title: Gene expression of CD66 expressing cells in cervical precancer cell line

city: Bangalore

first: Chitra

last: Pattabiraman

state: Karntaka

address: GKVK Campus, Bellary Road

institute: National Centre for Biological Sciences, TIFR

summary:
Gene Expression profiles of sorted CD66High and CD66Low cells were generated from CIN612-9E cells grown in Emedia.
We have analyzed the gene expression pattern of CD66High and CD66Low cells from CIN612 9E.  These cells are derived from a cervical precancer lesion (M. Bedell, J. Hudson, T. Golub  et al, 1991, J. Virol)

overall_design: Two sets of experiments (biological replicates) were performed for CD66High and CD66Low cells.

first: Sudhir

last: Krishna


title: RFTS-deleted DNMT1 enhances tumorigenicity with focal hypermethylation and global hypomethylation

status: Public on Sep 30 2014

city: Dallas

first: Duojia

last: Pan

state: Texas

address: 6001 Forest Park

department: Physiology

country: USA

institute: UT Southwestern Medical Center

type: Methylation profiling by genome tiling array

summary: Site-specific hypermethylation of tumor suppressor genes accompanied by genome-wide hypomethylation are epigenetic hallmarks of malignancy. However, molecular mechanisms that drive these linked changes in DNA methylation remain obscure. DNA methyltransferase 1 (DNMT1), the principle enzyme responsible for maintaining methylation patterns is commonly dysregulated in tumors. Replication foci targeting sequence (RFTS) is an N-terminal domain of DNMT1 that inhibits DNA-binding and catalytic activity, suggesting that RFTS deletion would result in gain of DNMT1 function. However, earlier data suggested that RFTS is required for DNMT1 activity. Here, we determined cellular consequences of RFTS deletion from DNMT1 in immortalized human bronchial epithelial cells. Compared to full-length DNMT1, ectopic expression of DNMT1- ΔRFTS caused greater malignant transformation and enhanced promoter methylation that silenced DAPK and DUOX1 gene expression and increased intensity of promoter methylation across the genome. Strikingly, DNMT1-ΔRFTS also produced genomic hypomethylation and demethylation of Satellite 2 repeat sequences. Because deletion of RFTS is sufficient to induce focal hypermethylation and global hypomethylation in parallel, evidence suggests that the RFTS domain is a target responsible for epigenetic changes in cancer.

overall_design: DNA samples from HBEC3 cells transfected with vector control and HBEC3 cells with full-length and RFTS-deleted DNMT1 were assessed for genome-wide methylation using the microarray-based high resolution HpaII tiny fragment enriched by ligation-mediated PCR (HELP) assay.

first: Bo-Kuan

last: Wu

first: Szu-Chieh

last: Mei

first: Charles

last: Brenner


title: Fission yeast Cactin restricts telomere transcription and elongation by promoting Rap1 pre-mRNA splicing and protein stabilization

status: Public on Sep 27 2014

city: Zürich

first: Claus

middle: M

last: Azzalin

address: Otto-Stern-Weg 3

department: Institute of Biochemistry

country: Switzerland

institute: ETH Zürich

type: Expression profiling by genome tiling array

summary:
RNA transcriptome analysis of S.pombe fission yeast cells deleted for cay1+/SPBC2F12.12c (cay1D) and wildtype
The transcriptome of cay1+ deleted fission yeast cells was characterized and compared to wildtype yeasts to identify differentially expressed genes controlled by Cay1 on a transcriptional or post-transcriptional level.

overall_design: 3 biological replicates of wildtype and cay1D fission yeast cells were prepared in parallel. Based on poor quality array hybridization one cay1D replicate was excluded from further analysis

first: Luca

middle: E

last: Lorenzi

first: Amadou

last: Bah

first: Harry

last: Wischnewski

first: Vadim

last: Shchepachev

first: Charlotte

last: Soneson

first: Marco

last: Santagostino


title: Wound healing process after TBI in zebrafish: time course (zebrafish)

city: Hsinchu

first: Yung-Jen

last: Chuang

state: Taiwan

address: No. 101, Sec. 2, Kuang Fu Road

department: Department of Medical Science

country: Taiwan

institute: National Tsing Hua University

summary: The interaction between neurogenesis and angiogenesis after traumatic brain injury is a complex and dynamic process. To resolve this, we chose the zebrafish model organism for studying brain wound healing via systems biology approach. Transcriptome microarray data and histological analysis of injured fish were sampled at different time points during recovery process. Time-course microarray data following wound healing of zebrafish were obtained. From this set of data, we constructed two intracellular protein–protein interaction (PPI) networks for the traumatic brain injury healing mechanism.

overall_design: Each fish in each group was injured by a 1.5 mm, 27G needle tip from day 0 to 28, respectively. These injured fish were collected at 0, 0.25, 1, 3, 6, 10, 15, 21, 28 dpi (day post injury).  0.625μg of Cy3 cRNA for C. albicans array and 1.65 μg of Cy3 cRNA for zebrafish array was fragmented to an average size of about 50-100 nucleotides by incubation with fragmentation buffer at 60°C for 30 minutes. Each time point contain two biological repeats.

first: Che

last: Lin

first: Bor-Sen

last: Chen

first: Wen-Ping

last: Hsieh

first: David

middle: S

last: Wong


title: Affymetrix Mouse Diversity Genotyping Array Data for p53 deficient mice

status: Public on Sep 29 2014

city: New Brunswick

first: SAURABH

middle: V

last: LADDHA

state: NEW JERSEY

address: 195 Little Albany Street

department: Center for Systems and Computational Biology

institute: Rutgers Cancer Institute of New Jersey

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

summary: We used an experimental mouse model to further evaluate whether constitutive p53 deficiency in the germ line may increase the rate of de novo CNV in the offspring. C57Bl6 mice with defined trp53 status (either +/+, +/- or -/-) were crossed with 129SvSL trp53+/+ mice and 129SvSL trp53-/- mice were crossed with C57Bl6 trp53+/+ mice.  CNV were analyzed in DNA isolated from whole F1 embryos at 17.5 days and compared with liver DNA from their parents. One out of 36 embryo from trp53+/+ parents was detected to have a potential de novo CNV.  No de novo CNV was detected in 84 embryos with a p53 deficient parent.  These observations suggest that, in this mouse model, partial or complete deficiency of p53 function in the germ line does not increase the rate of CNV formation in the offspring.

overall_design: Affymetrix Mouse Diversity Genotyping Array was performed at The Jackson Lab

first: Chang

last: Chan

first: Arnold

middle: J

last: Levine


title: Sequence specificity incompletely defines the genome-wide occupancy of Myc

status: Public on Sep 22 2014

city: Durham

first: Raluca

last: Gordan

state: NC

address: 101 Science Dr, CIEMAS 2179

department: Center for Genomic and Computational Biology

institute: Duke University

summary: The Myc-Max heterodimer is a DNA binding protein that regulates expression of a large number of genes. Genome occupancy of Myc-Max is thought to be driven by E-boxes (CACGTG or variants) to which the heterodimer binds in vitro. By analyzing ChIP-Seq datasets, we demonstrated that the positions occupied by Myc-Max across the human genome correlate with the RNA polymerase II (Pol II) transcription machinery better than with E-boxes. Metagene analyses showed that in promoter regions, Myc was uniformly positioned about 100 bp upstream of essentially all promoter proximal paused polymerases with Max about 10 bp upstream of Myc. We re-evaluated the DNA binding properties of full length Myc-Max proteins using electrophoretic mobility shift assays (EMSA) and protein-binding microarrays (PBM). EMSA results demonstrated Myc-Max heterodimers have high affinity for both E-box containing and non-specific DNA. Quantification of the relative affinities of Myc-Max for all possible 8- mers using PBM assays showed that sequences surrounding core 6-mers significantly affect binding. Comparing to the in vitro sequence preferences, Myc-Max genomic occupancy measured by ChIP-Seq was largely, although not completely, independent of sequence specificity. Our results suggest that the transcription machinery and associated promoter accessibility play an important role in genomic occupancy of Myc.

overall_design: Two protein binding microarray (PBM) experiments were performed: one for the heterodimer of the human transcription factors c-Myc and Max, and one for the Max-Max homodimer. Briefly, 4x44K arrays (Agilent Technologies; AmadID 015681) containing the ‘all 10-mer’ universal PBM design were used.  Arrays were incubated with a PBS buffer based protein mixture of wither 10nM His-tagged Myc-Max heterodimer or 10nM His-tagged Max-Max homodimer, 2% milk, 200ng/µL BSA, 50ng/µL Salmon Testes DNA, and 0.02% TX-100.  Bound protein was tagged with 10ng/µL anti-His antibody conjugated to Alexa 488 (Qiagen; 35310) in PBS with 2% milk.  Data were analyzed to obtain fluorescence intensities for all 8mers.  The PBM protocol is described in Berger et al., Nature Biotechnology 2006 (PMID 16998473).


title: Gene expression profile in DRG neurons over-expressing NRG1 type III intracellular domain

status: Public on Sep 26 2014

city: milano

first: Amelia

last: Trimarco

address: via olgettina 60

department: Divisione di Neuroscienze-INSPE

country: Italy

institute: Ospedale San Raffaele

summary: In DRG neurons NRG1 type III intacellular domain (ICD) moves to the nucleus upon contact with Schwann cells. We aimed to investigate genes up/down regulated by ICD.

overall_design: We analyzed total RNA from DRG neurons over-expressing ICD comparing it to RNA from wild-type DRG neurons and RNA from DRG neurons over-expressing EGFP. We used 4 biological replicates and two technical replicates for each condition.

first: Paola

last: Brambilla

first: Carla

last: Taveggia

first: Filippo

last: Martinelli Boneschi


title: MicroRNA expression in normal and tumoral esophageal squamous cell lines

status: Public on Sep 20 2014

city: Sakai

first: OSAMU

last: ISHIBASHI

address: 1-1 Gakuen-cho, Naka-ku

department: Grad Sch Life & Environmental Sciences

country: Japan

institute: Osaka Prefecture University

summary: This study was designed to identify microRNAs aberrantly expressed in esophageal squamous cell carcinoma (ESCC) cells.

platform_organism:
Homo sapiens
Human alphaherpesvirus 1
Human alphaherpesvirus 2
Cytomegalovirus
Lymphocryptovirus
Rhadinovirus
JC polyomavirus
Human immunodeficiency virus 1
Merkel cell polyomavirus
Betapolyomavirus hominis
Betapolyomavirus macacae

overall_design: Three esophageal squamous cell carcinoma-derived cell lines and one normal human esophageal squamous cell line were analyzed.

first: Ichiro

last: Akagi

first: Osamu

last: Ishibashi


title: ChIP-chip of MCF7 Sox2 regulatory region 2 transcription activity reporter unresponsive and reporter responsive breast cancer cells

status: Public on Sep 25 2014

city: Edmonton

first: Raymond

last: Lai

state: Alberta

address: 5-142 Katz Building, University of Alberta

department: Laboratory Medicine and Pathology

country: Canada

institute: University of Alberta

type: Genome binding/occupancy profiling by genome tiling array

summary: We found that MCF7 and ZR751 Sox2-expressing breast cancer cell lines comprise of cells with heterogeneous Sox2 transcription activity reporter response. A small subset of Sox2 reporter responsive cells are more tumourigenic than the bulk Sox2 reporter unresponsive cells. We questioned whether Sox2 exhibit differential gene promoter occupancies in the two cell subsets to govern differential gene expression patterns.

