title: Expression data from glioblastoma cells after ZFHX4 or CHD4 suppression.

status: Public on Jan 16 2014

city: New York

first: Milan

middle: Girish

last: Chheda

state: NY

address: 408 E. 69th Street

department: Neurology

country: USA

institute: Memorial Sloan-Kettering Cancer Center

summary:
ZFHX4 and CHD4 suppression independently shift tumor initiating cells out of a stem like state and toward a differentiated morphology.
After gene suppression via transduction of a lentivirally mediated shRNA construct, RNA was extracted 3 and 5 days later and was hybridized on Affymetrix microarrays.

overall_design: Total RNA was extracted 3 and 5 days after shRNA transduction of 0308 TICs, for 3 (for CHD4) or 5 (ZFHX4) independent experiments. Complementary RNA synthesis and hybridization/scanning of U133 plus 2.0 microarrays using GeneChip products (Affymetrix) was done as described in the GeneChip manual.

middle: G


title: Oryza sativa-Magnaporthe grisea interaction

status: Public on Jan 31 2014

city: 6 October

first: Yasser

middle: Bahaa-ElDin

last: Morsy

address: Flat 24, building 30, region 7, district 11, 6th October City, Giza, Egypt

department: Plant molecular biology

country: Egypt

institute: AGERI

summary: 5 leaves old rice plantlets were infected with Magnaporthe grisea spores and zero, two hours and twenty four houres after infection samples were collected

overall_design: control and 2 hour were mixed and hybridized with chip besides control and twenty four hours were mixed and hybridized with another chip. Both chips were performed in duplicate

middle: B

first: Ahmed

middle: M

last: Shokry

first: Sameh

middle: S

last: Hassnein

first: Hala

middle: F

last: Eissa


title: In situ synthesis of peptide microarrays - shadow mask design [3]

city: Tempe

first: Phillip

last: Stafford

state: Arizona

address: 727 E. Tyler St.

department: Biodesign Institute

institute: Arizona State University

summary: In this paper several computer programs were used to simulate in situ synthesis of peptides using shadow masks and BOC synthesis.  The peptides were designed to be random, or pseudo-random, but fulfill requirements of immunosignaturing.  This file contains data from actual 330,000 peptide arrays that used the first iteration of the peptide generation algorithm.  Monoclonal antibodies were bound to the microarrays and the total number of peptides that distinguished each monoclonal was measured.  This provides a baseline against which to compare purely random sequences.

overall_design: One replicate of each peptide was printed on 1 330k peptide microarray. One microarray were tested for each sample. Image was qualified using in-house metrics for quality assurance.

first: Lu

last: Wang

first: Neal

last: Woodbury

first: Stephen

last: Johnston

first: Zbigniew

last: Cichacz

first: Rebecca

last: Halperin


title: Lentiviral shRNA library screen to identify growth-related genes in malignant melanoma

status: Public on Jan 24 2014

city: Leipzig

first: Manfred

last: Kunz

address: Philipp-Rosenthal-Str. 23

department: Department of Dermatology

country: Germany

institute: University of Leipzig

summary:
Little is known about genes that promote melanoma cell growth and proliferation. siRNAs may be used to address the role of individual genesin these processes. RNAi library screens were used in the past to gain a comprehensive overview of all genes involved in cell growth, proliferation, migration and other cellular processes.
A large-scale loss-of-function screen for eight different melanoma cell lines was performed using a pooled lentiviral shRNA library (GeneNet Human 50K lentiviral shRNA Library,cat#SI206B-1, System Biosciences) to identify genes relevant for melanoma cell growth and proliferation. shRNAs that lead to cell death or reduced growth of transduced melanoma cells are negatively selected and thereby underrepresented in the final cellular shRNA pool and vice versa. The shRNAs of the shRNA library (3-5 per gene) have complementary sequences to probes on the custom Affymetrix microarray HG-U133Plus2 and were analysed using this array.

overall_design: Well-known melanoma cell lines SK-Mel-103, A375, SK-Mel-147, SK-Mel-19, SK-Mel-28, SK-Mel-29, SK-Mel-5, WM3523cln6 were transduced with the lentiviral shRNA library and grown for 10 days under puromycin selection (day 10), control cells of respective cell lines were transduced and frozen immediately after transduction and genomic integration of shRNAs (day 0). Totel DNA was extracted and genomically integrated shRNAs were hybridized to Affymetrix microarrays (HG-U133Plus2.0 array).


title: DNA methylation profiling in primary Diffuse Large B cell Lymphoma (DLBCL) and normal Germinal Center B Cells

status: Public on Jan 18 2014

city: Manhasset

first: Nyasha

last: Chambwe

address: 350 Community Drive

department: Institute of Molecular Medicine

institute: Feinstein Institutes for Medical Research

type: Methylation profiling by genome tiling array

summary: Diffuse Large B-Cell Lymphoma (DLBCL) is the most common aggressive form of non-Hodgkin lymphoma with variable biology and clinical behavior. The current classification does not fully explain the biological and clinical heterogeneity of DLBCLs. In this study we carried out genome-wide DNA methylation profiling of 140 DLBCL samples and 10 normal germinal center B-cells (NGCBs) using the HELP assay and hybridization to a custom Roche NimbleGen promoter array. We defined methylation disruption as a main epigenetic event in DLBCLs and designed a method for measuring the methylation variability of individual cases. We then used a novel approach for unsupervised hierarchical clustering based on the extent of DNA methylation variability. This approach identified 6 clusters (A-F). The extent of methylation variability was associated with survival outcomes, with significant differences in overall and progression-free survival. The novel clusters are characterized by disruption of specific biological pathways like cytokine-mediated signaling, ephrin signaling and pathways associated with apoptosis and cell cycle regulation. In a subset of patients, we profiled gene expression and genomic variation to investigate their interplay with methylation changes. This study is the first to identify novel epigenetic clusters of DLBCLs and their aberrantly methylated genes, molecular associations and survival.

overall_design: DNA methylation profiling in 140 primary denovo Diffuse Large B cell Lymphoma (DLBCL) samples from patients that had undergone R-CHOP chemotherapy and 10 purified normal Germinal Center B Cells

first: Matthias

last: Kormaksson

first: Huimin

last: Geng

first: Subhajyoti

last: De

first: Franziska

last: Michor

first: Nathalie

middle: A

last: Johnson

first: Ryan

middle: D

last: Morin

first: David

middle: W

last: Scott

first: Lucy

last: Godley

first: Randy

last: Gascoyne

first: Ari

last: Melnick

first: Fabien

last: Campagne

first: Rita

last: Shaknovich


title: Methylation profiling categorizes HIV-associated lymphomas in two distinctive groups

status: Public on Jan 30 2014

city: Shinjuku

first: Akihiro

last: Matsunaga

state: Tokyo

department: Intractable Disease

country: Japan

institute: National Center for Global Health and Medicine

summary: HIV-positive patients have a higher risk of non-Hodgkin's lymphoma with poor prognostic features. To characterize features of HIV-associated lymphoma, we compared the DNA methylation profiles of 803 cancer-related genes in between 9 HIV-associated and 12 non-HIV lymphoma samples by Illumina GoldenGate Methylation Cancer Panel I microarray.

overall_design: Bisulfite-converted DNA from the 42 samples  (duplicate analysis of 21 samples) were analyzed to obtain the methylation profiles of cancer-associated genes by using Illumina GoldenGate Methylation Cancer Panel I microarray.

first: Tsunekazu

last: Hishima

first: Noriko

last: Tanaka

first: Maria

last: Yamazaki

first: Makoto

last: Motizuki

first: Yukihito

last: Ishizaka

first: Mari

last: Shimura

first: Shotaro

last: Hagiwara


title: Signaling pathways in skeletal muscle of Amyotrophic Lateral Sclerosis mouse model

status: Public on Jan 22 2014

city: São Paulo

first: Renato

middle: David

last: Puga

state: São Paulo

address: Dr Ovidio Pires de Campos,785

department: Instituto de Psiquiatria

country: Brazil

institute: Universidade de São Paulo

summary: Gene expression analyses through cDNA microarray of fifteen gastrocnemius muscles from transgenic and wild-type SOD1G93A mouse model by the ages of 40 and 80 days old were performed. We used a customized cDNA array containing the cDNA platform comprised of 2352 spots, 326 of them orthologous to mouse, 1384 additional human cDNA sequences, 496 negative controls (DMSO) and 48 positive controls (the Q gene from λ-phage). Gene expression results for SOD1G93A and WT age matched mice pointed to eight up- (LOXL2, PIK4CA, FZD9, CUL1, CTNND1, SNF1LK, PRKX, DNER) and nine down-regulated genes (PIK3C2A, RIPK4, ID2, C1QDC1, EIF2AK2, RAC3, CDS1, INPPL1, TBL1X) at 40 days and also to one up- (PIK3CA) and five down-regulated genes (CD44, EEF2K, FZD2, CREBBP, PIKI3R1) at 80 days. Based on differentially expressed genes, analyses for gene priorization were performed and used to construct a network of protein-protein interaction. The network based on the genes of 40 and 80 days old mice was composed by 251 and 531 genes, respectively. GRB2 and SRC were identified as central genes of both networks. In conclusion, changes in gene expression of skeletal muscle from transgenic ALS mice in pre-symptomatic periods give further evidence of early neuromuscular abnormalities that precede motor neuron death.

sample_organism:
Homo sapiens
Mus musculus

overall_design: We performed gene expression analyses by customized cDNA array, using reference design, of fifteen gastrocnemius muscles from transgenic and wild-type SOD1G93A mouse model by the ages of 40 and 80 days old. These differentially expressed lists were submitted to analyses for gene priorization and used to construct a network of protein-protein interaction.

first: Alex

last: Fiorini


title: Gene expression profiles in the bacterial pustule-resistant soybean cultivars

status: Public on Jan 23 2014

city: Seoul

first: Jung Min

last: Kim

address: Gangnam-gu Teheran-ro 216

department: Department of Health Genomics

country: South Korea

institute: NAR Center, Inc. & Genoplan, Inc.

overall_design: To investigate the differential action between resistance and susceptible cultivars, we examined genome wide expression levels at five time points after X. axonopodis pv. Glycines (Xag) inoculation using microarray.

first: Jung

first: Seong-yun

first: In-soo

last: Choi


title: Role of microRNAs and microRNA machinery in the pathogenesis of Diffuse large B-cell Lymphomas

status: Public on Jan 27 2014

city: Stockholm

first: Stefano

last: Caramuta

address: CMM L8:01, Karolinska University Hospital

department: Molecular Medicine and Surgery

country: Sweden

institute: Karolinska Institutet

summary: We performed miRNA expression profiling in  a series of de novo DLBCLs, transformed DLBCLs and non-neoplastic lymph nodes using a microarray approach. Significant differentially expressed miRNAs among groups were identified using SAM analysis.

overall_design: Agilent microarray platform containing 470 miRNAs was used to determine miRNA expression profiles in 45 DLBCL cases (32 de novo and 13 transformed) and 10 lymph nodes. To validate the microarray platform, the expression levels of selected miRNAs were evaluated using qRT-PCR.

