title: Transcriptional profile Lactobacillus plantarum WCFS1 : p-coumaric acid (p-CA) treated cells

status: Public on Jan 16 2013

city: Madrid

first: Felix

last: Lopez de Felipe

address: Jose Antonio Novais

country: Spain

institute: ICTAN-CSIC

summary: Whole genome transcriptional profiling was used to characterize the response of Lactobacillus plantarum WCFS1 human isolate during challenge with p-coumaric acid (p-CA). Twelve independent experiments were performed and mixed at random in groups of four for total of three RNA samples. The transcriptional profile reveals a massive induction of genes involved in stress resistance and detoxification-related functions and a global shutdown of growth-associated processes.

overall_design: Biological triplicates: untreated cells: Control vs. p-coumaric treated cells: Experimental

first: Inés

last: Reverón

first: Blanca

last: de las Rivas

first: Rosario

last: Muñoz

first: Félix

last: López de Felipe


title: Targeting microRNAs for asthma treatment

status: Public on Jan 11 2013

city: San Francisco

first: Andrea

middle: J

last: Barczak

state: CA

address: 1550 4th St Rock Hall 545

country: USA

institute: UCSF Sandler Center Functional Genomics Core Facility

summary: Profiling miRNA expression in cells that directly contribute to human disease pathogenesis is likely to aid the discovery of novel drug targets and biomarkers. However, tissue heterogeneity and the limited amount of human diseased tissue available for research purposes present fundamental difficulties that often constrain the scope and potential of such studies. We established a flow cytometry-based method for isolating pure populations of pathogenic T cells from bronchial biopsy samples of asthma patients, and optimized a high-throughput nano-scale qRT-PCR method capable of accurately measuring 96 miRNAs in as little as 100 cells. Comparison of circulating and airway T cells from healthy and asthmatic subjects revealed asthma-associated and tissue-specific miRNA expression patterns. These results establish the feasibility and utility of investigating miRNA expression in small populations of cells involved in asthma pathogenesis, and set a precedent for application of our nano-scale approach in other human diseases. We analyzed the concordance in results obtained by nano-scale qPCR and miRNA microarrays. RNA extracted from human Th2 cells was used for parallel profiling by both nano-scale PCR and microarray method. Fifty nanograms (ng) of RNA was used for the microarray method and cDNA from 1 ng (~1000 cell equivalent) of RNA, pre-amplified by 18 cycle PCR reaction, was used for miRNA detection by the nano-scale qPCR method (G.Seumois et al. in submission). Out of the 92 miRNAs assayed, 51 were detected by nano-scale qPCR. Of these, 45 were detected by microarray analysis, including the 32 miRNAs with the strongest signal intensities on the nano-scale qPCR platform.

platform_organism:
Caenorhabditis elegans
Drosophila melanogaster
Danio rerio
Gallus gallus
Homo sapiens
Mus musculus
Rattus norvegicus

overall_design: One sample; one color design. This is a single array from a larger normalized set of data investigating targeting microRNAs for asthma treatment that is to published separately.

first: Gregory

last: Seumois

first: Pandurangan

last: Vijayanand

first: K

middle: M

last: Ansel


title: Klebsiella pneumoniae: WT vs. Hfq mutant

city: Taichung

first: Yichyi

last: Lai

address: No.110, Sec. 1 Jianguo N. Road

department: Microbiology and Immunology

country: Taiwan

institute: Chung Shan Medical University

summary:
Transcriptional profiling of K. pneumoniae comparing the wild type strain (S5) with a hfq deletion mutant (H0201).
Goal was to determine the effects of Hfq absence on global K. pneumoniae gene expression.

platform_organism: Klebsiella pneumoniae subsp. pneumoniae NTUH-K2044

overall_design: WT vs. Hfq mutant. Eight replicates for each ORF presented in the 44K array.

first: Mingko

last: Chiang


title: Circulating microRNAs to predict neurological outcome after sudden cardiac arrest

city: Luxembourg

first: Yvan

last: Devaux

address: 120 route d'Arlon

country: Luxembourg

institute: LIH

summary: Studies of miRNA profiling to predict outcome in cardiac arrest patients treated with therapeutic hypothermia (TH)

overall_design: Venous blood was collected in citrated tubes prior discharge. Plasma was harvested by centrifugation and stored at -80°C until assayed. Identical volumes of plasma from the 14 patients of a group (cerebral performance category (CPC): 1-2 or CPC: 3-5) were pooled to reach a final volume of 400µL for each group. The two pools were processed conjointly. Total RNA was extracted using miRVana isolation kit (Applied Biosystems), dephosphorylated and labeled using miRNA Complete Labeling and hybridization kit (Agilent). Hybridization was performed on miRNA Human Microarray Release 12.0 slides (Agilent). 4 arrays per pool were hybridized. Scanning was achieved with the Genepix 4000B Scanner (Molecular Devices, Sunnyvale, USA). Raw data were acquired with the Genepix Pro software (Molecular Devices).


title: Floral transition in maize infected with Sporisorium reilianum disrupts compatibility with this biotrophic fungal pathogen

status: Public on Jan 29 2013

city: wuhan

first: shaopeng

last: zhang

address: No.1,Shizishan Street · Hongshan District

country: China

institute: Huangzhong agricultural university

summary: Sporisorium reilianum f. sp. zeae is an important biotrophic pathogen that causes head smut disease in maize. Head smut is not obvious until the tassels and ears emerge. S. reilianum has a very long life cycle that spans almost the entire developmental program of maize after the pathogen successfully invades the root. The aim of this study was to understand at a molecular level how this pathogen interacts with the host during its long life cycle, and how this interaction differs between susceptible and resistant varieties of maize after hyphal invasion. We investigated transcriptional changes in the resistant maize line Mo17 at four developmental stages using a maize 70mer-oligonucleotide microarray. We found that there was a lengthy compatible relationship between the pathogen and host until the early 8th-leaf stage. The resistance in Mo17 relied on the assignment of auxins and regulation of flavonoids in the early floral primordium during the early floral transition stage. We propose a model describing the putative mechanism of head smut resistance in Mo17 during floral transition. In the model, the synergistic regulations among auxins, flavonoids, and hyphal growth play a key role in maintaining compatibility with S. reilianum in the resistant maize line

overall_design: After inoculation using the hyphae of S. reilianum, the shoot apexes of inoculated Mo17 (resistant maize line) that contained hyphae but displayed normal morphology were collected for RNA extraction at at four vegetative stages; the 2nd-, 4th-, 6th-, and 8th-leaf stages. RNA samples from mock-inoculated and inocultated Mo17 were hybridized to the 46K maize 70-mer oligonucleotide microarray. Hybridization was performed in three biological replicates with Cy5/Cy3 dye swap as technical replicates.

first: Shaopeng

last: Zhang

first: Jack

last: Gardiner

first: Yannong

last: Xiao

first: Jiuran

last: Zhao

first: Fengge

last: Wang

first: Yonglian

last: Zheng


title: Imatinib/Rapamycin mRNA abundance

status: Public on Jan 10 2013

city: Stanford

first: Jamie

middle: Geier

last: Bates

address: 279 Campus Dr.

department: Biochemistry

institute: Stanford U.

summary:
Measurement of mRNA abundance from the following cells lines (red) versus universal mouse reference RNA (green). Wildtype v-Abl transformed pre-B cells were treated for 12 hours with 2.5 uM imatinib mesylate, 10ng/mL rapamycin or nothing.
Compound Based Treatment: wildtype v-Abl transformed pre-B cells were treated with imatinib mesylate (IMA), rapamycin (RAP) or nothing (NONE)

last: Geier


title: Genomic profiles vary with race and subtype in young African American and European American breast cancer (aCGH)

city: Birmingham

first: Theresa

middle: V

last: Strong

state: AL

address: 1530 3rd Avenue South

department: Medicine

institute: University of Alabama at Birmingham

type: Genome variation profiling by genome tiling array

summary: In the United States, African-American (AA) women are more likely to develop early-onset breast cancer and have historically poorer outcomes due to this disease compared to European-American (EA) women. Here, we analyzed genomic profiles of breast tumors from young women (<50 years old), matched by tumor subtype, histological grade, and ethnicity (African-American, AA, compared to European-American, EA). DNA copy number alterations (CNAs) were analyzed using a 32K BAC tiling path array. The study provides insight into the genetic component of ethnicity-related breast cancer health disparities.

overall_design: Breast tumor samples from young women (< 50 years old) were matched as follows: a matched pair consists of one AA and one EA sample, matched for tumor grade and tumor subtype (based on immunohistochemical analysis of ER, PR, and HER2 status). 44 experiments; each experiment is tumor DNA versus reference control DNA (AF) isolated from the blood of a 25-year-old African-American female with no familial or personal history of breast cancer. Additional control experiments included the AF reference versus the well-characterized F1 reference, and 3 self-self hybridization controls (AF versus AF).

first: Tyesha

middle: L

last: Farmer


title: Gene expression signatures for Normal-looking, fibrotic foci and hyperplastic (adjacent to fibrotic foci) area in IPF lungs

city: Pittsburgh

first: Guoying

last: Yu

state: PA

address: 3500 Terrace St., W1200

department: Departmnet of Medicine

institute: University of Pittsburgh

summary: To further understand the pathologic microenvironment in IPF, we have employed whole genome microarray expression profiling as a discovery platform to identify genes with the potential to distinguish normal and IPF lung in normal-looking, fibrotic foci and hyperplastic areas of IPF lung.   Four IPF lungs were dissected into normal-looking, fibrotic foci and hyperplastic areas by Laser-Capture-Microdissection. Gene expression analysis showed that 638 significantly different genes were identified that clearly distinguished the different IPF microenvironments . Among them, MMP19 was revealed as one of the most significantly up-regulated genes that distinguished normal looking epithelial cells (N) to hyperplastic epithelial cells, MMP19 up-regulation in IPF lungs was verified by immunohistochemical (IHC), qRT-PCR and Western-blot.

overall_design: IPF lungs are heterogeneity complex, which comprise normal looking area, fibrotic foci and hyperplastic area. In this study we separated the normal, fibrotic foci and hyperplastic area by LCM and employed Agilent whole genome gene expression microarray profiling to identify genes with the potential to distinguish the unique microenironment of IPF

first: Elisabetha

last: Kovkarova-Naumovski


title: Haloarcula hispanica wild-type strain cultured in different media: MG vs 168

status: Public on Jan 22 2013

city: Beijing

first: Hailong

last: Liu

address: West Beichen Road, Chaoyang District

institute: Institute of Microbiology, Chinese Academy of Sciences

summary: Transcriptional profiling of Haloarcula hispanica wild-type strain cultured in different media comparing MG medium with 168 medium. H. hispanica wild-type strain can accumulate PHBV in MG medium, while can not in 168 medium. Goal was to explore the PHA biosynthesis and its impact on central metabolism in H. hispanica.

overall_design: Total RNA from MG and 168 were used to generate target cDNA, and then hybridized to 8*15K Haloarcula hispanica genome array genechips, representing about 3800 genes.

first: Hua

last: Xiang


title: Comparative gene-expression analysis on the first-generation offspring of irradiated male and female mice

city: Leicester

first: Yuri

middle: E

last: Dubrova

address: University Road

department: Genetics

country: United Kingdom

institute: University of Leicester

summary:
Invstigation of whole genome gene expression level changes in kidney of the male offspring of BALB/c male and female mice exposed to 1 Gy of acute X-rays
The design of this study is further described in Abouzeid Ali, H. E., R. C. Barber, and Y. E. Dubrova. 2012. The effects of maternal irradiation during adulthood on mutation induction and transgenerational instability in mice. Mutat. Res. 732(1): 21-25. (PMID: 22289278).

