title: Effect of Epigallocatechin gallate (EGCG), a green tea ployphenol, on estrogen regulated genes in breast cancer cell line MCF7.

status: Public on Apr 01 2015

city: Guwahati

first: Anil

middle: Mukund

last: Limaye

state: Assam

address: IIT Guwahati

department: Department of Biosciences and Bioengineering

institute: Indian Institute of Technology Guwahati

summary: Epigallocatechin gallate (EGCG), the major green tea polyphenol, has been a subject of global interest as a potential chemopreventive or chemotherapeutic supplement for breast cancer. While on one hand epidemiological studies suggest inverse correlation between green tea consumption and breast cancer risk, investigations using cell culture and animal models of breast carcinogenesis on the other hand have demonstrated antiproliferative, antitumor, anti-invasive and anti-metastatic properties of EGCG. Mechanism of how EGCG affects cell proliferation, apoptosis, migration and cell cycle by affecting the function of a wide range of molecular targets have also been studied. However, the question as to how EGCG impacts on estrogen responsive genes has not been addressed. This issue is of relevance to our notion of EGCG as a potential chemopreventive or chemotherapeutic agent against breast cancer, which is estrogen dependent in majority of the newly diagnosed cases. Here, using the estrogen receptor α (ERα) positive MCF-7 breast cancer cells as a model, we have examined the effect of EGCG on the estrogen regulated genes.

overall_design: MCF7 cells were treated with vehicle (Ethanol) or EGCG in the presence or absence of estrogen for 24hrs. Total RNA was extracted; Cy3 labeled cRNA was hybridized to Genotypic Technology designed Custom Human Whole Genome 8x60k Microarray (Agilent-027114). Median signal intensities were used for the analysis. After background subtraction (normexp) and normalization (quantile) differentially expressed genes were identified using linear models.

first: Mohan

last: Manjegowda

first: J

middle: M

last: Dixcy Jaba Sheeba

first: Marine

last: Hussain

first: Gauri

last: Deb

first: Neeraj

last: Kumar


title: Neosartorya fischeri Comparative Transcriptome when the fungi uses a differente carbon source, petroleum asphaltenes or glucose-peptona

status: Public on Apr 23 2015

city: Ensenada

first: RAFAEL

last: VAZQUEZ DUHALT

state: Baja California

address: Km 107 Carretera Tijuana-Ensenada

department: Bionanotechnology

country: Mexico

institute: Nanoscience and Nanotechnology Center-UNAM

summary: Neosartorya fischeri is a fungi that is able to grow in petroleum asphaltenes as sole carbon source. Here,  was investigated which enzymes were up regulated

overall_design: Analysis used glucose-peptone condition RNA as control samples for comparison to the experimental samples when the fungi was growth in asphaltenes as sole carbon source.

first: Rafael

last: Vazquez-Duhalt

first: E

middle: L

last: Hernandez-Lopez


title: Expression of Wigglesworthia glossinidia endosymbiont of Glossina morsitans morsitans genes

status: Public on Mar 10 2015

city: Montpellier

first: Anne

last: Geiger

address: Laboratoire de Recherches et de Coordination sur les Trypanosomoses TA,A-17 / G Campus international de Baillarguet

country: France

institute: UMR 177 IRD-CIRAD

summary:
Transcriptome analysis of Wigglesworthia glossinidia endosymbiont derived from uninfected and infected samples at 3 time points (3, 10 and 20 days).
Expression profiling by array -  Wigglesworthia glossinidia endosymbiont of Glossina morsitans morsitans

overall_design: RNAs are a mix of Wigglesworthia, Sodalis and glossina. RNAs were extracted from 24 samples including 6 conditions (with 4 replicates per condition).


title: Altered neurotrophin expression profiles in the nucleus of the solitary tract of spontaneously hypertensive rats

status: Public on Apr 15 2015

city: Tokyo

first: Sabine

last: Gouraud

address: 3-10-2  Osawa, Mitaka

country: Japan

institute: International Christian University

summary:
Our previous findings suggest that the nucleus of the solitary tract (NTS), a pivotal region for regulating the set-point of arterial pressure, exhibits abnormal inflammation in pre-hypertensive and spontaneously hypertensive rats (SHRs) together with elevated anti-apoptotic and low apoptotic factor levels compared with that of normotensive Wistar–Kyoto (WKY) rats.
Whether this chronic condition affects neuronal growth and plasticity in the NTS remains unknown.
To unveil the characteristics of the neurodevelopmental environment in the NTS of hypertensive rats, we investigated the gene expression profile of neurotrophins and their receptors in SHRs compared to that of normotensive rat WKY.

overall_design: The NTS was dissected from the brain of 6 SHRs and 6 WKY rats and the total RNA was extracted. In both groups of rats (SHRs & WKY rats, n = 6 each), a total of 2 ug mRNA extracts from each NTS were pooled together, treated with RNase-free DNAse I (Invitrogen Life technologies) to remove any genomic contamination, and further purified using the RNeasy mini kit (Qiagen) according to the manufacturer’s instructions. Reverse transcription was subsequently performed on 1 ug total RNA using SuperArray’s RT2 First Strand Kit (SABiosciences); the resulting cDNA was submitted for real-time quantitative PCR reactions on RT2 ProfilerTM PCR array plates using Superarray RT2 SYBR Green qPCR Master Mix (SAbiosciences) and iCycler iQ thermal cycler (Bio-rad), following the manufacturer’s instructions. The experiment was performed in duplicate in each group.

first: S

middle: S

first: H

last: Waki


title: Genome-wide transcriptional analyses of islet-specific CD4+ T cells identify Idd9 genes controlling diabetogenic T cell function

status: Public on Mar 04 2015

city: Hershey

first: Hanspeter

last: Waldner

address: 500 University Dr.

country: USA

institute: PSU College of Medicine

summary: Analysis of gene expression levels in ex-vivo and p79-stimulated splenic CD4+ T cells.

overall_design: Total RNA obtained from ex-vivo CD4+TCRVβ4+ T cells from BDC-Idd9 mice compared to BDC mice and p79-stimulated CD4+TCRVβ4+ T cells from BDC-Idd9 mice compared to BDC mice.

first: Gregory

last: Berry

first: Christine

last: Frielle

first: Robert

last: Brucklacher

first: Willard

last: Freeman


title: Whole-genome gene expression profiling revealed genes and pathways potentially involved in regulating interactions of soybean with cyst nematode (Heterodera glycines Ichinohe)

city: Columbia

first: Henry

middle: T.

last: Nguyen

state: Missouri

address: Hitt Street

department: Plant Sciences

institute: University of Missouri

summary: Background: Soybean cyst nematode (SCN, Heterodera glycines Ichinohe) is the most devastating pathogen of soybean. Many gene expression profiling studies have been conducted to investigate the responses of soybean to the infection by this pathogen using primarily the first-generation soybean genome array that covered approximately 37,500 soybean transcripts. However, no study has been reported yet using the second-generation Affymetrix soybean whole-genome transcript array (Soybean WT array) that represents approximately 66,000 predicted soybean transcripts. Results: In the present work, the gene expression profiles of two soybean plant introductions (PIs) PI 437654 and PI 567516C (both resistant to multiple SCN races) and cultivar (cv.) Magellan (susceptible to SCN) were compared in the presence or absence of the SCN inoculum at different time points (3 and 8 days post-inoculation). For this purpose, the Soybean WT array, which covers many more predicted soybean transcripts than the first-generation Affymetrix soybean array, was employed. Data analysis revealed that the two resistant soybean lines showed distinctive gene expression profiles from each other and from Magellan not only in response to the SCN inoculation, but also in the absence of SCN. Overall, 1,413 genes and many pathways, such as defense and hormonal pathways, were revealed to be differentially regulated. Among them, 297 genes were constitutively regulated in the two resistant lines (compared with cv. Magellan) and 1,146 genes were responsive to the SCN inoculation in the three lines, with 30 genes regulated both constitutively and by SCN. In addition to the findings similar to those in the published work, many genes involved in ethylene, protein degradation, and phenylpropanoid pathways were also revealed differentially regulated in the present study. GC-rich elements (e.g., GCATGC) were found over-represented in the promoter regions of certain groups of genes. These have not been observed before, and could be new defense-responsive regulatory elements. Conclusions: Different soybean lines showed different gene expression profiles in the presence and absence of the SCN inoculum. Both inducible and constitutive gene expression may contribute to resistance to multiple SCN HG Types in the resistant soybean PI lines. Ethylene, protein degradation, and phenylpropanoid pathways, as well as many other pathways reported previously, may play important roles in mediating the soybean-SCN interactions. The revealed genes, pathways, and promoter elements can be further explored to regulate or engineer soybean for resistance to SCN.

overall_design: Three soybean lines were compared in the study:  Magellan (susceptible to SCN), PI 437654 (PI654; resistant to SCN), and PI 567516C (PI516C; resistant to SCN). Overall, thirty samples, including two biological replicates for each sample, were analyzed.

first: Tri

last: Vuong

first: Yongqing

last: Jiao

first: Jinrong

last: Wan


title: Natriuretic Peptide Receptor 3 (NPR3) is regulated by microRNA-100

status: Public on Mar 23 2015

city: Singapore

first: Lee Lee

last: Wong

address: 14 Medical Drive, 08-01

department: Medicine

country: Singapore

institute: National University of Singapore

summary: The cardiac natriuretic peptide (NPs) plays an important role in the regulation of cardiovascular and renal function. We examined the miRNAs that could be regulating NPs by subjecting the cardiomyocytes, HCMa cells, to hypoxia.

overall_design: In the study presented, 839 miRNAs were profiled in two samples- control normoxia and hypoxia. Each samples were pooled from 3 independent experiments.

first: Lee

first: Arunmozhiarasi

last: Armugam

first: Kandiah

last: Jeyaseelan

first: Arthur

last: Richards

first: Yei-Tsung

last: Chen


title: Gene expression change in the cerebellum and prefrontal cortex of depression rats

status: Public on Feb 26 2015

city: Wakayama city

first: Yuta

last: Yamamoto

address: 811-1 Kimiidera

institute: Wakayama Medical  University

summary: The depressive-like behavior in animals is usually assessed by standardized behavioral tests such as the forced swimming test. However, the findings of these tests may be affected by individual variability among animals, which may hinder the discovery of genes responsible for depression. Few reports have showed the influence of individual variability in identifying the genes associated with depressive-like behavior. In this study, we measured the immobility ratio (% immobility in 5 min) in the forced swimming test in 106 male Wistar rats. According to the distribution of individual immobility ratio, the rats were divided into three groups: the control group with immobility ratio -1 to +1 standard deviation (SD) from the mean, the depressive group with immobility ratio +1 to +2 SD above the mean, and the anti-depressive group with immobility ratio -1 to -2 SD below the mean. Microarray analysis was used to identify the genes differentially expressed by depressive group rats in the prefrontal cortex and cerebellum. The differentially expressed genes in both brain regions of the depressive group were Alas2, Gh1, Hba-a2, Hbb, Hbb-b1, Hbe2, LOC689064, Mrps10, Mybpc, Olf6415, and Pfkb1. Ingenuity pathway analysis identified Gh1 as a hub gene in the networks of the differentially expressed genes in both brain regions. This study indicates that inherent differences in depressive-like behavior may be related to the Gh1 expression in the cerebellum and prefrontal cortex.