first: Mattias

last: Berglund

first: Linkiat

last: Lee

first: Deniz

last: Özata

first: Pinar

last: Akçakaya

first: Patrik

last: Georgii-Hemming

first: Xie

last: Hong

first: Rose-Marie

last: Amini

first: Gunilla

last: Enbland

first: Catharina

last: Larsson

first: Weng-Onn

last: Lui


title: Drosophila temperature sensitive col4a1 mutant (DTS-3) and control (OreR) comparison at permissive and at restrictive temperature

city: Szeged

first: Márton

last: Kiss

address: 52 Közép fasor

department: Genetics

country: Hungary

institute: University of Szeged

summary: We have recently reported an allelic series of dominant, conditional, temperature-sensitive (DTS) mutations in the type IV collagen gene col4a1 in Drosophila and the onset of severe myopathy by massive degradation of striated muscle fibers, degeneration of epithelial and circular smooth muscle cells of the gut. In order to get a closer look at the molecular causes of the observed phenomena we have executed microarray experiments with the aforementioned mutant.

overall_design: Two growth temperatures for both DTS-3 and OreR flies with dye-swap technical control replicates.


title: Hes1 and Glucocorticoid Signaling in Bone Sarcoma Cells

status: Public on Jan 21 2014

city: RTP

first: NIEHS

last: Microarray Core

state: NC

address: 111 T.W. Alexander Drive

department: DIR

institute: NIEHS

summary: To investigate the role of HES1 during glucocorticoid signaling in bone sarcoma cells (U2OS-GR cells) , we employed whole-genome microarray expressions in  mRNA extracted from control U2OS-GR and Hes1-overexpressed U2OS-GR cells.

overall_design: RNA isolated from control U2OS-GR and Hes1-overexpressed U2OS-GR cells treated with VEH or Dexamethasone.

first: Nick

last: Lu

first: John

last: Cidlowski


title: Transcriptional adaptation of L. monocytogenes EGD to oxygen availability

city: Freising

first: Stefanie

last: Müller-Herbst

address: Weihenstephaner Berg 3

department: ZIEL and Chair for Microbial Ecology

institute: Technical University Munich

summary:
Comparison of aerobic and anaerobic transcriptome of L. monocytogenes EGD
L. monocytogenes EGD cells used in this study were grown either aerobically or anaerobically to an OD600 = 0.70 - 0.75 and the transcriptome of these two conditions was compared

overall_design: Six biologically independent cultures of each aerobically and anaerobically grown L. monocytogenes EGD were used for total RNA isolation (six RNA sets). 4 array experiments were performed with Cy5-labelled cDNA derived from aerobically grown Listeria and Cy3-labelled cDNA derived from anaerobcially grown cells. For the two other RNA sets a dye swap was performed, that means the two other array experiments were performed with Cy3-labelled cDNA derived form aerobically grown Listeria and Cy5-labelled cDNA from anaerobically grown cells. As all oligonuceotides are spotted twice on an array, technical duplicates were performed for each experiment. The overall design results in 12 data points for the expression of each gene.

last: Wüstner

first: Daniela

last: Eder

first: Claudia

last: Held

first: Armin

last: Ehrenreich


title: Real-time quantitative PCR analysis of human malignant pleural mesothelioma tissue specimens

status: Public on Jan 25 2014

city: Copenhagen

first: Morten

last: Andersen

address: Frederik V's vej 11

department: Department of Pathology, section 5432

country: Denmark

institute: Rigshospitalet

summary:
BACKGROUND: Malignant pleural mesothelioma (MPM) is difficult to distinguish from reactive mesothelial proliferations (RMPs). MicroRNAs (miRNAs) are small non-coding RNA-strands (~22 nucleotides) that post-transcriptionally regulate gene-expression. Studies have shown that miRNAs are potential diagnostic markers in other cancers; however, it is uncertain whether miRNAs are useful biomarkers for differentiating MPM from RMP.
OBJECTIVE: To identify differentially expressed microRNAs which can aid in the diagnostics of MPM.
METHODS: We screened with a quantitative RT-PCR (RT-qPCR)-based platform the expression of 742 miRNAs in formalin-fixed paraffin-embedded (FFPE) preoperative diagnostic biopsies, surgically resected MPM-specimens previously treated with chemotherapy, and corresponding non-neoplastic pleura (NNP) from 5 patients.
RESULTS: By comparing the change in microRNA expression in patient-matched tissue samples, we identify 14 miRNAs which exhibit statistically significant deregulation between sample groups.
CONCLUSION: Based on this initial screening of miRNA expression, we have identified 14 miRNAs which are potential diagnostic biomarkers and may aid in diffferentiating RMP from MPM.

overall_design: qPCR microRNA expression profiling. MicroRNA expression in surgical tissue samples and presurgery diagnostic biopsies of malignant pleural mesotheliomas was compared to corresponding patient-matched non-neoplastic pleura. Patient-matched diagnostic biopsies from still chemotherapy-naïve patients were included to test for chemotherapy-induced changes in microRNA expression.

last: Grauslund

first: Eric

last: Santoni-Rugiu


title: Blastocyst Formation

city: Fort Collins

first: Ahmed

last: Gad

state: Colorado

address: 3107 Rampart Rd

department: Biomedical Sciences

institute: Colorado State University

summary: In this study we aimed to examine the effect of alternative in vivo and in vitro culture conditions during the time of blastocyst formation on the transcriptome profile of bovine blastocysts.

overall_design: Two different blastocyst groups were produced. The first group (Vitro_morula) was matured, fertilized and cultured in vitro until morula stage then transferred to synchronized recipients and blastocysts were collected at day 7 by uterine flushing. The second group (Vivo_morula) was matured, fertilized and cultured in vivo until morula stage then flushed out and cultured in vitro until day 7. Complete in vitro (IVP) and in vivo blastocysts were produced and used as controls.


title: Gene expression pattern after insertion of dexamethasone-eluting electrode into the guinea pig cochlea.

status: Public on Jan 17 2014

city: Matsumoto

first: Shin-ya

last: Nishio

state: Nagano

address: 3-1-1 Asahi

department: Department of Otorhinolaryngology

institute: Shinshu University School of Medicine

summary: To investigate the effect of the dexamethasone-eluting electrode in the guinea pig cochlea, and compared the gene expression after 7 days insertion with that of a normal electrode or non-treated control by microarray.

overall_design: Male Hartley guinea pigs (SLC, Shizuoka, Japan) with an age of seven weeks were used for the study. Three were implanted with normal electrodes while three others received a dexamethasone-eluting electrode. The cochleae from two animals, which did not undergo surgery. Seven days after electrode implantation the whole temporal bone was removed and placed into RNAlater solution (Ambion, Life Technologies Co., Grand Island, NY) to stabilize and protect cellular RNA. The whole cochlea was dissected out under a microscope and total RNA were extracted.

first: Yutaka

last: Takumi

first: Kenneth

last: Mugridge

first: Tomohiro

last: Oguchi

first: Shigenari

last: Hashimoto

first: Nobuyoshi

last: Suzuki

first: Satoshi

last: Iwasaki

first: Claude

last: Jolly

first: Shin-ichi

last: Usami


title: Variation in genomic islands contribute to genome plasticity in Cupriavidus metallidurans

city: Mol

first: Rob

last: Van Houdt

address: Boeretang 200

department: Interdisciplinary Biosciences

country: Belgium

institute: SCK-CEN

type: Genome variation profiling by genome tiling array

summary: Different Cupriavidus metallidurans strains isolated from metal-contaminated and other anthropogenic environments were genotypically and phenotypically compared with C. metallidurans type strain CH34. The latter is well-studied for its resistance to a wide range of metals, which is carried for a substantial part by its two megaplasmids pMOL28 and pMOL30. Comparative genomic hybridization (CGH) indicated that the extensive arsenal of determinants involved in metal resistance was well conserved among the different C. metallidurans strains. Contrary, the mobile genetic elements identified in type strain CH34 were not present in all strains but clearly showed a pattern, although, not directly related to a particular biotope nor location (geographical). One group of strains carried almost all mobile genetic elements, while these were much less abundant in the second group. This occurrence was also reflected in their ability to degrade toluene and grow autotrophically on hydrogen gas and carbon dioxide, which are two traits linked to separate genomic islands of the Tn4371-family. In addition, the clear pattern of genomic islands distribution allowed to identify new putative genomic islands on chromosome 1 and 2 of C. metallidurans CH34. Metal resistance determinants are shared by all C. metallidurans strains and their occurrence is apparently irrespective of the strain's isolation type and place. Cupriavidus metallidurans strains do display substantial differences in the diversity and size of their mobile gene pool, which may be extensive in some (including the type strain) while marginal in others.

sample_organism:
Cupriavidus metallidurans
Cupriavidus metallidurans CH34

overall_design: Comparative genome hybridization experiments. Comparing genomic DNA samples of different strains with a common reference strain (CH34).

first: Pieter

last: Monsieurs

first: Kristel

last: Mijnendonckx

first: Ann

last: Provoost

first: Ilse

last: Coninx

last: Jannsen

first: Max

last: Mergeay

first: Natalie

last: Leys


title: Comparative Transcriptomic Response from Fathead Minnow Liver and Blood Exposed to Environmentally Relevant Perfluorochemicals Concentrations

city: Gainesville

first: Ignacio

middle: Alejandro

last: Rodriguez-Jorquera

state: Florida

address: Mowry Drive 471

department: Soil and Water Science

institute: University of Florida

summary: The Nation’s streams and rivers contain several contaminants in the form of complex mixtures. These cocktails of chemicals are not equivalent in concentrations, some pollutants such as nutrients can be found in the range of mg/L (macro-pollutants) but others components (micro-pollutants) such as endocrine disrupting chemicals (EDCs) are in amounts thousands to millions of times less concentrated ug/L to ng/L. These mixtures hamper the determination of particular effects of contaminants in aquatic biota. Nonetheless, the fact that toxicity is preceded by alteration in gene expression in an organism allows the use of gene expression profiling (from microarray studies) to detect early toxic effects and identify mechanisms of action. The microarray technology, a collection of DNA fragments attached to a solid surface, can be used to measure the expression levels of large numbers of genes. This facilitates establishment of links between toxicants and effects on biota. In urban waters, micropollutants such as EDCs, are known to cause effects at very low concentrations. One common class of EDCs found in low levels in urban waters is the class of perfluorochemicals (PFCs). Previously, we observed that urban waters with wastewater influence containing PFCs in the 300 ng/L range exerted effects in fish by altering the expression of cholesterol metabolism and DNA repair genes in the liver. To determine whether low concentrations in the range of the PFCs found in the environment can elicit gene expression changes, we investigated the impact of 7 different types of PFCs in a controlled laboratory study by exposing fathead minnows for 48h to environmentally relevant concentrations of PFCs. Additionally, we use blood as starting material for microarray analysis in order to explore non-invasive techniques. No fish mortality was observed in any treatment exposures, but gene expression was altred. Surprisingly, low levels of PFCs that we used altered gene expression in fish liver and blood. Several of the same genes were altered in both liver and blood from exposed fish. Micorarray analysis yields information on altered molecular pathways that predict changes at higher levels of biological organization such as survival and reproduction.

