title: Effect of miR-144/miR451 expression on TC-1 lung epithelial cell responses to influenza infection for 24 hours [Expression]

status: Public on Aug 01 2012

city: seattle

first: madhumati

last: gundapuneni

address: 401 Terry avenue North

institute: Institute for systems biology

summary: Antiviral responses must be regulated to rapidly defend against infection while minimizing inflammatory damage, but the mechanisms for establishing the magnitude of response within an infected cell are not well understood. miRNAs are small non-coding RNAs that negatively regulate protein levels by binding target sequences on their cognate mRNA. Here we identify miR-144 as a negative regulator of the host antiviral response. Ectopic expression of miR-144 resulted in increased replication of three RNA viruses, influenza, EMCV, and VSV, in primary mouse lung epithelial cells. To elucidate the mechanism whereby miR-144 increases influenza replication within lung epithelial cells, TC-1 cells stably over-expressing miR-144 were infected with influenza A for 24 hours and the transcriptional profile was compared with those of infected control cells. This systems biology approach identified the transcriptional network regulated by miR-144 and demonstrate that it controls the TRAF6/IRF7 antiviral response by post-transcriptionally suppressing TRAF6 levels. In vivo ablation of miR-144 reduced influenza replication within the lung.

overall_design: TC-1 lung epithelial cells stably expressing miR144+miR451 or control vector were unstimulated (n=1) or infected with Influenza A/PR/8/34 (MOI=5) for 24 hours (n=3).

first: Carrie

middle: M

last: Rosenberger

first: Rebecca

last: Podyminogin

first: Jacques

last: Peschon

first: David

last: Rodriguez

first: Madhumati

last: Gundapuneni

first: Mitchell

last: Weiss

first: Alan

last: Aderem


title: Comparative genomic and transcriptomic analysis revealed genetic characteristics related to solvent formation and xylose utilization in Clostridium acetobutylicum EA 2018

status: Public on Jul 23 2012

city: Shanghai

first: Shiyuan

last: Hu

address: 300# fenglin road

country: China

institute: Institute of plant physiology and ecology, Shanghai institutes for biological sciences, Chinese academy of sciences

summary: Transcriptomic profiling of gene expression in EA 2018 relative to that of ATCC824 revealed several key genes related to solvent formation. For example, spo0A and adhEII have higher expression level, and most of the acid formation related genes have lower expression level in EA 2018.

sample_organism:
Clostridium acetobutylicum ATCC 824
Clostridium acetobutylicum EA 2018

overall_design: Cells for RNA isolation were grown on P2 medium and collected at 9 h, 13 h, 17 h, 21 h, 24 h and 30 h by centrifugation at 4°C and 4500 x g for 10 min. Total RNA was extracted and purified by using Trizol (Invitrogen, Carlsbad, CA, USA) and RNeasy cleanup kit (Qiagen, Inc., Valencia, CA, USA) according to the manufacturer’s protocol. The total RNA yield was quantified by spectrophotometric analysis (NanoDrop Technology, Cambridge, UK) and the quality was verified by gel electrophoresis. Agilent oligonucleotide microarrays technology was used for monochromic analysis, in which probes (size: 60bp; three replicates for each ORF) from the two groups were labeled by incorporation of cyanine 3 (Cy3) (Agilent Technologies, Palo Alto, CA, USA). Average linkage hierarchical clustering was performed using Cluster 3.0, and gene clusters were visualized in Treeview

first: Huajun

last: Zheng

first: Yang

last: Gu

first: Jingbo

last: Zhao

first: Weiwen

last: Zhang

first: Yunliu

last: Yang

first: Shengyue

last: Wang

first: Guoping

first: Sheng

first: Weihong

last: Jiang


title: Effect of miR-144/miR451 expression on TC-1 lung epithelial cell responses to influenza infection for 24 hours

first: madhumati

country: USA

type:
Expression profiling by array
Other

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

overall_design: Refer to individual Series


title: Zinc finger nuclease knockouts of human ADP-glucokinase

status: Public on Jul 20 2012

city: Auckland

first: Cris

last: Print

address: Grafton Campus, Park Rd

country: New Zealand

institute: Auckland University

summary: Zinc finger nucleases (ZFN) are powerful tools for editing genes in cells. Here we use ZFNs to interrogate the biological function of human ADPGK, which encodes an ADP-dependent glucokinase (ADPGK), in tumour cell lines. The hypothesis tested is that ADPGK utilises ADP to phosphorylate glucose under conditions where ATP becomes limiting, such as hypoxia. We characterised two ZFN knockout clones in each of two tumour cell lines (H460 and HCT116). All four lines had frameshift mutations in all alleles at the target site in exon 1 of ADPGK, and were ADPGK-null by immunoblotting.  ADPGK knockout had little or no effect on cell proliferation, but compromised the ability of H460 cells to survive siRNA silencing of hexokinase-2 under oxic conditions, with clonogenic survival falling from 21±3% for the parental line to 6.4±0.8% (p=0.002) and 4.3±0.8% (p=0.001) for the two knockouts. A similar increased sensitivity to clonogenic cell killing was observed under anoxia. No such changes were found when ADPGK was knocked out in HCT116 cells, for which the parental line was less sensitive than H460 to anoxia and to hexokinase-2 silencing. While knockout of ADPGK in HCT116 cells caused few changes in global gene expression, knockout of ADPGK in H460 cells caused notable up-regulation of mRNAs encoding cell adhesion proteins. Surprisingly, we could discern no effect on glycolysis as measured by glucose consumption or lactate formation under oxic or anoxic conditions, or extracellular acidification rate (Seahorse XF analyser) under oxic conditions in a variety of media. However, oxygen consumption rates were generally lower in the ADPGK knockouts, in some cases markedly so.  Collectively, the results demonstrate that ADPGK can contribute to tumour cell survival under conditions of high glycolytic dependence, but the phenotype resulting from knockout of ADPGK is cell line dependent and appears to be unrelated to priming of glycolysis.

overall_design: Use Affymetrix microarrays to examine the effecs of knockout of the gene ADPGK using Zinc Finger nucleases in two cultured cell lines: (i)  HCT116 cells (three wild type cultures compared to three ADPGK-knockout cultures), (ii) H460 cells (two wild type cultures compared to two ADPGK-knockout cultures). Ten microarrays in total.

first: Susan

last: Richter

first: Shona

last: Morrison

first: Tim

last: Connor

first: Jiechuang

last: Su

first: Cristin

first: Ron

middle: S

last: Ronimus

first: Sean

middle: L

last: McGee

first: William

middle: R

last: Wilson


title: Different effects of 17 beta estrodial and soy protein isolate on bone gene expression in the pre-pubertal female rats

status: Public on Jul 15 2012

city: Little rock

first: Kartik

last: Shankar

state: AR

address: 1120 Marshall Street, Slot 512-20B

department: Pharmacology and Toxicology

institute: University of Arkansas for Medical Sciences/Arkansas Childrens Nutrition Center

summary: Beneficial effects of a soy diet on bone quality have been assumed to be due to the putative estrogenic actions of isoflavones. We studied the effects of soy protein isolate (SPI) on bone quality and compared these effects to 17β-estradiol (E2) in pre-pubertal rats. Female rats were weaned to a control diet with or without E2 (0.1, 1, 10 µg/kg/d), or SPI-containing diet with or without E2 (10 µg/kg/d) for 14 days beginning on postnatal day 20. In long bones from SPI-fed rats, only cancellous bone mineral density (BMD) was increased (p<0.05), while cortical BMD was decreased accompanied by lower bone strength compared to control casein-fed rats (p<0.05). In sharp contrast, 10 µg/kg/d E2 not only increased trabecular BMD, but also cortical BMD compared to controls. Rats treated with the combination of SPI and E2 had an intermediate bone effect. SPI increased while E2 decreased bone turnover, and increased trabecular BMD by both E2 and SPI was associated with decreased serum sclerostin levels. Microarray analysis revealed 652 genes regulated by SPI diet, 491 genes regulated by E2, and 266 genes regulated in common by both SPI diet and E2 compared to rats fed casein. The expression of caveolin-1, a protein localized in cell membrane, was down-regulated (p<0.05) in rats fed SPI, but not by E2 compared to rats fed casein. Down-regulated caveolin-1 by SPI was associated with increased BMP2, Smad and Runx2 expression in bone and osteoblasts (p<0.05). These results suggest SPI consumption results in significant non-classical estrogenic stimulation of cancellous bone formation prior to puberty, but may have adverse effects on overall bone quality and strength at this developmental stage as a result of reduced cortical bone formation.

overall_design: The study was designed to compare expression of bone development associated genes between soy protein isolate fed and estrogen treated pre pubertal female rats. Therefore, total RNA was isolated from bone from rats fed with control casein diet, SPI diet, 17 beta estrodial treated and SPI diet plus 17 beta estrodial.

first: Jian

first: Oxana

middle: P

last: Lazarenko

first: Xianli

last: Wu

first: Yudong

last: Tong

first: Michael

last: Blackburn

first: Jamie

middle: V

last: Badeaux

first: Thomas

last: Badger

first: Martin

middle: J

last: Ronis

first: Jin-Ran

last: Chen


title: Effect of miR-144/miR451 expression on TC-1 lung epithelial cell responses to influenza infection for 24 hours [RT-PCR]

first: madhumati

last: gundapuneni

summary: Antiviral responses must be regulated to rapidly defend against infection while minimizing inflammatory damage, but the mechanisms for establishing the magnitude of response within an infected cell are not well understood. miRNAs are small non-coding RNAs that negatively regulate protein levels by binding target sequences on their cognate mRNA. We profiled microRNA expression in the lungs of mice infected for 24 h with Influenza A/PR/8/34 to identify microRNAs that may regulate host response to influenza infection.

overall_design: Mice were infected intranasally with 10e5 pfu Influenza A/PR/8/34. Lungs were isolated after 24 hours and total RNA extracted using Trizol. Equivalent quantities of RNA from 3 infected mice were pooled.

first: Carrie

last: Rosenberger

first: Rebecca

last: Podyminogin

first: Jacques

last: Peschon

first: David

last: Rodriguez

first: Madhumati

last: Gundapuneni

first: Mitchell

last: Weiss

first: Alan

last: Aderem


title: Expression profiling in VCP-associated myopathy

status: Public on Jul 19 2012

city: Washington

first: Svetlana

last: Ghimbovschi

state: DC

address: 111 Michigan Ave., NW

department: Research Center for Genetic Medicine

institute: Children's National Medical Center

summary:
Inclusion body myopathy associated with Paget disease of bone and frontotemporal dementia (IBMPFD) is caused by mutations in the Valosin Containing Protein (VCP) gene on chromosome 9p12-13.
To elucidate affected signaling transduction axes in IBMPFD, we determined expression profiles using microarray technology in quadriceps muscle from patients and unaffected relatives.

overall_design: Muscle from 10 individuals  (7 affected, 3 unaffected first degree relatives) was obtained after informed consent for the muscle biopsy was obtained.

first: V

last: Kimonis

first: S


title: Comparative transcriptomic profiling of peripheral blood mononuclear cells (PBMCs) isolated from patients in secondary prevention of CVD taking placebo, grape extract or resveratrol-enriched grape extract

status: Public on Jun 30 2012

city: Espinardo

first: María-Teresa

last: García-Conesa

state: Murcia

address: Campus de Espinardo

department: Quality, Safety and Bioactivity of Plant Foods

country: Spain

institute: CEBAS-CSIC

summary: We used Affymetrix microarrays to investigate gene expression changes in PBMCs isolated from male patients ongoing secondary prevention of CVD to determine significant modulatory effects that may have been induced by the intake of an initial dose of 8 mg of resveratrol-enriched grape extract for 6 months and then, 16 mg for a further 6 months.