overall_design: We measured the immobility ratio of 106 normal rats using the forced swimming test and statistically analysis. We selected the rats exhibitting depressive-like behavior or average in the 106 rats. Total RNA was prepareted from the cerebellum and prefrontal cortex. An equal amount of RNA from 4 rats in each group was pooled and used for microarray analysis.

first: Takao

last: Ito

first: Takashi

last: Ueyama

first: Yoshihiro

last: Tsuruo


title: Increased sucrose levels mediate selective mRNA translation in Arabidopsis

status: Public on Jan 28 2015

city: Umea

first: Johannes

last: Hanson

address: KBC

department: Plant Physiology, Umeå University

country: Sweden

institute: Umeå Plant Science Centre

summary: Background  Protein synthesis is a highly energy demanding process and is regulated according to energy availability in plant cells. Light and sugar availability affect mRNA translation but the specific roles of these factors remain unclear. In this study, sucrose was applied to Arabidopsis seedlings kept in the light or in the dark, in order to distinguish sucrose and light effects on transcription and translation. These were studied using microarray analysis of steady state mRNA and mRNA bound to translating ribosomes.   Results  Steady state mRNA levels were affected differently by sucrose in the light and in the dark but general translation increased to a similar extend in both conditions. Alterations in polysomal mRNA association closely followed the changes induced on the transcript level. However, for 243 mRNAs, a change in ribosome occupancy was observed after sucrose treatment in the light, but not in the dark condition. Many of these mRNAs are annotated as encoding ribosomal proteins, supporting specific translational regulation of this group of transcripts. Unexpectedly, the numbers of ribosomes bound to each mRNA decreased for mRNAs with increased ribosome occupancy.   Conclusions  Our results suggest that sucrose regulate translation of these 243 mRNAs but specifically in the light, through a novel regulatory mechanism. Our data sows that increased polysomal association is not necessarily leading to more ribosomes per transcript, suggesting a mechanism of translational induction not solely dependent on increased translation initiation rates.

overall_design: Four different samples groups were used: Control, Darkness, Sucrose, Simultaneous Darkness and sucrose treatments. All sample groups was represented by both total mRNA hybridization and of mRNAs from polysomal enrichment. All sample groups were represented by three biological replicates.

first: Magdalena

last: Gamm


title: Tumor circulating DNA profiling in xenografted mice exposed to intermittent hypoxia

status: Public on Feb 24 2015

first: Rene

middle: Gabriel

last: Cortese

state: MO

address: 1 Hospital Dr. MA104E

department: Child health Research Institute

type: Genome variation profiling by genome tiling array

summary: Intermittent hypoxia (IH) is a hallmark of obstructive sleep apnea (OSA), which has been proposed as the major determinant of processes involving tumor invasion and metastasis. To study whether circulating DNA (cirDNA) in blood plasma reflects the changes that the tumor cells undergo under IH conditions, we used a xenografted murine model. Mice engrafted with TC1 epithelial lung and controls were exposed to IH or room air (RA) conditions. Plasma cirDNA amounts were significantly increased in mice exposed to IH (p<0.05). We found a significant correlation between plasma cirDNA concentration and tumor size, weight and invasiveness (p<0.05). Using a microarray-based approach, we identified 2,094 regions showing significant differential cirDNA modifications. System biology analysis revealed an association with molecular pathways misregulated in cancer progression and with distal and TSS-associated transcription factor binding sites. We detected clusters of highly variable regions in chromosomes 7, 13, 14 and X, which may highlight hotspots for DNA deletions. Single locus displayed high intragroup variation, suggesting cellular heterogeneity within the tissue may be associated to cirDNA release. Our result showed that exposure to IH increases the shedding of cirDNA into circulation, which carries epigenetic modifications that may characterize cell populations within the tumor that preferentially release their DNA upon IH exposure.

overall_design: 6 xenografted mouse samples were analyzed by microarray analysis: Mouse exposed to IH (n=3, XenoIH group) and mouse exposed to room air conditions (n=3, XenoRA group)

first: Isaac

last: Almendros

first: Yang

last: Wang

first: David

last: Gozal


title: Selective Loss of RB in Resistant EGFR Mutant Lung Adenocarcinomas that Transform to SCLC [CGH]

status: Public on Jan 30 2015

city: Boston

first: Kenneth

middle: N

last: Ross

state: MA

address: 450 Brookline Ave., Rm M640

department: Pediatric Oncology

institute: Dana-Farber Cancer Institute

summary:
The study was designed to identify the molecular changes that occur in EGFR mutant NSCLCs that become resistant to TKI by transforming to SCLC.
Tyrosine kinase inhibitors (TKIs) are effective treatments for non-small cell lung cancers (NSCLCs) with epidermal growth factor receptor (EGFR) mutations.  However, they do not lead to cures, and, on average, relapse occurs after one year of continuous treatment.  In a subset of patients, a fundamental histological transformation from NSCLC to small cell lung cancer (SCLC) is observed in the resistant cancers, but the molecular changes associated with this transformation remain unknown. Analysis of a cohort of tumor samples and cell lines derived from resistant EGFR mutant patients with SCLC transformation revealed that RB is lost in 100% of these cases, but rarely in those that remain NSCLC.  Global changes in gene expression, including increased neuroendocrine marker expression and absence of EGFR expression, are observed in cancers that transformed to SCLC.  Consistent with their genetic and epigenetic similarities to classical SCLC, cell lines derived from resistant EGFR mutant SCLC biopsies are substantially more sensitive to ABT-263 treatment compared to those derived from resistant EGFR mutant NSCLCs.  Together, these findings suggest that despite developing initially as EGFR mutant adenocarcinomas, this subset of resistant cancers ultimately take on many of the molecular and phenotypic characteristics of classical SCLC.

overall_design: Overall, we completed array CGH analysis on 4 tumor specimens from EGFR mutant, TKI-resistant patients.  Three of these samples had transformed to SCLC and one remained NSCLC.

first: Matthew

middle: J

last: Niederst

first: Jeffrey

middle: A

last: Engelman

first: Anthony

last: Iafrate


title: SMC2: a candidate gene associated with Cornelia de Lange Syndrome

status: Public on Jan 23 2015

city: Beijing

first: wang

last: liang

address: 7A North Yongchang Road BDA

country: China

institute: BioChainBJ

summary: whole-genome aCGH analysis also showed us that the patient carried a 12.01-1M Mb deletion region at chromosome bands 9q31.1-q32 (105,190,105-117,195,154). The deleted region encompasses 22 genes including SMC2

overall_design: Two-condition Samples, Cornelia de Lange Syndrome vs. Normal cells.

first: Ruixue

last: Cao

first: Fei

last: Long

first: Shaohai

last: Fang

first: Yuejuan

last: Xu

first: Rang

first: Sun


title: microRNA expression in parotid acinar cells during terminal differentiation

status: Public on Jan 27 2015

city: Louisville

first: Douglas

last: Darling

state: KY

address: 501 S. Preston St.

department: Oral Immunology and Infectious Diseases

institute: University of Louisville

summary:
Terminal differentiation in parotid acini relies on sustained changes in gene expression during the first few postnatal weeks. Little is known about what drives these changes. Expression measurements along with knowledgebased network analysis was used to develop a prospective gene regulatory network that drives differentiation.
We used both microRNA and mRNA expression measurements along with knowledgebased network analysis was used to develop a prospective gene regulatory network that drives differentiation.

platform_organism:
Mus musculus
Rattus norvegicus

overall_design: laser capture microdissection was used to isolate acinar cells from the parotid at four timepoints in triplicate (E20, P5, P15, and P25). RNA was isolated, and used to measure microRNA expression.


title: microRNA expression profiling of different T cell subset in human tonsils

status: Public on Jan 10 2015

city: Canberra

first: Monika

last: Srivastava

state: ACT

address: Building 131, Garran Road

department: Pathogen and Immunity

country: Australia

institute: JCSMR, ANU

summary:
Tight control of follicular helper T(Tfh) cells is required for optimal maturation of the germinal center (GC) response. The molecular mechansims controlling Tfh cell differentiation remain incompletely understood. Here we sought to to identfiy miRNAs that might regulate Tfh cell development and/or function.
To identfiy miRNAs that are differentially expressed in Tfh cells, we performed Agilent microRNA microarray analysis comparing Tfh cells with the other main T cell subsets (naive T cells, non-Tfh effector or non-Tfh memory T cells, CD57+ Tfh cells and CD57- Tfh cells).

overall_design: RNA was extracted from 4 separate human tonsils (biological replicates) using mirVANA RNA isolation kit (Ambion) according to the manufacturer’s protocol. Each biological sample was analysed individually. Live lymphocytes were sorted based on negative 7AAD staining, and thefollowing four subsets were purified: Naive T cells (CD4+ CD45RO-); CD57+ Tfh cells (CD4+ CD45RO+ PD-1_high CXCR5_high CD57+); CD57- Tfh cells (CD4+ CD45RO+ PD-1_high CXCR5_high CD57-) and non-Tfh effector or memory T cells  (CD4+ CD45RO+ PD-1_neg CXCR5_neg). RNA quantity and quality was determined using a Nanodrop 1000 and an Agilent 2100 Bioanalyzer respectively. Hybridization on Agilent Human miRNA Microarray (V1) Kit, 8x15K and was performed at The Ramaciotti Center for Genomics (University of New South Wales, Australia). The mean of 3-4 biological replicates from each population of each population were calculated and values were plotted using Prism.

first: Alvin

last: Pratama

first: Robert

last: Rigby

first: Carola

middle: G

last: Vinuesa


title: Analysis of the transcriptional responses in inflorescence buds of Jatropha curcas exposed to cytokinin treatment

status: Public on Dec 14 2014

city: Mengla

first: MaoSheng

last: Chen

state: Yunnan

address: Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences

department: Molecular breeding of energy plants

summary: Jatropha curcas L. is a potential biofuel plant. Application of exogenous cytokinin (6-benzyladenine, BA) on its inflorescence buds can significantly increase the number of female flowers, thereby improving seed yield. To investigate which genes and signal pathways are involved in the response to cytokinin in J. curcas inflorescence buds, we monitored transcriptional activity in inflorescences at 0, 3, 12, 24, and 48 h after BA treatment using a microarray. We detected 5,555 differentially expressed transcripts over the course of the experiment, which could be grouped into 12 distinct temporal expression patterns. We also identified 31 and 131 transcripts in J. curcas whose homologs in model plants function in flowering and phytohormonal signaling pathways, respectively. According to the transcriptional analysis of genes involved in flower development, we hypothesized that BA treatment delays floral organ formation by inhibiting the transcription of the A, B and E classes of floral organ-identity genes, which would allow more time to generate more floral primordia in inflorescence meristems, thereby enhancing inflorescence branching and significantly increasing flower number per inflorescence. BA treatment might also play an important role in maintaining the flowering signals by activating the transcription of GIGANTEA (GI) and inactivating the transcription of CONSTITUTIVE PHOTOMORPHOGENIC 1 (COP1) and TERMINAL FLOWER 1b (TFL1b). In addition, exogenous cytokinin treatment could regulate the expression of genes involved in the metabolism and signaling of other phytohormones, indicating that cytokinin and other phytohormones jointly regulate flower development in J. curcas inflorescence buds. Our study provides a framework to better understand the molecular mechanisms underlying changes in flowering traits in response to cytokinin treatment in J. curcas inflorescence buds. The results provide valuable information related to the mechanisms of cross-talk among multiple phytohormone signaling pathways in woody plants.