overall_design:
Gene expression after 48 hours of exposure to prefluorochemicals in male liver of FHM
Exposure Water Preparation Four different treatment were prepared. A control (0 ug/L); two PFOS concentrations: PFOS high (25 ug/L), PFOS low (0.5 ug/L); and a PFCs mixture, consisting in 7 types of PFCs at concentrations similar than those found in a previous research downstream to a wastewater treatment plant (Rodriguez-Jorquera et al., in prep.) in an attempt to mimic the mixtures usually found in waters with wastewater influence. The preparation of all exposure treatments was completed dissolving the needed amount of PFCs for each concentration first on a 50 ml polypropylene falcon tube and 1, 9 ul of TEG (Triethylene glycol) as vehicle. For the control group, Milli-Q water and TEG was mixed in a falcon tube. Then, the 50 ml preparation were poured into a pre cleaned fiberglass cylinder containing 38 liters of carbon filtered and de-chlorinated city water. All PFCs were purchased from Wellington labs. Water samples were collected at the end of the exposures from the distribution cylinders. 1 L sample was collected for each treatment in a polypropylene bottles for PFCs analysis of 7 types of perfluorinated carboxylic acids (including PFOA) using EPA Method 537. Fish Exposure and Tissue Collection  Thirty two males were separated from the common tank two weeks before the experiment and placed in the treatment aquaria for 48 h. The exposure system consisted of 10 L glass aquaria. Each exposure was conducted in quadruplicate and each aquarium contained two male FHM in 4 L of treatment water. The water used in the control treatment was carbon filtered, dechlorinated tap water. The positions of the treatment tanks were randomized and test initiation times were staggered to ensure an exposure/sampling interval of 48 h. The fish were not fed during the experiment. The temperature range of the water was 24- 26 °C with a photoperiod of 16 h light: 8 h dark. At the conclusion of the exposures, fish were anesthetized with MS-222 and weighed to the nearest 0.1 g .The testes were removed and preserved for histological analysis to check sex and sexual stage. Liver tissue and whole blood was flash frozen using liquid nitrogen and stored at -80 °C until RNA extraction. Liver and blood were isolated from all males. The liver and blood from same individuals (four for each treatment) were used for RNA extraction. All procedures involving live fish were reviewed and approved by the University of Florida Institutional Animal Care and Use Committee (IACUC). After the exposure of fish to each treatment, four biological replicates were used to isolate RNA from FHM livers and blood using the same individuals in order to diminish variability among fish.Then microarrays were washed according to the Agilent protocol and, kept in the dark until scanning.

first: Nancy

last: Denslow


title: Expression analysis and in silico characterization of intronic long noncoding RNAs in renal cell carcinoma: emerging functional associations (RCC malignancy)

city: New York

first: Angela

middle: A.

last: Fachel

state: New York

address: 1300 York Ave

institute: Weill Cornell Medicine

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

summary: Intronic and intergenic long noncoding RNAs (lncRNAs) are emerging gene expression regulators. The molecular pathogenesis of renal cell carcinoma (RCC) is still poorly understood, and in particular, limited studies are available for intronic lncRNAs expressed in RCC. Microarray experiments were performed with two different custom-designed arrays enriched with probes for lncRNAs mapping to intronic genomic regions. Samples from 18 primary clear cell RCC tumors and 11 nontumor adjacent matched tissues were analyzed with 4k-probes microarrays. Oligoarrays with 44k-probes were used to interrogate 17 RCC samples (14 clear cell, 2 papillary, 1 chromophobe subtypes) split into four pools. Meta-analyses were performed by taking the genomic coordinates of the RCC-expressed lncRNAs, and cross-referencing them with microarray expression data from three additional human tissues (normal liver, prostate tumor and kidney nontumor samples), and with large-scale public data for epigenetic regulatory marks and for evolutionarily conserved sequences. A signature of 29 intronic lncRNAs differentially expressed between RCC and nontumor samples was obtained (false discovery rate (FDR) <5%). An additional signature of 26 intronic lncRNAs significantly correlated with the RCC five-year patient survival outcome was identified (FDR <5%, p-value ≤0.01). We identified 4303 intronic antisense lncRNAs expressed in RCC, of which 25% were cis correlated (r >|0.6|) with the expression of the mRNA in the same locus across three human tissues. Gene Ontology (GO) analysis of those loci pointed to ‘regulation of biological processes’ as the main enriched category. A module map analysis of all expressed protein-coding genes in RCC that had a significant (r ≥|0.8|) trans correlation with the 20% most abundant lncRNAs identified 35 relevant (p <0.05) GO sets. In addition, we determined that 60% of these lncRNAs are evolutionarily conserved. At the genomic loci containing the intronic RCC-expressed lncRNAs, a strong association (p <0.001) was found between their transcription start sites and genomic marks such as CpG islands and histones methylation and acetylation. Intronic antisense lncRNAs are widely expressed in RCC tumors. Some of them are significantly altered in RCC in comparison with nontumor samples. The majority of these lncRNAs is evolutionarily conserved and possibly modulated by epigenetic modifications. Our data suggest that these RCC lncRNAs may contribute to the complex network of regulatory RNAs playing a role in renal cell malignant transformation.

overall_design: A total of 22 human kidney tissue samples consisting of 11 primary renal tumors and 11 matched adjacent nontumor tissues from clear cell renal cell carcinmoa (RCC) patients were evaluated in this study. We compared the expression profiles of tumor and non-tumor samples obtained from patients with clear cell RCC to evaluate a possible correlation of the lncRNAs with renal malignancy. The set of clear cell RCC expression profiles was generated using a custom-designed cDNA microarray platform with 4,608 unique elements in replicate (9,216) enriched in gene fragments that map to intronic regions of known human genes (GPL3985).

first: Ana

middle: C

last: Tahira

first: Santiago

last: Vilella-Arias

first: Vinicius

last: Maracaja-Coutinho

first: Etel

middle: R

last: Gimba

first: Giselle

last: Vignal

first: Franz

last: Campos

first: Eduardo

last: Reis

first: Sergio

last: Verjovski-Almeida


title: Maize gene expression after infection of Ustilago maydis SG200 and SG200Δtin2

status: Public on Jan 28 2014

city: Marburg

first: Regine

last: Kahmann

address: Karl-von-Frisch-Strasse 10

department: Organismic Interactions

institute: Max Planck Institute for Terrestrial Microbiology

summary:
Anthocyanin induction in plant is considered a general defense response against biotic and abiotic stresses. The infection by Ustilago maydis, the corn smut pathogen, is accompanied with anthocyanin induction in leaf tissue. We revealed that anthocyanin is intentionally induced by the virulence promoting secreted effector protein Tin2. Tin2 protein functions inside plant cells where it interacts with cytoplasmic maize protein kinase ZmTTK1. Tin2 masks an ubiquitin-proteasome degradation motif in ZmTTK1 leading to a more stable active kinase. Active ZmTTK1 controls transcriptional activation of genes in the anthocyanin biosynthesis pathway rerouting phenylalanine away from lignin biosynthesis.
Therefore, we performed microarray analysis to understand how maize gene transcription in phenylpropanoid pathway is differentially changed after infection with Ustilago maydis SG200 (wild type) and SG200Dtin2 (anthocyanin-inducing effector mutant).

overall_design: We prepared three biological replicates for mock-inoculated maize (control), SG200-infected maize and SG200Δtin2-infected maize. For 1 sample, we harvested the leaves (1-3cm below injection hole) from 20 plants and pooled them. At 4 days post inoculation, total RNA was extracted.

first: Shigeyuki

last: Tanaka

first: Nina

last: Neidig


title: Antimicrobial mechanism analysis of an oil-in-water micro-emulsion by DNA microarray-mediated transcriptional profiling of Escherichia coli

city: Hangzhou

first: Cai

last: Haiying

address: #866 Yuhangtang Road

country: China

institute: Zhejiang Universtiy

summary: The DNA microarray was employed in this study to investigate the gene expression profiles of Escherichia coli treated by an oil-in-water (o/w) microemulsion, in order to better understand the antimicrobial mechanism of the microemulsion as a promising food-grade antimicrobial system. 5,440 open reading frames (ORFs) of E. coli were investigated.

overall_design: 5 ml bacterial cultures with a known inoculum of E. coli cells (1.0 × 109 cfu/ml) was added at 1:1 (v/v) to the microemulsion and incubated on a tube rotator at 200 rpm for 4 h at 37 °C for the subsequent DNA microarray analysis.

first: Haiying

last: Cai

first: Liyi

last: Yu

first: Yang

last: Li

first: Hui

last: Zhang

first: Fengqin

last: Feng


title: Deciphering life history transcriptomics in different environments

city: Las Vegas

first: Allen

middle: G.

last: Gibbs

state: Nevada

address: 4505 S Maryland Parkway

department: School of Life Sciences

institute: University of Nevada

summary: Investigation of whole genome transcription expression level changes in Drosophila mojavensis wild-type populations (Las Bocas:LB and Punta Prieta:PP). The experiment was designed to investigate life history transcriptomics in different environments.

overall_design: A total of  172 hybridizations were performed in this entire experiment. We used 135K 12-plex NimbleGen arrays. Total RNA was recovered from each sample listed below. The experimental design consisted a total of two populations (Las Bocas:LB; Punta Prieta:PP),  two host diets (Agria:AG and Organ pipe:OP) and fourteen life stages (6 hr egg:E6; 1st instar larvae:L1; 2nd instar larvae:L2; 3rd instar larvae:L3; Early pupal stage:EP; Late pupal stage:LP; 0 Day old adult:0D; 3 Day old adult:3D; 4 Day old adult: 4D; 6 Day old adult:6D; 10 Day old adult:10D; 14 Day old adult:14D; 18 Day old adult:18D & 24 Day old adult:24D). Each chip measures the expression level of 14528 transcripts. Two to 5 replicates were used for each type (R1, R2, R3 etc.). Fly source details are as follows: Las Bocas 2009: LB09; Punta Prieta 2008:PP08.

first: William

middle: J

last: Etges

first: Shripad

last: Tuljapurkar

first: Meredith

middle: V

last: Trotter

first: Cassia

last: de Oliveira

first: Subhash

last: Rajpurohit


title: NcRNA profiling after Influenza A/WSN/33 infection II

status: Public on Jan 29 2014

city: Berlin

first: Carla

last: Winterling

address: Charitéplatz 1

institute: Max Planck Institute for Infection Biology

summary:
8h and 24h after A/WSN/33 infection (MOI 1) ncRNA profiling was performed
A growing body of evidence suggests gene regulatory functions for the majority of non-protein-coding RNAs (ncRNAs). Besides small RNAs (sRNAs), the diverse class of long ncRNAs (lncRNAs) recently came into focus of research. So far, the relevance of lncRNAs in infection processes remains elusive. Here, we report the differential expression of several classes of lncRNAs during influenza A virus (IAV) infection in human lung epithelial cells.

overall_design: 2 biological replicates of 8h and 24h infection were hybridzed in an independent color-swap

first: Fernando

last: Garcia

first: Manuel

last: Koch

first: Alexander

last: Karlas

first: Max

last: Köppel

first: Thomas

last: Meyer


title: Human peripheral blood cells (PB): Effect of Tocilizumab/MRA compared to methotrexate(MTX) treatments on rheumatoid arthritis(RA) patients.

city: Ibaraki

first: Norihiro

last: Nishimoto

state: Osaka

address: 7-7-20, Saito-Asagi

institute: Wakayama Medical University

summary: This microarray study was conducted along with SATORI study, the clinical trial evaluated 125 patients with active RA with an inadequate response to low dose of MTX. Patients were allocated to receive either Tocilizumab(TCZ) 8 mg/kg every 4 weeks (TCZ group) or MTX 8 mg/week (MTX/control group) for 24 weeks. Gene expression profiles (GEP) of 112 patients -  54 patients from TCZ group and 58 patients from MTX group - were obtained in this study.