overall_design:
The aim of this work was to determine whether the daily intake of dietary levels of resveratrol (RES) for a total of 12 months exerted any modulatory effects, at the level of gene expression, in PBMCs isolated from patients in secondary prevention of CVD. Male patients were divided in 3 groups: placebo (A), grape extract (B) and resveratrol-enriched grape extract (C). Total RNA was extracted from isolated PBMCs belonging to a total of 18 diabetic male patients (6 from each group) in 3 time points (at day 0, after 6 months and after 12 months) to compare differential gene expression between the groups.
Differential gene expression after 6 and 12 months of the study for each group: placebo (A), grape extract (B) and resveratrol-enriched grape extract (C)

first: Joao

last: Tomé-Carneiro

first: Juan-Carlos

last: Espín de Gea


title: Age-dependent changes in the gene expression profile of mice over-expressing mutant APP, PS1 and phosphorilated tau

status: Public on Jun 28 2012

city: Chieti

first: Valentina

last: Gatta

state: Abruzzo

address: Via Colle dell'Ara

department: Aging Research Center (CESI)

country: Italy

institute: G. d’Annunzio University Foundation Chieti

summary: In this study, using a microarray approach, we investigated the age-dependent changes in the gene expression profile of  hippocampi obtained from young and old 3xTg-AD and WT control mice, in order to identify the molecular mechanisms involved in the development of AD and assess the role of aging in the development of the disease. A global gene expression profile in the hippocampi obtained from 3xTgAD (expressing mutant human APP, PS1, and tau) and WT mice at 3 and 12 months of age was studied by employing a Mouse OneArray Whole Genome DNA microarray. Data were analyzed with the Ingenuity Pathways Analysis (IPA) in order to achieve a classification of the results on the basis of their biological functions and disclose functional networks and/or pathways.

overall_design: In this study we performed gene expression profiles for a total of 9 experiments. Hippocampi were collected from 2 3xTG and 2 WT mice at 3 months of age and from 2 3xTG and 2 WT mice at 12 months of age. Three MicroArray experiments were performed for each condition (WT 12 moa versus WT 3 moa; 3xTG 3 moa versus WT 3 moa; 3xTG 12 moa versus WT 12moa). On the total of 9 experiments 6 were biological replicates and 3 were technical replicates.

first: Marco

last: D'Aurora

first: Liborio

last: Stuppia

first: Stefano

last: Sensi

first: Teresa

last: Caporale


title: Gene expression profiling of MT-2 cells treated with interferon-alpha and ascorbic acid (dose response)

status: Public on Jun 14 2012

city: Leuven

first: Rekin's

last: Janky

address: Herestraat 49 Box 816

department: Nucleomics Core

country: Belgium

institute: VIB

summary:
Background: Clear guidelines for therapy of HTLV-1-associated myelopathy/tropical spastic paraparesis (HAM/TSP) are missing due to the lack of randomized double-blind controlled clinical trials. Moderate yet similar clinical benefit has been demonstrated for IFN-a monotherapy and high-dose ascorbic acid (AA) monotherapy in open clinical trials. However, there is no clear evidence to support the value of one of these specific treatment approaches, due to the lack of in vivo and in vitro studies exploring and comparing the effects of high-dose AA and IFN-a treatment in the context of HAM/TSP.

Principal Findings: Based on flow cytometry and thymidine incorporation, we demonstrated for the first time that high-dose AA displays superior antiproliferative and immunomodulatory effects over IFN-a in HAM/TSP PBMCs ex vivo. In addition, high-dose AA induces cell death in HTLV-1-infected T-cell lines in vitro. Microarray combined with Ingenuity Pathway Analysis revealed AA-induced modulation of genes associated with cell death and cell cycle.

Conclusions: In comparison with IFN-a, high-dose AA is preferred as anti-HTLV-1 treatment in vitro, due to its superior cell death-inducing, antiproliferative and immunomodulatory effects. Considering the lack of treatment options, the mild in vivo side effects and the low cost price, high-dose AA should be further explored for its therapeutic potential in HAM/TSP treatment.

overall_design: In total, 15 samples were analyzed. One microarray experiment was performed, including triplicate samples for each treatment condition (untreated, IFN-a, 10 µg/ml ascorbic acid, 50 µg/ml ascorbic acid, 100 µg/ml ascorbic acid). Triplicate samples were obtained from three separate RNA experiments.

first: Britta

last: Moens

first: Anne-Mieke

last: Vandamme

first: Johan

last: Van Weyenbergh


title: A Salmonella-encoded microRNA-like RNA facilitates bacterial invasion and intracellular replication via suppressing host cell inducible nitric oxide synthase

status: Public on Dec 23 2014

city: Nanjing

first: Zhen

last: Zhou

state: Jiangsu

address: 22th,Hankou Road

department: School of Lifesciences

institute: Nanjing University

type: Expression profiling by high throughput sequencing

summary: As the leading cause of food-borne illness in the world, Salmonella have evolved a sophisticated machinery to alter host cell function to promote virulence and survival.In this study, we compare production of non-coding RNAs between Salmonella-infected cells and mock infection cells. Using Solexa deep sequencing, we detected a panel of 19-24nt Salmonella-derived non-coding RNA fragments with considerable large copy numbers in human colonic epithelial HT-29 cells following Salmonella infection.The fragment with the highest copy number, Sal-1, was further validated by both quantitative reverse transcription polymerase chain reaction (qRT-PCR) and northern blot. The generation of Sal-1 requires the infection of host cells by Salmonella, and the processing of the Sal-1 “primary” or “precursor” to the mature Sal-1 in Salmonella-infected cells is Dicer-independent but Argonaute 2 (Ago2)-dependent. Functionally, Sal-1 suppresses the expression of colonic epithelial cell endogenous inducible nitric oxide synthase (iNOS) via targeting its open reading frame and thus reduces the bacterial resistance of host cells.

overall_design: Screening and identification of Salmonella-encoded microRNA-like RNA fragments

first: Hongwei

last: Gu

first: Tianfu

last: Zhang

first: Chen-Yu

first: Ke

last: Zen


title: Adipose Tissue MicroRNAs as Regulators of CCL2 Production in Human Obesity (differentiation data)

status: Public on Aug 13 2012

city: Stockholm

first: Ingrid

last: Dahlman

address: Karolinska Huddinge

country: Sweden

institute: Karolinska

summary: We used an unbiased systems biology approach to study the regulation of gene expression in human adipose tissue focusing on inflammation. We show that microRNAs play a major role as regulators of CCL2 production in obesity.

overall_design: Subcutaneous adipose tissue was obtained from healthy subjects undergoing cosmetic liposuction (n=12). There was no selection for age, sex or BMI. From the tissue, we isolated preadipocytes and in vitro differentiated them to adipocytes. The cells were lysed at day 4/5 (early), 8 (middle) and 12 (late) of differentiation. From the samples, we prepared and hybridised biotinylated complementary RNA to GeneChip Human Gene 1.0 ST Arrays (Affymetrix Inc., Santa Clara, CA). Pre-processing was performed using the Affymetrix Expression Console version 1.1 and the following settings: Summarization: PLIER; Background Correction: PM-GCBG; Normalization: Global Median.

first: Niklas

last: Mejhert

first: Erik

last: Arner

first: Peter


title: Chromosomal aberrations in ETV6/RUNX1 positive cases using high-resolution 244K oligo-based array-CGH

status: Public on Jun 20 2012

city: Kuala Lumpur

first: Zubaidah

last: Zakaria

address: Jalan Pahang

department: Haematology Unit

country: Malaysia

institute: Institute for Medical Research

type: Genome variation profiling by genome tiling array

summary:
Identification of chromosomal deletion and duplications in childhood acute lymphoblastic leukemia with t(12;21). This study was performed to correlate clinical parameters with chromosomal aberrations by array-CGH and to identify other potential novel cancer genes involved in leukaemia.

In brief, PALL-6 was a Malay male diagnosed with B-ALL, had undergone a remission but late relapse and passed away. He was assessed under medium risk. PALL-7 is a Malay male and has a medium risk assessment, and is currently in remission. PALL-8 is a Malay female and has a medium risk assessment, and is currently in remission. PALL-9 is a Chinese male and has a high risk assessment, and is currently in remission. PALL-10 is a Malay male and has a standard risk assessment, had a relapse but is currently in remission. PALL-11 was a Malay male and had a medium risk assessment, but died during transplant.

overall_design: array-CGH was carried out on 11 cases of childhood acute lymphoblastic leukemia with t(12;21) diagnosed by molecular and FISH techniques. Commercial male and female genomic DNA were used as the references.

first: Nor

last: Kamaluddin

first: Mohd

middle: F

last: Ahid

first: Norlin

last: Ahmat

first: Ezza

last: Sharmiza


title: Twist1 Transcriptional targets in the developing atrio-ventricular canal of the mouse

status: Public on Jun 01 2012

city: Vancouver

first: Pamela

last: Hoodless

state: BC

address: 675 W 10th Ave

department: Terry Fox Laboratory

country: Canada

institute: BC Cancer Agency - Research Centre

summary: Malformations of the cardiovascular system are the most common type of birth defect in humans, affecting predominantly the formation of valves and septa. During heart valve and septa formation, cells from the atrio-ventricular canal (AVC) and outflow tract (OFT) regions of the heart undergo an epithelial-to-mesenchymal transformation (EMT) and invade the underlying extracellular matrix to give rise to endocardial cushions. Subsequent maturation of newly formed mesenchyme cells leads to thin stress-resistant leaflets. TWIST1 is a basic helix-loop-helix transcription factor expressed in newly formed mesenchyme cells of the AVC and OFT that has been shown to play roles in cell survival, cell proliferation and differentiation. However, the role and downstream targets of TWIST1 during heart valve formation remain unclear. To identify genes important for heart valve development downstream of Twist1 we performed global gene expression profiling of AVC, OFT, atria and ventricles of the embryonic day 10.5 mouse heart by tag-sequencing (Tag-seq). Using this resource we identified a novel set of 1246 genes, including 201 regulators of transcription, enriched in the valve forming regions of the heart. We compared these genes to a Tag-seq library from the Twist1 null developing valves revealing significant gene expression changes. These changes were consistent with a role of TWIST1 in controlling differentiation of mesenchymal cells following their transformation from endothelium in the mouse. To study the role of TWIST1 at the DNA level we performed chromatin immunoprecipitation and identified novel direct targets of TWIST1 in the developing heart valves. Our findings are consistent with a role for TWIST1 in the differentiation of AVC mesenchyme post-EMT in the mouse, and suggest that TWIST1 exerts its function by direct DNA binding to activate valve specific gene expression.

overall_design: Profiled the AVC, OFT, atria and ventricles of the embryonic day 10.5 mouse heart by tag-sequencing (Tag-seq) (no replicates). We also produced a Tag-seq library from Twist1 null developing valves to reveal the gene expression changes associated with loss of this gene.

