title: Genome-wide expressing profiling of nasopharyngeal carcinoma primary tumors versus non-cancerous nasopharyngeal tissues.

status: Public on Jan 05 2014

city: Guangzhou

first: ChaoNan

last: Qian

state: Guangdong

address: 651 Dongfeng East Road

department: State Key Laboratory of Oncology in South China

institute: Sun Yat-sen University Cancer Center

summary: To explore differentially expressed genes between nasopharyngeal carcinoma (NPC) primary tumors and non-cancerous nasopharyngeal tissues, 18 NPC tissue samples versus 18 control samples were utilized to perform genome-wide expressing profiling. Consequently, 2992 genes were found to be differentially expressed in NPC tissues relative to the control (FC>2, P<0.05). Among these 2992 genes, uPA was ranked as the top one in all upregulated genes sorted by ascending order of P-value. Moreover, expression of uPAR was also upregulated in NPC tissues with FC=3.34 and P=7.52×105.

overall_design: 18 nasopharyngeal carcinoma primary tumors and 18 non-cancerous nasopharyngeal tissues were used to perform genome-wide expressing profiling. The median ages of patients were 46 (range, 19-77) for NPC patients and 45 (range, 18-78) for the non-cancerous cohort. Almost one third of patients were female. All samples were collected before any anti-cancer treatment.

last: Bao

first: Xue

last: Cao

first: Dong

middle: H

last: Luo

first: Li

middle: X

last: Peng

first: Yong

last: Yan

last: Zheng

first: Ping

last: Xie

first: Yun

last: Liang

first: Fang

first: Bi

last: Huang

last: Zeng

first: Chao


title: Analysis of potential transcriptomic biomarkers for doxorubicin cardiotoxicity in peripheral blood

status: Public on Dec 31 2013

city: Little Rock

first: Valentina

last: Todorova

state: AR

address: 4301 W. Markham

country: USA

institute: UAMS

summary: The aim of this study is the characterize and compare heart and PBMC transcriptomes of rats treated with doxorubicin in order to isolate a list of similarly differentially regulated genes with an ultimate goal to indentify PBMC biomarkers for early prediction of doxirubicinduced cardiotoxicity

overall_design: Total RNA was isolated from PBMC and hearts of rats treated with doxirubicin or saline for 48 hrs and used for gene expression

first: Val

first: Marjorie

middle: L

last: Beggs

first: Ishwori

last: Dhakal


title: Gene expression profile in HEK293T cells infected with Chikungunya virus

status: Public on Jan 20 2014

city: New Delhi

first: Dr. Ritu

last: Kulshreshtha

state: New Delhi

address: Room 134, Block I

department: Dept of Biochemical Engineering and Biotechnology

country: India

institute: Indian Institute of Technology

summary:
HEK293T grown in 6 well plates were infected with CHIKV and total RNA was isolated from cells at 0, 12 and 24 hrs post infection.
CHIKV gene expression signature was generated.

overall_design: Cells grown on 6-well plates. Three biological replicates of uninfected and two biological replicates of infected samples

first: Tanvi

last: Saxena

first: Bhavna

last: Tandon

first: Shivani

last: Sharma

first: Pratima

last: Ray

first: Alok

middle: R

first: Ritu


title: Transcriptional response to tetanus toxoid in pigs with divergent humoral and lean growth performance

city: Dummerstorf

first: Klaus

last: Wimmers

address: Wilhelm-Stahl-Allee 2

country: Germany

institute: Leibniz Institute for Farm Animal Biology (FBN)

summary: In vivo microarray study of transcriptional changes in porcine peripheral blood mononuclear cells (PBMCs) during the immune response to tetanus vaccination

overall_design:
Comparisons of high (hiLG) vs. low lean growth (loLG) and high antibody titer (hiAB) vs. low AB (loAB)
Expt type: Mixed model including repeated measures

first: Siriluck

last: Ponsuksili

first: Marcel

last: Adler


title: Role of CD26 on oncogenic gene expression

status: Public on Dec 01 2014

city: Kamakura

first: Satoshi

last: Kondo

state: Kanagawa

address: Tebiro 6-10-1

department: New Projects Development Division

country: Japan

institute: Toray Industries,Inc.

summary:
Purpose: Investigate a mechanism of CD26 to promote tumor progression in mesothelioma.
Background: CD26 play a role on tumor progression and is expressed in many kinds of human malignancy, including mesothelioma, renal cell carcinoma, and T cell leukemia/lymphoma. In mesothelioma, expression of CD26 is observed in mesothelioma cells, but not in non-neoplastic mesothelioma cells, suggesting a role of CD26 on tumor progression (Clin Cancer Res 13:4191-4200, 2007). CD26 is known to activate T-cells through associating with adenosine deaminase, mannose 6-phosphatic/insulin-like growth factor II receptor, or with CD45RO (Immunol Res 161:55-70, 1998). However, mechanism of CD26 to promote tumor progression was not known.

overall_design: In order to examine a mechanism of CD26 to promote tumor progression in mesothelioma, changes of gene expression profile on CD26-depletion or CD26-overexpression in mesothelioma cells were investigated by microarray analysis. CD26 was depleted by transfection of CD26 siRNA into mesothelioma cell line ACC-MESO1, while CD26 overexpression was conducted by transfecting CD26 into mesothelioma cell line MSTO-211H. Total RNAs were isolated from these cell lines and subjected to microarray analysis.

first: T

last: Okamoto

first: S

last: Iwata

first: C

last: Morimoto


title: Comparison of the expression profiles of R20291 strain : a wild type strain, a fliC mutant and a fliC mutant complemented after 14h of growth in PY and a wild type strain and a fliC mutant after 14h of mouse infection in vivo

city: Paris

first: Monot

last: Marc

address: 25, rue du docteur roux

department: Genomes and Genetics

country: France

institute: Institut Pasteur

summary: Transcriptionnal profiling of C. difficile R20291 strain : a wild type strain, a fliC mutant and a fliC mutant complemented after 14h of growth in PY and a wild type strain and a fliC mutant after 14h of mouse infection in Vivo

overall_design: two-conditions experiments, R20291 strain : a wild type strain, a fliC mutant and a fliC mutant complemented in Vitro and a wild type strain and a fliC mutant in Vivo, 4 biological replicates for each condition, in an direct design.

first: Amira

last: Barketi

first: Marc

last: Monot


title: Effects of tocilizumab versus methotrexate therapy on gene expression profiles in the early rheumatoid arthrtis synovium

status: Public on Dec 30 2013

city: Brussels

first: Bernard

middle: Robert

last: Lauwerys

address: Avenue Hippocrate 10

department: Institut de Recherches Expérimentales et Cliniques

country: Belgium

institute: Université catholique de Louvain

summary:
Rheumatoid arthritis (RA) is a chronic, systemic autoimmune inflammatory disease that is characterized by the presence of inflammatory cytokines, including interleukin-6 (IL-6). Here, we investigated the global molecular effects of Tocilizumab, an approved humanized anti-IL6 Receptor antibody, versus Methotrexate therapy, in synovial biopsy samples collected prospectively in early RA before and 12 weeks after administration of the drug. The results were compared with our previous data, generated in prospective cohorts of Adalimumab- and Rituximab-treated (Methotrexate- and anti-TNF-resistant, respectively) RA patients.
We found that Tocilizumab induces a significant down-regulation of genes included in specific pathways: cytokines & chemokines (e.g. IL-6, IL-7, IL-22, CCL8, CCL11, CCL13, CCL19, CCL20), and T cell activation. By contrast, Tocilizumab induces a significant up-regulation of genes associated with healing processes. These effects are significantly more pronounced as compared to Methotrexate, Rituximab, or Adalimumab therapies. By opposition to the effects of Adalimumab, Tocilizumab therapy does not induce a decreased expression of genes involved in cell proliferation.

overall_design: Paired synovial biopsy samples were obtained from the affected knee of early RA patients before and 12 weeks after initiation of Tocilizumab (n=12) or Methotrexate (n=8) therapy. SDAI remission criteria were computed prospectively before, 3 months and 6 months after administration of the drugs and patients’ responses were defined according to their SDAI remission status at 6 months. Gene expression studies were performed using GeneChip Human Genome U133 Plus 2.0 arrays.

first: Julie

last: Ducreux

first: Patrick

last: Durez

first: Adrien

middle: N

last: Toukap

first: Frédéric

middle: A

last: Houssiau


title: Genome-wide analysis of anti_GBM antibody responsive gene expression in the kidney of different mouse strains using Illumina microarrays

status: Public on Dec 24 2013

city: Dallas

first: yun

last: lian

state: TX

address: 5323 Harry Hines Blvd.

institute: UT Southwestern Medical Center

summary: Different mosue strains showed different sensitivity to anti-GBM antibody induced glomerulai nephritis. By analyze the renal gene expressin profiles in different mouse stains after challenging with anti-GBM antibody, we will be able to identify the genes and pathway underlining the anti-GBM nephritis.

overall_design: 5 mice strains (BALB/C and B6 strains are resistant to anti-GBM nephritis, DBA1, 129/svj and NZW are anti-GBM sensitive strains) were challenged by anti-GBM antibody. Total RNA were extracted from kidney cortex of each mice and subject to microarray analysis using Illumina Mouse WG-6 v1 Beadchips. Data was analyzed using BeadStudio.

first: Quan-Zhen

last: Li

first: Chandra

last: Mohan


title: Characterization of Nicotiana attenuata plants with reduced expression of HD-Zip HD20 (ir-hd20 plants).

city: Jena

first: Klaus

last: Gase

address: Hans-Knoell-Strasse 8

department: Molecular Ecology

institute: Max-Planck-Institute for Chemical Ecology

summary: Identification of transcripts that change expression in corollas of Nicotiana attenuata plants with reduced expression of the transcription factor HD20.

overall_design: Gene expression in opening corollas of Nicotiana attenuata wild type and ir-hd20 plants was measured from isolated corollas collected at 12 pm. Three independent experiments were performed with wild type plants and three independent experiments were performed with ir-hd20 plants. A total of 274 genes were identified as differentially regulated in ir-hd20 plants compared to wild type plants.

first: Delfina

last: Re

first: Gustavo

last: Bonaventure


title: To analyze the effect of loss of mitochondria on the transcriptome of Candida albicans

status: Public on Dec 05 2013

city: Delhi

first: Sneh

middle: Lata

last: Panwar

state: Delhi

address: New Mehrauli Road

department: Scholo of Life Sciences

institute: Jawaharlal Nehru University

summary: This set of experiment was done in order to analyze the effect of a dysfunctional mitochondria on C. albicans. The mutant was obtained by deleting the gene FZO1, which is known to be involved in mitochondrial biogenesis in S. cerevisiae. We show that the deletion of FZO1 leads to a change in mitochondrial morphology, which affects the mitochondrial membrane potential and causes the loss of mtDNA. Upon performing a transcriptome analysis, we observed that the mutant showed upregulation of genes like AOX2, MDR1 etc., while the genes involved in iron uptake were dysregulated. Besides, genes involved in cell wall biosynthesis were also downregulated.

overall_design: Genotypic Technology Pvt. Ltd. designed Custom Whole Genome Candida albicans 8x15k GE Microarray (AMADID-026377).