overall_design: PB samples were collected directly into PAXGene tubes before and after the treatments. Total RNA was extracted using PAXGene Blood RNA Kit with the optimal on-column DNase digestion. Two-color microarray was used to directly compare the samples before versus after the treatment. Total RNA was amplified and amino allyl aRNA of the sample before/after treatments was further labeled with Cy3/Cy5. The labeled aRNAs (mixture of Cy3 and Cy5) was hybridized onto microarray slide. Dye swapping was done with each investigation to account for dye bias in microarray experiments.

first: Hooi-Ming

last: Lee

first: Satoru

last: Ishikawa

first: Chieko

last: Aoki

first: Kenichi

last: Matsubara


title: Expression analysis and in silico characterization of intronic long noncoding RNAs in renal cell carcinoma: emerging functional associations (RCC survival)

first: Angela

last: Fachel

overall_design: A total of 16 human renal tumors from clear cell renal cell carcinoma (RCC) patients were evaluated in this study. We compared the expression profiles of tumor samples obtained from patients with clear cell RCC who died as a consequence of the disease versus those alive without disease (5-years follow-up) to evaluate a possible correlation of the lncRNAs with patient survival. The set of clear cell RCC expression profiles was generated using a custom-designed cDNA microarray platform with 4,608 unique elements in replicate (9,216) enriched in gene fragments that map to intronic regions of known human genes (GPL3985).

first: Ana

last: Tahira

first: Santiago

last: Vilella-Arias

first: Vinicius

last: Maracaja-Coutinho

first: Etel

last: Gimba

first: Giselle

last: Vignal

first: Franz

last: Campos

first: Eduardo

last: Reis

first: Sergio

last: Verjovski-Almeida


title: AB001

city: Utrecht

first: Marian

last: Groot Koerkamp

state: Utrecht

address: Heidelberglaan 25

department: Research

country: Netherlands

institute: Princess Maxima Center for Pediatric Oncology

summary: Diamond-Blackfan anemia (DBA) is a congenital disorder that results predominantly from mutations in various ribosomal protein genes. In order to determine how these mutations affect the translation of specific mRNAs, we performed microarray analysis of polysomal transcripts isolated from lymphoblast cells derived from DBA patients carrying different haploinsufficient mutations in either RPS19 or RPL11. One of the few overlapping transcripts that we found significantly decreased on the polysomes codes for branched-chain aminotransferase-1 (BCAT-1). We go on to determine that translation of BCAT-1 is especially impaired in cells carrying mutations in the small ribosomal protein genes, and provide evidence that this effect is due to its unusually long 5’UTR. The BCAT-1 enzyme is critical for synthesis of the branched-chain amino acids, including leucine. It is known that DBA patients respond well to orally administered leucine, and large-scale clinical trials as such are currently underway. Our results suggest that the haploinsufficient loss of ribosomal protein genes results in a decrease of BCAT-1 translation and provide an explanation for why leucine administration is beneficial for DBA patients.

overall_design: In this expression study duplicate mRNA samples were generated from polysomes isolated from celllines with mutations in RPS19 or RPL11 or normal controls. In each group 3 cellines were tested. Duplicate samples were analyzed in dyeswap. As common reference the commercial universal human reference RNA (Stratagene) was used.

first: Tamara

last: Pereboom

first: Albert

last: Bondt

first: Lina

last: Pallaki

first: Tim

last: Klasson

first: Paul

last: Essers

middle: G

last: Koerkamp

first: Frank

last: Holstege

first: Alyson

last: MacInnes


title: Transcriptomic profiles of Japanese medaka (Oryzias latipes) in response to alkalinity stress

city: Shanghai

first: Zongli

last: Yao

address: No.300 Jungong Road

institute: East China Sea Fisheries Research Institute

summary: Alkalinity stress is considered to be one of the major stressors for fish in saline-alkali water. Thus, it is of great significance from both aquaculture and physiological viewpoint to understand the molecular genetic response of aquatic organisms to alkalinity stress. The objective of this study is to determine genome-wide gene expression profiles to better understand the physiology response of medaka (Oryzias latipes) to high carbonate alkalinity stress. In lab-based cultures, adult fish were exposed to freshwater and high carbonate alkalinity water .We designed a microarray containing 26429 oligonucleotides and describe our experimental results for measuring gene expression changes in the gill of carbonate alkalinity stress exposed fish.

overall_design: The fish were exposed to freshwater (FW) and high carbonate alkalinity water (AW) for 96h, each with three replicates.

first: Qifang

last: Lai


title: Identification of Lgr5-independent spheroid-generating progenitors of the mouse fetal intestinal epithelium

city: Brussels

first: Frederick

last: Libert

address: 808 route de Lennik

department: IRIBHM

institute: ULB

summary: Immortal spheroids were generated from fetal mouse intestine using the culture system developed to culture organoids from adult intestinal epithelium. Spheroids are made of a monostratified polarized epithelium displaying a poorly differentiated intestinal phenotype. The proportion of spheroids generated from intestinal explants progressively decreases from fetal to postnatal period, with a corresponding increase in production of organoids. Spheroid cells show indefinite self-renewing properties but exhibit a transcriptome strikingly different from that of adult intestinal stem cells reminiscent of incompletely caudalized progenitors. The receptor Lgr4, but not Lgr5, is essential for their growth. Trop2/Tacstd2 and Cnx43/Gja1, two markers highly enriched in spheroids, are expressed throughout the E14 intestinal epithelium. Comparison of in utero and neonatal lineage tracing using Cnx43-CreER and Lgr5-CreERT2 mice identified spheroid-generating cells as developmental progenitors involved in generation of the prenatal intestinal epithelium. Ex vivo, spheroid cells have the potential to differentiate into organoids, thus qualifying them as a new type of intestinal stem-like cells.

overall_design: Two-channel microarray experiments were performed from spheroid/organoid pairs isolated each from a given embryo. Following initial seeding of small intestine from a given embryo/mouse (at E16, E18 or P0), spheroids and organoids were selectively picked up for each animal and replated for 3 passages to reach sample homogeneity. Hybridization was performed on the 4 independent pairs with dye-swap.

first: Roxana

last: Mustata

first: Gabriela

last: Vasile

first: Valeria

last: Fernandez-Vallone

first: Sandra

last: Strollo

first: Anne

last: Lefort

first: Frédérick

first: Daniel

last: Monteyne

first: David

last: Pérez-Morga

first: Gilbert

last: Vassart

first: Marie-Isabelle

last: Garcia


title: Mechanisms of TGFB1 induced atrial fibrosis

city: San Francisco

first: Andrea

last: Barczak

state: CA

address: 1550 4th St Rock Hall 545

institute: UCSF Sandler Center Functional Genomics Core Facility

summary: This project aims to compare gene expression in transgenic mice that overexpress TGFB1 to wild type mice. Transgenic mice have a fibrotic response in the atria, but not the ventricle.

overall_design: This is a 2 color design; dye swaps and a loop design were incorporated. Each group has N=4, with the exception being WT atria which has N=3 and was hybridied twice, the groups are Wt atria, WT ventricle, Transgenic atria, Transgenic ventricle. Comparisons of interest : Tg atria vs WT atria, Tg ventricle vs WT ventricle, WT atria vs.dWT ventricle, Tg atria vs Tg ventricle


title: Cross-Species Comparison Identifies Proneural specific patterns of genetic alterations in Glioblastoma

first: Richard

last: Leung

address: 1130 Saint Nicholas Avenue

department: Department of Neurosurgery

institute: Columbia University

summary: The determinants of the genetic complexity of Glioblastoma are poorly understood. We generated murine Glioblastomas by transforming glial progenitors in the adult brain with PDGF expression and PTEN deletion +/- p53 deletion. PDGF+PTEN-/- tumors developed additional deletions of specific genes in up to 100% of the tumors, whereas PDGF+PTEN-/-p53-/- tumors did not. Cross-species comparison with data from tCGA database and published in Verhaak, 2010, showed that consistent genetic deletions observed in mouse tumors were specific to human Proneural Glioblastoma. These findings show that the genetic alterations that accumulate during tumor progression are determined by the initiating genetic alterations and by the cellular context in which they occur.

overall_design: Murine gliomas were induced in vivo by retroviral mediated PDGF overexpression, PTEN deletion with or without p53 deletion using Cre/lox system. Tumors were subsequently harvested for sequencing and aCGH analysis. Paired liver DNA was used for hybridization. For PDGF+PTEN-/- tumors, different timepoints were obtained including 21, 35 days post tumor induction, as well as endstage tumors.

first: Adam

last: Sonabend


title: Expression analysis and in silico characterization of intronic long noncoding RNAs in renal cell carcinoma: emerging functional associations (RCC expression)

first: Angela

last: Fachel

overall_design: Tumor kidney tissue samples expression was measured with a 44k-element oligo-array (GPL4051) using 4 pools of tumor samples from 17 RCC patients (14 clear cell RCC, 2 papillary RCC and 1 chromophobe RCC). Pools were obtained from equal amounts of 300ng of DNase-treated total RNA of each tissue sample.

first: Ana

last: Tahira

first: Santiago

last: Vilella-Arias

first: Vinicius

last: Maracaja-Coutinho

first: Etel

last: Gimba

first: Giselle

last: Vignal

first: Franz

last: Campos

first: Eduardo

last: Reis

first: Sergio

last: Verjovski-Almeida


title: ROS homeostasis and pimaricin production in Streptomyces natalensis ATCC 27448

status: Public on Jan 15 2014

city: Porto

first: Tiago

last: Beites

address: rua do campo alegre, 823

country: Portugal

institute: IBMC

summary:
The aim of this work was to unveil the molecular mechanisms by which Streptomyces respond to a ROS intracellular imbalance and the effect of such response on the biosynthesis of secondary metabolites.
The study was focused on the industrial actinomycete S. natalensis ATCC 27448 producer of the polyene pimaricin - an antifungal agent widely used in the food industry and promising for antiviral activity and stimulation of immune response.

overall_design: Two-color microarray with common reference. The transcriptomes of S. natalensis ATCC 27448 (wild-type), S. natalensis CAM.02 (DsodF) and S. natalensis CAM.04 (DahpCD) were compared. Two time points were included: late exponential (T1) and early stationay (T2) phase. Biological triplicates were performed for each strain/time point. Genomic DNA of S. natalensis ATCC 27448 was used as common reference.

first: Antonio

last: Rodríguez-García

first: Pedro

last: Moradas-Ferreira

first: Jesús

last: Aparicio

first: Marta

last: Mendes


title: In situ synthesis of peptide microarrays - shadow mask design [1]

city: Tempe

first: Phillip

last: Stafford

address: 727 E. Tyler St.

department: Biodesign Institute

institute: Arizona State University

summary: A computer program was used to create random amino acid sequences based on and restricted by physical shadow masks which will be used for lithography-based synthesis of peptides.  The output from this algorithm was used to create peptides that were synthesized by Sigma Aldrich, and printed onto glass slides.  The arrays contained 384 peptides printed in duplicate for each of 4 different mask designs.  52 different monoclonal antibodies were incubated on these microarrays and analyzed for their propensity to bind the peptides created from each mask set.  The diversity of binding served as a proxy for the 'randomness' of these peptides, and provided information about how many masks are needed to truly generate random sequence peptides.

overall_design: two replicates of each peptide was printed on 1 Mask peptide microarray. A minimum of Two microarrays were tested for each sample. Image was qualified using in-house metrics for quality assurance.