first: Pavle

last: Vrljicak

first: Rebecca

last: Cullum

first: Erix

last: Xu

first: Alex

middle: C

last: Chang

first: Elizabeth

middle: D

last: Wederell

first: Marco

middle: A

last: Marra

first: Aly

last: Karson


title: Exosomal tumor microRNA modulates premetastatic organ cells [Agilent]

status: Public on Jun 13 2012

city: Heidelberg

first: Sanyukta

last: Rana

address: Im Neuenheimerfeld 365

department: Tumor Cell Biology

country: Germany

institute: University Hostipal Heidelberg

summary: Exososmes, potent intercellular communicators, are supposed to contribute to metastasis formation, which we confirmed for exosomes of the metastatic rat pancreatic adenocarcinoma line BSp73ASML that promote metastatic settlement in lymph nodes and lung of poorly metastatic BSp73ASML cells with a selective CD44v4-v7 (BSp73ASML-CD44vkd) knockdown. To define the molecular pathway(s), whereby exosomes contribute to premetastatic niche preparation, we profiled mRNA miRNA of BSp73ASMLwt and BSp73ASML-CD44vkd- exosomes and evaluated the impact on potential target cells. BSp73ASML exosomes are recovered in the draining lymph node after subcutaneous injection. In vitro, they preferentially bind and are taken-up by lymph node stroma cells (LnStr) and lung fibroblasts (LuFb) that were chosen as exosome targets. BSp73ASMLwt and BSp73ASML-CD44kd exosomes contain a restricted repertoire of mRNA and miRNA, hwere the lattter differe significantly between the two lines and even more pronounced, exosomes derived thereof with a not yet explored dominance of tumor-suppressor miRNA in ASML-CD44kd cells and exosomes. Both, exosomal mRNA and miRNA are recovered in target cells and exosome-uptake is accompanied by significant changes in gene expression. We didn't  observe a correlation between exosomal mRNA and changes in target cell mRNA or proteins. Instead transferred miRNA significantly affected target cell mRNA translation as demonstrated for selected, most abundant ASML exosomal miRNA besides others, miR-494 known target MAL (myelin and lymphocytes protein)/cadherin17, and miR-542-3p which targets TRAF/cadherin17. Furthermore, MMP transcription suggested to accompany cadherin17 dwon-regulation was upregulated in miR-494 or miR542-3p transfected or exosome co-cultured LnStr. Taken together, tumor exosomes target in vivo non-transformed cells in premetastatic organs. Exosome uptake induced altered target celll gene expression is strongly  promoted by exosomal miRNA where we demonstrate for the first time that exosomes/exosomal miRNA from a metastasizing tumor line can modulate stroma cells from premetastatic organs.

overall_design: Endothelial cells lines were treated with pancreatic adenocarcinoma (AS) derived exosomes or pancreatic adenocarcinoma derived exosomes expressing tetraspanin 8. Total RNA was isolated and used to perform the Agilent gene expression microarrays. In this assay a replicate of endothelial cell lines treated with ASTspan8 were also included. Moreover, total RNA from both base line expression of endothelial cells and rat endothelial fibroblasts were also used to perfrom gene expression microarrays. RNA isolated from Rat endothelial fibroblasts treated with the exosomes derived from rat pancreatic adenocarcinoma and exosomes derived from rat pancreatic adenocarcinoma expressing tetraspanin8 were individually used to perfrom gene expression microarrays. RNA isolated from exosomes derived from rat pancreatic adenocarcinoma cell lines expressing tetraspanin were used to peform gene expresiion to see the base line expression. Another replicate were also used. RNA isolated from base line or control of rat pancreatic adenocarcinoma wild type cells and also base line RNA isolated from rat pancreatic adenocarcinoma cells lines where CD44 was knock-down.

first: Kamilla

last: Malinowska

first: Margot

last: Zoller


title: Nascent-seq indicates widespread cotranscriptional RNA editing in Drosophila

status: Public on May 31 2012

city: Waltham

first: Joseph

last: Rodriguez

address: 415 South Street

department: Biology

institute: Brandeis University

summary: The RNA editing enzyme ADAR chemically modifies adenosine (A) to inosine (I), which is interpreted by the ribosome as a guanosine. Here we assess cotranscriptional A-to-I editing in Drosophila, by isolating nascent RNA from adult fly heads and subjecting samples to high-throughput sequencing. There are a large number of edited sites within nascent exons. Nascent RNA from an ADAR null mutant strain was also sequenced, indicating that almost all A-to-I events require ADAR. Moreover, mRNA editing levels correlate with editing levels within the cognate nascent RNA sequence, indicating that the extent of editing is set cotranscriptionally. Surprisingly, the nascent data also identify an excess of intronic over exonic editing sites. These intronic sites occur preferentially within introns that are poorly spliced cotranscriptionally, suggesting a link between editing and splicing. We conclude that ADAR-mediated editing is more widespread than previously indicated and largely occurs cotranscriptionally.

overall_design:
GSM914095: Fly genomic DNA sequencing. Sequenced on the Illumina GA II.
GSM914102-GSM914113: Fly head nascent RNA profiles over 6 time points of a 12hr light:dark cycle in duplicate; sequenced on the Illumina GA II.
GSM914114-GSM914119: Fly head nascent RNA profiles of yw, FM7, ADAR0 males in duplicate; sequenced on the HiSeq2000.
GSM915213-GSM915214: Fly head mRNA profiles over 2 time points of a 12hr light:dark cycle; sequenced on the Illumina GA II.
GSM915215-GSM915220: Fly head mRNA profiles over 6 time points of a 12hr light:dark cycle; paired-end sequenced on the Illumina GA II.
GSM915221-GSM91526: Fly head mRNA profiles over 6 time points of a 12hr light:dark cycle; sequenced on the Illumina GA II.

first: Jerome

last: Menet

first: Michael

last: Rosbash


title: Defective uncoupled differentiations after nuclear reprogramming

status: Public on Jun 08 2012

city: Jouy en Josas

first: Isabelle

last: Hue

address: Domaine de Vilvert

department: PHASE

country: France

institute: INRA

summary: Somatic cell nuclear transfer (SCNT) is the most efficient cell reprogramming technique available, especially when working with bovine species. Although SCNT blastocysts performed equally well or better than controls in the weeks following embryo transfer at Day 7, elongation and gastrulation defects were observed prior to implantation. To understand the developmental implications of embryonic/extra-embryonic interactions, the morphological and molecular features of elongating and gastrulating tissues were analysed. At Day 18, 30 SCNT conceptuses were compared to 20 controls (AI and IVP: 10 conceptuses each); one-half of the SCNT conceptuses appeared normal while the other half showed signs of atypical elongation and gastrulation. SCNT was also associated with a high incidence of discordance in embryonic and extraembryonic patterns, as evidenced by morphological and molecular ‘‘uncoupling’’. Elongation appeared to be secondarily affected; only 3 of 30 conceptuses had abnormally elongated shapes and there were very few differences in gene expression when they were compared to the controls. However, some of these differences could be linked to defects in microvilli formation or extracellular matrix composition and could thus impact extra-embryonic functions. In contrast to elongation, gastrulation stages included embryonic defects that likely affected the hypoblast, the epiblast, or the early stages of their differentiation. When taking into account SCNT conceptus somatic origin, i.e. the reprogramming efficiency of each bovine ear fibroblast (Low: 0029, Med: 7711, High: 5538), we found that embryonic abnormalities or severe embryonic/extra-embryonic uncoupling were more tightly correlated to embryo loss at implantation than were elongation defects. Alternatively, extra-embryonic differences between SCNT and control conceptuses at Day 18 were related to molecular plasticity (high efficiency/high plasticity) and subsequent pregnancy loss. Finally, because it alters redifferentiation processes in vivo, SCNT reprogramming highlights temporally and spatially restricted interactions among cells and tissues in a unique way.

overall_design: Amplified material from each extra-embryonic tissue was indirectly labelled using "random" hexamers. One independent target per tissue was generated and hybridised onto one array. 10 measurements per reproduction mode were generated.

first: S

last: Degrelle

first: F

last: Jaffrezic

first: E

last: Campion

first: K-A

last: Le Cao

first: D

last: Lebourhis

first: C

last: Richard

first: N

last: Rodde

first: R

last: Fleurot

middle: E

last: Everts

first: J

last: Lecardonel

first: Y

last: Heyman

first: X

last: Vignon

last: Yang

last: Tian

first: H

last: Lewin

last: Renard

first: I


title: Gene expression profiling in erythroid progenitors through ontogeny

city: Belgrade

first: Vladan

middle: Predrag

last: Cokic

address: Dr Subotica 4

country: Serbia

summary: Background: It has been reported that the phosphatidylinositol 3-kinase (PI3K)-AKT signaling pathway regulates erythropoietin (EPO)-induced survival, proliferation, and maturation of early erythroid progenitors. Erythroid cell proliferation and survival has also been related to activation of the JAK-STAT pathway. The goal of this study was to observe the function of EPO activation of JAK-STAT and PI3K/AKT pathways in the development of erythroid progenitors from hematopoietic CD34+ progenitor cells, as well as to distinguish early EPO target genes in human erythroid progenitors during ontogeny. Methods: Hematopoietic CD34+ progenitor cells, isolated from fetal and adult hematopoietic tissues, were differentiated into erythroid progenitor cells. We have used microarray analysis to examine JAK-STAT and PI3K/AKT related genes, as well as broad gene expression modulation in these human erythroid progenitor cells. Results: In microarray studies, a total of 1755 genes were expressed in fetal liver, 3844 in cord blood, 1770 in adult bone marrow, and 1325 genes in peripheral blood-derived erythroid progenitor cells. The erythroid progenitor cells shared 1011 common genes. Using the Ingenuity Pathways Analysis software, we evaluated the network pathways of genes linked to hematological system development, cellular growth and proliferation. The KITLG, EPO, GATA1, PIM1 and STAT3 genes represent the major connection points in the hematological system development linked genes. Some JAK-STAT signaling pathway-linked genes were steadily upregulated throughout ontogeny (PIM1, SOCS, MYC, PTPN11), while others were downregulated (PTPN6, PIAS, SPRED2). In addition, some JAK-STAT pathway related genes have specific expression just at certain stages of ontogeny (STATs, GRB2, CREBB). Beside continuously upregulated (AKT1, PPP2CA, CHUK, NFKB1) and downregulated (FOXO1, PDPK1, PIK3CG) genes in the PI3K-AKT signaling pathway, we also observed intermittently regulated gene expression (NFKBIA, YWHAH). Conclusions: This broad overview of gene expression in erythropoiesis revealed transcription factors with a prevalence at certain stages of ontogenesis. Finally, our results show that EPO-mediated proliferation and survival of erythroid progenitors occurs mainly through modulation of JAK-STAT pathway associated STATs, GRB2 and PIK3 genes, as well as AKT pathway- coupled NFKBIA and YWHAH genes.

overall_design:
Adult peripheral blood mononuclear cells were isolated from buffy coats of 3 healthy donors using Lymphocyte Separation Medium (BioWhittaker, Walkersville, MD). We washed mononuclear cells twice with Dulbecco's phosphate-buffered saline (PBS, Invitrogen Corporation, Carlsbad, CA), and CD34+ cells were purified by positive immunomagnetic selection using the MACS cell isolation system (Miltenyi Biotec, Auburn, CA). Fresh bone marrow CD34+ cells were collected (AllCells LLC, Berkeley, CA). Cord blood CD34+ cells (AllCells LLC) and fetal liver CD34+ cells (Cambrex Bio Science, Inc., Walkersville, MD) were collected and frozen. For analysis, CD34+ cells were resuspended in medium, which contained 30% FBS, 2 mmol/L glutamine, 100 U/ml penicillin, 100 µg/ml streptomycin, 1% deionized BSA, 10 mmol/L beta-mercaptoethanol, 1 mmol/L dexamethasone, 33 µg/ml holo-transferrin, 10 ng/ml SCF, 1 ng/ml IL-3 and 1 ng/ml GM-CSF (Sigma, St. Louis, MO), and 1 U/ml human recombinant EPO (Amgen Inc, Thousand Oaks, CA)
Erythroid progenitor cells differentiated from hematopoietic CD34+ progenitor cells of fetal liver, cord blood, bone marrow and peripheral blood origin
Biological replicates: 2 fetal liver, 3 cord blood, 3 bone marrow, 3 peripheral blood origin

first: Bhaskar

last: Bhattacharya

first: Raj

middle: K

last: Puri


title: Molecular basis for the specification of floral organs by APETALA3 and PISTILLATA (ChIP-Seq)

city: Zurich

first: Samuel

middle: Elias

last: Wuest

address: Winterthurerstrasse 190

department: Institute of Evolutionary Biology and Environmental Studies

country: Switzerland

institute: University of Zurich

type: Genome binding/occupancy profiling by high throughput sequencing

summary: Characterization of the activities of the transcription factors that AP3 and PI encode throughout flower development using perturbation and ChIPSeq assays in combination with a floral induction system (FIS) that allows a stage-specific analysis of flower development.