title: Dicer-like proteins and their role in plant-herbivore interactions in Nicotiana attenuata

summary: DICER-like proteins produce small RNAs that silence genes involved in development and defenses against viruses and pathogens. Which DCLs participate in plant-herbivore interactions remains unstudied. We identified four distinct DCL genes and stably silenced their expression by RNAi in Nicotiana attenuata, a model system for the study of plant-herbivore interactions. Silencing DCL1 expression was lethal to the plants. Manduca sexta larvae performed significantly better on ir-dcl3and ir-dcl4 plants, but not on ir-dcl2 plants compared to wild type plants. Phytohormones, defense metabolites and microarray analyses revealed that when DCL3 and DCL4 were silenced separately, herbivore resistance traits were regulated in distinctly different ways. Crossing of the lines revealed complex interactions in the patterns of regulation. Single ir-dcl4 and double ir-dcl2/ ir-dcl3 plants were impaired in JA accumulation, while JA-Ile was increased in ir-dcl3 plants. Ir-dcl3 and ir-dcl4 plants were impaired in nicotine accumulation; silencing DCL2 in combination with either DCL3 or DCL4 restored nicotine levels to those of WT. Trypsin proteinase inhibitor activity and transcripts were only silenced in ir-dcl3 plants. We conclude that DCL2/3/4 interact in a complex manner to regulate anti-herbivore defenses and that these interactions significantly complicate the already challenging task of understanding smRNA function in the regulation of biotic interactions.

overall_design: Gene expression in leaves of Nicotiana attenuata wild type, irDCL3 and irDCL4 plants was measured at 1 hour after elicitation with oral secretions of Manduca sexta larvae. Three independent experiments were performed with wild type plants and three independent experiments were performed with irDCL3 and irDCL4 plants. A total of 811 genes were identified as differentially regulated in irDCL3 and irDCL4 compared to wild type plants.

first: Tohir

last: Bozorov


title: MicroRNA transcriptional regulation in lung cancer

status: Public on Dec 10 2013

city: Madrid

first: Gema

last: Moreno-Bueno

state: Madrid

address: Arturo Duperier

department: Biochemistry

country: Spain

institute: IIB

summary:
Squamous cell lung cancer (SCC) and adenocarcinoma are the most common subtypes of the lung tumours. The search for cancer-directed treatments has increased the need for understanding molecular features of either histological subtype. The aim of this study was to identify transcriptional regulation differences due to miRNA expression profiles between SCC and adenocarcinoma. For this propose, a total of 44 patients were evaluated to assess the correlation between the miRNA and messenger RNA (mRNA) expression levels. Total RNA were isolated, amplified, labeled and hybridized on Agilent human whole genome V2 22 K microarray chip. qRT-PCR was conducted to validate our microarray data. MicroRNA expression was detected and quantified using the TaqMan Low Density Arrays. Predicted miRNA-mRNA interactions were taken from miRanda, miRWalk and TargetScan. After processing data, changes in 56 mRNAs as well as in 9 miRNAs were detected between SCC and adenocarcinoma. Nearly 20% of overall deregulated genes were targeted by at least one of the 9 miRNAs (miR-149, miR-205, miR-375, miR-378, miR-422a, miR-483-5p, miR-494, miR-601 and miR-708) differentially expressed between SCC and adenocarcinoma. Genes predicted (CEACAM6, CGN, CLDN3, ABCC3, MLPH, ACSL5, TMEM45B, MUC1) to be targeted by several miRNAs were individually validated by qRT-PCR.  We found genes involved in tight junctions and other involved in resistance to anticancer agents. These genes were reliable biomarkers, with high sensitivity and specificity, to detect differences between the two most common histological subtypes of lung cancer. In conclusion, our data demonstrate that the transcriptional regulation differences through miRNA expression play an important role in key hallmarks of non-small cell lung cancer.
Identification of new molecular markers in  lung carcinoma

overall_design:
44 tumour samples following surgical resection for clinical early stage NSCLC (SCC and adenocarcinoma)
This series represents the mRNA profiling only (not miRNA). The related miRNA data are in Series GSE43000.

first: Sonia

last: Molina-Pinelo

first: Gabriel

last: Pozo

first: MariaDolores

last: Pastor

first: Marta

last: Hergueta

first: Rocio

last: García-Carbonero

first: Ana

last: Nogal

first: Raul

last: Suárez

last: Salinas

first: Francisco

last: Pozo-Rodríguez

first: Fernando

last: Lopez-Rios

first: MariaTeresa

last: Agulló-Ortuño

first: Amancio

last: Carnero

first: Luis

last: Paz-Ares


title: Time course profiles in salt shock roots of Ceriops tagal

first: SH

last: Shi

address: 135 Xin Gang Xi

country: China

institute: Sun Yat-Sen University

summary: Transcriptional differentiation in response to environmental stresses plays critical roles in adaptation. Mangroves are dominant in intertidal zones and form dense forest at the sea-land interface, but little is known about the impact of transcriptional phenotype on their adaptation to the saline environments. To address this issue, we prepared customized chips containing cDNA from the root cDNA library of a mangrove species, Ceriops tagal, and then monitored the time-course transcript profiles in the roots by conducting a series of microarray experiments. Five durations of salt shock with 500 mM NaCl, namely 2, 5, 10, 24 and 192 hours, were included. A total of 88 unigenes that were recognized to be up- or down-regulated by salt shock and both gene categories in relation to stresses-induced responses and transcription factor activity were over-predominant. The stresses-responsive genes were significantly overrepresented, some of which were regulated in differential manners from their homologues genes in Arabidopsis. Specific transcriptional regulations were employed by C. tagal to cope with salt shock, which could benefit the salt-tolerant lifestyle of this mangrove species and possibly contribute to establishment of adaptation to the saline environments.

overall_design: A reference design was used to analyze gene expression differences. Salt stressed young roots were harvested from seedlings of C. tagal at the ends of each shock duration. Young roots of unshocked seedlings were used as controls and harvested at the same time. Three biological replicates were set up for each treatment and corresponding control, respectively, each containing a pool of total RNA from 4 seedlings. Salt stressed samples were compared with the corresponding controls at each time point by co-hybridizing to the customized cDNA arrays

first: Shan

last: Liang

first: Suhua


title: Wnt Pathway Contributes to the Protection of Acute Lymphoblastic Leukemia Cells by Bone Marrow Stromal Cells and May Be a Therapeutic Target

status: Public on Jan 01 2014

city: Houston

first: Xiaoping

last: Sun

address: 1515 Holcombe Blvd

institute: M.D. Anderson Cancer Center

summary: Acute lymphoblastic leukemia (ALL) is the most common cancer in children and one of the most common cancers in adults. Although most children with ALL can be cured, approximately 60% of adults with ALL develop drug resistance or experience relapse and cannot be cured with traditional chemotherapy. One possible reason that treatment fails to eradicate ALL cells is that residual leukemia cells are protected by various components of the bone marrow microenvironment, such as marrow stromal cells (MSCs). To evaluate the effects of MSCs on ALL cell survival and response to chemotherapy, we co-cultured ALL cells with human or murine MSCs. We found that both human and murine MSCs protected human ALL cell lines and primary ALL cells from spontaneous and Ara-C-induced apoptosis. MSCs also modulated the cell cycle and increased ALL cell proliferation. Specifically, we found that Wnt signaling activation contributed to MSC-mediated drug resistance. In contrast, blocking the Wnt pathway led to decreased ALL cell viability. Chemotherapy plus the β-catenin inhibitor XAV939 resulted in a decreased tumor burden and improved overall survival in an ALL mouse model compared with chemotherapy alone. Our data demonstrate that targeting the Wnt pathway may represent an innovative approach to the treatment of ALL.

overall_design: Reh cells were harvested after being treated with Ara-C for 48 hours, with or without HS and HS-5 human stromal cells. Independent triplicate samples were used in the experiments. Total RNA was prepared using TRI reagent (Ambion, Austin, TX) and amplification and synthesis of cRNA was performed using Illumina TotalPrep RNA amplification kit (Ambion). cRNA was then hybridized to the HumanHT-12 v3 Expression BeadChip (Illumina, San Diego, CA) according to the manufacturer's instructions.

first: Yang

last: Yang

first: Saradhi

last: Mallampati

first: Baohua

first: Jing

last: Zhang

first: Yun

last: Gong

first: Zhen

last: Cai


title: MG-treated vs non-treated ST2 cells Mouse 32K

status: Public on Nov 19 2013

city: Toon

first: Sohei

last: Kitazawa

state: Ehime

address: Shitsukawa

department: Molecular Pathology

institute: Ehime University

summary: In diabetics, methylglyoxal (MG), a glucose-derived metabolite, plays a noxious role by inducing oxidative stress, which causes and exacerbates a series of complications. With the use of microarray analysis, we comprehensively screened the gene expression profiles of ST2 cells, derived from a multipotent bone marrow stromal cell line, in the presence or absence of oxidative stress induced by100 μM methylglyoxal (MG) treatment to charactrize genes related to diabetic complications.

overall_design: Mouse bone marrow stromal cell-line ST2 (RIKEN, Tsukuba, Japan) was cultured in α-MEM (Sigma, St. Louis, MO) supplemented with 10% FBS (Sigma), 100 μg/ ml penicillin/ streptomycin (ICN Biomedicals, Inc., Aurora, OH) and 100 μM methylglyoxal (MG), and maintained at 37°C in a humidified atmosphere with 5% CO2. Total RNA was isolated from ST2 cells treated with or without 100 μM methylglyoxal (MG) or 1 μM of 5-aza-2’-deoxycytidine (5-aza-dC) by standard methods with the use of an RNeasy Protect Mini kit (Qiagen KK, Tokyo, Japan) according to the manufacturer’s instructions. Cy3, Cy5 differential expression asasy by Mouse 32K Filgen array


title: Genome-wide analysis of gene expression in cancerous and normal human bladder tissues

status: Public on Nov 20 2013

city: Moscow

first: Anastasia

last: Zabolotneva

address: Miklukho-Maklaya 16/10

country: Russia

institute: Intitute of Bioorganic chemistry

summary: Analysis of differential gene expression in urothelium cancer cells compared to healthy bladder cells. The goal of researh was to discover any differences in signaling pathways regulation between cancer and normal cells and searching potential molecular markers for early cancer diagnostics.

overall_design: Total RNA was isolated from 9 cancerous tissue samples obtained during cystectomy and 3 normal bladder tissue samples obtaind post mortem from donors without bladder cancer.

first: Anton

last: Buzdin

first: Peter

middle: V

last: Shegay

first: Nurshat

middle: M

last: Gaifullin

first: Andrew

last: Garazha


title: U87 cells implanted on a chick CAM (Chorioallantoic Membrane)

status: Public on Dec 02 2013

city: Birmingham

last: Turan

address: University of Birmingham, Edgbaston

country: United Kingdom

institute: University of Birmingham

summary: Glioblastoma multiforme (GBM) brain tumours have one of the shortest mean survival times (<1 year). In vivo models of GBM in mice and rats have been developed to study aspects of glioma that cannot be observed in cell culture such as angiogenesis, invasion and metastasis. Gliomas can be induced by implantation of rodent glioma cell lines into the brain or flank of nude mice. The disadvantages of rodent models however include variable growth rate and poor penetrance, which leads to difficulties in collecting clearly graded samples (pre-vascular/vascular). Bikfalvi et al have previously established a human GBM model that addresses these issues based on the chicken egg chorio-allantoic membrane (CAM), a highly vascularised extra-embryonic tissue. We have used DNA microarrays and a CAM model of GBM to study gene expression during the recruitment and development of the tumour vasculature. Over a 5 day period samples were taken every 12 hours from the tumour implantation site consisting of tumour cells and stroma cells, and also from a site distant from the implantation site consisting of just CAM cells. This study will shed light on the dynamic transcriptional signature of pathological angiogenesis.