overall_design: Sox2 ChIP in reporter unresponsive (RU) and reporter responsive (RR) cells (duplicate samples) were compared. IgG ChIP in RU and RR cells served as the negative controls.

first: Karen

last: Jung


title: Tumor Cell Heterogeneity and Dormancy in Single Disseminated Prostate Cancer Cells

status: Public on Sep 16 2014

city: Seattle

first: Ilsa

last: Coleman

state: WA

address: 1100 Fairview Ave N, E2-112

department: Human Biology

institute: Fred Hutchinson Cancer Center

summary: Prostate cancer (PCa) disseminated tumor cells (DTC) in the bone marrow (BM) can remain dormant for prolonged periods before recurrence.  Our aim was to characterize individual prostate DTC, analyze tumor cell heterogeneity, and identify markers of tumor dormancy.

overall_design: Custom Agilent 44K whole human genome expression oligonucleotide microarrays were used to profile single disseminated tumor cells isolated from bone marrow (BM) samples of four patients with no evidence of disease (NED) upon follow-up and six advanced disease (ADV) prostate cancer patients. Essentially, a two-step selection process was employed, in which anti-CD45 and anti-CD61 conjugated to immunomagnetic beads were used for negative selection, and anti-HEA was used for positive selection. Cells were then fluorescently stained for BerEP4, counter stained with RPE anti-CD45, and individually selected (10 single cells each per patient) under fluorescent light using a micropipette system for further analysis. RNA was amplified using the WT-Oviation one-direct system and hybridized against a common reference pool of prostate tumor cell lines.

first: Lisly

last: Chéry

first: Hung-Ming

last: Lam

first: Bryce

last: Lakely

first: Sandy

last: Larson

first: Roger

first: Julio

last: Aguirre-Ghiso

first: Jing

last: Xia

first: Roman

last: Gulati

first: Peter

last: Nelson

first: Bruce

last: Montgomery

first: Paul

last: Lange

first: Linda

middle: A

last: Snyder

first: Robert

middle: L

last: Vessella

first: Colm

last: Morrissey


title: Mouse Bone-marrow Stromal Cell Lines Genetic Expression Comparison

city: Madison

first: Igor

last: Slukvin

state: WI

address: 1220 Capitol Court

department: Department of Pathology and Laboratory Medicine

institute: University of Wisconsin

summary: OP9 stromal cells are strong inducers of mesoendodermal differentiation of human embryonic stem cells. They acquire inductive function after prolonged post-confluence culture. The experiment is designed to determine the genes specifically expressed in these highly inductive OP9 cells compared to non-confluent OP9 cultures as well as other stromal cell lines (MS5, S17).

overall_design: OP9, MS5, and S17 cells were plated on gelatin-coated 10cm dishes in alphaMEM/20%FBS. Cells were collected at confluence (day 4) and after additional 4 days post-confluence culture. Half of the medium was replaced with fresh medium on day 4. Cells were collected by trypsin-EDTA, lysed in TRIReagent and strored at -80C up to 1 month. RNA was isolated and treated with DNase using Ambion RiboPure RNA isolation kit and TURBO DNAfree reagents. One sample was analyzed per condition.

first: Maxim

last: Vodyanik

first: Scott

last: Swanson


title: Expression data from primary bovine mammary epithelial cells (pbMEC) primed with 100 ng/ml LPS and subsequently challenged with heat inactivated E. coli particles after a short or long waiting period

status: Public on Sep 13 2014

city: Dummerstorf

first: Juliane

last: Guenther

address: Wilhelm-Stahl-Allee 2

country: Germany

institute: Leibniz-Institute for Farm Animal Biology (FBN)

summary:
Background:  Udder infections with environmental pathogens like Escherichia coli are a serious problem for the diary industry. Reduction of incidence and severity of mastitis is desirable and mild priming of the immune system either through vaccination or with low doses of an immune stimulant like lipopolysaccharide LPS was previously found to dampen detrimental effects of a subsequent infection. Monocytes / macrophages are known to develop tolerance to the endotoxin (ET) LPS as adaptation strategy to prevent exuberant inflammation.   We have recently observed that application of 1 µg of LPS/udder quarter effectively protects the cow for several days from an experimentally elicited mastitis. We have modelled this process in primary cultures of Mammary Epithelial Cells (MEC) from the cow. This is by far the most abundant cell type in the udder coming into contact with invading pathogens and little is known about the role of MEC in establishing ET in the udder.
Results: We primed primary MEC cultures for 6 h with LPS (100 ng/ml) and stimulated some cultures 12 h or 42 h later with 107/ml of E. coli particles. Affymetrix microarrays were used to profile priming related alterations in the global transcriptome of those cells. Corner stone data were validated with quantitative real time PCR. LPS-priming alone caused differential expression of 40 genes and mediated significantly different response to a subsequent E. coli challenge of 226 genes. Expression of 38 genes was enhanced while that of 188 was decreased. Higher expressed were anti-microbial factors (ß-defensin LAP, SLPI), cell and tissue protecting factors (DAF, MUC1, TGM1,-3) as well as mediators of the sentinel function of MEC (CCL5, IL-8). Dampened was the expression of potentially harmful pro-inflammatory master cytokines (IL-1B, IL-6, TNF-alpha and immune effectors (iNOS, matrix metalloproteases). Functional network analysis highlighted the reduced expression of IL-1B and of IRF7 as key to this modulation.
Conclusion: LPS-primed MEC are fitter to repel pathogens and better protected against misguided attacks of the immune response. Attenuated is the exuberant expression of factors potentially promoting immunopathological processes. MEC therefore recapitulate many aspects of ET known so far from professional immune cells.

overall_design: Each experiment was performed in triplicate using separate pbMEC cultures (80% confluence) prepared from the udders of udders of three healthy, pregnant (d130 of gestation) cows in the mid of their first lactation. Controls (C.) were cultured for 12 h in GM, washed 3x with PBS and cultivated for additional 18 h (short waiting experiment) or 48 h (long waiting experiment). For the priming experiment (P.) the pbMEC cultures were stimulated (“primed”) at time 0 h with 100 ng/ml LPS , washed three times with PBS and cultivated for another 18 h or 48 h. For the induction trial (I.) cells were challenged with 107/ml particles of heat inactivated E. coli1303 for 6 h. The cultures were handled exactly like the control group (C.) prior to the E. coli challenge. For the induction post priming experiment (I.p.P.) cultures were primed for 12 h with LPS, just as described for the priming group (P.). After 3x washing with PBS and waiting for 12 h or 42 h in GM the I.p.P. cultures were also challenged with 107/ml particles of E. coli1303. Cells were harvested at time 30 h (short waiting experiments) or 60 h (long waiting experiments) and total RNA was prepared.

last: Günther

first: Wolfram

last: Petzl

first: Holm

last: Zerbe

first: Hans-Joachim

last: Schuberth

first: Dirk

last: Koczan

first: Leopold

last: Goetze

first: Hans-Martin

last: Seyfert


title: Prediction of antibiotic resistance by large-scale phenotypic and genotypic data

status: Public on Sep 17 2014

city: Suita

first: Chikara

last: Furusawa

state: Osaka

address: 6-2-3 Furuedai

department: Quantitative Biology Center (QBiC)

institute: RIKEN

summary: The evolution of antibiotic resistance is a clear example of adaptation by natural selection. Although a number of mutations contributing to the resistance have been identified, the relationship between the mutations and the related phenotypic changes responsible for the resistance has yet to be fully elucidated. To better characterize phenotype-genotype mapping for drug resistance, we performed parallel laboratory evolution of Escherichia coli under the selection of single antibiotics and after 90 days propagation obtained resistant strains. We find that an acquisition of resistance to one drug drastically changes the resistance and susceptibility to other drugs. Based on transcriptome data of these strains, we demonstrated that the resistances could be quantitatively predicted by the expression changes of a small number of genes. Whole-genome resequencing analysis provided several candidate mutations contributing to the resistances, while phenotype-genotype mapping was suggested to be complex and included various mutations that caused similar phenotypic changes. The integration of transcriptome and genome data enables us to extract essential phenotypic changes for drug resistances.

overall_design: To examine the contribution of the gene expression changes to the antibiotic resistances, transcriptome of the parent strain (duplicated) and 40 resistant strains (4 parallel-evolved resistant strains for 10 antibiotics) were analyzed.

first: Shingo

last: Suzuki


title: Muscle specific proteasome deficient mice

city: Sendai

first: Naoki

state: Miyagi

address: 1-1 Seiryo-machi, Aoba-ku

department: Department of Neurology

institute: Tohoku University School of Medicine

summary: The ubiquitin-proteasome and autophagy-lysosome pathways are the two major routes for protein and organelle clearance. In skeletal muscle, both systems’ excessive activation induces severe muscle loss. Although altered proteasomal function has been observed in various myopathies, the specific role of proteasomal activity in skeletal muscle has not been determined by loss-of-function approaches. Here, we report that muscle-specific deletion of a crucial proteasomal gene, Rpt3, resulted in profound muscle atrophy and decrease in force. Rpt3 null muscles showed reduced proteasomal activity in early age, accumulation of basophilic structure, disorganization of sarcomere, and formation of vacuoles and concentric membranous structures in electronmicroscope. We also observed accumulation of ubiquitin, p62, LC3, TDP43, FUS and VCP proteins. Proteasomal activity is important to preserve muscle mass and to maintain myofiber integrity. Our results suggest that inhibition/alteration of proteasomal activity can contribute to myofiber degeneration and weakness in muscle disorders, such as inclusion body myositis, characterized by accumulation of abnormal inclusions.

overall_design: Tibialis anterior muscles from Rpt3 null and control mice. each 3 mice.

first: Yasuo

last: Kitajima

first: Yoshihiro

last: Tashiro

first: Maki

last: Tateyama

first: Risa

last: Ando

first: Rumiko

last: Izumi

first: Hitoshi

last: Warita

first: Masaaki

last: Kato

first: Ryoichi

last: Nagatomi

first: Ryosuke

last: Takahashi

first: Masashi

last: Aoki


title: Expression data from primary rat aortic smooth muscle cells

status: Public on Sep 05 2014

city: Moscow

first: Sergei

last: Orlov

address: 1/b.12 Leninskie Gory

country: Russia

institute: Moscow State Univeristy

summary:
Electrochemical gradients of monovalent cations across the plasma membrane (high intracellular potassium, [K+]i vs low intracellular sodium, [Na+]i) are created by the Na+,K+-pump and determine a large variety of physiologically important processes. We hypothesized that transcriptomics changes triggered by hypoxia are at least partially caused by Na+i/K+i-mediated excitation-transcription coupling .
We used microarrays for identification and functional characterization of [Na+]i/]K+]i-sensitive transcriptome in RASMC

overall_design: Quiescent cells were washed with K+-free DMEM and incubated for 6 hr at 37oC in a humidified atmosphere with 5% CO2/balance air in control DMEM, K+-free DMEM and DMEM containing 3 mM ouabain. Total RNA was extracted from cells grown in 6-well plates with TRIzol® reagent and purified with RNeasy® MinElute cleanup kit, following the manufacturers’ protocols. Microarray experiments were performed with GeneChip® Rat Gene 1.0 ST array.

middle: N

first: Svetlana

last: Koltsova

first: Pavel

last: Hamet


title: Streptococcus pyogenes MGAS5005: control vs heme exposure

city: College Park

first: Yoann

last: Le Breton

state: Maryland

address: 3217 Bioscience Research Building (413)

department: Cell Biology and Molecular Genetics

institute: University of Maryland

summary: Transcriptional profiling of Streptococcus pyogenes MGAS5005 cells comparing control untreated GAS cells with GAS cells exposed to 4uM heme for 1.5 h

overall_design: Two-condition experiment, untreated vs. heme-treated MGAS5005 cells. Biological replicates: 3 control, 3 Heme-treated, independantly grown and harvested. One replicate per array.

