title: Transcriptional Analysis of Rind Separation in Mandarin Oranges

status: Public on May 08 2010

city: Riverside

first: Livia

last: Tommasini

state: CA

address: 2150 Batchelor Hall

department: Botany and Plant Science

country: USA

institute: University of California, Riverside

summary: In mandarin (Citrus reticulata Blanco), rind separation is an essential trait for marketing, as it confers easy-peeling, an inheritable trait whose genetic basis has not yet been characterized. To this end, we used the 30 K Affymetrix Citrus GeneChip to compare gene expression in albedo tissues of an easy-peeling genotype (Clementine Nules) to a less easy-peeling hybrid genotype (Lee x Nova, USDA 88-2) at three time points: before, at and after the onset of rind separation. A high percent of genes were detected reliably by the chip (76.1 %), and Principal Component Analysis (PCA) based on these genes showed that three replicates were well clustered, indicating the reliability of the data set. Functional analysis of genes showing >5-fold difference in expression between Clementine Nules and Lee x Nova across three developmental points suggested that the transcriptome of the two varieties diverges as the maturation process advances. A pectin methylesterase was expressed at levels more than 100-fold higher in Clementine Nules than in Lee x Nova at all three time points and two genes encoding for pectinases were more than 10-fold higher in Clementine Nules than in Lee x Nova during the last sampling time. Different hydrolases, a glucanase and a carbohydrate kinase were higher in Nules than in Lee x Nova. Higher expression of two cellulose synthases, an expansin and an aquaporin was observed in the easy peel genotype Clementine Nules. The difference between Clementine Nules and Lee x Nova at the transcript level suggests that three main molecular mechanisms are involved in the easy peeling trait: 1) lower cell adhesion, 2) pronounced degradation of albedo cell wall polysaccharides, and 3) high and extended cell expansion rate of the rind.

overall_design: We used the 30 K Affymetrix Citrus GeneChip to compare gene expression in albedo tissues of an easy-peeling genotype (Clementine Nules) to a less easy-peeling hybrid genotype (Lee x Nova, USDA 88-2) at three time points (16 arrays): before, at and after the onset of rind separation.

first: Timothy

last: Close

first: Mikeal

last: Roose

first: Chandrika

last: Ramadugu

first: Claire

last: Federici

first: Raymond

last: Fenton


title: Array comparative genomic hybridization analysis of flat epithelial atypia (DIN1a) and lobular intraepithelial neoplasia

status: Public on May 05 2010

city: Berlin

first: Reinhard

last: Ullmann

department: Human Molecular Genetics

country: Germany

institute: MPIMG

type: Genome variation profiling by genome tiling array

summary: Low grade flat ductal intraepithelial neoplasia (DIN1a, flat epithelial atypia) is one of the earliest morphologically recognizable neoplastic lesions of the breast. Frequently, it occurs in association with lobular intraepithelial neoplasia (LIN). The aim of this study was to elucidate chromosomal aberrations in these early neoplastic breast lesions using array comparative genomic hybridization (CGH) analysis. Laser capture microdissection of 12 archival formalin-fixed, paraffin-embedded specimens harbouring both foci of DIN1a as well as LIN was performed. All analyzed cases of DIN1a and LIN showed chromosomal gains and losses. The aberration encountered most often was loss on 16q in 7 DIN1a (70%) and 10 LIN (91%) cases. Regarding changes in chromosome 1, four DIN1a (40%) and 7 LIN (64%) cases showed a gain on 1q. The results of our study show concurrent chromosomal aberrations of 1q gains and 16q losses in several cases with coexisting LIN and low grade flat DIN. These aberrations are known to be common in low grade invasive ductal carcinomas as well as more advanced (conventional) types of low grade DIN (low grade ductal carcinoma in-situ). Our results raise the possibility of similar molecular-genetic pathways in most of the cases with coexisting LIN and low grade flat DIN.

overall_design:
In this study, 11 cases of classic lobular intraepithelial neoplasias and 10 cases with several areas of low grade flat DIN (DIN1a or flat epithelial atypia) were analyzed by array CGH. Sections of formalin-fixed paraffin-embedded (FFPE) specimens cut at 7-8µm were mounted on special foil-coated slides (Molecular Devices, San Diego, USA). The sections were then deparaffinized with Xylene, processed in decreasing concentrations of ethanol and stained with haematoxylin. Lasercapture microdissection for both lesions was performed at multiple sites using Veritas Arcturus. For reference-DNA, female mammary tissue without histomorphological changes obtained from reduction mammoplasty specimens was procecessed and laser-microdissected as explained above.

Cells were digested in 10µl TE, pH 9, and 0.5µl proteinase K (20mg/ml) for 48h at 55°C. After inactivation of proteinase K at 99°C for 10min, the digest was stored at -20°C. Without any further purification, the complete digest was used for whole genome amplification by means of the WGA (Whole Genome Amplification) kit from Sigma following the manufacturer’s recommendations. Array CGH was performed as described previously. In brief, two µg of amplified tumor and reference DNA were labelled by random priming (BioPrime® Total Genomic Labeling System, Invitrogen, Carlsbad, CA) with Alexa Fluor® 3 and Alexa Fluor® 5, respectively, and hybridized onto a tiling path BAC array, consisting of the human 32k BAC Re-Array Set (BACPAC Resources Center; http://bacpac.chori.org/pHumanMinSet.htm; DNA kindly provided by Pieter de Jong) and a 1Mb Resolution BAC set (clones kindly provided by Nigel Carter, Wellcome Trust Sanger Centre). All protocols are provided in detail on our website (http://www.molgen.mpg.de/~abt_rop/molecular_cytogenetics/) and more information concerning this platform have been submitted to the Gene Expression Omnibus (GEO; http://www.ncbi.nlm.nih.gov/geo/; GPL5114). For the analysis and visualization of array CGH data, our software-package CGH-PRO was employed. No background subtraction was applied. Raw data were normalized by “Subgrid LOWESS”. For the assessment of copy number gains and losses, we used circular binary segmentation in combination with log2 ratio thresholds of 0.15 and -0.15, respectively.

first: R


title: Microarray analyses of lymph node dendritic cells (DCs) stimulated in vitro with papain or LPS

city: SÃO PAULO

first: Helder

middle: I.

last: Nakaya

state: SÃO PAULO

address: AVENIDA PROFESSOR LINEU PRESTES, 580, Block 17

country: Brazil

institute: Universidade de São Paulo

summary:
T helper type 2 (Th2) responses are induced by protease allergens and helminthes. However the molecular mechanisms that initiate Th2 responses are poorly understood. To obtain insight into this mechanism, we performed a microarray analysis of lymph node DCs stimulated in vitro with the protease allergen papain, or with LPS, a Th1 inducing stimulus.
Key words: Th2 response, LPS, dendritic cells, Papain

overall_design: CD11c+ DCs were isolated from the lymph nodes of C57BL/6 mice, and cultured in vitro (1x106 DCs per ml) with 500 3T3-CD40L fibroblasts, either alone, or in the presence of papain (25 µg/ml) or LPS (1 µg/ml).  4h and 17h later, the cells were harvested and RNA isolated and processed for microarray analyses. RNA was extracted and processed from freshly isolated LN DCs. For a given time point, the expression profile of DCs treated with papain or LPS, were compared to that of untreated DCs

first: Hua

last: Tang

first: Bali

last: Pulendran


title: Gene expression profile of N+ and N0 HNSCC

status: Public on May 28 2010

city: Sao Paulo

first: Anna

last: Coló

address: Rua Professor Antonio Prudente, 211

institute: Hospital A.C. Camargo

summary:
Head and neck squamous cell carcinomas (HNSCCs) is the seventh most common solid malignancy in the United States, accounting for more than 47,000 new cancer cases. Surgery of patients clinically diagnosed with lymph node metastasis (N+) also involves neck dissection, which causes disfigurement and pain. However, after histological examination, more than 30% of clinically N+ patients turn out to be metastasis-free (N0).
Clinically negative lymph node patients have occult node metastasis in up to 50% of the cases. Within two years of follow-up these patients may or may not develop metastatic disease. On the other hand, around 50% of N0 patients do not have occult node metastasis. Therefore, many N0 patients undergo neck dissection unnecessarily. Due to limitations in detecting lymph node metastasis before surgery, both N+ and N0 patients may receive inappropriate treatment. This indicates that a better understanding of the biology of HNSCC is urgently needed.
Despite tumor complexity, many studies have tried unsuccessfully to test single genes to be used as prognostic markers in HNSCC. A group of tumor samples can be characterized in terms of the behavior of modules. These modules include clusters of coexpressed genes, such as genes that belong to the same pathway or functional category.
Cancer is a multifaceted phenomenon that involves activation and/or disruption of various cellular processes. Thus, the identification of pathways or group of genes such as those involved in the development of lymph node metastasis and recurrent disease may help understanding the complex biology of cancer.

overall_design:
Samples were obtained during surgery and neck dissection of 81 patients with primary untreated HNSCC at the Head and Neck Surgery Department from the Hospital AC Camargo (São Paulo, Brazil) between 1998 and 2003. Diagnosis of HNSCC was determined by biopsy. All patients signed a pre-informed consent and the study was approved by our institutional review board. After surgery, all patients were treated with adjuvant radiotherapy. Tumor samples were snap-frozen in liquid nitrogen. Before RNA extraction, diagnosis was confirmed by hematoxylin-eosin staining. Frozen samples were hand dissected for removal of normal cells, necrosis, and infiltrating inflammatory cells.
Total RNA was extracted using TRIzol. RNA quality was accessed by spectrophotometry and gel electrophoresis. To be considered as high-quality, the RNA had to have a 260/280 ratio higher than 1.7 and a 18S/28S rRNA ratio ~2. Amplifictaion of the mRNA was done using a T7-based protocol and cDNA was indirectly labeled with Alexa Dye 555 or 647. Samples and a common RNA reference were hybridized overnight at 42oC in dye-swap to a 4,800-element in-house printed microarray, enriched with cancer-related ESTs derived from the Human Cancer Genome Project. After washing, slides were scanned on a confocal laser scanner and data were extracted.

first: Alex

last: Carvalho

first: Luiz

last: Reis

first: André

last: Kowalski

first: Ana

last: Simões

first: Eduardo

last: Neves

first: Lucas

last: Fahham

first: Louise

last: Mota

first: Waleska

last: Martins

first: Hugo

last: Campos

first: Bianca

last: Barreto

last: Pagotto

first: Sarah

last: Marques

first: Mariana

first: Chamberlein

last: Neto


title: Expression analysis of Clostridium acetobutylicum ATCC 824 grown on different carbohydrates

status: Public on May 15 2010

city: Adelphi

first: Christian

last: Sund

state: MD

address: 2800 Powder Mill Road

institute: US Army Research Laboratory

summary: Investigation of whole genome gene expression levels in Clostridium acetobutylicum strain 824 grown individually on starch, galactose, lactose, mannose, fructose, glucose, arabinose, xylose, cellobiose, maltose, sucrose

overall_design: A 33 array study using total RNA recovered from three separate wild-type cultures of Clostridium acetobutylicum 824 grown on each of the following sugars: starch, galactose, lactose, mannose, fructose, glucose, arabinose, xylose, cellobiose, maltose, sucrose.  RNA extraction, cDNA production, and labeling were performed independently on three separate cultures for each carbohydrate.  Each independent sample was hybridized to one array equating to one technical replicate for each biological sample and three biological replicates for each condition tested.  Each array contains 2 replicates of 9 probes approximately 60 bp in length for each of the 3,842 open reading frames annotated in the C. acetobutylicum 824 genome.

