title: Athero-susceptibility of inbred mouse strains

city: Chapel Hill

first: Yukako

last: Kayashima

state: NC

address: 701 Brinkhous-Bullitt Building

institute: University of North Carolina at Chapel Hill


title: Expression data from thioglycollate-elicited peritoneal macrophages from 129S6/SvEvTac and C57BL/6 mice

status: Public on Dec 01 2014

country: USA

summary:
Strain differences influence susceptibility to atherosclerosis. Apolipoprotein E-null mice on a C57BL/6 genetic background (B6-apoE) are highly susceptible to atherosclerosis in the aortic root area compared with those on a 129S6/SvEvTac background (129-apoE).
To explore strain-specific differences affecting the susceptibility to atherosclerosis, we performed microarray analysis of macrophages from wild type mice of each strains.

overall_design: Peritoneal macrophages were harvested from 3-month-old male and female 129S6/SvEvTac and C57BL/6 mice after the intraperitoneal injection of thioglycollate medium.

first: Nobuyo

last: Maeda


title: Gene expression profiling in ovarian cancer

status: Public on Dec 06 2014

city: Gliwice

first: Katarzyna

middle: Marta

last: Lisowska

address: ul. Wybrzeże Armii Krajowej 15

department: Center for Translational Research  and Molecular Biology of Cancer

country: Poland

institute: MSC Memorial Cancer Center and Institute of Oncology, Gliwice Branch

summary: The introduction of microarray techniques to cancer research brought great expectations for finding biomarkers that would improve patients’ treatment; however, the results of such studies are poorly reproducible and critical analyses of these methods are rare. In this study, we examined global gene expression in 97 ovarian cancer samples. Also, validation of results by quantitative RT-PCR was performed on 30 additional ovarian cancer samples. We carried out a number of systematic analyses in relation to several defined clinicopathological features. The main goal of our study was to delineate the molecular background of ovarian cancer chemoresistance and find biomarkers suitable for prediction of patients’ prognosis. We found that histological tumor type was the major source of variability in genes expression, except for serous and undifferentiated tumors that showed nearly identical profiles. Analysis of clinical endpoints [tumor response to chemotherapy, overall survival, disease-free survival (DFS)] brought results that were not confirmed by validation either on the same group or on the independent group of patients. CLASP1 was the only gene that was found to be important for DFS in the independent group, whereas in the preceding experiments it showed associations with other clinical endpoints and with BRCA1 gene mutation; thus, it may be worthy of further testing. Our results confirm that histological tumor type may be a strong confounding factor and we conclude that gene expression studies of ovarian carcinomas should be performed on histologically homogeneous groups. Among the reasons of poor reproducibility of statistical results may be the fact that despite relatively large patients’ group, in some analyses one has to compare small and unequal classes of samples. In addition, arbitrarily performed division of samples into classes compared may not always reflect their true biological diversity. And finally, we think that clinical endpoints of the tumor probably depend on subtle changes in many and, possibly, alternative molecular pathways, and such changes may be difficult to demonstrate.

overall_design: Here, we provide gene expression data from 101 ovarian cancer surgical samples: 73 serous, 12 endometrioid, 9 clear cell and 7 undifferentiated.   The majority of patients (98 out of 101) were tested for BRCA1 gene mutation: 27 patients had germline BRCA1 gene mutation, one had somatic mutation, 70 had no BRCA1 mutation detected.   We also checked for somatic TP53 gene mutation: 75 tumors had somatic mutation in TP53, 15 had no mutation detected, 11 were not analyzed (NA). The p53 protein accumulation in the cancer cells was analyzed by immunohistochemistry: 54 tumors had protein accumulation, 42 had no accumulation, 5 - NA.   For 75 samples we provide extensive pathological and clinical data: tumor grade, histological type, FIGO stage, disease free survival time (DFS), overall survival (OS), residual tumor size (R), clinical status post first-line chemotherapy and at last follow-up, platinum sensitivity. The tumors were graded in a four-grade scale, according to the criteria given in [1].   The results of data analyses were published in [2].   [1] HRK Barber, SC Sommers, R Snyder, TH Kivon; Histologic and nuclear grading and stromal reaction as indices for prognosis in ovarian cancer. Am. J. Obstet. Gynecol, 121 (1975), p. 795-807  [2] K. Lisowska, M. Olbryt, V. Dudaladava, J. Pamuła-Piłat, K. Kujawa, E. Grzybowska, M. Jarząb, S. Student, I. K. Rzepecka, B. Jarząb J. Kupryjańczyk (2014) Gene expression analysis in ovarian cancer – faults and hints from DNA microarray study.

first: Jolanta

last: Kupryjańczyk


title: Genome-wide DNA Microarray Analysis Unravels Rapid Changes in the Transcriptome of MK-801 treated Rat Brain

status: Public on Nov 26 2014

city: Tsukuba

first: RANDEEP

last: RAKWAL

state: Ibaraki

address: 1-1-1 Tennodai

department: Institute of Health and Sport Sciences

country: Japan

institute: University of Tsukuba

summary: N-Methyl-D-aspartate receptors (NMDAr), widely located around the central nervous system, are known to be involved in behavioral disorders. Dizocilpine (commonly referred to as MK-801) is a well known non-competitive NMDAr antagonist. We treated rats with intraperitoneal injection [0.08 (low-dose) and 0.16 (high-dose) mg/kg] of MK-801. In one experiment, 40 min after NaCl (vehicle control) and MK-801 (0.08 mg/kg) injection, electrocorticogram (ECoG) signals were analyzed. In the second experiment, 40 min post-injection, the whole brain of each animal was rapidly removed and separated into amyglada, cerebral cortex, hippocampus, hypothalamus, midbrain and ventral striatum) on ice, followed by analysis using a 4x44K DNA microarray chip. Spectral analysis revealed that a single systemic injection of MK-801 significantly and selectively augmented the power of baseline  (30-80 Hz) frequency oscillations. DNA microarray analysis showed the largest number (up- and down- regulations) of gene expressions in the cerebral cortex (378), midbrain (376), hippocampus (375), ventral striatum (353), amygdala (301), and hypothalamus (201) under low-dose of MK-801. Under high-dose, ventral striatum (811) showed the largest number of gene expression changes. Gene expression changes were functionally categorized to reveal expression of genes and function varies with each brain region. MK-801 increases the synchrony of baseline oscillations, causing very early changes in gene expressions in rat brain after acute MK-801 treatment, a first report.

overall_design: The overall goal of the present study was to identify gene expression patterns along rat chromosomes in different brain regions after a single injection of MK-801, which exerts a longer acute effect than ketamine on ongoing brain activities. Two approaches were taken, first electrophysiological and send molecular analysis, where the brain of MK-801-treated rats was subjected to a genome-wide transcriptome mapping analysis (~4400 genes) in the cerebral cortex, midbrain, hippocampus, ventral striatum, amygdala, and hypothalamus regions.

first: Yuka

last: Kobayashi

first: Sofya

middle: P

last: Kulikova

first: Junko

last: Shibato

first: Randeep

last: Rakwal

first: Hiroyuki

last: Satoh

first: Didier

last: Pinault

first: Yoshinori

last: Masuo


title: Microarray expression profiling of Runx1-null and wildtype mouse mammary epithelial cells

city: Boston

first: Zhe

last: Li

state: MA

address: 77 Avenue Louis Pasteur, Room 466

department: Medicine, Genetics Division

institute: Brigham and Women's Hospital

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

overall_design: Refer to individual Series


title: Microarray expression profiling of distinct subsets of mouse mammary epithelial cells

summary: The purpose of this microarray experiment was to obtain reference gene expression patterns of a number of epithelial cell populations [mammary stem cells (MASC), luminal progenitors (LP), alveolar luminal stem/progenitor cells (WC virgin-these are mammary epithelial cells genetically marked by Wap-Cre in virgin females), mature luminal cells (ML, mainly represent ductal luminal cells in virgin females), and alveolar luminal cells (WC preg – these are alveolar cells genetically marked by Wap-Cre during mid-gestation)] present in the mammary gland of wildtype adult mice on a C57BL6 genetic background.

overall_design: For the isolation of RNA from mammary stem cells (MASC, Lin-CD24+CD29hi), luminal progenitors (LP, Lin-CD24hiCD29+CD61+), and mature luminal cells (ML, lin-CD24hiCD29+CD61-), the thoracic and inguinal mammary glands from 3 adult virgin female mice were harvested, minced and digested into a single cell suspension. Form each of these 3 single cell suspensions, the above populations were sorted by FACS. For alveolar luminal stem/progenitor cells and alveolar luminal cells, Lin-YFP+ mammary epithelial cells were isolated from virgin or midgestation mice genetically marked by Wap-Cre;R26Y. R26Y is a conditional YFP reporter that would be turned on upon Cre-mediated recombination.

first: Maaike

last: van Bragt


title: Murine Myeloid-Erythroid Progenitors (MEPs): WT vs. Bmi1-/-

status: Public on Nov 18 2014

city: Chicago

first: Yan

last: Liu

state: IL

address: 303 E. Superior Street, Lurie 5-107, Northwestern University

department: Department of Medicine

institute: Northwestern University

summary: Transcriptional profiling of MEPs purified from wild type and Bmi1-/- mice.

overall_design: Two-condition experiment, WT vs. Bmi1-/- MEPs. Biological replicates: 3 WT replicates, 3 Bmi1-/- replicates.


title: Expression data from thioglycollate-elicited peritoneal macrophages from 129S6/SvEvTac and DBA2/J mice

summary:
Strain differences influence susceptibility to atherosclerosis. Apolipoprotein E-null mice on a DBA/2J genetic background (DBA-apoE) are highly susceptible to atherosclerosis in the aortic root area compared with those on a 129S6/SvEvTac background (129-apoE).
To explore strain-specific differences affecting the susceptibility to atherosclerosis, we performed microarray analysis of macrophages from wild type mice of each strains.

overall_design: Peritoneal macrophages were harvested from 3-month-old male and female 129S6/SvEvTac and DBA2/J mice after the intraperitoneal injection of thioglycollate medium.


title: Expression data from the aorta of DBA, B6 and 129 mice

summary:
Strain differences influence susceptibility to atherosclerosis. Apolipoprotein E-null mice on a DBA/2J genetic background (DBA-apoE) and C57BL/6 (B6-apoe) are highly susceptible to atherosclerosis in the aortic root area compared with those on a 129S6/SvEvTac background (129-apoE).
To explore strain-specific differences affecting the susceptibility to atherosclerosis, we performed microarray analysis of aortic arch and root from wild type mice of each strains.

overall_design: Aortia were dissected from wild-type DBA-apoe, B6-apoe and 129-apoe male mice, and tissues from 4-6 mice were pooled per sample.


title: Murine Proerythroblasts (ProEs): WT vs. Bmi1-/-

summary: Transcriptional profiling of ProEs purified from wild type and Bmi1-/- mice.

overall_design: Two-condition experiment, WT vs. Bmi1-/- ProEs. Biological replicates: 3 WT replicates, 3 Bmi1-/- replicates.


title: Staphylococcus aureus gene expression in a rat model of infective endocarditis

status: Public on Nov 01 2014

city: Rochester

first: Paul

last: Dunman

state: NY

address: 601 Elmwood Avenue

department: Microbiology and Immunology

institute: University of Rochester

summary:
S. aureus has a propensity to cause endocarditis; diabetes mellitus is a frequent underlying comorbitity in patents with S. aureus endocarditis.
S. aureus Affymetrix GeneChips were used to compare S. aureus expression properties in cardiac vegatations isolated from diabetic and nondiabetic rats.
S. aureus Affymetrix GeneChips were also used to compare the S. aureus expression properties of cardiac vegatations (both diabetic and nondiabetic) in comparsions to planktonic cells.
Few differences were observed between the expression properties of S. aureus harvested from diabetic vs. nondiabetic cardiac vegatations.
Significant differences were observed between the expression properties of S. aureus harvested from cardiac vegetations in comparison to exponential and/or stationary phase planktonically grown cells.