sample_organism:
Gallus gallus
Homo sapiens

platform_organism:
Gallus gallus
Homo sapiens

overall_design: On day 10 of embryonic development 3-5 million U87 cells were deposited onto the surface of the CAM after gentle laceration. The cells were contained within a plastic ring and each tumour was size matched based on its volume. Tumour/stroma and distant CAM samples were cut out at 12 hour intervals post implantation for 5 days, equalling 10 time points. Each time point consisted of three replicates. U87 cells in culture (pre-implantation) were also included in the study in triplicate.

first: Kim

last: Clarke


title: lncRNAs expression signatures of gastric cancer

status: Public on Dec 09 2013

city: shanghai

first: wei

last: gu

address: No.197,Rui Jin Er Road

institute: ruijin hospital

summary: Long noncoding RNAs (LncRNAs) are an important class if pervasive genes involved in a variety of biological functions. LncRNAs have been recently implicated as having oncogenic and tumor suppressor roles. To further investigate the function of lncRNA in gastric cancer, we use lncRNA microarray to describe LncRNAs profiles in 6 pairs of human gastric adenocarcinoma and the corresponding adjacent nontumorous tissues.

overall_design: The experimental samples  are divided into two groups(normal and tumor) to compare lncRNA expression profiling of those

first: Wei

last: Gu


title: Bovine nose tissues: Yellow nose vs. Black nose

status: Public on Dec 26 2013

city: Anseong

first: Sang Hwan

last: Kim

state: Kyonggi-do

address: Chungang-no

department: Institute of Genetic Engineering

country: South Korea

institute: Hankyong national university

summary: The coat color of mammals is determined by the melanogenesis pathway, which is responsible for maintaining the balance between black-brown eumelanin and yellow-reddish phaeomelanin. It is also believed that the color of the bovine nose is regulated in a similar manner; however, the molecular mechanism underlying pigment deposition in the black nose has yet to be elucidated. The aim of the present study was to identify melanogenesis-associated genes that are differentially expressed in the black vs. yellow nose of native Korean cows.

overall_design: Experiment, Yellow nose vs. Black nose HanWoo

first: Sang-Hwan

first: Jong-Taek

last: Yoon


title: miRNA expression signatures in Tif1b-deficient hematopoietic stem cell

status: Public on Nov 12 2013

city: Chiba

first: Satoru

last: Miyagi

state: Chiba

department: Graduate school of Medicine

institute: Chiba university

summary: miRNA expression analyses of Tif1b-deficient hematopoietic stem cells (HSCs). Tif1b loss leds to  rapid depletion of HSCs. Expression analyses provide insight into the role of Tif1b in the maitenance of HSC.

overall_design: HSCs (c-Kit+ Sca1+ Lineage- )  are sorted from adult bone marrow and are subjected into microarray analyses.

first: Atsushi

last: Iwama


title: Gene expression changes during hematopoietic cell differentiation

status: Public on Nov 06 2013

summary: Gene expression analyses of hematopoietic stem cells (HSCs), progenitor cells (HPCs), and differentiated cell. Gene expressions of long-term HSCs (CD34-ckit+Sca1+Lineage-),  short term HSCs (CD34+ckit+Sca1+Lineage-), Progenitor cells (ckit+Sca1- Lineage-), and differentiated cels (Lineage+)  were examined by microarray. Results provide insight into the mechanism of hematopoietic cell differentiation.

overall_design: Long-term HSCs (CD34-ckit+Sca1+Lineage-), Short term-HSCs (CD34+ckit+Sca1+Lineage-), Progenitor cells (ckit+Sca1- Lineage-, and Lineage+), and differentiated cell (Lineage+) were sorted from mouse bone marraw and were examined by microarray. Results provide insight into the mechanism of hematopoietic cell differentiation.


title: The Tif1Beta-Hp1 system maintains transcriptional integrity of hematopoietic stem cells

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

overall_design: Refer to individual Series


title: Differentially Expressed Wound Healing-Related microRNAs in the Human Diabetic Cornea

status: Public on Nov 09 2013

city: Los Angeles

first: Vincent

middle: Anthony

last: Funari

state: CA

address: 8700 Beverly Drive

department: Medical Genetics

institute: Cedars Sinai

summary: MicroRNAs are powerful gene expression regulators, but their corneal repertoire and potential changes in corneal diseases remain unknown. Our purpose was to identify miRNAs altered in the human diabetic cornea by microarray analysis, and to examine their effects on wound healing in cultured telomerase-immortalized human corneal epithelial cells (HCEC) in vitro. Using microarrays, 29 miRNAs were identified as differentially expressed in diabetic samples. Two miRNA candidates showing the highest fold increased in expression in the diabetic cornea were confirmed by Q-PCR and further characterized. HCEC transfection with h-miR-146a or h-miR-424 significantly retarded wound closure, but their respective antagomirs significantly enhanced wound healing vs. controls. Cells treated with h-miR-146a or h-miR-424 had decreased p-p38 and p-EGFR staining, but these increased over control levels close to the wound edge upon antagomir treatment. In conclusion, several miRNAs with increased expression in human diabetic central corneas were found. Two such miRNAs inhibited cultured corneal epithelial cell wound healing. Dysregulation of miRNA expression in human diabetic cornea may be an important mediator of abnormal wound healing.

overall_design: Total RNA was extracted from age-matched human autopsy normal (n=6) and diabetic (n=6) central corneas, Flash Tag end-labeled, and hybridized to Affymetrix® GeneChip® miRNA Arrays. Select miRNAs associated with diabetic cornea were validated by quantitative RT-PCR (Q-PCR) and by in situ hybridization (ISH) in independent samples.

first: Mehrnoosh

last: Saghizadeh


title: Gene expression profiling of paired pterygium and conjunctiva tissues

status: Public on Nov 02 2013

city: Singapore

first: Aihua

last: Hou

address: 11 Third Hospital Avenue, #06-18, SNEC Building

department: Ocular Surface Research Group

country: Singapore

institute: Singapore Eye Research Institute

summary: To identify dysregulated molecules between pterygium tissues and uninvolved conjunctiva tissues from the same eye,  we performed whole genome microarray expression profiling.

overall_design: Total RNA from four pairs of pterygium and uninvolved conjunctiva tissues from the same eye was extracted and used for microarray experiments.

first: Wanwen

last: Lan

first: Louis

last: Tong


title: The genomic distribution of sex-biased genes in Drosophila serrata: X-chromosome demasculanisation, feminisation, and hyper-expression in both sexes

status: Public on Nov 05 2013

city: St Lucia

first: Stephen

last: Chenoweth

state: QLD

address: The School of Biological Sciences, The University of Queensland

department: Biological Sciences

country: Australia

institute: The University of Queensland, Australia

summary: Data from whole-body, head, thorax, abdomen, ovaries, testes and accessory glands was used to assess possible causes of a non-random distribution of sex-biased genes (sexually dimorphic expression). All samples were derived from virgin adult flies.

overall_design: We measured gene expression of male and female Drosophila serrata from 43 lines (whole-body) and multiple tissues sampled from outbred laboratory stock. All flies were originally samples from Brisbane, Queensland, Australia. Data from two replicates for each sex/line are presented, plus 3-5 replicates per sex/tissue. 24 adult whole-body samples were not used in analyses due to poor quality, giving a total of 176 arrays.

first: Scott

last: Allen

first: Russell

last: Bonduriansky

middle: F


title: Solanum torvum transcriptional responses to nematodes

status: Public on Nov 01 2013

city: Fiorenzuola D'Arda

first: Paolo

last: Bagnaresi

address: Via S. Protaso 302

department: Genomics

country: Italy

institute: CRA-GPG

summary: Solanum torvum Sw is worldwide employed as rootstock for eggplant cultivation because of its vigour and resistance/tolerance to the most serious soil-borne diseasesas bacterial, fungal wilts and root-knot nematodes.  A 30,0000 features custom combimatrix chip was designed and microarray hybridizations were conducted for both control and 14 dpi (day post inoculation) with Meloidogyne incognita-infected roots samples. We also tested the chip with samples from the phylogenetically-related nematode-susceptible eggplant species Solanum melongena.The genes identified from S. torvum catalogue, bearing high homology to knownnematode resistance genes, were further investigated in view of their potential role in the nematode resistance mechanism.

sample_organism:
Solanum torvum
Solanum virginianum

overall_design: total RNA was extracted from control and 14 days post-infection (infection with root-knot nematode Meloidogyne  incognita)  from roots of Solanum torvum and Solanum melongena. Three biological replicates were used for each condition and genotype for a total of 12 samples.


title: Microarray gene expression analysis of tumorigenesis and regional lymph node metastasis in laryngeal squamous cell carcinoma

city: beijing

first: Demin

last: Han

address: beijing  100730

institute: Beijing Tongren Hospital ofCapital Medical University

summary:
Objective: The purpose of this study was to investigate the molecular basis of tumorigenesis and regional lymph node metastasis in LSCC, and provide a set of genes that may be useful for the development of novel diagnostic markers and/or more effective therapeutic strategies.

Methods: A total number of 10 patients who underwent surgery for primary laryngeal squamous cell carcinoma were recruited for microarray analysis. LSCC tissues compared with corresponding adjacent non-neoplastic tissues were analysed by Illumina mRNA microarrays,and LSCC tissues with regional lymph node metastasis and LSCC tissues without regional lymph node metastasis were analyzed in the same manner.The most frequently differently expressed genes screened by microarrays were also validated by qRT-PCR in another 42 patients diagnosed for LSCC .

Results: Analysed by Illumina mRNA microarrays,there were 361 genes significantly related to tumorigenesis while 246 genes significantly related to regional lymph node metastasis in LSCC. We found that the six genes (CDK1,CDK2,CDK4,MCM2,MCM3,MCM4) were most frequently differently expressed functional genes related to tumorigenesis while eIF3a and RPN2 were most frequently differently expressed functional genes related to regional lymph node metastasis in LSCC. The expressions of these genes were also validated by qRT-PCR.