overall_design: A six 12x135K chip study using total RNA extracted from kidney of control and treated BALB/c male mice. The expression of 42,575 genes was measured with at least two-fold technical redundancy.


title: Gene expression analysis comparing between dormant and released leaf bud from Japanese pear 'Kosui'

city: Tsukuba

first: Chikako

last: Nishitani

state: Ibaraki

country: Japan

institute: National Institutes of Fruit Tree Science

summary: Dormancy of buds is a critical developmental process that allows plants to survive extreme seasonal variations in climate. Dormancy transition in leaf buds of Japanese pear leading cultivar ‘Kosui’ were investigated using 10 K cDNA microarray. Leaf buds collected on October (early endodormancy) and February (breaking stage) were used to monitor the changes in the transcriptome. Over 1000 genes were differentially expressed (p value < 0.05 and 2 fold change) when the early endodormant stage and breaking one were compared to each other. Functional classification revealed that the majority of genes were involved in response to abiotic/biotic stimulus and stress, signal transduction, and transcription. Among them, 76 and 22 genes were significantly (over 10 fold change) highly expressed in early endodormant stage and breaking stage, respectively, this result suggests that even in the endodormant stage, gene expression in the buds is high. Among them, several transcriptional factors were included. The quantitative real-time PCR analysis showed that at least three of their seasonal changes during endodormancy transition phases were similar to two DAM (dormancy-associated MADS box) genes isolated from Japanese pear, suggesting that they might be novel candidate genes associated to dormancy.

overall_design: The gene expression profiles between dormant and released leaf bud were compared.

first: Takanori

last: Saito

first: Benjamin

last: Ubi

first: Takaya

last: Moriguchi

first: Toshiya

last: Yamamoto


title: Gene expression profiles in lymph nodes from ferrets infected with A/California/07/2009

status: Public on Jan 28 2013

city: Toronto

first: Longsi

last: Ran

state: ON

address: 101 College Street

department: Division of Experimental Therapeutics

country: Canada

institute: Toronto General Research Institute

summary: Pandemic H1N1 influenza A Human infection leads to symptoms ranging from mild to severe with lower respiratory complications observed in a small but significant number of infected individuals. Microarray analysis of the lymph nodes from ferrets infected with A/California/07/2009 shows intense gene upregulation during days 3 and 5 post-infection, and followed by marked downregulation during days 7 and 14 post infection. Gene expression profiles during the upregulation phase show intense chemokine activity, cell replication and activation of the lymphocyte-related signaling pathways.

overall_design: 15 ferrets were randomly allocated to 5 groups: Day 0 (before infection), and Day 3, 5, 7 and 14 (post infection) with 3 biological replicates for each group. Infection was performed with 10E6 EID50 of influenza A/California/07/2009 (H1N1). Ferrets were euthanized and lymph nodes were excised for RNA purification on the scheduled date. The subsequent gene expression analysis was performed with Affymetrix GeneChip Canine Genome 2.0 Array. Day 0 groups were used as control.

first: David

last: Kelvin


title: Long term intake of pea fiber affects the colonic barrier, bacterial and transcriptional profile using pig as model

status: Public on Jan 30 2013

city: Chengdu

first: Lianqiang

last: Che

address: Huiming Road 211,Wenjiang

institute: Sichuan Agricultural University

summary: The aim of this study was to investigate whether long term intake of pea fiber would improve colonic barrier, bacterial profile and alter colonic gene expression using DNA microarray. Fifty weaned pigs were randomly allocated into 2 groups receiving control and fibrous diet with inclusion of pea fiber from weaning age until d 160. The two diets had similar nutrient levels. Pigs fed pea fiber diet (PF diet) had markedly decreased overall average daily feed intake (ADFI) and Feed:Gain in growing and finishing period (P<0.05). In addition, long term intake of PF diet induced deeper crypt  (+50 %, P<0.05), increased protein expression of colonic mucin and sIgA (+13～16 %, P<0.05). Resulting from the increased lactobacillus content (P<0.05), moreover, pigs fed PF diet had significantly higher concentration of colonic total short chain fatty acid (SCFA) and acetic acid. DNA microarray results indicated that feeding PF diet induced alterations in the expression of colonic cancer, immune response and lipid metabolism-related genes, as well as genes involved in signal pathway such as intestinal immune network for IgA production, PPAR signaling pathway and nutrient metabolism-related pathways. Collectively, our results suggested that long term intake of PF diet would improve colonic health via altering colonic bacteria profile, colonic barriers, immune and metabolism related protein or gene expressions.

overall_design: A total of 50 weaned pigs (Duroc×Landrace×Yorkshire, initial body weight: 7.2±0.5 kg) were randomly allocated to 2 groups with 5 pens each group and 5 pig each pen.  Pigs were fed control (Control) and fibrous diets (10～20 % inclusion of pea fiber, PF) from weaning at 28 day  to 160 day-old-age, which is subjected to phase feeding by weaning diet (weaning to d 30 post-weaning), growing diet (d 30～90 postweaning) and finishing diet  (d 90～160 postweaning) according to their physiological stage. At d 160 postweaning, four pigs each group were selected to be slaughtered for collection of colonic tissues and DNA microarray was applied to the colonic tissues for analysis of gene expression.

first: Hong

last: Chen

first: Bing

first: Jun

last: He

first: Ping

last: Zheng

first: Xiangbing

last: Mao

first: Jie

first: Daiwen


title: EH001: Lmx1a is an activator of Rgs4 and Gbr10 and is responsible for the correct specification of rostral and medial mdDA neurons

status: Public on Jan 08 2013

city: Utrecht

first: Marian

last: Groot Koerkamp

state: Utrecht

address: Heidelberglaan 25

department: Research

country: Netherlands

institute: Princess Maxima Center for Pediatric Oncology

summary: The LIM homeodomain transcription factor Lmx1a is a very potential inducer of stem cells towards dopaminergic neurons. Despite several studies on the function of this gene, the exact in vivo role of Lmx1a in mesodiencephalic dopamine (mdDA) neuronal specification is still not understood. To analyze the genes functioning downstream of Lmx1a, we performed expression microarray analysis of LMX1A overexpressing MN9D dopaminergic cells. Several interesting regulated genes were identified, based on their regulation in other, previously generated expression arrays, and their expression pattern in the developing mdDA neuronal field. Post analysis through in vivo expression analysis in Lmx1a mouse mutant (drJ/drJ) embryos demonstrated a clear decrease in expression of the genes Grb10 and Rgs4, in and adjacent to the rostral and dorsal mdDA neuronal field and within the Lmx1a expression domain. Interestingly, the DA marker Vmat2 was significantly up-regulated as a consequence of increased LMX1A dose, and subsequent analysis on Lmx1a mutant E14.5 and adult tissue revealed a significant decrease in Vmat2 expression in mdDA neurons. Taken together, microarray analysis of an LMX1A overexpression cell system resulted in the identification of novel downstream targets of Lmx1A in mdDA neurons: Grb10, Rgs4 and Vmat2.

overall_design: RNA was isolated from MN9D cells. Each experimental sample consisted of a RNA pool derived from 3 separate 10-cm dishes containing Lmx1a overexpressing MN9D cells (transfected with pcDNA3.1(-)-Lmx1a). microarray analysis was performed in triplicate, each experimental sample was hybridized to the same reference pool of RNA derived from 9 10-cm dishes containing control MN9D cells (transfected with empty pcDNA3.1(-)). On each of three microarray samples, dye swap was performed to correct for dye effects.

first: Elisa

last: Hoekstra

first: Lars

last: von Oerthel

first: Annemarie

last: van der Linden

first: Raymond

middle: D

last: Schellevis

first: Gerard

last: Scheppink

first: Frank

middle: C

last: Holstege

first: M

middle: P

last: Smidt


title: Genes differentially expressed Haloarcula hispanica strains: PHB (ΔphaEC mutant) vs 960 (wild type)

first: Hailong

last: Liu

summary: Transcriptional profiling of Haloarcula hispanica comparing PHB with 960. PHB represents the PHA synthase genes mutant (i.e., ΔphaEC) which is deficient in PHBV accumulation when grown in MG medium. 960 represents the wild-type strain which can produce PHBV when grown in MG medium. Goal was to explore the PHBV biosynthesis and its impact on central metabolism in H. hispanica.

overall_design: Total RNA from PHB and 960 were used to generate target cDNA, and then hybridized to 8*15K Haloarcula hispanica genome array genechips, representing about 3800 genes.

first: Hua

last: Xiang


title: Proteome reference map of Haloarcula hispanica and comparative proteomic and transcriptomic analysis of polyhydroxyalkanoate biosynthesis under genetic and environmental perturbations

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

overall_design: Refer to individual Series


title: Global gene profiling comparison between hydrogen sulfide- and N-methyl-D-aspartate-induced neuronal deaths

status: Public on Jan 23 2013

city: Hobart

first: Minghui Jessica

state: Tasmania

address: Menzies Research Institute, University of Tasmania, Private Bag 24

department: Neuroscience group

country: Australia

institute: Menzies Research Institute

summary: Hydrogen sulfide (H2S), present in abundance in the mammalian brain, has recently been demonstrated to induce a dose- and time-dependent apoptotic-necrotic continuum in murine primary cortical neurons, which was successfully attenuated upon application of N-methyl-D-aspartate (NMDA) receptor antagonist. The current study focused on gaining an insight into the molecular mechanisms of H2S–mediated neuronal death pertaining to NMDA receptors activation through global gene expression  comparisons.

overall_design:
A total of 24 RNA samples were analyzed. There are 2 treatment conditions, namely 200uM sodium hydrosulfide and 200uM N-methyl-D-asparate. 3 replicates were collected for each of the selected time-points (5h, 15h and 24h), in addition to 6 replicates of shared vehicle control.