overall_design: S. aureus strain COL was used to establish cardiac vegetations in diabetic and nondiabetic rats or grown in laboratory medium to exponential or stationary phase, total bacterial RNA was isolated, labeled and applied to Affymetrix GeneChips.  We sought to determine whether the transcriptional profiles of S. aureus differed in diabetic vs. nondiabetic rats and whether vegetations differed from that of planktonic S. aureus.

middle: M

first: Frank

last: Hanses


title: Metabolomic heterogeneity of severe pulmonary arterial hypertension

status: Public on Nov 14 2014

city: Toronto

first: Yidan

last: Zhao

state: Ontario

address: 101 College Street

country: Canada

institute: University Health Network

summary: Although multiple gene and protein expression have been extensively profiled in human pulmonary arterial hypertension (PAH), the mechanism for the development and progression of pulmonary hypertension remains elusive.  Analysis of the global metabolomic heterogeneity within the pulmonary vascular system leads to a better understanding of disease progression. Using a combination of high-throughput liquid-and-gas-chromatography-based mass spectrometry, we showed unbiased metabolomic profiles of disrupted glycolysis, increased TCA cycle, and fatty acid metabolites with altered oxidation pathways in the severe human PAH lung. The results suggest that PAH has specific metabolic pathways contributing to increased ATP synthesis for the vascular remodeling process in severe pulmonary hypertension. These identified metabolites may serve as potential biomarkers for the diagnosis of severe PAH. By profiling metabolomic alterations of the PAH lung, we reveal new pathogenic mechanisms of PAH in its later stage, which may differ from the earlier stage of PAH, opening an avenue of exploration for therapeutics that target metabolic pathway alterations in the progression of PAH.

overall_design:
Global profiles were determined in human lung tissue and compared across 11 normal and 12 severe pulmonary arterial hypertension patients.
Using a combination of microarray and high-throughput liquid-and-gas-chromatography-based mass spectrometry, we showed unbiased metabolomic profiles of disrupted glycolysis, increased TCA cycle, and fatty acid metabolites with altered oxidation pathways in the severe human PAH lung.

first: Jenny

last: Peng

first: Catherine

last: Lu

first: Michael

last: Hsin

first: Marco

last: Mura

first: Licun

last: Wu

first: Lei

last: Chu

first: Ricardo

last: Zamel

first: Tiago

last: Machuca

first: Thomas

last: Waddell

first: Mingyao

first: Shaf

last: Keshavjee

first: John

last: Granton

first: Marc

last: de Perrot


title: STAT1 and IRF8 orchestrate IFNγ and LPS-mediated signal integration in the vasculature that leads to amplified pro-atherogenic responses

status: Public on Nov 04 2014

city: Poznań

first: Hans

last: Bluyssen

address: Umultowska 89

department: Department of Human Molecular Genetics

institute: Faculty of Biology, University of Adam Mickiewicz

summary: The transcription factor Signal Transducer and Activator of Transcription (STAT) 1 is activated by Interferon gamma (IFNγ) but also Lipopolysaccharide (LPS) is the trigger of inflammation. STAT1 together with downstream activated Interferon Regulatory Factors (IRF) create a platform for signal integration between IFNγ and the Toll-Like Receptor (TLR) 4 ligand in immune cells. Little is known about the role of STAT1 and IRFs on potential synergism between LPS- and INFγ-signaling in cells from the vasculature. We investigated whether vascular cells can promote inflammatory signaling by the STAT1-IRFs pathway.

overall_design: To study signal integration between LPS and IFNγ pathways and the role of STAT1, aortic Vascular Smooth Muscle Cells (VSMCs) from C57BL/6 and STAT1 mice were isolated and treated either with IFNγ or LPS or pretreated with IFNγ followed by LPS. Experiment was prepared in three independent biological repeats for each cell type.

first: Stefan

last: Chmielewski

first: Adam

last: Olejnik


title: Microarray analysis of the therapeutic effects of the mixture of salvianolic acids from Salvia miltiorrhiza and total flavonoids from Anemarrhena asphodeloides on sulfur mustard-induced damages

status: Public on Nov 05 2014

city: ShangHai

first: Jian-Zhong

last: Li

address: Guo He Road 325#

country: China

institute: Second Military Medical University

summary: To further investigate the potential molecular basis of the therapeutic effects of the mixture of salvianolic acids from Salvia miltiorrhiza and total flavonoids from Anemarrhena asphodeloides (MSTF) on sulfur mustard (SM) damage, gene expression analysis was conducted on rats liver tissues using microarrays.

overall_design: Rats were randomly assigned to one of the three following treatment groups (10 rats per group): normal control, SM and SM + MSTF. SM was dissolved in propylene glycol. The SM was applied with subcutaneous injection as a single dose of 3.5 mg/kg body weight equivalent to 0.7 LD50. The equivalent volume of solvent was given to control rats. MSTF (120 mg/kg body weight/day) dissolved in double distilled water were administered intragastrically to the rats 1 h after SM treatment. Twenty-four hours following SM treatment, the rats were subjected to anesthesia and then sacrificed by cervical dislocation. Liver was dissected out from each animal. 3-4 of these liver tissues were processed for the microarray experiment.

first: Jian

middle: Z


title: Comparative analysis of transcriptome profiles of G. arboreum L. cv. and its fuzzy-lintless mutant (ANOI 1960) during fibre development stages.

city: New Delhi

first: Mogilicherla

last: Kanakachari

state: Delhi

address: LBS Building, PUSA Campus

department: Molecular Biology and Biotechnology

country: India

institute: National Research Centre on Plant Biotechnology

summary:
Comparative analysis of transcriptome profiles of G. arboreum L. cv. and its fuzzy-lintless mutant (ANOI 1960) at 0 and 10 dpa.
Cotton is one of the most commercially important fibre crops in the world and used as a source for natural textile fibre and cottonseed oil. The fuzzy-lintless ovules of cotton mutants are ideal source for identifying genes involved in fibre development by comparing with fibre bearing ovules of wild-type. To decipher molecular mechanisms involved in fibre cell development, transcriptome analysis has been carried out by comparing G. arboreum cv. (wild-type) with its fuzzy-lintless mutant (ANOI 1960). Fuzzed-lintless mutant line was generated by back cross breeding between FL and Fl (recurrent parent) lines (personal communication by Dr. I. S. Katageri). Basically Fibre less type was a RIL, first recovered from cross between G.arboreum (linted) and G. anomalum (lint less). This RIL was used as donor parent and crossed with normal arboreum (as recurrent parent) to develop G. arboreum FL and G. arboreum Fl isogenic lines. This G. arboreum Fl line is named as ANOI 1960. Cotton bolls were collected at fibre initiation (0 dpa/days post anthesis) and elongation (10 dpa) and gene expression profiles were analyzed in wild-type and ANOI 1960 mutant using Affymetrix cotton GeneChip Genome array.

platform_organism:
Gossypium barbadense
Gossypium hirsutum
Gossypium arboreum
Gossypium raimondii

overall_design: Cotton plants were grown under field condition. Flowers were tagged and cotton bolls were collected during fibre development stages. Total RNA was isolated from fibre bearing ovules of wild-type (WT) and fuzzy-lintless ovules of mutant (ANOI 1960) collected at various (0 and 10 dpa) fibre development stages using SpectrumTM Plant Total RNA kit (Sigma, USA) according to the manufacturer’s protocol. Affymetrix cotton GeneChip Genome array (Affymetrix, USA) having 23,977 probe sets representing 21,854 cotton transcripts was used for transcriptome analysis. Three biological replicates were maintained to test the reproducibility and quality of the chip hybridization. cDNA labeling, array hybridization, staining and washing procedures were carried out as described in the Affymetrix protocols. CEL files having estimated probe intensity values were analyzed with GeneSpring GX-11.5 software (Agilent Technologies, USA) to get differentially expressed transcripts. The Robust Multiarray Average (RMA) algorithm was used for the back ground correction, quantile normalization and median polished probe set summarization to generate single expression value for each probe set. Normalized expression values were log2-transformed and differential expression analysis was performed using unpaired t-test. The p-values were corrected by applying the false discovery rate (FDR) correction (Benjamini and Hochberg, 2000).

first: A

middle: S

last: Hande

first: K

middle: V

last: Padmalatha

first: G

last: Dhandapani

first: M

first: S

middle: G

last: Savita

middle: U

last: Solanke

first: V

last: Reddy

first: Polumetla

middle: A

last: Kumar

first: H

last: Vamadevaiah

first: I

last: Katageri


title: Genome-wide mapping proteins at replication forks in the yeast S. cerevisiae

status: Public on Oct 29 2014

city: New York

first: zhiguo

last: zhang

address: 1130 St. Nicholas Avenue

department: Pediatric and Genetics and Development

institute: Columbia University

type: Genome binding/occupancy profiling by high throughput sequencing

summary: Faithful duplication of DNA is essential for the maintenance of genomic stability in all organisms. DNA synthesis proceeds bi-directionally with continuous synthesis of leading strand DNA and discontinuous synthesis of lagging strand DNA. Herein, we describe a method of enriching and Sequencing of Protein-Associated Nascent strand DNA (eSPAN) to detect whether a protein binds the leading- and lagging-strands of DNA replication forks. We show that Pol-epsilon, PCNA, Cdc45, Mcm6 and Mcm10 preferentially associate with leading strands, whereas Pol-alpha, Pol32, Pol-delta, Rfa1 and Rfc1 associate with lagging strands of hydroxyurea (HU)-stalled replication forks. In contrast, PCNA is enriched at lagging strands of normal replication forks in wild type cells and HU-stalled forks in cells lacking Elg1. These studies demonstrate a strategy to reveal proteins at leading and lagging strands of DNA replication forks, and suggest that the unloading of PCNA from lagging strands of HU-stalled replication forks helps maintain genome integrity.

overall_design: We synchronized yeast cells at G1 and released into early S phase in the presence of BrdU, a nucleotide analog that can be incorporated into newly synthesized DNA strand, and hydroxyurea (HU), a ribonucleotide reductase inhibitor. HU has no effect on initiation of DNA replication at early replication origins, but inhibit late replication firing. In addition, replication forks are stalled due to depletion of dNTPs. We then performed chromatin-immunoprecipitation of 12 proteins of interest following a standard procedure. Protein-bound DNAs were then reverse-crosslinked and double strand DNA was denatured. Nascent DNA was enriched by immunoprecipitation using anti-BrdU antibodies. The recovered ssDNA was first marked with ligation to one oligo at 3’ end before conversion to dsDNA for library preparation and sequencing. In this way, the directionality of ssDNA and therefore strand information of each sequenced DNA were known. The sequencing tag was mapped to both Watson (red) and Crick (blue) strands of the reference genome. In addition to ChIP-eSPAN, we also performed BrdU-IP and single strand DNA sequence (BrdU-ssSeq) and protein ChIP followed by single-strand DNA sequencing (ChIP-ssSeq) for each corresponding ChIP-eSPAN experiment. We also performed Mcm4 and Mcm6 ChIP-seq using cells synchronized at G1 phase of the cell cycle for identification of replication origins in comparison with published dataset. Some protein ChIP-ssSeq and ChIP-eSPAN experiments were repeated and the data fits well each other. Therefore, we did not repeat all protein ChIP-ssSeq and ChIP-eSPAN experiments.