Conclusions: The research revealed a gene expression signature of tumorigenesis and regional lymph node metastasis in laryngeal squamous cell carcinoma.Of the total, the deregulation of several genes (CDK1, CDK2, CDK4, MCM2, MCM3, MCM4, EIF3a and RPN2) were potentially associated with disease development and progression. The result will contribute to the understanding of the molecular basis of LSCC and help to improve diagnosis and treatment.

first: Jugao

last: Fang


title: Transcriptional events during lung recovery from MRSA infection: a mouse pneumonia model

city: Chicago

first: Jiwang

last: Chen

state: IL

address: 840 S Wood Street

institute: University of Illinois at Chicago

summary: Community-associated methicillin-resistant Staphylococcus aureus (CA-MRSA) is an emerging threat to human health throughout the world. Rodent MRSA pneumonia models mainly focus on the early innate immune responses to MRSA infection. However, the molecular pattern and mechanisms of recovery from MRSA lung infection are largely unknown. In this study, a nonlethal mouse MRSA pneumonia model was employed to investigate events during lung recovery from MRSA infection. We compared lung bacterial clearance, bronchoalveolar lavage fluid (BALF) characterization, lung histology, and gene expression profiling between Day 1 and Day 3 post-MRSA infection. Compared to Day 1 post-infection, bacterial colony counts and both BALF total cell number and protein concentration significantly decreased at Day 3 post-infection. Lung cDNA microarray analysis identified 47 significantly up-regulated and 35 down-regulated genes (p<0.01, 1.5-fold change [up and down]). Changes in eight genes were confirmed by real-time PCR. The pattern of gene expression suggests lung recovery is characterized by enhanced cell division, vascularization, and wound healing and by adjustment in host adaptive immune responses. Collectively, this data helps elucidate the molecular mechanisms of lung recovery after MRSA infection.

overall_design: RNA expression analysis was performed using the Illumina MouseRef-8 v2.0 BeadChip (Illumina, San Diego, CA), which provides coverage of approximately 25,700 genes and expressed sequence tags. Four independent mouse lung tissue samples at Day 1 and Day 3 post-MRSA infection were used in this study.

first: Richard

last: Wunderink

first: Gilbert

last: Feng

first: Simon

last: Lin


title: Gene expression signatures in Tif1b-deficient hematopoietic stem cell

first: Satoru

last: Miyagi

summary: Gene expression analyses of Tif1b-deficient hematopoietic stem cells (HSCs). Tif1b loss leads to  rapid depletion of HSCs. Expression analyses provide insight into the role of Tif1b in the maitenance of HSC.

overall_design: HSCs (c-Kit+ Sca1+ Lineage- )  are sorted from fetal liver or adult bone marrow and are subjected into microarray analyses.


title: Global gene expression profiles in ovarian cancer linked to Lynch syndrome

status: Public on Oct 14 2013

city: Lund

first: Katarina

last: Bartuma

address: Barn garan 2b

country: Sweden

institute: department of Oncology

summary: Heredity is a major cause of ovarian cancer. Lynch syndrome is associated with 10-12% risk of ovarian cancer, diagnosis at young age and a predilection for endometrioid and clear cell tumors. Global gene expression profiling applied to 25 Lynch syndrome-associated and 42 sporadic ovarian cancers revealed 335 differentially expressed genes and involvement of the mTOR and the MAPK/ERK pathways. The clear cell tumors had distinct expression profiles with upregulation of HER2 and apoptosis signaling pathways. The distinct expression profiles provide clues relevant for hereditary tumorigenesis and may be relevant for therapeutic strategies and refined diagnostics in ovarian cancer linked to Lynch syndrome.

overall_design: Ovarian cancers linked to Lynch syndrome (n=25) were compared to a matched series of sporadic ovarian cancers (n=42), selected from a population-based consecutive series in which hereditary was excluded based on family history, normal MMR protein staining and lack of mutations in BRCA1 and BRCA2.

first: Jenny-Maria

last: Jönsson

first: Mev

last: Cominguez-Valentin

first: Katja

last: Harbst

first: Zohreh

last: Ketabi

first: Susanne

last: Malander

first: Mats

first: Ana

last: Carneiro

first: Anna

last: Måsbäck

first: Göran

first: Mef

last: Nilbert


title: Molecular Profiles of Human Breast Cancer and Their Association with Tumor Subtypes and Disease Prognosis (Illumina)

city: Bethesda

first: Atsushi

last: Terunuma

state: MD

address: 37 Convent Drive, 37/3050

department: Dermatology Branch

institute: National Cancer Institute

summary: This study identified DNA methylation patterns that were associated with tumor subtypes, disease outcome, and distinct metabolome and gene expression patterns.

overall_design: This study performed a large scale DNA methylation (Illumina HumanMethylation450 BeadChip [HumanMethylation450 15017482 v.1.1], N=72), gene expression (Affymetrix Human Gene 1.0 ST Array [HuGene-1_0-st], N=108), and metabolome (Metabolon, Inc. Durham, NC) analysis of fresh-frozen human breast tumors from African-American and European-American patients from the greater Baltimore area, Maryland (US), with survival follow-up.

first: Robert

middle: S

last: Hudson

first: Stefan

last: Ambs


title: Molecular Profiles of Human Breast Cancer and Their Association with Tumor Subtypes and Disease Prognosis (Affymetrix)

overall_design: This study performed a large scale DNA methylation (Illumina HumanMethylation450 BeadChip [HumanMethylation450 15017482 v.1.1], N=73), gene expression (Affymetrix Human Gene 1.0 ST Array [HuGene-1_0-st], N=108), and metabolome (Metabolon, Inc. Durham, NC) analysis of fresh-frozen human breast tumors from African-American and European-American patients from the greater Baltimore area, Maryland (US), with survival follow-up.


title: mRNA and lncRNA expression profiles in MCF-7 breast cancer cells stably overexpressing pcDNA3.1-PinX1 and Empty Vector

status: Public on Sep 30 2013

city: Guangzhou

first: Rong

last: Shi

address: 7th Floor, Building of Life Science, 1023 Sha Tai Nan Road

institute: Southern Medical University

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

summary: To elucidate the molecular mechanism and signaling pathways that PinX1 is involved in, a Human LncRNA Array V2.0 (Arraystar, USA)-based genome wide screen of the alterations in lncRNA and mRNA expression profiles was performed in MCF-7 cells stably overexpressing PinX1.

overall_design: MCF-7 breast cancer cells were transfected with the pcDNA3.1-PinX1 and pcDNA3.1 empty vector and the microarray analysis were performed after the  clonal selection of cells  with a high expression level.

first: Shi

last: Rong

first: Zhou

last: Jueyu


title: Comprehensive analysis of gene expression profiles of Spodoptera exigua larvae challenged with Bacillus thuringiensis VIP3A toxin

status: Public on Sep 27 2013

city: Burjassot

first: Agata

middle: K

last: Jakubowska

state: Valencia

address: Dr. Moliner 50

department: Genetics

institute: University of Valencia

summary: Host-pathogen interactions result in complex relationship, many aspects of which are not completely understood. Vip proteins, which are Bacillus thuringensis (Bt) insecticidal toxins produced during the vegetative stage, are selectively effective against specific insect pests. This new group of Bt proteins represents an interesting alternative to the classical Bt Cry toxins because current data suggests that they do not share the same mode of action. We have designed and developed a genome-wide microarray for the beet armyworm Spodoptera exigua, a serious lepidopteran pest of many agricultural crops, and used it to better understand how Lepidopteran larvae respond to the treatment with the insecticidal protein Vip3Aa. With this approach, the goal of our study was to evaluate the changes in gene expression levels caused by treatment with sublethal doses (causing 99% growth inhibition) of Vip3Aa at 8 and 24 h after treatment. Results indicated that the toxin provoked a wide transcriptional response, with 19% of unigenes in the microarray responding significantly to treatment. The number of up- and down-regulated unigenes was very similar.. The number of genes whose expression was regulated at 8 h was similar to the number of genes whose expression was regulated after 24 h of treatment. The up-regulated sequences were enriched for genes involved in innate immune response and in pathogen response such as antimicrobial peptides (AMPs) and repat genes. The down-regulated sequences were mainly unigenes with homology to genes involved in metabolism. Genes related to the mode of action of Bt Cry proteins were found, in general, to be slightly overexpressed. The present study is the first genome-wide analysis of the response of lepidopteran insects to Vip3Aa intoxication. An insight into the molecular mechanisms and components related to Vip intoxication will allow designing of more effective management strategies for pest control.

overall_design: Changes in gene expression levels caused by treatment with sublethal doses (causing 99% growth inhibition) of Vip3Aa were measured at 8 and 24 h after treatment by means of custom Spodoptera exigua microarray. Six to seven larvae were used for each time point and three independent experiments were performed at each time point.

first: Yolanda

last: Bel

first: Juliana

last: Costa

first: Salvador

last: Herrero

first: Baltasar

last: Escriche


title: Microarray Analysis of Tomato's Early and Late Wound Response Reveals New Regulatory Targets for Leucine Aminopeptidase A

status: Public on Oct 31 2013

city: Riverside

first: Linda

middle: Lee

last: Walling

address: 900 University Avenue

department: Botany and Plant Sciences

institute: University of California

summary: Wounding due to mechanical injury or insect feeding causes a wide array of damage to the cell including cell disruption, desiccation, metabolite oxidation, and disruption of primary metabolism. In response, plants regulate a variety of genes and metabolic pathways to cope with injury. Tomato (Solanum lycopersicum) is a model for wound signaling but few studies have examined the comprehensive gene expression profiles in response to injury. A cross-species microarray approach using the TIGR potato 10-K cDNA array was analyzed for large-scale temporal (early and late) and spatial (locally and systemically) responses to mechanical wounding in tomato leaves. These analyses demonstrated that tomato regulates many primary and secondary metabolic pathways and this regulation is dependent on both timing and location. To determine if LAP-A, a known modulator of wound signaling, influences gene expression beyond the core of late wound-response genes, changes in RNAs from healthy and wounded Leucine aminopeptidase A-silenced (LapA-SI) and wild-type (WT) leaves were examined. While most of the changes in gene expression after wounding in LapA-SI leaves were similar to WT, overall responses were delayed in the LapA-SI leaves. Moreover, two pathogenesis-related 1 (PR-1c and PR-1a2) and two dehydrin (TAS14 and Dhn3) genes were negatively regulated by LAP-A. Collectively, this study has shown that tomato wound responses are complex and that LAP-A's role in modulation of wound responses extends beyond the well-described late-wound gene core.

overall_design: A reference design hybridization strategy was used with WT (0-hr) being the reference RNA. The reference RNA was a pool from five WT 0-hr RNAs. RNAs from wounded or unwounded leaves labeled with Cy3 and the reference RNA labeled with Cy5 were co-hybridized to the potato cDNA array. Three dye bias experiments were performed in which WT 0-hr RNAs were labeled with Cy3 and co-hybridized with the Cy5-labeled reference RNA (WT 0-hr RNAs from a different pool). After normalization, no dye bias was detected on these experiments (p-value<0.05).

first: Melissa

last: Scranton

first: Jonathan

last: Fowler

first: Thomas

last: Girke


title: The Stress-Regulated Transcription Factor CHOP Promotes Hepatic Inflammatory Gene Expression, Fibrosis, and Oncogenesis

city: Iowa City

first: David

middle: Thomas

last: Rutkowski

state: IA

address: 51 Newton Rd.