The supplementary file 'GSE16035_non-normalized_data.txt' contains non-normalized data for Samples GSM401312-GSM401335.

first: Nam

middle: S

last: Cheung

first: Minghui

first: Zhao

middle: F

last: Peng

first: Jayapal

last: Manikandan


title: Identification of transcripts predominantly expressed in cultured chicken primordial germ cells and embryonic fibroblasts.

city: Seoul

first: JAE

middle: YONG

last: HAN

address: 1 Gwanak-ro, Gwanak-gu

department: Department of Agricultural Biotechnology

country: South Korea

institute: Seoul National University

summary:
The present investigation was to identify the signaling and metabolic pathways of expressed genes by microarray comparison between Primordial Germ Cells (PGCs) and their somatic counterpart, chicken embryonic fibroblasts (CEFs).
We identified a total of 2,605 expressed transcripts. Among these, 1,197 were predominantly expressed in PGCs, and 1,408 were predominantly expressed in CEFs.

overall_design: Cell culture and microarray data generation were performed in triplicate. Blood PGCs from E2.5 embryos (N=20 for each replication) and CEFs from E6.5 embryos (N=5 for each replication) were cultured in appropriate culture medium. Total RNA was extracted from cultured PGCs (1,500,000 cells for each replication) and cultured CEFs (6,000,000 cells for each replication) with a Qiagen RNeasy kit. About 5 µg of total RNA from each replication was used for labeling. Probe synthesis from total RNA samples, hybridization, detection, and scanning were performed according to standard protocols from Affymetrix.

first: Deivendran

last: Rengaraj

first: Jae

middle: Y

last: Han


title: Global transcriptome analysis of eukaryotic genes affected by Gromwell extract

first: Yong-Sun

last: Bahn

address: 134 Shinchon-dong Seodaemun-gu

department: Biotechnology

institute: Yonsei University

summary:
BACKGROUND: Lithospermum erythrorhizon, popularly known as Gromwell, is a perennial herb belonging to the family of Boraginaceae and its extract is known to have diverse pharmacological, cosmetic, and nutritional values for human. Nevertheless the biological influence of Gromwell extract on general physiology of eukaryotic cells remains unknown. In this study, we for the first time performed a global transcriptome analysis by using DNA microarray analysis to identify genes affected by the addition of Gromwell extract (GE) by using a eukaryotic microorganism, basidiomycete fungus Cryptococcus neoformans, as a model system.
RESULTS: The transcriptome analysis revealed that a total of 1932 genes are differentially regulated in a statistically significant manner and expressions of 715 genes are up- (315 genes) or down-regulated (457 genes) more than twofold upon GE treatment. In response to GE treatment, genes involved in signal transduction genes are immediately regulated and the evolutionarily conserved set of genes involved in the core cellular functions, including DNA replication, RNA transcription/processing, and protein translation/processing, are generally upregulated. In contrast, a number of genes involved in carbohydrate metabolism and transport, inorganic ion transport and metabolism, post-translational modification/protein turnover/chaperone functions, and signal transduction are downregulated by the GE treatment. Among the GE-responsive genes that are also evolutionarily conserved in the human genome, we confirmed expression patterns of YSA1, TPO2, FET5 (CFO1), and PZF1 by Northern blot analysis. Based on the functional characterization of some GE-responsive genes through phenotypic analysis of gene knockout mutants, we found that GE treatment may promote cellular tolerance against a variety of environmental stresses in eukaryotes.
CONCLUSIONS: A significant portion of the Cryptococcus genome is affected in expression levels by treatment of GE, implying that the general physiology of eukaryotic cells is significantly affected by the GE treatment.

overall_design: There are more than 95% of genome homology between JEC21 and H99. Therefore 6 slides of JEC21 (Cryptococcus neoformans var. neoformans serotype D) 70-mer oligo are used in this analysis, 3 biological replicate experiments are performed, total RNAs are extracted from H99 (H99 Wild type strain (Cryptococcus neoformans var. grubii serotype A)) with 6.4 mg/ml Gromwell extract in 0, 10, 30, 60 min. We use the mixed all of total RNAs from this experiment as a control RNA. We use Cy3 as Sample dye and Cy5 as a control dye.

first: Soohyun

last: Bang

first: Dohyun

last: Lee

first: Hanhe

last: Kim


title: Expression data from mouse T cells after CLIP (Crosslinking immunoprecipitation) procedures (microRNA)

status: Public on Jan 19 2013

city: Ann Arbor

first: yaping

last: sun

state: Michigan

address: 1500 E Medical Center Dr.

department: internal medicine

institute: university of michigan

summary:
Molecular networks based on genome-wide mRNA and miRNA expression in activated T cells are integrated by co-regulation with miRNA and protein-coding genes during immune responses, however, accurate prediction of miRs and their targets remains a challenge. Furthermore, the specific changes in the expression of miRNAs and/or mRNAs in allogeneic activated T cells during HCT would be distinct from those responding to non-specific stimulation.
Recently, Ago-CLIP has been demonstrated to provide a robust platform for identification of precise miRNA-mRNA interactions by definitively distinguishing direct from indirect miRNA-target interactions. We utilized CLIP procedure followed by screening with standard microarray platforms for miRNA and mRNA transcripts to demonstrate the miR-mRNA landscape and identify novel molecular targets for modulating T cell responses.

overall_design: Mixed cell culture was performed with T cells in the presence of syngeneic 57BL/6, or allogeneic BALB/c Dendritic cells or cultivated with anti-CD3e and anti-CD28 mAB for 24 h.  Purified T cells were processd for CLIP procedures and followed RNA isolation (miReasy Kit and TRIzol LS)  and hybridization on Exiqon 6th generation miRCURY LNA microRNA Arrays and Affymetrix microarrays. We sought to obtain that the specific changes in the expression of miRNAs and/or mRNAs from those responding to non-specific stimulation and in allogeneic activated T cells.

first: Yaping

last: Sun

first: Pavan

last: Reddy


title: Imatinib/Rapamycin Gradient Encoding, mRNA abundance

first: Jamie

last: Bates

type:
Expression profiling by array
Other


title: Imatinib/Rapamycin Gradient Encoding

summary:
The purpose of this study was to compare changes in translation (using Gradient Encoding, described below) to changes in mRNA abundance. Lysates of wildtype v-Abl transformed pre-B cells harvested before and after 12 hours of treatment either with 2.5 uM imatinib, a v-Abl kinase inhibitor, or 10ng/mL (10.9 nM) rapamycin, an mTOR inhibitor, were fractionated by sedimentation through linear sucrose gradients.  Gradient fractions were encoded such that the mRNA from successive fractions was labeled with increasing ratios of Cy5 to Cy3.  mRNAs derived from fractions in the lighter portion of the gradient therefore have a lower Cy5 to Cy3 ratio, whereas those deeper in the gradient have a higher Cy5 to Cy3 ratio.  The ratio of Cy5 to Cy3 for each mRNA therefore reflects its average position within the gradient. We thus encoded the sedimentation rate of each mRNA across the entire gradient.  The resulting ratios were quantitatively measured for each mRNA species by hybridization to DNA microarrays, and related to the 260 nm absorbance peaks representing different numbers of ribosomes bound per mRNA
Compound Based Treatment: wildtype v-Abl transformed pre-B cells were treated with imatinib mesylate (IMA), rapamycin (RAP) or nothing (NONE)

last: Geier


title: CBFb Stabilizes HIV Vif to Counteract APOBEC3 at the Expense of RUNX1 Target Gene Expression [gene expression]

status: Public on Jan 17 2013

first: Nevan

last: Krogan

address: 1700 4th Street

department: Cellular & Molecular Pharmacology

institute: University of California, San Francisco

summary:
The HIV-1 accessory protein Vif hijacks a cellular
Cullin-RING ubiquitin ligase, CRL5, to promote
degradation of the APOBEC3 (A3) family of restriction factors. Recently, the cellular transcription
cofactor CBFb was shown to form a complex with
CRL5-Vif and to be essential for A3 degradation
and viral infectivity. We now demonstrate that
CBFb is required for assembling a well-ordered
CRL5-Vif complex by inhibiting Vif oligomerization
and by activating CRL5-Vif via direct interaction.
The CRL5-Vif-CBFb holoenzyme forms a welldeﬁned heterohexamer, indicating that Vif simultaneously hijacks CRL5 and CBFb. Heterodimers of
CBFb and RUNX transcription factors contribute
toward the regulation of genes, including those with
immune system functions. We show that binding of
Vif to CBFb is mutually exclusive with RUNX heterodimerization and impacts the expression of genes
whose regulatory domains are associated with
RUNX1. Our results provide a mechanism by which
a pathogen with limited coding capacity uses one
factor to hijack multiple host pathways.

overall_design: Analysis of Vif-dependent effects on gene expression in Jurkats when cells are activated for 4 or 6 hours with PMA and PHA

first: Paul

last: Hartley


title: MicroRNA profiling in primary and metastatic HCC cell lines using PLC8024 and MHCC97H derived cell lines

status: Public on Jan 12 2013

city: Pokfulam, Hong Kong

first: Wing Lung

middle: Simon

last: Yau

address: 21 Sassoon Road

department: Surgery

country: Hong Kong

institute: The University of Hong Kong

summary: Goal for this study is to identified miRNA involved in metastasis development using PLC8024 and MHCC97H derived cell lines.

platform_organism:
Caenorhabditis elegans
Drosophila melanogaster
Danio rerio
Homo sapiens
Mus musculus
Rattus norvegicus

overall_design: PLC8024 derived cell lines, PLC-PT (Primary Tumor) and PLC-LM (Lung Metastasis), and MHCC97H derived cell lines, MHCC97H-PT and MHCC97H-LM were compared using the Ncode miRNA microarray platform. The experiment were repeat twice with dye-swap.

first: Wing

last: YAU


title: Epididymal Adipose Tissue Profiling In HMDP

status: Public on Jan 09 2013

city: Los Angeles

first: Calvin

last: Pan

address: 675 Charles Young Dr South

institute: UCLA

summary: Identify genes in the epididymal adipose tissue whose expression is under genetic regulation in the hybrid mouse diversity panel.  The hybrid mouse diversity panel is comprised of classical inbred and recombinant inbred wild type mice.  The RMA values of genes were used for genome wide association as described in Bennett et al Genome Research 2010.  These data are used to identify candidate genes at loci associated with obesity and dietary responsiveness.

overall_design: GWAS for expression of epididymal adipose tissue in inbred strains

first: Aldons

last: Lusis

first: Brian

last: Parks

last: Bennett


title: Pig Longissimus muscle in Basque and Large White pigs reared in 3 different rearing systems

city: saint-gilles

first: marie

last: damon

address: domaine de la prise

country: France

institute: INRA

summary: Transcriptional profiling of pig skeletal muscle in 2 breeds [(Large white , LW, conventional) and (Basque, B, local, indigeneous)] and 3 rearing systems [(Conventional, C), (Alternative, A) and (Extensive, E)].

overall_design: 5 groups (BC,BA,BE,LWC and LWA) of 10 samples (i.e. biological replicates).  One replicate per array.

first: Marie

last: Damon

first: Bénédicte

last: Lebret


title: Gene expression profile in mouse tumor RIF-1 cell line after knockdown of Bre1a (Rnf20) or Bre1b (Rnf40).

first: Sophia

last: Chernikova

email: sophiac1@stanford.edu, sbcher@gmail.com

address: 269 Campus Dr

department: Radiation Oncology

institute: Stanford University

summary:
Mammalian Bre1 complexes (BRE1A/B (RNF20/40) in humans and Bre1a/b (Rnf20/40) in mice) function similarly to their yeast homolog Bre1 as ubiquitin ligases in monoubiquitination of histone H2B. This ubiquitination facilitates methylation of histone H3 at K4 and K79, and accounts for the roles of Bre1 and its homologs in transcriptional regulation. Recent studies by others suggested that Bre1 acts as a tumor suppressor, augmenting expression of select tumor suppressor genes and suppressing select oncogenes. In this study we present an additional mechanism of tumor suppression by Bre1 through maintenance of genomic stability.  We track the evolution of genomic instability in Bre1-deficient cells from replication-associated double-strand breaks (DSBs) to specific genomic rearrangements that explain a rapid increase in DNA content and trigger breakage-fusion-bridge cycles. We show that aberrant RNA-DNA structures (R-loops) constitute a significant source of DSBs in Bre1-deficient cells. Combined with a previously reported defect in homologous recombination, generation of R-loops is a likely initiator of replication stress and genomic instability in Bre1-deficient cells. We propose that genomic instability triggered by Bre1 deficiency may be an important early step that precedes acquisition of an invasive phenotype, as we find decreased levels of BRE1A/B and dimethylated H3K79 in testicular seminoma and in the premalignant lesion in situ carcinoma.
A cellular modification design type is where a modification of the transcriptome, proteome (not genome) is made, for example RNAi, antibody targeting.
Knock down by RNA interference: gene knocked down in RIF-1 cell line


title: Direct reprogramming of human astrocytes into neural stem cells and neurons (MeDIP)

status: Public on Jan 05 2013

city: Milan

first: Stefania

last: Corti

address: via F. Sforza 35

department: Neurological Sciences

country: Italy

institute: University of Milan

type: Methylation profiling by genome tiling array

summary:
Ectopic expression of the reprogramming factors OCT4, SOX2, or NANOG into human astrocytes in specific cytokine/culture conditions activated the neural stem gene program and induced generation of cells expressing neural stem/precursor markers (ASTRO-NSC).
To evaluate the epigenetic changes associated with this reprogramming, we analyzed the DNA methylation patterns of Astro-NSC relative to untransfected astrocytes.