first: Chuanhe

last: Yu

first: Haiyun

last: Gan

first: Zhiguo

last: Zhang


title: Recurrent breakpoint genes in colorectal cancer

city: Amsterdam

first: Daoud

last: Sie

address: De Boelelaan 1117

department: Pathology

country: Netherlands

institute: Vrije Universiteit Medical Center

type: Genome variation profiling by genome tiling array

summary: In this study our aim was to document recurrent DNA copy number aberration associated breakpoints in primary tumors of colorectal cancer patients that ultimately received systemic treatment in the context of metastatic disease. Such data can be used to catalogue copy number aberration associated breakpoints and thereby affected genes. To this end, high quality arrayCGH data set of clinically well annotated colorectal cancer specimens was generated using FFPE tumor samples from patients from two phase III clinical trials, namely CAIRO and CAIRO2.

overall_design: arrayCGH data of colorectal cancers of patients from 2 clinical trials. 108 patients were treated with capecitabine first line, 110 patients were treated with capecitabine and irinotecan first line and 134 patients were treated with capecitabine, oxaliplatin and bevacizumab.

first: Evert

last: van den Broek

first: Josien

middle: C

last: Haan

first: Miriam

last: Koopman

first: Jolien

last: Tol

first: Danielle

last: Israeli

first: Hendrik

middle: F

last: van Essen

first: Mark

last: van de Wiel

first: Nicole

last: van Grieken

first: Quirinus

middle: J

last: Voorham

first: Beatriz

last: Carvalho

first: Mariette

last: Labots

first: Henk

last: Verheul

first: Iris

middle: D

last: Nagtegaal

first: Bauke

last: Ylstra

first: Johan

middle: H

last: van Krieken

first: Cornelis

last: Punt

first: Gerrit

last: Meijer

first: Remond

last: Fijneman


title: Microarray-based Analysis of Gene Expression in Lycopersicon esculentum Roots in Response to Cadmium, Chromium, Mercury and Lead

status: Public on Nov 06 2014

city: Beijing

first: Jing

last: Hou

address: No. 19, XinJieKouWai St., HaiDian District

institute: Beijing Normal University

summary: We hypothesize that microarray-based analysis of Lycopersicon esculentum is a sensitive tool for the early detection of potential toxicity of heavy metals, as well as an effective tool for identifying the heavy metal-specific genes. To test the hypothesis, the Agilent whole-genome cDNA microarrays were used to assess the effects of heavy metal on L. esculentum at relatively low concentrations (1/10 LC50 of heavy metals). Results showed that the characteristic gene expression profiles induced by Cd, Cr, Hg and Pb were not only distinct from the control but also distinct from one another, demonstrating the feasibility of discriminating between the effects of these four heavy metals present at relatively low concentrations. Moreover, heavy metal-specific genes were identified by microarray analysis. These findings support the above hypothesis.

overall_design: A total of fifteen microarrays (4*44K tomato gene expression microarray; G2519F-022270) were used to hybridize with RNA extracted from Cd-, Cr-, Hg-, Pb-treated and the untreated roots (control) of Lycopersicon esculentum. Each treatment was carried out for three replicates. A total of thirty seedlings were used for each treatment. Root samples from ten seedlings randomly selected from each Petri dish were pooled together to obtain three biological replicates.

first: Xinhui

last: Liu


title: Essential oils affect populations of some rumen bacteria as revealed by microarray analysis

status: Public on Oct 23 2014

city: Columbus

first: Amlan

middle: Kumar

last: Patra

state: OHIO

address: 2029 Fyffe Road

department: Animal Science

institute: The Ohio State University

summary: Origanum oil (ORO), garlic oil (GAO), and peppermint oil (PEO) were shown to effectively lower methane production, decrease abundance of methanogens, and change abundances of several bacterial populations important to feed digestion in vitro. In this study, the impact of these essential oils (EOs, at 0.50 g/L), on the rumen bacterial community composition was further examined using the recently developed RumenBactArray.

overall_design: In vitro rumen mixed cultures (three replicates) received 0.50 g/L each EO in the present study. The control culture (three replicates) that did not receive EO was included in parallel.

first: Zhongtang

last: Yu


title: Expression diversity of Phytophthora ramorum from canyon live oak

status: Public on Oct 24 2014

city: Davis

first: Takao

last: Kasuga

state: CA

address: 382 Huchison Hall

institute: USDA-ARS

summary: Expression diversity of P. ramorum isolates belonging to the NA1 clonal lineage growing on solid CV8 was examined.  We found that phenotypes and transcriptomes change when isolates were passing through oak trees.

overall_design: Global expression patterns of 8 isolates originating from coastal live oak and California bay laurel  and re-isolates from canyon live oaks were investigated.  No biological replicates were generated.  The sequenced strain Pr102 was included.  Gene models Phytophthora ramorum v1.0 were used to construct NimbleGen 72K x4 custom arrays.

first: Lilian

last: Diep

first: Mai

last: Bui

first: David

last: Rizzo

first: Matteo

last: Garbelotto


title: Expression data from Rhesus immune cells responding to YFV

status: Public on Oct 22 2014

city: Riverside

first: Ilhem

last: Messaoudi

address: 3401 Watkins Dr.

department: Biomedical Science

institute: UC Riverside

summary:
Immune response to infection involves the regulation of numerouse genes in numerous cell types. The number and type of genes that become differentially expressed in response to infection can result in very different pathophysiologic presentations and disease course. Wild type YFV and 17D despite having very few genetic differences result in very different disease outcomes in human and monkey hosts.
We used microarrays to detail the global programme of gene expression of Rhesus macaque immune cells responding to both wild type and 17D strains of YFV. We identified distinct classes of gene expression as well as marked differences in differential gene expression between responses to 17D and wild type strains of YFV.

overall_design: Rhesus PBMC were isolated before and on day 3 of either vaccination with 17D or infection with wild type YFV with an n of 3 per group. Total RNA was extracted and hybridized on Affymetrix microarrays.

first: Flora

last: Engelmann

first: Laurence

last: Josset

first: Thomas

last: Girke

first: Byung

last: Park

first: Mark

middle: K

last: Slifka


title: Predicting genome-wide DNA methylation

city: Druham

first: Weiwei

last: Zhang

address: 101 Research Drive

department: Biostatistics and Bioinformatics

institute: Duke University

type: Methylation profiling by genome tiling array

summary: Genome wide DNA methylation profiling of normal whole blood samples. The data consist of 100 samples with Illumina HumanMethylation450 BeadChip data.

overall_design: Bisulphite converted DNA from the 100 samples were hybridized to the Illumina HumanMethylation450 BeadChip

first: Jordana

last: Bell


title: Alteration of the transcriptome upon plakophilin3 loss in FBM cell line

status: Public on Sep 23 2014

city: navi mumbai

first: Srikanta

last: Basu

state: Maharashtra

address: Kharghar, sector 22

department: Sorab's Lab

institute: TMC-ACTREC

summary: To understand alterations in gene expression upon plakophilin3 (PKP3) loss, we generated two FBM derived plakophilin3 knockdown clones. One of these clones named shpkp3-2 was used for the experiment. The gene expression profile of shpkp3-2 was compared with the vector control named vec.

overall_design: RNA used for this experiment was obtained from two biological replicates of vec (vec1 and vec2) and shpkp3-2 ( shpkp3-2-1 and  shpkp3-2-2 ). RNA from the clones were obtained at separate time points  in 2 groups. The first group was vec1 and shpkp3-2-1 and the second group was of clones vec2 and shpkp3-2-2 respectively.

first: Sorab

middle: N

last: Dalal


title: Nasal Mucosal miRNA expression in RSV positive infants with mild or severe disease, compared to healthy controls

status: Public on Oct 15 2014

city: Lørenskog

first: Christopher

middle: Stephen

last: Inchley

address: Sykehusveien

department: Department of Pediatric and Adolescent Medicine

country: Norway

institute: Akershus University Hospital

summary: The aim of this investigation was two-fold: i) to describe miRNAs involved in the immune response to Respiratory syncytial virus (RSV) in a clinical setting in order to inform further research of immune system regulation by miRNAs in RSV or other infections; ii) to discover differences in miRNA expression between disease severity groups. We have therefore profiled miRNA in cytology brushings of the nasal mucosa in infants with RSV disease, comparing them to healthy infants. miRNA microarray identified 26 differentially regulated miRNA which were subsequently analyzed by RT-qPCR.

overall_design: Nasal mucosal samples were taken from RSV positive infants using cytology brushes on admission to hospital after aspiration of nasal secretions. Samples were taken from healthy controls without clinical symptoms of respiratory infection using the same procedure.

first: Tonje

last: Sonerud

first: Hans

middle: O

last: Fjærli

first: Britt

last: Nakstad


title: Characterization of changes in global genes expression in the distal colon of loperamide-induced constipation SD rats in response to the laxative effects of Liriope platyphylla

status: Public on Oct 04 2014

city: Miryang

first: Dae Youn

last: Hwang

address: 50 Cheonghak-ri, Samnangjin-eup

country: South Korea

institute: Pusan National University

summary: In order to characterize the changes in global gene expression in the distal colon of constipated SD rats in response to the laxative effects induced by aqueous extract of Liriope platyphylla (AEtLP) including isoflavone, saponin, oligosaccharide, succinic acid and hydroxyproline, total RNA extracted from the distal colon of AEtLP-treated constipation rats was hybridized to oligonucleotide microarrays.Overall, 581 genes were up-regulated and 216 genes were down-regulated by constipation induced by loperamide, while 67 genes were up-regulated and 421 genes were down-regulated by AEtLP treatment in constipated rats compared to controls. Among the transcripts up-regulated by constipation, 89 were significantly down-regulated and 20 were recovered to normal levels by AEtLP treatment. The major genes in the down-regulated categories included Slc9a5, klk10, Fgf15 and Alpi, while the major genes in the recovered categories were Cyp2b2, Ace, G6pc and Setbp1. However, nine of these genes that were down-regulated by constipation were significantly up-regulated and four were recovered to normal levels by AEtLP treatment. The major genes in the up-regulated categories included Serpina3n, Lcn2 and Slc5a81, while the major genes in the recovered categories were Tmem45a, Rerg and Rgc32.

overall_design: Constipation was induced in SD rats by subcutaneous injection of loperamide for 3 days. At 15 hr after the final treatment of loperamide, each animal were received a consistent volume of water or 15 uL/g body weight of AEtLP (1,000 mg/kg weight) via oral administration for once at 9 AM.

first: Dae

middle: Y

first: Ji

middle: E

last: Kim


title: Analysis of gene expression changes during long-term induction of EMT in EpRas tumor cells by TGF-b1.

status: Public on Sep 01 2014

city: Stockholm

first: Jonas

last: Fuxe

address: Scheeles v. 2

department: Medical Biochemistry and Biophysics

country: Sweden

institute: Karolinska Institutet

summary:
EMT is a developmental process, which can be reactivated in cancer cells. Cancer cells maintaining EMT in the circulation may have pro-metastatic properties.
We used microarrays to profile EMT-related gene expression changes after 14 d of TGF-b1 treatment.

overall_design: EpRas cells were cultured in standard conditions either in the presence of absence of recombinant TGF-b1 (2 ng/ml) for 14 d. After this period, RNA was isolated from triplicate wells of treated and non-treated cells, and hybridized on Affymetrix microarrays.