department: Anatomy and Cell Biology

institute: University of Iowa Carver College of Medicine

summary: Viral hepatitis, obesity, and alcoholism all represent major risk factors for hepatocellular carcinoma (HCC). Although these conditions also lead to integrated stress response (ISR) or unfolded protein response (UPR) activation, the extent to which these stress pathways influence the pathogenesis of HCC has not been tested. Here we provide multiple lines of evidence demonstrating that the ISR-regulated transcription factor CHOP promotes liver cancer. We show that CHOP expression is upregulated in liver tumors in human HCC and two mouse models thereof. Chop-null mice are resistant to chemical hepatocarcinogenesis, and these mice exhibit attenuation of both apoptosis and cellular proliferation. Chop-null mice are also resistant to fibrosis, which is a key risk factor for HCC. Global gene expression profiling suggests that deletion of CHOP reduces the levels of basal inflammatory signaling in the liver. Our results are consistent with a model whereby CHOP contributes to hepatic carcinogenesis by promoting inflammation, fibrosis, cell death, and compensatory proliferation. They implicate CHOP as a common contributing factor in the development of HCC in a variety of chronic liver diseases.

overall_design: 24 samples were analyzed from 9 month old male C57BL/6J or backcrossed Chop-/- male mice, injected with either PBS or a single dose of 25 mg/kg diethylnitrosamine (DEN) at 15 d.o. Samples are either from whole liver or liver tumors.

first: D

middle: T


title: The GtaR quorum-sensing protein negatively regulates a capsular polysaccharide gene transfer agent (RcGTA) receptor on Rhodobacter capsulatus cells

status: Public on Sep 19 2013

city: St. John's

first: Ryan

middle: G

last: Mercer

state: Newfoundland

address: 232 Elizabeth Avenue

department: Biology

country: Canada

institute: Memorial University

summary: Expression profiles of wild type and gtaI mutant in logarithmic and stationary phase of growth. The objective was to search for differentially regulated genes potentially associated with EPS production in R. capsulatus.

overall_design: A single sample of each strain in both growth phases for basic comparison of expression profiles.

first: Cedric

last: Brimacombe

first: Aaron

last: Stevens

first: Andrew

last: Lang

middle: J

last: Beatty


title: DNA microarray analysis of E.coli K12 MG1655 exposed to prolonged stationary phase

status: Public on Sep 12 2013

city: Hyderabad

first: kotakonda

last: Arunasri

state: Andhra Pradesh

address: Habsiguda

institute: Centre for Cellular and Molecular biology

summary:
This study explores the effects of prolonged stationary phase, on whole genome expression of Escherichia coli.
In summary these results imply that prolonged stationary phase cells have shown less growth rate compared to fresh cells due to the low abundance of transcripts for translation initiation factor infC, and for all the seven rrn operons of 5S, 16S, 23S ribosomal RNA which further delayed in protein synthesis leading to low biomass in prolonged stationary phase cells.

overall_design: 28 days old E.coli cells were grown in the presence of LB broth and LB broth supplemented with 10% v/v glycerol. RNA was extracted from these samples, cDNA was prepared, fragmented cDNA was labled with labeling reagent and hybridized with Affymetrix E.coli2.0 genome array chips.Data was analysed to get the effect of glycerol on E.coli gene expression

first: S

last: Shivaji

first: K

first: M

last: Adil


title: Methylation Profiling of Human Kidney Tubules

status: Public on Sep 14 2013

city: Philadelphia

first: Yi-An

last: Ko

state: Pennsylvania

address: 415 curie blvd

department: Genetics & Gene Regulation

institute: UPeenn

summary: We sought to decrease the cell type heterogeneity of kidney tissues to increase the resolution of methylation profiles. To that end, microdissected human kidney tissue from patients are used and hybridized on Illumina HumanMethylation450 BeadChip arrays.

overall_design: We extract genomic DNA from microdissected human kidney tubule samples. And used these genomic DNA for the Illumina 450K beads array.

first: Sang

middle: Y

last: Han

first: Ae

middle: D

last: Park

first: Katalin

last: Susztak


title: Expression data from preadipocytes isolated from laying hen

status: Public on Sep 17 2013

city: Winnipeg

first: Alemu

middle: Regassa

last: Hunde

state: Manitoba

address: 12 Dafoe Road

department: Animal Science

institute: University of Manitoba

summary: Adipogenesis is one of the most intensively studied models of cellular differentiation, and transcriptional activities involved in the process have been extensively investigated. We analyzed transcripts differentially expressed between hen preadipocytes treated with adipogenic cocktail containing 500 nM dexamethasone, 0.5 mM 3-isobutyl-1-methylxanthine, 20 ug/mL insulin and 300 uM OA (DMIOA) and non-treated control cells and transcripts differentially expressed between preadipocytes treated with DMIOA alone and those treated with a combination of DMIOA and 20(S)-hydroxycholesterol (DMIOA + 20(S)) using Affymetrix GeneChip Chicken Genome Array containing 28,000 transcripts.

overall_design: Preadipocytes were isolated from hen abdominal tissue, cultured and treated with different treatments

last: Regassa

first: Woo-Kyun

last: Kim


title: The genome and development-dependent transcriptomes of Pyronema confluens: a window into fungal evolution

status: Public on Sep 20 2013

city: Bochum

first: Minou

last: Nowrousian

address: Universitaetsstr. 150

department: Molecular and Cellular Botany

institute: Ruhr-University Bochum

type: Expression profiling by high throughput sequencing

summary: This transcriptome analysis accompanies the genome sequencing of Pyronema confluens for purposes of annotation and gene expression quantification. P. confluens is a basal filamentous ascomycete that forms primitive fruiting bodies (apothecia) to generate its sexual spores. We have performed RNA-seq for two growth conditions allowing only vegetative growth and one condition allowing sexual development to identify genes that are differentially regulated during fruiting body formation.

overall_design: The samples sex (sexual development), DD (growth in darkness, no sexual development), and vegmix (pool of several conditions, no sexual development) were sequenced as paired-end reads on an Illumina HiSeq 2000, two independent biological replicates for each sample, two technical replicates for each biological replicate (each library was sequenced twice in two independent flow cells).

first: Stefanie

last: Traeger

first: Florian

last: Altegoer

first: Michael

last: Freitag

first: Toni

last: Gabaldon

first: Frank

last: Kempken

first: Abhishek

last: Kumar

first: Marina

last: Marcet-Houben

last: Pöggeler

first: Jason

middle: E

last: Stajich


title: Expression data from canine osteosarcoma stem cells

city: Edinburgh

first: Lisa

last: Pang

address: Easter Bush Estate

institute: Roslin Institute

summary: Osteosarcoma is the most common primary bone tumours of dogs. Canine osteosarcoma contains a sub-population of cancer stem cells. Here we used canine-specific microarrays to compare the global gene expression profiles of osteosarcoma stem cells to adherent cancer cells and canine mesenchymal stem cells.

overall_design: Canine osteosarcoma spheres were isolated by their ability to form tumourspheres. Spheres, adherent cells and mesenchymal stem cells were harvested and used for RNA extraction and hybridisation on Affymetrix microarrays (Canine 2.0). Four biological replicates of each sample were included.

first: David

last: Argyle


title: Combinatory microarray and SuperSAGE analyses identify pairing-dependently transcribed genes in Schistosoma mansoni males, including follistatin

status: Public on Sep 09 2013

city: Giessen

first: Silke

last: Leutner

address: Rudolf-Buchheim-Straße 2

institute: Institute for Parasitology

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

overall_design: Refer to individual Series


title: Mutational Variation in Gene Expression

status: Public on Sep 01 2013

city: Nouzilly

first: Julie

last: Collet

address: Centre INRAE

institute: INRAE

summary:
Transcript abundance was measured in whole-body virgin male Drosophila serrata from 41 inbred lines that had diverged through 27 generations of mutation accumulation.
Pleiotropic mutations are the ultimate source of genetic variation in complex traits, including many human diseases. However, the nature and extent of mutational pleiotropy remain largely unknown. Here, we investigate the variation in 11,604 gene expression traits among 41 mutation accumulation lines of Drosophila serrata, which had diverged for 27 generations. We detected significant mutational variance in 4.6% of ESTs, but 70% of ESTs were invariant among lines, allowing us to reject a null hypothesis of phenome-wide universal pleiotropy. Mutational covariance among ESTs was detected at a frequency of only 1 in 193 random pairs of variable EST, bu t was detected among random combinations of five ESTs in 1 in 5 cases, revealing that mutational covariance among multiple ESTs was common.  The observed frequency of significant multivariate covariance among random ESTs implied that a substantial number of ESTs (>70) must be pleiotropically affected by at least some mutations.

overall_design: We measured gene expression of male Drosophila serrata from 41 mutation accumulation lines (whole-body). Data from two replicates for each line are presented.

first: Katrina

last: McGuigan

first: Elizabeth

middle: A

last: McGraw

first: Yixin

middle: H

last: Ye

first: Mark

middle: W

last: Blows


title: Genome-wide analysis of mRNA expression alterations of mucosa associated lymphoid tissue lymphoma translocation gene 1 (Malt1) -/- or Wild Type (WT) Naïve T cells induced to differentiate into (T helper) Th1 or Th17 cells

city: Toronto

first: carl

last: virtanen

state: Ontario

address: 101 College St

department: Princess Margaret Genomics Centre

institute: University Health Network

summary: Microarrays were used to examine gene expression changes at two time points following the induction of differentiation of Malt1 deficient Naive T cells into Th1 or Th17 cells.  The present study aims to find the effect that Malt1 deficiency has on lineage specific T cell differentiation.  Malt1 is a NF kappa B regulator and plays a key role in peripheral T cell activation and proliferation, but its role in T cell differentiation is not clear. Aspects of the latter are what the current data set investigates.

overall_design: Total RNA obtained from naïve T cells at two time points following induction to lineage specific T helper cells.

first: Dirk

last: Brenner

first: Anne

last: Brustle

first: Carl

last: Virtanen

first: Tak

last: Mak


title: Genetic Differences in the Immediate Transcriptome Response to Stress Predict Risk-Related Brain Function and Psychiatric Disorders

city: Munich

first: Janine

last: Arloth

address: Kraepelinstr. 2-10

institute: Max Planck Institute of Psychiatry

summary: Depression risk is exacerbated by genetic factors and stress exposure; however, the biological mech- anisms through which these factors interact to confer depression risk are poorly understood. One putative biological mechanism implicates variability in the ability of cortisol, released in response to stress, to trigger a cascade of adaptive genomic and non-genomic processes through glucocorticoid receptor (GR) activation. Here, we demonstrate that common genetic variants in long-range enhancer elements modulate the immediate transcriptional response to GR activation in human blood cells. These functional genetic variants increase risk for depression and co-heritable psychiatric disorders. Moreover, these risk variants are associated with inappropriate amygdala reactivity, a transdiagnostic psychiatric endophenotype and an important stress hormone response trigger. Network modeling and animal experiments suggest that these genetic dif- ferences in GR-induced transcriptional activation may mediate the risk for depression and other psy- chiatric disorders by altering a network of function- ally related stress-sensitive genes in blood and brain.

overall_design: A Dexamethasone Suppression Test was performed in 160 male subjects. Baseline and stimulated (3 hours after 1.5 mg dexamethasone p.o.) whole blood samples were analyzed using Illumina Human HT-12 v3 arrays.