first: Lu

last: Wang

first: Neal

last: Woodbury

first: Stephen

last: Johnston

first: Zbigniew

last: Cichacz

first: Rebecca

last: Halperin


title: In situ synthesis of peptide microarrays - shadow mask design [2]

summary: An experiment was designed to use a computer program to create lithography masks using a pseudo-random pattern generator.  The data in this file are results from immunosignaturing 8 different monoclonals using a 10,000 peptide random-sequence microarray.  Peptides were synthesized by Sigma Aldrich, and printed onto glass slides and used to test several different parameters.

overall_design: One replicate of each peptide was printed on 1 CIM_10K_v2 peptide microarray. One microarray were tested for each sample. Image was qualified using in-house metrics for quality assurance.


title: Cryptochrome 1 regulates growth and development in Brassica through alteration in the expression of genes involved in light, phytohormone and stress signalling

status: Public on Jan 10 2014

city: New Delhi

first: Pooja

last: Sharma

state: New Delhi

address: Benito Juarez Road

department: Department of Plant Molecular Biology

country: India

institute: University of Delhi South Campus

summary: To cover a comprehensive understanding of the complex regulatory networks controlling cryptochrome 1(CRY1)-mediated photomorphogenic response in Brassica, a genome-wide differential expression analysis was performed for the 5-day-old T3 BnCRY1-OE and wild type seedlings grown under white light (100 µmol m–2s–1) on 0.8% agar-gelled MS (Murashige and Skoog) medium containing 2% sucrose. Total RNA was extracted and cleaned up with the Qiagen RNeasy Plant Mini Prep Kit as per the manufacturer’s instructions (Qiagen). The yield and RNA purity were determined spectrophotometrically. Integrity of the RNA was checked using Agilent Bioanalyzer (Agilent Technologies, USA). 500 ng RNA of each of the sample was processed for microarray analysis according to Agilent protocol.   Keywords: Cryptochrome, Brassica, photomorphogenesis, differential expression.

overall_design: Agilent one-color experiment, Organism: B. napus (Brassica) Oligo Microarray, Agilent-022520 B. napus (Brassica) Oligo Microarray 4x44K, Labeling kit: Agilent Quick-Amp labeling Kit (p/n5190-0442)

first: Jitendra

middle: P

last: Khurana


title: Transcriptomic-Based Effects Monitoring for Endocrine Active Chemicals—Assessing Relative Contribution of Treated Wastewater to Downstream Pollution

status: Public on Jan 04 2014

city: Costa Mesa

first: Alvine

last: Mehinto

address: 3535 Harbor Blvd, Suite 110

institute: Southern California Coastal Water Research Project

summary: Many biomonitoring tools/approaches have been proposed to assess presence of endocrine active chemicals (EACs) and their biological effects in the field. Although these tools have provided valuable information, they are often limited by their specificity for certain groups of EACs and they may not account for interactions between EACs. This study aims to evaluate utility of transcriptomic and metabolomic technologies for effects monitoring in the field, and to advance integration of omic and environmental chemistry data sets. The objective was to utilize transcriptomic biomonitoring to determine the relative contribution of wastewater treatment plant effluents to biological effects observed in fish exposed to ambient waters receiving the effluents.

overall_design: Adult male fathead minnow were exposed to treated wastewater effluent or stream water up or downstream the plant in three different watersheds for 4 days. After exposure, the liver of 5-7 fish per treatment per site (i.e 19-21 fish from each watershed) were analyzed by microarrays. The transcriptomic profiles were compared to control fish exposed to Lake Superior filtered water.

first: Dalma

last: Martinovic-Weigelt

first: Gerald

last: Ankley

first: Nancy

last: Denslow

first: Larry

last: Barber

first: Kathy

last: Lee

first: Ryan

last: King

first: Heiko

last: Schoenfuss

first: Dan

last: Villeneuve


title: Elimination of hydrogenase post-translational modification blocks H2 production and increases ethanol yield in Clostridium thermocellum

city: Oak Ridge

first: Dawn

middle: Marie

last: Klingeman

state: TN

address: 1 Bethel Valley Rd building 15056 Rm 366  MS 6038

department: Biosciences Division

institute: Oak Ridge National Lab

summary: Clostridium thermocellum is a leading candidate organism for implementing a consolidated bioprocessing (CBP) strategy for biofuel production due to its native ability to rapidly consume cellulose and its existing ethanol production pathway. C. thermocellum converts cellulose and cellobiose to lactate, formate, acetate, H2, ethanol, amino acids, and other products. Elimination of the pathways leading to products such as H2 could redirect carbon flux towards ethanol production. Rather than delete each hydrogenase individually, we targeted a hydrogenase maturase gene (hydG), which is involved in converting the three [FeFe] hydrogenase apoenzymes into holoenzymes by assembling the active site. This functionally inactivated all three Fe-Fe hydrogenases simultaneously, as they were unable to make active enzymes. In the ∆hydG mutant, the [NiFe] hydrogenase-encoding ech was also deleted to obtain a mutant that functionally lacks all hydrogenase. The ethanol yield increased nearly 2-fold in ∆hydG∆ech compared to wild type, and H2 production was below the detection limit. Interestingly, ∆hydG and ∆hydG∆ech exhibited improved growth in the presence of acetate in the medium. Transcriptomic and proteomic analysis reveal that genes related to sulfate transport and metabolism were up-regulated in the presence of added acetate in ∆hydG, resulting in altered sulfur metabolism. Further genomic analysis of this strain revealed a mutation in the bi-functional alcohol/aldehyde dehydrogenase adhE gene, resulting in a strain with both NADH- and NADPH-dependent alcohol dehydrogenase activities, whereas the wild type strain can only utilize NADH. This is the exact same adhE mutation found in ethanol-tolerant C. thermocellum strain E50C, but ∆hydG∆ech is not more ethanol tolerant than the wild type. Targeting protein post-translational modification is a promising new approach to target multiple enzymes simultaneously for metabolic engineering.

overall_design: A seventeen array study using total RNA recovered from fermentation cultures of three strains (parental, ∆hydG and ∆hydG∆ech) of Clostridium thermocellum DSM1313. Cells were harvested at an OD 0.4-0.5 from cultures grown in the presence of additional 5mM acetate and compared to untreated controls. At least two biological replicates were performed for each treatment and control condition.

first: Ranjita

last: Biswas

first: Charlotte

last: Wilson

first: Tianyong

last: Zhang

first: Richard

last: Giannone

first: Robert

middle: L

last: Hettich

first: Daniel

last: Olson

first: Lee

last: Lynd

first: Steven

last: Brown

first: Adam

last: Guss


title: Gene expression profiles of Day 30 embryos from diet-restricted sows

city: Edmonton

first: Stephen

last: Tsoi

state: Alberta

address: 4-32G Agriculture/Forestry Cen

department: AFNS

country: Canada

institute: University of Alberta

summary: In our previous sow study, two subpopulations of feed-restricted sows (60% of anticipated feed intake) were identified: ‘Restrict (Risk)’ that mobilized higher levels of body tissue stores (>40MJ ME day-1) compared to ‘Restrict (Non-Risk)’ sows (Patterson et al. Reprod. Fert. Deveopl., 2011, 23, 889-898) and although Risk sows maintain higher litter growth in the weaned litter, this was at the expense of lower embryonic weight in their subsequent litter compared with Non-Risk sows. To understand the underlying molecular mechanisms involved, we investigated the gene expression profiles of embryos from Risk and Non-Risk litters in this experiment.

overall_design: Two-condition experiment, Risk vs Non Risk. Biological replicates: 20 risk, 20non-risk, independently compared to reference (all the 80 samples pooled from ch 1).

first: Zhuqing

last: Ren

first: Gina

last: Oliver

first: Walter

last: Dixon

first: George

last: Foxcroft


title: Expression profiling of extensively drug-resistant tuberculosis isolates and H37Rv exposed to anti-TB compounds

status: Public on Jan 07 2014

first: Yu

last: Guohua

state: Shanghai

address: Handan road

institute: Fudan university

summary: To explore the mechanism of drug resistance, most works focused on resistance associated genetic mutations, whereas concerns for resistance related gene expression are relatively low. Here a global expression analysis was performed between a reference strain H37Rv and two clinical extensively drug-resistant (XDR) strains with three anti-TB drug exposures {isoniazid (INH), capreomycin (CAP), rifampicin (RIF)}

overall_design: Strains were grown in Middlebrook 7H9 broth supplemented with ADC, 0.05% Tween 80 and 0.2% glycerol to an OD600 of 0.5-0.6, and then respectively treated with control (water), 10×MIC INH, 1×MIC RIF and CAP for 6hr.

first: Yao

last: Li

first: Guohua

last: Yu


title: Effects on the hepatic transcriptome due to caloric restriction are not altered by milking frequency

status: Public on Jan 08 2014

city: Auckland

first: Talia

last: Grala

address: 3 Symonds St

country: New Zealand

institute: DairyNZ

summary: The ruminant liver has multiple roles in the dairy cow and many of these are crucial in nutrient supply during lactation. Reduced feed intake alters the expression of many genes and pathways in the liver, inducing a period of negative energy balance. Once-daily milking is a management strategy to reduce the effects of periods of negative energy balance so the objective of this study was to determine if once-daily milking altered hepatic gene transcription during a period of negative energy balance induce by caloric restriction. Multiparous Holstein-Friesian and Holstein-Friesian x Jersey cows (n = 120) were grazed on pasture and milked twice daily (2X) from calving until 34 ± 6 days in milk (mean ± standard deviation). Cows were then allocated to one of four treatments in a 2 x 2 factorial arrangement. Treatments consisted of two milking frequencies (2X or once daily; 1X) and two feeding levels for three weeks: adequately fed (AF), consuming 14.3 kg dry matter intake/cow per d, or underfed (UF) consuming 8.3 kg dry matter intake /cow per d.  After the treatment period, all cows were fed to target grazing residuals ? 1600 kg DM/cow per d and milked 2X for 20 wk. Liver tissue was collected from 12 cows per treatment by subcutaneous biopsy at 3 wk relative to treatment start, RNA extracted and transcript abundance of genes quantified.

overall_design: 48 animals were enrolled in this study, a liver sample from 45 animals was used for microarray analysis. A reference design was used for hybridisation, whereby each of the 46 samples were hybridised to individual microarrays along with a pooled reference sample. The reference sample was generated by taking equal concentrations of each of the experimental samples.

middle: M

first: Jane

middle: K

last: Kay

first: Claire

last: Phyn

first: Caroline

last: Walker

first: Russell

last: Snell

first: John

last: Roche


title: Transcriptomics profilling of B. anthracis grown under different environmental perturbation

first: Gurudutta

last: Panda

address: New Mehrauli Road

department: School of Biotechnology

institute: Jawaharlal Nehru University

summary: The effect of factors that affect toxin production i.e. glucose, bicarbonate and growth temperature was investigated by transcriptional profilling using microarrays.

overall_design: Sequential environmental perturbations were carried out in R media, wherein glucose was replaced by glycerol (0.25%) [referred as 'R(-)Glucose'] or no bicarbonate [referred as 'R(-)Bicarbonate'] was added or the growth temperature was 28°C instead of 37°C [referred as 'R-28C']. The strain was grown in a chemically defined media called R medium in the presence of 5%CO2 at 37°C to simulate host like conditions and induce toxin production (referred as ‘R-Full’), which is used as control in this study.