middle: J

first: Matthew

middle: D

last: Servinsky

first: James

middle: T

last: Kiel

first: Nicole

middle: F

last: Dupuy


title: MicroRNA expression in Sézary syndrome: Identification, function and diagnostic potential.

status: Public on May 12 2010

city: Oxford

first: charles

last: lawrie

address: John Radcliffe Hospital

department: NDCLS

country: United Kingdom

institute: University of Oxford

summary: MicroRNAs are commonly aberrantly expressed in many cancers. Very little is known of their role in T-cell lymphoma, however. We therefore elucidated the complete miRNome of purified T-cells cells from 21 patients diagnosed with Sézary syndrome (SzS), a rare aggressive primary cutaneous T-cell (CD4+) lymphoma. Unsupervised cluster analysis of microarray data revealed that the microRNA expression profile was distinct from CD4+ T-cell controls and B-cell lymphomas. The majority (104/114) of SzS-associated microRNAs (P < 0.05) were down-regulated and their expression pattern was largely consistent with previously reported genomic copy number abnormalities and were found to be highly enriched (P < 0.0001) for aberrantly expressed target genes. Levels of miR-223 distinguished SzS samples (n = 32) from healthy controls (n = 19) and patients with mycosis fungoides (n = 11) in >90% of samples. Furthermore, we demonstrate that the down-regulation of intronically encoded miR-342 plays a role in the pathogenesis of SzS by inhibiting apoptosis and describe a novel mechanism of regulation for this microRNA via binding of miR-199a* to its host gene. We also provide the first in vivo evidence for down-regulation of the miR-17-92 cluster in malignancy and demonstrate that ectopic miR-17-5p expression increases apoptosis and decreases cell proliferation in SzS cells.

platform_organism:
Gallus gallus
Homo sapiens
Mus musculus
Rattus norvegicus

overall_design: CD4+ cells were purified from peripheral blood of 21 Sz patients and compared with 6 healthy controls.

first: Erica

last: Ballabio

first: Tracey

last: Mitchell

first: Marloes

last: van Kester

first: Stephen

last: Taylor

first: Heather

last: Dunlop

first: Jianxiang

last: Chi

first: Isabella

last: Tosi

first: Maarten

last: Vermeer

first: Daniela

last: Tramonti

first: Nigel

last: Saunders

first: Jackie

last: Boultwood

first: Jim

last: Wainscoat

first: Francesco

last: Pezzella

first: Sean

last: Whittaker

first: Cornelius

last: Tensen

first: Chris

last: Hatton

first: Charles

last: Lawrie


title: aCGH of neuroblastic tumors

city: Helsinki

first: Maija

middle: K

last: Wolf

address: Biomedicum Helsinki 2U, Tukholmankatu 8,

country: Finland

institute: Institute for Molecular Medicine Finland (FIMM)

summary:
Title: Array-based gene expression, CGH and tissue data define a 12q24 gain in neuroblastic tumors with prognostic implication.
Background: Neuroblastoma has successfully served as a model system for the identification of neuroectoderm-derived oncogenes. However, in spite of various efforts, only a few clinically useful prognostic markers have been found. Here, we present a framework, which integrates DNA, RNA and tissue data to identify and prioritize genetic events that represent clinically relevant new therapeutic targets and prognostic biomarkers for neuroblastoma.
Methods: A single-gene resolution aCGH profiling was integrated with microarray-based gene expression profiling data to distinguish genetic copy number alterations that were strongly associated with transcriptional changes in two neuroblastoma cell lines. FISH analysis using a hotspot tumour tissue microarray of 37 paraffin-embedded neuroblastoma samples and in silico data mining for gene expression information obtained from previously published studies including up to 445 healthy nervous system samples and 123 neuroblastoma samples were used to evaluate the clinical significance and transcriptional consequences of the detected alterations and to identify subsequently activated gene(s).
Results: In addition to the anticipated high-level amplification and subsequent overexpression of MYCN, MEIS1, CDK4 and MDM2 oncogenes, the aCGH analysis revealed numerous other genetic alterations, including microamplifications at 2p and 12q24.11. Most interestingly, we identified and investigated the clinical relevance of a previously poorly characterized amplicon at 12q24.31. FISH analysis showed low-level gain of 12q24.31 in 14 of 33 (42%) neuroblastomas. Patients with the low-level gain had an intermediate prognosis in comparison to patients with MYCN amplification (poor prognosis) and to those with no MYCN amplification or 12q24.31 gain (good prognosis) (P = 0.001). Using the in silico data mining approach, we identified elevated expression of five genes located at the 12q24.31 amplicon in neuroblastoma (DIABLO, ZCCHC8, RSRC2, KNTC1 and MPHOSPH9). Among these, DIABLO showed the strongest activation suggesting a putative role in neuroblastoma progression.
Conclusions: The presented systematic and rapid framework, which integrates aCGH, gene expression and tissue data to obtain novel targets and biomarkers for cancer, identified a low-level gain of the 12q24.31 as a potential new biomarker for neuroblastoma progression. Furthermore, results of in silico data mining suggest a new neuroblastoma target gene, DIABLO, within this region, whose functional and therapeutic role remains to be elucidated in follow-up studies.

overall_design:
High-resolution aCGH was utilized to identify novel genetic alterations in two neuroblastoma cell lines, NGP and IMR-32. Through the integration of gene copy number and gene expression data, the impact of copy number changes on expression levels was determined. Fluorescence in situ hybridization (FISH) on a tissue microarray (TMA) format was used to assess the clinical significance of the identified copy number increase at 12q24.31 in neuroblastoma patients. Finally, we used in silico data mining of publicly available transcriptomics data, to evaluate the transcriptional consequences of the detected 12q24.31 alteration and to identify subsequently activated gene(s).

Here, aCGH of the NGP and IMR-32 cell lines was performed. Male genomic DNA was used as reference.

first: Miikka

last: Korja

first: Ritva

last: Karhu

first: Henrik

last: Edgren

first: Sami

last: Kilpinen

first: Kalle

last: Ojala

first: Spyro

last: Mousses

first: Anne

last: Kallioniemi

first: Hannu

last: Haapasalo


title: Methylation status in human sperm

city: Sendai

first: Hitoshi

last: Hiura

address: 2-1 Seiryo-cho, Aoba-ku

department: Obstetrics and Gynecology

country: Japan

institute: Tohoku University Graduate School of Medicine

type: Methylation profiling by genome tiling array

summary: Genomic imprinting describes the expression of a subset of mammalian genes from one parental chromosome. The parent-of-origin specific expression of imprinted genes relies on DNA methylation of CpG-dinucleotides at differentially methylated regions (DMRs) during gametogenesis. We identified the paternally methylated DMR at human chromosome 2 near the imprinted ZDBF2 gene using a methylated-DNA immunoprecipitation-on-chip (meDIP-on-chip) method applied to DNA from sperm.

overall_design: To analyze whether or not the GPR1-ZDBF2 DMR is conserved in human genome, methylation analysis of human sperm sample was performed using MeDIP and genome tiling array.

first: Atsushi

last: Sugawara

first: Hidehiko

last: Ogawa

first: Rosalind

middle: M

last: John

first: Naoko

last: Miyauchi

first: Yusuke

last: Miyanari

first: Tokumasa

last: Horiike

first: Yufeng

last: Li

first: Nobuo

last: Yaegashi

first: Hiroyuki

last: Sasaki

first: Tomohiro

last: Kono

first: Takahiro

last: Arima


title: Transcriptional profiling of flatfish (Solea senegalensis) spermatogenesis: early versus late spermatogenesis

status: Public on May 07 2010

city: Barcelona

first: Josep

middle: V

last: Planas

address: Av. Diagonal 643

department: Fisiologia i Immunologia (Biologia)

country: Spain

institute: Universitat de Barcelona

summary: The Senegalese sole (Solea senegalensis) is a marine flatfish of high economic value and a target species for aquaculture. Here, we used a transcriptomic approach to investigate changes in genes expressed in the Senegalese sole testis throughout spermatogenesis in wild-caught fish adapted to captivity. We identified approximately 400 genes that are differentially expressed during the progression of spermatogenesis and that participate in processes such as activation of the ubiquitin-proteasome system, sperm maturation and motility, cell adhesion or cytoskeletal remodeling. The results from this study contribute to our understanding of the molecular changes ocurring during spermatogenesis in the Senegalese sole.

overall_design:
This study represents spermatogenesis in Solea senegalensis: early versus late spermatogenesis.

Total RNA from testes at different stages in spermatogenesis (early, mid, late and functional maturation) from F0 wild Senegalese sole (3-4 animals at each stage) was extracted using the RNeasy extraction kit (Qiagen) and treated with DNAse following the manufacturer’s instructions. Quantitative and qualitative analysis of total RNA was performed using the Agilent 2100 bioanalyzer. RNA samples from each stage were pooled and amplified, labelled and hybridized to a custom-made oligonucleotide microarray containing 5,087 Senegalese sole Unigene sequences. In brief, pooled testicular RNAs from each stage were amplified and the resulting cRNAs labelled with Cy3 and Cy5, respectively, mixed in equal amounts and hybridized to the microarray for 17 h at 60 ºC. Each hybridization was performed at least in duplicate.

first: Ignasi

last: Forné

first: Barbara

last: Castellana

first: Rubén

last: Marín-Juez

first: Joan

last: Cerdà

first: Joaquin

last: Abián


title: Interactions between Streptococcus thermophilus and Lactobacillus bulgaricus in yoghurt

city: Ede

first: Sander

last: Sieuwerts

address: Kernhemseweg 2

department: Health

country: Netherlands

institute: NIZO Food Research

summary: Many food fermentations are carried out by mixed cultures of lactic acid bacteria. Interactions between strains are of key importance for the performance of these fermentations. Yoghurt fermentation by Streptoccus thermophilus and Lactobacillus delbrueckii subsp. bulgaricus (L.bulgaricus) is one of the best-described mixed culture fermentations. These species stimulate each other’s growth by the exchange of metabolites such as folic acid and carbon dioxide. Recently, post-genomic studies have been applied to reveal the global physiological response to mixed culture growth in S. thermophilus, but an in-depth molecular analysis of mixed culture growth of both strains remains to be established. Here we report the application of mixed culture transcriptome profiling and a systematic analysis of candidate interaction compounds on growth, which allowed the unraveling of the molecular responses associated with co-culture growth in batch of S. thermophilus CNRZ1066 and L. bulgaricus ATCC BAA-365 in milk.