first: Elisabeth

middle: B

last: Binder


title: Combinatory microarray and SuperSAGE analyses identify pairing-dependently transcribed genes in Schistosoma mansoni males, including follistatin [SuperSAGE]

summary: Comparing the transcriptomes of pairing-experienced (EM) and pairing-unexperienced (UM) male Schistosoma mansoni (in biological triplicates) we detected 253 genes to be significantly differeantially (p < 1-10; log2ratios < -0.585 or > +0.585)  transcribed.

overall_design: pairing-experienced (EM) and pairing-unexperienced (UM) male Schistosoma mansoni were compared by SuperSAGE (Matsumura et al., 2003; with minor changes: Molina et al., 2008), sequencing Illumina (Solexa)

first: Katia

middle: C

last: Oliveira

first: Björn

last: Rotter

first: Joao

middle: P

last: Kitajima

first: Svenja

last: Beckmann

first: Christin

last: Buro

first: Steffen

last: Hahnel

first: Sergio

last: Verjovski-Almeida

first: Peter

last: Winter

first: Christoph

last: Grevelding


title: Molecular Profiles of Human Breast Cancer and Their Association with Tumor Subtypes and Disease Prognosis

first: Atsushi

last: Terunuma

type:
Expression profiling by array
Methylation profiling by array


title: Combinatory microarray and SuperSAGE analyses identify pairing-dependently transcribed genes in Schistosoma mansoni males, such as follistatin [Microarray]

first: Silke

last: Leutner

summary: Transcriptional profiling of  S. mansoni pairing-experienced males (EM)  vs. pairing unexperienced males (UM)

overall_design: Two conditions (EM vs. UM) with three biological samples of EM and in parallel other three biological samples of UM. For each sample (three EM and three UM) were performed four technical replicas.


title: Gene expression data of untreated and RA-treated wild type and RXRα-deficient mice liver

status: Public on Aug 21 2013

city: Sacramento

first: Yuqi

last: He

state: California

address: Rm3400, Research III, UC Davis Medical Center, 4645 2nd Ave

institute: UC Davis Medical Center

summary:
Our project focuses on retinoic acid (RA) effect on hepatic lipid homeostasis. Even though RA has more than one receptor including retinoids x receptor (RXR) and retinoic acid receptor (RAR), most probably, RA effect on lipid homeostasis is mediated by RXR and its partners such as PXR, FXR, and PPAR. So we treated the wild type and RXRα-knockout mice by retinoic acid to check the global gene expression especially for lipid homeostasis genes.
We used microarrays to observe the global gene expression underlying hepatic lipid homeostasis.

overall_design: We treated both the wild type and RXRα-KO mice with normal diet and RA-containing diet for 7 days. For each group, three replicates were done. Liver total RNA were used to test global gene expression by microarray.

first: Yu-Jui

last: Wan

first: Lei

last: Gong

first: Lois

last: Lehman-McKeeman

first: Qi

last: Zhan

first: Yanliu

last: Lu

first: Hui-Xin

last: Liu


title: Expression data from stable clones of BE(2)M17 cell line expressing miR-142 or miR-null

status: Public on Aug 23 2013

city: Omaha

first: Amrita

last: Datta Chaudhuri

state: NE

address: 985800 Nebraska Medical Center

department: Pharmacology & Experimental Neuroscience

institute: University of Nebraska Medical Center

summary:
MiR-142 is upregulated in neurons in HIV and SIV encephalitis. We have created stable clones of the BE(2)M17 human neuroblastoma cell line overexpressing miR-142.
Gene expression in these miR-142-expressing clones was compared to stable clones transfected with control miR-null in order to identify miR-142 targets relevant to neuronal dysfunction in HIV encephalitis.

overall_design: RNA was extracted from 3 independent  miR-142-expressing clones (6B, 6C, 6G) and 3 independent miR-null expressing clones (1A, 2A, 2B) for expression analysis. Partek genomics suite was used for data analysis. Genes that had fold change > -2.5 and p <0.001 were chosen for validation by RT-PCR

last: Chaudhuri

first: Sowmya

middle: V

last: Yelamanchili

first: Howard

middle: S

last: Fox


title: Expression data from Soybean leaves under drought stress and normally irrigated

status: Public on Aug 29 2013

city: Viçosa

first: Humberto

middle: Henrique

last: de Carvalho

state: Minas Gerais

address: PH Rolfs

department: Biologia Vegetal

country: Brazil

institute: Universidade Federal de Viçosa

summary:
BiP overexpression confers resistance to drought, through an as yet unknown mechanism that is related to ER functioning, has been described  that the delay in leaf senescence by BiP overexpression might relate to the absence of the response to drought.
We used microarrays to detail the global programme of gene expression underlying in soybean leaves overexpressing BiP and with different water potentials to elucidate the mechanisms by which BiP protects plant cells against cell death induced by dehydration.

overall_design: BiP overexpressing plants and wild type as a control were subjected to dry slowly for 25 days. Third or fourth trifoliate leaves were collected from plants in water potential next 1.0 MPa, 1.5 MPa and 1.7 MPa for test weak and strong stress and subject RNA extraction and hybridization on Affymetrix microarrays maintaining the hybridization of two chips per treatment.

first: Elizabeth

last: Fontes

last: Carvalho


title: Expression time-series from Streptomyces coelicolor germination

status: Public on Aug 01 2013

city: Prague

first: Jiri

last: Vohradsky

address: Videnska 1083

country: Czech Republic

institute: Institute of Microbiology Czech Academy of Sciences

summary: Transcriptome time-courses during the S. coelicolor germination were used to reveal processes that underlie the gene expression at the transcriptional level within transition from dormancy to vegetative growth.

overall_design: Samples from 13 time points at the initial 5.5 h (30 min time intervals) of germination. 2-3 biological (and technical) replicates for each time point. Altogether 37 samples.

first: Eva

last: Strakova


title: MIcroRNA expression profiling of chemotherapy resistant esophageal adeno- and squamous cell carcinoma cell lines

status: Public on Aug 28 2013

city: Bedford Park

first: Damian

middle: James

last: Hussey

address: Flinders Drive

institute: Flinders University

summary:
Chemotherapy resistance adversely impacts the treatment of some individuals with esophageal cancer. Identifying chemotherapy resistance might help tailor clinical treatments. In this study the impact of microRNAs on chemotherapy resistance in esophageal cancer was investigated.
We used microarrays to detail the global programme of microRNA expression underlying chemotherapy resistance and identified distinct classes of up-regulated microRNAs in generated chemotherapy resistant cell lines.

overall_design: An in-vitro model of acquired chemotherapy resistance in esophageal adeno- (EAC) and squamous cell carcinoma (SCC) cells was used, and microRNA expression profiles for cisplatin or 5-fluorouracil (FU) resistant variants vs. chemotherapy sensitive controls were compared using microarray. These results were further validated using qRT-PCR techniques (not shown in this submission).

first: Mark

last: Van der Hoek

first: Richard

last: Hummel

first: Corina

last: Sie

first: David

middle: I

last: Watson

first: Tingting

last: Wang

first: Alfiya

last: Ansar

first: Michael

middle: Z

last: Michael

first: Joerg

last: Haier


title: Olig1 is a Smad cofactor involved in cell motility induced by transforming growth factor-b

status: Public on Jul 01 2013

city: Chuoshi

first: Kunio

last: Miyake

state: Yamanashi

address: 1110 Shimokato

institute: Yamanashi University

summary: Transforming growth factor (TGF)-β plays crucial roles in embryonic development and adult tissue homeostasis by eliciting various cellular responses in target cells. TGF-β signaling is principally mediated through receptor-activated Smad proteins, which regulate expression of target genes in cooperation with other DNA-binding transcriptionfactors (Smad cofactors).  In this study, we found that the basic helix-loop-helix transcription factor Olig1 is a Smad cofactor involved in TGF-b-induced cell motility. Knockdown of Olig1 attenuated TGF-β-induced cell motility in chamber migration and wound healing assays. In contrast, Olig1 knockdown had no effect on bone morphogenetic protein-induced cell motility, TGF-β-induced cytostasis or epithelial-mesenchymal transition. Furthermore, we observed that cooperation of Smad2/3 with Olig1 is regulated by a peptidyl-prolyl cis/trans isomerase, Pin1. TGF-b-induced cell motility, induction of Olig1-regulated genes, and physical interaction between Smad2/3 and Olig1 were all inhibited after knockdown of Pin1, indicating a novel mode of regulation of Smad signaling. We also found that Olig1 interacts with the L3 loop of Smad3. Using a synthetic peptide corresponding to the L3 loop of Smad3, we succeeded in selectively inhibiting TGF-b-induced cell motility. These findings may lead to a new strategy for selective regulation of TGF-b-induced cellular responses.

overall_design: NMuMG cells were transfected with siRNAs (siControl, siOlig1 or siPin1) and treated with or without TGF-b for 1h. We compared genes affected by knockdown of Olig1 and that of Pin1.

first: Mitsuyoshi

last: Motizuki

first: Kazunobu

last: Isogaya

first: Hiroaki

last: Ikushima

first: Takeo

last: Kubota

first: Kohei

last: Miyazono

first: Masao

last: Saitoh

first: Keiji

last: Miyazawa


title: Murine Schistosoma-Induced Pulmonary Hypertension: RNA-seq Data

status: Public on Jul 23 2013

city: Aurora

first: Brian

last: Graham

state: CO

department: Medicine

country: USA

institute: University of Colorado Denver

summary: Whole lung RNA-seq of 8 mice with experimental Schistosoma-induced pulmonary hypertension, compared to 8 control mice. All mice on a C57Bl6/J background. 3 schisto-PH and 3 control mice (#s 1-3 in each group) were also processed by Affy microarray and separately submitted. 3 of the mice in each group (labeled 1D11) were also treated with the pan-TGF-beta neutralizing antibody 1D11. Illumina HiSeq 2000 used. Data published in: Protective Role of IL6 in Vascular Remodeling in Schistosoma-Pulmonary Hypertension.  Graham BB, Chabon J, Kumar R, Kolosionek E, Gebreab L, Debella E, Edwards M, Diener K, Shade T, Bifeng G, Bandeira A, Butrous G, Jones K, Geraci M, Tuder RM. Am J Respir Cell Mol Biol. 2013 Jul 1. [Epub ahead of print] PMID: 23815102

overall_design: Whole lung transcriptome of 8 mice with experimental Schistosoma-induced pulmonary hypertension, compared to 8 control mice. All mice on a C57Bl6/J background.