first: Vedrana

last: Tabor

first: Joel

last: Johansson


title: Gamma radiation and HZE treatment of seedlings in Arabidopsis

status: Public on Sep 18 2014

first: Anne

last: Britt

address: One Shields Drive

department: Plant Biology

institute: UC Davis

summary:
Plants exhibit a robust transcriptional response to gamma radiation which includes the induction of transcripts required for homologous recombination and the suppression of transcripts that promote cell cycle progression. Various DNA damaging agents induce different spectra of DNA damage as well as “collateral” damage to other cellular components and therefore are not expected to provoke identical responses by the cell.
Here we study the effects of two different types of ionizing radiation (IR) treatment, HZE (1 GeV Fe26+ high mass, high charge, and high energy relativistic particles) and gamma photons, on the transcriptome of Arabidopsis thaliana seedlings. Both types of IR induce small clusters of radicals that can result in the formation of double strand breaks (DSBs), but HZE also produces linear arrays of extremely clustered damage. We performed these experiments across a range of time points (1.5-24 h after irradiation) in both wild-type plants and in mutants defective in the DSB-sensing protein kinase ATM. The two types of IR exhibit a shared double strand break-repair-related damage response, although they differ slightly in the timing, degree, and ATM-dependence of the response. The ATM-dependent, DNA metabolism-related transcripts of the “DSB response” were also induced by other DNA damaging agents, but were not induced by conventional stresses. Both Gamma and HZE irradiation induced, at 24 h post-irradiation, ATM-dependent transcripts associated with a variety of conventional stresses; these were overrepresented for pathogen response, rather than DNA metabolism. In contrast, only HZE-irradiated plants, at 1.5 h after irradiation, exhibited an additional and very extensive transcriptional response, shared with plants experiencing “extended night.” This response was not apparent in gamma-irradiated plants.

overall_design: We treated 5-day-old WT and atm-1 seedlings of Arabidopsis thaliana with 100 Gy of Gamma radiation (over a span of 15 minutes) or 30 Gy of HZE (over a span of approximately 12 minutes).  Gamma irradiations were completed at 8:40 am, while HZE irradiations were conducted in two runs (due to space limitations) which were completed at 1:09 and 1:28pm respectively.  Gamma treated seedlings were sampled at 10:10 am, 11:40 am, 2:55 pm, 8:40 pm, and 8:40 am.  HZE treated seedlings were sampled at 2:39 pm, 4:09 pm, 7:24 pm, 1:09 am, and 1:09 pm.  Un-irradiated WT and atm-1 control seedlings were sampled at 10:45 am on Day #1 and 9:15 am on Day #2.  There are a total of 22 experimental or control conditions, with two replicates per condition, yielding 44 samples overall.

first: Kevin

middle: M

last: Culligan

first: Neil

last: Huefner

first: Victor

last: Missirian

first: Phillip

last: Conklin

middle: B


title: Muscle Transcriptomic Investigation of Late Fetal Development Identifies Candidate Genes for Key Roles in Piglet Maturity

status: Public on Sep 19 2014

city: Castanet tolosan

first: Laurence

last: Liaubet

address: chemin de borde rouge

department: Animal Genetic

country: France

institute: INRA

summary: To further knowledge of piglet maturity, we have developed a microarray analysis to describe biological processes and to find candidate genes for key roles in piglet maturity. The objective was to identify which genes and biological processes are specifically involved in the difference between two extreme breeds: Large White (LW) and Meishan (MS). The LW breed is a selected breed known to show an increased rate of mortality at birth, while the MS breed presents more robust piglets at birth. MS and LW sows were inseminated with mixed semen (LW and MS) hence each litter was composed of pure fetuses (LW or MS) and crossed fetuses (LWMS from MS sows and MSLW from LW sows).

overall_design: To assay for changes in gene expression during piglet maturity, mRNA was isolated from 61 fetal skeletal muscle samples with 8 different conditions: two fetal gestational ages (90 or 110 days of gestation), associated with four genotypes (two extreme breeds for mortality at birth (MS and LW) and two crossed breeds (MSLW and LWMS)). MS fetuses are known to have a better survival at birth than LW fetuses. An understanding of maturity is possible with the comparison between the fetal gestational ages and between the two extreme breeds. The impact of parental genotypes is studied with the presence of crossed fetuses. After quality control and normalization, only 61 samples were conserved (represented here).

first: V

last: Voillet

first: M

last: San Cristobal

first: Y

last: Lippi

first: P

last: Martin

first: N

last: Iannuccelli

first: C

last: Lascor

last: Billon

first: L

last: Canario


title: Inhalation of rod-like carbon nanotubes causes unconventional asthma

status: Public on Oct 01 2014

city: Tampere

first: Dario

last: Greco

address: Arvo ylpön Katu 34

department: Faculty of Medicine and Health Technology

country: Finland

institute: Tampere University

summary: Exposure to rod-shaped carbon nanotubes reveals novel innate immunity mediated asthma-like inflammation in mice. Inhalation of rCNT elicited a drastic infiltration of eosinophils into the lungs but only minor infiltration of neutrophils and lymphocytes. Transcriptomic study revealed remarkable effects of rCNT exposure, affecting almost exclusively pathways essential for innate immunity.

overall_design: Mice were exposed to rCNT or tCNT for 4 h and sacrificed immediately or 24 h after the exposure. The total RNA was extracted from lung samples, hybridized to Agilent microarray and analyzed with BioConductor package Limma. Untreated mice were used as control.

first: Elina

last: Rydman

first: Marit

last: Ilves

first: Joonas

last: Koivisto

first: Pia

last: Kinaret

first: Vittorio

last: Fortino

first: Terhi

last: Savinko

first: Maili

last: Lehto

first: Ville

last: Pulkkinen

first: MinnaMari

last: Vippola

first: Kaarle

last: Hämeri

first: Sampsa

last: Matikainen

first: Henrik

last: Wolff

first: Kai

last: Savolainen

first: Harri

last: Alenius


title: sRNA from strawberry flower

city: Guangzhou

first: Rui

last: Xia

state: Guangdong

address: 483 Wushan Rd, Tianhe

department: Horticulture

institute: South China Agricultural University

type: Non-coding RNA profiling by high throughput sequencing

summary: Identifing the miRNA-TASL-PPR-siRNA pathway in strawberry

overall_design: one library was constructed and sequenced

first: Songqing

last: Ye

first: Zhongchi

last: Liu

first: Zongrang


title: Effect of tamoxifen on early gene expression in T47D cells

status: Public on Aug 29 2014

city: Heraklion

first: George

last: Notas

address: PO BOX 2208

department: Medicine

country: Greece

institute: University of Crete

summary: Tamoxifen is the treatment of choice in estrogen receptor alpha breast cancer patients. However, ~50% of ERα-positive tumors exhibit intrinsic or rapidly acquire resistance to endocrine treatment, requiring chemotherapy. Ιt has been difficult to predict de novo resistance to endocrine therapy and/or assess the likelihood of early relapse, while no concrete mechanism regulating the acquisition and the maintenance of endocrine resistance has been identified. We have performed a whole transcriptome analysis of an ER-positive (T47D) and a triple-negative (MDA-MBA-231) breast cancer cell line exposed to tamoxifen for a short time frame (hours) in order to study resistance mechanisms that are initiated early after initiation of tamoxifen treatment.

overall_design: Cells after a 4h incubation with medium containing 10% charcoal stripped FBS were incubated with vehicle, E2 (10-6M) or tamoxifen (10-6M) in RPMI 1640 supplemented with 10% charcoal stripped FBS, for 3 hours. Total RNA was isolated using Nucleospin II columns (Macheray-Nagel, Dttren, Germany), according to the manufacturer’s instructions. RNA was labeled and hybridized according to the Affymetrix protocol (Affymetrix Gene-Chip Expression Analysis Technical Manual), using the HGU133A plus 2 chip, analyzing a total of 54675 transcripts. Signals were detected by an Affymetrix microarray chip reader.

first: Marilena

last: Kampa

first: Elias

last: Castanas


title: Effect of tamoxifen on early gene expression in MDA-MB-231 cells

overall_design: Cells after a 4h incubation with medium containing 10% charcoal stripped FBS were incubated with vehicle,E2 (10-6M) or tamoxifen (10-6M) in RPMI 1640 supplemented with 10% charcoal stripped FBS, for 3 hours. Total RNA was isolated using Nucleospin II columns (Macheray-Nagel, Dttren, Germany), according to the manufacturer’s instructions. RNA was labeled and hybridized according to the Affymetrix protocol (Affymetrix Gene-Chip Expression Analysis Technical Manual), using the HGU133A plus 2 chip, analyzing a total of 54675 transcripts. Signals were detected by an Affymetrix microarray chip reader.


title: Effect of tamoxifen on early gene expression in T47D and MDA-MB-231 cells

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

overall_design: Refer to individual Series


title: Global transcriptome analysis in fast-growing Arabidopsis thaliana with elevated level of ATP [roots]

status: Public on Aug 25 2014

city: Hong Kong

first: Boon Leong

last: Lim

address: 5N01, Kaddorie Biological Sciences Building, the University of Hong Kong, Pokafulam Road

department: School of Biological Sciences

country: Hong Kong

institute: The University of Hong Kong

summary:
Higher ATP supply in AtPAP2 overexpression line is the driving force for its fast-growth phenotypes, leading to massive changes in its transcriptome and metabolome.
The OE lines are previously described in Sun et al., New Phytol. 2012 Apr;194(1):206-19.

overall_design: 20-day-old Arabidopsis seedlings at middle of day under long day growth conditions were collected for RNA extraction and microarray analysis

first: Feng

last: Sun

first: Chao

last: Liang

first: Boon

middle: L


title: Global transcriptome analysis in fast-growing Arabidopsis thaliana with elevated level of ATP [shoots]


title: Global transcriptome analysis in fast-growing Arabidopsis thaliana with elevated level of ATP


title: STAT3-mediated CD133 upregulation promotes hepatocellular carcinoma

status: Public on Aug 08 2014

city: Seoul

first: Byung-Hak

last: Kim

state: Seoul

address: 103 Daehangno, Jongno-gu

department: Pharmacology

institute: Seoul National University College of Medicine

summary:
We identified a novel mechanism by which IL-6/STAT3 signaling up-regulates CD133 expression and promotes HCC progression.
STAT3 activation upregulates the expression of CD133 during liver carcinogenesis. Targeting STAT3-mediated CD133 overexpression may represent a promising therapeutic strategy for HCC patients via eradicating the liver tumor microenviornment.

overall_design: To develop novel cancer therapeutic strategies by identification of signaling pathways or biomarkers and understanding their functions on cancer stem cell biology, we determined CD133 expression and STAT3 activation with tumor microenvironment in HCC patient tissues. The relation of STAT3 activation and CD133 expression was investigated by luciferase assay, shRNA knock-down, and chromatin immunoprecipitation assay in HCC cells, and in vivo xenograft model.

first: Cheolhee

last: Won

first: Eun

last: Yi

first: Kyung-Ju

last: Choi

first: Eun-Kyung

first: Jae-Ho

last: Lee

first: Ja-June

last: Jang

first: Jung-Hwan

last: Yoon

first: In-Chul

last: Park

first: Tae-Woo

first: Sun

middle: S

last: Bae

first: Valentina

last: Factor

first: Stephanie

last: Ma

first: Snorri

last: Thorgeirsson

first: Yun-Han

first: Sang-Kyu


title: Expression analysis of Arabidopsis thaliana wild-type Col-0 and selected RNA silencing mutant plants

status: Public on Aug 20 2014

city: Canberra

first: Ming-Bo

last: Wang

state: ACT

address: Clunies Ross Street

department: Agriculture Flagship

country: Australia

institute: CSIRO

summary:
Investigation of whole genome gene expression level changes in several Arabidopsis thaliana mutants (nrpd1, nrpe1, ros1 dml2 dml3) compared to  wild-type Col-0.
The mutants analyzed in this study are further described in Le et al. 'DNA demethylases target promoter transposable elements to positively regulate stress responsive genes in Arabidopsis' . Genome Biology (in press).