sample_organism: Lactobacillus delbrueckii subsp. bulgaricus ATCC BAA-365

overall_design: Comparisons of mono cultures versus mixed cultures, at four time-points in batch fermentation, and comparisons between the four time-points within each fermentation, all in duplicate

first: Douwe

last: Molenaar

first: Sacha

middle: A

last: van Hijum

first: Marke

last: Beerthuyzen

first: Marc

last: Stevens

first: Patrick

middle: W

last: Janssen

first: Frank

last: de Bok

first: Willem

last: de Vos

first: Johan

middle: E

last: van Hylckama Vlieg


title: Comparison of glioblastoma tissue, glioblastoma primary culture, and normal brain

status: Public on May 06 2010

city: Seattle

first: Biaoyang

last: Lin

state: WA

address: 550 17th Ave, James Tower suite 550

department: Swedish Neuroscience Institute

institute: Swedish Medical Center

summary: Pooled samples of primary GBM tissues, primary cultures, and normal tissues were analyzed by MPSS.

overall_design: 2 Samples


title: Insert in CovS Gene Distinguishes a Pharyngeal and a Blood Isolate of Streptococcus pyogenes Found in the Same Individual.

status: Public on May 01 2010

city: Honolulu

first: Alan

middle: Francis

last: Garcia

state: Hawaii

address: 651 Ilalo Street

department: Tropical Medicine, Medical Microbiology and Pharmacology

institute: John A Burns School of Medicine

summary: Expression of the extensive arsenal of virulence factors by Streptococcus pyogenes are controlled by many regulators, of which covR/S is one of the best characterized and can influence ~15% of the genome. Animal models have established that mutants of CovR/S arise spontaneously in vivo resulting in highly invasive organisms. We analyzed a pharyngeal and a blood isolate of S. pyogenes recovered from the same individual 13 days apart. The two isolates varied in many phenotypic properties including speB production, which were reflected in transcriptome analyses. Pulsed field gel electrophoresis, multilocus sequence typing, and partial sequencing of some key genes failed to show any differences except for an 11-base insert in the covS gene in the blood isolate. These results showing that pharyngeal and blood isolates from a single individual which differ by a simple insertion, provide evidence for the model that regulatory gene mutations allow S. pyogenes to invade different niches in the body.

overall_design: A chip study using total RNA recovered from two separate wild-type cultures of group A Streptococcus, Streptococcus pyogenes UH322 and UH328. Each chip measures the expression level of 1865 genes replicated twice from 7 fully sequenced strains of Streptococcus pyogenes (M1_GAS NC_002737; MGAS10394 NC_006086; MGAS315 NC_004070; MGAS5005 NC_007297; MGAS6180 NC_007296; MGAS8232 NC_003485; SSI-1 NC_004606 with fourteen 24-mer probe pairs (PM/MM) per gene, with three-fold technical redundancy.

first: Lucienne

last: Abe


title: Analysis of extracellular matrix and adhesion molecules expression in ALL cell line

city: Morgantown

first: Stephen

last: Akers

state: WV

address: 1 Medical Center Drive P.O. Box 9300 West Virginia University Health Sciences Center

institute: West Virginia University

summary: The acute lymphoblastic leukemia cells lines JM-1, REH, Nalm-27, and SUP-B15 were analyzed for baseline expression of extacellular matrix and adhesion molecules using a pathway focused cDNA microarray (SABiosciences).

overall_design: RNA isolated from the ALL cell lines JM-1, REH, Nalm-27, and SUP-B15 was analyzed using the Extracellular Matrix and Adhesion Molecules Oligo GEArray (SABIosciences).

first: Laura

last: Gibson


title: Methylation status in AG- and PG-derived cells and sperm

first: Hitoshi

last: Hiura

summary: Genomic imprinting describes the expression of a subset of mammalian genes from one parental chromosome. The parent-of-origin specific expression of imprinted genes relies on DNA methylation of CpG-dinucleotides at differentially methylated regions (DMRs) during gametogenesis. We identified the paternally methylated DMRs at mouse chromosome 1 near the imprinted Zdbf2 gene using a methylated-DNA immunoprecipitation-on-chip (meDIP-on-chip) method applied to DNA from parthenogenetic (PG)- and androgenetic (AG)-derived cells and sperm.

overall_design: To identify novel DMRs, genome-wide methylation analysis of three samples were performed using MeDIP and whole genome tiling array.

first: Atsushi

last: Sugawara

first: Hidehiko

last: Ogawa

first: Rosalind

last: John

first: Naoko

last: Miyauchi

first: Yusuke

last: Miyanari

first: Tokumasa

last: Horiike

first: Yufeng

last: Li

first: Nobuo

last: Yaegashi

first: Hiroyuki

last: Sasaki

first: Tomohiro

last: Kono

first: Takahiro

last: Arima


title: Copy number variation in the porcine genome

city: Tjele

first: Jakob

last: Hedegaard

address: PO-box 50

department: Department of Genetics and Biotechnology

country: Denmark

institute: Aarhus University, Faculty of Agricultural Sciences

summary:
Copy number variations (CNVs), which represent a significant source of genetic diversity in mammals, are currently being associated with phenotypes of clinical relevance, mostly in humans and mice. Notwithstanding, little is known about the extent of CNV that contributes to genetic variation in farm animals, including pig.
This Nimblegen experiment reports a genome-wide high resolution map of copy number variation in the porcine genome. After remapping the initial CNV sequences to the latest genome assembly (Sus scrofa v.9), 84 CNV regions (CNVRs) were identified among the genomes of 21 related porcine samples from Duroc breed. We used a set of NimbleGen CGH arrays that tile across the assayable portion of the pig genome with approximately 2.1 million probes, at a 502 bp average probe spacing (Sus scrofa pre assembly version 6). These CNVRs covered 2 Mb of the genome, and ranged in size from 4 to 352 kb (median size of 12 kb).
Together, this analysis provides a useful resource to assist with the assessment of CNVs in the contexts of porcine variation, health and productive efficiency.

overall_design: 21 samples were analyzed in a dye swap loop design. In order to cover the latest, at the time of the experiment, porcine genome assembly (Sus scrofa v.6) with high density, custom Nimblegen HD2 CGH arrays were planned to cover all the chromosomes available with 2.1M probes, which yielded 502 bp of average probe spacing.

first: João

last: Fadista

first: Christian

last: Bendixen


title: Stp1 regulated genes in Streptococcus agalactiae strain A909

status: Public on Apr 29 2010

first: Lakshmi

last: Rajagopal

address: 1900 9th Ave

department: Pediatric Infectious Disease

institute: Seattle Children's Hospital Research Institute

summary: Genes that showed altered expression between wild type A909 and the isogenic Stp1 mutant were identified by microarray analysis

overall_design: Deletion mutants were examined for changes in gene expression

first: Kellie

last: Burnside

first: Melissa

last: delosReyes


title: Analysis of human neurotrophins and receptors in bone marrow stromal cells (BMSC) treated with NGF or BDNF

first: Stephanie

last: Rellick

summary: BMSC gene expression profiling was completed to examine the baseline neurotrophin and receptor gene expression in BMSC and to evaulate changes in gene expression in response to NGF or BDNF stimulation

overall_design: In the study, primary BMSC were treated with recombinant human NGF or BDNF for 24 hours.  Following treatment,  RNA isolated from the BMSC were analyzed using the Human Neurotrophin and Receptor Gene Array HS-018

first: Fariba

last: Rezaee

middle: L

first: Laura

last: Gibson


title: Dermatophytes CGH based on a Trichophyton rubrum cDNA microarray

status: Public on May 04 2010

city: Beijing

first: Qi

last: Jin

state: Beijing

address: No.6 Rongjing East Street, BDA

country: China

institute: National Institute for Viral Disease Control and Prevention

summary:
A cDNA microarray was constructed from the expressed sequence tags (ESTs) of different developmental stages, and comparative genome hybridization based on microarray procedures were carried out.

Dermatophyte species are classified into three genera: Epidermophyton, Microsporum, and Trichophyton. To determine the relationship between these three groups comparative genome hybridization were used in our experiment. Trichophyton rubrum genmic DNA was reference DNA and labelled by Cy3 while the other dermatophytes genomic DNA were test DNA and labelled by CY5. Test and reference DNA were co-hybridized with the T. rubrum cDNA microarray and the numbers of genes shared between each species and T. rubrum were determined.
Keywords: Comparative Genomic Hybridization

sample_organism:
Trichophyton rubrum
Trichophyton schoenleinii
Trichophyton violaceum
Epidermophyton floccosum
Trichophyton benhamiae
Nannizzia gypsea
Microsporum canis
Trichophyton verrucosum
Trichophyton soudanense
Arthroderma uncinatum
Microsporum ferrugineum
Microsporum distortum
Nannizzia nana
Nannizzia racemosa
Trichophyton longifusum
Paraphyton cookei
Lophophyton gallinae
Arthroderma terrestre

overall_design: We used a Trichophyton rubrum cDNA microarray prepared in our lab through comparative genome hybridization of genomic DNA of 21 dermatophyte strains (belonging to 20 species) to elucidate the taxonomy and evolution profiles of 20 dermatophyte species. The numbers of genes shared between each species and T. rubrum were determined. Each strain DNA hybridized for 3 times. The slides were separated into three groups base on different datasets.

first: Lingling

last: Wang

first: Li

last: Yang


title: Investigating the epigenetic effects of a prototype smoke-derived carcinogen in human cells

city: Duarte

first: Xiwei

last: Wu

address: 1500 E. Duarte Rd.

department: Computational and Quantitative Medicine

institute: City of Hope National Medical Center

summary: Global loss of DNA methylation and locus/gene-specific gain of DNA methylation are two distinct hallmarks of carcinogenesis. Aberrant DNA methylation is implicated in smoking-related lung cancer. In this study, we have comprehensively investigated the modulation of DNA methylation consequent to chronic exposure to a prototype smoke-derived carcinogen, benzo[a]pyrene diol epoxide (B[a]PDE), in genomic regions of significance in lung cancer, in normal human cells. We have used a pulldown assay for enrichment of the CpG methylated fraction of cellular DNA combined with microarray platforms, followed by extensive validation through conventional bisulfite-based analysis. Here, we demonstrate strikingly similar patterns of DNA methylation in non-transformed B[a]PDE-treated cells vs control using high-throughput microarray-based DNA methylation profiling confirmed by conventional bisulfite-based DNA methylation analysis. The absence of aberrant DNA methylation in our model system within a timeframe that precedes cellular transformation suggests that following carcinogen exposure, other as yet unknown factors (secondary to carcinogen treatment) may help initiate global loss of DNA methylation and region-specific gain of DNA methylation, which can, in turn, contribute to lung cancer development. Unveiling the initiating events that cause aberrant DNA methylation in lung cancer has tremendous public health relevance, as it can help define future strategies for early detection and prevention of this highly lethal disease.

overall_design: Methylated fragments in genomic DNA extracted from benzo[a]pyrene diol epoxide (B[a]PDE)-treated normal human fibroblasts versus control (solvent [dimethylsulfoxide (DMSO)-treated counterpart cells] were enriched with the MIRA assay and hybridized together with input genomic DNA to NimbleGen's whole genome tiling array.

first: Ahmad

last: Bearatinia

first: Stella

last: Tommasi

first: Sang-in

last: Kim

first: Xueyan

last: Zhong

first: Gerd

middle: P

last: Pfeifer


title: Variation of the genomic expression pattern after exposed to 17beta-estradiol in Japanese medaka (Oryzias latipes)

city: Tsukuba

first: Katsuyuki

last: Kadota

address: Tokodai 5-13-11

department: Research

institute: Japan Pulp and Paper Research Institute, Inc.