first: Jacob

last: Chabon


title: Murine Schistosoma-Induced Pulmonary Hypertension: Microarray Data

status: Public on Jul 16 2013

summary:
Rationale: Schistosomiasis is one of the most common causes of pulmonary arterial hypertension worldwide, but the pathogenic mechanism by which the host inflammatory response contributes to vascular remodeling is unknown. We sought to identify signaling pathways that play protective or pathogenic roles in experimental Schistosoma-induced pulmonary vascular disease by whole-lung transcriptome analysis. Methods: Wildtype mice were experimentally exposed to S. mansoni ova by intraperitoneal sensitization followed by tail vein augmentation, and the phenotype assessed by right ventricular catheterization and tissue histology, RNA and protein analysis. Whole-lung transcriptome analysis by microarray and RNA sequencing was performed, the latter analyzed using 2 bioinformatic methods. Functional testing of the candidate IL-6 pathway was determined using IL6-knockout mice and the STAT3 inhibitor STI-201. Results: Wild-type mice exposed to S. mansoni had increased right ventricular systolic pressure and thickness of the pulmonary vascular media. Whole lung transcriptome analysis identified the IL6-STAT3-NFATc2 pathway as being upregulated, which was confirmed by PCR and immunostaining of lung tissue from S. mansoni-exposed mice and patients who died of the disease. Mice lacking IL6 or treated with STI-201 developed pulmonary hypertension associated with significant intima remodeling after exposure to S. mansoni. Conclusions: Whole lung transcriptome analysis identified upregulation of the IL6-STAT3-NFATc2 pathway, and IL6 signaling was found to be protective against Schistosoma-induced intimal remodeling.
Affy Mouse ST1.0 chip used. Data published in: Protective Role of IL6 in Vascular Remodeling in Schistosoma-Pulmonary Hypertension.  Graham BB, Chabon J, Kumar R, Kolosionek E, Gebreab L, Debella E, Edwards M, Diener K, Shade T, Bifeng G, Bandeira A, Butrous G, Jones K, Geraci M, Tuder RM. Am J Respir Cell Mol Biol. 2013 Jul 1. [Epub ahead of print] PMID: 23815102

overall_design: Whole lung transcriptome of 3 mice with experimental Schistosoma-induced pulmonary hypertension, compared to 3 control mice. All mice on a C57Bl6/J background.


title: Extrauterine growth restriction on pulmonary vascular endothelial dysfunction in adult male rats: the role of epigenetic mechanisms

status: Public on Jul 10 2013

city: Hangzhou

first: Liyan

last: Zhang

state: Zhejiang

address: #57 Zhugan Lane

department: the children's Hospital

institute: Zhejiang university school of medicine

type: Methylation profiling by genome tiling array

summary:
Early postnatal life is considered as a critical time window for determination of long-term metabolic states and organ functions. Extrauterine growth restriction (EUGR) causes the development of adult onset chronic diseases, including pulmonary arterial hypertension (PAH). However, the effects of nutritional disadvantages during early postnatal period on pulmonary vascular consequences in later life are not fully understood. Our study was designed to test whether epigentic dysregulation mediates the cellular memory of this early postnatal event. To test this hypothesis, we isolated pulmonary vascular endothelial cells (PVEC) by magnetic-activated cell sorting (MACS) from EUGR and control rats. A postnatal insult, nutritional restriction-induced EUGR caused development of an increased pulmonary artery pressure at 9-week of age in male rats. MeDIP-chip (Methyl-DNA immune precipitation chip), genome-scale mapping studies to search for differentially methylated loci between control and EUGR rats revealed significant difference in cytosine methylation between EUGR and control rats. We validated candidate dysregulated loci with quantitative assays of cytosine methylation and gene expressions. EUGR changes cytosine methylation at ~500 loci in male rats at 9 weeks of age, preceding the development of PAH and these represent candidate loci for mediating the pathogenesis of pulmonary vascular disease that occurs later in life. These results demonstrate that epigenetic dysregulation is a strong mechanism for propagating the cellular memory of early postnatal events, causing changes in expression of genes and long term susceptibility to PAH, and further providing a new insight into prevention and treatment of EUGR-related PAH.
MeDIP together with microarray analysis demonstrated that significant differences in cytosine methylation between EUGR and control rats.

overall_design: Comparison of EUGR(n=3) vs Control (n=3) male rats' pulmonary vascular endothelial cells in 9-week age old rats

first: Lili

last: Tang


title: The acclimation of Chlamydomonas reinhardtii to anaerobiosis involves plant and animal strategies

city: Los Angeles

first: Sabeeha

last: Merchant

address: 607 Charles E. Young Drive East

department: Department of Chemistry and Biochemistry

institute: University of California Los Angeles

summary: The absence of oxygen (O2) is a stress condition for aerobic organisms and requires extensive acclimation responses. Previously, Chlamydomonas reinhardtii has been used as a reference organism for understanding these acclimation responses. In this work, we use RNA-Seq for a whole genome view of the acclimation of the organism to dark-anoxic conditions. To distinguish the responses dependent on the COPPER RESPONSE REGULATOR 1 (CRR1), which is also involved in hypoxic gene regulation, we compared the transcriptome of crr1 mutants to that of complemented strains. Nearly 10% of the genome (~ 1,400 genes) are affected by hypoxia based on pairwise comparisons of all strains and two time-points. Comparing transcript profiles from early (hypoxic) with those from late (anoxic) time-points indicated that the cells activated oxidative energy generation pathways before employing fermentative enzymes. Probable substrates included not only carbohydrates but also amino acids and fatty acids (FAs). Lipid profiling of the C. reinhardtii cells revealed that they degraded FAs but also accumulated triacylglycerols (TAGs). In contrast to N-deprived cells, the TAGs accumulating in hypoxic cells are enriched in desaturated FAs, which distinguishes the contribution of individual pathways for Chlamydomonas TAG accumulation. In crr1 mutants, about 140 genes were aberrantly regulated , re-affirming the importance of CRR1 for the hypoxic response, but indicating also the contribution of additional O2-sensors and signaling strategies to account for the remaining differentially regulated transcripts. We conclude that nitric oxide (NO) dependent signaling cascades, employing both known and novel components, are operative in C. reinhardtii.

overall_design: The transcriptome of four different Chlamydomonas strains (wild type CC-124, crr1 mutant, crr1:CRR1 rescued strain and crr1dCys rescued strain) are profiled by RNA-Seq in the dark at different times after the transition from light-oxic to dark-anoxic conditions

first: Anja

last: Hemschemeier

first: David

last: Casero

first: Bensheng

last: Liu

first: Christoph

last: Benning

first: Matteo

last: Pellegrini

first: Thomas

last: Happe


title: Protective Role of IL6 in Vascular Remodeling in Schistosoma-Pulmonary Hypertension


title: A variant in the neuropeptide receptor npr-1 is a major determinant of Caenorhabditis elegans growth and physiology

status: Public on Jul 30 2013

city: Princeton

first: Leonid

last: Kruglyak

state: NJ

address: 110 Carl Ichan Laboratory

institute: Princeton University

summary: The mechanistic basis for how genetic variants cause differences in phenotypic traits is often elusive. We identified a quantitative trait locus in C. elegans that affects three seemingly unrelated phenotypic traits: lifetime fecundity, adult body size, and susceptibility to the human pathogen Staphyloccus aureus. We found a QTL for all three traits arises from variation in the neuropeptide receptor gene npr-1. Moreover, we found that variation in npr-1 is also responsive for differences in 247 gene expression traits. Variation in npr-1 is known to determine whether animals disperse throughout a bacterial lawn or aggregate at the edges of the lawn. We found that the allele that leads to aggregation is associated with reduced growth and reproductive output. The altered gene expression pattern caused by this allele suggests that the aggregation behavior might cause a weak starvation state, which is known to reduce growth rate and fecundity. Importantly, we show that variation in npr-1 causes each of these phenotypic differences through behavioral avoidance of ambient oxygen concentrations. These results suggest that variation in npr-1 has broad pleiotropic effects mediated by altered exposure to bacterial food.

overall_design: Two-channel experiment comparing mixed stage sample to mixed stage mixed 50:50 N2,CB4856 common reference

first: Erik

last: Andersen

first: Joshua

last: Bloom


title: Detection of Bacillus anthracis DNA in complex soil and air samples using next-generation sequencing [NimbleGen Array data]

status: Public on Jun 27 2013

city: Livermore

first: Kevin

last: McLoughlin

state: CA

address: PO Box 808

department: Global Security

institute: Lawrence Livermore National Laboratory

summary: One of the cornerstones of an effective biodefense strategy is the ability to detect infectious agents with a high degree of sensitivity and specificity in the context of a complex sample background.  The nature of the B. anthracis genome, however, renders specific detection difficult, due to close homology with B. cereus and B. thuringiensis.  We therefore elected to determine the efficacy of next-generation sequencing analysis and microarrays for detection of B. anthracis in an environmental background.  We applied next-generation sequencing to titrated genome copy numbers of B. anthracis in the presence of background nucleic acid extracted from aerosol and soil samples.  We found next-generation sequencing to be capable of detecting as few as 10 genomic equivalents of B. anthracis DNA per nanogram of background nucleic acid.  Detection was accomplished by mapping reads to either a defined subset of reference genomes or to the full GenBank database.  Moreover, sequence data obtained from B. anthracis could be reliably distinguished from sequence data mapping to either B. cereus or B. thuringiensis.  We also demonstrated the efficacy of a microbial census microarray in detecting B. anthracis in the same samples, representing a cost-effective and high-throughput approach, complementary to next-generation sequencing.

overall_design:
This Series contains the NimbleGen array data only (no next-generation sequencing data). The next-gen sequencing data from this study are accessible in the BioProject database under accession PRJNA206989.
B. anthracis DNA was spiked at 6 different concentrations (1, 10, 100, 1000, 10000 and 100000 genome copies) into 1 ng of background nucleic acids extracted either from a soil sample or from an aerosol (air filter) sample. Two replicates of each combination of B. anthracis copy number and background sample were analyzed.

first: Nicholas

last: Be

first: James

last: Thissen

first: Shea

middle: N

last: Gardner

first: Viacheslav

last: Fofanov

first: Heather

last: Koshinsky

first: Sally

middle: R

last: Ellingson

last: Brettin

first: Paul

middle: J

last: Jackson

first: Crystal

last: Jaing


title: Expression profiling of BMP9-stimulated mesenchymal stem cells

city: Chicago

first: Tong-Chuan

last: He

state: IL

address: 5841 South Maryland Avenue, MC 3079

department: Department of Orthopaedic Surgery

institute: The University of Chicago Medical Center

summary: To identify potential target genes regulated by BMP9 in MSCs, we used microarray to profile expression patterns of BMP9- vs. GFP-stimulated MSCs.

overall_design: Subconfluent mouse C3H10T1/2 cells were transduced with adenoviral vector expressing BMP9 or GFP for 30h. Total RNA was isolated for microarray analysis using Affymetrix mouse MOE430A GeneChips. Experiments were done in triplicate.

first: Tong


title: Charting a dynamic DNA methylation landscape of the human genome

status: Public on Aug 09 2013

first: Michael

middle: Johannes

last: Ziller

address: Kraepelinstrasse 2-10

department: Translational Psychiatry

country: Germany

type: Methylation profiling by high throughput sequencing

summary: DNA methylation is a defining feature of mammalian cellular identity and is essential for normal development. Most cell types, except germ cells and pre-implantation embryos, display relatively stable DNA methylation patterns, with 70-80% of all CpGs being methylated. Despite recent advances we still have a too limited understanding of when, where and how many CpGs participate in genomic regulation. Here we report the in depth analysis of 42 whole genome bisulfite sequencing (WGBS) data sets across 30 diverse human cell and tissue types. We observe dynamic regulation for only 21.8% of autosomal CpGs within a normal developmental context, a majority of which are distal to transcription start sites. These dynamic CpGs co-localize with gene regulatory elements, particularly enhancers and transcription factor binding sites (TFBS), which allow identification of key lineage specific regulators. In addition, differentially methylated regions (DMRs) often harbor SNPs associated with cell type related diseases as determined by GWAS. The results also highlight the general inefficiency of WGBS as 70-80% of the sequencing reads across these data sets provided little or no relevant information regarding CpG methylation. To further demonstrate the utility of our DMR set, we use it to classify unknown samples and identify representative signature regions that recapitulate major DNA methylation dynamics. In summary, although in theory every CpG can change its methylation state, our results confirm that only a fraction does so as part of coordinated regulatory programs. Therefore our selected DMRs can serve as a starting point to help guide novel, more effective reduced representation approaches to capture the most informative fraction of CpGs as well as further pinpoint putative regulatory elements.

overall_design:
Analysis of 42 human WGBS libraries comprising 30 distinct primary cell lines, tissues, in vitro derived cell types and cell lines.