overall_design: A twelve chip study using total RNA recovered from three week-old plants grown on Murashige Skoog sucrose agar. The number of biological replicates for each plant genotype were as follows: Col-0 (3 biological replicates), rdd (2), nrpd1 (2) and nrpe1 (2) respectively. Each array contains 60-mer probes targeting 39,042 genes (TAIR 9.0) with 4 probes per gene.

first: Tuan-Ngoc

last: Le

first: Sameer

last: Tiwari

first: Danny

last: Llewellyn

first: Jen

last: Taylor

first: Elizabeth

last: Dennis


title: Microarray analysis adherent peripheral blood mononuclear cells stimulated with IL-10, IL-15, and IL-4

city: Sacramento

first: Dennis

middle: Jay

last: Montoya

address: 2700 Stockton Blvd #2354

department: Biochemistry and Molecular Medicine

institute: UC Davis School of Medicine

summary: Tuberculosis remains a major cause of death from an infectious disease worldwide, yet only 10% of people infected with Mycobacterium tuberculosis develop disease.  Defining both necessary and sufficient immunologic determinants of protection remains a great scientific challenge.  Analysis of peripheral blood gene expression profiles of active tuberculosis patients has identified correlates of risk for disease or pathogenesis.  We sought to identify human potential candidate markers of host defense by studying gene expression profiles of macrophages, cells which, upon infection by M. tuberculosis, can mount an antimicrobial response.  Weighted gene co-expression network analysis revealed an association between the cytokine, IL-32, and the vitamin D antimicrobial pathway in a network of IFN-γ and IL-15 induced ‘defense response’ genes.  IL-32 was sufficient for induction of the vitamin D-dependent antimicrobial peptides, cathelicidin and DEFB4, and generation of antimicrobial activity in vitro, dependent on the presence of adequate 25-hydroxyvitamin D.  The IL-15 induced ‘defense response’ macrophage gene network was integrated with ranked pairwise comparisons of gene expression from five different clinical data sets of latent vs. active tuberculosis or healthy controls, and a co-expression network derived from gene expression in patients with tuberculosis undergoing chemotherapy.  Together, these analyses identified eight common genes, including IL-32, as molecular markers of latent tuberculosis and the IL-15 induced gene network.  Inferring that maintaining M. tuberculosis in a latent state and preventing transition to active disease represents host resistance, we believe these results identify IL-32 as one functional marker and potential correlate of protection against active tuberculosis.

overall_design: Adherent peripheral blood monuclear cells were derived by Ficoll-Hypaque from the whole blood of four healthy donors.  Cells adhered to tissue culture-treated plates for 2 h in 1% Fetal Bovine Serum (FBS) in RPMI.  Cells were washed then stimulated with IL-10 (10ng/ml), IL-15 (10ng/ml) (R&D Systems), or IL-4 (1U/ml) in RPMI 1640 supplemented with 10% FBS at 37°C, 5% CO2. Cells were harvested at 6 h and 24 h after stimulation and monocytes purified by CD14 microbeads (Miltenyi Biotec) for a confirmed monocyte purity of at least 90%.   RNA from purified monocytes extracted by Trizol and purified by Qiagen RNeasy Kit.  RNA probe and microarray performed by UCLA Clinical Microarray Core using Ambion labeling kit and Affymetrix Human U133 Plus 2.0 array.


title: TM4SF20 is reduced by TGF-β in A549 cells

status: Public on Aug 04 2014

city: Dallas

first: Qiuyue

last: Chen

state: TX

address: 5323 Harry Hines Blvd.

department: Molecular Genetics

institute: UT Southwestern Medical Center

summary: To find out genes regulated by TGF-β in A549 cells, we compared gene expression of cells treated with 1ng/ml TGF-β versus non-treated cells and find out that expression of  one transmembrane protein, TM4SF20, is reduced by TGF-β.

overall_design: A549 cells were treated with or without 1ng/ml TGF-β for 12h. RNA was extracted and hybridized on Affymetrix microarrays


title: SEQC Toxicogenomics Study: RNA-Seq data set

city: Shanghai

first: Leming

last: Shi

address: 2005 Songhu Road

department: School of Life Sciences

institute: Fudan University

type: Expression profiling by high throughput sequencing

summary: The comparative advantages of RNA-Seq and microarrays in transcriptome profiling were evaluated in the context of a comprehensive study design. Gene expression data from Illumina RNA-Seq and Affymetrix microarrays were obtained from livers of rats exposed to 27 agents that comprised of seven modes of action (MOAs); they were split into training and test sets and verified with real time PCR.

overall_design:
105 samples were selected from the DrugMatirx tissue/RNA bank that is now owned by the National Toxicology Program (NTP). The samples were split into 2 sets, training and test, to allow for the evaluation of classifiers derived from the data. There were 63 samples in the training set and 42 in the test set. Of the 63 samples in the training set 45 were derived from rats treated with test agent and 18 were control samples (3 sets of 6). 39 of the test set samples were derived from test agent treated animals and 6 were from vehicle and route matched controls.   Five MOAs were represented in the training set and 4 MOAs were in the test set.  Two of the MOAs were duplicated from the test set and two were without representation in the training set. For each test agent there were three rats treated, in accordance with the common practice in the field of toxicology. For each MOA there were three representative test agents to ensure adequate power for detecting the MOA signatures. 6 samples from the training set had duplicate libraries sequenced and duplicate sequencing runs for the first library.
DrugMatrix, National Toxicology program (NTP)
Sequencing was carried out in Dr. Charles Wang's Functional Genomics Core at City of Hope Comprehensive Cancer Center, Duarte, CA

first: Charles

first: Scott

last: Auerbach

first: Weida

last: Tong


title: Effect of 48 h aldosterone treatment on late-gestation fetal lung

status: Public on Aug 07 2014

city: Gainesville

first: Maureen

last: Keller-Wood

state: FL

department: Pharmacodynamics

institute: University of Florida

summary: The late-gestation fetal lung has relatively high levels of expression of the mineralocorticoid receptor (MR) as well as the glucocorticoid receptor (GR), suggesting that endogenous corticosteroids may act in the lung through binding at MR as well as GR. This study was designed to determine the effects of physiologically relevant increases in steroids on MR and GR in the late-gestation lung. The GR agonist, betamethasone, the MR agonist, aldosterone, or both agonists were infused intravenously for 48 hours in ovine fetuses of approximately 130 days gestation. Effects on airway pressures during stepwise inflation of the in situ lung, expression of ENaC and Na,K ATPase, and elastin and collagen content were determined at the end of the infusions. We found that aldosterone significantly reduced the initial airway pressures measured in situ during inflation. This effect did not occur with betamethasone alone or in combination with aldosterone. Conversely, betamethasone, but not aldosterone, significantly increased expression of the epithelial sodium channel (ENaC) subunit mRNAs, and collagen and elastin content in the lungs. Aldosterone altered novel gene pathways in the fetal lung, suggesting effects on lung compliance via genes which influence immune pathways and lung stiffness. The results are consistent with corticosteroid-induced fluid reabsorption at birth through GR rather than MR, but suggest that MR contributes effects facilitating lung inflation with the first breaths via nonclassical mechanisms.

overall_design: 4 sets of twin sheep fetuses at approximately 130d gestation (term is 147d) were used. One twin was infused with 0.2 mg aldosterone for 48 h, the other received vehicle.

first: Jarret

last: McCartney

first: Elaine

last: Richards

last: Wood


title: M2 cytokines alter the miRNA expression profile in macrophages

status: Public on Jul 12 2014

first: Shicheng

last: Su

address: 107 Yanjiang West Road

institute: Sun-Yat-Sen Memorial Hospital

summary: To examine the miRNA expression profile of the profibrogenic macrophages, we compared miRNA expression in untreated versus IL-4 or IL-13-treated macrophages using miRNA microarray.IL-4 and IL-13 treatment resulted in marked changes in 18 and 19 miRNAs in macrophages, respectively.(n=3, fold changes>2, P<0.05)

overall_design: Total RNA from human primary macrophages (n=3) treated with or without 20 ng/ml IL-4 or 20ng/ml IL-13 for 48 hr was isolated with a mirVana miRNA Isolation kit (Ambion, Foster, CA). The miRNA expression profile of the samples were examined using miRCURY LNA™ arrays (v18.0; covering 1921 human miRNAs, Exiqon ,Vedbaek, Denmark).


title: mRNA expression profile in IL-4-treated macrophages transfected with miR-142-5p ASO or miR-130a-3p mimics

summary: To identify target genes of miR-142-5p and miR-130a-3p that are involved in M2 polarization, we examined the mRNA expression profile changes after altering miR-142-5p or miR-130a-3p expression in IL-4-treated macrophages.

overall_design: Macrophages were transfected with control ASO, miR-142-5p ASO, control mimics or miR-130-3p mimics using lentiviral vectors.Each treatment contained 3 replicates. After 24 hr, the cells were treated with IL-4 for 24h.mRNA was purified from total RNA after removal of rRNA (mRNA-ONLY Eukaryotic mRNA Isolation Kit, Epicentre). Then, each sample was amplified, transcribed into fluorescent cRNA along the entire length of the transcripts without 3' bias utilizing a random priming method and labeled by Agilent Gene Expression Hybridization Kit (Agilent p/n 5188-5242). The labeled cRNAs were hybridized onto the Agilent_Whole Human Genome Microarray 4x44K v2. After having washed the slides, the arrays were scanned by the Agilent Microarray Scanner (Agilent p/n G2565BA).


title: DUX4-induced gene expression is the major molecular signature in FSHD skeletal muscle

status: Public on Jul 03 2014

city: Seattle

first: Stephen

last: Tapscott

state: WASHINGTON

address: 1100 Fairview N. Ave

department: Human Biology

institute: Fred Hutch Cancer Research Center

summary: Facioscapulohumeral dystrophy (FSHD) is caused by decreased epigenetic repression of the D4Z4 macrosatellite array and recent studies have shown that this results in the expression of low levels of the DUX4 mRNA in skeletal muscle. Several other mechanisms have been suggested for FSHD pathophysiology and it remains unknown whether DUX4 expression can account for most of the molecular changes seen in FSHD. Since DUX4 is a transcription factor, we used RNA-seq to measure gene expression in muscle cells transduced with DUX4, and in muscle cells and biopsies from control and FSHD individuals. We show that DUX4 target gene expression is the major molecular signature in FSHD muscle together with a gene expression signature consistent with an immune cell infiltration. In addition, one unaffected individual without a known FSHD-causing mutation showed expression of DUX4 target genes. This individual has a sibling with FSHD and also without a known FSHD-causing mutation, suggesting the presence of yet unidentified modifier locus for DUX4 expression and FSHD. These findings demonstrate that expression of DUX4 accounts for the majority of the gene expression changes in FSHD skeletal muscle together with an immune cell infiltration.

overall_design: RNA-seq for muscle cells and biopsies from control and FSHD individuals.

first: Zizhen

last: Yao

first: Lauren

last: Snider

first: Judit

last: Balog

first: Richard

last: Lemmers

first: Silvère

last: van der Maarel

first: Rabi

last: Tawil


title: The differential miRNA expression  induces M2 macrophage polarization and mediates their profibrogenic effects