summary: We assess gene expression patterns upon 17beta-estradiol (E2) exposure to Japanese medaka (Oryzias latipes) in order to appere the E2 effects using DNA microarray analysis. Larval medaka were exposed to 0, 3, 30 and 100 ng/L of E2 and concentration-dependent changes in gene expressions were examined using Agilent medaka DNA microarrays. At 7 day, fish were sacrificed and mRNA was extracted for gene expression analysis. In an effort to link gene expression changes to effects on higher levels of biological organization, sex characteristics, gonadal histology, GSI, and egg production and fertility were examined. In microarray experiments, the correlation factors between the controls were from 0.91 to 1.00 among control samples. We observed highly induced O. latipes Gene Indices (OLGI) related to egg-yolk protein such as vitellogenin and L-SF precursor etc., which were significantly affected in a concentration-dependent manner by E2 exposure. To clarify the function of expressed genes by E2 treatments, we selected statistically expressed genes from the microarray experiments. We found 190 genes and 72 genes which were statistically expressed in E2 treatment as induced and repressed genes, respectively. In the induced gene list, there were characteristic induced-genes in the categories of lipid metabolism, stress (oxidative stress, DNA and protein damage), and apoptosis with MAPK pathway. On the other hands, there were characteristic repressed genes in the categories of heat shock protein. Our result may suggest that gene expressions in yolk medaka is able to be used for detection of E2 effect by DNA microarray analysis.

overall_design: Larval medaka were exposed to 0, 3, 30 and 100 ng/L of E2 and concentration and time-dependent changes in gene expressions were examined using Agilent medaka DNA microarrays. At 7 day, three independent samples (one sample contained thirty whole medakas) were sacrificed and mRNA was extracted for gene expression analysis.

first: Satomi

last: Mizukami-Murata


title: Gene expression in failing and non-failing atrial canine myocardium

city: Baltimore

first: Andreas

middle: Sebastian

last: Barth

address: 720 Rutland Ave.

department: Medicine, Division of Cardiology

institute: Johns Hopkins University

summary: Gene expression in right atrial myocardium was compared between non-failing control and tachypaced dogs (heart failure was induced by tachycardic pacing for 6 weeks).

overall_design:
Dyssynchronous heart failure (DHF): One week after ablation of the left bundle branch, animals were paced at 200 beats per minute for 6 weeks from the right atrium (via epicardial pacing leads).
Control dogs (NF): No heart failure, no pacing, no left bundle branch block.

middle: S

first: David

last: Kass

first: Gordon

last: Tomaselli


title: Genome-wide analysis of germ cell proliferation in C. elegans

city: New Haven

first: Valerie

last: Reinke

state: CT

address: 333 Cedar St

department: Genetics

institute: Yale University School of Medicine

summary: Proliferating germ cells in C. elegans provide a useful model system for deciphering fundamental mechanisms underlying the balance between proliferation and differentiation.  Using gene expression profiling of mutants with excess germ cell proliferation, we identified approximately 200 genes expressed in the proliferating germ cells of C. elegans.

overall_design: RNA isolated from young adult C. elegans hermaphrodites of the genotype unc-32(e189) (control) and from unc-32(e189)glp-1(oz112gf) (excess germ cell proliferation) was directly compared on DNA arrays representing >90% of C. elegans genes.  Four biological replicates were performed, with balanced dye swaps.

first: Katherine

last: Waters

first: Alison

middle: Z


title: miRNA profiling of late stage metastatic Her2+ breast cancer

city: Galway

first: Paul

last: Geeleher

address: University Road

department: Mathematics

country: Ireland

institute: National University of Ireland, Galway

summary: We have assayed differential miRNA expression between late stage (stage IV) metastatic Her2+ and Her2- breast cancer.

overall_design: 4 late stage metastatic Her2- samples were compared to 3 late stage metastatic Her2+ samples. There are 4 within array replicates for each sample.

first: Eamonn

last: Mulvee

first: Breege

last: Howley

first: Vladimir

last: Benes

first: Sabine

last: Schmidt

first: Jonathan

last: Blake

first: Nicola

last: Miller

first: Michael

last: Kerin

first: Howard

last: Fearnhead

first: Aaron

last: Golden


title: Changes in bone marrow resident monocyte gene expression upon induction of ischemia

status: Public on Apr 26 2010

city: Saint Louis

first: Alyssa

last: Gregory

state: MO

address: 660 S Euclid Ave.

department: Medicine

institute: Washington University in St. Louis

summary: There is considerable interest in the potential of cell-based approaches to mediate therapeutic angiogenesis for acute and chronic vascular syndromes. Using a mouse model of HLI, we showed previously that adoptive transfer of a small number of donor monocytes enhanced revascularization significantly. Herein, we provide data suggesting that the BM resident monocytes sense systemic signals that influence their future functional capacity. Specifically, following induction of distant ischemia, the angiogenic capacity of BM resident monocytes is reduced markedly. We provide evidence that G-CSF and IL-6 represent such conditioning signals. Systemic levels of G-CSF and IL-6 are increased significantly following induction of HLI. Accordingly, BM resident monocytes from ischemic mice exhibited increased pSTAT3 and STAT3 target gene expression. Finally, G-CSFR(-/-) and IL-6(-/-) mice were resistant to the deleterious effects of ischemic conditioning on monocyte angiogenic potential. RNA expression profiling suggested that ischemia-conditioned monocytes in the BM up-regulate the well-described M2 polarization markers Chi3l4 and Lrg1. Consistent with this observation, M2-skewed monocytes from SHIP(-/-) mice also had impaired angiogenic capacity. Collectively, these data show that G-CSF and IL-6 provide signals that determine the angiogenic potential of BM resident monocytes.

overall_design: Bone marrow was harvested from CX3CR1+/GFP heterozygous mice and CX3CR1-GFP+ monocytes were sorted at baseline and at 24 hours post-induction of hindlimb ischemia by femoral artery ligation.  Paired samples from three independent experiments were analyzed.

first: Daniel

middle: C

last: Link


title: mRNA profiling of genetically matched ESCs and iPSCs

status: Public on Apr 28 2010

city: Boston

first: Matthias

last: Stadtfeld

state: MA

address: 185 Cambridge Street

institute: MGH

summary: Induced pluripotent stem cells (iPSCs) can be generated by enforced expression of defined transcription factors in somatic cells. It remains controversial whether iPSCs are equivalent to blastocyst-derived embryonic stem cells (ESCs). Using genetically matched cells, we found that the overall mRNA  expression patterns of these cell types are indistinguishable with the exception of a few transcripts encoded on chromosome 12qF1.

overall_design: iPSCs were derived from somatic tissues of chimeric mice generated with ESCs that carry an inducible cassette encoding for the reprogramming factors myc, Klf4, Oct4 and Sox2.

first: Konrad

last: Hochedlinger


title: Light-regulated genes in Cryptococcus neoformans

status: Public on Apr 23 2010

city: Kansas City

first: Alexander

last: Idnurm

address: 5007 Rockhill Road

department: School of Biological Sciences

institute: University of Missouri-Kansas City

summary: Light is a universal environmental signal perceived by many organisms, including the fungi in which light regulates both common and unique biological processes depending on the species. We conducted a whole-genome microarray analysis on the basidiomycete fungus Cryptococcus neoformans to identify light-regulated genes.

overall_design: Two-condition experiment, cells grown in complete darkness or exposed to white light.  Six biological replicates independently grown and harvested.  One replicate per array.

first: Joseph

last: Heitman


title: Time-series analyses of Monterey Bay coastal microbial picoplankton using a “genome proxy” microarray

status: Public on Apr 24 2010

city: Tucson

first: Virginia

middle: Isabel

last: Rich

state: AZ

address: 1041 E. Lowell St.

institute: University of Arizona

summary:
To gain improved temporal, spatial and phylogenetic resolution of marine microbial communities, in this study we expanded the original prototype genome proxy array (an oligonucleotide microarray targeting marine microbial genome fragments and genomes), evaluated it against metagenomic sequencing, and applied it to time series samples from the Monterey Bay long term ecological research site. The expanded array targeted 268 microbial genotypes (vs. 14 in the original prototype) across much of the known diversity of cultured and uncultured marine microbes. The target abundances measured by the genome proxy array were highly correlated to pyrosequence-based abundances (linear regression R2 = 0.85-0.91, p<0.0001). Fifty-seven samples from ~4-years in Monterey Bay were examined with the array, spanning the photic zone (0m), the base of the surface mixed layer (30m), and the subphotic zone (200m). A significant portion of the expanded genome proxy array’s targets showed signal (95 out of 268 targets present in ≥ 1 sample). The multi-year community survey showed the consistent presence of a core group of common and abundant targeted taxa at each depth in Monterey Bay, higher variability among shallow than deep samples, and episodic occurrences of more transient marine genotypes. The abundance of the most dominant genotypes peaked after strong episodic upwelling events. The genome-proxy array’s ability to track populations of closely-related genotypes indicated population shifts within several abundant target taxa, with specific populations in some cases clustering by depth or oceanographic season. Although 51 cultivated organisms were targeted (representing 19% of the array) the majority of targets detected and of total target signal (85% and ~92%, respectively) were from uncultivated lineages, often those derived from Monterey Bay. The array provided cost-effective (~$15 per array, for construction and use) insights into the natural history of uncultivated lineages in the wild.
To gain improved temporal, spatial and phylogenetic resolution of marine microbial communities, in this study we expanded the original prototype genome proxy array (an oligonucleotide microarray targeting marine microbial genome fragments and genomes), evaluated it against metagenomic sequencing, and applied it to time series samples from the Monterey Bay long term ecological research site. The expanded array targeted 268 microbial genotypes (vs. 14 in the original prototype) across much of the known diversity of cultured and uncultured marine microbes. The target abundances measured by the genome proxy array were highly correlated to pyrosequence-based abundances (linear regression R2 = 0.85-0.91, p<0.0001). Fifty-seven samples from ~4-years in Monterey Bay were examined with the array, spanning the photic zone (0m), the base of the surface mixed layer (30m), and the subphotic zone (200m). A significant portion of the expanded genome proxy array’s targets showed signal (95 out of 268 targets present in ≥ 1 sample). The multi-year community survey showed the consistent presence of a core group of common and abundant targeted taxa at each depth in Monterey Bay, higher variability among shallow than deep samples, and episodic occurrences of more transient marine genotypes. The abundance of the most dominant genotypes peaked after strong episodic upwelling events. The genome-proxy array’s ability to track populations of closely-related genotypes indicated population shifts within several abundant target taxa, with specific populations in some cases clustering by depth or oceanographic season. Although 51 cultivated organisms were targeted (representing 19% of the array) the majority of targets detected and of total target signal (85% and ~92%, respectively) were from uncultivated lineages, often those derived from Monterey Bay. The array provided cost-effective (~$15 per array, for construction and use) insights into the natural history of uncultivated lineages in the wild.