BiSeq raw sequencing reads were aligned using maq in bisulfite mode (Li et al. 2008) or bsmap 2.7 (Xi et al. 2009) against human genome version hg19/GRCh37, discarding duplicate reads. DNA methylation calling was performed based on an extended custom software pipeline published previously for RRBS (Gu et al., 2010). The bed files contain all seen CpGs within the given library. The number of methylated reads/number of total reads is listed in the score column.

This study includes a re-analysis of Samples from the NIH Roadmap Epigenomics Mapping Consortium (REMC; GSE16256, GSE17312), Hodges et al. 2011 (GSE31971), Molaro et al. 2011 (GSE30340), and Xi et al. 2013.

WARNING: This submission is incomplete pending further deposits of raw data files from Meissner via EDACC.

first: Alex

last: Meissner


title: AGO-PAR-CLIP of DG75 and BCBL-1

city: Würzburg

first: Florian

last: Erhard

address: Versbacher Str. 7

department: Institut für Virologie und Immunbiologie

institute: Julius-Maximilians-Universität Würzburg

type: Non-coding RNA profiling by high throughput sequencing

summary: AGO-PAR-CLIP was employed to identify microRNA binding sites in BCBL-1, a Kaposi's sarcoma-associated herpesvirus (KSHV) infected B-cell line and DG75, a KSHV negative B-cell line as a control. By using our novel computational method (PARma) and differential analysis of PAR-CLIP data, highly accurate target sites of KSHV microRNAs can be defined.

overall_design: Examination of microRNA target sites in two different cell lines using replicate PAR-CLIP experiments

first: Lukasz

last: Jaskiewicz

first: Mihaela

last: Zavolan

first: Lars

last: Doelken

first: Ralf

last: Zimmer


title: Expression data from Lbx1-EGFP+ flow sorted cells from Pitx2 WT, HT, Null forelimb tissue

status: Public on Jun 11 2013

city: Corvallis

first: Adam

middle: Lee

last: Campbell

state: OR

address: 301 Pharmacy Building

department: College of Pharmacy

institute: Oregon State University

summary:
Determing the gene network regulated by Pitx2 in during forelimb muscle development of mouse embryos at E12.5.  Lbx1 is coexpressed in Pitx2+ cells during forelimb development, thus Pitx2-LacZ and Lbx1-EGFP+ mice were cross bred to allow us to purify Lbx1-EGFP+|Pitx2 -wildtype, het, or null cells by flow sorting
We used microarray analysis to determine the genes misregulated in Pitx2 null mice compared to Pitx2 wildtype and heterozyogtes.

overall_design: Lbx1-EGFP+|Pitx2(+/+, LacZ/+, or LacZ/LacZ) cells were flow sorted, RNA extracted, labelled cDNA was hybridized to Affymetrix mouse genome 430 2.0 arrays

first: Chrissa

last: Kioussi

last: Gross

first: Hung-Ping

last: Shih


title: Gene expression profilling of six species of Brassica and early four generation of resynthesized B. napus (F1-F4)

city: Yangzhou

first: Jinjin

last: Jiang

address: Wenhui East Road No.12

institute: Yangzhou University

summary: Analysis of the different gene expression profiles of natural and resynthesized Brassica polyploids with Illumina deep sequencing technology could help to improve our knowledge of polyploid genome evolution. We obtained approximately 6 million sequence tags per sample,and 6018254, 5930726, 6022170, 5950123, 5991210, 5798939, 5823113, 5772449,5858527 and 5657697 clean tags were obtained in libraries of B. rapa, B. oleracea, B. napus-F1, B. napus-F2, B. napus-F3, B. napus-F4, natural B. napus, B. nigra, B. juncea and B. carinata, respectively.16574, 15970, 22059, 18155, 16479, 18196, 17448, 13867, 19424 and 16645 genes of B. rapa genome were unambigously mapped by sequence tags of these ten DGE libraries, respectively. Differentially expressed genes during polyploidization were broadly discovered by comparing the tetraploids with their progenitors.

sample_organism:
Brassica juncea
Brassica napus
Brassica nigra
Brassica rapa
Brassica oleracea
Brassica carinata

overall_design: mRNA obtained from young leaves of 28-days-old seedlings were compared during polyploidization.

first: Youping

last: Wang


title: Gene expression profiling of mouse uterine epithelial cells isolated on morning of day 4 of pregnancy

city: urbana

first: Sandeep

last: Pawar

state: Illinois

address: apt 6

department: Molecular and Integrative Physiology

institute: University of Illinois

summary:
Embryo implantation into a receptive endometrium is tightly regulated by a variety of maternal factors, including cytokines, growth factors and transcription factors. Previous studies identified the leukaemia inhibitory factor (LIF), produced in uterine glands, as an essential factor for implantation. It was shown that LIF acts via its cell surface receptor to activate the transcription factor STAT3 in the uterine epithelial cells. However, the mechanisms via which STAT3 promotes uterine receptivity remain unknown. To address the molecular pathways regulated by STAT3 in the uterus, we created mice in which Stat3 gene is conditionally inactivated in uterine epithelium. These mutant mice are infertile due to implantation failure and exhibit a lack of embryo attachment to the luminal epithelium. Gene expression profiling of the epithelial tissue impaired in STAT3 activation revealed dysregulated expression of specific components of junctional complexes, including E-cadherin, β-catenin, and claudins, which critically regulate epithelial cell polarity and embryo attachment. Additionally, mice lacking functional epithelial STAT3 showed markedly reduced stromal proliferation and differentiation, indicating that this transcription factor controls stromal function via a paracrine mechanism. The stromal defect arose from a drastic reduction in the production of several members of the epidermal growth factor (EGF) family in luminal epithelium of mutant uteri and consequent lack of activation of EGF receptor signaling and mitotic activity in the stromal cells. Collectively, our results uncovered intricate signaling networks operating downstream of STAT3 in uterine epithelium that regulate epithelial cell polarity, and stromal proliferation and differentiation, which are critical determinants of successful implantation.
To identify the downstream targets of STAT3 in mouse uterine epithelial cells during pregnancy, we performed gene expression profling of mouse uterine epithelial cells on day 4 of pregnancy between Stat3 flox control and SW d/d mice. This led to the identification of several junctional molecules (Claudins and Catenins) that are negatively regulated by STAT3 at the time of implantation.

overall_design: Mouse uteirne epithelial cells were isolated from control and knockout mice on the morning of day 4 of pregnancy. (n=3 for each sample), pooled total RNA from these cells was then hybridized to high density affymetrix microarrays according to the Affymetrix protocol (Mouse Genome 430A 2.0 Array) .

first: Indrani

last: Bagchi

first: Milan

middle: K


title: Post-weaning selenium and folate supplementation affects gene and protein expression and global DNA methylation in mice fed high-fat diets

status: Public on Jun 01 2013

city: Palmerston North

first: Helge

last: Dzierzon

address: Bachelar Road

department: Bioinformatics

country: New Zealand

institute: Plant and Food Research Ltd.

summary:
Background: Consumption of high fat diets has negative impacts on health and well-being, some of which may be epigenetically regulated. Selenium and folate are two compounds which influence epigenetic mechanisms. We investigated the hypothesis that post-weaning supplementation with adequate levels of selenium and folate in mouse offspring fed a high fat, low selenium and folate diet during gestation and lactation will lead to epigenetic changes of potential importance for long-term health. Female offspring of mothers fed the experimental diet were either maintained on this diet (HF-low-low), or weaned onto a high-fat diet with sufficient levels of selenium and folate (HF-low-suf), for 8 weeks. Gene and protein expression, DNA methylation, and histone modifications were measured in colon and liver of female offspring.
Results: Adequate levels of selenium and folate post-weaning affected gene expression in colon and liver of offspring, including decreasing Slc2a4 gene expression. Protein expression was only altered in the liver. There was no effect of adequate levels of selenium and folate on global histone modifications in the liver. Global liver DNA methylation was decreased in mice switched to adequate levels of selenium and folate, but there was no effect on methylation of specific CpG sites within the Slc2a4 gene in liver.
Conclusions: Post-weaning supplementation with adequate levels of selenium and folate in female offspring of mice fed high-fat diets during gestation and lactation can alter global DNA methylation in liver. This may be one mechanism by which the negative effects of a poor diet during early life can be ameliorated. Further research is required to establish what role epigenetic changes play in mediating observed changes in gene and protein expression, and the relevance of these changes to health.

overall_design: Female wild type C57BL/6 mice (Animal Resource Centre, Western Australia) were fed a High Fat diet containing low levels of selenium and folate (HF-Low) for 7 days prior to mating with male C57BL/6 mice (Ruakura Small Animal Facility, Hamilton, New Zealand). Mothers were maintained on the HF-Low diet throughout gestation and lactation. Offspring of these female mice were randomly assigned to one of two different dietary treatments: either the same diet as the mothers (HF-Low), or a High Fat diet containing adequate selenium and folate (HF-Suf). At 12 weeks of age, mice were euthanized and colon and liver samples taken for microarray, proteomics, and DNA methylation analyses. Genomic DNA, total RNA and protein from whole colon and liver tissue was extracted using an AllPrep® DNA/RNA/Protein mini kit (Qiagen, Cat number 80004). Colon and liver RNA from six female offspring on the HF-Low diet was compared with colon and liver RNA from six female offspring on the HF-Suf diet. All individual RNA samples were hybridized against a common reference RNA on separate arrays. The reference RNA was prepared by pooling in equimolar proportions RNA extracted from the intestine and liver of twelve female C57BL/6 mice, these being all of the mice from which samples were derived for microarray analysis in the current study.

first: Emma

last: Bermingham

first: Shalome

middle: A

last: Bassett

first: Wayne

last: Young

first: Nicole

last: Roy

first: Warren

last: McNabb

first: Janine

middle: M

last: Cooney

first: Di

middle: T

last: Brewster

first: William

last: Laing

first: Matthew

last: Barnett


title: Elevated pulmonary arterial pressure and altered expression of Ddah1 and Arg1 in mice lacking Cavin-1/PTRF

city: Lund

first: Catarina

last: Rippe

address: BMC, D12

department: Experimental Sciences

institute: Lund University

summary: Lungs from newborn cavin-1/PTRF-deficient and wild-type mice were analyzed

overall_design: 6 cavin-1 deficient newborn mice and 6 wild-type mice

first: Karl

last: Swärd