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

platform_organism:
Homo sapiens
synthetic construct


title: Transcriptional response to cotton worm feeding in resistant and susceptible soybean lines

status: Public on Jul 07 2014

city: Nanjing

first: Yongli

last: Wang

address: Weigang No.1

department: Agricultural college

institute: Nanjing Agricultural University

summary:
The interaction between soybean and its destructive insect (cotton worm) is complicated. In this paper, the timecourse of induced responses to cotton worm were characterized in two soybean lines, suggesting complex results with different timepoints of peak induced resistance in resistant (WX) and susceptible (NN) soybean lines.
To get a better understanding of induced resistant mechanisms of soybean against herbivory, two sets of transcriptome profiles of WX and NN at their peak induced resistant timepoints were compared by microarrays

overall_design: The common phenomenon was that no matter in resistant or susceptible line, there always exist a peak level of induced resistance timepoint. Here we are aimed to focus on transcriptional changes induced by insect feeding at the peak timepoints (5 dai and 24 hai) in WX and NN, three biological replicates were used for each of the four treatments (WX treated (WX-T) and control (WX-CK); NN treated (NN-T) and control (NN-CK) ) with three biological replicates.

first: Yong-Li

first: De-Yue

last: Yu


title: Analysis and expansion of the eosinophilic esophagitis transcriptome by RNA sequencing

status: Public on Jun 27 2014

city: Mason

first: Joe

last: Sherrill

state: Ohio

address: 8700 Mason-Montgomery Rd

institute: Procter and Gamble

summary: We utilized RNA sequencing to expand and better define the molecular entities involved in the transcriptional programming within the eosphagus in eosinophilic esophagitis (EoE)

overall_design: Examination of differentially expressed genes from RNA sequencing data performed on esophageal biopsy specimen from 6 healthy controls and 10 patients with active EoE

first: Joseph

first: Marc

last: Rothenberg


title: miRNA expression profiling and to explore the role of miRNAs in DC120-mediated Sox2 down-regulation

status: Public on Jul 18 2014

first: jiao

last: ji

address: 651 Dongfeng Road East

department: State Key Laboratory of Oncology in Southern China

institute: Sun Yat-Sen University Cancer Center

summary: From the results of microarray, 7616 miRNAs with significantly different expression ratios were selected when CNE-2-S-18/SP cells were treated with DC120. Among these, 80 miRNAs were up-regulated and 78 were down-regulated. We then chose 20 miRNAs through the qRT – PCR, and our results showed that 9 miRNAs were up-regulated after treatment with DC120, which was consistent with the results of the microarray. Among these, miR-30a were significantly up-regulated. These results indicated that miR 30a expression was up-regulated by DC120. We then investigated the role of miR 30a in DC120-treated cells, we explored its potential targets using a bioinformatics approach of complementary base pairing. The relative luciferase activity of the reporter that contained the wild type 3' UTR was significantly suppressed when miR 30a was contransfected. In contrast, the luciferase activity of the mutant reporter was unaffected by the contransfection of miR 30a, indicating that miR 30a suppressed Sox2 gene expression using the miR 30a binding sequence at the 3' UTR of the Sox2 gene. Additionally, the ectopic expression of miR 30a caused a decrease in Sox2 protein expression and mRNA levels in CNE-2-S-18 cells. These data demonstrate that miR 30a may directly target the Sox2 gene via seed matches on both 3' UTR. Taken together, our results demonstrate that DC120 regulates Sox2 via up-regulation of miR 30a.

overall_design: In this study, two samples were used to acquire the miRNA expression profiling. We analyzed the differences in miRNA profiles between control (DMSO solution) and DC120 treatment in CNE-2-S-18/SP cells from miRNA microarrays. The CNE-2-S-18/SP cells were separately cultured with a DMSO solution or 10μmol/L DC120 for 15h, and total RNA from all of the cells was extracted. Then we chose 20 up-regulated miRNAs through the qRT – PCR, and our results showed that 9 miRNAs were up-regulated after treatment with DC120. Among these, miR-30a were significantly up-regulated. Then we investigated the role of miR 30a in DC120-treated cells by bioinformatic methods and Dual luciferase reporter system, the function of miR-30a was analyzed through ectopic expression of miR 30a. Taken together, our results demonstrate that DC120 regulates Sox2 via up-regulation of miR 30a.

first: Juan

last: Qin

first: Jiao

last: Ji


title: Expression data from shMiwi/shCaf1 transduced mouse elongating spermatids

status: Public on Jul 11 2014

first: Lantao

last: Gou

address: 320 Yue Yang Road

institute: Institute of Biochemistry and Cell Biology

summary:
We reasoned that the pi-RISC, by virtue of the enormous sequence portfolio of piRNAs, might mediate elimination of a large variety of mRNAs in late stages of spermiogenesis. Both Miwi-null and Caf1-null mice showed early spermiogenic arrest, preventing us from determining the role of MIWI and CAF1 in elongating spermatids using the existing genetic models.
We therefore used microarrays to detail the global effect of MIWI or CAF1 on mRNA levels in mouse elongating spermatids.

overall_design: Using GFP+ elongating spermatids sorted from mouse testes transduced with shMiwi:GFP, shCaf1:GFP, or control pSilencer:GFP, we performed transcriptome profiling on Affymetrix mouse arrays.

first: Lan-Tao

first: Peng

last: Dai


title: Human memory T cells of the bone marrow are resting and maintain long-lasting memory

status: Public on Jun 17 2014

city: Berlin

first: Pawel

last: Durek

address: Charitéplatz 1

country: Germany

institute: Deutsches Rheuma-Forschungszentrum

summary: To compare human memory CD4+ T cell subsets in peripheral blood (PB) and bone marrow (BM) of healthy individuals at transcriptional level, we analyzed the global gene expression of ex vivo PB CD69- as well as BM CD69- and CD69+ memory CD4+ T cells from 4 paired PB and BM samples. The gene expression of these subsets was additionally compared to the transcriptional profile of 8 PB samples taken ex vivo or stimulated with phorbol myristate acetate (PMA) and Ionomycin for 3 hours.

overall_design: Three ex vivo memory CD4+ T cell subsets (CD4+CD45RO+CD69+ and CD4+CD45RO+CD69- cells from bone marrow; CD4+CD45RO+CD69- cells from peripheral blood) were isolated from 4 paired bone marrow and blood samples (two males and two females) or from a different cohort of 8 blood samples (3 males and five females). The purity of sorted cells was higher than 95% as assessed by FACS. Subsequently, a fraction of purified cells from the 8 blood samples were stimulated with phorbol-myristic-acid/ionomycin (PMA/iono) for 3 h and used as high controls. Total RNA of each cell subset was extracted using a NucleoSpin RNA XS Kit (Macherey-Nagel) or 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). Double-stranded complementary RNA was synthesized from 1 µg total RNA using Message AmpII Biotin (Ambion, USA). Fifteen micrograms of fragmented cRNA of each sample were hybridized to 28 HG-U133A plus 2.0 GeneChips (Affymetrix). Hybridization was performed in a Hybridization Oven 640, and chips were washed and stained in the Fluidics Station 400 (both Affymetrix). Finally, the arrays were scanned with a GeneChip Scanner 3000 using the GCOS software, version 1.4, 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.

first: Anna

last: Okhrimenko

first: Joachim

middle: R

last: Grün

first: Kerstin

last: Westendorf

first: Zhuo

last: Fang

first: Simon

last: Reinke

first: Philipp

last: von Roth

first: Georgi

last: Wassilew

first: Anja

middle: A

last: Kühl

first: Robert

last: Kudernatsch

first: Sonya

last: Demski

first: Carmen

last: Scheibenbogen

first: Koji

last: Tokoyoda

first: Mairi

last: McGrath

first: Martin

last: Raftery

first: Günther

last: Schönrich

first: Alessandro

last: Serra

first: Hyun

last: Chang

first: Andreas

last: Radbruch

first: Jun

last: Dong


title: Identification of significant gene regulations for breast cancer from human tissues

status: Public on May 08 2014

first: Xin

last: Qi

address: 1600 SW Archer Rd

department: Medicinal Chemistry

summary: To discover individual genes with potential diagnostic and therapeutic utilities, we use gene expression profiling from real patient tissues to identify significantly regulated genes out of a broad coverage of human transcriptome. We use Agilent gene expression microarray technologies to measure gene expressions of 32 cancerous and normal tissues from breast cancer patients. Total RNAs were extracted and analyzed using Agilent microarray technologies. The whole genome expression profiling has been proformed and several significantly differently expressed genes (such as HS3ST4, MMP1, MMP11) were quatified by qPCR to verify their up/down-regulations, leading to discovery of important genes related to breast cancer metastasis.

overall_design: We examined 32 human breast tissues of three different breast cancer subtypes (including Luminal A, Luminal B, Triple Negative) and normal controls to perform microarray gene expression profiling.

first: Zhuofan

last: Ma


title: Genome-wide immunity studies in the rabbit: transcriptome variations in PBMCs after in vitro stimulation by LPS or PMA/ionomycin

status: Public on Jul 10 2014

city: JOUY EN JOSAS

first: Vincent

last: Jacquier

address: INRA CEA GABI GIS Domaine de Vilvert bat 320

department: GABI

institute: INRA

summary:
Background: Our purpose was to obtain non-existing genome-wide expression data for the rabbit species on the responses of peripheral blood mononuclear cells (PBMCs) after in vitro stimulation by lipopolysaccharide (LPS) or phorbol myristate acetate (PMA) and ionomycin. This transcriptomic study was carried out using microarrays enriched with immunity-related genes, and annotated with the most recent data available for the rabbit genome.    Results: The LPS affected 15 to 20 less genes than PMA/Ionomycin after 4 hours (T4) or 24 hours (T24), of in vitro stimulation, by comparison with mock-stimulated PBMCs. LPS induced an inflammatory response as shown by a significant up-regulation of IL12A and CXCL11 at T4, followed by an increased transcription of IL6, IL1B, IL1A, IL36, IL37, TNF, CCL4 and SAA1 at T24. Surprisingly, we could not find an up-regulation of IL8 either at T4 or at T24.  PMA/ionomycin induced a very early expression of Th1, Th2, iTreg, and Th17 responses by PBMCs at T4. The Th1 response was increased at T24 as shown by the increase of the transcription of IFNG and by contrast to other cytokines that significantly decreased from T4 to 24 (IL2, IL4, IL10, IL13, IL17A, CD69). The granulocyte-macrophage colony-stimulating factor (CSF2) was by far the most over-expressed gene at both T4 and T24 by comparison to mock-stimulated cells, confirming a major impact of PMA/ionomycin on cell growth and proliferation. A significant down-regulation of IL16 was observed at T4 and T24, in agreement with a role of IL16 in in PBMC apoptosis.
Conclusion:  We report new data on the responses of PBMCs to LPS and PMA/ionomycin for the rabbit species, thus enlarging the set of mammalian species for which such reports exist. The availability of the rabbit genome assembly together with highly performing genomic tools should pave the way for more intense genomic studies for this species known to be a very relevant animal model in immunology and physiology.

overall_design: To characterize gene expression changes in peripheral blood mononuclear cells (PBMCs), we collected blood from 4 adult rabbits. PBMCs were isolated and stimulated with LPS or a mixture of  PMA/Ionomycin, versus a control group (C). Cells were harvested either 4h or 24h after activation.