sample_organism:
unidentified
marine metagenome

platform_organism: Prochlorococcus marinus subsp. pastoris str. CCMP1986

platform_organism: uncultured marine gamma proteobacterium EBAC31A08

platform_organism: uncultured marine group II euryarchaeote 37F11

platform_organism: uncultured gamma proteobacterium eBACHOT4E07

platform_organism: uncultured marine group II euryarchaeote EF100_57A08

overall_design: The expanded genome proxy array was designed as in (Rich et al., 2008). Briefly, each genotype was targeted using suites of ~20 70-mer oligonucleotide probes designed using the program ArrayOligoSelector (Zhu et al., 2003). Probes had approximately the same %GC (40%) and were distributed across the target genome or genome fragment, with no more than one probe per gene and avoiding 16S and 23S rRNA genes. The array included positive and negative control probes designed using the same method, to Halobacterium salinarum NRC-1 and a random genome sequence, respectively.    The expanded array had a broader scope than the prototype of Rich et al., 2008 (268 target genotypes, as opposed to the prototype’s 14) and included a co-spot oligo for spot alignment and gridding purposes (using the “alien” oligo sequence of (Urisman et al., 2005). The targets were selected from fully-sequenced marine microbial genomes, publicly-available marine-derived BAC and fosmid clone sequences, and fully-sequenced clones from the lab’s Monterey Bay and Hawaii environmental BAC- and fosmid-based genomic libraries. Targeted genotypes are detailed in Table S1, summarized in Table S2, and presented in a schematic phylogenetic overview in Fig. 1. Previously-unpublished sequences used for array design were submitted to Genbank under accession numbers GU474833-GU474949.   This submission presents the analysis of 57 samples, each hybridized to >= 3 arrays. In addition to negative control probes, for each hyrbdization date and run a negative control array was hyrbdized for which the input DNA was TE, taken through the entire aplification, labeling, and hybridization process.

middle: I

first: Edward

last: DeLong


title: Tissue-specific dysregulation of DNA methylation in aging

city: Bronx

first: Reid

last: Thompson

state: NY

address: 1301 Morris Park Avenue

department: Molecular Genetics

institute: Albert Einstein College of Medicine

summary: The normal aging process is a complex phenomenon associated with physiological alterations in the function of cells and organs over time.  Although an attractive candidate for mediating transcriptional dysregulation, the contribution of epigenetic dysregulation to these progressive changes in cellular function remains unclear.  In this study, we employed the genome-wide HELP assay to define patterns of cytosine methylation throughout the rat genome, and the LUMA assay to measure global levels of DNA methylation in the same samples. We studied both liver and visceral adipose tissue, and demonstrated significant differences in DNA methylation with age at >5% of sites analyzed.  Furthermore, we showed that epigenetic dysregulation with age is a highly tissue-dependent phenomenon.  The most distinctive loci were located at intergenic sequences and conserved non-coding elements, and not at promoters nor at CG-dinucleotide dense loci.  Finally, we demonstrated that changes in methylation occur consistently near genes that are involved in metabolism and metabolic regulation, implicating their potential role in the pathogenesis of age-related diseases.  We conclude that different patterns of epigenetic dysregulation occur in each tissue over time and may cause some of the physiological changes associated with normal aging.

overall_design: Direct comparison of DNA methylation in 18 samples belonging to four groups: young liver (n=6), young adipose tissue (n=4), old liver (n=5), old adipose tissue (n=3), isolated from F344*BN rats (young at ~3 months, old at ~18 months).  Each microarray consists of a two-color comparison of a methylation-sensitive representation of the genome (HpaII) with an internal methylation-insensitive control/reference (MspI).

first: Gil

last: Atzmon

first: Hong

middle: Q

last: Liang

first: Christina

last: Lowes

first: John

last: Greally

first: Nir

last: Barzilai


title: Cyclin K and cyclin D1b are oncogenic in myeloma cells

city: Illkirch

first: Doulaye

last: Dembele

address: 1 rue Laurent Fries

department: Biopuces

country: France

institute: IGBMC

summary: To study the oncogenic potential of cyclin D1b in the context of mature B cells we generated several cell clones derived from LP-1 MM cell line expressing either cyclin D1b, Myc or cyclin K oncogenes. Transcriptomic analysis allowed us to describe several mechanisms of cyclin D1b- and K-mediated oncogenesis.

overall_design: Three-condition experiment: LP-1cl1, LP-1K and LP-1D1b. Multiple myeloma LP-1 cell lines. Biological replicates: 4 control (LP-1cl1), 4 transfected with cyclin K (Lp-1K) and 4 transfected with cyclin D1b (LP-1D1b) independently grown and harvested. One replicate per array.

first: Veronique

last: Marsaud

first: Guergana

last: Tchakarska

first: Geoffroy

last: Andrieux

first: Jian-Miao

last: Liu

first: Bernard

last: Jost

first: Joanna

last: Wdzieczak-Bakala

first: Jack-Michel

last: Renoir

first: Brigitte

last: Sola


title: Stp1 and Stk1 regulated genes during S. aureus post-exponential phase growth

status: Public on Apr 22 2010

first: Lakshmi

last: Rajagopal

summary:
Genes that showed altered expression in Stk1 and Stp1 deficient Staphylococcus aureus Newman were identified.
strain comparison, global regulation

overall_design: Deletion mutants were examined for alterations in gene expression.

first: Kellie

last: Burnside

first: Melissa

middle: D

last: Reyes


title: Genome changes associated with a Zymomonas mobilis sodium acetate-tolerant mutant (AcR)

city: Raleigh

first: Stan

last: Martin

state: NC

address: 1404 Crete Dr.

institute: Science Apps, L3C

summary: We report the genome changes associated with a Zymomonas mobilis sodium acetate-tolerant mutant (AcR). We used comparative genomics, transcriptomics, and genetics to show nhaA over-expression conferred sodium acetate (NaAc) tolerance in Z. mobilis. We observed a synergistic effect for sodium and acetate ions that enhanced toxicity against the wild-type strain (ZM4), which was not observed for similar concentrations of potassium and ammonium acetate under controlled laboratory conditions. We extended our studies and demonstrated that Saccharomyces cerevisiae sodium-proton antiporter genes contribute to NaAc tolerance for this important ethanologen. The application of classical and systems biology tools is a paradigm for industrial strain improvement and combines benefits of few a priori assumptions with detailed, rapid, mechanistic studies. Finally, our studies reinforce the idea that one obtains what one selects for in mutant screens and that a genetic system is important for industrial strain development.

overall_design:
ZM4_ACr_NaCl_NaAc_study.
Whole-genome expression profiles of exponential and stationary phase cells were analyzed for the wild-type Zymomonas mobilis ZM4 and the acetate-tolerant mutant AcR under 12g/L sodium acetate and same molar concentration of sodium chloride (8.55g/L) control conditions.


title: miRNA expression in granulopoiesis

city: Rotterdam

first: Su Ming

last: Sun

address: Dr. Molewaterplein 50

department: Hematology

institute: Erasmus University Medical Center

summary: Normal human neutrophil development is a complex biological process, where the balance between cell proliferation, differentiation and apoptosis is tightly regulated by a transcriptional program that results in the production of appropriate numbers of circulating mature neutrophils. MicroRNAs (miRNAs) are small non-coding RNAs of 18~25 nt that affect cellular protein levels. Only limited data is available on miRNA expression patterns during normal granulocytic differentiation of primary human cells.   We have examined miRNA expression patterns in distinct stages of granulocytic differentiation sorted from human bone marrow and identified highly stage-specific expressed miRNAs. Some of these differentially expressed miRNA are related to each other in terms of seed sequence (miRNA families) and location on the genome (miRNA clusters). These data reveal distinct expression patterns of specific miRNA sets that closely follow the transition of discrete maturation stages along the myeloblast-neutrophil pathway.

overall_design: In total 13 samples were measured, 2 myeloblast, 3 myeloblast/promyelocyte, 4 metamyelocytes and 3 neutrophils

first: Su

first: Menno

middle: K

last: Dijkstra

first: Andre

last: Bijkerk

first: Rik

last: Brooimans

first: Peter

last: Valk

first: Stefan

middle: J

last: Erkeland

first: Bob

last: Lowenberg

first: Mojca

last: Jongen-Lavrencic


title: Deregulated expression programs in the hypomorphic Dnmt3b mutant mice

status: Public on Apr 21 2010

city: TOURS

first: Jérome

last: Rollin

address: av de la republique

department: Hematology-Hemostasis

institute: CHU-Tours

summary: The function of Dnmt3b, of which deregulated activity is linked to several human pathologies, was studied using Dnmt3b hypomorphic mutant mice with reduced catalytic activity. Microarray analysis of deregulated expression programs in the hypomorphic Dnmt3b mutant mice (m3/m24) was combined to an analysis of the molecular mechanisms involved in the illegitimate activation of a specific set of genes.

overall_design:
Mouse embryonic fibroblasts and thymus tissues isolated from 12.5 dpc and 18.5 dpc, respectively, wild-type and hypomorphic embryos (129SvJae x C57BL/6 hybrid genetic background).
Total RNA was isolated using RNeasy Mini kit (QIAGEN), amplified, labeled, and hybridized following a previously described protocol (Le Brigand et al., Nuc Acid Res, 2006). Total RNA was coupled with Cyanine 3 or 5 and then hybridized in competition with reference RNA composed of a pool of total RNA isolated from wild-type thymus or MEF cells (thymus, n=5; MEF, n=5); two dye-swap were realized leading to the analysis of 18 microarrays for thymus (2 microarrays were excluded for unsufficient quality) and 20 for MEF cells. Arrays were then scanned with Agilent G2565AA Microarray Scanner (Agilent Technologies).

first: Guillaume

last: Velasco

first: Florent

last: Hubé

first: Jérôme

first: Damien

last: Neuillet

first: Angélique

last: Galvani

first: Cathy

last: Philippe

first: Haniaa

last: Bouzinba-Segard

first: Evani

last: Viegas-Péquignot

first: Claire

last: Francastel


title: MicroRNA Profiling in Ischemia-Reperfusion Injury of the Gracilis Muscle in Rats (miRNA data)

city: Kaohsiung Hsien

first: Ching-Hua

last: Hsieh

state: Kaohsiung

address: 123, Ta-Pei road, Naio-Sung Hsiang

department: Plastic and Reconstructive Surgery

country: Taiwan

institute: Kaohsiung Chang Gung Memorial Hospital

summary:
Profile the microRNA expression in the Gracilis muscle of rat after 4h ischemia and 24 h reperfusion
Following 4 h of ischemia and subsequent reperfusion for 4 h of the gracilis muscles, the specimens were analyzed with an Agilent rat miRNA array to detect the expressed miRNAs in the experimental muscles compared to those from the sham-operated controls.

overall_design: Two-condition experiment, Gracilis muscle after 4h ischemia and reperfusion injury for 24 h v.s. Gracilis muscle (sham control), Biological replicates: 2 control replicates, 2 experiement replicates


title: MicroRNA Expression Profiles Associated with Mutational Status and Survival in Malignant Melanoma

city: Stockholm

first: Stefano

last: Caramuta

address: CMM L8:01, Karolinska University Hospital

department: Molecular Medicine and Surgery

country: Sweden

institute: Karolinska Institutet

summary: In order to improve our understanding of microRNA (miRNA) deregulation in melanoma development and possible consequences for patient survival, miRNA expression profiles were determined, using an array based approach, in melanoma tumors, melanoma cell lines and normal melanocytes. Differentially expressed miRNAs were evaluated in relation to clinical characteristics, patient prognosis in terms of melanoma-specific survival, and mutational status for BRAF and NRAS.