overall_design: Examination of genomic regions bound by fully functional AP3-GFP and PI-GFP proteins at approx floral stage 4-5 as compared to a negative control sample

first: Diarmuid

last: O'Maoileidigh

first: Frank

last: Wellmer


title: Intra-myocellular fatty acid synthesis and breakdown plays a critical role in mediating responses to dietary restriction in Drosophila melanogaster

status: Public on Jun 15 2012

city: Novato

first: Simon

last: Melov

state: CA

address: 8001 Redwood Blvd

institute: Buck Institute for Research on Aging

summary: Dietary restriction (DR) is a robust environmental intervention that slows aging in various species. Changes in fat content have been associated with DR, but whether they play a causal role in mediating various responses to DR remains unknown. We demonstrate that upon DR, Drosophila melanogaster shift their metabolism towards increasing both fatty acid synthesis and breakdown. Inhibition of acetyl CoA carboxylase (ACC), a critical enzyme in fatty acid synthesis, or fatty acid oxidation genes specifically in the muscle tissue inhibited the lifespan extension observed upon DR, suggesting a critical role for intra-myocellular fatty acid metabolism. DR enhances spontaneous activity of flies which was found to be dependent on the enhanced fatty acid metabolism. Furthermore, this increase in activity upon DR was found to partially mediate the lifespan extension upon DR. Over-expression of adipokinetic hormone (dAKH) in whole flies, which increases fat metabolism, led to an increase in spontaneous activity and lifespan in a nutrient dependent manner. Together these results suggest that in Drosophila melanogaster enhanced fat metabolism in the muscle is a key metabolic adaptation in response to DR.

overall_design: 24 experimental samples were analyzed using Nimblegen oligo microarrays. Wild type samples (AL without RU486) were used as the Cy3 reference/control for all experimetal comparisons.

first: Subhash

last: Katewa

first: Fabio

last: Demontis

first: Marysia

last: Kolipinski

first: Allan

last: Hubbard

first: Matthew

last: S Gill

first: Norbert

last: Perrimon

first: Pankaj

last: Kapahi


title: Molecular basis for the specification of floral organs by APETALA3 and PISTILLATA

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

overall_design: Refer to individual Series


title: MicroRNAome of pig adipose and muscle tissues

status: Public on May 16 2012

city: Ya'an

first: Mingzhou

last: Li

state: Sichuan

address: No.46  Xinkang Road

department: College of Animal Science and Technology

institute: Sichuan Agricultural University

type: Non-coding RNA profiling by high throughput sequencing

summary: Although the well-known importance of pig in agriculture, as well as a model for human biology, the miRNA catalog of pig has been largely undefined. Identification and preliminary characterization of adipose- and muscle-specific miRNAs would be a prerequisite for a thorough understanding of their roles in regulating adipose deposition and muscle growth. In the present study, we get insight into the miRNA transcriptome in eight adipose tissues, two skeletal muscles and cardiac muscle of pig using deep sequencing technology, and to elucidate their characteristic tissue-specific profiles and genomic context.

overall_design: Eleven small RNA libraries from eight adipose tissues, two skeletal muscle tissues and cardiac muscle of pig were sequenced.

first: Xuewei

first: Haosi

last: Chen

first: Xiaolian

last: Gao


title: Expression data from mammary macrophages isolated from MMTV-iFGFR1 transgenic mice

city: Minneapolis

first: Kaylee

last: Schwertfeger

state: MN

address: 420 Delaware St. SE MMC 609

department: Lab Medicine and Pathology

institute: University of Minnesota

summary: The goal of this experiment was to profile macrophages from mammary glands isolated from transgenic mice that express inducible FGFR1 in mammary epithelial cells (MMTV-iFGFR1 transgenic mice). The mice were treated with with dimerizer to activates iFGFR1 for 48 hours and 4 weeks to induce mammary hyperplasias. Control mice included non-transgenic littermates treated with dimerizer for the same amount of time.

overall_design: Macrophages were sorted from mammary glands of MMTV-iFGFR1 transgenic mice and non-transgenic mice following dimerizer treatment using Cd11b-PE. Macrophages from 3 mice were pooled for each sample. RNA was extracted and analyzed using the Affymetrix Mouse 2.0 chip.

first: Kathryn


title: Simvastatin treated Lymphoblastoid Cell lines from Cholesterol and Pharmacogenomics (CAP) Trial

status: Public on Jul 01 2012

city: Seattle

first: Lara

last: Mangravite

state: WA

address: 1100 Fairview Ave North

institute: Sage Bionetworks

summary: Statins reduce cardiovascular disease risk by lowering plasma low density lipoprotein (LDL)-cholesterol.  To identify novel pathways that modulate statin response, we assessed the influence of simvastatin exposure on expression quantitative trait locus (eQTL) associations across the genome in 480 lymphoblastoid cell lines (LCLs).  Cell lines were derived blood samples collected ant entry visit from participants in the Cholesterol and Pharmacogenomics (CAP) trial, who underwent a 6 week 40mg/day simvastatin trial. We identified 4590 cis-eQTLS that were independent of treatment status (FDR=1%) and six cis-eQTLS for which there was evidence of an interaction with treatment (FDR=20%).  Genotypes and Phenotypes derived from these indivudals are available through dbGaP (Accession Number).  eQTL results are available at: http://eqtl.uchicago.edu/cgi=bin/gbrowse/eqtl/

overall_design: Dataset consists of 960 expression beadarrays (Illumina HumanRef-8v3) representing  paired samples derived from 24-hour exposures of 480 lymphoblastoid cell lines (LCLs) to 2 micromolar simvastatin acid or control buffer.

first: Ronald

last: Krauss


title: Larval epidermis of the swallowtail butterfly Papilio xuthus

status: Public on May 12 2012

city: Tsukuba

first: Ryo

last: Futahashi

address: Central6, Higashi 1-1-1

country: Japan

institute: National Institute of Advanced Industrial Science and Technology

summary: Transcriptional profiling of larval epidermis at specific markings were examined using 11 developmental stages. Gene expression level was compared between mimetic white, cryptic thorax, and cryptic abdomen vs. mimetic black, cryptic eyespot, and cryptic V-shaped markings in all stages.

overall_design: For initial screening of marking-specific genes, 6 developmental stages for mimetic pattern, and 5 developmental stages for cryptic pattern was used. Mimetic white, cryptic thorax, and cryptic abdomen were independently labelled with Cyanine 3-CTP (Cy3), and mimetic black, cryptic eyespot, and cryptic V-shaped markings were independently labelled with Cyanine 5-CTP (Cy5) in all stages.

first: Haruhiko

last: Fujiwara


title: Cardiac gene expression analysis in porcine model of  heart failure

city: La Coruña

first: Mario

last: Torrado

state: La Coruña

address: Campus de Oza, Edificio El Fortin

department: Institute of Health Sciences

institute: University of La Coruña

summary:
A gene expression topology of the developing, postnatal and diseased heart resulted in re-interpretation of ventricular remodeling in terms of rearrangement of key gene regulatory networks that are imbalanced, attenuated, or abnormally activated in the failing myocardium. The underlying principle, “Shaping the heart in development and disease” becomes a focus of current cardiovascular research with the goal of developing innovative diagnostic and therapeutic strategies to combat cardiovascular disease. In this line, our interests focus on regulatory molecular pathways and identification of novel candidate genes associated with ventricular remodeling in normal and pathological states. The general goal of the project was to establish a piglet model of heart failure induced by the cardiotoxic agent Doxorubicin.
Transcriptomic analysis on Affymetrix GeneChip Porcine Genome Array was used to used to identified the genes associated with  pathological ventricular remodeling.

overall_design: Six 8-day old piglets were randomized in two groups, the experimental group (n=3) received a single intravenous administration of 2.0 mg/kg Doxorubicin, whereas the control group (n=3) was injected with PBS. Piglets were euthanized 3 weeks later to harvest cardiac tissue for RNA isolation. Piglets were used in accordance with protocols approved by the Institutional Animal Care and Use Ethical Committee.

first: Alexander

last: Mikhailov


title: An atlas of DNA methylomes in pig adipose and muscle tissues

type: Methylation profiling by high throughput sequencing

summary: It is evident that epigenetic factors, especially DNA methylation, play essential roles in obesity development. To learn systematic association of DNA methylation to obesity, we used pig as a model, and sampled eight diverse adipose tissues and two distinct skeletal muscle tissues from three pig breeds with distinguished fat levels: the lean Landrace, the fatty Rongchang, and the feral Tibetan pig. We sequenced 180 methylated DNA immunoprecipitation (MeDIP) libraries, generated 1,381 Gbp sequence data, and provided a genome-wide DNA methylation map for pig adipose and muscle studies. The analysis showed global similarities and differences between breeds, genders and tissues, and identified the differentially methylated regions (DMRs) that are preferentially located in intermediate CpG promoters and CpG island shores. The DMRs in promoters are highly associated to obesity development. We also analyzed methylation and regulation of the known obesity-related genes and predicted novel candidate genes. The comprehensive map here provides a solid base for exploring epigenetic mechanisms of adipose deposition and muscle growth.

overall_design: We collected eight diverse adipose tissues and two phenotypically distinct skeletal muscle tissues from three well-defined pig models with distinct fat rates, and studied genome-wide DNA methylation differences among breeds, males and females, and tissues.

first: Honglong

last: Wu

first: Ruiqiang


title: Expression differences related to phenobarbital feeding in worker honey bees

city: Wooster

first: Reed

last: Johnson

state: OH

address: 1680 Madison Ave.

department: Entomology

institute: The Ohio State University

summary:
The drug phenobarbital induces cytochrome P450 monooxygenase (P450) gene expression in many animals, but no changes in P450 expression, or expression of any detoxification genes, were observed in worker honey bees fed on phenobarbital-candy relative to bees fed plain candy.