overall_design: We compared three human AstroNANOG-NSC clones to the astrocytes from which they were derived using NimbleGen 3x720K CpG Island Plus RefSeq Promoter Arrays


title: Transcriptome  of Staphylococcus aureus Response to Spermine

status: Public on Jan 03 2013

city: Atlanta

first: Xiangyu

last: Yao

state: Georgia

address: 100 piedmont ave., petit science center

department: Biology

institute: Georgia State University

summary: To explore the Spermine(Spm)-based antibacterial targets in S. aureus, time course-dependent transcriptome analysis was conducted on Mu50 (MRSA) in the absence and presence of Spm.

sample_organism: Staphylococcus aureus subsp. aureus Mu50

overall_design: We conducted five independent microarray experiments in the absence (control) and the presence (experimental) of Spm. We calculated fold change as the ratio between the signal of untreated (control) and Spm-treated (experimental) cultures for 15, 30 and 60 min exposures.

first: Chung-Dar

last: Lu


title: Expression profiles of water deficit stress (WDS) regulated genes in rose petals

first: Junping

last: Gao

address: Department of Ornamental Horticulture, China Agricultural University

department: Ornamental Horticulture

institute: China Agricultural University

summary: Water deficit stress (WDS) is a crucial factor that causes the inhibition of petal expansion and abnormal flower opening in rose. The regulatory mechanisms of petal expansion by WDS at transcriptional level were investigated by analysis expression profiles under WDS.

overall_design: Analysis used total RNA samples of petals taken from flowers treated by WDS comparison to those from control flowers. Transcriptome dynamics during treatment time responsive to WDS.

first: Fanwei

last: Dai

first: Changqing

last: Zhang


title: SNP data from 82 lung carcinomas and 2 cell lines.

city: Paris

first: Eric

last: Letouzé

address: 15 rue de l'école de médecine

institute: Ligue Contre Le Cancer

summary: SNP profiles from 82 lung carcinomas and 2 cell lines were analyzed to detect potential tumor suppressors in lung cancer. Homozygous deletions revealed two interesting candidates with ARID domains, which were further characterized by sequencing in the whole series.

overall_design: 82 lung carcinomas and 2 cell lines were analyzed with Illumina HumanCNV370-Duo v1.0 chips.

first: Gilles

last: Manceau

first: Audrey

last: Didelot

first: Aurélie

last: Cazes

first: Elodie

last: Guichard

first: Karine

last: Pallier

first: Jessica

last: Zucman-Rossi

first: Pierre

last: Laurent-Puig

first: Hélène

last: Blons


title: Overexpression of four and a half LIM domains protein 2 promotes epithelial-mesenchymal transition-like phenotype in fish pre-osteoblasts

city: Legnaro (PD)

first: Serena

last: Ferraresso

state: Padova

address: Viale dell'Università

department: Dept of Comparative Biomedicine and Food Science

institute: University of Padova

summary: Four and a half LIM domains protein 2 (FHL2) is a co-regulator of gene transcription relevant for many signalling pathways and physiological processes. In this work, the role of FHL2 in cell differentiation has been investigated during in vitro mineralization using a Sparus aurata pre-osteoblast cell line (VSa16, [1]). A global microarray analysis was then performed to characterize the molecular pathways affected by FHL2 overexpression.  [1] Pombinho, A.R., Laizé, V., Molha, D.M., Marques, S.M.P. and Cancela, M.L. (2004). Development of two bone-derived cell lines from the marine teleost Sparus aurata; evidence for extracellular matrix  mineralization and cell-type specific expression of matrix Gla protein and osteocalcin. Cell Tissue Res. 315, 393-406.

overall_design: Sparus aurata oligo-DNA microarray (GPL6467) was used to compare gene expression profiles between Control (WT) and FHL2-transfected (F2) VSa16 cell lines. Gene expression profiles of both WT and F2 cells were assessed either at T0 (initial confluent cultures) or T4 (4 weeks of cell confluency). Four (4) pools of cells were taken from both WT and F2 groups at each time point and stored in RNA later at -20°C until RNA extraction.

first: Marta

last: Rafael

first: Vincent

last: Laizé

first: Luca

last: Bargelloni

first: M

last: Cancela


title: Aberrant microRNA expression in radiation-induced rat mammary cancer: the potential role of miR-194 overexpression in cancer cell proliferation.

status: Public on Jan 07 2013

city: Chiba

first: Daisuke

last: IIZUKA

address: 4-9-1, Anagawa, Inage-ku

institute: Research Institutes for Quantum Science and Technology

summary: Aberrant expression of microRNAs (miRNAs) is frequently associated with a variety of cancers, including breast cancer. We and others have demonstrated that radiation-induced rat mammary cancer exhibits a characteristic gene expression profile and a random increase in aberrant DNA copy number; however, the role of aberrant miRNA expression is unclear. We performed a microarray analysis of frozen samples of eight mammary cancers induced by gamma-irradiation (2 Gy), eight spontaneous mammary cancers, and seven normal mammary samples. We found that a small set of miRNAs was characteristically overexpressed in radiation-induced cancer. Quantitative RT-PCR analysis confirmed that miR-135b, miR-192, miR-194, and miR-211 were significantly upregulated in radiation-induced mammary cancer compared with spontaneous cancer and normal mammary tissue. The expression of miR-192 and miR-194 also was upregulated in human breast cancer cell lines compared with non-cancer cells. Manipulation of the miR-194 expression level using a synthetic inhibiting RNA produced a small but significant suppression of cell proliferation and upregulation in the expression of several genes that are suggested to act as tumor suppressors in MCF-7 and T47D breast cancer cells. Thus, the induction of rat mammary cancer by radiation involves aberrant expression of miRNAs, which may favor cell proliferation.

overall_design: We performed miRNA microarray analysis on mammary carcinomas in Sprague-Dawley rat to identify radiation-specific miRNA expression patterns compared with spontaneous mammary carcinomas and normal mammary tissues.

first: D

last: Iizuka

first: T

last: Imaoka

last: Nishimura

first: H

last: Kawai

first: F

last: Suzuki

first: Y

last: Shimada


title: Definition of the σ(W) Regulon of Bacillus subtilis in the Absence of Stress

status: Public on Jan 02 2013

city: Coventry

first: Emma

last: Denham

address: Gibbet Hill Road

department: Warwick Medical School

institute: University of Warwick

type: Expression profiling by genome tiling array

summary:
Comprison of the transcriptome of wild type Bacillus subtilis to the mutants sigW, rasP and prsW to select all candidate sigW regulated genes.
We identified 89 genes as being sigW regulated, including several non-coding RNA's.
The effects of rasP and prsW mutations on sigW regulated genes were relatively mild, implying that RasP or PrsW are not strictly required for sigW activation.
The rasP mutant has a peliotropic phenotype, affecting competence development, protein secretion and membrane protein production.  We show that these are not mirrored in the transcriptome, suggesting that RasP exerts its effects at the post transcriptional level.

sample_organism: Bacillus subtilis subsp. subtilis str. 168

overall_design:
RNA samples prepared from B. subtilis 168 and mutants sigW, rasP, and prsW were grown in Luria Bertani broth to O.D 600nm 1.0 were reverse transcribed, labeled and hybridized to tiling arrays.
All hybridizations (except prsW which was in duplicate) were performed in triplicate using RNA isolated from independent cultures.

last: Zweers

last: Nicholas

first: Thomas

last: Wiegert

first: Jan

last: van Dijl


title: miRNA expression profile in the Squalius alburnoides complex

city: Lisbon

first: Angela

last: Inácio

address: Campo Grande

country: Portugal

institute: centro de Biologia Ambiental

summary: The Squalius alburnoides complex (Steindachner) is one of the most intricate hybrid polyploid systems known in vertebrates. In this complex, the constant switch of the genome composition in consecutive generations, very frequently involving a change on the ploidy level, promotes repetitive situations of potential genomic shock. Previously in this complex, it was shown that in response to the increase in the genome dosage, triploid hybrids could regulate gene expression to a diploid state. In this work, we compared the small RNA profiles in the different genomic compositions interacting in the complex. Using high-throughput arrays and sequencing technologies, we were able to verify that diploid and triploid hybrids were closely related: they shared most of their sequences and their miRNA expression profiles were highly correlated. However, an overall view indicates an up-regulation of a substantial number of miRNAs in triploids. Also, the global miRNA expression in triploids was higher than predicted from an additive model. These results point to a participation of miRNAs in the cellular functional stability needed when the ploidy change.

sample_organism:
Squalius alburnoides
Squalius pyrenaicus

platform_organism:
Caenorhabditis elegans
Drosophila melanogaster
Danio rerio
Gallus gallus
Homo sapiens
Mus musculus
Rattus norvegicus
Takifugu rubripes

overall_design: In this study, miRNA expression from 3 adult tissues (brain, muscle and liver) from 3 individuals of each genomic composition (PAA, PA, AA and PP) was analysed using microarrays.

first: A

first: J

last: Pinho

first: P

last: Pereira

first: L

last: Comai

last: Coelho


title: Microarray analysis of toxicogenomic effect of Para-Tertiary Amyl Phenol (PTAP) on Staphylococcus aureus.

status: Public on Jan 01 2013

city: Ft. Meade

first: Prashanthi

last: Mulinti

state: MD

address: 701 Mapes Road

department: OPP/BEAD

institute: USEPA

summary: Global gene expression analysis of Staphylococcus aureus following Para-Tertiary Amyl Phenol (PTAP) treatment using Affymetrix GeneChip arrays. Results from this study provide insight into the molecular mechanisms underlying the cellular response of Staphylococcus aureus to PTAP.

overall_design: We conducted four independent microarray experiments (biological replicates) in the absence (control) and the presence (experimental) of Para-Tertiary Amyl Phenol (PTAP). Fold change was calculated as a ration between the signal averages of five untreated (control) and five PTAP-treated (experimental) cultures after 0, 10 and 60 min exposure time.

last: Toghrol


title: Conditional Essentiality of vicK (walKSpn) Histidine Kinase for Anaerobic Growth of Streptococcus pneumoniae D39

status: Public on Jan 04 2013

city: Bloomington

first: Ho-Ching

middle: Tiffany

last: Tsui

state: IN

address: 1001 E. Third St.