overall_design: Gene expression of flower buds in response to BA was measured at 0h, 3h, 12h, 24h and 48h after 1mM 6-benzylaminopurine treatment. Three biological replicates were prepared for each time point.

first: Zeng

middle: F

first: Mao

first: Bang

middle: Z

last: Pan

first: Gui

first: Jun

last: Ni

first: Long

last: Niu


title: Expression analysis of individual homoeologous wheat genome- and rye genome-specific transcripts in a 2BS.2RL wheat-rye translocation

city: Urbana

first: Tong Geon

last: Lee

state: IL

address: 1101 W Peabody

institute: University of Illinois

summary: To distinguish transcripts expressed from each of the three wheat genomes and those from the rye chromatins, genomic probes generated from diploid progenitors of wheat and rye were synthesized

sample_organism:
Secale cereale
Triticum aestivum
Triticum urartu
Aegilops speltoides
Aegilops tauschii

overall_design: Consensus sequences for probe design were generated from local unigene clusters. EST and cDNA sequences were downloaded from NCBI. A total of 52,589 pairs of probes were designed. Two 60 bp probes were designed from each consensus sequence. The array was manufactured by NimbleGen and synthesized on 12-plex arrays. Two independent biological replicates were used in separate hybridizations. Each biological replicate was a total RNA sample extracted from the whole tissue of two seedlings.

first: Tong

first: Yong

middle: W

last: Seo


title: Transcriptome of the NWMN_0641 deletion mutant strain and the wild-type Staphylococcus aureus Newman strain

status: Public on Nov 04 2014

city: Shanghai

first: Lefu

last: Lan

address: 555 Zu Chong Zhi Road

department: Shanghai Institute of Materia Medica

institute: Chinese Academy of Sciences

summary:
To study the roles of NWMN_0641, we used microarray to compare the transcriptome of the NWMN_0641 deletion strain with that of the wild-type Staphylococcus aureus Newman strain.
Transcriptome of the NWMN_0641 deletion mutant strain and the wild-type Newman strain

sample_organism: Staphylococcus aureus subsp. aureus str. Newman

overall_design: We sought to obtain the transcriptomes of the NWMN_0641 deletion mutant strain and the wild-type Newman strain when bacteria were grown TSB medium (without glucose)

first: Yue

last: Ding


title: Altered Gene Expression Profiles of Wheat Genotypes against Fusarium Head Blight

city: Yokohama

first: Alagu

last: Manickavelu

state: Kanagawa

address: Maioka 641-12

institute: Yokohama City University

summary: Fusarium graminearum is responsible for Fusarium head blight (FHB), which is a destructive disease of wheat that makes its quality unsuitable for end use. To understand the temporal molecular response against this pathogen, microarray gene expression analysis was carried out at two time points on three wheat genotypes, the spikes of which were infected by Fusarium graminearum. The greatest number of genes was upregulated in Nobeokabouzu-komugi followed by Sumai 3, whereas the minimum expression in Gamenya was at three days after inoculation (dai). In Nobeokabouzu-komugi, high expression of detoxification genes, such as multidrug-resistant protein, multidrug resistance-associated protein, UDP-glycosyltransferase and ABC transporters, in addition to systemic defense-related genes, were identified at the early stage of infection. This early response of the highly-resistant genotype implies a different resistance response from the other resistant genotype, Sumai 3, primarily containing local defense-related genes, such as cell wall defense genes. In Gamenya, the expression of all three functional groups was minimal. The differences in these molecular responses with respect to the time points confirmed the variation in the genotypes. For the first time, we report the nature of gene expression in the FHB-highly resistant cv. Nobeokabouzu-komugi during the disease establishment stage and the possible underlying molecular response.

overall_design: F. graminearum inoculated (3 and 7 days after inoculation) and water inoculated Mock samples were used for cRNA synthesis and further hybridization with 3 biological replications. Total 12 samples per genotype

first: Ayumi

last: Kosaka

first: Daniela

last: Kajihara

first: Tomohiro

last: Ban


title: Microarray analysis of med16, med8, elp2, and wild type (Col-0) infected with the necrotrophic fungal pathogen Sclerotinia sclerotiorum

status: Public on Jan 22 2015

city: Gainesville

first: Zhonglin

last: Mou

state: FL

address: 981 Museum Road

department: Microbiology and Cell Science & Plant Molecular and Cellular  Biology

institute: University of Florida

summary: The goal of the microarray experiment was to identify defense genes that were differentially expressed in the Arabidopsis mutants med16, med8, elp2, wild type in response to infection of the necrotrophic fungal pathogen Sclerotinia sclerotiorum.  Results indicated that, compared with the wild type, the jasmonic acid (JA) biosynthesis genes LOX3, AOC3, and OPR3, ethylene (ET) biosynthesis genes ACS2 and ACS8, as well as salicylic acid (SA) biosynthesis genes ICS1 and EDS5 were up-regulated in med16 in local tissues at 1 day post-inoculation (dpi) and/or systemic tissues at 4 dpi.  Surprisingly, however, while a number of SA pathway genes (EDS1, PAD4, NPR1, WRKY18, WRKY38, WRKY53, PR1, and PR2) and several JA-regulated wound-responsive genes (MYC2, JAR1, VSP1, and VSP2) were up-regulated in med16, a group of JA/ET-regulated defense genes (ORA59, ERF1, ERF14, PDF1.2, PDF1.2b, PDF1.2c, PDF1.3, PR4, and ChiB) and PR5 were down-regulated.  On the other hand, only a few of these genes were differentially expressed between med8 or elp2 and the wild type.

overall_design: Three biological replicates with leaves from 8-12 plants per sample were collected at 0, 1, 2, and 4 days post-inoculation (dpi) after inoculation with the necrotrophic fungal pathogen Sclerotinia sclerotiorum.  Leaf tissues were collected as controls at 0 dpi, the inoculated leaves were collected as local tissues at 1 dpi, and the upper uninoculated leaves were collected as systemic tissues at 2 and 4 dpi.  After extraction, RNA concentration was determined on a NanoDrop Spectrophotometer (Thermofisher Scientific, Waltham, MA) and sample quality was assessed using the 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).  Equal amount of RNA from the 3 biological replicates were used for microarray analysis.

first: Chenggang

last: Wang

first: Jin

last: Yao

first: Yanping

last: Zhang

first: Yijun

last: Sun

first: Jeffrey

last: Rollins


title: Differential expressed miRNAs between tumor tissues and adjecent normal tissues from a patient with glioblastoma

status: Public on Sep 17 2014

city: Chongqing

first: Yu

last: Shi

state: Chongqing

address: Gao-tan Yan Street

department: Southwest Hospital

institute: Institute of Pathology and Southwest Cancer Center

summary: Glioblastoma is the most aggressive and lethal malignant brain tumor. miRNA expression profiling could be useful in improving the classification of tumors and predicting their behavior. In this study, the miRNA expression patterns in glioblastoma tumor tissues and adjacent normal tissues were identified through expression profiling of a patient with glioblastoma. The results will hopefully enhance our understandings of the epigentic changes in glioblastoma progression and provide candidates for miRNAs-based targeting tharapy.

overall_design: A paired miRNAs tumor tissues and adjacent tissues of a glioblastoma patient was used in this study. miRNAs were isolated using miRNeasy FFPE Kit (Qiagen). Profiling was established by applying the Agilent human miRNA Microarray (8 × 60K, v16.0) (Agilent Technologies).

first: Yi-fang

last: Ping


title: Microarray correpsonding to the paper manuscript titled: Targeted expression profiling of single disseminated cancer cells isolated from bone marrow of prostate cancer patients

status: Public on Oct 20 2014

city: Regensburg

first: Zbigniew

middle: Tadeusz

last: Czyz

address: Josef-Engert-Strasse 9

department: Project Group Personalized Tumor Therapy, Regensburg

country: Germany

institute: Fraunhofer Institute for Toxicology and Experimental Medicine

summary: Bone is the most frequent site of metastasis in prostate cancer (PCa) and patients with bone metastases are deemed incurable. Targeting prostate cancer cells that disseminated to the bone marrow (BM) prior to surgery and before metastatic outgrowth may therefore prevent lethal metastasis. This prompted us to directly analyse the transcriptome of disseminated cancer cells (DCC) isolated from non-metastatic (UICC stage M0) prostate cancer patients. We screened 105 BM samples of M0-stage prostate cancer patients and 18 BM samples of patients without malignancy for the presence of EpCAM+ single cells. In total we isolated 270 cells from both groups by micromanipulation and globally amplified their mRNA. We used targeted transcriptional profiling to unambiguously identify DCCs for subsequent in-depth analysis. Transcriptomes of all cells were examined for the expression of EPCAM, KRT8, KRT18, KRT19, KRT14, KRT6a, KRT5, KLK3 (PSA), MAGEA2, MAGEA4, PTPRC (CD45), CD33, CD34, CD19, GYPC, SCL4A1 (band 3), and HBA2. Using these transcripts we found it impossible to reliably identify true DCCs. We then applied combined genome and transcriptome analysis of single cells and found that EpCAM+ cells from controls expressed transcripts thought to be epithelial-specific, while true DCCs may express haematopoietic transcripts. These results point to an unexpected plasticity of epithelial cancer cells in bone marrow and question common transcriptional criteria to identify DCCs.

overall_design: Array-CGH was used to analyze EpCAM-positive single cells isolated from bone marrow of M0-stage prostate cancer patients, and individuals without cancer. The purpose was to demonstrate that cells with genomic aberrations are true tumour cells.

first: Miodrag

last: Guzvic

first: Bernhard

last: Braun

first: Roman

last: Ganzer

first: Maximilian

last: Burger

first: Michael

last: Nerlich

first: Sebastian

last: Winkler

first: Melanie

last: Werner-Klein

middle: T

last: Czyż

last: Polzer

first: Christoph

last: Klein


title: Molecular profiling of single circulating tumor cells with diagnostic intention

status: Public on Nov 05 2014

summary: About 230 clinical trials currently explore the role of circulating tumor cell (CTC) analysis for therapy decisions, but no assays enable comprehensive molecular characterization of CTCs with diagnostic precision. We therefore combined a workflow for CTC enrichment and isolation with 100% purity with a non-random whole genome amplifiation method for single cells and applied it to 510 single CTCs and 189 leukocytes of 66 breast cancer patients. We defined a genome integrity index (GII) to identify cells suited for molecular chracterization by different molecular assay in more than 90% of single cells, such as diagnostic profiling for point mutations, gene amplifications and whole genomes of single cells. The high reliability on clinical samples enabled assessing the molecular heterogeneity of single CTCs of metastatic breast cancer patients. We readily identified therapeutically relevant genomic disparity between primary tumors and CTCs. Microheterogeneity analysis among individual CTCs uncovered preexisting cells reistsant to ERBB2 targeted therapies suggesting ongoing microevolution at late stage disease whose exploration may provide essential information for personalized treatment decisions.

overall_design: The analysis aimed to indentify profiles of copy number changes in genomic DNA of single circulating tumor cells (CTCs). For this, CTCs were enrched using the FDA approved CellSearch System and single-cell were isolated using the DEPArray System. Subsequently, single-cell DNA was amplified using the Ampli1 WGA Kits and subjected to single-cell aCGH analysis according to previously published protocol (Czyz ZT et al., PLoS One. 2014 Jan 21;9(1):e85907). The analysis included 38 single CTCs and 10 white blood cells (WBCs) obtained from 16 breast cancer patient. WBCs were used as controls for the analysis. In addition, four CTC cell pools were included in the analysis. This was done to show the discrepancies between the profiles of individual cells and corresponing average genomic profile of CTCs in a patient material (cell pools), thereby demonstrating the importance of the analysis on the cell-by-cell basis. The reference sample used for all aCGH experiments consisted of a pool of four single-cell WGA products generated from WBCs of a healthy female donor.