first: Rakesh

last: Bhatnagar


title: The impact of exposure to serum lipids during in vitro culture on the transcriptome of bovine blastocysts

status: Public on Jan 09 2014

city: Montréal

first: Gael

middle: Louis Max

last: Cagnone

state: QC

address: 3175 Chemin de la Côte-Sainte-Catherine

department: The Montreal single-cell Academy

institute: CHU Sainte Justine

summary: EtOH-Lipid form serum have been added in BSA-supplemented SOF during post-compaction development of IVP bovine embryos. Lipid-treated blastocysts were compared with control treated blastocysts (no lipid addition to BSA, EtOH balanced).

overall_design: Amplified anti-sense RNA from each sample (4 pools of control and 4 pools of treated blastocysts) were labeled then hybridized on oligonucleotide microarrays following a dye-swap design (ex: pool 1 ctl in red vs. pool 1 treatment in green and then pool 1 ctl in green vs. pool 1 treatment in red).

first: Marc-André

last: Sirard


title: MicroRNA profiling of monocytes in LTNPs and Chronic HIV patients (CHI)

status: Public on Jan 16 2014

city: Sydney

first: daniel

last: murray

address: cnr West and Boundary Streets

country: Australia

institute: Kirby Institute

summary: We extracted total RNA from monocytes in 3 different patient groups, LTNPs, CHIs and Healthy Controls (HCs) in order to determine differentially expressed miRNA between these groups and to compare the results to a previous study on the same patients CD4+ T cells (GSE24022).

overall_design: In this study total RNA was extracted from 8 LTNPs, 8 CHIs and 8 HCs before being run on an agilent miRNA microarray

first: Daniel

middle: D

last: Murray

first: Sanjay

last: Swaminathan


title: Heme oxygenase-1 knocked down rat mesangial cells treated with hydrogen peroxide

city: Hsin Chu City

first: Hui-Teng

last: Cheng

address: No. 25, Lane 422, Section 1, Jingguo Road

department: Internal Medicine

country: Taiwan

institute: National Taiwan University Hospital Hsin-Chu Branch

summary: HO-1 cells denote the cultured rat mesangial cells with heme oxygenase-1 knocked down by RNA interference (using lentiviral vector). GFP cells denote the cultured rat mesangial cells that are transfected with empty lentiviral vector containing GFP cassette. Cells are treated with hydrogen peroxide 100 micromolar for 2 hours, or without. RNA are then harvested for array analysis. Biological replicates are performed (two independent experiment sets).

overall_design: GFP cell and HO-1 cell are untreated, or treated with hydrogen peroxide (100 micromolar for 2 hours).


title: Alternative splicing changes in A. fumigatus sensitized mice

status: Public on Jan 14 2014

city: New York

first: Dennis

last: Lazarev

state: NY

address: 1212 Amsterdam Av

department: Biological Sciences

country: USA

summary: Dysregulation of alternative splicing of mRNA precursors is known to  contribute to numerous human diseases. In this study we carried out  the first systematic search for asthma-associated changes in  alternative splicing events, using a model of Aspergillus fumigatus (A.  fumigatus)-sensitized mice and an exon junction microarray to detect  potential changes in alternative splicing. One of the  sensitization-associated changes identified in the search was a shift  in alternative splicing of the mRNA encoding cFLIP, a modulator of the  caspase- mediated extrinsic apoptosis pathway. Expanding these studies  to human asthma patients, we discovered a significant decrease in the  expression of both cFLIP isoforms in severe corticosteroid- resistant  asthmatics. Although it is unclear whether these changes were due  solely to differences in alternative splicing, these findings provide evidence that dysregulation of the extrinsic apoptosis pathway is part  of the underlying immunopathogenesis of severe refractory asthma.

overall_design: The technical side of the microarray experiment was essentially the  Illumina protocol.


title: Targeted chromatin profiling reveals novel enhancers in Ig heavy and light chain loci.

status: Public on Jan 03 2014

first: Eugene

last: Oltz

state: MO

address: 660 S Euclid Avenue

department: Pathology and Immunology

institute: Washington Univeristy in St.Louis

type: Genome binding/occupancy profiling by genome tiling array

summary:
Chip-chip from pro-B cells from Rag1KO mice for H3K27ac and RNA Pol II
Identification of novel enhancers from Ig heavy and light chain loci

overall_design: Rag1KO pro-B epigenetic landscape at Ig heavy and light chain loci

first: S

last: Gopalakrishnan

first: Alexander

last: Predeus

first: Maxim

last: Artyomov


title: The Genomics of the Fetal Hypothalamic Cellular Response to Transient Hypoxia: Endocrine, Immune, and Metabolic Responses

city: GAINESVILLE

first: Charles

middle: Evans

last: Wood

address: 1345 Center Drive/Room M552

department: Physiology and Functional Genomics

institute: University of Florida

summary: Fetuses respond to transient hypoxia (a common stressor in utero) with cellular responses that are appropriate for promoting survival of the fetus.  The present experiment was performed to identify the acute genomic responses of the fetal hypothalamus to transient hypoxia.  Three fetal sheep were exposed to 30 min of hypoxia and hypothalamic mRNA extracted from samples collected 30 min after return to normoxia. These samples were compared to those from 4 normoxic control fetuses using the Agilent 019921 ovine array.  Differentially-regulated genes were analyzed by network analysis and by gene ontology analysis, identifying statistically significant overrepresentation of biological processes.  Real-time PCR of selected genes supported the validity of the array data.  Hypoxia induced increased expression of genes involved in response to oxygen stimulus, RNA splicing, anti-apoptosis, vascular smooth muscle proliferation, and positive regulation of Notch receptor target.  Downregulated genes were involved in metabolism, antigen receptor-mediated immunity, macromolecular complex assembly, S-phase, translation elongation, RNA splicing, protein transport, and post-transcriptional regulation.  We conclude that these results emphasize that the cellular response to hypoxia involves reduced metabolism, the involvement of the fetal immune system, and the importance of glucocorticoid signaling.

overall_design: 3 Ventilatory Hypoxia (VH) and 4 Control (con) fetuses.  All fetuses were chronically catheterized and in late gestation. Hypoxia produced by low PO2 in maternal inspired gas for 30 min, followed by normoxia recovery for 30 min. Control fetuses maintained at normoxia for 30 min, followed by another 30 min of normoxia.  Hypothalami collected for mRNA at end of normoxic recovery period.

middle: E

first: Maria

middle: B

last: Rabaglino

first: Eileen

last: Chang

first: Nancy

last: Denslow

first: Maureen

last: Keller-Wood

first: Elaine

last: Richards


title: Subcutaneous adipose tissue gene expression in PCOS, compared with age and BMI-matched healthy controls

city: Dublin

first: Melissa

last: Morine

address: Belfield

country: Ireland

institute: University College Dublin

summary: Subcutaneous adipose tissue gene expression profiles from women with PCOS, compared with age and BMI matched healthy controls (matched at group-level).

overall_design: A cross-section comparison was made between women with and without PCOS

first: Annalouise

last: O'Connor


title: Subcutaneous adipose tissue gene expression in PCOS

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

overall_design: Refer to individual Series


title: Influence of lysophosphatidic acid (LPA) and LPA together with interferon tau (IFNt) on transcriptional profiling of bovine endometrial cells.

city: Olsztyn

first: Dorota

last: Boruszewska

address: Tuwima 10

department: Department of Reproductive Immunology and Pathology

country: Poland

institute: PAS

summary:
The endometrium plays a crucial role in the reproductive organs in the aspect of embryo-maternal communication and pregnancy. This study investigated transcriptome profiles of endometrial cells stimulated with PBS, LPA and LPA in combination with IFNt. LPA, one of the signaling molecule, is locally produced and released from the bovine endometrium during estrous cycle and early pregnancy. The highest concentration of LPA and expression of its active receptor (LPAR1) were detected in bovine endometrium at the time of maternal recognition of pregnancy, when the conceptus announces its presence by increased IFNt production.
Using transcriptomic approach we compared the influence of LPA and LPA together with IFNt on the gene expression profiles in bovine endometrial cells.

overall_design: A total of nine normally cycling Holstein/Polish Black and White (75/25% respectively) cows were used in this study. Global transcriptional profiling was performed using co-cultured stromal and epithelial cells (ratio - 3:1) isolated from bovine endometrium. Three experimental conditions (control (PBS), LPA and LPA plus IFNt) with three replicates per condition were prepared. Total RNAs were extracted from 9 pooled samples (n=3 for each sample) amplified and hybridized onto Affymetrix microarrays.

first: Ilona

last: Kowalczyk-Zieba

first: Emilia

last: Sinderewicz

first: Izabela

last: Woclawek-Potocka


title: miRNA expression profiles in the 19 candidate urines (prostate cancer, CaP, patients and non-cancer subjects with benign prostatic hyperplasia, BPH)

city: Seoul

first: Jung Min

last: Kim

address: Gangnam-gu Teheran-ro 216

department: Department of Health Genomics

institute: NAR Center, Inc. & Genoplan, Inc.

summary:
The aims of the study were investigated whether expression of urinary cell-free miRNAs would be different between prostate cancer (CaP) patients and non-cancer subjects with benign prostatic hyperplasia (BPH).
Urinary cell-free miRNAs will provide potential benefits for detecting CaP, and virus-encoded hsv1-miR-H18 and hsv2-miR-H9-5p could be the important urinary diagnostic markers of CaP. It would be interesting because this is the first report about virus-encoded miRNAs related to CaP, and two miRNAs showed good diagnostic performance even in patients with PSA gray zone.

overall_design: A total 14 urines from patients with CaP (7 localized and 7 advanced stage) and 5 of BPH controls were used for miRNA array analysis.

first: Seok

last: Yun

first: Pildu

last: Jeong

first: Jung

first: Wun-Jae


title: Identification of novel mechanosensitive genes differentially regulated at 48 h timepoint in vivo using mouse carotid   artery endothelium exposed to disturbed blood flow

status: Public on Jan 13 2014

city: Atlanta

first: Sandeep

last: Kumar

state: GA

address: 1760 Haygood Dr.

department: Biomedical Engineering

institute: Emory University

summary: Recently, we showed that disturbed ﬂow caused by a partial ligation ofmouse carotid artery rapidly induces atherosclerosis. Analysis of mechanosenstive microRNA in the mouse carotid endothelium.  In this study, we examined the microRNAs that respond differentially to blood flow pattern in the mouse carotid endothelium.  We surgically induced disturbed blood flow in the left common carotid cartery (LCA) using partial carotid ligation surgery while the right carotid artery was left undisturbed.  The hypothesis tested here is that turbulent or disturbed blood flow across the left carotid artery endothelium will affect endothelial genes and microRNAS.  Identifying flow-sensitive microRNAs will provide important information about how endothelium responds to d-flow and regulates endothelial function and progression of atherosclerosis. Deter-  mining the functional importance of these novel mechanosensitive microRNAS may provide important insights into understanding vascular biology and atherosclerosis.

overall_design: We used 6- to 8-week-old male C57Bl/6 mice (The Jackson Laboratory) according to the approved Institutional Animal Care and Use Committee protocol by Emory University. Mice were subjected to partial carotid ligation surgery under anesthesia.  Brieﬂy, 3 of 4 caudal branches of LCA (left external carotid, internal carotid, and occipital artery) were ligated with 6-0 silk suture, although the superior thyroid artery was left intact. Development of low and oscillatory blood flow in the Left Carotid Artery of each mouse was determined by ultrasound measurements.