institute: Indiana University

summary: The VicRK two-component system of S. pneumoniae (Pneumococcus) is a member of the essential WalRK (YycFG) family found in low G+C gram positive bacteria. Previously, we showed that phosphorylated VicR response regulator (RR) is essential, because of its strong positive regulation of the pcsB gene, which mediates cell division. Little is known about the signals sensed by the VicK or WalK histidine kinases (HK), and it is unknown why pneumococcal VicK is not essential under aerobic growth conditions, whereas other the WalK HKs in other species are essential. VicK contains the only PAS domain in the Pneumococcal genome. PAS domains in other HKs have been shown to sense oxygen or other metabolic signals, such as NAD+, and it has been speculated that VicK may be involved in sensing oxygen in S. pneumoniae. Contrary to previous reports, we found that delta vicK mutants do not grow anaerobically, implying a conditional requirement for the VicK HK. Point mutations and domain deletions in vicK indicated that the autokinase activity of VicK is required for anaerobic growth, whereas the PAS domain and VicK phosphatase activity are not required. These combined results are consistent with the idea that maintenance of VicR~P level is required for anaerobic growth. The inability of delta vicK mutants to grow anaerobically was suppressed by spontaneous high- and low-growth yield mutants. Spontaneous suppressor mutants were still VicR dependent and did not result in bypass of the VicR signaling pathway. The genome of a high yield suppressor was sequenced using the Illumina method, which identified three mutations in the suppressor, two of which are predicted to play roles in phosphate transport (pnpR RR and phosphate ABC transporter). Manual sequencing of regions in additional independently isolated ΔvicK suppressor mutants identified similar mutations, and deletion of the pnpR RR gene in the ΔvicK background fully suppressed the anaerobic growth requirement for the VicK HK. Ongoing experiments will determine whether this suppression requires the PnpS HK or is mediated through changes in signaling. Finally, Western blotting showed that the level of VicK during anaerobic growth is about 3-fold less than that of aerobic cultures. This result suggests that the level of VicRKX operon expression is lower anaerobically, which may prevent crosstalk that occurs during aerobic culture to phosphorylate VicR.

overall_design: Three independent hybridizations using independent RNA preparations from the strain IU1781 (reference strain) and strain IU1896 (a strain with vicK deletion) were performed. Dye swap was performed with the reference strain labeled with Cy3 in two hybridizations and Cy5 in one hybridization.

first: Kyle

last: Wayne

middle: T

first: Malcolm

last: Winkler


title: Deep Sequencing Identifies IDH1 R132S Mutation in Adult Medulloblastoma (Nanostring)

city: Boston

first: Matija

last: Snuderl

state: MA

address: 55 Fruit St.

department: Pathology

institute: MAssachusetts General Hospital

summary:
Here we present the case of adult medulloblastoma with minimal chromosomal rearrangements but Shh expression profile and IDH1 mutation.
Data presented here are NanoString analyses of two biopsies of adult patient with a medulloblastoma which was classified as a Shh subtype

overall_design: Analyses were performed on 2 archival specimens of medulloblastoma, WHO Grade IV, seen at the Department of Pathology, Massachusetts General Hospital in 2007.


title: Transcriptional responses of resistant and susceptible fish clones to the bacterial pathogen Flavobacterium psychrophilum

city: Jouy-en-Josas

first: Jouneau

last: Luc

address: Domaine de Vilvert

summary: Comparison of the transcriptional response to the bacteria in the pronephros of a susceptible and a resistant line by micro-array analysis five days after infection

overall_design: Four to seven individual fishes have been analyzed for each experimental condition : Infected or Control ; Susceptible or resistant line

first: Christelle

last: Langevin

first: Mar

last: Blanco

first: Samuel

middle: A

last: Martin

first: Luc

last: Jouneau

first: J-F

last: Bernardet

first: Armel

last: Houel

first: Aurélie

last: Lunazzi

first: Eric

last: Duchaud

first: Christian

last: Michel

first: Edwige

last: Quillet

first: Pierre

last: Boudinot


title: Microarray analysis of toxicogenomic effect of Ortho-Benzyl-Para-Chloro Phenol (OBPCP) on Staphylococcus aureus.

first: Prashanthi

last: Mulinti

summary: Global gene expression analysis of Staphylococcus aureus following Ortho-Benzyl-Para-Chloro Phenol (OBPCP) treatment using Affymetrix GeneChip arrays. Results from this study provide insight into the molecular mechanisms underlying the cellular response of Staphylococcus aureus to OBPCP.

overall_design: We conducted five independent microarray experiments (biological replicates) in the absence (control) and the presence (experimental) of Ortho-Benzyl-Para-Chloro Phenol(OBPCP). Fold change was calculated as a ration between the signal averages of five untreated (control) and five OBPCP-treated (experimental) cultures after 0, 10 and 60 min exposure time.

first: P

first: F

last: Toghrol


title: Comparative analysis of the toxicogenomic effects of Ortho-Benzyl-Para-ChloroPhenol (OBPCP) and Para-Tertiary AmylPhenol (PTAP) on Staphylococcus aureus

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

overall_design: Refer to individual Series


title: Transcriptional profiling of FeHm effects on Haemophilus influenzae 86-028NP

city: Oklahoma City

first: Timothy

last: VanWagoner

state: OK

address: 940 SL Young Blvd, BMS340

department: Pediatrics

institute: University of Oklahoma Health Sciences Center

summary: Recently described microarray studies have defined the genes that are regulated in response to iron and heme levels in three isolates of Haemophilus influenzae.  Comparison of the data sets have allowed us to develop a putative core iron/heme modulon.  Included in the core modulon are thirty seven genes that are preferentially expressed under iron/heme limitation.  The majority of these genes are involved with iron and or heme acquisition such as hitA, tonB, exbD, exbB, hgpB, hgpC and the hxu and tbp operons.  In addition, we identified several other loci with roles potentially related to iron and heme metabolism such as protection against oxidative stress, iron and heme storage and detoxification and biofilm formation.  In this report, we describe the further definition of the core iron/heme modulon following transcriptomic analysis of H. influenzae strains 86028NP and R2846.   With the defined core, we then test our original hypothesis that “iron and heme regulated genes are upregulated, and important, during clinical infection”.  The in vivo expression profiles of the core genes were determined following inoculation of select isolates into the bullae of chinchillas.  Isolates selected included 86028NP and a previously un-characterized isolate HI1722.  To facilitate studies with the latter isolate, we sequenced the genome and annotated the identified CDS to ensure that oligonucleotides selected for Q-PCR would correctly target each gene of interest.   The results from the in vitro studies show that the operons identified as core are actively upregulated in the chinchilla ear during otitis media.  For isolate 86-028NP, 70% of the operons were significantly upregulated while isolate NTHI1722 had 100% of the operons upregulated.

overall_design: Three replicate cultures were grown in iron and heme depleted media for 90 minutes and samples taken for expression analyses. Fe and heme were supplemented to the remaining cultures and the cultures allowed to incubate an additional 20 minutes. Microarray analyses were used to determine changes in gene expression resulting from transfer from FeHm-deplete to FeHm-replete conditions.

middle: W

last: Whitby

first: T

last: Seale

first: D

middle: J

last: Morton

last: Stull


title: Genome-Wide Characterization of the Phosphate Starvation Response in Schizosaccharomyces pombe [gene expression data]

city: Cambridge

first: Ian

middle: O'Brien

last: Carter-O'Connell

address: 52 Oxford St. NW 440

department: MCB

institute: Harvard University

summary: Inorganic phosphate is an essential nutrient required by organisms for growth. During phosphate starvation, Saccharomyces cerevisiae activates the phosphate signal transduction (PHO) pathway leading to the expression of the secreted acid phosphatase, PHO5. The fission yeast, Schizosaccharomyces pombe, regulates expression of the ScPHO5 homolog (pho1+) via a non-orthologous PHO pathway. The genes induced by phosphate limitation and the molecular mechanism by which the genetically identified positive (pho7+) and negative (csk1+) regulators function are not known. Here we use a combination of molecular biology, expression microarrays, and chromatin immunoprecipitation coupled with high-throughput sequencing (ChIP-Seq) to characterize the role of pho7+ and csk1+ in the PHO response. We define the set of genes that comprise the initial response to phosphate starvation in S. pombe. We identify a conserved PHO response for the ScPHO5 (pho1+), ScPHO84 (spbc8e4.01c+), and ScGIT1 (spbc1271.09+) orthologs. We use ChIP-Seq to identify members of the Pho7 regulon and characterize Pho7 binding in response to phosphate-limitation and Csk1 activity. We demonstrate that activation of pho1+ requires Pho7 binding to a UAS in the pho1+ promoter and that Csk1 repression does not regulate Pho7 enrichment. Further, we find that Pho7-dependent activation is not limited to phosphate-starvation, as additional environmental stress response pathways require pho7+ for maximal induction. We provide a global analysis of the PHO pathway in S. pombe. Our results elucidate the conserved core regulon required for responding to phosphate starvation between distantly related ascomycetes and a better understanding of flexibility in environmental stress response networks.

overall_design: Schizosaccharomyces pombe 972 h- cells were starved for inorganic phosphate for 0, 30, 60, 120, or 240 minutes pior to microarray preparation to determine the extent and temporal resolution of the phosphate starvation response. At 120 minutes post-starvation we define a set of genes that are directly and specifically induced by phosphate starvation, providing a time-point at which all other experiments were performed. We characterize the pho7+- and csk1+- dependency of this PHO response at 120 minutes post-starvation in pho7+csk1+, pho7Δ, csk1Δ, and pho7Δcsk1Δ cells. In a seperate set of experiments we characterized the S. pombe stress response to copper limitation, iron limitation, and carbon switching at 120 minutes post-stress and osmotic shift at 20 minutes post-stress in both pho7+ and pho7Δ cells.

middle: O

first: Michael

last: Peel

first: Dennis

last: Wykoff

first: Erin

middle: K

last: O'Shea


title: Transcriptional profiling of FeHm effects on Haemophilus influenzae R2846

middle: M

middle: L


title: Single-Stranded Annealing Induced by Re-Initiation of Replication Origins Provides a Novel and Efficient Mechanism for Generating Copy Number Expansion via Non-Allelic Homologous Recombination.

city: San Francisco

first: Kenneth

last: Finn

address: 600 16th Street

department: Department of Biochemsitry and Biophysics

institute: University of California, San Francisco

summary: Copy number expansions such as amplifications and duplications contribute to human phenotypic variation, promote molecular diversification during evolution, and drive the initiation and/or progression of various cancers. The mechanisms underlying these copy number changes are still incompletely understood, however. We recently demonstrated that transient, limited re-replication from a single origin in Saccharomyces cerevisiae efficiently induces segmental amplification of the re-replicated region. Structural analyses of such re-replication induced gene amplifications (RRIGA) suggested that RRIGA could provide a new mechanism for generating copy number variation by non-allelic homologous recombination (NAHR). Here we elucidate this new mechanism and provide insight into why it is so efficient. We establish that sequence homology is both necessary and sufficient for repetitive elements to participate in RRIGA and show that their recombination occurs by a single-strand annealing (SSA) mechanism. We also find that re-replication forks are prone to breakage, accounting for the widespread DNA damage associated with deregulation of replication proteins. These breaks appear to stimulate NAHR between re-replicated repeat sequences flanking a re-initiating replication origin. Our results support a RRIGA model where the expansion of a re-replication bubble beyond flanking homologous sequences followed by breakage at both forks in trans provides an ideal structural context for SSA–mediated NAHR to form a head-to-tail duplication. Given the remarkable efficiency of RRIGA, we suggest it may be an unappreciated contributor to copy number expansions in both disease and evolution.