first: Gianni

last: Medoro

first: Sophie

last: Pasch

first: Francesca

last: Fontana

first: Laura

last: Zorzino

first: Aurelia

last: Pestka

first: Ulrich

last: Andergassen

first: Franziska

last: Meier-Stiegen

first: Barbara

last: Alberter

first: Steffi

last: Treitschke

first: Thomas

last: Schamberger

last: Sergio

first: Giulia

last: Bregola

first: Anna

last: Doffin

first: Stefano

last: Gianni

first: Alex

last: Calanca

first: Giulio

last: Signorini

first: Chiara

last: Bolognesi

first: Arndt

last: Hartmann

first: Peter

last: Fasching

first: Maria

last: Sandri

first: Brigitte

last: Rack

first: Tanja

last: Fehm

first: Giuseppe

last: Giorgini

first: Nicolò

last: Manaresi


title: Expression of Sodalis glossinidius genes derived from self-cleared and control Glossina palpalis gambiensis flies

status: Public on Dec 23 2014

city: Montpellier

first: Anne

last: Geiger

address: Laboratoire de Recherches et de Coordination sur les Trypanosomoses TA,A-17 / G Campus international de Baillarguet

institute: UMR 177 IRD-CIRAD

summary: Transcriptome analysis of Sodalis glossinidius derived from uninfected (controls) and Trypanosoma brucei gambiense infection self cleared Glossina palpalis gambiensis. 10 days after infectived blood meal, flies anal drop were analysed by PCR to isolate the infected self cleared flies. Then, uninfected  (controls) and infection self cleared 10 days-flies midgut were dissected for RNA extraction.

overall_design: Total RNAs were extracted from 8 samples including: 4 control and 4 infection self-cleared flies.

first: Illiassou

last: Hamidou Soumana

first: Béatrice

last: Loriod

first: Pascal

last: Rihet


title: Array CGH from mouse SFME cells and SFME cells differentiated with TGFB and FCS

status: Public on Jan 01 2015

city: Homburg

first: Andreas

last: Keller

address: Building 60

institute: Saarland University

summary: SFME cells (ATCC)  were grown as spheres or differentiated with TGFß for 24 h or 10%FCS for 12 h. ArrayCGH experiments were performed on all three samples.

overall_design: ArrayCGH from SFME sphere cells, 24h differentiated SFME cells in the presence of TGFß and 12h differentiated SFME cells in the presence of 10% FCS

first: Ulrike

middle: H

last: Fischer

first: Eckart

middle: U

last: Meese


title: Depletion of yeast PDK1 orthologs triggers a stress-like transcriptional response

status: Public on Apr 30 2015

city: Cerdanyola

first: Antonio

last: Casamayor

state: Barcelona

address: Edifici IBB, Campus UAB

country: Spain

institute: Universitat Autonoma de Barcelona

summary:
The yeast proteins Pkh1 and Pkh2 are functional counterparts of the mammalian 3-phosphoinositide-dependent protein kinase 1 (PDK1). Cells carrying simultaneous deletion in both genes, PKH1 and PKH2 are not viable, at least in some genetic backgrounds (Casamayor et al., 1999; Inagaki et al., 1999). Consequently, a different strategy is needed to study the function of these apparently redundant gene products. The approach that has been successfully used to dissect the functions of these proteins consist in the use of a strain that combine the disruption of PKH2 with the temperature sensitive pkh1D398G allele (Inagaki et al., 1999). Since Pkh1 and Pkh2 phosphorylate Pkc1 in vitro in its activation loop (Thr983), and the cell lysis defects of the pkh1D398G pkh2 strain at the restrictive temperature are partially restored by constitutive activation of the Pkc1-Slt2 MAPK pathway, it has been suggested that the Pkh activity is important for maintenance of the cell wall integrity in S. cerevisiae (Inagaki et al., 1999; Friant et al., 2001). We considered it necessary that a different genetic strategy would be convenient in order to carry out specific studies about the functions of the Pkh proteins. In order to avoid incubation at temperatures that activate the Slt2 pathway, and induce cellular lysis, we decided to use a strategy based on the use of a regulatable promoter. We replaced 487 bp located immediately upstream the start PKH2 codon by a cassette containing the doxycycline-repressed promoter tetO7. In this strain (MB002) the PKH2 expression could be switched off by addition of doxycycline. In order to deplete the cell for the Pkh activity, we disrupted both, the PKH1 and PKH3 coding regions, obtaining the new SDP8 strain.
Our results show that the long term depletion of Pkh results in a cell transcriptional response that include overexpression of genes typically induced in response to oxidative stress, as well as up-regulation of chaperons and genes that induce the unfolded protein response.

overall_design:
Four samples were analyzed: the SDP8 strain, a tetO7 conditional mutant, and its isogenic WT strain both, in the presence and in the absence of doxycyline (for 8 and 24 h).

We compared the expression profile of:
1) SDP8 + Dox after 8h vs WT + Dox after 8h
2) SDP8 + Dox after 24h vs WT + Dox after 24h

A Dye-swap was carried out for each comparison of samples.

Total number of chips analyzed: 4.

first: Daniel

last: Pastor-Flores

first: Ricardo

last: Biondi

first: Jofre

last: Ferrer-Dalmau

first: Anna

last: Bahí


title: Uncapped mRNAs during heat stress

status: Public on Nov 21 2014

city: Uppsala

first: Emilio

last: Gutierrez Beltran

state: Sweden

address: Almas Allé 5

department: Department of Plant Biology

institute: Swedish University of Agricultural Sciences and Linnean Center for Plant Biology, SLU (Biocenter)

summary: Tudor staphylococcal nuclease (TSN or Tudor-SN; also known as SND1) is an evolutionarily conserved protein involved in transcriptional and post-transcriptional regulation of gene expression in animals. Although TSN was found to be indispensable for normal plant development and stress tolerance, the molecular mechanisms underlying these functions remain elusive. Here we show that Arabidopsis thaliana TSN is essential for integrity and function of cytoplasmic messenger ribonucleoprotein (mRNP) complexes called stress granules (SG) and processing bodies (PB), sites of post-transcriptional gene regulation during stress. TSN associates with SG following their microtubule-dependent assembly and plays a scaffolding role in both SG and PB. The enzymatically active tandem repeat of four SN domains is crucial for targeting TSN to the cytoplasmic mRNA complexes, and is sufficient for the cytoprotective function of TSN during stress. Furthermore, our work connects the cytoprotective function of TSN with its positive role in stress-induced mRNA decapping. While stress led to a pronounced increase in the accumulation of uncapped mRNAs in wild type plants, this increase was abrogated in TSN knockout plants. Taken together, our results establish TSN as a key enzymatic component of catabolic machinery responsible for the processing of mRNAs in the cytoplasmic mRNP complexes during stress.

overall_design: Five-day Arabidopsis seedlings  were grown vertically on MS agar plates under 16/8-h light/dark cycle and light intensity 150 µE m−2 s−1 for 5 days. For heat stress, plates with seedlings were incubated for 40 min on a thermoblock at 39 ºC. Root tissue was collected and used to purify uncapped and total mRNA. Two independent sets of biological samples were used for the experiments.

first: E

last: Gutierrez-Beltran

first: P

last: Moschou

first: A

middle: P

last: Smertenko

middle: V

last: Bozhkov


title: Smad3 ChIP-chip analysis on human breast epithelial cells of the MCF10A series

city: Bethesda

first: Howard

last: Yang

state: MD

address: 37 CONVENT DR, Room 5120

department: CCR

institute: NCI

type: Genome binding/occupancy profiling by genome tiling array

summary:
TGF-betas have complex roles in tumorigenesis, with context-dependent effects that can either suppress or promote tumor progression. Our goal was to use integrated genomic approaches in a model of human breast cancer progression to identify core TGF-beta-regulated genes that specifically reflect the tumor suppressor activity of TGF-beta. The model consisted of the non-tumorigenic MCF10A (“M1”), the premalignant MCF10AT1k.cl2 (“M2”), the early malignant MCF10Ca1h (“M3”) and the highly malignant, metastatic MCF10Ca1a.cl1 (“M4”) cell lines.  We have previously shown that tumor suppressor activity of TGF-beta is dependent on Smad3, and is lost in M4 cells.
To identify how TGF-beta/Smad3 targets change with cancer progression, we performed promoter-wide Smad3 ChIP-chip on all four cell lines of the breast cancer progression model (M1-M4), following treatment with TGF-beta or vehicle control.

overall_design: Subconfluent cultures of the four cell lines (M1-M4) were serum-starved for 16 h and then treated  with 5ng/ml of TGF-beta1 (plus condition) or vehicle alone (minus condition) for 1hour.  Smad3 ChIP was performed using the Abcam #28379 anti-Smad3 antibody. Four biological replicates were performed for each condition (plus and minus) for M1 and M2 cells, and two biological replicates for each condition for M3 and M4 cells; total of 24 samples.

first: Misako

last: Sato

first: Mitsutaka

last: Kadota

first: Binwu

last: Tang

first: Robert

last: Clifford

first: Aleksandra

middle: M

last: Michalowski

first: Maxwell

last: Lee

first: Lalage

last: Wakefield


title: Attachment of Bacillus subtilis to the hyphae of Aspergillus niger results in altered metabolism and defense mechanisms in both partner

status: Public on Sep 09 2014

city: Jena

first: Akos

last: Kovacs

address: Neugasse 23

department: Institute of Microbiology

institute: Friedrich Schiller University of Jena

summary:
Transcriptome comparison of Bacillus subtilis NCIB3610 attached to the hyphae of Aspergillus niger CB 119.1 compared to Bacillus subtilis NCIB3610 cells in the supernatant of the same culture.
Detailed description (other than provided below) of growth conditions, RNA preparation, cDNA synthesis and hybridization conditions can also be found in the submitted paper.

sample_organism:
Bacillus subtilis
Aspergillus niger

platform_organism: Bacillus subtilis subsp. subtilis str. 168

overall_design: B subtilis NCIB3610 cells were grown in the presence of Aspergillus niger CB 119.1 hyphae for 3 hours. The mycelium and the attached bacteria were separated from the non-attached B. subtilis cells via filtration through Miracloth. The mycelia and attached bacteria were briefly rinsed with TY medium, dried, and the sample was frozen in liquid nitrogen. Bacterial cells in the flow-through medium fraction were harvested by centrifugation at 10.397 g for 1 min. To extract RNA mainly from the bacterial cells, lysozyme solution and RiboLock (Thermo  Scientific) was added followed by incubation at 37 C for 30 minutes. Further RNA extraction was performed with the Macaloid/Roche method as described before (van Hijum et al., 2005, Kovács and Kuipers, 2011) but omitting the bead beater treatment and using RiboLock.