first: Ankita

last: Sachla

first: Fahmina

last: Akhter

first: Kevin

last: McIver

first: Zehava

last: Eichenbaum


title: Transgenic Eµ-myc mouse lymphoma array CGH data

status: Public on Sep 10 2014

first: Daphne

middle: R

last: Friedman

address: 101 Science Drive, Room 2121, CIEMAS Bldg

institute: Duke University Medical Center

summary: We used array CGH data from Eµ-myc lymphomas to assess significant differences in DNA copy number variation between Cluster 1 and Cluster 2 lymphomas.

overall_design: When Eµ-myc mice had evidence of lymphoma and/or ill appearance, they were humanely sacrificed and dissected.  Lymphoma tissue was obtained and flash frozen in liquid nitrogen.  Later, lymphoma tissue was homogenized, and genomic DNA was extracted.  Array CGH was performed on genomic DNA, with genomic DNA from normal background strain mice used as the reference.

first: Joseph

last: Nevins

first: Seiichi

last: Mori

first: Xiaolei

last: Jiang


title: GeoChip data of soil microbial communities in the maize rhizosphere and bulk soils

status: Public on Sep 12 2014

city: Chengdu

first: Junpeng

last: Rui

state: Sichuan

address: No. 9 Section 4, Renmin Nan Road

country: China

institute: Chengdu Institute of Biology, Chinese Academy of Sciences

summary:
Microbial communities in the rhizosphere make significant contributions to crop health and nutrient cycling. However, their ability to perform important biogeochemical processes remains uncharacterized.
Important functional genes, which characterize the rhizosphere microbial community, were identified to understand metabolic capabilities in the maize rhizosphere using GeoChip 3.0-based functional gene array method.

overall_design: Triplicate samples were taken for both rhizosphere and bulk soil, in which each individual sample was a pool of four plants or soil cores. To determine the abundance of functional genes in the rhizosphere and bulk soils, GeoChip 3.0 was used.

first: Xiangzhen

last: Li

first: Jingbo

last: Xiong

first: Jiabao

first: Zhili

last: He

first: Jizhong

last: Zhou

first: Anthony

middle: C

last: Yannarell

first: Roderick

middle: I

last: Mackie


title: Comparative epigenomics of human and mouse erythropoiesis

status: Public on Dec 01 2014

city: Cambridge

first: Vijay

middle: G

last: Sankaran

state: MA

address: 7 Cambridge Center

institute: Broad Institute

type: Expression profiling by high throughput sequencing

type: Genome binding/occupancy profiling by high throughput sequencing

summary: Erythropoiesis is one of the best understood examples of cellular differentiation. Morphologically, erythroid differentiation proceeds in a nearly identical fashion between humans and mice, but recent evidence has shown that networks of gene expression governing this process are divergent between species. We undertook a systematic comparative analysis of six histone modifications and four transcriptional master regulators in primary pro-erythroblasts and erythroid cell lines to better understand the underlying basis of these transcriptional differences. Our analyses suggest that while chromatin structure across orthologous promoters is strongly conserved, subtle differences are associated with transcriptional divergence between species. Many transcription factor (TF) occupancy sites were poorly conserved across species (~25% for GATA1, TAL1, and NFE2), but these factors were considerably more conserved between proerythroblasts and cell lines derived from the same species. We found that certain cis-regulatory modules co-occupied by GATA1, TAL1, and KLF1 are under strict evolutionary constraint and localize to genes necessary for erythroid cell identity. More generally, we show that conserved TF occupancy sites are indicative of active regulatory regions and strong gene expression sustained during maturation. Our results suggest that evolutionary turnover of TF binding sites drives transcriptional divergence partially by mediating changes in the underlying chromatin structure. We provide examples of how this framework can be applied to understand epigenomic variation in specific regulatory regions, such as the Beta-globin gene locus. Our findings have important implications for understanding epigenomic changes that mediate variation in cellular differentiation across species, while also providing a valuable resource for studies of hematopoiesis.

sample_organism:
Homo sapiens
Mus musculus
Austrofundulus limnaeus

overall_design:
Examination of 6 histone marks and 4 transcription factors across human pro-erythroblasts, mouse pro-erythroblasts, K562 cells, and G1E cells
'Extract protocol' and 'library construction protocol' were performed as detailed in: GSE53983, GSE40522, GSE52924, GSE47492, GSE50406, GSE36028, GSE48020, GSE43626, GSE36985, GSE36589, GSE31477, GSE30142, GSE18868, GSE27893, GSE26501

first: Jacob

last: Ulirsch


title: Real-time quantitative PCR analysis of mouse pre-implantation embryos

status: Public on Sep 01 2014

city: Blacksburg

first: Fernando

middle: H

last: Biase

state: VA

address: 175 West Campus Drive

department: School of Animal Sciences

institute: Virginia Tech

summary: Adult female mice (C57BL/6) were super-ovulated by intraperitoneal hormone injections with the interval of 48 hours between injections. The hormones administered were PMSG followed by hCG (5IU/0.1ml, Sigma-Aldrich). Following the second hormonal treatment, the females were mated with males (1:1, C57BL/6). Zygotes, 2-cell and 4-cell and blastocysts were collected 26, 48 and 52 hours post hCG.  Prior to cell collection, the zona pelucida was removed by Tyrode   s acid solution. The 2- and 4-cell embryos were then immersed in Trypsin solution (Invitrogen) with RNase inhibitor (1 IU/ul, Clontech) and BSA (50 ug/ul) for the separation of the blastomeres. The separated blastomeres were snap frozen, and maintained at -80  C until processed. Twelve zygotes, 20 2-cell and 9 4-cell embryos were collected for single cell qPCR. In addition, we prepared with a pool of 10 zygotes and a pool of 50 zygotes as positive controls. The cells and pools were subjected to reverse transcription with SuperScript  VILO    cDNA Synthesis kit (Life Technologies) as recommended by the manufacturer. DELTAgene    Assays were custom designed for 94 genes associated with embryonic development or regulation of gene expression, as well as 2 housekeeping genes. The cDNA from cells and pools were subjected to target specific amplification for 20 cycles. Pre-amplified template was diluted and subjected to primer specific amplification with SooFast   EvaGreen  Supermix (Biorad) on 96.96 array chip and BiomarkHD    System (Fluidigm). Relative quantification of gene expression (log2 space) was obtained by subtracting the Ct values from the baseline value of 22.

overall_design: 12 zygotes, 10 2-cell, and 9 4-cell mouse (C57BL/6) embryos were collected and multi-cell embryos were separated into blastomeres

first: Sheng

last: Zhong


title: Access to follicular dendritic cells is a pivotal step in murine chronic lymphocytic leukemia B cell activation and proliferation

city: Münster

first: Michael

last: Grau

state: Nordrhein-Westfalen

address: Albert-Schweitzer-Campus 1

department: Faculty of Medicine

institute: University of Münster

summary: In human chronic lymphocytic leukemia (CLL) pathogenesis B cell antigen receptor signaling seems important for leukemia B cell ontogeny, whereas the microenvironment influences B cell activation, tumor cell lodging and provision of antigenic stimuli. Using the murine Eμ-Tcl1 CLL model, we demonstrate that CXCR5-controlled access to follicular dendritic cells (FDCs) confers proliferative stimuli to leukemia B cells. Intravital imaging revealed a marginal zone B cell-like leukemia cell trafficking route. Murine and human CLL cells reciprocally stimulated resident mesenchymal stromal cells through lymphotoxin-β-receptor activation, resulting in CXCL13 secretion and stromal compartment remodeling. Inhibition of lymphotoxin/lymphotoxin-β-receptor signaling or of CXCR5 signaling retards leukemia progression. Thus, CXCR5 activity links tumor cell homing, shaping a survival niche, and access to localized proliferation stimuli.

overall_design: This GEO dataset is comprised of GEP measurements for EµTCL mouse CD5+CD19+ tumor cells and healthy WT controls, including healthy MZB cells and B1 cells. 6 measurements are for WT EµTCL1 mice, 5 for the CXCR5-KO EµTCL1 genotype. MZB and B1 cells were pooled from 15 animals. WT reference was obtained from 5 WT animals

first: Uta

last: Höpken

first: Armin

last: Rehm

first: Georg

last: Lenz


title: The SET-2/SET1 histone H3K4 methyltransferase maintains pluripotency in the caenorhabditis elegans germline.

status: Public on Sep 04 2014

city: Lyon

first: Valerie

last: Robert

address: 46 Allee d'Italie

department: LBMC

country: France

institute: ENS Lyon

summary: Histone H3 Lys 4 methylation (H3K4me) is deposited by the conserved SET1/MLL methyltransferases acting in multiprotein complexes including Ash2 and Wdr5. While individual subunits contribute to complex activity, how they influence gene expression in a specific tissue remains largely unknown. In caenorhabditis elegans, SET-2/SET1, WDR-5.1 and ASH-2 are differentially required for germline H3K4 methylation. Using expression profiling on germlines from animals lacking set-2, ash-2 or wdr-5.1, we show that these subunits play unique and redundant functions to promote expression of germline genes and repress somatic genes. We further show that in set-2 and wdr-5.1 deficient germlines, somatic gene misexpression is associated with conversion of germ cells into somatic cells, and that nuclear RNAi acts in parallel with SET-2 and WDR-5.1 to maintain germline identity. These findings uncover a unique role for SET-2 and WDR-5.1 in preserving germline pluripotency, and underline the complexity of the cellular network regulating this process.

overall_design: Gene misregulation in SET1/set-2, wdr-5.1 and ash-2 defective germlines

first: Valérie

first: Marine

last: Mercier

first: Stéphane

last: Janczarski

first: Francesca

last: Palladino


title: Mycoplasma gallisepticum Lipid Associated Membrane Proteins Up-regulate Inflammatory Genes in Chicken Tracheal Epithelial Cells via TLR-2 Ligation Through an NF-κB Dependent Pathway

status: Public on Sep 19 2014

city: Storrs

first: Frank

last: Zappulla

state: CT

address: 61 North Eagleville Road

department: Pathobiology

institute: University of Connecticut

summary: To identify differential gene expression profiles of chicken tracheal epithelial cells (TECs) upon exposure to Mycoplasma gallisepticum virulent strain Rlow and avirulent strain Rhigh and corresponding lipid associated membrane proteins(LAMP) at 1.5 hours in vitro. Goal of this experiment was to identify relative comtribution of LAMPs in up-regulation of inflammatory gene compared to the live strains. Several genes were identified to be differentially regulated in all exposures, but the virulent strain up-regulated more number genes as well as at a higher extent. We identified 6 important inflammatory mediators and did confirmatory RT-qPCR analysis at 1.5, 6 and 24 hours in vitro as well as at 1.5 and 6 hours ex-vivo. RT-qPCR was also employed to identify expression of these 6 genes in presence of different signalling inhibitors and we were able to identify that Mycoplasma gallisepticum LAMPs up-regulate these inflammatory genes via TLR-2 in an NF-κB dependent pathway.