overall_design: The arrays in this series are primary comparative genomic hybridizations to determine genomic changes after re-replication.  Genomic DNA was purified from reference Saccharomyces cerevisiae cells or survivors of re-replication, differentially labeled with Cy3 and Cy5, and competitively hybridized to a spotted microarray containing ORF and intergenic PCR products. Cy5/Cy3 ratios (or the inverse in the case of dye swapped samples) are normalized so that the average ratio of all elements was 1 (except for arrays measuring re-replication induction where this ratio was set to 2). A small number of the arrays were used to determine the extent and location of re-replication under different conditions. For those, genomic DNA was purified from non-replicating and re-replicating cells and treated as above. Series contains a total of 333 hybridizations.  Note that the VALUE field reported for all of the sample tables in this series are the log2 of the normalized Cy5/Cy3 (or Cy3/Cy5) ratio.  To convert these into usable copy number profiles raise 2 to the indicated VALUE.

first: Joachim

last: Li

first: May

last: Szeto

first: Stephane

last: Ricoult


title: Transcriptional profiling of FeHm effects on Haemophilus influenzae 86-028NP and R2846


title: Streptomyces coelicolor A3(2) strain M600 wild type transcriptome ChIP-chip with the bldC null mutant

city: Norwich

first: Chris

last: den Hengst

state: Norfolk

address: Colney

department: Molecular Microbiology

institute: John Innes Centre

type: Genome binding/occupancy profiling by array

summary: Global regulation by the Streptomyces coelicolor atypical MerR-like transcription factor BldC. BldC is a transcriptional regulator essential for morphological development and antibiotic production in Streptomyces coelicolor. Here we identify the BldC regulon by means of chromatin immunoprecipitation (ChIP) microarray analysis. The BldC regulon encompasses at least 201 transcriptional units, which include many genes that play key roles in Streptomyces development (e.g., bldC itself, bldB, bldM, whiB, whiD, whiI, sigF, smeA-sffA, hupS), antibiotic production (e.g., afsK) and stress response (e.g., clpB, nsrR, sigE, sigF). All BldC-binding sites identified by ChIP-chip are present in the promoters of the target genes. In vitro DNA-binding experiments show that BldC is capable of binding DNA specifically in the absence of other proteins and suggest that BldC is a minor-groove DNA-binding protein. The regulon of BldC partially overlaps with that of the pleiotropic regulator BldD. BldC and BldD bind to distinct sites in the promoter region of smeA, where they simultaneously repress its transcription.

overall_design: ChIP-chip experiment using an anti-BldC antibody and a total DNA control. Comparison of IP in wild-type strain vs. IP in a bldC null mutant strain.

first: Ngat

last: Tran

first: Govind

last: Chandra

first: Ray

last: Dixon

first: Mark

last: Buttner


title: Response to elevated pCO2 in Strongylocentrotus purpuratus larvae

city: Santa Barbara

first: Tyler

middle: G

last: Evans

state: California

address: Marine Science Institute

department: Ecology, Evolution and Marine Biology

institute: University of California Santa Barbara

summary: Transcriptional profiling of purple sea urchin (Strongylocentrotus purpuratus) larvae cultured under three different seawater CO2 concentrations 400, 800, 1200 µatm. The goal was to determine the effects of CO2, an important climate change variable, on global gene expression

overall_design: Larvae were cultured under three different seawater CO2 concentrations 400, 800, 1200 µatm, each with four replicate cultures, and sampled at two developmental stages (gastrula and pluteus)


title: Transcriptomic analysis of differential genetic expression under CosR-knockdown condition compared with wild-type

city: Seoul

first: Sunyoung

last: Hwang

address: 599 Gwanak-ro

department: Department of Food and Animal Biotechnology

institute: Seoul National University

summary: We perfomed the transcriptomic analysis of differential genetic expression in the CosR-knockdown condition with a DNA microarray. CosR-specific antisense-PNA was used for CosR-knockdown. The results revealed that CosR significantly affected the expression of several genes involved in various cellular function in Campylobacter. Final goal of this study is to figure out the importance and the role of CosR in Campylobacter by identification of the CosR regulons.

overall_design: Two-condition experiment, WT vs. CosR-knockdown. Biological replicates: 3 wild type (control) replicates, 3 CosR-knockdown replicates.  For preparing the total RNA, C. jejuni cells were grown at 42°C in MH broth supplemented with 1.5 μM CosR-PNA for CosR knockdown to the mid-exponential phase for approximately 8 hr with shaking.

first: Qijing

last: Zhang

first: Sangryeol

last: Ryu

first: Byeonghwa

last: Jeon


title: Functions for the Magnaporthe oryzae Flb3p and Flb4p transcription factors in the regulation of conidiation

city: Kaiserslautern

first: Karsten

last: Andresen

address: Erwin-Schroedinger-Str. 56

country: Germany

institute: IBWF

first: S

last: Matheis

first: E

last: Thines

first: D

last: Scheps

first: A

last: Yemelin

first: K

last: Foster


title: Comparison of transcript abundance in aerial mycelium of the Magnaporthe oryzae FLB4-deleted mutant and its parental strain 70-15

summary: Genes potentially regulated by the Flb4p transcription factor were identified by microarray-based transcriptome analysis of the flb4- mutant and the parental strain 70-15.

overall_design: Two-condition experiment, wild-type vs. FLB4-deleted mutant. 6 biological replicates with dye-swaps


title: Comparison of transcript abundance in aerial mycelium of the Magnaporthe oryzae FLB3-deleted mutant and its parental strain 70-15

summary: Genes potentially regulated by the Flb3p transcription factor were identified by microarray-based transcriptome analysis of the flb3- mutant and the parental strain 70-15.

overall_design: Two-condition experiment, wild-type vs. FLB3-deleted mutant. 3 biological replicates with dye-swaps


title: Transcriptome profiling of low temperature-treated cassava apical shoots reveals dynamic responses of a tropical plant to cold stress

city: Shanghai

first: Jun

last: Yang

address: 300 Fenglin Road

institute: SIPPE

summary:
Background: Cassava is an important tropical root crop adapted to a wide range of environmental stimuli such as drought and acid soils. Nevertheless, it is an extremely cold-sensitive tropical species. Thus far, there is limited information about gene regulation and signaling pathways related to the cold stress response in cassava. The development of microarray technology has accelerated the study of global transcription profiling under certain conditions.

Results: A 60-mer oligonucleotide 4X44K Agilent microarray representing 20,840 genes was used to perform transcriptome profiling in cassava apical shoots subjected to cold at 7°C for 0 h, 4 h, and 9 h. A total of 508 transcripts were identified as early cold-responsive genes in which 319 sequences had descriptions when they were aligned with Arabidopsis proteins. Gene ontology (GO) annotation analysis identified many interesting categories including ‘Response to abiotic and biotic stimulus’, ‘Response to stress’, ‘Transcription factor activity’, and ‘Chloroplast’. Various stress-associated genes comprising signal transduction components (e.g., MAP kinase 4), transcription factors (TFs; e.g., RAP2.11), and ROS scavenging enzymes (e.g., catalase 2), as well as photosynthesis-related genes (e.g., PSAL), were found. Seventeen major TF families were also identified as being involved in the early response to cold stress (e.g., AP2-EREBP). Meanwhile, KEGG pathway analysis uncovered many important pathways, including ‘Plant hormone signal transduction’, ‘Starch and sucrose metabolism’, and ‘Plant-pathogen interaction’. Furthermore, the expression changes of 18 genes under cold and other abiotic stresses conditions were validated by real-time RT-PCR. As a response to cold stress in cassava, an increase in the ROS scavenging enzyme activities of catalase and superoxide dismutases and the accumulation of total soluble sugars were also detected. Importantly, most of the tested stress-responsive genes were primarily expressed in mature leaves, stem cambia, and fibrous roots rather than apical buds and young leaves.

Conclusions: The dynamic expression changes reflect the integrative controlling and transcriptome regulation of the networks in the early cold stress response of cassava. The biological processes involved in the signal perception and physiological response might shed light on the molecular mechanisms related to cold tolerance in tropical plants and provide useful candidate genes for genetic improvement.

overall_design: Apical shoots subjected to cold at 7°C for 0 h, 4 h, and 9 h were collected for RNA extractions from three independent healthy 3-month-old cassava (cultivar TMS60444) plants in the greenhouse.

first: Dong

last: An

first: Peng


title: MicroRNA profiling of the failing heart after myocardial infarction induction and doxorubicin treatment

status: Public on Jan 29 2013

city: London

first: Laura

last: Roca-Alonso

address: Du Cane Rd

department: Surgery and Cancer

institute: Imperial College London

summary: The use of anthracycline antibiotics such as doxorubicin (DOX) has greatly improved the mortality and morbidity of cancer patients. However, the associated risk of cardiomyopathy has limited their clinical application. DOX-associated cardiotoxicity is irreversible and progresses to heart failure (HF). For this reason, a better understanding of the molecular mechanisms underlying these adverse cardiac effects is essential to develop improved regimes that include cardioprotective strategies. MicroRNAs (miRNAs) are short non-coding RNAs that are able to post-trascriptionally regulate gene expression. MiRNAs have been demonstrated to be involved in both cancer and cardiovascular disease. Therefore, we were interested in unveiling the potential role of miRNAs in chemotherapy-induced HF. We used a combination of three different models to recreate this cardiac toxicity (acute in vitro DOX treatment, DOX-induced HF in vivo and a myocardial infarction -MI- leading to failure model) to study the pattern of dysregulated miRNAs. Using RNA from all three conditions, miRNA microarray profiling was performed and a common miRNA signature was identified. Interestingly, these dysregulated miRNAs have been previously identified as involved in the failing heart.  Our results suggest that DOX is able to alter the expression of miRNAs implicated in HF, in vitro as well as in vivo.

overall_design: The present study is a microRNA profiling of the damaged cardiac muscle (cardiomyocyte cell population), following either myocardial infarction (MI) induction or doxorubicin (DOX) treatment. Two DOX-treated models were included: ARC exposed to DOX in vitro and a validated DOX-induced heart failure model generated by repeated administration of DOX injections.

last: Lyon

first: L

last: Castellano

first: J

last: Stebbing


title: miRNA Profiles of Long-Lived Individuals (>=90 years)

city: Homburg

first: Andreas

last: Keller

address: Building 60

institute: Saarland University

summary: This project analyzes peripheral blood profiles of patients of age 90 or above and aims to detect profiles that distinguish them from younger controls.

overall_design: n = 55 normal controls and n = 15 long lived individuals have been screened for the complete miRNA repertoire. Please note that each miRNA has been measured in seven replicates and the median of the replica has been computed.

first: Abdou

last: ElSharawi


title: Global transcriptional profiling in porcine liver and lymph node tissues during acute pleuropneumoni

city: Tjele

first: Jakob

last: Hedegaard

address: PO-box 50

department: Department of Genetics and Biotechnology

country: Denmark

institute: Aarhus University, Faculty of Agricultural Sciences

summary: Expression profiles of porcine liver and tracheobronchial lung lymph node tissues were studied to identify genes being significantly affected by bacterial infection of the lungs. Samples were taken from liver and tracheobronchial lung lymph node tissues in pigs experimentally infected with A. pleuropneumoniae, serotype 5b, and from healthy non-inoculated control pigs from the same herd. Samples were investigated for changes in gene expression by means of global cDNA microarrays.

overall_design: Expression profiling of samples of liver and lung lymph node tissues from ten pigs challenged with Actinobacillus pleuropneumoniae and from five healthy control pigs was conducted by hybridising all 2x15 samples against a tissue specific common reference consisting of a pool of equal amount of total-RNA from all samples of each tissue type and were balanced with respect to control and challenged animals.