first: Marielle

last: van den Esker

first: Oscar

last: Kuipers


title: Gene expression of Ustilago maydis SG200, SG200∆hxt1 and the avirulent SG200∆hxt1 hxt1(R164K) on maize leaf surface

status: Public on Sep 04 2014

city: Karlsruhe

first: Jörg

middle: Thomas

last: Kämper

address: Hertzstrasse 16, Geb. 06.40

department: Department for Applied Biosciences

institute: Karlsruhe Institute of Technology

summary: Hxt1 is a high affinity hexose transporter important for virulence of the phytopathogenic  basidiomycete Ustilago maydis on its host plant maize. Hxt1 shows the highest similarities to the glucose sensors Rgt2 and Snf3 from S. cereviciae (42% and 39% identity on amino acid level, respectively). In these sensors, the substitution of a highly conserved arginine to lysine leads to a constitutive active signal, resulting in expression of several glucose induced genes. Introduction of an analogous mutation in Hxt1 leads to loss of transport activity in the resulting Hxt1(R164K) protein. Expression of Hxt1(R164K) in hxt1 deletion strains results in a completely avirulent phenotype. Pathogenic developement of ∆hxt1 hxt1(R164K) strains is blocked immediately after plant penetration. Expression analysis of ∆hxt1 hxt1(R164K) cells 24 hours post inoculation revealed downregulation of a set of genes involved in carbohydrate metabolism indicating a role of Hxt1 in carbohydrate signaling during initiation of the pathogenic stage.

overall_design: To analyze expression changes of SG200 and SG200∆hxt1 and SG200∆hxt1 hxt1(R164K) cells were harvested from the surface of maize leaves 24 hour post inoculation. For each strain three independent replicates were conducted.

first: D

last: Schuler

first: J

last: Kaemper


title: Identification of Lrig3 target genes in Xenopus animal caps injected with wnt3a and chordin

status: Public on Sep 01 2014

city: Shatin

first: Hui

last: Zhao

address: The Chinese University of Hong Kong

department: School of Biomedical Sciences

country: Hong Kong

institute: The Chinese University of Hong Kong

summary:
During embryonic development, the neural crest is a transient, migratory cell population that differentiates into a large variety of tissues and contributes much to the formation of vertebrate body. In Xenopus, lrig3 is involved in neural crest formation by modulating FGF and Wnt signaling. Lrig3 functions downstream of pax3 and zic1 to regulate the expression of neural crest markers.
We used microarrays to identify the lrig3 target genes during neural crest formation.

overall_design: Xenopus embryos were injected with mRNAs or MO at two-cell stage. When developing to stage 9, the animal caps were dissected for RNA extraction and hybridization on Affymetrix microarrays. According to the mRNAs and MO injected, the animal caps (AC) were divided into four groups, including (1) uninjected control AC; (2) AC injected with chordin; (3) AC injected with chordin and wnt3a; (4) AC injected with chordin, wnt3a and lrig3MO.  The injected animal caps were cultured till stage 15 and then collected for RT-PCR and microarray assay. Each group had two repeats.

first: Kin

last: Kam


title: Circulating miRNAs Bear a Signature of Acute Hepatitis C Viremia

city: Baltimore

first: Ashwin

last: Balagopal

address: 855 North Wolf Street, Rangos Building Room 520

institute: Johns Hopkins Univ. School of Medicine

summary:
miRNAs were purified from frozen plasma from injection drug users in the Baltimore Before and After the Start of Hepatitis (BBAASH) Study before, during and after acute hepatitis C infection.
Acute HCV outcome of 'Clear' indicates spontaneous resolution of infection. 'Time 3' in these individuals indicates the last known viremic specimen from these individuals before resolution and 'Time 4' indicates a plasma sample greater than one month after resolution of infection. Acute HCV outcome of 'Persist' indicates progression to chronic infection and 'Time 3' and 'Time 4' samples from these individuals are plasma samples time-matched to those of the clearers with the same name.

overall_design: qPCR miRNA expression profiling. 22 individuals HCV negative at enrollment were profiled for miRNA abundance in plasma, before, during, and after HCV infection.

first: Ramy

last: El-Diwany


title: RNA-Seq reveals an unprecedented complexity of the neuroblastoma transcriptome and is suitable for clinical endpoint prediction [microarray]

status: Public on Oct 21 2014

first: Leming

last: Shi

address: 2005 Songhu Road

department: School of Life Sciences

institute: Fudan University

summary:
We generated gene expression profiles from 498 primary neuroblastomas using RNA-Seq and microarrays. We sought to systematically evaluate the capability of RNA deep-sequencing (RNA-Seq)-based classification for clinical endpoint prediction in comparison to microarray-based ones. The neuroblastoma cohort was randomly divided into training and validation sets, and 360 predictive models on six clinical endpoints were generated and evaluated. While prediction performances did not differ considerably between the two technical platforms, the RNA-Seq data processing pipelines, or feature levels (i.e., gene, transcript, and exon junction levels), RNA-Seq models based on the AceView database performed best on most endpoints. Collectively, our study reveals an unprecedented complexity of the neuroblastoma transcriptome, and provides guidelines for the development of gene expression-based predictive classifiers using high-throughput technologies.

Sample clinical characteristics definitions:

dataset: Expression data set used for classification training (1) or validation (2)
Sex: M = male; F= female
age at diagnosis: the age in days at diagnosis
mycn status: Amplification status of the MYCN proto-oncogene (amplified = 1, no amplification = 0; no information = N/A)
high risk: Clinically considered as high-risk neuroblastoma (yes=1, no= 0)
INSS stage: disease stage according to International Neuroblastoma Staging System (INSS) (1, 2, 3, 4 and 4S)
class label: Maximally divergent disease courses - unfavorable (= 1): patient died despite intensive chemotherapy, favorable (=0): patient survived without chemotharapy for at least 1000 days post diagnosis; not applicable (N/A)
progression: Occurrence of a tumor progression event (yes=1; no=0)
death from disease: Occurrence of death from the disease (yes=1; no=0)

overall_design: Gene expression of 498 neuroblastoma samples was quantified by RNA sequencing as well as by microarray analyses in order to understand the neuroblastoma transcriptome and predict clinical endpoints.

first: Wenqian

last: Zhang

first: Falk

last: Hertwig

first: Zhiyu

last: Peng

first: Matthias

last: Fischer


title: Acute (2 hr) response to rxLeptin injection in preoptic area/hypothalamus/pituitary of juvenile Xenopus laevis

status: Public on Aug 05 2014

city: Ann Arbor

first: Robert

last: Denver

state: Michigan

address: 1105 North University Ave

department: MCDB

institute: University of Michigan

summary:
Leptin binding to the leptin receptor (LepR) causes rapid signaling to the nucleus. We investigated the early (2 hr) transcriptional response to acute leptin injectio (intracerebroventricular)
in the preoptic area/hypothalamus/pituitary of juvenile Xenopus laevis frogs.

overall_design: Frogs were given i.c.v. injections of 0.6% saline or recombinant X. laevis leptin (rxLeptin; 20 ng/g BW) and 2 hrs later killed and the preoptic area/hypothalamus/pituitary dissected.

first: Melissa

last: Cui


title: Perturbation of the Notch pathway in Xenopus laevis embryos

status: Public on Aug 06 2014

city: Willimsburg

first: Margaret

last: Saha

state: VA

address: 540 Landrum Drive

department: Biology

institute: College of William and Mary

summary: The Notch signaling pathway functions in a number of processes during embryologic development, especially the maintenance or aquisition of cell fate. We purturb the Notch signalling pathway in embryonic Xenopus laevis in order to 1) better characterize the downstream targets of Notch signalling, and 2) determine the extent to which early embryos can recover from transient purturbations to critical signalling pathways, if at all.

overall_design: Xenopus laevis embryos were unilaterally injected at the two cell stage with either GFP, GFP and ICD (Notch intracellular domain, an up-regulator of the Notch pathway), or GFP and DBM (domain-binding mutant, a downregulator of the Notch pathway). At stages 18, 28, and 38, for each injection, pooled total RNA from 10 embryos was extracted. Extraction was performed for three biological replicates for each time/injection condition. cDNA from total RNA was hybridized on Affymetrix Xenopus laevis Genome 2.0 arrays.

middle: S

first: Molly

last: McDonough

first: Brian

last: Rabe

first: Samuel

last: Clamons


title: Pathogenic response of Glycine max to the stem parasitic plant Cuscuta

status: Public on Jun 27 2014

first: Takeshi

last: Furuhashi

address: 1-7-22 Suehiro, Tsurumi

institute: RIKEN CSRS

summary: Little is known about plant pathogenic response to parasitic plants, although some parasitic plants affect crop production in certain areas. To study this, we chose Glycine max as the model host plant and investigated changes in expression patterns after parasitization by Cuscuta using microarrays.

overall_design: Transcriptional change of Glycine max stem with and without Cuscuta at 2 different stages were compared


title: Hepatic transcriptomic profiling reveals early toxicological mechanisms of uranium in Atlantic salmon (Salmo salar)

status: Public on Jun 26 2014

city: Oslo

first: You

last: Song

address: Økernveien 94

department: Ecotoxicology and Risk Assessment

country: Norway

institute: Norwegian Institute for Water Research (NIVA)

summary: To study the short term (48 h) hepatic transcriptional changes and identify potential modes of action, Atlantic salmon (Salmo salar) were exposed to 0.25 mg/L, 0.5 mg/L and 1.0 mg/L depleted uranium. A combination of high density (60 k) custom oligonucleotide salmonid miacroarray and quantitative real-time reverse transcription polymerase chain reaction (qPCR) was employed to perform gene expression analyses. Differentially expressed genes (DEGs) were determined using one-way analysis of variance (ANOVA) and Tukey posthoc tests. Functional enrichment analysis based on Gene Ontology (GO) was performed to link DEGs to their biological functions. The Salmo salar DEGs were further mapped to mammlian orthologs. By using ortholog DEGs, gene networks were built based on well-curated mammlian protein-protein interactions and pathways analyses were performed to link DEGs to specific toxicological/biological functions. The results obtained from microarray analysis were further verified using qPCR.

overall_design: Juvenile Atlantic salmon were exposed to waterborne depleted uranium for 48 h. Liver were samples and used for gene expression analysis.

first: Brit

last: Salbu

first: Hans-Christian

last: Teien

first: Lene

last: Heier

first: Bjørn

middle: O

last: Rosseland

first: Tore

last: Høgåsen

first: Knut

middle: E

last: Tollefsen


title: Patients SAHGEN: cerebral vasospasm after subarachnoid hemorrhage

status: Public on May 08 2014

city: Luxembourg

first: Yvan

last: Devaux

address: 120 route d'Arlon

country: Luxembourg

institute: LIH

summary: The diagnosis of cerebral vasospasm after Subarachnoid-Hemorrhage is currently very difficult, additional tools such as blood biomarkers are necessary. We tested the ability of gene expression profiles of blood cells to predict vasospasm.