overall_design: Agilent microarray platform containing 470 miRNAs was used to determine miRNA expression profiles in 3 normal melanocytes (as non-neoplastic control), 21 melanoma cell lines and 16 clinical samples from fresh frozen regional lymph node metastases. To validate the microarray platform, the expression levels of some miRNAs were evaluated using RT-PCR and the correlation between the two platforms was assessed using Pearson Correlation analysis. The results obtained were further verified and confirmed by RT-PCR in an independent set of melanoma samples. Association between deregulated miRNAs and survival was determined by Univariate Cox proportional hazards model and log rank test.

first: Suzanne

last: Egyházi


title: Expt 2: The contribution of vjbR and N-dodecanoyl homoserine lactone on gene regulation in Brucella melitensis

city: College Station

first: Jenni

last: Weeks

state: TX

address: 4467 TAMU

institute: Texas A&M University

summary:
Quorum sensing (QS) is a communication system in bacteria that regulates gene expression in response to a small diffusible signal indicative of the bacterial population present.  QS has been shown to regulate virulence genes, biofilm formation, cell division and secretion systems in a diverse set of bacteria.  Brucella melitensis produces a QS signaling molecule, N-dodecanoyl homoserine lactone (C12-HSL), that interacts with a LuxR transcriptional regulator, VjbR.  Deletion of vjbR has been found to highly attenuate intracellular survival of B. melitensis.  The importance of QS in the regulation of genes necessary for the establishment and maintenance of B. melitensis infection has already been described for the virB and fla operons, however, a complete description of the vjbR regulon has not been described.  Genome mining revealed seven luxR-like genes in B. melitensis, only one of which, vjbR, was confirmed to be attenuated for intracellular survival using macrophage assays.  Using custom B. melitensis microarrays, we compared transcripts from wild type and ∆vjbR strains in the presence and absence of exogenous C12-HSL.  Comparison of the transcriptomes obtained from culture grown bacteria revealed bi-phasic gene regulation with expression peaks during exponential and early stationary growth phase; characterized by the regulation of 226 and 246 genes (respectively) by VjbR and 349 and 146 (respectively) altered by the addition of C12-HSL.  Comparison of the VjbR and C12-HSL regulated genes provided confirmation that expression of 134 genes are regulated by both conditions with all but 3 genes inversely regulated.  Overall, these results indicate that VjbR is an activator of gene expression at the exponential growth phase and exerts an equal effect on gene expression at the stationary growth phase; while C12-HSL has a repressive effect on gene expression at both growth stages examined and acts as an antagonist to VjbR activity.  Direct transcript analysis comparing ∆vjbR with and without the addition of C12-HSL revealed that the AHL signal is able to direct gene expression in the absence of VjbR and exclusively exerted a positive influence on the expression of 56 genes, including a 93-fold increase in the expression of BabR, a second LuxR homologue.  Genes regulated by these QS components included adhesins, proteases, antibiotic and toxin resistance genes, stress survival aids, including DNA repair genes and protein chaperones, transporters and porins, cellular membrane biogenesis genes, amino acid metabolism and transport, transcriptional regulators, and energy production genes.  From these data, we conclude that QS is a global regulator of gene expression, and present potential virulence genes that may provide insight into the bacteria’s ability to establish and maintain the replicative vacuole (BCV) within the host cell.

Keywords: Microarray comparison of a genetic deletion mutant and the addition of an effector molecule.

overall_design: Samples consist of RNA isolated from Brucella melitensis grown to logarithmic or stationary phase.  RNA was extracted from a ∆vjbR mutant with and without exogenously added C12-HSL. There are three biological replicates of each sample.  Every Brucella melitensis open reading frame was printed in quadruplicate on each microarray.  Each replicate was normalized against labeled Brucella melitensis 16M genomic DNA.

middle: N

first: Cristi

last: Galindo

first: Carlos

last: Rossetti

first: Sarah

last: Lawhon

first: Harold

middle: R

last: Garner

first: Thomas

last: Ficht

first: L

middle: G

last: Adams


title: Copy number variation in the bovine genome

city: Tjele

first: Jakob

last: Hedegaard

address: PO-box 50

institute: Aarhus University, Faculty of Agricultural Sciences

summary:
Copy number variations (CNVs), which represent a significant source of genetic diversity in mammals, are currently being associated with phenotypes of clinical relevance, mostly in humans and mice. Notwithstanding, little is known about the extent of CNV that contributes to genetic variation in cattle.
This study reports the highest resolution map of copy number variation in the cattle genome, with 304 CNV regions (CNVRs) being identified among the genomes of 20 bovine samples from 4 dairy and beef breeds. We used a set of NimbleGen CGH arrays that tile across the assayable portion of the cattle genome with approximately 6.3 million probes, at a 301 bp median probe spacing. These CNVRs covered 0.68% (23 Mb) of the genome, and ranged in size from 1.7 to 2,031 kb (median size 16.7 kb). About 20% of the CNVs colocalized with segmental duplications while 30% encompassed genes, mostly related with environmental response. About 10% of the orthologous CNV cow-human genes are related with human disease susceptibility and, hence, may have important phenotypic consequences.
Together, this analysis provides a useful resource to assist with the assessment of CNVs in the contexts of bovine variation, health and productive efficiency.

overall_design: 20 samples were analyzed in a dye-swap loop design. In order to cover the latest bovine genome assembly (bt4) with high density, custom Nimblegen HD2 CGH arrays were planned in 3 designs. Each design covered a specific set of chromosomes with 2.1M probes, which yielded 420 bp of average probe spacing (301 bp median probe spacing).

first: João

last: Fadista

first: Christian

last: Bendixen


title: Expt 1: The contribution of vjbR and N-dodecanoyl homoserine lactone on gene regulation in Brucella melitensis

summary:
Quorum sensing (QS) is a communication system in bacteria that regulates gene expression in response to a small diffusible signal indicative of the bacterial population present.  QS has been shown to regulate virulence genes, biofilm formation, cell division and secretion systems in a diverse set of bacteria.  Brucella melitensis produces a QS signaling molecule, N-dodecanoyl homoserine lactone (C12-HSL), that interacts with a LuxR transcriptional regulator, VjbR.  Deletion of vjbR has been found to highly attenuate intracellular survival of B. melitensis.  The importance of QS in the regulation of genes necessary for the establishment and maintenance of B. melitensis infection has already been described for the virB and fla operons, however, a complete description of the vjbR regulon has not been described.  Genome mining revealed seven luxR-like genes in B. melitensis, only one of which, vjbR, was confirmed to be attenuated for intracellular survival using macrophage assays.  Using custom B. melitensis microarrays, we compared transcripts from wild type and ∆vjbR strains in the presence and absence of exogenous C12-HSL.  Comparison of the transcriptomes obtained from culture-grown bacteria revealed bi-phasic gene regulation with expression peaks during exponential and early stationary growth phase; characterized by the regulation of 226 and 246 genes (respectively) by VjbR and 349 and 146 (respectively) altered by the addition of C12-HSL.  Comparison of the VjbR and C12-HSL regulated genes provided confirmation that expression of 134 genes are regulated by both conditions with all but 3 genes inversely regulated.  Overall, these results indicate that VjbR is an activator of gene expression at the exponential growth phase and exerts an equal effect on gene expression at the stationary growth phase; while C12-HSL has a repressive effect on gene expression at both growth stages examined and acts as an antagonist to VjbR activity.  Direct transcript analysis comparing ∆vjbR with and without the addition of C12-HSL revealed that the AHL signal is able to direct gene expression in the absence of VjbR and exclusively exerted a positive influence on the expression of 56 genes, including a 93-fold increase in the expression of BabR, a second LuxR homologue.  Genes regulated by these QS components included adhesins, proteases, antibiotic and toxin resistance genes, stress survival aids, including DNA repair genes and protein chaperones, transporters and porins, cellular membrane biogenesis genes, amino acid metabolism and transport, transcriptional regulators, and energy production genes.  From these data, we conclude that QS is a global regulator of gene expression, and present potential virulence genes that may provide insight into the bacteria’s ability to establish and maintain the replicative vacuole (BCV) within the host cell.

Keywords: Microarray comparison of a genetic deletion mutant and the addition of an effector molecule.

overall_design: Samples consist of RNA isolated from Brucella melitensis grown to logarithmic or stationary phase.  RNA was extracted from wild type with and without exogenously added C12-HSL, and a ∆vjbR mutant. There are three biological replicates of each sample.  Every Brucella melitensis open reading frame was printed in quadruplicate on each microarray.  Each replicate was normalized against labeled Brucella melitensis 16M genomic DNA.

middle: A


title: Plasmodium falciparum treated with cyclohexylamine

status: Public on Apr 19 2010

city: Brummeria

first: John

middle: van Wyk

last: Becker

state: Gauteng

address: Meiring Naude Road

department: Biosciences

country: South Africa

institute: Council for Scientific and industrial Research

summary:
Transcriptional profiling of P. falciparum cultures treated with cyclohexylamine over time (18, 25 and 30 hours post invasion)
A control experiment was also set up in which P. falciparum was not treated with cyclohexylamine, and samples were taken at 18, 25 and 30 h post invasion).

Background
Plasmodium falciparum, the causative agent of severe human malaria, has evolved to become resistant to previously successful antimalarial chemotherapies, most notably chloroquine and the antifolates. The prevalence of resistant strains has necessitated the discovery and development of new chemical entities with novel modes-of-action. Although much effort has been invested in the creation of analogues based on existing drugs and the screening of chemical and natural compound libraries, a crucial shortcoming in current Plasmodial drug discovery efforts remains the lack of an extensive set of novel, validated drug targets. A requirement of these targets (or the pathways in which they function) is that they prove essential for parasite survival. The polyamine biosynthetic pathway, responsible for the metabolism of highly abundant amines crucial for parasite growth, proliferation and differentiation, is currently under investigation as an antimalarial target. Chemotherapeutic strategies targeting this pathway have been successfully utilized for the treatment of Trypanosomes causing West African sleeping sickness. In order to further evaluate polyamine depletion as possible antimalarial intervention, the consequences of inhibiting P. falciparum spermidine synthase (PfSpdSyn) were examined on a morphological, transcriptomic, proteomic and metabolic level.
Results
Morphological analysis of P. falciparum 3D7 following application of the PfSpdSyn inhibitor cyclohexylamine confirmed that parasite development was completely arrested at the early trophozoite stage. This is in contrast to untreated parasites which progressed to late trophozoites at comparable time points. Global gene expression analyses confirmed a transcriptional arrest in the parasite. Several of the differentially expressed genes mapped to the polyamine biosynthetic and associated metabolic pathways. Differential expression of corresponding parasite proteins involved in polyamine biosynthesis was also observed. Most notably, uridine phosphorylase, adenosine deaminase, lysine decarboxylase (LDC) and S-adenosylmethionine synthetase were differentially expressed at the transcript and/or protein level. Several genes in associated metabolic pathways (purine metabolism and various methyltransferases) were also affected. The specific nature of the perturbation was additionally reflected by changes in polyamine metabolite levels.
Conclusions
This study details the malaria parasite’s response to PfSpdSyn inhibition on the transcriptomic, proteomic and metabolic levels. The results corroborate and significantly expand previous functional genomics studies relating to polyamine depletion in this parasite. Moreover, they confirm the role of transcriptional regulation in P. falciparum, particularly in this pathway. The findings promote this essential pathway as a target for antimalarial chemotherapeutic intervention strategies.