overall_design: Primary chicken tracheal epithelial cells (TECs) were exposed to either 500 MOI of a virulent Mycoplasma gallisepticum strain Rlow or an avirulent strain Rhigh and the corresponding lipid associated membrane proteins (LAMPs) at 5µg/mL for 1.5 hours. 4 biological replicates along with a dye swap technique totalling 8 replicates were utilized for all microarray experiments

first: Sanjukta

last: Majumder


title: Gene Co-Expression Network Analysis in Rhodobacter capsulatus and Application to Comparative Expression Analysis of Rhodobacter sphaeroides

status: Public on Sep 08 2014

city: St. John's

first: Ryan

last: Mercer

state: Newfoundland

address: 232 Elizabeth Avenue

department: Biology

institute: Memorial University

summary: Transcriptomic data has been previously used to determine expression patterns in various R. capsulatus strains using custom made Affymetrix microarrays. Additional expression analyses have since been carried out to obtain preliminary data on certain wild type and mutant strains that have not been reported on. We used all current microarray expression data available and constructed an R. capsulatus gene co-expression network and performed functional analysis of identified gene modules.

overall_design: RNA was harvested from various wild type and mutant R. capsulatus strains grown under photoheterotrophic conditions to different growth phases. The samples were hybridized to custom made R. capsulatus Affymetrix microarrays according to manufacturers recommendations. The raw data was RMA normalized and log transformed.

first: Lourdes

last: Peña-Castillo

first: Anastasia

last: Gurinovich

first: Andrew

last: Lang


title: Cyclin C is a haploinsufficient tumour suppressor

status: Public on Sep 02 2014

city: Boston

first: Tobias

last: Otto

address: 450 Brookline Avenue

department: Cancer Biology

institute: Dana-Farber Cancer Institute

summary: Cyclin C was cloned as a growth-promoting G1 cyclin, and was also shown to regulate gene transcription. Here we report that in vivo cyclin C acts as a haploinsufficient tumour suppressor, by controlling Notch1 oncogene levels. Cyclin C activates an 'orphan' CDK19 kinase, as well as CDK8 and CDK3. These cyclin-C-CDK complexes phosphorylate the Notch1 intracellular domain (ICN1) and promote ICN1 degradation. Genetic ablation of cyclin C blocks ICN1 phosphorylation in vivo, thereby elevating ICN1 levels in cyclin-C-knockout mice. Cyclin C ablation or heterozygosity collaborates with other oncogenic lesions and accelerates development of T-cell acute lymphoblastic leukaemia (T-ALL). Furthermore, the cyclin C encoding gene CCNC is heterozygously deleted in a significant fraction of human T-ALLs, and these tumours express reduced cyclin C levels. We also describe point mutations in human T-ALL that render cyclin-C-CDK unable to phosphorylate ICN1. Hence, tumour cells may develop different strategies to evade inhibition by cyclin C.

overall_design: Comparison of wild-type mouse embryonic fibroblasts (n=3 biological replicates) versus cyclin C knockout MEFs (n=3), wild-type mouse embryonic stem cells (n=3) versus cyclin C knockout ESC (n=3), wild-type mouse embryonic brain (n=3) versus cyclin C knockout embryonic brain (n=3)

last: Li

first: Clifford

last: Meyer


title: Using RNA sequencing for identifying gene imprinting and random monoallelic expression in human placenta (SNP genotyping)

city: Tartu

first: Tauno

last: Metsalu

address: Liivi 2

country: Estonia

institute: University of Tartu

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

summary: Given the possible critical importance of placental gene imprinting and random monoallelic expression on fetal and infant health, most of those genes must be identified, in order to understand the risks that the baby might meet during pregnancy and after birth. Therefore, the aim of the current study was to introduce a workflow and tools for analyzing imprinted and random monoallelic gene expression in human placenta, by applying whole-transcriptome (WT) RNA sequencing of placental tissue and genotyping of coding DNA variants in family trios. Ten family trios, each with a healthy spontaneous single-term pregnancy, were recruited. Total RNA was extracted for WT analysis, providing the full sequence information for the placental transcriptome. Parental and child blood DNA genotypes were analyzed by exome SNP genotyping microarrays, mapping the inheritance and estimating the abundance of parental expressed alleles. Imprinted genes showed consistent expression from either parental allele, as demonstrated by the SNP content of sequenced transcripts, while monoallelically expressed genes had random activity of parental alleles. We revealed 4 novel possible imprinted genes (LGALS8, LGALS14, PAPPA2 and SPTLC3) and confirmed the imprinting of 4 genes (AIM1, PEG10, RHOBTB3 and ZFAT-AS1) in human placenta. The major finding was the identification of 4 genes (ABP1, BCLAF1, IFI30 and ZFAT) with random allelic bias, expressing one of the parental alleles preferentially. The main functions of the imprinted and monoallelically expressed genes included: i) mediating cellular apoptosis and tissue development; ii) regulating inflammation and immune system; iii) facilitating metabolic processes; and iv) regulating cell cycle.

overall_design: Ten family trios (mother, father, child) were analysed using SNP genotyping. Raw data contains additional two samples that were not used.

first: Triin

last: Viltrop

first: Airi

last: Tiirats

first: Balaji

last: Rajashekar

first: Ene

last: Reimann

first: Sulev

last: Kõks

first: Kristiina

last: Rull

first: Lili

last: Milani

first: Ganesh

last: Acharya

first: Purusotam

last: Basnet

first: Jaak

last: Vilo

first: Reedik

last: Mägi

first: Andres

last: Metspalu

first: Maire

last: Peters

first: Kadri

last: Haller-Kikkatalo

last: Salumets


title: Exonic variants associated with development of Aspirin Exacerbated Respiratory Diseases

city: Bucheon-si

first: Seung-Woo

last: Shin

state: Gyeonggi-do

address: 1174 Jung-dong, Wonmi-gu

department: Genome research Center for Allergy and Respiratory Diseases

country: South Korea

institute: Soon Chun Hyang University hospital

summary: Aspirin-exacerbated respiratory disease (AERD) is one phenotype of asthma, often in the form of a severe and sudden attack. Due to time consuming and laborious oral aspirin challenge (OAC) for diagnosis of AERD, non-invasive biomarkers have been searched. Therefore, we scrutinize AERD-associated exonic SNPs and examine the diagnostic potential of combination of these candidate SNPs to predict AERD

overall_design: DNA obtained from 164 AERD subjects, 397 subjects with aspirin-tolerant asthma (ATA), 398 normal controls and 10 null samples were subjected to Exome Chip assay of 240K SNPs. 1023 model (210-1) were generated from combination of the top 10 SNPs selected by p-values. The area under the curve (AUC) value of receiver operating characteristic (ROC) curves was calculated for each model. SNP functional Portal and PolyPhen-2 was used to validate the functional significance of the candidate SNPs

first: Byung

last: Park


title: Study of PB1-F2 functions in avian host.

city: Jouy-en-Josas

first: Ronan

last: Le Goffic

state: Please select one below:

address: Domaine de Vilvert

department: SA

institute: INRA

summary: Highly pathogenic avian influenza virus (HPAIV) is a permanent threat due to its capacity to cross species barriers and generate severe infections and high mortality in humans. Recent findings have highlighted the potential role of PB1-F2, a small accessory influenza protein, in the pathogenesis process mediated by HPAIV in mammals. In this study, using a recombinant H5N1 HPAIV (wt) and its PB1-F2-deleted mutant (ΔF2), we studied the effects of PB1-F2 in a chicken model. Unexpectedly, when using low inoculation dose we observed that the wt-infected chickens had a higher survival rate than the ΔF2-infected chickens, a feature that contrasts with what is usually observed in mammals. High inoculation dose had similar mortality rate for both viruses, and comparison of the bio-distribution of the two viruses indicated that the expression of PB1-F2 allows a better spreading of the virus within chicken embryos. Transcriptomic profiles of lungs and blood cells were characterized at two days post-infection in chickens inoculated with the wild type (wt) or the ΔF2 mutant viruses. In lungs, the expression of PB1-F2 during the infection induced pathways related to calcium signaling and repressed a large panel of immunological functions. In blood cells, PB1-F2 was associated to a gene signature specific for mitochondrial dysfunction and down-modulated leucocytes activation. Finally we compared the effect of PB1-F2 in lungs of chickens and mice. We identified that gene signature associated to tissue damages is a PB1-F2 feature shared by the two species; by contrast, the early inhibition of immune response mediated by PB1-F2 observed in chickens is not seen in mice. In summary, our data suggest that PB1-F2 expression deeply affect the immune host response in chickens in a way that may attenuate pathogenicity, a feature differing from what was previously observed in mammal species.

overall_design: Three-condition experiment, virus-infected (wt or ΔF2) vs. Mock-infected chickens. Biological replicates: 2x5 control replicates, 5 wt replicates, 5 ΔF2 replicates.

first: Hana

last: Weingartl


title: Genome-wide 10K SNP profiles in heterogeneous stock rats that differ in glucose tolerance

status: Public on Sep 18 2014

city: Milwaukee

first: Leah

last: Solberg Woods

address: 8701 Watertown Plank Road

department: Pediatrics

institute: Medical College of Wisconsin

summary: Using heterogeneous stock (HS) rats, we have identified a region on rat chromosome 1 that maps multiple diabetic traits.  We sought to use global expression analysis to determine if genes within this region are differentially expressed between HS rats with normal glucose tolerance and those with glucose intolerance

overall_design: HS rats were euthanized at 17 weeks of age and tail sample was taken.  Genomic DNA was extracted from tail of 23 HS rats with glucose intolerance and 23 HS rats with normal glucose.  The Affymetrix 10K SNP array was used to genotype these animals.

first: Shirng

middle: W

last: Tsaih

first: Katie

last: Holl

first: Shuang

last: Jia

first: Mary

last: Kaldunski

first: Michael

last: Tschannen

first: Hong

last: He

first: Jaime

last: Andrae

first: Shun

last: Li

first: Alexander

last: Stoddard

first: John

last: Parrington

first: Margarida

last: Ruas da Silva

first: Antony

last: Galione

first: James

last: Meigs

first: Raymond

last: Hoffmann

first: Pippa

last: Simpson

first: Howard

last: Jacob

first: Martin

last: Hessner


title: Effect of Titanium dioxide nanoparticles on Escherichia coli K12 MG1655 genes expression

city: METZ

first: Bénédicte

last: SOHM

address: 8 rue du Gal Delestraint

institute: CNRS

summary: In the present study, we investigated the transcriptional expression patterns of the model strain E. coli exposed to titanium dioxide nanoparticles (NP-TiO2), under dark conditions by using a microarray. Expression profiles were compared to unexposed E.coli and ratio of expression were analysed.

sample_organism: Escherichia coli str. K-12 substr. MG1655

overall_design: Cell exposure to NP-TiO2 was conducted in 10 mM NaCl, E. coli bacterial suspension and NP-TiO2 stock suspension (or mQ water for the control) were added to the NaCl solution to obtain final concentrations of 10E7 cells/ml and 100 mg/l of TiO2 nanoparticles. The flasks were then incubated at 20°C on a dark rotary shaker for 5 h. Exposed NP-TiO2: 4 biological replicats. Control: 4 biological replicats.

last: Sohm

first: Christophe

last: Pagnout


title: Nanostring nCounter human miRNA assay (v1) of eosinophilic esophagitis

city: Aurora

first: Calies

last: Menard-Katcher

state: CO

institute: University of Colorado School of Medicine

summary: Nanostring nCounter Human miRNA assay (v1) of esophageal mucosal biopsies from children with eosinophilic esophagitis and controls

overall_design: Individual esophageal mucosal biopsies from children with eosinoniphilic esophagitis and controls were analysed for detection of microRNA

first: Adam

last: Zahm

first: Josh

last: Friedman


title: TaqMan microRNA array of human serum from children with eosinophilic esophagitis

summary: Serum from children with active and inactive treated eosinophilic esophagitis was analyzed for detection of microRNA

overall_design: Individual serum samples from children with eosinophilic esophagitis were analyzed for detection of microRNA. (n=5 for active EoE and n=5 for inactive EoE)


title: MicroRNA assays of eosinophilic esophagitis

type:
Expression profiling by RT-PCR
Other

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

overall_design: Refer to individual Series


title: VSL#3 supplementation of mice is associated primarily with changes in ileal microbiota composition and amelioration of DSS-induced colitis.