overall_design: 32 patients suffering subarachnoid-hemorrhage were included in this prospective  monocentre study. They were grouped according to have a complicated cerebral vasospasm (Vasospasm) or not (Control) and Paired according to age (+/- 10 years), sex, Fisher grade (+/- 1), location, smoking (at least 3 first parameters). Gene expression profiles of blood cells were determined using 25,000~gene microarray. Blood  sample: 2.5 mL harvested in PAXgene® Blood RNA tubes (PreAnalytix) RNA extraction: PAXgene® Blood RNA kit (Qiagen). We used a Universel Reference RNA (Stratagene). RNA amplification and labelling: kit Amino Allyl MessageAmp II (Ambion). We hybridized 4 microarrays per patient using pangenomic microarrays from the "Réseau National des Génopôles" (Illkirch, France). 2 slides were hybridized with reference RNA labelled Cy3 and patient RNA labelled Cy5, and 2 slides were hybridized with reference RNA labelled Cy5 and patient RNA labelled Cy3. Hybridation : Agilent protocol with few modifications : 750 ng of each labelled RNA were hubriddized at 60°C during 17 hours in an Aglient hybridization oven. After washings, Slides were scanned with a GenePix 4000B scanner (Molecular Devices). Image intensity data were extracted with GenePix Pro 6.0 analysis software. Quantification of Cy3 and Cy5 and selection of good spots were performed using the MAIA software (Novikov E and Barillot E. Software package for automatic microarray image analysis (MAIA). The ACUITY software was then used to normalize log ratios Cy3/Cy5 with Lowess non linear normalization, to filter out genes not present in at least 3 slides out of 4, to evaluate the reproducibility of the 4 microarrays of each patient (hierarchical clustering, Self Organizing Maps). Statistical analyses to insure reproducibility was performed using Excel (correlation coefficients, ANOVA). Only slides that passed all reprocubility tests were validated.


title: Expression data of hAEC, hAFSC and hBMSC before and after osteogenic induction in vitro

status: Public on May 04 2014

city: Shanghai

first: Jiawen

last: Si

address: 639, Zhizaoju Road

department: Department of Oral and Maxillofacial Surgery

institute: Ninth People’s Hospital, Shanghai Jiao Tong University School of Medicine

summary:
The in vitro osteogenic differentiation of hAEC, hAFSC and hBMSC have been reported.The final tissue-forming potential of all three cell types may vary in terms of different anatomical origin and molecular response to osteogenic induction.
We used microarrays to detail the global genes expression profiles of hAEC, hAFSC and hBMSC before and after osteogenic induction in vitro.

overall_design: Global gene expression profiles of hAECs, hBMSCs and hAFMSCs were evaluated before and after 7-day osteogenic induction in vitro. Samples were subjected to gene expression analysis using the Affymetrix human HTA2.0 microarray.

first: Guofang

last: Shen


title: Expression of Sodalis glossinidius genes derived from self-cleared and infected Glossina palpalis gambiensis flies

status: Public on Mar 20 2014

first: Anne

last: Geiger

summary: Transcriptome analysis of Sodalis glossinidius derived from Trypanosoma brucei gambiense infection self cleared and infected Glossina palpalis gambiensis. At 3 time points (3, 10 and 20 days) after infectived blood meal, flies were analysed by PCR to isolate the infected and infection self cleared flies. Then, infected and infection self cleared flies midgut were dissected for RNA extraction.

overall_design: Total RNAs were extracted at 3 time points (3, 10 and 20 days) from 24 samples including, for each time, 4 infected and 4 infection self-cleared flies.

first: Illiassou

last: Hamidou Soumana

first: Béatrice

last: Loriod

first: Pascal

last: Rihet


title: Submicroscopic and asymptomatic Plasmodium falciparum and P. vivax infections are common in western Thailand - molecular and serological evidence

status: Public on Jun 22 2014

city: Irvine

first: Elisabeth

last: Baum

state: CA

address: Med Surge II

institute: University of California Irvine

summary:
Background: Malaria is a public health problem in parts of Thailand, where Plasmodium falciparum and Plasmodium vivax are the main causes of infection. In the northwestern border province of Tak parasite prevalence is now estimated to be less than 1% by microscopy. Nonetheless, microscopy is insensitive at low-level parasitaemia. The objective of this study was to assess the current epidemiology of falciparum and vivax malaria in Tak using molecular methods to detect exposure to and infection with parasites; in particular, the prevalence of asymptomatic infections and infections with submicroscopic parasite levels.
Methods: Three-hundred microlitres of whole blood from finger-prick were collected into capillary tubes from residents of a sentinel village and from patients at a malaria clinic. Pelleted cellular fractions were screened by quantitative PCR to determine parasite prevalence, while plasma was probed on a protein microarray displaying hundreds of P. falciparum and P. vivax proteins to obtain antibody response profiles in those individuals.
Results: Of 219 samples from the village, qPCR detected 25 (11.4%) Plasmodium sp. infections, of which 92% were asymptomatic and 100% were submicroscopic. Of 61 samples from the clinic patients, 27 (44.3%) were positive by qPCR, of which 25.9% had submicroscopic parasite levels. Cryptic mixed infections, misdiagnosed as single-species infections by microscopy, were found in 7 (25.9%) malaria patients. All sample donors, parasitaemic and non-parasitaemic alike, had serological evidence of parasite exposure, with 100% seropositivity to at least 54 antigens. Antigens significantly associated with asymptomatic infections were P. falciparum MSP2, DnaJ protein, putative E1E2 ATPase, and three others.

platform_organism:
Plasmodium falciparum
Plasmodium vivax

overall_design: Antibody profiling against P. falciparum and P. vivax proteins was performed on sera from residents of Thailand's Tak province as part of Southeast Asia International Centers for Excellence in Malaria Research (ICEMR). Ninety-three samples collected during community-based surveys (Active Case Detection) and 60 hospital outpatient samples (Passive Case Deterction), and 12 unexposed USA controls were probed on a protein microarray displaying 500 P. falciparum and 500 P. vivax proteins.

first: Jetsumon

last: Prachumsri

first: Jeeraphat

last: Sirichaisinthop

first: Aarti

last: Jain

first: Douglas

last: Molina

first: Xiaowu

last: Liang

first: Phillip

last: Felgner

first: Guiyun

last: Yan


title: Genome-Wide Analysis Reveals Divergent Patterns of Gene Expression During Zygotic and Somatic Embryo Maturation of Theobroma cacao L., The Chocolate Tree

status: Public on Mar 07 2014

city: University Park

first: Mark

last: Guiltinan

state: Pennsylvania

address: 422 Life Sciences Bldg.

department: Plant Molecular Biology

institute: Penn State University

summary: With the goal to better understand somatic embryogenesis (SE) development and improve the efficiency of SE conversion in Theobroma cacao L.  we examined the differences between zygotic and somatic embryo at gene expression level using a whole genome microarray. A gene expression microarray representing 28,752 genes was used to compare the expression profiles at 4 developmental time points during zygotic embryogenesis (ZE) and 2 time points during somatic embryogenesis (SE). Within the ZE time course, 10,288 differentially expressed genes were identified which were enriched for functions related to responses to abiotic and biotic stimulus, metabolic and cellular processes. A comparison of expression profiles of ZE and SE identified 10,175 differentially expressed genes. 463 and 714 transcription factor (TF) genes are differentially expressed during ZE and SE maturation respectively, of which, an overlapping set of 128 genes were regulated during both processes. Large numbers of TFs, putatively involved in ethylene metabolism and ethylene response, were expressed at higher levels during SE as compared to ZE.  Expression levels of genes involved in fatty acid metabolism, flavonoid biosynthesis and seed storage protein genes were also differentially expressed in the two types of embryos.

overall_design: A 12-plex Nimblegen expression microarray representing 28,752 genes was manufactured on which only 46 of the predicted cacao genes were not represented with at least one probe. Total RNA was isolated from four biological replicates of six different types and stages of embryo development: zygotic embryo tissues: torpedo (T-ZE), early-full (EF-ZE), late-full (LF-ZE) and mature (M-ZE) embryos; and somatic embryos: late torpedo (LT-SE) and mature (M-SE) stages

first: Siela

last: Maximova

first: Sergio

last: Florez

first: Xiangling

first: Nicolas

last: Niemenak

first: Yufan

last: Zhang

first: Wayne

last: Curtis


title: Transcriptional changes in soybean nodules with the loss of expression of GmbHLHm1

status: Public on Mar 14 2014

city: Urrbrae

first: Brent

middle: N

last: Kaiser

state: SA

address: Waite Campus

department: School of Agriculture Food and Wine

institute: The University of Adelaide

summary: This study was conducted to investigate the changes in gene expression that occurs with the silencing of GmbHLHm1. GmbHLHm1 is a membrane localised DNA binding transcription factor that is important for nodule development.  Its activity is linked to ammonium transport.

overall_design: 7 samples

first: David

last: Chiasson

first: Patrick

middle: C

last: Loughlin

first: Danielle

last: Mazurkiewicz

first: Manijeh

last: Mohammadidehcheshmeh

first: Elena

last: Fedorova

first: Mamoru

last: Okamoto

first: Elizabeth

last: McLean

first: Anthony

middle: D

last: Glass

first: Sally

last: Smith

first: Ton

last: Bisseling

first: Stephen

last: Tyerman

last: Day


title: The omega subunit of the RNA polymerase core directs transcription efficiency in cyanobacteria

status: Public on Jan 30 2014

city: Turku

first: Taina

last: Tyystjarvi

address: Pharmacity/Itäinen Pitkäkatu 4 C, 6th floor

department: Biochemistry

country: Finland

institute: University of Turku

summary: The catalytic core of the RNA polymerase of most eubacteria is composed of two α subunits and β, β’ and ω subunits. In Escherichia coli, the ω subunit (encoded by the rpoZ gene) has been suggested to assist β’ during RNA polymerase core assembly. The function of the ω subunit is particularly interesting in cyanobacteria because the cyanobacterial β’ is split to N-terminal γ and C-terminal β’ subunits. The ∆rpoZ strain of the cyanobacterium Synechocystis sp. PCC 6803 grew well in standard conditions although the mutant cells showed low light-saturated photosynthetic activity, low Rubisco content and accumulated high quantities of protective carotenoids and α-tocopherol. The ∆rpoZ strain contained 15% less of the primary σ factor, SigA, than the control strain, and recruitment of SigA to the RNA polymerase core was inefficient in ∆rpoZ. Thus, a cyanobacterial RNA polymerase holoenzyme lacking the ω subunit contains less frequently the primary σ factor. A DNA microarray analysis revealed that this leads to specific down-regulation of highly expressed genes, like genes encoding subunits for Rubisco, ATP synthase, NADH-dehydrogenase and carbon concentrating mechanisms. On the contrary, many genes showing only low or moderate expression in the control strain were up-regulated in ∆rpoZ. A conserved -10 region was detected in promoters showing up or down-regulation in ∆rpoZ, but -35 regions of down-regulated genes completely differed from -35 regions of up-regulated genes.

overall_design: Cells from cyanobacteria Synechocystis sp. PCC 6803 named as control strain (CS) and RNA polymerase omega subunit inactivation strain, ΔrpoZ, were harvested (A730=1, 40 mL) directly from standard growth conditions (continuous illumination at the PPFD of 40 µmol m-2s-1, 32°C, ambient CO2). From three to four independent experiments were performed at each conditions.