first: Jordi

last: Estellé

first: Barbara

last: Panneau

first: Jérôme

last: Lecardonnel

first: Marco

last: Moroldo

first: Gaëtan

last: Lemonnier

first: Thierry

last: Gidenne

first: Isabelle

middle: P

last: Oswald

first: Véronique

last: Duranthon

first: Claire

last: Rogel-Gaillard


title: Global transcriptome analysis of gene expression changes in Mesorhizobium alhagi CCNWXJ12-2 under salt stress

status: Public on May 06 2014

city: Yangling

first: Xiaodong

last: Liu

state: Shaanxi

address: NO. 22 Xinong Road

department: College of Life Sciences

institute: Northwest Agriculture & Forestry University

summary: Analysis of gene expression changes of Mesorhizobium alhagi CCNWXJ12-2 under high salt stress. Mesorhizobium alhagi CCNWXJ12-2 is isolated  from Alhagi sparsifolia in northwest of China.

overall_design: Total RNA extracted from Mesorhizobium alhagi CCNWXJ12-2 growing in TY medium containing 0.4 M NaCl and 0 M NaCl.

first: Gehong

last: Wei


title: 89 NSCLC patients with gene expression profiles and matching CT imaging data available at TCIA.

status: Public on Jun 19 2014

city: Boston

first: Patrick

last: Grossmann

address: 450 Brookline Ave

department: Radiation Oncology

institute: Dana-Farber Canacer Institute

summary: The Lung3 data set consists of 89 NSCLC patients that were treated at MAASTRO Clinic, The Netherlands. For these patients pretreatment CT scans, tumour delineations and gene expression profiles were available. We used this data set to associate imaging features with gene-expression profiles.

overall_design: 89 samples from NSCLC patients. Samples were obtained by biopsies from cancerous tissue. Tumors were classified as Adenocarcinoma, Papillary, NOS; Squamous Cell Carcinoma, NOS; Non-Small Cell; Papillary Type; or Solid Type.

first: Hugo

middle: J

last: Aerts


title: Perinatal Calorie Restriction with IUGR Perturbs Hepatic Circadian Cycling in Rat Male Offspring

status: Public on Jun 01 2014

city: Los Angeles

first: William

middle: Alexander

last: Freije

address: 650 Charles Young Drive, South CHS B8-127

department: Obstetrics and Gynecology

institute: UCLA

summary: Aside from the perinatal complications associated with low birth weight, individuals born with intra-uterine growth restriction suffer from chronic diseases late in life that ultimately lead to a shortened lifespan. These late life metabolic sequelae of low birth weight include obesity and metabolic syndrome, diabetes mellitus, cardiovascular disease, hypertension, stroke, dyslipidemia, and non-alcoholic fatty liver disease/steatohepatitis. Animal models employing perinatal calorie restriction recapitulate the observations made in humans. Interestingly, if continued calorie restriction is employed post-natally the late life sequelae of intra-uterine growth restriction are ameliorated. These observations linking both fetal and early post natal growth to later health is now termed the developmental origins of health and disease. To further our understanding of the mechanism of how early growth affects late life health we have employed Affymetrix microarray-based expression profiling to characterize hepatic gene expression in a rat model of maternal semi-nutrient restriction. In these experiments we have limited maternal calorie intake to 50% of normal so as to create 3 groups of animals: Control (Con) male offspring born to mothers who were fed normally throughout gestation and lactation; intra-uterine calorie restricted male offspring (IUCR) born to mothers who had 50% restriction of calories from e11 to e21; and combined intra-uterine and post-natal calorie restriction (IPCR) male offspring who were born to mothers who received calorie restriction during both fetal growth (e11 to e21) and post-natally (p1-p21). Livers were collected at p21(day 21 of life) for Con and IPCR groups (IUCR withheld owing to ‘catch up” growth), and at p450 (day 450 of life) for Con, IUCR, and IPCR. The profiling data reveals clear alteration of circadian cycling at P21, and subtle changes for circadian gene expression at p450. In addition, a clear transcriptional response is found during active calorie restriction at p21 but an absence of a transcriptional response late in life at p450.

overall_design: Transcritional studies have been performed using Affymetrix Rat Gene 1.0 arrays for the following treatment groups, with each group run in triplicate (each replicate from separate littermates): Day 21 Control, Day 21 IPCR, Day 450 Con, Day 450 IUCR, Day 450 IPCR

first: Sherin

last: Devaskar


title: Novel biomarkers for distributed stem cells: asymmetric self-renewal associated (ASRA) genes identification by combined cDNA micro-array orthogonal intersection and sparse feature analysis

status: Public on Jun 30 2014

city: clayton

first: Dave

last: Winkler

address: bayview ave

summary: Biomarkers unique for distributed stem cells (DSCs) have proven elusive.  Previous searches for proteins expressed specifically in DSCs were hampered by difficulty obtaining pure DSCs and challenges to successfully mining complex molecular expression data.  To identify novel candidates for DSC biomarkers, we combined a sparse feature selection method with combinatorial molecular expression data focused on asymmetric self-renewal, a defining DSC property.  Our analyses revealed reduced expression of the histone H2A variant H2A.Z as a superior discriminator for asymmetric self-renewal, which proved to be a novel pattern-specific biomarker of DSCs.

overall_design:
Overview:
Sixteen cDNA micro-array samples were analyzed, with four replicates for each of four biologically orthogonal comparisons of congruent asymmetrically self-renewing versus symmetrically self-renewing cells. Sparse feature selection was used to identify a uniquely robust discriminator of these two different DSC self-renewal patterns.

General Approach:
An orthogonal-intersection strategy for identification of asymmetric self-renewal associated genes

Previously, we used non-tumorigenic, immortalized mouse mammary epithelial C127 cells and mouse embryo fibroblasts (MEFs) to derive lines with conditional self-renewal patterns.  The self-renewal pattern of these cells can be reversibly switched between symmetric and asymmetric by varying either culture temperature or Zn concentration, respectively, as a consequence of controlling p53 expression from respectively responsive promoters (1-6).  These and related cell lines were used to design a 2 x 4 orthogonal-intersection microarray analysis for the purpose of identifying genes whose expression consistently showed the same pattern of change between asymmetric self-renewal versus symmetric self-renewal.  Four different pair-wise comparisons were developed in which a state of asymmetric self-renewal was compared to a congruent state of symmetric self-renewal.  The first 3 comparisons were based on a difference in p53 expression, but each had a different biological context.  For asymmetric versus symmetric, respectively, these comparisons were: 1) Zn-inducible p53 MEFs (Ind-8 cells) versus p53-null control MEFs (Con-3 cells), both cultured in Zn-supplemented medium (65 micromolar ZnCl2); 2) Zn-inducible p53 MEFs in Zn-supplemented medium versus in Zn-free medium (1,3-6); and 3) low temperature (32.5˚C)-inducible p53 mouse mammary epithelial cells (MMECs; 1h-3 cells) versus vector-control MMECs (i.e., no p53 transgene; 1g-1 cells), both cultured at 32.5˚C (2,5,6).

The fourth comparison had a special purpose.  It provided a comparison of asymmetric versus symmetric self-renewal that was not due to a difference in p53 expression (1).  Two previously described derivatives of the Zn-responsive p53-inducible MEFs were used to make this comparison.  One line (tI-3 cells) is stably transfected with a constitutively expressed type II inosine monophosphate dehydrogenase (IMPDH II) gene (1,3,5).  IMPDH II is the rate-limiting enzyme for guanine ribonucleotide biosynthesis.  Its down-regulation by p53 is required for asymmetric self-renewal (3,5).  Therefore, even in Zn-supplemented medium, which induces normal p53 expression, cells derived with a stably expressed IMPDH II transgene continue to undergo symmetric self-renewal (3,5).  This abrogation of p53 effects on self-renewal pattern occurs even though other p53-dependent responses remain intact (3).  Under the same conditions, control vector-only transfectants (tC-2 cells) continue to exhibit asymmetric self-renewal (3,5).  Thus, this fourth comparison could be used to exclude genes whose change in expression was primarily due to changes p53 expression and not specifically transitions in self-renewal symmetry as well (1).

We identified genes whose expression varied consistently for all 4 orthogonal comparisons of cells in states of asymmetric self-renewal versus symmetric self-renewal (7).  We developed a new quality control metric called the population division cycle ratio (PDC ratio) to insure consistent degrees of asymmetric self-renewal and symmetric self-renewal across all 4 orthogonal comparisons (6,7).  Prefabricated cDNA microarrays constructed with the National Institute for Aging (NIA) mouse 15K mouse clone set were used for the analysis (8,9).  As detailed in supplemental Materials and Methods (see below), for each of the 4 experimental comparisons, we isolated two independent samples of RNA; and each of the RNA samples was labeled independently with Cy5 and Cy3 fluorescent dyes.  Each independent set of fluorescent RNA samples was used to develop two reciprocal co-hybridizations for each experimental comparison.  Thus, data from 4 microarrays, representing 2 independent experiments, were available for each of the 4 orthogonal contexts for asymmetric versus symmetric self-renewal.

Materials and Methods:

cDNA Microarray Data Analysis
Cells for total RNA extraction were harvested at the time estimated for PDC = 2 (36 hours for Ind-8 and Con-3, 48 hours for tC-2, tI-3, 1h-3, and 1g-1), and were selected for microarray experiments based on the actual PDC ratio curves derived from replicate cell cultures grown in parallel.  The same PDC ratio values were maintained to obtain similar fractions of cycling stem-like cells and non-cycling differentiating cells for all compared asymmetric models.  Total RNA was extracted with the Trizol reagent (Invitrogen, Carlsbad, CA) and impurities were removed with the Qiagen RNeasy kit (Qiagen, Valencia, CA).  Fifty to seventy μg of total RNA was used for cDNA syntheses.  Arabidopsis thaliana mRNAs (Stratagene, La Jolla, CA) were introduced as internal probe standards into reverse transcription reactions to normalize data between different arrays. Cy3- or Cy5-fluorescently labeled cDNAs were hybridized onto the NIA 15K mouse cDNA prefabricated arrays (8), supplied by the Massachusetts Institute of Technology (MIT)-BioMicro Center, using the procedure provided by the MIT-BioMicro Center. Hybridized microarrays were scanned with the arrayWoRxeTM Biochip Reader (Applied Precision LLC, Northwest Issaquah, WA).  The fluorescence intensity of each spot was analyzed from the scanned tiff images by using the DigitalGenomeTM software (MolecularWare, Inc. Cambridge, MA).  The Cy3 and Cy5 fluorescence intensities were normalized by calculating the normalization factor from total intensity normalization (10). Analyses for each self-renewal pattern comparison were performed as duplicate independent experiments.  For each comparison, we performed two chip hybridizations with reciprocally labeled Cy3 or Cy5 target cDNAs to each biological sample. The entire analysis incorporated data from 16 independent chips.

A gene was selected for data analyses only if the mean value of foreground pixels of the spot was greater than the sum of the mean and two standard deviations of the background pixels.  For individual gene probe spots, the expression intensities of Cy5 and Cy3 channels were estimated by subtracting mean backgrounds from mean foregrounds.  The ratios of the final gene expression intensities for the asymmetrically self-renewing states to the respective symmetrically self-renewing states were calculated.  These ratio values (7) were used for sparse feature selection.

References:

1. M. Noh, J. L. Smith, Y. H. Huh, J. L. Sherley, J. L., A resource for discovering specific and universal biomarkers for distributed stem cells. PLoS ONE 6(7): e22077. doi:10.1371/journal.pone.0022077 (2011).

2. J. L. Sherley, P. B. Stadler, D. R. Johnson, Expression of the wild-type p53 antioncogene induces guanine nucleotide-dependent stem cell division kinetics. Proc. Natl. Acad. Sci. USA 92, 136-140 (1995).