first: Dong

last: Son

first: Wakako

last: Takabe

first: Chan

middle: W

first: Chih-Wen

last: Ni

first: Hanjoong

last: Jo


title: The Histone H3 Lysine 9 Methyltransferases G9a and GLP Regulate Polycomb Repressive Complex 2-Mediated Gene Silencing [Affymetrix]

city: Paris

first: PONTIS

last: Julien

address: 35, rue Hélène BRION

country: France

institute: UMR7216 CNRS

summary: G9a/GLP and Polycomb Repressive Complex 2 (PRC2) are two major epigenetic silencing machineries, which in particular methylate histone H3 on lysines 9 and 27 (H3K9 and H3K27), respectively. Although evidence of a crosstalk between H3K9 and H3K27 methylations has started to emerge, their actual interplay remains elusive. Here, we show that PRC2 and G9a/GLP interact physically and functionally. Moreover, combining different genome-wide approaches, we demonstrate that Ezh2 and G9a/GLP share an important number of common genomic targets, encoding developmental and neuronal regulators. Furthermore, we show that G9a enzymatic activity modulates PRC2 genomic recruitment to a subset of its target genes. Taken together, our findings demonstrate an unanticipated interplay between two main histone lysine methylation mechanisms, which cooperate to maintain silencing of a subset of developmental genes.

overall_design: Microarray has been perform in triplicate on total extract RNA from mES cell (TT2 : Wildtype and KOs G9a-/-, GLP-/-, G9a-/- and GLP-/-)

first: Julien

last: Pontis

first: Chiara

last: Mozzetta

first: Slimane

last: Ait-Si-Ali


title: Circadian behavior is light-reprogrammed by plastic DNA methylation

city: Zurich

first: Steven

last: Brown

state: Switzerland

address: Winterthurerstrasse 190

department: Institute of Pharmacology and Toxicology

country: Switzerland

institute: University of Zurich

summary:
The timing of daily “circadian” behavior can be highly variable among different individuals, and twin studies suggest that about half of this variability is environmentally controlled.  Similar plasticity can be seen in mice exposed to an altered lighting environment – for example, 22-hour days instead of 24-hour ones – which stably alters the genetically determined period of circadian behavior for months.  The mechanisms mediating these environmental influences are unknown.  Here, we show that transient exposure of mice to such lighting stably alters global transcription in the suprachiasmatic nucleus of the hypothalamus (the SCN, the “master clock” tissue determining circadian behavior in mammals). We have also showed that, these changes in transcription are due to change in DNA methylation in the SCN. Indeed, genome-wide methylation profiling revealed global alterations in promoter DNA methylation in the SCN.  Importantly, infusion of a methyltransferase inhibitor to the SCN during 22-hour days suppressed period changes.  We also found that these behavioral and DNA methylation changes are reversible upon entrainment to 24-hours days. We conclude that the SCN utilizes DNA methylation as a mechanism to drive circadian clock plasticity.
MeDIP array of profiling,  demonstrated that genomicDNA methylation changes in mice entrained to short-T cycle.

overall_design: comparison of methylation profile in the suprachiasmatic nuclei of mice entrained to normal T-cycle and short T-cycle

first: Abdelhalim

last: Azzi


title: ChIP-chip from lymph node-derived primary lymphocytes with anti-E2F2 and anti-SV40TAg

city: Cambridge

first: Usue

last: Laresgoiti

address: Tennis Court Road

country: United Kingdom

institute: University of Cambridge

summary:
E2F2 is essential for the maintenance of T lymphocyte quiescence. To identify the full set of E2F2 target genes, and to gain further understanding of the role of E2F2 in transcriptional regulation, we have performed ChIP-chip analyses across the genome of lymph node-derived T lymphocytes.
Here we show that during quiescence, E2F2 binds the promoters of a large number of genes involved in DNA metabolism and cell cycle regulation, concomitant with their transcriptional silencing.

overall_design: We performed 3 ChIP-chip experiments with an antibody against E2F2 and another 3 ChIP-chip experiments with an antibody against SV40TAg (irrelevant antibody).

first: Usua


title: scAT gene expression from women with PCOS following LC n-3 PUFA or placebo supplementation

first: Melissa

last: Morine

summary:
Gene expresion profiles from the scAT following 6 week LC n-3 PUFA and 6 week placebo supplementation were compared
Women with PCOS were supplemented with 4g n-3 PUFA (containing 1.8g EPA and DHA) daily for 6 weeks and changes in subcutaneous adipose tissue gene expression was compared with 6 week placebo supplementation.

overall_design: This was a cross-over placebo, controlled dietary intervention wherein women with PCOS received both treatments.

first: Annalouise

last: O'Connor


title: In situ synthesis of peptide microarrays - shadow mask design

city: Tempe

first: Phillip

last: Stafford

state: Arizona

address: 727 E. Tyler St.

institute: Arizona State University


title: Formaldehyde-induced changes in microRNA signaling [Agilent]

city: Chapel Hill

first: Rebecca

middle: Catherine

last: Fry

address: 1213 MHRC

department: Environmental Sciences and Engineering

institute: UNC-Chapel Hill

summary: MicroRNAs (miRNAs) are critical regulators of gene expression, yet much remains unknown regarding miRNA changes resulting from environmental exposures and whether they influence pathway signaling across various tissues and time. To gain knowledge on these novel topics, we set out to investigate in vivo miRNA responses to inhaled formaldehyde, an important air pollutant known to disrupt miRNA expression profiles. Rats were exposed by inhalation to either 0 or 2 ppm formaldehyde (6 hours/day) for 7 days, 28 days, or 28 days followed by a 7 day recovery. Genome-wide miRNA expression profiles and associated signaling pathways were assessed within the nasal respiratory mucosa, circulating mononuclear white blood cells (WBC), and bone marrow (BM).

overall_design: Male Fischer rats received nose-only inhalation exposures of 2 ppm formaldehyde. Three exposure durations were investigated: (1) 2 ppm formaldehyde exposure, 6 hours/day, for 7 days (7-day group), (2) 2 ppm formaldehyde exposure, 6 hours/day, for 28 days (28-day group), and (3) 2 ppm formaldehyde exposure, 6 hours/day, for 28 days, with a 7 day recovery period following the last exposure (28-day plus recovery group). Control (unexposed) rats were placed in nose-only exposure tubes containing room air for the same duration. After the last exposure period (or the last recovery period for the 28-day plus recovery group), animals were euthanized. RNA were assessed from sampes collected from the nasal epithelium, circulating white blood cells, and bone marrow cells. Genome-wide miRNA expression profiles were evaluated using microarrays.

first: Julia

last: Rager

first: Lisa

last: Smeester

first: Benjamin

middle: C

last: Moeller

first: Melanie

last: Doyle-Eisele

first: James

middle: A

last: Swenberg


title: miRNA expression data in tooth germs at embryonic day 11, 12, 14, and 16

first: Eun-Jung

last: Kim

address: 50 Yonsei-ro

department: Department of Oral Biology

country: South Korea

institute: Yonsei Universiry

summary: miRNAs are not well known their expression and function in tooth development. To identify the miRNAs expression during tooth development, tooth germs were dissected from the initiation bud, cap and bell stages.

overall_design: miRNA-chip expression analysis was performed with RNAs of the molar tooth germs from embryos of pregnant mice at emrbryonic day 11, 12, 14, and 16, using Agilent's miRNA microarray.

first: Eun

middle: J

first: Min

last: Lee

first: Liwen

last: Li

first: Kyung

middle: S

last: Yoon

first: Kye

first: Han

last: Jung


title: Involvement of viral miRNA in the regulation of antiviral apoptosis in shrimp

city: hangzhou

first: Tianzhi

last: Huang

address: HANGZHOU

institute: ZJU

summary: In this study, the viral miRNAs from white spot syndrome virus (WSSV) were characterized in shrimp in vivo. On the basis of our previous study and small RNA sequencing in this study, a total of 89 putative WSSV miRNAs were identified. As revealed by miRNA microarray analysis, the expressions of viral miRNAs were tissue-specific in vivo.

overall_design: In this study, the viral miRNAs from white spot syndrome virus (WSSV) were characterized in shrimp in vivo. On the basis of our previous study and small RNA sequencing in this study, a total of 89 putative WSSV miRNAs were identified. As revealed by miRNA microarray analysis and Northern blots, the expressions of viral miRNAs were tissue-specific in vivo. Therefore, our study presented the first report on the in vivo molecular events of viral miRNA in the antiviral apoptosis.

first: Yalei

last: Cui

first: Xiaobo

last: Zhang


title: use of aCGH in a large series of prenatal samples

city: BARCELONA

first: Lluis

last: Armengol

state: Catalonia

address: Doctor Aiguader, 88

country: Spain

institute: qGenomics

summary: we have conducted a comparative study of the different technologies available for the detection of chromosomal abnormalities in prenatal samples. Here we include results of the aCGH experiments

overall_design:
this series is composed of internal controls plus a year-long (2009-2010) consecutive series of pregnant women with indication for prenatal screening of chromosomal abnormalities
a pdf and txt version of the table with 'sample name' plus relevant sample characteristics, including chromosomal abnormalities identified in our work is provided as a supplementary file on the Series record (below).


title: An Ribonuclease T2 Family Protein Modulates Acinetobacter baumannii Abiotic Surface Colonization

status: Public on Jan 01 2014

city: Rochester

first: Paul

last: Dunman

address: 601 Elmwood Avenue

department: Microbiology and Immunology

institute: University of Rochester

summary:
A. baumannii has the propensity to colonize abiotic surfaces and this is thought to mediate its transmission to susceptible patients.
We found that disruption of A. baumannii ribonuclease T2 family protein (ATCC 17978 locus A1S_3026) severely diminishes the organism's ability to colonize abiotic surfaces.
We used Affymetrix A. baumannii GeneChips (part number PMDACBA1) to compare the gene expression properties of wild type and isogenic ribonuclease T2 family protein mutant cells.

overall_design: A. baumanni strain 98-37-09 (wild type) or isogenic ACJ7 (harboring a EZ-Tn5 insertion in A1S_3026) cells were grown to mid-exponential phase growth in Luria Burtani medium, total bacterial RNA was isolated and subjected to GeneChip hybridization and analysis.  We sought to determine the regulatory effects of A1S_3026.

first: Yoshihiko

last: Murata


title: Comparison of hypoxia (4 % O2) cultured human embryonic stem cells (hESCs) to normoxia (21 % O2) cultured

status: Public on Jan 02 2014

city: Turku

first: Elisa

last: Närvä

address: Tykistökatu 6

department: Turku Centre for Biotechnology

country: Finland

institute: University of Turku

summary:
We compared the transcriptome at gene expression level in hypoxic and normoxic conditions.
The transcriptome of cells cultured at three different timepoints, 2h, 24 h and 7 days with three different cell lines in normoxia and hypoxia was compared

overall_design: 18 samples total, 3 replicates in each conditions, 2h, 24 h and 7day timepoints in hypoxia and normoxia

first: Asta

last: Laiho


title: Effect of selection on residual feed intake on gene expression in porcine subcutaneous adipose tissue (20 kg body weight)

city: Saint-Gilles

first: Annie

last: Vincent

address: domaine de la prise

institute: INRA

summary: Transcriptional profiling in subcutaneous adipose tissue of 16 pigs of 20 kg body weight from lines divergently selected for residual feed intake (RFI): low-RFI pigs (RFIneg), high-RFI pigs (RFIpl) .