first: T

first: L

last: Gunnelius

first: K

last: Hakkila

first: H

last: Matthijs


title: Natural anitsense transcripts in Plasmodium vivax clinical isolates

status: Public on Jan 16 2014

city: Pilani

first: Ashis

middle: Kumar

last: Das

state: Rajasthan

address: Vidya Vihar

department: Biological Sciences

country: India

institute: Birla Institute of Technology & Science,Pilani (Pilani Campus)

summary: Plasmodium vivax is the most geographically widespread human malaria parasite causing approximately 130-435 million infections annually. It is an economic burden in many parts of the world and poses a public health challenge along with the other Plasmodium sp. The biology of this parasite is very little understood.  Emerging evidences of severe complications due to infections by this parasite provides an impetus to focus research on the same. Investigating this parasite directly from the infected patients is the most feasible way to study its biology and any pathogenic mechanisms which may exist. Gene expression studies of this parasite directly obtained from the patients has provided evidence of gene regulation resulting in varying amount of transcript levels in the different blood stages. However, the mechanisms regulating gene expression in malaria parasites are not well understood. Discovery of natural antisense transcripts (NATs) in P. falciparum has suggested that these might play an important role in regulating gene expression. We report here the genome-wide occurrence of NATs in P. vivax parasites from patients with differing clinical symptoms. A total of 1348 NATs against annotated gene loci have been detected using a custom designed strand specific microarray. Majority of NATs identified from this study shows positive correlation with the expression pattern of the sense transcript. Our data also shows condition specific expression patterns of varying S and AS transcript levels. Genes with AS transcripts enrich to various biological processes. This is the first report detailing the presence of NATs from clinical isolates of P. vivax. The data suggests differential regulation of gene expression in diverse clinical conditions and would lead to future detailed investigations of genome regulation.

overall_design: Plasmodium vivax isolates  were collected from patients (n = 8) with differing clinical conditions.The patients exhibited symptoms categorized as un-complicated (n =1) or complicated malaria (n = 7). Criteria for determination of complicated disease were based on World Health Organization year 2010 guidelines. Microarray array based transcriptional profiling was carried out to detect prevalence of natural antisense transcripts.

first: P

middle: A

last: Boopathi

first: Amit

middle: K

last: Subudhi

first: Shilpi

last: Garg

first: Deepak

last: Pakalapati

first: Vishal

last: Saxena

first: Raja

last: Mugasimangalam

first: Mohamed

last: Aiyaz

first: Bipin

last: Chand

first: Dhanpat

last: Kochar

first: Sanjay

first: Sheetal

last: Middha

first: Jyoti

last: Acharya


title: Human Multipotent Stromal Cells: Passage 3 vs. Passage 5 vs. Passage 7

status: Public on Apr 01 2014

city: Silver Spring

first: Raj

last: Puri

state: Maryland

address: 10903 New Hampshire Ave

institute: FDA

summary:
Gene Markers of Cellular Aging in Human Multipotent Stromal Cells in Culture
Identifying gene markers of cellular aging as determined by cellular passaging of human multipotent stromal cells (MSCs) derived from bone marrow

overall_design: Repeated Measures Experiment; MSC from different donors at 3 passages (passages 3, 5, & 7) with 3 technical replicates at each passage; a total of 54 microarrays in original data set. 9 additional arrays added on October 23, 2015.

first: Ian

last: Bellayr

first: Jennifer

middle: G

last: Catalano

first: Samir

last: Lababidi

first: Amy

middle: X

last: Yang

first: Jessica

middle: L

last: Lo Surdo

first: Steven

middle: R

last: Bauer


title: Classifying leukemia types with chromatin conformation data (5C)

status: Public on Feb 27 2014

city: Montreal

first: Josée

last: Dostie

state: QC

address: 3655 Promenade Sir-William-Osler

country: Canada

institute: McGill University

summary:
Background: Although genetic or epigenetic alterations have shown to affect the three-dimensional organization of genomes, the utility of chromatin conformation in the classification of human disease has never been addressed.
Results: Here, we explore whether chromatin conformation can be used to classify human leukemia. We map the conformation of the HOXA gene cluster in a panel of cell lines with 5C chromosome conformation capture technology, and use the data to train and test a support vector machine classifier named 3D-SP. We show that 3D-SP is able to accurately distinguish leukemias expressing MLL-fusion proteins from those expressing only wild-type MLL, and that it can also classify leukemia subtypes according to MLL fusion partner, based solely on 5C data.
Conclusions: Our study provides the first proof-of-principle demonstration that chromatin conformation contains the information value necessary for classification of leukemia subtypes.

overall_design: Analysis of 38 samples using 5C technology. All data normalized using a 'master' BAC consisting of 5C data from 6 samples.

first: Mathieu

last: Rousseau

first: Maria

last: Ferraiuolo

last: Crutchley

first: Xue

middle: Q

last: Wang

first: Hisashi

last: Miura

last: Blanchette


title: Natural anitsense transcripts in Plasmodium falciparum clinical isolates

status: Public on Apr 30 2014

first: Ashis

last: Das

summary: Mechanisms regulating gene expression in malaria parasites are not well understood. Little is known about how this parasite regulates its gene expression during transition from one developmental stage to another and in response to various environmental conditions. Parasites in a diseased host face environments which differ from the static, well adapted in vitro conditions in culture. Parasites thus need to adapt quickly and effectively to these conditions by establishing transcriptional states which is best suited for better survival. With the discovery of natural antisense transcripts (NATs) in this parasite and considering the various proposed mechanisms by which NATs might regulate gene expression, it has been speculated that these might be playing a critical role in gene regulation. We report here the diversity of NATs that exist in this parasite, using isolates taken directly from patients with differing clinical symptoms caused by malaria infection. A total of 797 NATs targeted against annotated loci have been detected using a custom designed strand specific microarray. Out of these, 545 are unique to this study. The majority of NATs were positively correlated with the expression pattern of the sense transcript. Many were found to be differentially regulated in response to disease conditions. Antisense transcripts mapped to a wide variety of biochemical/ metabolic pathways, especially pathways pertaining to the central carbon metabolism and stress related pathways. Our data strongly suggests that a large group of NATs detected here are unannotated transcription units antisense to annotated gene models. The results reveal a previously unknown set of NATs that prevails in this parasite, their differential regulation in disease conditions and mapping to functionally well annotated genes. The results detailed here call for studies to deduce the possible mechanism of action, which would help in understanding the in vivo pathological adaptations of these parasites.

overall_design: Plasmodium falciparum isolates were collected from patients (n = 11) with differing clinical conditions.The patients exhibited symptoms categorized as un-complicated (n =2) or complicated malaria (n = 9). Criteria for determination of complicated disease were based on World Health Organization year 2000 guidelines. Microarray array based transcriptional profiling was carried out to detect prevalence of natural antisense transcript.

first: Amit

last: Subudhi

first: P

last: Boopathi

first: Shilpi

last: Garg

first: Vishal

last: Saxena

first: Raja

last: Mugasimangalam

first: Mohamed

last: Aiyaz

first: Harsha

middle: B

last: Orekondy

last: Kochar


title: Microarray data from aerial tissue of Williams 82 soybean exposed to submergence and reoxygenation

status: Public on Feb 18 2014

city: Blacksburg

first: Takeshi

last: Fukao

address: 1880 Pratt Drive

institute: Virginia Tech

summary: Submergence is a major constraint for soybean production worldwide and transient inundation after seeding causes serious loss of soybean productivity. To characterize genome-scale adjustment of gene expression to submergence and reoxygenation,  whole transcriptome analysis was conducted using Affymetrix Soybean Gene 1.0 ST Arrays.

overall_design: Aerial tissue of soybean which were treated with 1 d submergence, 5 d submergence, and 5 d submergence + 1 d reoxygenation were subjected to RNA extraction and hybridization on Affymetrix microarrays (Soybean Gene 1.0 ST arrays). Non-submerged were used as control. Two independent biological replicates were analyzed for each treatment.

first: Bishal

last: Tamang


title: Human milk miRNAs primarily originate from the mammary gland resulting in unique miRNA profiles of fractionated milk

status: Public on Mar 30 2015

city: Crawley

first: Mohammed

last: Alsaweed

state: WA

address: 35 stirling hwy

institute: UWA

summary: Human milk (HM) contains an array of regulatory biomolecules including miRNAs, the origin, properties, distribution and functional significance of which are still undetermined. In this study, we used the TaqMan OpenArray System to profile 681 human mature miRNAs in two fractions of HM (cells and lipids) collected from healthy mothers in month 2 of lactation (n=10). Comparisons were performed with maternal peripheral blood mononuclear cells (PBMCs) and plasma collected from the same individuals, as well as with a bovine- and a soy-based infant formulae. HM cells (292 miRNAs) and PBMCs (345 miRNAs) had higher miRNA content than HM lipids (242 miRNAs) and plasma (219 miRNAs), respectively (p<0.05). Despite the wide variation in miRNA profiles and expression between mothers, a strong association was found between HM cells and lipids within a mother, whilst PBMCs and plasma were distinctly different to the two milk fractions, with plasma displaying marked inter-individual variation. Considering the dominance of epithelial cells in mature milk of healthy women, these results suggest that HM cell and lipid miRNAs primarily originate from the mammary epithelium, whilst the maternal circulation may have a smaller contribution. Infant formulae contained very few human miRNA compared to HM. Our findings demonstrate that unlike infant formulae, human milk is a rich source of lactation-specific miRNA, which could be used as a biomarker of the performance and health status of the lactating gland. Given the recently identified stability and gene regulatory functions of food-derived miRNAs, HM miRNAs may contribute to infant protection and development.

sample_organism:
Glycine max
Homo sapiens
Bos taurus

overall_design:
10 exclusively breastfeeding mothers were recruited.
10 whole milk and 10 whole blood samples were collected and fractionated to obtain 10 milk cells, 10 milk lipid, 10 mononeucleoted blood cells (PBMCs), and 10 plasma.
In addition to the above 40 samples, 2 infant formula were profiled.
4 different extraction kits were used, miRNeasy mini Kit for human milk cell and PBMC samples. miRCURY RNA Isolation-Biofluids Kit for human milk lipid samples and both infant formulae. mirVana PARIS Kit for plasma samples.
NanoDrop 2000 and Bioanalyzer 2100 were used to determine concentration and purity of the extracted miRNA from all samples (n=42).
miRNA OpenArray panel system (Life Technologies, CA, USA) was used to profile 758 human mature miRNAs in samples.
RNU48, RNU44 and U6 rRNA were used as housekeeping controls for normalisation. ath-miR159a was used as a negative control for human samples.