Keywords: Expression profiling by array

overall_design: Five replicate microarray hybridizations were performed comparing transcript abundance in phenobarbital-fed and control-fed adult worker bees.  Each total RNA pool was derived from an independent collection of 10 worker bees.

first: May

last: Berenbaum


title: An atlas of mRNA expression in pig adipose and muscle tissues

summary: Obese and lean-type pig breeds show obvious differences in adipose deposition and muscle growth; however, the molecular mechanisms underlying this phenotypic variation remains unclear.  Landrace (a leaner, Western breed), Rongchang (a fatty, Chinese breed) and Tibetan (a feral, indigenous Chinese breed that has not undergone artificial selection) pig breeds were used in this study. We collected eight diverse adipose tissues and two phenotypically distinct skeletal muscle tissues from three well-defined pig models with distinct fat rates, and studied mRNA expression differences among breeds, males and females, and tissues.  These results highlight some possible candidate genes for porcine adipose deposition and muscle growth and provide some data on which to base further studies of the molecular basis of energy metabolism.

overall_design: The mRNA expression differences of eight diverse adipose tissues and two phenotypically distinct skeletal muscle tissues from three well-defined pig models with distinct fat rates are measured.


title: A cross-species analysis of microRNAs in the developing avian face

status: Public on May 02 2012

city: Saint Louis

first: Kara

last: Powder

state: MO

address: 4566 Scott Ave

department: Genetics

institute: Washington University in St Louis

summary: Avian beaks show extreme species-specific variability in morphology, though they develop from the same primordial structures. In both humans and birds, cranial neural crest cells are the primary source of mesenchyme for the frontonasal prominence; previous work has shown that these cells contain molecular information that regulate species-specific facial variation. To determine the molecular basis of avian craniofacial patterning, we have used Next-Generation sequencing to profile all 20-40nt microRNAs from micro-dissected cranial neural crest cells from the frontonasal prominence of three bird species (chickens, quails, and ducks). Samples for each species were isolated at two developmental stages, before (Hamilton Hamburger stage [HH] 20) and after (HH25) morphological distinctions between the species are evident.

sample_organism:
Anas platyrhynchos
Gallus gallus
Coturnix japonica

overall_design: Examination of microRNA expression in frontonasal neural crest cells of 3 bird species at two developmental stages.  Includes some biological replicates and one technical replicate.

first: Yuan-Chieh

last: Ku

first: Michael

last: Lovett


title: Expression analysis of strains Streptococcus pneumoniae KCTC 5080T, Streptococcus mitis KCTC 3556T, Streptococcus oralis KCTC 13048T, and Streptococcus pseudopneumoniae CCUG 49455T

status: Public on Apr 27 2012

city: Seoul

first: Heekuk

last: Park

address: Heukseok-dong

department: Department of Medical Microbiology

country: South Korea

institute: Chung-Ang University College of Medicine

summary: Investigation of whole genome gene expression level changes in S. pneumoniae KCTC 5080T, S. mitis KCTC 3556T, S. oralis KCTC 13048T, and S. pseudopneumoniae CCUG 49455T.  This proves that transcriptional profiling can facilitate in elucidating the genetic distance between closely related strains.

sample_organism: Streptococcus pseudopneumoniae ATCC BAA-960 = CCUG 49455

overall_design: A one chip study using total RNA recovered from S. pseudopneumoniae CCUG 49455T with three  strain. For the the transcriptome of S. pseudopneumoniae CCUG 49455T was analyzed using the S. pneumoniae R6 microarray platform and compared with those of S. pneumoniae KCTC 5080T, S. mitis KCTC 3556T, and S. oralis KCTC 13048T strains.

first: Hee

first: Soon

last: Myung

first: Wonyong

last: Kim


title: Phytochrome Interacting Factors 4 and 5

status: Public on May 03 2012

city: Lausanne

first: Markus

middle: Volker

last: Kohnen

state: Vaud

address: Genopode Building

department: Center for Integrative Genomics (CIG)

institute: Université de Lausanne


title: Liver transcriptome of sexually mature hens in relation to the formation of the egg yolk

status: Public on Apr 01 2012

city: Nouzilly

first: Joel

last: Gautron

address: UR83 Recherches avicoles

summary: We used a transcriptomic approach based on the comparison of the expression between the liver of sexually mature hens versus pre-laying pullets to better appreciate which hepatic proteases and antiproteases are specifically expressed in relation to vitellogenesis. Using a 20K chicken oligoarray corresponding to 12 595 different chicken genes, a total of 582 genes were shown to be over-expressed in the liver at sexual maturity of hens (1.2 to 67 fold- difference).  Most of the top ten over-expressed genes are known components of egg yolk or of the perivitelline membrane. The combination of different bioinformatic tools reveals 12 proteases and 3 antiproteases amongst the over-expressed genes, including many predicted proteins with yet unknown functions.

overall_design: 8 samples of each condition( liver of 38 weeks old mature hens and of 10 weeks old immature pullets) were analysed, with an experimental design in dye switch (half of the slides labeled with fluorophore Alexa 555 and half with Alexa 647 for each condition)

first: M

last: Bourin

first: J

last: Berges

first: C

last: Hennequet-Antier

last: Cabau

first: Y

last: Nys

first: S

last: Réhault-Godbert


title: Phosphate Starvation of Maize Inhibits Lateral Root Formation and Alters Gene Expression in the Lateral Root Primordium Zone

status: Public on Mar 09 2012

city: jinan

first: juren

last: zhang

address: shanda nanlv 27

institute: shandong university

summary:
Low phosphate concentrations are frequently a constraint for maize growth and development, and therefore, enormous quantities of phosphate fertilizer are expended in maize cultivation, which increases the cost of planting. Low phosphate stress not only increases root biomass but can also cause significant changes in root morphology. Low phosphate availability has been found to favor lateral root growth over primary root growth by dramatically reducing primary root length and increasing lateral root elongation and lateral root density in Arabdopsis. While in our assay when inbred line Q319 subjected to phosphate starvation, The numbers of lateral roots and lateral root primordia were decreased after 6 days of culture in a low phosphate solution (LP) compared to plants grown under normal conditions (sufficient phosphate, SP), and these differences were increased associated with the stress caused by phosphate starvation. However, the growth of primary roots appeared not to be sensitive to low phosphate levels. This is very different to Arabidopsis.
To elucidate how low phosphate levels regulate root modifications, especially lateral root development, a transcriptomic analysis of the 1.0-1.5 cm lateral root primordium zone (LRZ) of maize Q319 treated after 2 and 8 days by low phosphate was completed respectively. The present work utilized an Arizona Maize Oligonucleotide array 46K version slides, which contained 46,000 maize 70-mer oligonucleotides designated by TIGR ID, and the sequence information is available at the website of the Maize Oligonucleotide Array Project as the search item representing the >30,000 identifiable unique maize genes (details at http://www.maizearray.org).   Keywords: low phosphate, Lateral Root Primordium Zone, maize

overall_design: Two-condition experiment, low phosphate treated lateral root primordium zone of maize root vs. normal cultrued lateral root primordium zone. Biological replicates: 9 control, 9 treated, independently grown and harvested. One replicate per array.

first: Li

last: Zhaoxia

first: Xu

last: Changzheng

last: Kunpeng

first: Yan

last: Shi

first: Qu

last: Xun

first: Zhang

last: Juren


title: Expression data of yeast genes treated with rapamycin and compound CID 3528206

status: Public on May 01 2012

city: Albuquerque

first: Jun

last: Chen

state: NM

address: 2325 Camino de Salud NE

department: Health Science Center

institute: University of New Mexico

summary:
Compound CID 3538206 inhibits yeast TORC1 activity and functionally mimic rapamycin.
We used microarrays to compare the global gene expression with the treatment of  CID 3528206 and rapamycin.

platform_organism:
Schizosaccharomyces pombe
Saccharomyces cerevisiae

overall_design: BY4741 yeast cells were treated with1% DMSO, 20 uM CID 3528206 and 200 nM rapamycin in duplicate for 3hrs. RNA extracted and labeled to probe yeast gene arrays

first: Larry

last: Sklar


title: Whole genome gene expression profiles of normo- and dyslipidemic men after fish oil supplementation

status: Public on May 30 2012

city: Hannover

first: Simone

last: Schmidt

address: Am kleinen Felde 30

department: Institute of Food Science and Human Nutrition

institute: Leibniz University of Hannover

summary:
Beneficial effects of long-chain omega-3 polyunsaturated fatty acids (n-3 FAs) are generally well-known from epidemiological studies, but the various mechanisms of action are not completely clarified. Regulation of gene expression is one known mechanism of action, but only very limited data of regulated pathways in humans after n-3 FA supplementation are available. Up to now, no studies compared gene expression changes after n-3 FA supplementation between normolipidemic and dyslipidemic subjects. Therefore, the aim of this study was to investigate the effects of n-3 FA administration on whole genome expression profiles in the blood of normo- and dyslipidemic subjects.

We conducted an intervention study with normo- and dyslipidemic men aged between 29 and 51 years, which were subdivided into four groups with a balanced age distribution and randomized to either six fish oil capsules per day providing 1.5 g docosahexaenoic acid and 1.0 g eicosapentaenoic acid or corn oil capsules rich in linoleic acid per day for a period of 12 weeks. Venous blood samples were collected at baseline as well as after 4 hours, 1 week and 12 weeks of supplementation. For each investigation time point, the samples of each group were pooled together to minimize inter-individual variability. All subjects have successfully completed the study, but for the microarray experiments, nine subject samples were excluded. Therefore, the microarray experiments are based on the following group characteristics:
normolipidemic fish oil group (FO-N): pool of nine RNAs from normolipidemic subjects supplemented with fish oil;
normolipidemic corn oil group (CO-N): pool of six RNAs from normolipidemic subjects supplemented with corn oil;
dyslipidemic corn oil group (CO-D): pool of eight RNAs from dyslipidemic subjects supplemented with corn oil;
dyslipidemic fish oil group (FO-D): pool of nine RNAs from dyslipidemic subjects supplemented with fish oil.

overall_design:
The twenty normolipidemic and the twenty dyslipidemic subjects were subdivided into two groups. Thus, a total of four groups with ten men per group passed through the study. To realize a comparable mean age between groups, the formation of groups was performed by stratified allocation according to subject's age. The four study groups were randomly assigned to different study products by an uninvolved collaborator. Subjects ingested either six FO or six corn oil (CO) capsules per day for a period of twelve weeks. The daily n-3 PUFA intake via FO capsules was 2.7 g (1.14 g DHA and 1.56 g EPA). The predominant FA of the CO capsules was the omega-6 (n-6) PUFA linoleic acid (LA, 18:2n-6). Thus, the daily LA intake via CO capsules was 3.05 g LA. The subjects were instructed to ingest the capsules together with food, three in the morning and three in the evening, and to maintain their usual exercise and dietary habits throughout the intervention time. As an exception, at the first intervention day, all six capsules were ingested at the same time in the morning after a standardised breakfast. During each visit, fasting blood samples were collected by venepuncture. Additionally, participants completed a questionnaire to obtain information about changes in medication, dietary (e.g., changes in weekly fish intake, preferred fish dishes or species, respectively) and lifestyle habits (e.g., physical activity), as well as the tolerability of the capsules.