first: Kerstin

last: Skovgaard

first: Shila

last: Mortensen

first: Henrik

last: Hornshøj

first: Christian

last: Bendixen

first: Peter

last: Heegaard


title: In vitro transcriptional profiling of Bacteroides thetaiotaomicron in lactose, galactose and human milk oligosaccharides

city: Stanford

first: Angela

last: Marcobal

address: 299 Campus Drive

department: Microbiology and Immunology

institute: Stanford University

type:
Expression profiling by array
Third-party reanalysis

summary: Investigation of the overall in vitro response of Bacteroides thetaiotaomicron to human milk oligosaccharides. Comparison with response to MM-lactose and MM-galactose (Analysis performed using as a baseline datasets GSM301635 and GSM301637 corresponding to Bacteroides thetaiotaomicron response in MM-Glucose)

platform_organism:
Bacteroides thetaiotaomicron
Bifidobacterium longum

overall_design: In vitro transcriptional profiles of Bacteroides thetaiotaomicron obtained from biological duplicate cultures taken: (i) at middle log phase in minimal media galactose (MM-Gal) and minimal media lactose (MM-L) and (ii) at two timepoints during log phase in minimal media human milk oligosaccharides (MM-HMO).

first: Justin

last: Sonnenburg


summary: Co-expression network analysis using DNA oligonucleotide microarrays of experimentally infected pigs. The expression profiles of liver from ten experimentally infected pigs were compared with the profiles of liver from five non-infected contol pigs.

first: Gabriel

middle: C

last: Abreu

first: Rodrigo

last: Labouriau


title: Sarcoidosis miRNA Blood Profiles

summary: This project analyzes peripheral blood profiles of Sarcoidosis patients. Since miRNAs are known to be valuable diagnostic markers we asked whether respective patterns of patients can be detected in peripheral blood samples rather than in biopsies. The project aimed at an impoved understanding of complex profiles rather than single markers. Thus, a high-throughput technique was necessary, profiling all known miRNAs integratively.

overall_design: n = 55 normal controls and n = 45 Sarcoidosis samples have been screened for the complete miRNA repertoire. Please note that each miRNA has been measured in seven replicates and the median of the replica has been computed.


title: Gene expression studies to identify skeletal muscle genes related to stress in pigs

summary: Expression profiles of porcine muscle Semimembranosus were studied to identify genes beeing significantly affected by pre-slaughter stress or no stress treatment in pigs of different breed (Italian Duroc, Italian Large White or Pietrain) and differnt Halothane genotype (RYR1 locus CC-NN, CT-Nn or TT-nn) in Pietrain pigs.

overall_design: All 36 samples were hybridised together with a common reference.

first: Vincenzo

last: Russo

first: Roberta

last: Davoli

first: Paolo

last: Zambonelli

first: Luca

last: Fontanesi

first: Leonardo

last: Nannicosta

first: Michela

last: Colombo

first: Alessandra

last: Stella


title: Gene expression profiling in a Duroc/Landrace pig population differing in intramuscular fat content

first: Jakob

last: Hedegaard

summary:
The experiment aimed at studying gene expression differences in longissimus dorsi muscle from pigs from two groups: High versus low intramuscular fat (IMF). The animals were selected from a crossbred population of Landrace x Yorkshire/Landrace x Duroc animals, where we have previously found a highly significant QTL for IMF (Grindflek et al. 2001: "Detection of quantitative trait loci for meat quality in a commercial slaughter pig cross", Mammalian Genome 12(4): 299-304), and by microarray analysis we hoped to identify candidate genes for the QTL and/or pathways that are affected by the genes responsible for the QTL.

Keywords: phenotype comparison

overall_design: Direct dye-swap design, with 14 animals in each group (high IMF and low IMF) on 14 separate arrays

first: Ina

middle: S

last: Widerøe

first: Eli

last: Grindflek

first: Sigbjørn

last: Lien


title: serum microRNA profile of human nasopharyngeal carcinoma

status: Public on Dec 31 2012

city: Guangzhou

first: Jun

last: Ma

address: 651 Dongfeng Road East

institute: Sun Yat-sen University Cancer Center

summary: To evaluate whether serum microRNAs can predict survival in nasopharyngeal carcinoma (NPC) patients, we analyzed the serum microRNA expression profiles in 8 NPC patients with shorter-survival time and 8 age- and gender-matched NPC patients with longer-survival time using microarray. We identified a four-microRNA signature can predict survival of NPC patients.

overall_design: 8 serum samples from nasopharyngeal carcinoma patients with shorter-survival time and 8 serum samples from nasopharyngeal carinoma patients with longer-survival time

last: Liu


title: Comparative analysis of rice plants infected with Rice tungro bacilliform virus

city: Sapporo

first: Kouji

last: Satoh

state: Hokkaido

address: Hitsujigaoka 1

institute: NARO/HARC

summary:
Rice tungro bacilliform virus (RTBV) is determinant of the rice tungro disease symptom. We compare the gene responses by RTBV infection between RTBV susceptive (TN1) and resistant cultivar (TW16). TN1 infected with RTBV shows the mild stunting and leaf yellowing, although TW16 shows only mild stunting at only early infection stage, and recovers the symptoms.
Keywords: virus infection, disease response

overall_design: Comparison between RTBV and mock infected rice. Biological replicates: 3 control, 3 infected, independently grown and harvested. 1 samples derived from 5 plants grown under same conditons

first: Il-Ryong

last: Choi

first: Hiroaki

last: Kondoh

first: Hiromi

first: Setsuko

last: Kimura

first: Toshihiro

last: Omura

first: Shoshi

last: Kikuchi


title: Transcriptome of MEFs with BMP2 and DNA damage reagents

city: Singapore

first: Shuet Theng

last: Lee

address: 60 Biopolis Street

country: Singapore

institute: GIS

summary: The tightly controlled BMP-Smad1 pathway is essential for embryonic development and postnatal tissue homeostasis.  Dysfunction of BMP-Smad1 signaling also leads to tumor development such as juvenile polyposis and Cowden syndromes and various tumors in mouse models, with unknown pathological mechanisms. Here we establish a link between the BMP-Smad pathway and the prominent tumor suppressor Atm-p53 pathway.  We identify activated nuclear Smad1 as an Atm substrate under genotoxic stress.  Atm-mediated Smad1 S239 phosphorylation disrupts Smad1 interaction with protein phosphatase PPM1A and enhances Smad1 activation and up-regulation, which not only turns on target genes including Cdk1nc but also interacts with p53 and inhibits Mdm2-mediated p53 ubiquitination, leading to p53 stabilization.  Functionally, Smad1 acts like a tumor suppressor in DNA damage response, cell transformation and tumorigenesis in a p53-dependent manner. Sequencing of the gastric cancer samples revealed that Smad1 is frequently mutated, with S239 as mutational hotspot.  This study thus establishes the BMP-Smad1 pathway as an integral part of DNA damage response, which can suppresses tumorigenesis via p53.

overall_design: Transformed MEFs (Smad1f/f, Smad1f/f Cre) treated with 50ng/ml BMP2, 1 ug/ml doxorubincin, or both for different periods of time.  The mRNA levels of all genes were compared using microarray analysis.

first: Jenny

last: Chau

first: Qiang

last: Yu

first: Baojie

last: Li


title: CD3/CD28 Stimulated versus unstimulated Double-negative T Cells From Sooty Mangabeys

city: Seattle

first: Ramsey

last: Saleem

state: Washington

address: 307 Westlake Ave N

country: USA

institute: Seattle Biomedical Research

summary: Transcriptional profiling of Double Negative (CD4-/CD8-) T-cells isolated from SIV infected Sooty Mangebys. DN T-cells were stimulated through the T-Cell receptor using anti CD3/CD28 antibodies for 4 hours and compared to unstimulated DN T-cells.

overall_design: Two condition experiment, Stimulated vs Unstimulated. 4 animals tested, each with Stim vs Unstim, a dye flip of Stim vs Unstim, Stim vs Stim and Unstim vs Unstim.

first: Vasudha

last: Sundaravaradan

first: Donald

last: Sodora


title: microRNA expression in autonomous thyroid adenomas: correlation with mRNA regulation

city: Anderlecht

first: sebastien

last: floor

state: Bruxelles

address: Route de Lennik 808

country: Belgium

institute: IRIBHM - ULB

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

summary: MicroRNA (miRNA) are a class of small non-coding RNAs that act on the stability and the translation efficiency of their mRNA targets. Several evidences suggest that they play a role in tumorigenesis. So far, all types of thyroid tumors have been studied for miRNA expression except autonomous adenomas (AA), benign tumors characterized by the constitutive activation of the cAMP-dependent pathway, leading to a functional hyperactivity of the tissues. The objective of the study was to identify the deregulated miRNA in AA and to correlate the data with mRNA regulation observed in the same samples. AA and their corresponding adjacent tissues were hybridized on miRNA and mRNA microarrays. In order to investigate the correlation between both datasets and to identify mRNA regulations, bioinformatic mRNA target prediction softwares were used. 12 miRNAs were found as downregulated and 1 as upregulated in the tumors. Members of 3 different miR-families (miR-19, miR-29 and miR-135 families) were found among the regulated miRNA. By bioinformatic predictions we searched, among the mRNA microarray data, for regulated mRNA which could be targeted by the modulated miRNA. A great enrichment in mRNA encoding proteins involved in the extracellular matrix organization, as well as different phosphodiesterases were identified among the putative targets. The global miRNA profiles are not greatly modified, confirming the definition of these tumors as minimal deviation tumors. These results support a role for miRNA in ECM regulation and tissue remodelling occurring during tumor development, as well as in the retrocontrol of the activated cAMP pathway.

overall_design: 7 tumors hybridized in dey-swap, compared to thier adjacent normal tissues.

first: Sébastien

last: Floor

first: Christophe

last: Trésallet

first: F

last: Libert

first: M

last: Capello

first: G

last: Andry

first: Jaques

middle: E

last: Dumont

first: Wilma

last: van Staveren

first: Carine

last: Maenhaut


title: Metabolic features of Cryptosporidium parvum oocysts: Control vs. UV treatment.

city: College Station

first: haili

last: zhang

address: Texas A&M University 4467 TAMU

department: VTPB

institute: TAMU

summary:
Global gene expression in C. parvum environmental stage (oocysts) and the oocysts treated with UV comparing control untreated ones.
Goal was to uncover the metabolic features in oocysts and the oocysts treated with UV.

overall_design: two-condition experiment, UV treatment vs. UV untreatment; two time points, 0.5h and 5h. Each time point, two Biological replicates(1, 2) with two technique replicates(1-1,1-2 ; 2-1, 2-2).

first: Haili

last: Zhang

first: Fengguang

last: Guo

first: Huaijun

last: Zhou

first: Guan

last: Zhu


title: Exploring the potential of a Functional Gene Array (FGA) for fluvial biofilms

city: Girona

first: Chloé

last: Bonnineau

address: Campus Montilivi, s/n

country: Spain

institute: Institute of Aquatic Ecology, University of Girona

summary: Microarrays offer a comprehensive tool for a system-wide analysis of cell functioning based on the simultaneous detection of the activity of thousands of genes. While transcriptome analyses are usually related with the study of gene expression and regulation within single species in laboratory experiments or environmental samples, in the present study, the possibility of studying gene expression in river biofilm communities was explored. To this aim a Functional Gene array (FGA), based on consensus sequences from genes of key physiological processes, was designed including 83 functional genes chosen to reflect several essential biochemical pathways and specific stress response pathways. Probes of these genes were designed from consensus sequences from up to 6 microalgal species (diatoms and chlorophytes). Furthermore, species specific probes were included resulting in 1556 unique oligonucleotide probes for 83 different genes. RNA extracted from Chlamydomonas reinhardtii, Scenedesmus vacuolatus and multi-species biofilms was then hybridized to oligonucleotide arrays at different hybridization temperatures (55, 60 and 65ºC). Signal intensity was affected by sequence divergence but results showed that hybridisation temperature of 55ºC allowed a good compromise between cross-hybridization and specificity. Due to the limited number of probes and available sequence information the designed FGAs is at present particularly useful for the comparison of similar biofilms exposed to different conditions in laboratory experimental studies.