Please note that normalization of miRNAs was done in R but without generating deltaCT values, thus [1] only the list of normalized miRNA with Ct vlaue between 8 and 29 in each sample ('normalized_miRNAs_list.txt') [2] the sample data tables contain raw data.

first: Foteini

last: Hassiotou

first: Donna

middle: T

last: Geddes

first: Peter

last: Hartmann

first: John

last: Newnham

first: Chin-Tat

last: Lai

last: Savigni


title: Genome-wide analysis of long noncoding RNA (lncRNA) expression in hepatoblastoma tissues

status: Public on Dec 31 2013

first: Rui

last: Dong

address: 399 Wan Yuan Roa

department: Department of Pediatric Surgery

institute: Children’s Hospital of Fudan University

summary: We performed a genome-wide analysis of lncRNA expression in hepatoblastoma tissues to identify novel targets for further study of hepatoblastoma.We found that 2736 lncRNAs were differentially expressed in hepatoblastoma tissues.

overall_design: The genome-wide analysis of lncRNA expression in these tissues was performed using a 4 × 180K lncRNA microarray and Sureprint G3 Human lncRNA Chips.Quantitative RT-PCR (qRT-PCR) was performed to confirm these results.

first: Deshui

last: Jia


title: Zygotic expression of Exostosin1 (Ext1) is required for establishment of dorsal-ventral pattern in Xenopus

status: Public on Oct 23 2013

city: Houston

first: Amy

middle: of

last: Sater

state: TX

address: 4800 Calhoun Rd

department: Biology and Biochemistry

institute: University of Houston

summary: Exostosin 1 (Ext1) is a glycosyltransferase involved in the biosynthesis of the extracellular matrix Heparan Sulfate Proteoglycan (HSPG). Knockdown of Ext1 caused gastrulation defects and formation of an abnormal body axis. Since ext1 has been implicated as an indirect contributor to multiple signaling  pathways in vertebrate development, microarray was used to identify genes expressed in gastrulae that would be affected by a reduction in ext1 expression. Microarray-based comparisons of gene expression in control vs. Ext1 MO embryos showed that Ext1 is involved in regulating genes that are related to metabolic process, development and signaling pathways. Half of the hits from the microarray are uncharacterized genes. Approximately forty-five percent of genes are related to metabolic process and thirty percent of genes are belonged to signaling and developmental process categories. Ten percent of each up-regulated and down-regulated gene set is predicted to function in establishment of localization by GO, which is consistent with EXT1 being involved in the movement of extracellular substances. The transcription factors or signaling protein, Isl1, Pitx2, TBX5A, Wnt5A, Wnt7A, WT1, Pax3, Wnt1, and Xbra were identified as Ext1 regulated genes. This analysis investigating the role of Ext1 during gastrulation and provide the information that EXT1 plays an important role in Xenopus early development.    Exostosin 1 (EXT1) is a glycosyltransferase involved in the biosynthesis of the extracellular matrix Heparan Sulfate Proteoglycan (HSPG). Knockdown of EXT1 caused gastrulation defects and formation of an abnormal body axis. Since ext1 has been implicated as an indirect contributor to multiple signaling  pathways in vertebrate development, microarray was used to identify genes expressed in gastrulae that would be affected by a reduction in ext1 expression. Microarray-based comparisons of gene expression in control vs. EXT1 MO embryos showed that EXT1 is involved in regulating genes that are related to metabolic process, development and signaling pathways. Half of the hits from the microarray are uncharacterized genes. Approximately forty-five percent of genes are related to metabolic process and thirty percent of genes are belonged to signaling and developmental process categories. Ten percent of each up-regulated and down-regulated gene set is predicted to function in establishment of localization by GO, which is consistent with EXT1 being involved in the movement of extracellular substances. The transcription factors or signaling protein, Isl1, Pitx2, TBX5A, Wnt5A, Wnt7A, WT1, Pax3, Wnt1, and Xbra were identified as EXT1 regulated genes. This analysis investigating the role of EXT1 during gastrulation and provide the information that EXT1 plays an important role in Xenopus early development.

overall_design: The embryos were injected with mispair or Ext1 MO were collected at St. 10.5. The RNA was extracted and for probe synthesis and the hybridization was performed on Affymetrix Xenopus laevis genome v2.0 array. The experiments were repeated for three times. Results of paired control and experimental samples were compared.

first: Shieh

middle: Y

last: Wells


title: Syndecan-2 and apoptosis in osteosarcoma

status: Public on Sep 23 2013

city: Valbonne - Sophia-Antipolis

first: Kevin

last: Lebrigand

address: 660 route des lucioles

institute: IPMC/CNRS

summary: Syndecan-2 was found to act as a tumor suppressor in osteosarcoma and to mediate the apoptotic response to cytotoxic agents. To determine new mechanisms that control cell survival and apoptosis in osteosarcoma cells, we aim to show target genes that are involved downstream of this proteoglycan during apoptosis induction. We aim to compare the modifications induced by syndecan-2 overexpression in two different human osteosarcoma cell lines using a lentiviral vector coding the human syndecan-2.

overall_design: Syndecan-2 lentiviral vector (SY) and control empty lentiviral vector (VV) were transducted in two different human osteosarcoma cell lines in a dye-swap experiment.

first: Dominique

last: Modrowski

first: Pascal

last: Barbry

first: Bernard

last: Mari

first: Oivia

last: Fromigue


title: Targeting of Painting of fourth to roX1 and roX2 proximal sites suggests evolutionary links between dosage compensation and the regulation of the 4th chromosome in Drosophila melanogaster

status: Public on May 27 2013

city: Umea

first: Jan

last: Larsson

address: Umea University

department: Molecular Biology

institute: Umea University

summary: In Drosophila melanogaster, two chromosome-specific targeting and regulatory systems have been described. The male-specific lethal (MSL) complex supports dosage compensation by stimulating gene expression from the male X-chromosome and the protein Painting of fourth (POF) specifically targets and stimulates expression from the heterochromatic 4th chromosome. The targeting sites of both systems are well characterized, but the principles underlying the targeting mechanisms have remained elusive. Here we present an original observation, namely that POF specifically targets two loci on the X-chromosome, PoX1 and PoX2 (POF-on-X). PoX1 and PoX2 are located close to the roX1 and roX2 genes, which encode ncRNAs important for the correct targeting and spreading of the MSL-complex. We also found that the targeting of POF to PoX1 and PoX2 is largely dependent on roX expression and identified a high-affinity target region which ectopically recruits POF. The results presented support a model linking the MSL-complex to POF and dosage compensation to regulation of heterochromatin.

overall_design: POF salivary glands ChIP

first: Lina

last: Lundberg

first: Maria

last: Kim

first: Anna-Mia

last: Johansson

first: Marie-Line

last: Faucillion

first: Rafael

last: Josupeit


title: Gene expression profile analysis of inducible melanotic and amelanotic melanoma in mice

status: Public on Jun 26 2013

summary: We analyzed an inducible melanoma model in TiRP Ink4a/ArfF/F B10.D2 mice based on the conditional deletion in melanocytes of two tumor suppressor genes INK4a/Arf coupled to the expression of the oncogene H-rasG12V and a known tumor antigen (Hujibers et al. Cancer Res. 66:3278,2006; Soudja et al. Cancer Res. 70:3515-3525,2010). About 40% of these mice develop melanomas. Some tumors are heavily pigmented melanotic melanoma and grow slowly (hereafter referred to as “Mela”), but most of the induced tumors are nonpigmented amelanotic melanomas which are more aggressive (hereafter referred to as “Amela”). Gene expression profiles of the two types of tumors and of Amela-derived cell lines established in vitro were analyzed to identify the transcriptional signatures of these two types of tumors (including stromal components and infiltrating cells), as well as that intrinsic to Amela-tumor cells.

overall_design: 4 Amela and 4 Mela ex-vivo tumors were compared in a dye-swap experiment (8 chips). 4 Amela and 4 Mela ex-vivo tumors were compared to healthy skin (CTRL) (8 chips). 4 Amela ex-vivo tumors and Amela cell lines were compared in a dye-swap experiment (8 chips).

last: Wehbe

first: Anne-Marie

last: Schmitt-Verhulst


title: Effects of Brca1 knock-down on Ezh2 targeting

status: Public on Jul 01 2013

city: ROCHESTER

first: Haojie

last: Huang

state: MINNESOTA

address: 200 1st ST SW

institute: Mayo Clinic

summary: The Polycomb repressive complex 2 (PRC2) is important for the maintenance of stem cell pluripotency and suppression of cell differentiation by promoting histone H3 lysine 27 trimethylation (H3K27me3) and silencing expression of genes regulating differentiation. Here we show decreased expression of BRCA1 promotes EZH2 re-targeting genome wide and enhances H3K27me3 levels at PRC2 target loci in mouse ES cells.

overall_design: R1 mouse ES cells were transfected with control siRNA and Brca1 specific siRNA. At 48h after transfection, cells were harvested and subjected to ChIP assay with Ezh2 antibody. Brca1 wild-type (AB2.2) and Brca1 deficient (PL2F8) mouse ES cells were harvested and subjected to ChIP assay with Ezh2 antibody. Fragmented DNA obtained from ChIP assay was repaired by DNA Terminator End Repair Kit (Lucigen Corporation, Middleton, WI) and purified by QIAquick PCR purification kit. Then two unidirectional linkers JW102 and JW103 were annealed and ligated to the blunt ends DNA at 16°C overnight. The purified products were amplified to 2 μg by LM-PCR. NimbleGen Mouse ChIP 3x720K RefSeq Promoter Array (Roche) were used for the hybridization. Relative enrichments were calculated by dividing the normalized level of ChIP DNA to that of input DNA at corresponding locus. Labeling, hybridization and washing were carried out according to manufacturer’s instructions. Experiments in AB2.2 and PL2F8 cells were performed in duplicate.

first: X

last: Zeng

first: L

last: Wang

first: H


status: Public on Jan 21 2014

city: Regensburg

first: Zbigniew

middle: Tadeusz

last: Czyz

address: Josef-Engert-Strasse 9

department: Project Group Personalized Tumor Therapy, Regensburg

institute: Fraunhofer Institute for Toxicology and Experimental Medicine

summary: Establishment and subsequent validation of a aCGH protocol for WGA (whole genome amplification) products originating from single cell or low amount of starting material (i.e. microdissected FFPE tissue samples). The establishment of the protocol involved testing of three DNA labeling protocols. Two labeling protocols were designed specifically for Ampli1(TM) WGA products. Additionally random primed isothermal (Klenow-based) labeling approach was tested (Möhlendick et al., PLoS One. 2013 Jun 25;8(6):e67031.). In addition two different types of reference samples were tested and reference based on single-cell WGA products was chosen as most suitable in the end. The validation of the protocol assessed the following aspects: (1) performance of the protocol on primary and reamplified WGA products, (2) accuracy of the protocol in term of sensitivity of the CNA detection, (3) accuracy in terms of recapitulation of complex patterns of CNAs, (4) accuracy in terms of quantitative assessment of the CNAs, (5) ability to detect genomic heterogeneity of single cells (obtained either from in vitro cultures or from clinical patient material), (6) ability to detect minimal regions of aberration within a panel of disseminated cancer cells and corresponding tumor tissues.

overall_design:
Establishment and validation of the single-cell aCGH protocol: two condition experiment (i.e. PCR-based labeling technique 1 vs. PCR-based labeling technique 2; PCR-based labeling technique 2 vs. random-primed isothermal (Klenow) labeling approach; reference DNA from cell pool WGA product vs. reference DNA from single-cell WGA products). Validation of the protocol: comparison of the CNA profiles between single-cell WGA products and corresponding bulk DNA. Analysis of the DCC and corresponding FFPE tumor tissue samples: single-condition experiment performed on samples collected at different stages of the disease (DCCs from bone marrow) and/or from different sites (primary tumor-breast; metastasis-lymph nodes; DCCs-bone marrow).
Microarray data is corresponding data depicted in the paper manuscript titled: Reliable single cell array CGH for clinical samples

first: Martin

last: Hoffmann

first: Günter

last: Schlimok

first: Bernhard

last: Polzer

first: Christoph

last: Klein


status: Public on Jun 01 2013

first: Yvan

last: Devaux

address: 120 route d'Arlon

institute: LIH

summary: Prediction of neurological outcomes shortly after cardiac arrest would represent a major breakthrough. We tested the ability of gene expression profiles of blood cells to predict outcome in cardiac arrest patients.

overall_design: 35 consecutive cardiac arrest patients treated with therapeutic hypothermia (33°C for 24h) were included in this prospective  monocentre study. Cerebral Performance Category (CPC) was determined at discharge and 6 months later. All patients had blood sampling at the end of hypothermia. Gene expression profiles of blood cells were determined using 25,000~gene microarray in two groups of patients: good outcome (CPC 1-2) and bad outcome (CPC 3-5).