city: San Francisco

first: Jordan

middle: Samuel

last: Mar

state: Ca

address: 513 Parnassus Ave., S-357

department: Medicine, Division of Gastroenterology

institute: University Of California, San Francisco

summary:
Inflammatory bowel diseases encompass gastrointestinal illnesseses typified by chronic inflammation, loss of epithelial integrity and gastrointestinal microbiota dysbiosis. In an effort to counteract these characteristic perturbations, we used stem cells and/or a probiotic preparation in a murine model of Dextran Sodium Sulfate induced colitis to examine both their efficacy in ameliorating disease and impact on niche-specific microbial communities of the lower GI tract.
Colitis was induced in C57BL/6 mice by administering 3% DSS in drinking water for 10 days prior to administering one of three treatment plans: daily probiotic (VSL#3) supplementation for 3 days, a single tail vein injection of 1x106 murine mesenchymal stem cells, or both. Controls included DSS-untreated mice and DSS-treated mice that received no therapy. Ileal, cecal and colonic sections were collected for microbiota and histological analyses.
Microbiota profiling revealed distinct bacterial community compositions in the ileum, cecum and colon of control untreated animals, all of which were predicted in silico to be enriched for a number of discrete KEGG pathways, indicating compositional and functional niche specificity in healthy animals. DSS- treatment perturbed community composition in all three niches with ileal communities exhibiting the greatest change relative to control animals.
Stem cell, VSL#3 and the combination treated animals exhibited treatment-specific microbiota composition in the lower GI tract, though disease scores were only improved in VSL#3 treated animals. This VSL#3-associated shift in the ileal microbiota was characterized by significant Enterobacteriaceae enrichment compared to colitic animals (p<0.05),

platform_organism: Bacteria Archaea

overall_design:
Mice (n=40) were randomly divided into five experimental groups, four of which received Dextran Sodium Sulfate (DSS; 3% solution in drinking water) for 10 days to induce colitis. Three of the DSS-treated groups received the following treatment modalities: VSL#3 (VSL#3, n=5), mesenchymal stem cells (MSC, n=5), or VSL#3 + mesenchymal stem cells (DUAL, n=5).
The fourth DSS-treated group received no intervention (DSS; n=10). The additional fifth group of animals received neither DSS nor any therapeutic intervention and acted as untreated controls (CNTL, n=15). Following colitis induction (Day 10), DSS administration was halted and mice in the VSL#3, MSC and DUAL groups received the following interventions respectively: daily oral supplementation with 5x106 CFUs per supplement of VSL#3 in 100ul PBS (VSL#3); a single tail vein injection of 1x106 murine mesenchymal stem cells in 100_l PBS on Day 10 (MSC) or a combination of both treatments
To provide control data for comparison, CNTL mice (n=5 per time point) were euthanized and sampled on days 1, 10, and 14, while DSS mice (n=5 per time point) were euthanized on days 10 and 14. All MSC, VSL#3, and DUAL mice were euthanized on Day 14. Samples collected from each animal included terminal ileum (1cm proximal to the cecum), cecum (divided transversely and stored as two separate samples), and proximal colon.
All samples were added to RNAlater, prior to storage at -80C for analysis. Additional colonic samples were obtained, proximal to the initial sample site for microbiome analyses, and were preserved in paraformaldehyde for histological analyses.

first: Nabeetha

last: Nagalingam

first: Yuanlin

last: Song

first: Michio

last: Onizawa

first: J

last: Lee

first: Susan

last: Lynch


title: Genomic responses to copper in Synechocystis

city: Sevilla

first: Luis

last: Lopez Maury

address: Av Americo Vespucio 49

country: Spain

institute: IBVF

summary: Analysis of genome-wide gene expression patterns in response to copper in WT and COPR mutant in the cyanobacterium Synechocystis sp PCC 6803.  Here we have used microarrays to interrogate the global responses to copper additions at non-toxic (0.3 micromolar) and toxic concentrations (3 micromolar) of copper in WT and in a mutant in the copR gene. Addition of the non-toxic copper concentration stimulated the metabolism and induced the switch in the use from cyitochrome c6 to plastocyanin. In contrast, high copper addition induced a stress response and affected the metabolism of several other metals. This included repression of ribosomal, photosynthetic and metabolic genes and induction of chaperones and antioxidant enzymes genes. Finally CopRS seems to control only the expression of the copMRS and copBAC operons as all other genes that were differentially expressed by copper seemed to be unaffected in copR strains.

overall_design: Cells treated with 0.3 µM or 3µM copper for 1h.

first: Joaquin

last: Giner-Lamia

first: Francisco

last: Florencio

last: Lopez-Maury


title: microRNA expression in HeLa cells under a mild hyperthermia

city: Kodaira

first: Hirohiko

last: Hohjoh

state: Tokyo

address: 4-1-1 Ogawahigashi

institute: National Institute of Neuroscience, NCNP

summary: We investigated expression profiles of miRNAs in HeLa cells that were subjected to a mild hyperthermia as well as normal temperature by means of DNA microarray. The data suggested similar expression profiles to each other.

overall_design: Small RNA samples prepared from HeLa cells exposed to a mild hyperthermia (40ºC) as well as normal temperature (37ºC) were examined by means of Genopal®-MICH07 DNA chips.

first: Masashi

last: Fukuoka


title: Maize gene expression during infection with the Ustilago maydis mutant for cluster 19A and subdeletions for individual genes of cluster 19A

city: Marburg

first: Gunther

last: Doehlemann

state: Hessen

address: Karl von Frisch Str.

department: Organismic Interactions

institute: Max Planck Institue for Terrestiral Microbiology

summary:
Many of the genes coding for secreted protein effectors are arranged in gene clusters in the genome of the biotrophic plant pathogen Ustilago maydis. The largest of these gene clusters, cluster 19A, encodes 24 secreted effectors. Deletion of the entire cluster results in severe attenuation of virulence. The generation and analysis strains carrying sub-deletions identified 9 genes significantly contributing to tumor formation after seedling infection. As the individual contributions of these genes to tumor formation were small, we studied the response of maize plants to the whole cluster mutant as well as to several individual mutants by array analysis. This revealed distinct plant responses, demonstrating that the respective effectors have discrete plant targets.     Many of the genes coding for secreted protein effectors are arranged in gene clusters in the genome of the biotrophic plant pathogen Ustilago maydis. The largest of these gene clusters, cluster 19A, encodes 24 secreted effectors. Deletion of the entire cluster results in severe attenuation of virulence. The generation and analysis strains carrying sub-deletions identified 9 genes significantly contributing to tumor formation after seedling infection. As the individual contributions of these genes to tumor formation were small, we studied the response of maize plants to the whole cluster mutant as well as to several individual mutants by array analysis. This revealed distinct plant responses, demonstrating that the respective effectors have discrete plant targets.
We used the Affymetrix maize genome array to analyze the transcriptional responses of maize to cluster 19A mutants and individual sub-deletions for the cluster 19A genes tin1, tin3, tin4 and tin5. We found plant responses to the mutants were significantly different although the macroscopic phenotypes of the individual mutants were very similar.

overall_design: U. maydis infected parts of maize seedling leaves were dissected 4 days after inoculation with strain SG200∆19A, SG200∆tin1, SG200∆tin3, SG200∆tin4 and SG200∆tin5, respectively. We previously submitted data of maize leaves that were treated with the progenitor wild type strain SG200 as well as mock-infections under identical experimetal conditions (GEO: GSE10023). These data served as controls for this experiment.

first: Thomas

last: Brefort

first: Shigeyuki

last: Tanaka

first: Nina

last: Neidig

first: Regine

last: Kahmann


title: Mytilus edulis blue mussel larval development Control vs. Fatty acid diet deficiency

status: Public on Aug 31 2014

city: Rimouski

first: Sleiman

last: Bassim

state: Quebec

address: 310, Allée des Ursulines

department: Oceanography

institute: UQAR

summary:
Blue mussel larvae were fed, in a first group, a balanced diet of essential fatty acids (EFAs) provided by a cocktail diet (COC) from three algal species. Larvae were cultured in three separate tanks from hatching, 0 day post-fertilization (DPF) until 42 DPF. Treated larvae were fed a deficient diet (Tiso) that contains low levels of arachidonic acid (AA) and eicosapentaenoic acid (EPA), two EFAs necessary for larval development, performance, and survival.
The goal is to identify coordinated patterns of gene expression and understand their predictive function in relation to growth and mortality during early developmental stages of the blue mussel Mytilus edulis. In order to understand the mechanisms by which growth and survival drive an organism to the full range of its adaptation, we de novo assembled of the mussel transcriptome during early development using next-generation sequencing (NGS) technology, then designed customized microarrays targeting every developmental stage, which encompass major transitions in tissue organization of the fast-evolved blue mussel

overall_design: Two experimental conditions, COC and Tiso diets. Biological replicates 3 culture replicate per stage of development for 5 stages of development. Eggs and trocophore larvae did not undertake treatments

first: Bassim

last: Sleiman

first: Tanguy

last: Arnaud


title: More than the sum of their parts: Metabolic crossfeeding and interkingdom communication in dual-species biofilms of Streptococcus mutans and Candida albicans

city: Třeboň

first: Jürgen

last: Tomasch

address: Novohradská 237

country: Czech Republic

institute: Center Algatech, Institute of Microbiology of the Czech Academy of Science

summary:
Polymicrobial biofilms are of large medical importance, but little is known about their physiology and the underlying interspecies interactions. Here we studied two human pathogens, the opportunistic fungus Candida albicans and the caries promoting bacterium Streptococcus mutans. Both species formed biofilms in monoculture, with C. albicans growing mainly in the virulence-associated hyphae form, and S. mutans forming a thick layer of extracellular polymeric substances (EPS). Biofilm growth was enhanced in dual-species biofilms, which reached twice the biomass of monospecies biofilms and higher cell numbers of both S. mutans and C. albicans. EPS production by S. mutans was strongly suppressed in dual-species biofilms.
Virulence traits of S. mutans, e.g. genetic competence, biofilm formation and bacteriocin synthesis are controlled by quorum sensing through activation of the alternative sigma factor SigX. SigX is induced by the pheromones CSP (competence stimulating factor) or XIP (sigX inducing peptide). Strong induction of sigX was observed in dual species biofilms indicated by fluorescence of a reporter strain for the sigX promoter, S. mutans PcomX-gfp, as well as by qRT-PCR of comX. The peak of sigX expression occurred after 10 h of biofilm growth. Conditioned media from mixed biofilms but not from C. albicans or S. mutans cultivated alone activated sigX in the reporter strain. Deletion mutants for the comC and comS genes encoding the precursors of CSP and XIP, respectively, were constructed. Conditioned media from mixed biofilms with S. mutans DcomS were unable to induce sigX in the reporter strain, while deletion of comC had no effect. These data show that synthesis of XIP was induced in S. mutans by coculture with C. albicans.
Transcriptome analysis of S. mutans in single and mixed biofilms confirmed strong induction of comS, sigX, and the downstream late competence genes in dual-species biofilms. Among the late competence genes, fratricins were discovered for the first time. The comCDE operon and bacteriocin related genes were also induced, but much weaker. Genes related to oxidative stress, chaperones and glycosyltransferase genes required for EPS synthesis from sucrose were down-regulated, while glycogen synthesis genes were up-regulated, indicating that S. mutans was protected from oxidative stress and provided with excess sugar for storage polymer synthesis in mixed biofilms. The data show that in dual-species biofilms, C. albicans improves growth of S. mutans, suppresses its EPS formation and induces the complete quorum sensing signalling system, thus fundamentally changing the virulence properties of the caries pathogen, including its potential interactions with other members of the polymicrobial dental plaque community.