overall_design: Two conditions experiment: low-RFI (RFIneg), high-RFI (RFIpl) . 8 pigs in RFIneg stain and 8 pigs in RFIpl stain . One replicate per array.

first: Isabelle

last: Louveau


title: Effect of selection on residual feed intake on gene expression in pig skeletal muscle (20 kg body weight)

summary: Transcriptional profiling in skeletal muscle of 15 pigs of 20 kg body weight from lines divergently selected for residual feed intake (RFI): low-RFI pigs (RFIneg), high-RFI pigs (RFIpl) .

overall_design: Two conditions experiment: low-RFI (RFIneg), high-RFI (RFIpl) . 7 pigs in RFIneg stain and 8 pigs in RFIpl stain . One replicate per array.


title: Effect of selection on residual feed intake on gene expression in pig subcutaneous adipose tissue (115 kg body weight)

summary: Transcriptional profiling in subcutaneous adipose tissue of 24 pigs of 115 kg body weight from lines divergently selected for residual feed intake (RFI): low-RFI pigs (RFIneg), high-RFI pigs (RFIpl) and high-RFI pigs restricted at RFIneg feeding level (RFIplR) to investigate the impact of feeding independently of selection.

overall_design: Three conditions experiment: low-RFI (RFIneg), high-RFI (RFIpl) and restricted high-RFI (RFIplR). 8 pigs per condition. One replicate per array.


title: Expression Data from E. faecalis V583 under exposure to 10ug/ml vancomycin

city: Oeiras

first: Neuza

last: Teixeira

address: Av. da República, Estação Agronómica Nacional

institute: ITQB

summary: The vancomycin resistant strain V583 was exposed to therapeutical dose of vancomycin in order to understand the cell response to the antibiotic besides the induction of the vanB genes

overall_design: E. faecalis V583 cells were collected at 10 minutes and 30 min after vancomycin addition and without vancomycin, for RNA extraction and hybridization on Affymetrix microarrays. The cells were collected when at 0.4. For each condition were made replicates.

first: Ribeiro

last: Tânia

first: Teixeira

last: Neuza

first: Yokohata

last: Ryoji

first: Nakayama

last: Jiro

first: Gilmore

last: Michael S.

first: Lopes

last: Maria de Fátima Silva


title: Genome-wide gene expression analysis of Cirh1a heterozygote state on early embryo in mice

city: Montreal

first: Andrea

last: Richter

state: Quebec

address: 3175 chemin Côte-Ste-Catherine

department: Service de Génétique Médicale

institute: CHU Sainte-Justine

summary:
CIRHIN is a transcription co-factor, shows postive effect on Hiv-1 LTR enhancer element(NF-κB site); and Cirh1a null is preimplantation lethal, but highly expressed in the early mice embryo (E6.0-E12.5). We hypothesis that Cirh1a's  effect on gene transcription of early embryo  can be detected with Cirh1a down regulated in Cirh1a+/- state.
Result shows that Cirh1a+/- has significant effect on early mice embryo gene transcription, Differentially expressed genes (DEGs) detected are mainly involved in cell proliferation/differenciation, cell cycle progress, embryo development and multi-orgnaogenesis.

overall_design:
Littermate embryos (E8.5) were dissected into RNAlater reagent for total RNA extraction, and yolk sac was used for genotyping PCR.
Littermate embryos (E9.5) were dissected into RNAlater reagent for total RNA extraction, and yolk sac was used for genotyping PCR.
Liver buds from littermate embryos (E11.5) were dissected into RNAlater reagent for total RNA extraction, and yolk sac was used for genotyping PCR.
Liver buds from littermate embryos were dissected into RNAlater reagent for total RNA extraction, and yolk sac was used for genotyping PCR.

first: Bin

last: Yu


title: Transcriptional profiles of wild-type NCTC11168 and Cj0480c mutant grown without fucose

city: SARANAC LAKE

first: Wayne

last: Muraoka

address: 154 Algonquin Ave

institute: Trudeau Institute

summary: Strain specific growth of C. jejuni on fucose has been linked to a plasticity region of the chromosome (PR2) and confers a competitive advantage during intestinal colonization.  Growth on fucose induces gene expression of PR2 genes, but the regulatory mechanism of the structural genes involved with fucose utilization is unknown.  A mutant was constructed to examine the role of Cj0480c, a putative IclR-type transcriptional regulator, on PR2 gene expression.  Transcriptional profiles of wild-type C. jejuni and the Cj0480c mutant strain grown without fucose may provide insight in to the extent of the fucose regulon and genes that are necessary for fucose utilization.

overall_design: The design utilized an available two color microarray slide for the entire transcriptome of Campylobacter jejuni wild type strain NCTC 11168. Each sample represents one competitive hybridization: wild-type NCTC 11168 v.s. Cj0480c isogenic mutant. There were four biological replicates of each sample with a dye swap introduced in alternating replicates. Samples were  independently grown, treated and harvested.

middle: T

first: Qijing

last: Zhang


title: Profiling of single murine bronchioalveolar stem cells

city: Regensburg

first: Bernhard

last: Polzer

address: Franz-Josef-Strauss-Allee 11

department: Chair of Experimental Medicine and Therapy Research

country: Germany

institute: University of Regensburg

summary: Murine bronchioalveolar stem cells play a key role in pulmonary epithelial maintenance and repair but their molecular profile is poorly described so far. In this study, we used antibodies directed against Sca-1 and CD34, two markers originally ascribed to pulmonary cells harboring regenerative potential, to isolate single putative stem cells from murine lung tissue. The mean detection rate of positive cells was 8 per 106 lung cells. We then isolated and globally amplified the mRNA of positive cells to analyze gene expression in single cells. The resulting amplicons were then used for molecular profiling by transcript specific polymerase chain reaction (PCR) and global gene expression analysis using microarrays. Single marker-positive cells displayed a striking heterogeneity for the expression of epithelial and mesenchymal transcripts on the single cell level. Nevertheless, they could be subdivided into two cell populations: Sca-1+/CD34- and Sca-1+/CD34+ cells. In these subpopulations, transcripts of the epithelial marker Epcam (CD326) were exclusively detected in Sca-1+/CD34- cells (p = 0.03), whereas mRNA of the mesenchymal marker Pdgfrα (CD140a) was detected in both subpopulations and more frequently in Sca-1+/CD34+ cells (p = 0.04). FACS analysis confirmed the existence of a Pdgfrα positive subpopulation within Epcam+/Sca-1+/CD34- epithelial cells. Gene expression analysis by microarray hybridization identified transcripts differentially expressed between the two cell types as well as between epithelial reference cells and Sca-1+/CD34+ single cells, and selected transcripts were validated by quantitative PCR. Our results suggest a more mesenchymal commitment of Sca-1+/CD34+ cells and a more epithelial commitment of Sca-1+/CD34- cells. In summary, the study shows that single cell analysis enables the identification of novel molecular markers in yet poorly characterized populations of rare cells. Our results could further improve our understanding of Sca-1+/CD34+,- cells in the biology of the murine lung.

overall_design: Single cells of 10 Sca-1+/CD34+/CD31-/CD45-, 7 Sca-1+/CD34-/CD31-/CD45-, and 12 Sca-1-/CD34-/CD31-/CD45- were analyzed. Although the raw data are two channel only Cy5 signal of each file as analyzed. The Cy5 channel for each gene is normalized to the average Cy5 intensity of the gene across all samples.

first: Markus

last: Hittinger

first: Zbigniew

last: Czyz

first: Yves

last: Hüsemann

first: Matthias

last: Maneck

first: Catherine

last: Botteron

first: Stephanie

last: Kaeufl

first: Christoph

last: Klein


title: Transcriptional profiles of NCTC11168 grown with or without 25mM fucose

summary: Strain specific growth of C. jejuni on fucose has been linked to a plasticity region of the chromosome (PR2) and confers a competitive advantage during intestinal colonization.  Growth on fucose induces gene expression of PR2 genes, but the regulatory mechanism of the structural genes involved with fucose utilization is unknown.  Additionally, the mechanism of fucose dissimilation by C. jejuni is not known since no fucose catabolism homologs are found in the C. jejuni genome. Transcriptional profiles of C. jejuni grown with and without fucose may provide insight in to the genes that are necessary for fucose utilization.

overall_design: The design utilized an available two color microarray slide for the entire transcriptome of Campylobacter jejuni wild type strain NCTC 11168. Each sample represents one competitive hybridization: sham-treated NCTC 11168 v.s. 25mM fucose treated NCTC 11168. There were four biological replicates of each sample with a dye swap introduced in alternating replicates. Samples were  independently grown, treated and harvested.


title: microRNA expression profile of wogonin treatment in HNSCC cell lines

city: Chiba city

first: Naohiko

last: Seki

state: Chiba

address: Inohana1-8-1, Chuo-ku

country: Japan

institute: Chiba University

summary: To identify microRNAs induced by wogonin treatment, human head and neck squamos cell carcinoma cell lines were subjected to miRCURY LNA microRNA Array.

platform_organism:
Homo sapiens
Mus musculus
Rattus norvegicus

overall_design: FaDu and SAS cell lines were treated with 10 ug/ml wogonin or DMSO for 72h and total RNAs were extracted. Defferentially expressed microRNAs were analyzed by miRCURY LNA microRNA Array.


title: Transcriptome of pvcA mutant as compared to parent strain of pseudomonas aeruginosa

city: Lubbock

first: Uzma

last: Qaisar

state: TX

institute: Texas Tech University

summary: Pseudomonas aeruginosa is a gram negative pathogen that infects acute wounds such as third degree skin injury and chronic wounds such as diabetic ulcers. Within infection sites, this pathogen exists in specific structures termed as biofilms. Biofilms contribute to enhanced resistance of microorganisms to the host defense and antibiotic treatments. Flagella, pilli and chaperon usher pathway (cup) fimbriae provide initial attachment to host tissue during biofilm development. pvcA-D operon codes for proteins which synthesize a secondary metabolite called paerucumarin. Paerucumarin is an isonitrile functionalized cumarin which is not extensively analyzed. We recently showed that paerucumarin enhances the expression of cup genes and biofilm development. We hypothesize that besides the cup genes pvcA-D operon regulates other P. aeruginosa genes. To test this hypothesis, we compared the transcriptome of P. aeruginosa strain MPAO1 with its pvcA mutant (MPAO1/pvcA). In comparison with MPAO1, 53 genes were differentially expressed in pvcA which included 19 up-regulated and 34 down-regulated genes. Functional characterization of differentially expressed genes indicated that 20 of these genes have been reported as iron regulated genes. Real time PCR confirmed these results and indicated that the expression of pvcAD operon is iron independent. However traditional chrome azurol S (CAS) iron binding assay showed that paerucumarin binds iron either within supernatants of MPAO1 or in solution. In addition, exogenously added paerucumarin enhances the expression of iron repressed genes pvdS and pvdA. Similarly, the level of pvdS gene expression in MPAO1?pvcA was significantly reduced as compared to MPAO1. Further analysis confirmed that paerucumarin binds iron in MPAO1 but does not deliver it inside the cell. The growth of a PAO1 double mutant strain (?pvdD?pchA), defective in iron scavenging systems, grown in iron deficient medium was restricted. However, the growth was restricted even further upon addition of exogenous paerucumarin to bacterial cultures. These results suggest that paerucumarin chelates iron but does not function as an iron scavenging system.

overall_design: 4 biological replicates of each strain were randomly paired

first: Muhammed

last: Azeem

first: Abdul

last: Hamood