Keywords: Time course experiment in response to a drug treatment

overall_design:
Reference design.  All timepoints compared with t = 18 hours (untreated) post invasion. Two biological replicates and one technical sample per treatment and per time point.

A reference design was employed for array hybridisation, utilising the URR pool described previously. All solvent-control and drug-treated sampled were hybridised to Operon slides, along with the URR. For each time point and each untreated/treated sample, three microarray slides were processed, such that a total of eighteen slides were processed in the study. Two independent cDNA samples (biological replicates) were prepared for each untreated and drug-treated sample at each time point. One of the biological replicate cDNA samples were additionally hybridised to a third slide (representing the technical replicate). GenePix results (gpr) files were generated using GenePix 6.0 (Molecular Devices) software, without normalization. For clustering analyses, results files were normalized with DNMAD (Diagnosis and Normalization for MicroArray Data) using print-tip loess. The normalized values were subsequently downloaded and analyzed with the Multiexperiment Viewer (MeV) in the TM4 software suite. Hierarchical Clustering (HCL, average linkage) was performed to estimate technical and biological variation between samples and at which point cytostasis most likely occurred for comparative purposes in downstream analyses. Intensity data for individual slides were imported into LIMMA (linear models for microarray data) in the R computing environment. Pre- and post-normalization diagnostic plots were performed using MARRAY. Data from each microarray slide was normalized using print-tip loess. Data between microarrays was normalized using rquantile normalisation. Pearson correlations were computed in ExCel to estimate variation between technical and biological replicates. Spots excluded from slide correlations and normalisation were those weighted by the limma script or flagged in the genepix results file (gpr). Additionally, spots termed Alien, Empty, Null and Operon Use Only were excluded from the correlation analyses. These spots were similarly excluded for correlations between untreated and treated samples at each time point following normalisation. Results from biological and slide replicates within each of the time points were collated, and linear models were computed to contrast gene expression between time points.  A two-fold change in gene expression was used as cut-off, in conjunction with correction for false discovery (false discovery rate (FDR) = 5%). Normalised data was deposited in the Gene Expression Omnibus (GEO) database, number GSE18075. Analysis of differentially expressed genes was performed in MADIBA (Micro Array Data Interface for Biological Annotation).

middle: V

first: Linda

last: Mtwisha

first: Bridget

last: Crampton

first: Stoyan

last: Stoychev

first: Anna

last: van Brummelen

first: Shaun

last: Reeksting

first: Abraham

last: Louw

first: Lyn-Marie

last: Birkholz

first: Dalu

last: Mancama


title: Effect of R568 on podocytes

status: Public on Apr 16 2010

city: Mannheim

first: Li

last: Li

address: Theodor-Kutzer-Ufer

institute: University Heidelberg

summary: Calcimimetics such as R568 are renoprotective and the underlying mechanism is not yet fully clarified. We consider the importance of podocytes in mediating the beneficial effect of calcimimetics on kidney. Affymetrix array type Moe430_2 was used to study the effect of R-568. Analysis of differential gene expression indicates that R-568 acts antioxidative, stabilizes cytoskeleton, enhances cell cycle control and suppresses apoptosis in podocytes. This suggests that calcimimetics limit podocyte damage by antiapoptotic and cytoskeleton stabilizing effects and may thus constitute a new pharmacological approach in the prevention and treatment of glomerular disease.

overall_design: Podocytes treated with and without R568 were used for RNA extraction and hybridization on Affymetrix microarrays.

first: Jun

last: Oh


title: Characterization of Missing Human Genome Sequences and Copy-number Polymorphic Insertions.

status: Public on Apr 20 2010

city: Santa Clara

first: Nick

last: Sampas

address: 5301 Stevens Creek Blvd

department: Life Science and Nanotechnology Department

institute: Agilent Technologies

summary: The high level of human genome structural variation among individuals suggests that there must be portions of the genome that have yet to be discovered, annotated and characterized at the sequence level. Using clone resources developed as part of the Human Genome Structural Variation Sequencing Project, we focused on the characterization of 2,363 novel sequence contigs not present in the human reference genome. We determined that these contigs corresponded to 720 distinct loci of which 400 now have an anchored position in the reference genome. We investigated the sequence properties of these loci and determined that 37% of these novel insertions are copy-number polymorphic. We find that they are significantly enriched within the last 5 Mb of chromosomes (a 2.9-fold enrichment, p=1.0e-18, binomial test) and that most arose as a result of deletions in the human lineage after separation from the African great apes. A subset of these sites shows evidence of marked population stratification among Asian, African and European populations, including a 3.9-kb insertion within the first intron of the lactase gene. Complete sequencing of clones from 192 genomic loci, including 156 completely spanned insertions, provides a detailed and contextual view of 1.67 Mb of inserted sequence. Analysis of this sequence identified 477 elements that show evidence of sequence constraint over evolutionary time, as well as matches to 22 RefSeq gene segments. Twenty-six of the insertions contain matches against mRNA-seq data indicating the potential presence of functionally important, unannotated human sequences. Taking advantage of this high-quality sequence, we develop a method to accurately genotype these novel insertions using next-generation whole-genome sequencing datasets.

overall_design: 29 samples including the reference sample (NA15110) which was used in both channels in a single self-self experiment.

first: Jeffrey

middle: M

last: Kidd

first: Francesca

last: Antonacci

first: Tina

last: Graves

first: Robert

last: Fulton

first: Hillary

last: Hayden

first: Can

last: Alkan

first: Maika

last: Malig

first: Mario

last: Ventura

first: Giuliana

last: Giannuzzi

first: Joelle

last: Kallicki

first: Paige

last: Anderson

first: Anya

last: Tsalenko

first: N

last: Yamada

first: Peter

last: Tsang

first: Rajinder

last: Kaul

first: Richard

last: Wilson

first: Laurakay

last: Bruhn

first: Evan

middle: E

last: Eichler


title: miRNA expression data in idiopathic pulmonary fibrosis

city: Pittsburgh

first: Kusum

middle: Vijay

last: Pandit

state: PA

address: 200, Lothrop street, W1200-25A Biomedical Science Tower

department: Medicine-PACCM

institute: University of Pittsburgh

summary:
Idiopathic pulmonary fibrosis (IPF) is an untreatable fibrotic lung disease characterized by fibroblast proliferation and epithelial mesenchymal transition. The expression and role of microRNAs (miRNA) has not been studied in IPF. Using miRNA expression microarrays we identified 46 differentially expressed miRNA in IPF lungs which included let-7d and the miR-30 family.

Keywords: miRNA expression

overall_design: Lung tissue samples for microarray analysis were obtained through the University of Pittsburgh Health Sciences Tissue Bank. Ten samples were obtained from surgical remnants of biopsies or lungs explanted from patients with IPF who underwent pulmonary transplant, and ten control normal lung tissues obtained from the disease free margins with normal histology of lung cancer resection specimens. The morphologic diagnosis of IPF was based on typical microscopic findings consistent with usual interstitial pneumonia. Total RNA was labeled with Cy3 and hybridized on Agilent 8X15K microRNA array (Agilent Technologies, Santa Clara, CA). After 20 hours hybridization, arrays were washed and scanned according to the manufacturer’s protocol.

first: David

last: Corcoran

first: Panayiotis

last: Benos

first: Naftali

last: Kaminski


title: Identification of differentially expressed genes in fibroblasts derived from patients with Dupuytren's Contracture

first: Latha

last: Satish

address: 320 E North Avenue

department: Center for Genomic Sciences

institute: Allegheny-Singer Research Institute

summary:
Dupuytren's contracture (DC) is the most common inherited connective tissue disease of humans and is hypothesized to be associated with aberrant wound healing of the palmar fascia. Fibroblasts and myofibroblasts are believed to play an important role in the genesis of DC and the fibroproliferation and contraction that are hallmarks of this disease. This study compares the gene expression profiles of fibroblasts isolated from DC patients and controls in an attempt to identify key genes whose regulation might be significantly altered in fibroblasts found within the palmar fascia of Dupuytren's patients. Total RNA isolated from diseased palmar fascia (DC) and normal palmar fascia (obtained during carpal tunnel release; 6 samples per group) was subjected to quantitative analyses using two different microarray platforms (GE Code Link™ and Illumina™) to identify and validate differentially expressed genes. The data obtained was analyzed using The Significance Analysis of Microarrays (SAM) software through which we identified 69 and 40 differentially regulated gene transcripts using the CodeLink™ and Illumina™ platforms, respectively. The CodeLink™ platform identified 18 upregulated and 51 downregulated genes. Using the Illumina™ platform, 40 genes were identified as downregulated, eleven of which were identified by both platforms. Quantitative RT-PCR confirmed the downregulation of three high-interest candidate genes which are all components of the extracellular matrix: proteoglycan 4 (PRG4), fibulin-1 (FBLN-1) transcript variant D, and type XV collagen alpha 1 chain. Overall, our study has identified a variety of candidate genes that may be involved in the pathophysiology of Dupuytren's contracture and may ultimately serve as attractive molecular targets for alternative therapies.
Dupuytren's contracture and may ultimately serve as attractive molecular targets for alternative therapies.

overall_design: 6 Samples from carpal-tunnel derived fibroblasts and 6 Samples from Dupuytren's contracture-derived fibroblasts were hybridized to Illumina's Sentrix Human-6 Expression Beadchip and GE Code Link arrays.

first: L


title: HOTAIR transfected Breast Cancer Cells

status: Public on Apr 15 2010

city: Stanford

first: Rajnish

last: Gupta

state: CA

address: CCSR Room 2155

institute: Stanford University

summary:
MDA-MB-231 Breast Cancer Cells were infected by retroviral expression with either VECTOR or HOTAIR.  To test the role of polycomb in HOTAIR mediated gene expression, MDA-MB-231 HOTAIR cells were infected with short hairpin retroviral vectors targeting SUZ12 or EZH2.
A genetic modification design type is where an organism(s) has had genetic material removed, rearranged, mutagenized or added, such as knock out.


title: Culture effects on rheumatoid arthrits synovial fibroblasts

city: Bad Nauheim

first: Elena

last: Neumann

address: Benekestr. 2-8

department: Internal Medicine and Rheumatolgy

summary:
Comparison between early passage to later passages of  rheumatoid arthritis synovial fibroblast (RASF) populations using two different AtlasTM Human Arrays
Gene expression changes during culture with increasing number of changes at higher passages depending on individual expression pattern of the respective cell populations

overall_design:
During every passage, half of the RASF populations were used for culture, the other half of the cells was used for RNA isolation. After collection of all RNA samples up to 8 passages, RNA was used for array analysis as described below.