sample_organism:
Candida albicans
Streptococcus mutans UA159

overall_design: Dual-species biofilms of S. mutans and C. albicans and single-species biofilms of S. mutans were cultivated in 24-well microtitre plates in YNBB medium. Transcriptional profiles of S. mutans in single- and dual-species biofilms were analysed at early (6 h) and late (10 h) logarithmic phase of the biofilm growth, as well as after 24 h when biofilms entered stationary phase. Transcriptional profiles of S. mutans grown in the dual-species biofilms were compared to profiles obtained for single-species biofilm from the same time point. Three biological and one to two technical replicas were used in the microarray study. RNA samples were labeled with Cy3 or Cy5 using the ULS fluorescent labeling kit (Kreatech, Germany). Seven hundred nanograms of Cy3 or Cy5 labeled RNA after fragmentation were hybridized to the microarray at 65°C for 17 h using the Agilent hybridization chamber according to the manufacturer's instructions. The arrays were scanned using the Agilent DNA microarray scanner and the raw data were extracted using Agilent Feature Extraction software (v. 10.7).

first: Helena

last: Sztajer

first: Szymon

last: Szafranski

first: Michael

last: Reck

first: Manfred

last: Nimtz

last: Rohde

first: Irene

last: Wagner-Doebler


title: Expression analysis of Streptococcus pyogenes isolate SF370 and its rgg2 mutant

status: Public on Aug 01 2014

city: Vermillion

first: SRIVISHNUPRIYA

last: ANBALAGAN

state: SD

address: 414 East Clark Street

department: Basic Biomedical Sciences

institute: University of South Dakota

summary: Differences in gene expression between the wild-typ SF370 and its rgg2 mutant was identified with samples collected from mid-exponential and post-exponential phases of growth

overall_design: Samples were collected from both the wild-type and rgg2 mutant at 2hrs and 5hrs of growth. RNA was extracted, amplified and hybridized on Affymetrix microarrays.

first: Srivishnupriya

last: Anbalagan


title: Expression data from the bladders of carcinogen-treated mice with genetic Hh pathway manipulation

status: Public on Aug 27 2014

city: Stanford

first: Agnes

last: Lim

state: CA

address: 265 Campus Drive

department: Developmental Biology

institute: Stanford University

summary:
Attenuation of Hedgehog (Hh) pathway activity leads to accelerated tumor progression in a mouse model of N-butyl-N-4-hydroxybutyl nitrosamine (BBN) – induced bladder carcinoma.
In order to identify genes regulated by the Hh pathway that might be involved in bladder cancer progression, we performed transcriptional profiling of bladders harvested from mice after BBN-exposure, comparing Gli1CreER/WT; Smoflox/WT mice to Gli1CreER/WT; Smoflox/flox mice, which express CreER under control of the Gli1 promoter and carry one or two floxed alleles of the essential Hh pathway transductory component Smoothened (Smo) respectively. Administration of Tamoxifen to these mice results in attenuation of Hh pathway activty to a greater extent in the Gli1CreER/WT;Smoflox/flox mice as compared to Gli1CreER/WT;Smoflox/WT mice, allowing identification of Hh-pathway regulated genes.

overall_design: 6 total samples were analyzed. 3 bladders from Gli1CreER/WT; Smoflox/WT mice and 3 bladders from Gli1CreER/WT; Smoflox/flox mice were analyzed.

first: Philip

last: Beachy


title: Refined Candidate Region for F4ab/ac Susceptibility situated proximal to MUC13 in Pigs

status: Public on Jul 31 2014

city: Merelbeke

first: Tiphanie

last: Goetstouwers

state: East Flanders

address: Heidestraat 19

department: Veterinary Medicine

country: Belgium

institute: Ghent University

summary: A GWAS study was then performed in 52 non-adhesive and 68 strong adhesive pigs for F4ab/ac ETEC originating from 5 Belgian farms. A new refined candidate region (chr13: 144,810,100-144,993,222) for F4ac ETEC susceptibility was identified with MUC13 adjacent to the distal part of the region.

overall_design: All pigs were phenotyped for the presence of the F4ab/ac receptor (F4ab/acR) using the in vitro villous adhesion assay with 4×108 F4ac E. coli (strain GIS26, serotype O149:K91, F4ac+) or F4ab E. coli (strain G7, serotype O8:K87, F4ab+) . A total of 120 F4ab/acR phenotyped pigs were genotyped using the Porcine SNP60 BeadChip (Illumina) containing 62,163 SNPs, according to the manufacturer’s protocol. The position of the SNPs was based on the current pig genome assembly (Sscrofa10.2).

first: Mario

last: Van Poucke

first: Wouter

last: Coppieters

first: Ut

last: Nguyen Van

first: Vesna

last: Melkebeek

first: Annelies

last: Coddens

first: Katleen

last: Van Steendam

first: Dieter

last: Deforce

first: Eric

last: Cox

first: Luc

last: Peelman


title: Genome-wide analysis of cartilage gene expression in response to cartilage-specific ablation of Site-1 protease (Mbtps1) in mice (S1Pcko mice)

city: St. Louis

first: Debabrata

last: Patra

state: MO

address: 425 S. Euclid Avenue

department: Orthopaedic Surgery

institute: Washington University School of Medicine

summary: Analysis of differential gene expression in chondrocytes due to S1P ablation in mice. The hypothesis tested in this study was that ablation of S1P in mice would result in differential gene expression in chondrocytes that may be responsible for the S1Pcko phenotype.

overall_design: The chondroepiphyseal cartilage from the tip of appendicular bones such as femur, tibia, humerus, radius, ulna were harvested from E16.5 wild type (WT) and S1Pcko embryos. In addition, the appendicular bones and calvarium from E16.5 WT and S1Pcko embryos also were harvested and processed for total RNA without removing the chondroepiphyseal cartilage. The chondroepiphyseal cartilage and bones were rolled on Whatman Filter paper to remove muscle and blood vessels, and total RNA was extracted, labeled, hybridized on Illumina Mouse WG-6 v1.1 and analyzed to identify genes that were differentially expressed in the S1Pcko skeletal elements when compared to WT.

first: Linda

last: Sandell


title: Early stages of yeast senescent cells

status: Public on Jul 27 2014

city: Nagahama

first: Yukio

last: Mukai

state: Shiga

address: 1266 Tamura-cho

department: Department of Bioscience

institute: Nagahama Institute of Bio-Science and Technology

summary: We performed transcriptional and metabolic profiling for yeast at early stages of senescence (4th, 7th and 11th generation), that is, for populations in which most cells are still alive. Transcriptional profiles showed up- and down-regulation for about 20% of the genes profiled after the first 4 generations, few further changes by the 7th generation, and an additional 12% of the genes were up- and down-regulated after 11 generations. Pathway analysis revealed that these 11th generation cells had accumulated transcripts coding for enzymes involved in sugar metabolism, the tricarboxylic acid (TCA) cycle and amino acid degradation, and showed decreased levels of mRNAs coding for enzymes involved in amino acid biosynthetic pathways. Stationary phase-induced genes were highly expressed after 11 generations even though the growth medium contained adequate levels of nutrients, indicating deterioration of the nutrient sensing and/or signaling pathways by the 11th generation. These changes are presumably early indications of replicative senescence.

overall_design: Cells of yeast strain BY4742 were labeled with biotin and cultivated in YPD medium at 30°C. The labeled cells at early stages of senescence (4th, 7th and 11th generation) were isolated using Dynabeads Biotin Binder (Invitrogen, Carlsbad, CA, USA). Total RNA samples were prepared from the senescent cells. Antisense RNA was synthesized and labeled with Cy3 for the 4th, 7th, and 11th generation and with Cy5 for the 1st generation. Each mixture of Cy3- and Cy5-labeled antisense RNA was hybridized on a 3D-Gene Yeast Oligo Chip 6K (Toray, Kanagawa, Japan). The hybridized array was scanned with a 3D-Gene Scanner 3000 (Toray).

first: Yuka

last: Kamei


title: Real-time quantitative PCR analysis of microRNA expression in neonatal and adult cardiovascular progenitors

city: Loma Linda

first: Mary

last: Kearns-Jonker

address: 25094 Daisy Ave

department: Anatomy

institute: Loma Linda University

summary: Human cardiovascular stem cells were isolated from adult (57-75 year old) and neonatal (<1 month old) atrial tissue.  Cardiovascular stem cells were then cloned by single cell dilution and compared using sabiosciences cell development & differentiation miRNA PCR array.

overall_design: microRNA expression profiling by RT-PCR,  3 cardiac progenitor cell clones isolated from adults were run separately and results were pooled and compared to 8 neonatal cardiovascular progenitor cell clones that were run separately and pooled.

first: Tania

last: Fuentes


title: Human Wnt signaling pathway (Realtime qPCR array)

status: Public on Aug 12 2014

city: Minneapolis

first: susanta

middle: k

last: hui

state: MN

address: 420 Delaware Street SE

department: Therapeutic Radiology

institute: University of Minnesota

summary: Human bone marrow mesenchymal stem cells (BMMSC) and human embryonic mesenchymal stem cells (ESMSC)were used. X-ray irradiation (2Gy) or 0Gy was delivered. After 4 hours, equal amount total RNA from each sample was extracted prior to gene expression analysis. After making cDNA, genes associated with Wnt signaling pathway were analyzed.

overall_design: qPCR gene expression profiling.  Human bone marrow mesenchymal stem cells and human embryonic mesenchymal stem cells were used. X-ray irradiation (2Gy) or 0Gy was delivered. After 4 hours, equal amount total RNA from each sample was extracted prior to gene expression analysis.

first: Mohammad

last: Islam

first: Susanta

middle: K

last: Hui


title: Aplysia Pleural Ganglia 24 Hours After Long-Term Habituation Training

status: Public on Jul 16 2014

city: River Forest

first: Robert

last: Calin-Jageman

state: IL

address: 7900 West Division

department: Psychology

institute: Dominican University

summary: We used a custom-designed microarray and qPCR to characterize the persistent transcriptional response to long-term habituation training in the marine mollusk Aplysia californica.  Aplysia were exposed to either 3 days of spaced long-term habituation training (10 rounds of stimulation/day; each round = 15 min brushing at a 10s ISI; 15 min rest between rounds); a matched set of controls was not exposed to any brushing (n = 8/group).  While reflex responsiveness remained stable in controls, trained animals exhibited a large reduction in siphon-withdrawal duration that was evident at stimulation sites across the entire dorsal surface of the body (head, tail, and siphon).  This habituation was retained for at least 24 hours after the end of training.  Immediately after 24 hour retention tests, pleural ganglia were harvested from each trained animal and its matched control.  The pleural ganglia contain the VC nociceptors, which we confirmed are activated by the brush stimulus used to produce habituation.  Microarray analysis from 8 biological replicates suggests that long-term habituation training persistently regulates 21 transcripts.  We used qPCR to test a subset of these transcripts and found persistent regulation of an putative Aplysia cornichon homolog.