3. Y. Liu, S. A. Bohn, J. L. Sherley, Inosine-5’-monophosphate dehydrogenase is a rate-limiting factor for p53-dependent growth regulation. Mol. Biol. Cell 9, 15-28 (1998).

4. L. Rambhatla et al., Cellular senescence: ex vivo p53-dependent asymmetric cell kinetics. J. Biomed. Biotech. 1, 28-37 (2001).

5. L. Rambhatla, S. Ram-Mohan, J. J. Cheng, J. L. Sherley, Immortal DNA strand co-segregation requires p53/IMPDH-dependent asymmetric self-renewal associated with adult stem cells. Cancer Research 65, 3155-3161 (2005).

6. Y. Liu et al., Comparison of bax, waf1, and IMP dehydrogenase regulation in response to wild-type p53 expression under normal growth conditions. J. Cell Physiol. 177, 364-376 (1998).

7. M. Noh, thesis, Massachusetts Institute of Technology (2006).

8. T. S. Tanaka et al., Genome-wide expression pr

first: Minsoo

last: Noh

first: James

last: Sherley

first: Frank

last: Burden

first: David


title: Expression data of mouse developmental T cells (CD4CD8DP, CD4SP and CD8SP) derived from Brd1 deficient thymocyte

status: Public on May 24 2014

city: Chiba

first: ATSUSHI

last: IWAMA

address: 1-8-1 Inohana, Chuo-ku

department: Department of Cellular and Molecular Medicine

institute: Graduate School of Medicine, Chiba University

summary:
Conditional knock out of Brd1(bromodomain containing 1) in muse developmental T cells (CD4CD8DP, CD4SP and CD8SP) by intercrossing with Tie2-Cre
Conditional knock out of Brd1(bromodomain containing 1) in muse MHC class l restricted T cells (CD8SP) by intercrossing with Tie2-Cre and OT-l

overall_design: Developmental T cells (defined by surface markers: CD4, CD8 and TCRβ) derived from control (Tie2-Cre) or Brd1 conditional knock out (Brd1flox/flox, Tie2-Cre) thymocytes were isolated by fluorescence activated cell sorting (FACS) and subjected to a microarray analysis. CD8SP T cells were also isolated from control (Tie2-Cre, OT-l) or Brd1 conditional knock out (Brd1flox/flox, Tie2-Cre, OT-l) thymocytes intercrossed with OT-l.

first: Yuta

last: Mishima

first: Atsushi

last: Iwama

first: Satoshi

last: Miyagi


title: Cell senescence abrogates the immunomodulatory therapeutic potential of human mesenchymal stem cells

city: Madrid

first: Manuel

middle: Angel

last: Gonzalez

address: Melchor Fernandez Almagro, 3

country: Spain

institute: CNIC

summary: In this study, we have addressed how cellular senescence influences the immunomodulatory potential of human mesenchymal stem cells (hMSCs). We induced cell senescence in a panel of bone marrow-derived hMSC samples by means of gamma-irradiation, and performed both gene expression and miRNA microarray analyses on the untreated and senescent samples. We also compared the gene expression profile of untreated and senescent hMSCs with those obtained from several hMSCs samples used in an ongoing allogeneic clinical study of Graft Versus Host Disease (GVHD), of which their therapeutic efficacy is known. We have identified several genes (PLEC, C8orf48, TRPC4, and ZNF14) differentially expressed in senescent hMSCs that are similarly regulated in hMSC samples that did not show a therapeutic effect in the GVHD study. These genes might be useful as markers to evaluate the therapeutic potential of hMSCs used in future clinical studies.

overall_design: We compared the gene and miRNA expression profiles of untreated (WT) control bone marrow-derived hMSCs with the same primary cell lines 10 days after gamma-irradiation (SEN) and with several hMSCs samples used in a clinical stydy of GVHD. The samples used in the clinical study were classified in two groups, depending on whether they elicited a therapeutic response (G1) or not (G2). A total of four independent samples (biological replicates) were used for WT and SEN conditions. For the samples used in the clinical study, a total of five samples were used for the G1 group, and three samples for the G2 group.

first: Juan

middle: C

last: Sepúlveda

first: María

last: Tomé

last: Fernández

first: Mario

last: Delgado

first: Judith

last: Campisi

first: Antonio

last: Bernad

last: González


title: Effect of EtOH on transcriptome signatures in human dental pulp stem cells

status: Public on May 03 2014

first: Yong

last: Kim

address: 10833 Le Conte Ave, 73-022 CHS

country: USA

summary: We have performed gene expression microarray analysis to profile transcriptomic signatures affected by EtOH in human dental pulp stem cells

overall_design: Established human dental pulp stem cells were treated with different dose of EtOH (0, 1, 5, 10, 20 and 50mM) for a different time periods (24 and 48 hrs). Total RNA was extracted and subjected to gene expression microarray analysis using Affymetrix human genome 2.0 plus array

first: Omar

last: Khalid

first: Jeffrey


title: MicroRNA-188 regulates age-related switch between osteoblast and adipocyte differentiation

status: Public on Apr 29 2014

city: Changsha

first: Peng

last: Cheng

state: Hunan

address: 139# Middle Renmin Road

department: The Second Xiangya Hospital

institute: Central South University

summary: To identify microRNAs which differentially expressed in the BMSCs of aged and young mice and and investigate its influences on BMSCs differentiation with ageing.

overall_design: The microRNAs expressions of BMSCs from 3 aged mice and 3 young mice were measured.

first: Changjun

last: Li

first: Jinyu

last: Wang

first: Yusi

last: Chen

first: Ting

last: Liu

first: Mengke

last: Liang

first: Hui

last: Xie

first: Xianghang

last: Luo


title: The transcriptional regulators TAZ and YAP direct Transforming Growth Factor-beta-induced tumorigenic phenotypes in breast cancer cells

status: Public on Apr 02 2014

first: Boston University

last: Microarray and Sequencing Resource

state: MA

address: 72 East Concord Street, E631

department: Microarray and Sequencing Resource

institute: Boston University

summary:
Uncontrolled Transforming growth factor-beta (TGFβ) signaling promotes aggressive metastatic properties in late-stage breast cancers. However, how TGFβ-mediated cues are directed to induce late-stage tumorigenic events is poorly understood, particularly given that TGFβ has clear tumor suppressing activity in other contexts. Here we demonstrate that the transcriptional regulators TAZ and YAP (TAZ/YAP), key effectors of the Hippo pathway, are necessary to promote and maintain TGFβ-induced tumorigenic phenotypes in breast cancer cells. Interactions between TAZ/YAP, TGFβ-activated SMAD2/3, and TEAD transcription factors reveal convergent roles for these factors in the nucleus. Genome-wide expression analyses indicate that TAZ/YAP, TEADs and TGFβ-induced signals coordinate a specific pro-tumorigenic transcriptional program. Importantly, genes cooperatively regulated by TAZ/YAP, TEAD, and TGFβ, such as the novel targets NEGR1 and UCA1, are necessary for maintaining tumorigenic activity in metastatic breast cancer cells. Nuclear TAZ/YAP also cooperate with TGFβ signaling to promote phenotypic and transcriptional changes in non-tumorigenic cells to overcome TGFβ repressive effects. Our work thus identifies crosstalk between nuclear TAZ/YAP and TGFβ signaling in breast cancer cells, revealing novel insight into late-stage disease-driving mechanisms.
Expression profiling was conducted following the repression of the transcriptional regulators TAZ and YAP (TAZ/YAP), the TEAD family of transcription factors (TEAD1/2/3/4), or the TGFb signaling pathway (with SB-431542, an inhibitor of the TBRI recpeptor) in human MDA-MB-231-LM2 breast cancer cells treated with TGFβ1.

overall_design: Human MDA-MB-231-LM2-4 breast cancer cells were transfected with control siRNA, or siRNAs targeting TAZ/YAP or all four TEADs and were treated 24 hours later with 500pM TGFβ1 or 5mM SB-431542 for an additional 24 hours. Total RNA was isolated and twelve microarrays in total were performed, with each condition carried out three times on separate days. The Boston University Microarray Core generated the data using the Affymetrix Human Gene 1.0 St Array.

first: Samantha

last: Hiemer

first: Xaralabos

last: Varelas


title: A Genomic Portrait of Resectable Hepatocellular Carcinomas: Implications of RB1 and FGF19 Aberrations for Patient Stratification.

status: Public on May 01 2014

city: Incheon

first: Farhan

last: Haq

address: 7-45, Songdo-dong, Yeonsu-gu

institute: Gachon University

summary: Whole exome sequencing and copy number analysis was performed on 231 hepatocellular carcinomas (72% with hepatitis B viral infection) that were classified as early-stage hepatocellular carcinomas, candidates for surgical resection. Recurrent mutations were validated by Sanger sequencing. Unsupervised genomic analyses identified an association between specific genetic aberrations and postoperative clinical outcomes.   Recurrent somatic mutations were identified in 9 genes, including TP53, CTNNB1, AXIN1, RPS6KA3, and RB1. Recurrent homozygous deletions in FAM123A, RB1, and CDKN2A, and high-copy amplifications in MYC, RSPO2, CCND1, and FGF19 were detected. Pathway analyses of these genes revealed aberrations in the p53, Wnt, PIK3/Ras, cell cycle, and chromatin remodelling pathways. RB1 mutations were significantly associated with cancer-specific and recurrence-free survival after resection (p = 0.016 and p = 0.001, respectively). FGF19 amplifications, known to activate Wnt signalling, were mutually exclusive with CTNNB1 and AXIN1 mutations, and significantly associated with cirrhosis (p = 0.017). RB1 mutations can be used as a prognostic molecular biomarker for resectable hepatocellular carcinoma. Further study is required to investigate the potential role of FGF19 amplification in driving hepatocarcinogenesis in patients with liver cirrhosis and to investigate the potential of anti-FGF19 treatment in these patients.

overall_design: HCC samples classified at a surgically curable stage were analysed (n = 231 cases). Clinical features include tumour size, microvascular invasion, early recurrence, the Edmondson-Steiner histological grade, the fibrosis stage of the non-neoplastic liver tissue, and the serum alpha-fetoprotein levels. All specimens were obtained with the approval of the Institutional Review Board of Asan Medical Center, Seoul, South Korea, and with documented informed consent from patients.

first: Sung-Min

last: Ahn

first: Se

last: Jang

first: Ju

middle: H

last: Shim

first: Deokhoon

first: Seung-Mo

last: Hong

first: Chang

last: Sung

first: Daehyun

last: Baek

first: Adnan

last: Ansari

first: Sun

last: Lee

last: Chun

first: Seongmin

last: Choi

first: Jongkyu

first: Sukjun

first: Shin

last: Hwang

first: Young-Joo

first: Jong-eun

first: Wang-rim

last: Jung

first: Hye

first: Eunho

last: Yang

first: Eunsil

last: Yu

first: Han

first: Gu

last: Kong


title: REST and Stress Resistance in Aging and Alzheimer’s Disease

status: Public on Mar 16 2014

first: Tun-Hsiang

address: 77 Avenue Louis Pasteur

department: Genetics

institute: HMS

summary: Comparison of the gene expression profiles of adult human brain samples from frontal cortical regions, including samples from young, middle aged, normal aged.

overall_design: Comparison of 12 young (<40yr), 9 middle aged (40-70yr), 16 normal aged (70-94yr), and 4 extremely aged (95-106yr)

first: Bruce

last: Yankner

first: Tao

last: Lu