This record summarizes the results of 16 microarrays. The samples originate from whole blood of normo- and dyslipidemic subjects supplemented with either fish oil or corn oil for 4 h, 1 week and 12 weeks. Microarrays were hybridized in a loop design with one common reference using a dye-swap approach.

first: Frank

last: Stahl

first: Kai-Oliver

last: Mutz

first: Thomas

last: Scheper

first: Andreas

last: Hahn

first: Jan

last: Schuchardt


title: Global Mapping at the Core of the Arabidopsis Circadian Clock Defines the Network Structure of the Oscillator

status: Public on Mar 08 2012

city: Bellaterra

first: Jose Luis

last: Riechmann

state: Barcelona

address: Campus UAB - Edifici CRAG

institute: Center for Research in Agricultural Genomics

summary: In many organisms, the circadian clock is composed of functionally coupled morning and evening oscillators that regulate the bouts of dawn and dusk activity. In Arabidopsis, oscillator coupling relies on a core loop in which the evening oscillator component TOC1 was proposed to activate a subset of morning-expressed oscillator genes. Our systems-biological approach overturns the current view of the Arabidopsis circadian clock showing that TOC1 does not function as an activator but as a timely-controlled general repressor of morning and evening oscillator components. Repression occurs through rhythmic binding to the promoters of all oscillator genes, suggesting a previously unexpected direct connection between the morning and evening loops.

overall_design: Examination of TOC1 genome-wide binding using TOC1 Minigene (TMG) seedlings expressing the genomic fragment of TOC1 fused to the Yellow Fluorescent Protein in a toc1-2 mutant background (TMG-YFP/toc1-2 seedlings) grown under LD cycles (12h light:12h dark).

first: José

first: Igor

last: Antoshechkin

first: Paloma

last: Mas


title: Transcriptional analysis of primary adult human skin cells that express stage-specific embryonic antigen 3 (SSEA-3)

status: Public on Mar 01 2012

city: Los Angeles

first: James

last: Byrne

address: 610 Charles E. Young Drive East

department: Department of Molecular and Medical Pharmacology

institute: University of California, Los Angeles

summary: Primary human skin cells were gated based on expression of stage-specific embryonic antigen 3 (SSEA3) with the high SSEA3 expressing cells (top 10%, categorized as SSEA3-positive or SSEA3-high) and negative SSEA3 expressing cells (bottom 10%, categorized as SSEA3-negative) purified into two different subpopulations.  Sorted cells were allowed to adhere overnight under DMEM/F12 + 10% FBS culture conditions before total RNA was collected and global transcriptional analysis was performed.

overall_design: We isolated primary adult human skin cells with either high SSEA3 expression or negative SSEA3 expression via FACS and analyzed via Affymetrix microarray analysis.

first: J


title: Genome-wide analysis of gene expression changes in miR-214 KO mouse hearts and skeletal muscle

status: Public on Jan 31 2012

city: Dallas

first: Arin

middle: B

last: Aurora

state: TX

address: 6000 Harry Hines Blvd

department: Molecular Biology

institute: UT Southwestern Medical Center

summary: Early reperfusion of ischemic cardiac tissue remains the most effective intervention for improving clinical outcome following myocardial infarction.  However, abrupt increases in intracellular Ca2+ during myocardial reperfusion cause cardiomyocyte death and consequent loss of cardiac function, referred to as ischemia/reperfusion (IR) injury.  Cardiac IR is accompanied by dynamic changes in expression of microRNAs (miRNAs), which inhibit specific mRNA targets.  miR-214 is up-regulated during ischemic injury and heart failure in mice and humans, but its potential role in these processes is unknown.  We show that genetic deletion of miR-214 in mice causes loss of cardiac contractility, increased apoptosis, and excessive fibrosis in response to IR injury.

overall_design: The microarray contains 6 samples, each containing cDNA pooled from 3 mice per group. There are no replicates.  The array was designed to make 3 different pairwise comparisons between the following: P14 WT and miR-214 KO hearts; adult WT and miR-214 KO skeletal muscle; adult WT and miR-214 KO hearts

first: Eric

middle: N

last: Olson


title: Gene Expression Profiling of Listeria monocytogenes in monoculture and in co-culture state in the presence of Bacillus subtilis both as planktonic cells and in biofilms.

status: Public on Jan 15 2012

city: Agra

first: Prem Saran

last: Tirumalai

state: Uttar Pradesh

address: Dayalbagh

department: Faculty of Science

country: India

institute: Dayalbagh Educational Institute

summary: To understand the behaviour in terms of special genome components that are expressed by L.monocytogenes in the presence of another bacterium as may be the condition in its natural environments was our objective, for which we have used microarray gene expression at different time intervals of growth from 4hrs to 24 hrs. Expression of L.monocytogenes as co-cultures, both in broth culture state and biofilm state were differentiated to that of 24hrs pure broth culture. Also genes regulated for and during biofilm formation as pure cultures were identified with comparision to 24hrs pure broth culture. Distinguishing features with notable variation in all of the three sample sets as L.monocytogenes in pure culture biofilm, co-culture broth and co-culture biofilm were observable. Genes that are specifically up-regulated at each of growth condition and time interval were identified, genes regulated with ascending and descending patterns in time were also noticable. These variation in the gene expression gives an insight into the alterations in the biosynthetic and metabolic pathways under different states of growth

overall_design: Agilent one-color experiment,Organism: Listeria monocytogenes , Genotypic Technology Pvt. Ltd. designed Custom Microarray Listeria monocytogenes  8x15k  (Agilent-30831) , Labeling kit: Agilent Quick-Amp labeling Kit (p/n5190-0442)

first: Prem

middle: S

first: Soam

last: Prakash


title: Oval cells from DDB1 mutant mouse

status: Public on Jan 01 2012

city: La Jolla

first: Roy

middle: M

last: Williams

address: 3030 Science Park Road

department: Regenerative Medicine

institute: The Scripps Research Institute

summary: Quiescent hepatic stem cells (HSCs) can be activated when hepatocyte proliferation is compromised. Chemical injury rodent models have been widely used to study the locazation, biomarkers, and signaling pathways in HSCs, but these models usually exhibit severe promiscuous toxicity and fail to distinguish damaged and non-damaged cells. Our goal is to establish new animal models to overcome these limitations, thereby providing new insights into HSC biology and application. We generated mutant mice with constitutive or inducible deletion of Damaged DNA Binding protein 1 (DDB1), an E3 ubiquitin ligase, in hepatocytes. We show that deletion of DDB1 abolishes self-renewal capacity of mouse hepatocytes in vivo, leading to compensatory activation and proliferation of DDB1-expressing OCs. Importantly, the DDB1 mutant mice exhibit very minor liver damage, compared to a chemical injury model. Microarray analysis reveals several previously unrecognized markers, enriched in oval cells. This genetic model in which irreversible inhibition of hepatocyte duplication results in HSC-driven liver regeneration. The DDB1 mutant mice can be broadly applied to studies of HSC differentiation, HSC niche and HSCs as origin of liver cancer.

overall_design: Total RNA obtained from isolated EpCAM+ cells from DDB1 mutant mice compared to wild type hepatocytes

first: Yoko

last: Endo

first: Yong

last: Cang


title: Genome-Wide binding sites of two MADS-domain transcription factors SOC1 and SVP in Arabidopsis during the floral transition

status: Public on Feb 01 2012

city: Singapore

first: Zhen

last: Tao

address: S1A 07-01, 14 Science Drive 4

department: Biological Sciences

country: Singapore

institute: National University of Singapore

type: Genome binding/occupancy profiling by genome tiling array

summary: The floral transition in Arabidopsis is tightly controlled by complex genetic regulatory networks in response to endogenous and environmental flowering signals. SUPPRESSOR OF OVEREXPRESSION OF CONSTANS 1 (SOC1) and SHORT VEGETATIVE PHASE (SVP), two key MADS-domain transcription factors, perceive these signals and function as antagonistic flowering regulators. To understand how they mediate the floral transition, we mapped in vivo binding sites of SOC1 and SVP using chromatin immunoprecipitation followed by hybridization to whole-genome tiling arrays (ChIP-chip). Genes encoding proteins with transcription regulator activity and transcription factor activity were the most enriched groups of genes bound by SOC1 and SVP, indicating their central roles in flowering regulatory networks. In combination with gene expression microarray studies, we further identified the genes whose expression was directly regulated by SOC1 or SVP. Among the common direct targets identified, APETALA2 (AP2)-like genes that repress FT and SOC1 expression were downregulated by SOC1, but upregulated by SVP, revealing a complex feedback regulation among key genes determining the integration of flowering signals. SOC1 regulatory regions were also accessed by SOC1 itself and SVP, suggesting that self-activation and repression by SVP contribute to the regulation of SOC1 expression. In addition, ChIP-chip analysis demonstrated that miR156e and miR172a, which are involved in the regulation of AP2-like genes, were direct targets of SOC1 and SVP, respectively. Taken together, these findings reveal that feedback regulatory loops mediated by SOC1 and SVP are essential components of the gene regulatory networks underpinning the integration of flowering signals during the floral transition.

overall_design: soc1-101D and 35S:SVP ChIPed with SOC1 or SVP polyclonal antibody respectively vs. soc1-2 or svp-41 in Arabidopsis 9-day-old whole seedlings

first: Lisha

last: Shen

first: Chang

last: Liu

first: Lu

first: Yuanyuan

last: Yan

first: Hao

last: Yu


title: Intratumoral genomic heterogeneity in submucosal-invasive gastric cancer

status: Public on Jan 20 2012

city: Yufu-city

first: Yoshiyuki

last: Tsukamoto

state: Oita

address: hasamacho idaigaoka 1-1

department: Molecular Pathology

institute: Oita university, Faculty of Medicine

summary: In this study, we investigated CNAs of 59 tumor samples from 27 patients with submucosal-invasive gastric cancers (SMGC) by 44k oligonucleotide-based array comparative genomic hybridization (array CGH).

overall_design: 23 mucosal portion of SMGC vs 23 paired submucosal (SM) portion of SMGC, 9 SM portion vs 9 paired lymph node (LN) metastasis, 12 SMGC with LN metastasis vs 15 SMGC without LN metastasis

first: Akiko

last: Kuroda

first: Tung

middle: L

last: Nguyen

first: Tsuyoshi

last: Noguchi

first: Ichiro

last: Takeuchi

first: Masahiro

last: Uchida

first: Tomohisa

first: Naoki

last: Hijiya

first: Chisato

last: Nakada

first: Tadayoshi

last: Okimoto

first: Masaaki

last: Kodama

first: Kazunari

last: Murakami

first: Keiko

last: Matsuura

first: Masao

last: Seto

first: Hisato

last: Ito

first: Toshio

last: Fujioka

first: Masatsugu

last: Moriyama


title: Expression profiles in PCa And BPH from Chinese patients

status: Public on Feb 28 2012

city: Guangzhou

first: Yifeng

last: Luo

state: Guangdong

address: 58 Zhongshan 2nd Road

department: Institute of Respiratory Diseases of Sun Yat-sen University

country: China

institute: The First Affiliated Hospital of Sun Yat-sen University

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

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

overall_design: Refer to individual Series

first: Weide

last: Zhong

first: Huichan

last: He

first: Xingyin

last: Liu

first: Qishan

last: Dai

first: Funeng

last: Jiang

first: Jin

last: Zhao

first: Dongjiang

last: Liao

first: Xinpeng

last: Lu


title: Genome-wide Expression Assay Comparison Across Frozen and Fixed Postmortem Brain Tissue Samples

status: Public on Apr 03 2012

first: Maggie

last: Chow

address: 8110 La Jolla Shores Dr. Ste 201

department: Neuroscience

country: USA

institute: NIH-UC San Diego Autism Center of Excellence

summary: Comparison between in vitro transcription- and cDNA-mediated annealing, selection and ligation (DASL)-based assays on brain-specific reference RNA, and postmortem frozen and formalin fixed brain tissue from autistic and control cases.  Investigation of data preprocessing techniques for DASL-assayed RNA samples from frozen brain tissue.

overall_design: IVT-  and DASL-based expression assays were performed on 10 reference RNA samples (brain and pooled artificially degraded at 0, 10, 30, and 60 min), 4 formalin-fixed tissue-extracted RNA samples with replicates, and 57 frozen tissue-extracted RNA samples with replicates.  A subset of the 57 (N=33 samples) from frozen brain tissue assayed using the DASL-based platform were then used to test different dataset preprocessing strategies implemented in the lumi package in R/Bioconductor.  The data from frozen-tissue extracted DASL-processed RNA samples passing exclusion criteria were log2 transformed and normalized using quantile normalisation with lumi in R (quantile-normalized data available as a supplementary file linked to the Series record).