sample_organism:
Chlamydomonas reinhardtii
Scenedesmus vacuolatus
environmental samples

platform_organism:
Bacillariophyta
Chlorophyta
Chlamydomonas
Tetradesmus obliquus

overall_design: Nine samples were used, three were extracted from biofilm communities and hybridized at 55, 60 and 65 ºC, respectively; three were extracted from Scenedesmus vacuolatus and hybridized at 55, 60 and 65 ºC, respectively; and the three last ones were extracted from Chlamydomonas reinhardtii and hybridized at 55, 60 and 65 ºC

first: Stefan

last: Scholz

first: Helena

last: Guasch

first: Mechthild

last: Schmitt-Jansen


title: Cross species hybridization of human cancer cells co-cultured with mouse astrocytes and fibroblasts (Illumina mouse-6)

city: Houston

first: Sangbae

last: Kim

state: TX

address: 1 Baylor plaza

department: HGSC

institute: Baylor Colleage of Medicine

summary: Brain metastases are highly resistant to chemotherapy. Brain metastases are surrounded and infiltrated by activated astrocytes. To examine the genes whose expression is associated with chemo-resistance of brain-metastasized cancer cells, gene expression data were collected and analyzed from breast cancer cells and lung cancer cells co-cultured with astrocytes. Fibroblast cells were used as control.

overall_design: Total RNAs were extracted from co-cultured cells and hybridized to human microarray and mouse microarrays to detect human cell and mouse cell specific gene expression data.

first: Eun

last: Park

first: Ju-Seog

last: Lee

first: Isaiah

last: Fidler

first: Sun-Jin


title: Identification of ZDHHC14 as a novel tumor suppressor gene commonly downregulated in human cancers

first: Xueying

last: Mao

address: Charterhouse Square

institute: Queen Mary

type:
Genome variation profiling by SNP array
SNP genotyping by SNP array

summary: Genomic changes affecting tumor suppressor genes (TSGs) are fundamental to cancer. We applied SNP array analysis on a panel of testicular germ cell tumors (TGCTs) to search for novel TSGs and identified a frequent small deletion on 6q25.3 containing just one gene; ZDHHC14. The expression of ZDHHC14, a putative protein palmitoyltransferase, was decreased both at RNA and protein levels in TGCTs and this decrease correlated with chemoresistance. ZDHHC14 expression was also significantly decreased in a panel of prostate cancer samples and cell lines. Through next generation sequencing of the ZDHHC14 genomic locus we discovered several mutations in both cancer types, confirming the clinical significance of our findings. Furthermore, inducible overexpression of ZDHHC14 led to reduced cell viability and increased apoptosis through the classic caspase-dependent apoptotic pathway. Finally, we confirmed our in vitro findings of the tumor suppressor role of ZDHHC14 in a mouse xenograft model, showing that overexpression of ZDHHC14 inhibits tumorigenesis. Thus we have identified a novel TSG that is commonly downregulated in human tumors, as well as given mechanistic insight into the functional role of ZDHHC14, a potential protein palmitoyltransferase about which almost nothing has been described in the literature.

overall_design: Copy number analysis of Affymetrix 10K SNP array was performed for a total of 36 testicular germ cell tumour cases.Five samples have case-matched normal controls. All unpaired samples were compared with a common normal control, which was generated from the five normal samples.

first: Marc

last: Yeste-Velasco

first: Richard

last: Grose

first: Sakunthala

last: Kudahetti

first: Dongmei

last: Lin

first: Tracy

last: Chaplin

first: Liyan

last: Xue

first: Maojia

last: Xu

first: Julie

last: Foster

first: Sharon

last: James

first: Athina-Myrto

last: Chioni

first: Sharanpal

last: Jeetle

first: Natasa

last: Vasiljevic

first: Jacek

last: Marzec

first: Alan

last: McIntyre

first: David

last: Gould

first: Louise

last: Jones

first: Attila

last: Lorincz

first: R

middle: D

last: Oliver

first: Stephen

last: Mather

first: Janet

last: Shipley

first: Daniel

last: Berney

first: Bryan

last: Young

first: Yong-Jie

last: Lu


title: Candidatus Liberibacter americanus induces significant reprogramming of the transcriptome of the susceptible citrus genotype

status: Public on Dec 17 2012

city: Cordeirópolis

first: Valéria

last: Mafra

state: São Paulo

address: Rod. Anhanguera

country: Brazil

institute: Centro de Citricultura Sylvio Moreira

summary: This study evaluated the transcriptional reprogramming of a susceptible genotype (Pera sweet orange) challenged with the pathogenic bacteria Candidatus Liberibacter americanus (CaLam), using a customized 385K microarray containing about 32,000 unigene transcripts.

overall_design: For the microarray experiment were used symptomatic leaves from two Pera sweet orange plants inoculated with either bark or bud pieces infected with Candidatus Liberibacter americanus and two non-infected control plants.

first: Valeria

first: Polyana

last: Martins

first: Carolina

last: Franscisco

first: Marcelo

last: Ribeiro-Alves

first: Juliana

last: Freitas-Astúa

first: Marcos

last: Machado


title: Gene profiling of Turnip Crinkle Virus (TCV) siRNA in mutants at generation G1 and G11

city: evry

first: Soubigou-Taconnat

last: Ludivine

address: 2 rue gaston crémieux

department: URGV

institute: INRA

summary: gnp06-03_microtrac - gene profiling of turnip crinkle virus (tcv) sirna in mutants at generation g1 and g11 - What are the genes (including miRNA precursors) that are differentially regulated in a set of viral siRNA in diferent mutants?  - Col-0, dcl2/4, dcl3/4 and dcl2/3/4 were grown until rosette state and inoculated with TCV. Ten days post-inoculation the leaves were harvested. The same was made at generation 1 (G1) and 11 (G11).

overall_design: 10 dye-swap - gene knock out,treated vs untreated comparison

first: Agnes

last: Yu

first: Virginia

last: Ruiz-Ferrer

first: Jean-Pierre

last: Renou

first: Sandrine

last: Balzergue

first: Marie-Laure

last: Martin-Magniette


title: Dietary administration of botanicals to modulate gene expression in peripheral blood cells of sheep under ACTH challenge

city: Trieste

first: alberto

last: Pallavicini

address: via Giorgierei 5

department: Life Sciences

institute: University of Trieste

summary: The aim of the research was to investigate the regulation of gene expression in ovine blood leukocytes during ACTH challenge and the effect of effects of dietary administration of botanicals to modulate the stress related response. Six homogeneous groups of Sarda sheep were used, one negative control (CT) and five injected with ACTH to mimic biological stress. Afterwards four of the five ACTH treated groups were separately and fed with extract from Echinacea angustifolia roots (PO), with extract from Echinacea angustifolia flowers (EA), with extracts from Andrographis paniculata (AP) and with Larix decidua sawdust (LB). Control groups (CT and ACTH) were fed with a basal diet. RNA was extracted from blood samples collected before (T0) and after 3 (T3) and 51 (T51) hours from the first ACTH injection and transcriptome analysis was performed using a custom oligoarray. The injection of ACTH caused a down regulation of transcripts (95.5%, 232 over 243; P<0.01) at T3, whilst the administration with the diet of AP, EA, LB and PO determined a predominant up regulation. At T51, the down regulated transcripts of the ACTH group in comparison to CT group were lower (36.2%, 142 over 392; P<0.01), whilst for the animals receiving plant extracts with the diet the percentage of down regulated transcripts increased, in particular for LB  group (85.8 %).   Biological pathways affected by the injection of the adrenocorticotrophic hormone include the MAPK signaling pathway, the p53 signaling pathway, the TGF-beta signaling pathway and the T-cell receptor signaling pathway. The most promising botanicals for the control of induced stress appeared Echinacea angustifolia and Larix decidua, in particular both showing a target for the NR4A1 gene, a glucocorticoid receptor involved in the cell trafficking after cortisol secretion.

overall_design: The RNA extracted from blood samples and depleted from globinic mRNA was used for the preparation of pools. Samples were pooled together within group (6 groups) and time of sampling (3 times), including in the pool an equal quantity of RNA for each sheep. Eighteen pools were obtained for the hybridizations, that were performed in duplicate (36 slides).

first: Sandy

last: Sgorlon

first: Monica

last: Colitti

first: Elisa

last: Asquini

first: Alberto

last: Ferrarini

first: Bruno

last: Stefanon


title: Reliable analysis of the catabolic gene landscape and transcriptome for pollutant degradation using a custom open source microarray with internal calibration

city: Braunschweig

first: Robert

last: Geffers

address: Inhoffenstr. 7

department: Dep. Molecular Bacteriology

institute: HCI - Helmholtz Centre for Infection Research

summary: Despite various efforts to develop tools to detect and compare the activity and catabolic potential and activity for pollutant degradation of microorganisms in environmental samples, an open-source, curated and reliable method is still required. Here we report on a customize normalization system that can be applied to any microarray design, allowing the assessment of reliability of signals and enabling cross-experiment comparisons. Probes for the underlying catabolic gene array were designed based on manually curated databases for catabolic key genes. Signals were assigned to the respective catabolic protein subfamily that allows to inferring the functions and substrate specificity. The placement of probes for critical degradation nodes and subsequent metabolic steps allows the retrieval of information on the metabolic net. Information on gene localization from genome surveys was correlated to signals of putative hosts to generate phylogenetic community information. Hence, this novel array system was validated using genomic DNA of genome sequenced bacterial strains hosting biodegradation functions and applied to genomic DNA and RNA extracted from environmental samples under aromatic pollution pressure.

sample_organism:
unidentified microorganism
Cupriavidus pinatubonensis JMP134
Paraburkholderia xenovorans LB400
Pseudomonas putida F1
Rhizorhabdus wittichii RW1

overall_design: Catabolic microarray was optimized for detection and expression of catabolic genes involved in the degradation of pollutant compounds using genome genomic DNA of type strains: Burkholderia xenovorans LB400, Cupriavidus necator JMP134, Pseudomonas putida F1 and Sphingomonas wittichii RW1. Afterwards, this microarray was applied for environmental samples. For microcosm experiments, 200 ml of each groundwater were incubated in closed 1 l Erlenmeyer flasks at 20  degree C and 50 rpm. Second sets of 200 ml microcosms were supplemented with naphthalene (100 mg), which had above been identified as a contaminant present in both groundwaters in similar amounts. Naphthalene was supplied via the vapor phase and incubated under identical conditions as the control microcosms. After 4 days of incubations, 50 ml of each of the 4 microcosms were subjected to genomic DNA extraction and another 50 ml to RNA extraction.

first: Ramiro

last: Vilchez-Vargas

first: Howard

last: Junca

first: Dietmar

last: Pieper