overall_design: Between-subjects comparison of a trained animal to a matched control (matching based on duration of pre-test responsiveness).  Conducted with 8 biological replicates, meaning 8 arrays, each comparing 1 trained and 1 matched control.

first: Irina


title: Non-clonal mosaicism in human somatic and embryonic stem cells revealed by single-cell array-based copy-number variation analysis

status: Public on Jun 24 2014

city: Brussels

first: Kurt

last: Jacobs

address: Laarbeeklaan 103

department: Faculty of Medicine and Pharmacy

institute: Vrije Universiteit Brussel (VUB)

type: Genome variation profiling by genome tiling array

summary: Although it is known that cultured human cells acquire copy number variations over time, little is known about the mutation frequency in individual cells. Here we describe that human somatic and embryonic stem cell cultures show significant fractions of cells carrying unique chromosomal abnormalities, forming a non-clonal genetic mosaic. We studied 85 human single cells by array-based comparative genomic hybridisation and found that 14-31% of hESC and 8-26% of somatic cells are chromosomally abnormal. Remarkably, only 2 cells showed full-chromosome aneuploidy, while 93% of detected abnormalities were segmental, most of them telomere-spanning. Furthermore, fluorescent in situ hybridisation confirmed this finding and revealed an increased instability of the subtelomeric regions in hESC as compared to somatic cells.

overall_design: We first validated the aCGH method by studying single cells with known genetic imbalances of different sizes. We analysed 2 amniocytes (Amniocyte C 01 - Amniocyte C 02) with a trisomy 18, eight amniocytes carrying a deletion of 5p33.3p15.55 and a duplication of 9q33q34.3 (Amniocyte A 01 - Amniocyte A 08), two amniocytes carrying a deletion of 5p15.33p15.1 (Amniocyte B 01 - Amniocyte B 02) and three hESC carrying a duplication of 3q26.33q27.3 (VUB07 P165BBB7 01 - VUB07 P165BBB7 03). From this, we found that we can reliably detect at the single-cell level CNVs that span seven consecutive BAC clones on the microarray.

first: Afroditi

last: Mertzanidou

first: Mieke

last: Geens

first: Catherine

last: Staessen

first: Claudia

last: Spits


title: Genome-wide changes in the circadian transcriptional program in Synechococcus elongatus PCC 7942

status: Public on Jul 08 2014

city: Chicago

first: Michael

middle: Joseph

last: Rust

address: 900 E 57th ST

department: Molecular Genetics and Cell Biology

institute: University of Chicago

summary: Circadian input kinas A (cikA) null cells severly distorts the genome-wide output of the circadian clock

sample_organism: Synechococcus elongatus PCC 7942 = FACHB-805

overall_design: Synechococcus cultures (both wildtype and ΔcikA null cells) were synchronized with two light-dark (12h:12h) cycle before release into continuous light. Samples were collected at 4 h intervals for the next 24 h, total RNA was isolated from samples collected at each time points and genome-wide expression was measured using custom-designed microarrays

first: Gopal

last: Pattanayak

first: Connie

last: Phong


title: 10nM insulin stimulation of Fao Cells

status: Public on Jul 01 2014

city: Fukuoka

first: Hiroyuki

last: Kubota

address: 3-1-1 Maidashi Higashi-ku

department: Medical Institute of Bioregulation

institute: Kyushu University

summary: To confirm how many and what kind of gene changes within 1 hour treatment of insulin stimulation,  we have performed whole genome microarray expression profiling. And we found that 276 genes increased (>2 fold) or decreased (<0.5 fold)

overall_design: 10nM insulin induced gene expression in Fao cells was measured at 0, 15, 30, 45, 60 min.


title: Human TaqMan MicroRNA Arrays A and B v2.0 of breast tissue

status: Public on Jul 15 2014

city: Malmö

first: Sofie

last: Björner

address: Jan Waldenströms gata 59

country: Sweden

institute: Lund University

summary: Columnar cell hyperplasia (CCH) is the earliest histologically identifiable breast lesion linked to cancer progression and is characterized by increased proliferation, decreased apoptosis and elevated oestrogen receptor a expression. The mechanisms underlying the initiation of these lesions have not been clarified but might involve early and fundamental changes in cancer progression. MiRNAs are key regulators of several biological processes, acting by influencing the posttranscriptional regulation of numerous targets, thus making miRNAs potential candidates in cancer initiation. Here we have defined novel epithelial as well as stromal miRNA signatures from columnar cell hyperplasia lesions compared to normal terminal duct lobular units by using microdissection and miRNA microarrays. MiR-27a, miR-92a and let-7c were among the identified downregulated epithelial miRNAs and their functions were delineated in unique CCH derived cells suggesting pro-apoptotic and anti-proliferative properties for the selected miRNAs and that downregulation of let-7c in CCH cells potentially increased proliferation via Myb. MiR-132 was upregulated in the stroma surrounding CCH compared to stoma surrounding TDLUs, and overexpression of miR-132 in immortalized fibroblasts and in fibroblasts co-cultured with epithelial CCH cells caused substantial expression changes. Global miRNA expression was also examined both epithelial and stroma of one patient displaying TDLU, CCH and additional invasive breast cancer. The miRNA signatures identified in CCH indicate concordant early changes in the epithelial and stromal compartment of CCH and could represent early key alterations in breast cancer progression that potentially could be targeted in novel prevention or treatment schedules.

overall_design: Normal tissue (TDLU) and premalignant tissue (CCH) from epithelial cells was collected from four patients and stromal tissue surrounding TDLUs and CCH was collected from two of these patients. Epithelial cells and stroma surrounding TDLU, CCH and invasive breast cancer (IBC) was collected from one additional patient.

first: Göran

last: Landberg


title: Transcriptional profiling analysis of S. pombe kinase deletin strains treated (60min) or untreated (0min) with nitrogen starvation in comparison with a common reference.

status: Public on May 31 2014

city: Singapore

first: Jianhua

last: Liu

address: 60 Biopolis Street

country: Singapore

institute: Genome Institute of Singapore

summary:
Kinase deletion strains treated with or without nitrogen starvation
Background:  Protein kinase-mediated signaling pathways play a pivotal role in regulation of stress responses.  Nitrogen starvation (NS) induces sexual development when mating partner available or entry into a quiescent state (G0) in heterothallic background.  However, it is unclear whether transcriptional profiles in response to NS allows distinguishing between kinase deletion strains defective in sexual development and/or G0-arrest. Results:  In this study, we used DNA microarray to analyze transcriptional profiles in 68 protein kinase deletion strains prior to and after NS.  Microarray analyses indicated that NS-induced transcriptional profiles of all kinase strains plus wild type are highly correlated with one another (i.e., Pearson¡¯s correlation coefficient r > 0.7) except for that of pka1¦¤, which showed no high correlation with other 11 kinase strains.  Significantly, 9 of 11 strains were defective in sexual development, suggesting that the NS-induced profile of pka1¦¤ serves as a signature with no high correlation with profiles of kinase strains defective in sexual development.  Furthermore, we show that expression of the NS-induced genes is elevated in pka1¦¤ and cyr1¦¤ strains prior to NS.  On the other hand, levels of the NS-induced genes expression in pka1¦¤, cyr1¦¤, sty1¦¤, and byr1¦¤ are significantly lower than that of wild type. Conclusions:  Taken together, our analyses indicate that the cAMP-dependent Pka1-mediated signaling pathway play a major role in regulation of the NS-induced genes prior to and after NS.  In addition, the ROS-activated kinase Sty1 and the pheromone-induced kinase Byr1 are also involved in up-regulation of NS-induced genes upon NS stress.

overall_design: 68 kinase deletion strains and other 5 deletion strains were treated with (60m) or without (0min) nitrogen starvation

first: Chu

last: Zhaoqing

first: Jia

last: Yonghui

first: Li

last: Juntao

first: Karuturi

last: Krishna

first: Liu

last: Jianhua


title: Comparison of the gene expression of periimplantitis affected peri-implant tissue and healthy peri-implant tissue in vivo in human.

status: Public on May 14 2014

city: Göttingen

first: Nicolai

last: Miosge

address: Robert-Koch-Str. 40

department: Prothetik, Oral biology and Tissue regeneration

institute: University Göttingen

summary: In this study we want to ascertain the differences and similarities of infected and inflammated peri implant tissue versus healthy peri implant tissue at the mRNA level.

overall_design: Six of the patients where affected by periimplantitis. In situ dental implants where explanted because of inflammation and non-integration. From two patients, implants were explanted because of wrong placement. They where classified as implants with healthy periimplant tissue.

first: Boris

last: Schminke

first: Simon

last: Schmitt

first: Lennart

last: Opitz

first: Gabriela

last: Salinas-Riester


title: Time-series of transcriptome analysis of Bacillus subtilis response to 25 mM potassium acetate and 0.85 µM CCCP

status: Public on Apr 11 2014

city: Amsterdam

first: Alexander

last: Ter Beek

address: Science Park 904

department: Molecular Biology & Microbial Food Safety

country: Netherlands

institute: University of Amsterdam - Swammerdam Institute for Life Sciences

summary: The advent of ‘omics’ techniques bear significant potential for the assessment of the microbiological stability of foods. This requires the integration of molecular data with their implication for cellular physiology. Here we performed a comparative physiological and transcriptional analysis of Bacillus subtilis stressed with three different weak organic acids: the commonly used food preservatives sorbic- and acetic- acid, plus the well-known uncoupler carbonyl cyanide-m-chlorophenyl hydrazone (CCCP). The concentration of each compound needed to cause a similar reduction of the growth rate negatively correlated with their membrane solubility, and positively with the concentration of undissociated acid. Intracellular acidification was demonstrated by expressing a pH-sensitive GFP derivative. The largest drop in intracellular pH was observed in CCCP-stressed cells and was accompanied by the transcriptional induction of the general stress response (GSR) and SigM regulon, responses known to be induced by acidification. The GSR was induced by acetate, but not by sorbate in mildly-stressed cells. Microarray analysis further revealed that all three acids activate transcriptional programs normally seen upon nutrient limitation and cause diverse responses indicative of an adaptation of the cell envelope. Based on the responses observed and the utilized pH measurements, the inhibitory effect of sorbic acid seems to be more focused on the cell membrane than that of acetic acid or CCCP.

overall_design: Time-series of B. subtilis response to 25 mM potassium acetate and 0.85 µM CCCP during controlled growth in batch-fermentors in defined minimal medium (pH 6.4). Samples for microarrays were taken from both the treated and control cultures at 0, 10, 20, 30, 40, and 50 min after addition of acetate and CCCP. Two biologically independent experiments were performed.

first: Janneke

last: Wijman

first: Anna

last: Zakrzewska

first: Rick

last: Orij

first: Gertien

last: Smits

first: Stanley

last: Brul


title: Effect of overexpression of OsTGAP1 in chitin oligosaccharide elicitor-treated rice cells

status: Public on Apr 01 2014

city: Tokyo

first: Kazunori

last: Okada

address: 1-1-1, Yayoi, Bunkyo-ku

department: Biotechnology Research Center

institute: The University of Tokyo

summary: To see the effect of overexpression of the bZIP transcription factor OsTGAP1, we compared the gene expression profiles in wild type rice cells and OsTGAP1-overexpressing rice cells.

overall_design: Expression profiling in the wild type rice cells and OsTGAP1-overexpressing rice cells treated with chitin oligosaccharide for 0, 6, and 24 h was compared using two-color method with four biological replicates.