first: Hai-Ri

last: Li

first: Mary

last: Winn

first: Craig

last: April

first: Cynthia

last: Carter Barnes

first: Jian-Bing

last: Fan

first: Anthony

last: Wynshaw-Boris

first: Xiang-Dong

last: Fu

first: Eric

last: Courchesne

first: Nicholas

last: Schork


title: Transcriptome and microRNA array analyses reveal a stimulatory effect of the phytochemical shikonin on epithelial–mesenchymal transition (EMT) in mouse skin

status: Public on Dec 31 2011

city: Taipei

first: Ning-Sun

last: Yang

state: Taiwan

address: No.128 Sec.2, Academia Rd.

department: Agricultural Biotechnology Research Center

country: Taiwan

institute: Academia Sinica

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


title: Transcriptome and microRNA array analyses reveal a stimulatory effect of the phytochemical shikonin on epithelial–mesenchymal transition (EMT) in mouse skin [microRNA expression profile]

summary:
We investigate and define here the in vivo biological effects of shikonin, at the transcriptome and microRNA levels, in mouse skin tissues. Through cross-examination between total RNA transcripts and microRNA data sets, we predicted that shikonin treatment may affect the epithelial–mesenchymal transition (EMT) process and the expression of related microRNAs, including 200a, 200b, 200c, 141, 205 and 429 microRNAs, in test skin tissue. Indeed, further in vivo tests on mouse abdominal skin tissue confirmed the stimulatory effect of shikonin on regulatory molecules of the EMT process in epidermal tissue. In addition, RT-PCR analyses confirmed the downregulating effects of shikonin on the expression of microRNA 205 and members of the microRNA 200 family, which are known to be involved in the EMT process. Gene expression of two RNA targets of the microRNA 200 family in EMT regulation, namely Sip1 (Zeb2) and Tcf8 (Zeb1), were consistently upregulated by shikonin treatment.
We demonstrate here that shikonin can confer a potent stimulatory effect on the EMT process and suppress the associated-microRNAs expression in vivo in skin tissues.

overall_design: In order to systematically evaluate the effects of shikonin on mouse skin tissues, we next compared the gene expression profiles in shikonin-treated and acetone-treated skin tissues at different time points. Total RNA samples were collected at indicated time points for transcriptome and microRNA array analyses.

first: Shu-Yi

last: Yin


title: Conditional ablation of the Notch2 receptor in the ocular lens

city: Rockville

first: Radu

last: Cojocaru

state: MD

address: 5635 Fishers Lane, Suite 510

institute: Elsevier

summary: Notch signaling is essential for proper lens development, however the specific requirements of individual Notch receptors has not been previously investigated. Here we report the lens phenotypes of Notch2 conditionally mutant mice, which exhibited severe microphthalmia, reduced pupillary openings, disrupted fiber cell morphology, eventual loss of the anterior epithelium, fiber cell dysgenesis, and cataracts. Notch2 mutants also had a persistent lens stalk phenotype at E11.5, and aberrant DNA synthesis in the fiber cell compartment by E14.5. Gene expression analyses showed elevated levels of the cell cycle regulators Cdkn1a (p21Cip1), Ccnd2 (CyclinD2) and Trp63 (p63) that negatively regulates Wnt signaling. Although removal of Notch2 phenocopied the increased proportion of fiber cells of Rbpj and Jag1 conditional mutant lenses, Notch2 is not required for AEL proliferation, suggesting that a different receptor regulates this process. Instead, we found that the Notch2 normally blocks progenitor cell death. Overall, we conclude that Notch2-mediated signaling regulates lens morphogenesis, apoptosis, cell cycle withdrawal, and secondary fiber cell differentiation.

overall_design: We have compared gene expression of ocular lenses of mice that are lens specific conditional mutants of Notch2 gene to that of littermate controls that had no ablation of Notch2 gene in the lens. Two lenses of each of the three conditional mutants and controls were pooled together and total RNA was harvested from embryonic day 19.5 (E19.5) lenses. Gene expression changes caused by absence of Notch2 gene in the lens were analyzed.

first: Senthil

last: Saravanamuthu

first: Tien

middle: T

last: Le

first: Chun

middle: Y

last: Gao

middle: I

first: Pushpa

last: Pandiyan

first: Chunqiao

last: Liu

first: Jun

last: Zhang

first: Peggy

last: Zelenka

first: Nadean

last: Brown


title: Weighted gene co-expression network analysis on microarray data from subregions of zebra finch (Taeniopygia guttata) basal ganglia

status: Public on Jan 04 2012

first: Austin

last: Hilliard

address: 610 Charles E Young Dr East

institute: UCLA

summary: Similarities between speech and birdsong make songbirds advantageous for investigating the neurogenetics of learned vocal communication; a complex phenotype likely supported by ensembles of interacting genes in cortico-basal ganglia pathways of both species. To date, only FoxP2 has been identified as critical to both speech and birdsong. We performed weighted gene co-expression network analysis on microarray data from singing zebra finches to discover gene ensembles regulated during vocal behavior. We found ~2,000 singing- regulated genes comprising 3 co-expression groups unique to area X, the basal ganglia subregion dedicated to learned vocal-motor behavior. These contained known targets of human FOXP2 and potential avian targets. We validated novel biological pathways for vocalization. Our findings show that higher-order gene co-expression patterns, rather than expression levels, molecularly distinguish area X from the ventral striato-pallidum during singing. The previously unknown structure of singing-driven networks enables prioritization of molecular interactors that likely bear on human motor disorders, especially those affecting speech.

overall_design: Gene expression was measured in 2 basal ganglia sub-regions (area X & ventral striato-pallidum (VSP)) of 27 adult male zebra finches that sang different amounts of song over a 2hr period in the morning. 18 birds were allowed to sing freely, 9 birds were discouraged from singing by the presence of an investigator and those that sang fewer than 10 song motifs were considered “non-singers”.

first: Julie

last: Miller

first: Elizabeth

last: Fraley

first: Steve

last: Horvath

first: Stephanie

last: White


title: Tissue specific diurnal rhythm of transcripts and their regulation during herbivore attack in Nicotiana attenuata

status: Public on Dec 29 2011

city: Jena

first: Klaus

last: Gase

address: Hans-Knoell-Strasse 8

department: Molecular Ecology

institute: Max-Planck-Institute for Chemical Ecology

summary: Idenfication and characterization of oscillating transcripts after elicitation with oral secretions from the sepcialist herbivore, Manduca sexta larvae

overall_design: Source leaves, sink leaves and roots were collected every 4 h for one days.

first: Sang-Gyu

last: Kim

first: Emmanuel

last: Gaquerel

first: Jyotasana

last: Gulati

first: Ian

last: Baldwin


title: Genome-wide Binding Site Analysis of FAR-RED ELONGATED HYPOCOTYL 3 Reveals Its Novel Function in Arabidopsis Development

city: Shenzhen

first: Bosheng

last: Li

address: SUStech Huiyuan #1 406

department: MCDB

institute: SUSTC (current, may different with previous institution )


title: Characterization of exosomes from highly metastatic pancreatic adenocarcinoma line: ASML and a CD44v kd of ASML based on their miRNA content

status: Public on Dec 28 2011

city: Heidelberg

first: Sanyukta

last: Rana

address: Im Neuenheimerfeld 365

department: Tumor Cell Biology

institute: University Hostipal Heidelberg

summary: Comparing the miRNA profile of exosomes from ASML vs ASML CD44v kd pancreatic adenocarcinoma line revealed that the expression level of 33 from the 40 most abundant miRNA differed significantly between ASMLwt and ASML-CD44vkd exosomes

platform_organism:
Homo sapiens
Mus musculus
Rattus norvegicus
Human alphaherpesvirus 1
Human betaherpesvirus 5
Murid betaherpesvirus 1
human gammaherpesvirus 4
JC polyomavirus
Human immunodeficiency virus 1
Murid gammaherpesvirus 4
Human gammaherpesvirus 8
Betapolyomavirus hominis
Betapolyomavirus macacae

overall_design: In this study tumor cell exosomes, deemed important for intercellular communication were analysed for their miRNA content. Exosomes from a highly metastatic pancreatic adenocarcinoma cell line, ASML and from a CD44v kd of ASML were used for RNA preparation using Trizol reagent, and the total RNA was sent to Genomics core facility,EMBL, Heidelberg for miRCURY LNA microRNA Array, v.11.0 - hsa, mmu & rno

first: Margot

last: Zoeller


title: Transcriptome and microRNA array analyses reveal a stimulatory effect of the phytochemical shikonin on epithelial–mesenchymal transition (EMT) in mouse skin [gene expression profile]

first: Ning-Sun

last: Yang

first: Shu-Yi

last: Yin


title: Characterization of the the L. plantarum  capsular polysaccharide clusters

status: Public on Dec 23 2011

city: Ede

first: Michiel

last: Wels

address: Kernhemseweg 2

country: Netherlands

institute: NIZO food research

summary: The bacterial cell envelope is a complex, multilayered structure that is not only essential to maintain cellular integrity, but also facilitates vital bacterial processes such as adaption, colonization and adhesion. Cell envelopes comprise a wide range of molecules, such as proteins and capsular polysaccharide (CPS), which collectively decorate the bacterial cell in a species- and strain specific manner. Here we characterized the 4 CPS gene cluster of L. plantarum and assessed the impact on CPS (combinatorial) gene deletions on surface polysaccharide composition.

overall_design: individual KOs of the cps clusters and the combination of all four together were compared with the WT expression in a loop design. The KO of 1-3 was directly compared to the WT (dye swapped)

first: Daniela

last: Remus

first: Iris

last: van Swam

first: Roger

last: Bongers

first: Peter

last: Bron

last: Kleerebezem


title: Exosomal tumor miRNA modulates premetastatic organ cells


title: Transcriptional profiling of ICAM-positive and -negative cells from the mouse olfactory epithelium

status: Public on Dec 07 2011

city: Berkeley

first: Russell

last: Fletcher

department: MCB, Functional Genomics Lab

institute: UC Berkeley

summary: We used trasncriptional profiling of fluorescent activated cell sorting (FACS) purified ICAM1-positive and negative cells from the olfactory epithelium (OE) of three-week old mice to identify genes enriched in the horizontal basal cells.

overall_design: The olfactory epithelia from P21-P25 CD1 mice (Charles River Laboratories, Wilmington, MA), were isolated, dissociated, and then purified by FACS using a FITC-conjugated antibody for ICAM1 (CD54).  ICAM1-positive and negative cell populations were collected and compared.  RNA was purified with TRIzol reagent (Invitrogen, Carlsbad, CA), subjected to two rounds of amplification, labeled, and hybridized to Affymetrix Mouse Genome 430.2 GeneChip microarrays (Affymetrix Inc., Santa Clara, CA, USA) using Affymetrix reagents and protocols (http://www.affymetrix.com). There were three experimental replicates, each consisting of the ICAM1 (+) and ICAM1 (-) FACS purified cell populations from individual litters of mice that were dissected/dissociated/FACS-purified using an ICAM1-FITC conjugated antibody; one microarray was used for each ICAM1 (+) and ICAM1 (-) sample for a total of six microarrays.  Microarray data were normalized using GCRMA.

first: R

first: M

last: Prasol

first: J

last: Estrada

first: Y

middle: G

last: Choi

first: K

last: Vranizan

last: Ngai


title: Comparative analysis of mRNA expression in untreated lymph node stroma cells and upon treatment with exosomes derived from ASMLwt, ASML cd44v knockdown cells.