*********Only differentially expressed genes are reported in the Sample data tables. Complete data tables were requested and reported to be unavailable by the submitter.*********

first: E

first: B

last: Riepl

first: A

last: Knedla

first: S

last: Lefèvre

first: I

middle: H

last: Tarner

first: J

last: Grifka

last: Steinmeyer

last: Gay

first: U

last: Müller-Ladner


title: SOS1 is a candidate gene for idiopathic hirsutis

city: Rome

first: Daniela

last: Minella

state: Italy

address: Via Montpellier 1

department: Dept. of Biopathology

country: Italy

institute: Tor Vergata University

summary:
Expression profiling of androgen and insulin pathway regulating genes unveils SOS 1 as candidate gene for idiopathic hirsutism
Background: Idiopathic Hirsutism (IH), defined as the presence of terminal hairs in females in a male-like pattern, affecting about 5% -15% of women, may result from the interaction between the androgen level and the sensitivity of the hair follicle to the androgen. The pathophysiology of IH is presumed to be linked to increased SRD5A activity, probably both isoenzyme types (SRD5A1 and SRD5A2) and generally related to an alteration in androgen receptor (AR) function.  IH is often associated to metabolic syndrome, visceral obesity, dyslipidemia, insulin resistance, and hypertension.Methodology/Principal Findings: With the aim of identifying genes involved in the pathogenesis of this disorder, we investigated the expression profile of 190 genes involved in the androgen biosynthesis and metabolism, and other genes coding for products active in the insulin pathway in skin genital fibroblasts. For this purpose we selected from a cohort of 240 women affected with androgen excess syndrome a group of 52 idiopathic hirsute patients (22%) and we selected 8 of them with the higher grade of hirsutism (Ferriman & Gallway score >20) for the genetic studies  comparing the data with 4 healthy women used as controls. The array gene signature in the IH patients identified 4 differentially expressed genes, 2 up-regulated and 2 down-regulated (FC≥± 1.5). Differentially expressed genes included products involved in insulin signalling while no androgens related genes were found altered in expression levels. We found that one of the over expressed transcript codes for the SOS1 gene product, which is overproduced in IH patients compared to controls. We did not identified any genomic variants or SNPs in the SOS1 promoter region and/or witin the 3’UTR with documented functional effects on SOS1 gene expression, although  some variants in the 3’UTR seems to be potentially active in modulating the binding of transcription factors.
Conclusions/Significance: In the cohort of women with androgen excess syndrome studied the 22% had neither hyperandrogenemia nor biochemical sign of hyperinsulinemia. We were able to demonstrate that  SOS1 mRNA is over-expressed resulting in over production of SOS1 protein in IH patients. This suggests that an increase of SOS1 protein production could reflect a situation with an increased SOS1 activity function in hirsute patients. These findings propose a role for SOS1, in cooperation with other insulin pathway genes, in the pathogenesis of IH.

overall_design: We used the microarray technology to study the expression profiles of 190 genes involved in the androgen biosynthesis and metabolism, and other genes coding for products active in the insulin pathway, in genital skin fibroblasts of 8 idiopathic hirsute women and 4 related controls. To reduce individual variation and other confounding events, such as spontaneous up- and down-regulation of genes, the patients and the controls were pooled into 2 distinct pools. The gene expression analysis have been just used to identify genes which expression profiles result alterated and which could represents new genes involved in the pathogenesis of hirsutism.

first: Franca

last: D'Amico

first: Michela

last: Biancolella

first: Francesca

last: Amati

first: Barbara

last: Testa

first: Irene

last: Predazzi

first: Susana

last: Bueno

first: Francesco

last: Raducci

first: Katia

last: Petrilli

last: Gullotta

first: Davide

last: Lauro

first: Giuseppe

last: Novelli

first: Costanzo

last: Moretti


title: Cytokine interactome alterations promote oropharyngeal Epstien-barr virus (EBV) replication and shedding during HIV infection

city: Central

first: R A P

last: Perera

address: 34, Hospital road

department: Faculty of Dentistry

country: Hong Kong

institute: The University of Hong kong

summary: Proteomic analysis of cytokines in unstimulated oropharyngeal secretions. Epstein-barr virus (EBV) is a type 1 carcinogen which causes many cancers in humans. Here we explored the cytokine involvement of the EBV replication process in the oropharynx. Cytokine interactomic profiles were geneerated to understand the involved signalling pathways in HIV infected group and the healthy group. Proteome profilers were used to understand the major cytokine expression levels that are related to infection and immune regulation.

overall_design:
We analyzed unstimulated oropharyngeal samples (UOPS) from 42 healthy subjects and 72 HIV positive subjects using the R & D Proteome Profiler array panels. No techinical replicates were performed.
14 samples in HIV group without therapy (NHAART group); 58 HIV patients with highly active antiretroviral therapy (HAART group); 42 samples in healthy group

first: R

first: C

middle: S

last: Tsang

first: K

last: Chan

first: M

middle: P

last: Lee

first: P

last: Li

last: Miller

first: L

last: Samaranayake


title: High-resolution aCGH analyses of copy number alterations in HER2-amplified breast cancer

status: Public on Apr 14 2010

city: Lund

first: Johan

last: Staaf

address: Medicon Village

institute: SCIBLU - Swegene Centre for Integrative Biology at Lund University

summary:
HER2 gene amplification and protein overexpression (HER2+) define a clinically challenging subgroup of breast cancer with variable prognosis and response to therapy. Although gene expression profiling has identified an ERBB2 molecular subtype of breast cancer, it is clear that HER2+ tumors reside in all molecular subtypes and represent a genomically and biologically heterogeneous group.

Genome-wide DNA copy number profiling, using BAC array comparative genomic hybridization (aCGH) were performed on 200 tumors with mixed clinical characteristics and amplification of HER2. Genomic Identification of Significant Targets in Cancer (GISTIC) was used to identify significant copy number aberrations (CNAs) in HER2+ tumors. This analysis sheds further light on the genomically complex and heterogeneous nature of HER2+ tumors in relation to other subgroups of breast cancer.

overall_design: Genomic profiling of 200 breast tumors using tiling BAC aCGH (32K, 33K and 38K). A number of cases were hybridized as replicates or dye-swaps.

first: Göran

last: Jönsson

first: Markus

last: Ringner

last: Vallon-Christersson

first: Dorthe

last: Grabau

first: Adalgeir

last: Arason

first: Haukur

last: Gunnarsson

first: Bjarni

last: Agnarsson

first: Per

last: Malmström

first: Oskar

last: Johannsson

first: Niklas

last: Loman

first: Rosa

middle: B

last: Barkardottir

first: Ake

last: Borg


title: RNA Pol III transcriptomes and relationships to Pol II promoters, enhancer-binding factors and chromatin domains

city: Bethesda

first: Andrew

last: Oler

state: MD

address: 31 Center Drive, Room 3B62E

department: Bioinformatics and Computational Biosciences Branch (BCBB)

country: USA

institute: NIAID/NIH

type: Genome binding/occupancy profiling by genome tiling array

summary: RNA polymerase III transcribes many noncoding RNAs (e.g. tRNAs) important for translational capacity and other functions.   Here, we localized RNA polymerase III, alternative TFIIIB complexes (BRF1/2) and TFIIIC in HeLa cells, determining the Pol III transcriptome, defining gene classes, and revealing ‘TFIIIC-only’ sites.  Pol III localization in other transformed and primary cell lines revealed both novel and cell-type specific Pol III loci, and one occupied miRNA.  Surprisingly, only a fraction of the in silico-predicted Pol III loci are occupied. Interestingly, many occupied Pol III genes reside within an annotated Pol II promoter. Outside of Pol II promoters, occupied Pol III genes overlap with enhancer-like chromatin and enhancer binding proteins such as ETS1 and STAT1. Remarkably, Pol III occupancy scales with the levels of nearby Pol II, active chromatin and CpG content.  Taken together, active promoter and enhancer-like chromatin appears to gate Pol III accessibility to the genome.

overall_design: Use of ChIP-array to identify genomic regions bound by RNA Polymerase III machinery

first: Ravi

last: Alla

first: Douglas

last: Roberts

first: Alexander

last: Wong

first: Peter

middle: C

last: Hollenhorst

first: Katherine

last: Chandler

first: Patrick

last: Cassiday

first: Cassie

last: Nelson

first: Curt

last: Hagedorn

first: Barbara

last: Graves

first: Bradley

last: Cairns


title: TLR 4 Signaling Inhibitory Pathway Induced by Green Tea Polyphenol Epigallocatechin-3-Gallate through 67-kDa Laminin Receptor

city: yokohama

first: kenjiro

last: ikuta

state: kanagawa

address: 10-1, Daikoku-cho, Tsurumi-ku

institute: MITSUBISHI RAYON CO.,LTD

summary: Epigallocatechin-3-gallate (EGCG), a major active polyphenol of green tea, has been shown to downregulate inflammatory responses in macrophages; however, the underlying mechanism has not been understood. Recently, we identified the 67-kDa laminin receptor (67LR) as a cell-surface EGCG receptor that mediates the anti-cancer action of EGCG at physiologically relevant concentrations (0.1-1 mM). Here we show the molecular basis for the downregulation of TLR4 signal transduction by EGCG at 1 mM in macrophages. Anti-67LR antibody treatment or RNAi-mediated silencing of 67LR resulted in abrogation of the inhibitory action of EGCG on LPS-induced activation of downstream signaling pathways and target gene expressions. Additionally, we found that EGCG reduced the TLR4 expression through 67LR. Interestingly, EGCG induced a rapid upregulation of Tollip protein, a negative regulator of TLR-signaling, and this EGCG action was prevented by 67LR silencing or anti-67LR antibody treatment. RNAi-mediated silencing of Tollip impaired the TLR4 signaling inhibitory activity of EGCG. Taken together, these findings demonstrate that 67LR plays a critical role in mediating anti-inflammatory action of a physiologically relevant EGCG and Tollip expression could be modulated through 67LR. These results provide a new insight into the understanding of negative regulatory mechanisms for TLR4 signaling pathway and consequent inflammatory responses which are implicated in the development and progression of many chronic diseases.

overall_design: We quantified expression profile of 210 inflammatory-relating genes in the 67LR-downregulated cells treated with LPS or/and EGCG by microarray

first: Byun

last: Hong

first: Yoshinori

last: Fujimura

first: Koji

last: Yamada

first: Hirofumi

last: Tachibana


title: Identification of MucR regulatory targets

first: Jenni

last: Weeks

summary:
The transcriptional regulator MucR was identified as highly attenuated in a mutagenesis screen conducted by this laboratory.  MucR has been described as a key regulator of exopolysaccharide synthesis in closely related Rhizobials soil symbionts.  The goal of this study was to apply custom Brucella melitensis oligonucleotide microarrays to identify the regulatory targets of MucR.  These studies revealed that MucR's regulation of exopolysaccharide synthesis is also conserved in Brucella melitensis and is also a key regulator of iron sequestering/storage and denitrification.

Keywords: Microarray comparison of a genetically modified organism compared to wild type.

overall_design: There are 3 biological replicates isolated from Brucella melitensis wild type 16M and from 16M∆mucR.

first: Cristi

middle: L

last: Galindo

first: Carlos

last: Rossetti

first: Sarah

middle: D

last: Lawhon

first: Harold

last: Garner

first: Thomas

last: Ficht

first: L

last: Adams