summary: Comparison of total RNA isolated from ASML and ASML CD44v knockdown exosomes; and RNA from untreated B12 lymph node stroma cells vs. cells treated for 24h with ASML wt or ASML CD44v kd exosomes

overall_design: The array consists of 12 samples. Samples 1-3 consist of total RNA from exosomes derived from ASML cells; samples 4-6 : total RNA from exosomes derived from ASML CD44v knockdown cell; samples 7,8 are total RNA from untreated B12 lymph node stroma cells; samples 9,10 are RNA from B12 cells treated for 24h with ASML wt exosomes and samples 11, 12 are RNA from B12 cells treated with ASML CD44v kd exosomes

first: Kamilla

last: Malinowska


title: The effect of 2-AA on P. aeruginosa PA14 and its mutants

status: Public on Dec 21 2011

city: Boston

first: Laurence

last: Rahme

state: MA

address: 50 Blosson St, Thier 340

department: Surgery

institute: Massachusetts General Hospital

summary:
The pqs operon of the bacteria P. aeruginosa is responsible for the production of at least 60 secreted compounds mainly hidroxy-quinolones (HAQs). Some of them, like PQS and HHQ, were found to be important signal that control the virulence of the bacteria. We have discover that one of the most abandon molecule produced by the pqs operon, 2 aminoacetophenone (2-AA), a volatile molecule serves as a unique signal. In contrast to the previous described PQS and HHQ, 2-AA is downregulating virulence and acute phase proteins and upregulating chronic phase proteins. In addition we have found that 2-AA promotes the formation of persisters cells that antibiotic tolerant.
we have compared the genes profile of wild-type PA14 strain and its derivatives topA which lacks Topoisomerase I and pqsA that do not produces HAQs or 2-AA to cultures that were treated with 3mM of 2-AA.

overall_design: Cell were grown with and without 2-AA (3mM) to OD 2.0.

first: Ronen

last: Hazan

first: Jianxin

last: He

first: Meenu

last: Kesarwani

first: Laurance


title: Gene Expression Profiling of Primary Male Breast Cancers Reveals Two Unique Subgroups and Identifies N-acetyltransferase-1 (NAT1) as a Novel Prognostic Biomarker

status: Public on Feb 03 2012

city: Lund

first: Ida

last: Johansson

address: Department of Oncology Clinical Sciences Lund University BMC C13

department: Oncology

institute: Lund University

summary: Male breast cancer (MBC) is a rare and inadequately characterized disease. The aim of the present study was to characterize MBC tumors transcriptionally, to classify them into comprehensive subgroups, and to compare them with female breast cancer (FBC). Methods: Sixty-six clinicopathologically well-annotated fresh frozen MBC tumors were analyzed using Illumina Human HT-12 bead arrays, and a tissue microarray with 220 MBC tumors was constructed for validation using immunohistochemistry. Two external gene expression datasets were used for comparison purposes; 37 MBCs and 359 FBCs. Results: Using an unsupervised approach, we classified the MBC tumors into two subgroups, luminal M1 and luminal M2, respectively, with differences in tumor biological features and outcome, and which differed from the intrinsic subgroups described in FBC. The two subgroups were recapitulated in the external MBCs dataset. Luminal M2 tumors were characterized by high expression of immune response genes and genes associated with estrogen receptor (ER) signaling. Luminal M1 tumors, on the other hand, despite being ER positive by immunohistochemistry showed a lower correlation to genes associated with ER signaling and displayed a more aggressive phenotype and worse prognosis. Validation of two of the most differentially expressed genes, class 1 human leukocyte antigen (HLA) and the metabolizing gene N-acetyltransferase-1 (NAT1), respectively, revealed significantly better survival associated with high expression of both markers (HLA, hazard ratio (HR) 3.6, P=0.002; NAT1, HR 2.5, P=0.033). Importantly, NAT1 remained significant in a multivariate analysis (HR 2.8, P=0.040) and may thus be a novel prognostic marker in MBC. Conclusions: We have detected two unique and stable subgroups of MBC with differences in tumor biological features and outcome. They differ from the widely acknowledged intrinsic subgroups of FBC. As such they may constitute two novel subgroups of breast cancer, occurring exclusively in men, and which may consequently require novel treatment approaches. Finally, we identified NAT1 as a possible prognostic biomarker for MBC, as suggested by NAT1 positivity corresponding to better outcome.

overall_design: Total RNA was extracted from 66 male breast cancer samples and were hybridized to Human HT-12 v3.0 Expression BeadChips in three batches at the SCIBLU Genomics Center at Lund University. Four samples each from hybridization batches one and two were re-hybridized in the third batch, resulting in a total of 74 experiments.

first: Cecilia

last: Nilsson

first: Pontus

last: Berglund

first: Martin

last: Lauss

first: Markus

last: Ringnér

first: Håkan

last: Olsson

first: Lena

last: Luts

first: Edith

last: Sim

first: Sten

last: Thorstensson

first: Marie-Lousie

last: Fjällskog

first: Ingrid

last: Hedenfalk


title: miR-182 induced gene expression alteration in glioma cells

status: Public on Nov 15 2011

first: Jun

last: Li

address: 74# Zhongshan Road II

department: Department of Biochemistry, Zhongshan School of Medicine

institute: Sun Yat Sen University

summary: This experiment is designed to evaluate gene expression alteration following miR-182 transfection in glioma cells. We find a significant elevation of NF kappa B transcriptional targets.

overall_design: Total RNA were extracted from SNB-19 glioma cells transfected with miR-182 mimic oligo or miRNA mimic negative control 36 hours after transfection, two biological replications for each treatment.

first: Zhe

last: Ying


title: MicroRNA-1 is a candidate tumor suppressor and prognostic marker

status: Public on Dec 01 2011

city: Bethesda

first: Robert

middle: Scott

last: Hudson

address: National Cancer Institute Room Blgd.37/3044

department: NCI

institute: NIH

summary: MicroRNAs (miRs) are small non-coding RNAs that can function as tumor suppressor genes. We previously reported that miR-1 is among the most consistently down-regulated miRs in primary human prostate tumors. In this follow-up study, we further corroborated this finding in an independent dataset and made the novel observation that miR-1 expression is further reduced in distant metastasis and is a predictor of disease recurrence. Moreover, we performed in vitro experiments to explore the candidate tumor suppressor function of miR-1. Cell-based assays showed that miR-1 is epigenetically silenced in human prostate cancer cells. Overexpression of miR-1 in these cells led to growth inhibition and down-regulation of genes in pathways regulating cell cycle progression, mitosis, DNA replication/repair, and actin dynamics. This observation was further corroborated with protein expression analysis and 3’-UTR-based reporter assays, indicating that genes in these pathways are either direct or indirect targets of miR-1. A gene set enrichment analysis revealed that miR-1-mediated tumor suppressor effects are globally similar to those of histone deacetylase inhibitors. Lastly, we obtained preliminary evidence that miR-1 alters gH2A.X marker expression and affects the cellular organization of F-actin and filipodia formation. In conclusion, our findings indicate that miR-1 acts as a tumor suppressor in prostate cancer by influencing multiple cancer-related processes and by inhibiting cell proliferation and motility.

platform_organism:
Homo sapiens
Mus musculus

overall_design:
In this study we monitored global miRNA expression changes in prostate cancer LNCaP cells treated with the epigenetic compounds 5-Azacytidine (5-AzaC) and/or trichostatin A (TSA). Cells were treated with epigenetic drugs for 36 hours and total RNA was isolated for hybridization to miRNA microarrays.  5 independent experiments were performed (n=4 for combined treatment).

The candidate prostate tumor suppressor miRNAs, miR-1, miR-206, and miR-27 were up-regulated in LNCaP cells for Affymetrix microarray analysis.  LNCaP cells were transfected with pre-miR oligos and 24 hr post-transfection total RNA was collected for microarray analysis; total of three independent experiments.

first: Stefan

last: Ambs

first: Ming

last: Yi


title: Transcriptional responses of the two-spotted spider mite (Tetranychus urticae) after transfer to different plant hosts

status: Public on Nov 23 2011

city: Salt Lake City

first: Richard

last: Clark

state: Utah

department: Department of Biology

institute: University of Utah

summary: We generated 38-bp Illumina reads from messenger RNA libraries from mites transferred from their preferred laboratory host, bean (Phaseolus vulgaris cv. California Red Kidney), to one of three hosts: bean, Arabidopsis thaliana (Bla-2 accession) and the tomato (Solanum lycopersicum; genotype Heinz 1706). Larvae were carefully collected from bean plants and transferred to the treatment plant. Mites were reared on these plants for ~24 hours, after which mites were collected for mRNA library preparation. Samples were a mix of males and females. The goal of the study was to identify genes that may underlie the ability of mites to be herbivores on different host plants.

overall_design: Mites were transferred from host bean plants to two non-preferred hosts (Arabidopsis thaliana and tomato). RNA was then collected, and RNA-seq was performed on the Illumina platform. For each of three host plants, three biological replicates were generated.

first: Edward

middle: J

last: Osborne

first: Mike

last: Grbic


title: The genome of Tetranychus urticae reveals herbivorous pest adaptations


title: Developmental stage-specific small RNA composition in the two-spotted spider mite (Tetranychus urticae)

summary: We generated 38-bp Illumina reads from single messenger RNA libraries from three diverse developmental stages of the two-spotted spider mite to capture small RNA diversity across development. Adult, nymphal+larvae and embryonic stages were separated using sieves of various pore sizes, and mites of various developmental stages were carefully selected for small RNA library preparation. Samples were a mix of males and females to capture male and female patterns of small RNA composition and were reared on beans (Phaseolus vulgaris cv California Red Kidney). Small RNA reads were used for miRNA prediction, piRNA discovery, and for quantitation of small RNA-generating loci (i.e. expression across development).

overall_design: Examination of small RNA from spider mites of adult, embryonic and pooled larval/nymphal developmental stages.


title: Developmental stage-specific gene expression in the two-spotted spider mite (Tetranychus urticae)

summary: We generated 77-bp Illumina reads from single messenger RNA libraries from four diverse developmental stages of the two-spotted spider mite to maximally capture the complement of transcribed sequences across development. Adult, nymphal, larvae and embryonic stages were separated using sieves of various pore sizes, and mites of various developmental stages were carefully selected for transcriptome library preparation. Samples were a mix of males and females to capture male and female patterns of transcription, and were reared on beans (Phaseolus vulgaris cv California Red Kidney). The RNA-Seq data was used for validation of gene models predicted by EuGene, and to study patterns of gene expression across development.

overall_design: Gene expression for spider mites from adult, nymph, larvae and embryonic developmental stages was examined (technical replicates were generated).


title: Spider mite preliminary feeding experiment with mites reared on bean and two Arabidopsis thaliana accessions

summary: We sequenced messenger RNA from mixed stages of the two-spotted spider mite (Tetranychus urticae) reared on bean (Phaseolus vulgaris cv California Red Kidney; the laboratory host plant for mites) and two Arabidopsis thaliana accessions which were considered to either be susceptible (Kondara) or resistant (Bla-2) to mite feeding. This pilot experiment was conducted to assess gene expression differences of mites grown on sensitive versus resistant Arabidopsis accessions, as well as differences in mites feeding on different host species. The expression data was used for gene model validation of genes predicted by EuGene in the spider mite genome and to assess gene expression levels.

overall_design: Examination of gene expression of spider mites reared on beans and two Arabidopsis accessions (Kondara and Bla-2).