first: Koji

last: Miyamoto

first: Hideaki

last: Nojiri

first: Hisakazu

last: Yamane


title: Targeted changes of cell wall proteome influence Candida albicans ability to form single- and multi-strain biofilms.

status: Public on Mar 31 2014

city: Paris

first: Sadri

last: ZNAIDI

address: 25 rue du Docteur Roux

department: Mycology Department

institute: Institut Pasteur

summary: Biofilm formation is an important virulence trait of the pathogenic yeast Candida albicans. We have combined gene overexpression, strain barcoding and microarray profiling to screen a library of 531 C. albicans conditional overexpression strains (~10% of the genome) for genes affecting biofilm development in mixed-population experiments. The overexpression of 16 genes increased strain occupancy within a multi-strain biofilm, whereas overexpression of 4 genes decreased it. The set of 16 genes was significantly enriched for those encoding predicted glycosylphosphatidylinositol (GPI)-modified proteins, namely Ihd1/Pga36, Phr2, Pga15, Pga19, Pga22, Pga32, Pga37, Pga42 and Pga59; eight of which have been classified as pathogen-specific. Validation experiments using either individually- or competitively-grown overexpression strains revealed that the contribution of these genes to biofilm formation was variable and stage-specific. Deeper functional analysis of PGA59 and PGA22 at a single-cell resolution using atomic force microscopy showed that overexpression of either gene increased C. albicans ability to adhere to an abiotic substrate. However, unlike PGA59, PGA22 overexpression led to cell cluster formation that resulted in increased sensitivity to shear forces and decreased ability to form a single-strain biofilm. Within the multi-strain environment provided by the PGA22-non overexpressing cells, PGA22-overexpressing cells were protected from shear forces and fitter for biofilm development. Ultrastructural analysis, genome-wide transcript profiling and phenotypic analyses in a heterologous context suggested that PGA22 affects cell adherence through alteration of cell wall structure and/or function. Taken together, our findings reveal that several novel predicted GPI-modified proteins contribute to the cooperative behaviour between biofilm cells and are important participants during C. albicans biofilm formation. Moreover, they illustrate the power of using signature tagging in conjunction with gene overexpression for the identification of novel genes involved in processes pertaining to C. albicans virulence.

overall_design:
A total of 8 samples are included in this study. For fitness profiling of planktonic cells, 2 biological replicates were analyzed (samples Pool_Fitness_planktonic_rep1 and Pool_Fitness_planktonic_rep2). For quantification of strain abundance during biofilm formation, 6 biological replicates were analyzed (Pool_Biofilm_rep1, Pool_Biofilm_rep2, Pool_Biofilm_rep3, Pool_Biofilm_rep4, Pool_Biofilm_rep5, Pool_Biofilm_rep6).
Genomic DNA was purified and used as template to PCR-amplify barcodes, which were then used as probes for microarray hybridization. This experiment was done twice independently. For  quantification of strain abundance during multi-strain biofilm formation, strain pools were grown in minimal GHAUM medium with or without doxycycline, each inoculum was then diluted to an OD600 of 1 in fresh minimal GHAUM medium with or without doxycycline and left at room temperature for 30 min, to allow further overexpression. Plastic slides (Thermanox™; Nunc) were immersed in the inoculum for 30 min at room temperature to allow adhesion of cells to the plastic substrate. The plastic slides were then transferred to the glass vessel of a 40-mL incubation chamber. This vessel has two glass tubes inserted to drive the entry of medium and air, while used medium is evacuated through a third tube. The flow of medium is controlled by a recirculation pump (Ismatec®) set at 0.6 mL.min-1 and pushed by pressured air supplied at 105 Pa, conditions minimizing planktonic phase growth and promoting biofilm formation. The chambers with the plastic substrate were incubated at 37C and biofilms were grown for 40h followed by genomic DNA extraction, barcode amplification and differential labeling (dox-treated samples with Cy5, untreated samples with Cy3) and hybridization to barcode microarrays.

last: Znaidi


title: Plasmodium falciparum custom resequencing array testing and validation

status: Public on Mar 28 2014

city: Baltiomore

first: Christopher

last: Jacob

state: MD

address: 685 W. Baltimore St.

department: Center for Vaccine Development

country: USA

institute: University of Maryland School of Medicine

summary:
A custom resequencing array for analysis of field isolates of plasmdium falciparum was created.
Test of DNA with genotypes known at all loci genotyped by the microarray as well as test of accuracy correlation with amounts of DNA added to each array

overall_design: Comparison of test DNA from lab and clinical isolates between genotyped generated by next-generation sequencing and this new custom DNA microarray.

last: Plowe


title: Chitin oligosaccharide elicitor-responsive genes in suspension cultured rice cells

summary: Chitin is a major component of fungal cell walls and serves as a molecular pattern for the recognition of potential pathogens in the innate immune systems of both plants and animals. In plants, chitin oligosaccharides have been known to induce various defense responses in a wide range of plant cells including both monocots and dicots. We identified chitine oligosaccharide-responsive genes in suspension-cultured rice cells 6 and 24 h  after treatment using rice 44k microarray.

overall_design: Expression profiling in rice cells treated with chitin oligosaccharide for 6 and 24 h was compared with that in untreated control using two-color method with four biological replicates.


title: Dectin-1-mediated signaling leads to characteristic gene expressions in rat mast cells

status: Public on Mar 27 2014

city: Eiheiji

first: Yukihiro

last: Kimura

state: Fukui

address: 23-3 Matsuoka-Shimoaizuki

institute: University of Fukui

summary:
Rat mast cell line RBL-2H3 was analyzed to investigate the molecular mechanism of Dectin-1-mediated activation and responses of mast cells.
Dectin-1-mediated signaling stimulated characteristic gene expression, such as MCP-1, IL-4, IL-13, TNF-αand Nfkbiz.

overall_design: RBL-2H3 cell line stably expressing Dectin-1 was established. Non-stimulated cells (control) compared to Dectin-1-stimulated (Curdlan) cells in order to comfirm Dectin-1-mediated signaling-inducible genes. Dectin-1-stimulated cells compared to Syk inhibitor R406-pretreated cells in order to examine the importance of Syk for Dectin-1-mediated gene up-regulations.

first: Kazuyasu

last: Chihara

first: Chisato

last: Honjoh

first: Kenji

last: Takeuchi

first: Shota

last: Yamauchi

first: Shigeharu

last: Fujieda

first: Kiyonao

last: Sada


title: Transcriptome profiling of dominant follicle development in the equine ovary

status: Public on Mar 15 2014

city: Midlothian

first: Xavier

last: Donadeu

address: Easter Bush

country: United Kingdom

institute: Roslin Institute, University of Edinburgh

summary: The Objective of this study was to establish global gene expression profiles associated with different stages of dominant follicle development  in the horse.  This was done by collecting ovaries at different stages of an ovulatory follicular wave, when the dominant follicle reached 22 mm (early dominant, ED), 33 mm (late dominant, LD) and 34 h after an i.v. injection of crude equine gonadotropins (CEG; 15 mg i.v.) when the largest follicle reached > 33 mm (preovulatory stage, PO). RNA was then separately collected  from granulosa cells and theca-rich follicular wall fractions and was hybridized to the Agilent Horse Gene Expression Microarray.  Gene expression was compared between ED and LD and between LD and PO stages within each of granulosa cells and theca walls. Significantly larger numbers of genes were differentially expressed in granulosa cells than in theca walls throughout development, and between LD and PO follicles than between ED and LF follicles. The most salient features were the downregulation of cell cycle genes in granulosa cells during both the ED-LD and LD-PO transitions and the upregulation of genes associated with inflammation, immunity, extracellular matrix remodelling and protection aganints toxic insult in both GCs and TCs, particularly during the LD-PO transition.

overall_design: Five to nine biological replicates per cell type and developmental stage (total of 34 samples) were used in a single dye experiment. Samples were distributed among slides so that each experimental groupeach was represented at least once in each slide.  For each gene, mean normalized intensities (n= 5 biological replicates/group) were compared between follicle stages (ED-LD and LD-PO) within each cell type (GC and TC).

first: F

middle: X


title: Co-culture of C. albicans with bacteria

status: Public on Mar 03 2014

city: San Francisco

first: Emily

middle: Patricia

last: Fox

address: 600 16th Street, GH - N374

department: Biochemistry and Biophysics

institute: University of California, San Francisco

summary: Transcriptional profiling of C. albicans when monocultured in suspension culture or in biofilms compared to  when co-cultured with C. perfringens in suspension culture, or with E. coli, K. pneumoniae, E. faecalis, C. perfringens, or B. fragilis in biofilms, or in the presence of N-acetylglucosamine in biofilms.

overall_design: At least 2 replicates for each condition except for biofilms +N-acetylglucosamine, some experiments are two-condition experiments: C. albicans +/- bacteria vs. C. albicans. Some experiments multiple condition: C. albicans +/- bacteria vs. mixed reference of all conditions in that experiment.

middle: P


title: Expression analysis of maize (Zea mays L.) genes in continuous light

status: Public on Mar 04 2014

city: Montpellier

first: Cecilio

middle: Frois

last: Caldeira

address: 2 place Viala

department: Herault

institute: INRA - Institut National de la Recherche Agronomique

summary:
Investigation of whole genome gene expression level changes in maize plants (standard maize line B73) in controlled conditions under continuous light.
Tissues of the leaf elongation zone were sampled from plants well watered every 12 hours before and after lights on.

overall_design: A nine chip (Biogemma Nimblegen Custom Array) study using total RNA recovered from three replicates (plants) sampled every 12 hours (1h before and 12 and 24h after lights on).

first: C

middle: F

first: J

last: Pichon

first: M

last: Bosio

last: Tardieu


status: Public on Mar 01 2014

city: Ithaca

first: John

middle: D.

last: Helmann

state: NY

address: 372 Wing Hall

department: Microbiology

institute: Cornell University

summary: Transcriptional profile of the sigA (G336C) mutant during log growth phase in LB medium.

overall_design: Bacillus subtilis W168, WT vs. sigA (G336C). The experiment was conducted two times using three independent total RNA preparations (biological triplicates). Each comparison was performed in dye-swap with the same RNA preparation. For each paried comparison, one sample was labeled with Alexa Fluor 555 and the other was with Alexa Fluor 647.

first: Yong

last: Lee

middle: D


title: The effect of GPR30 agonist G-1 on androgen-sensitive and castration-resistant LNCaP xenografts

status: Public on Feb 14 2014

city: Cincinnati

first: Mario

last: Medvedovic

state: OH

address: 3223 Eden Av. ML 56

department: Department of Environmental Health

institute: University of Cincinnati

summary: G-1 is an agonist to GPR30. Activation of GPR30 by G-1 inhibited prostate cancer cell growth in LNCaP xenografts regrown after catration of the host (nude mice), but not in the androgen-sensitive LNCaP xenograft grown in an intact host. Results provide insights into the molecular basis of G-1 action in castration-resistant prostate cancer.

overall_design: Male nude mice were injected with LNCaP cells. When the LNCaP tumors reached 150–300 mm3, mice were divided into two groups: intact (androgen-sensitive tumor) and castrated. For the intact group, mice were subcutaneously injected with vehicle alone (95% PBS, 2.5% DMSO, 2.5% ethanol) or G-1 (4 mg/kg/day in vehicle) daily for 16 days.   For the castrated group, tumors regressed and then regrew to ~300-400mm3. Mice were treated daily with vehicle or G-1 as described for 16 days. Tumors were harvested for RNA extraction and microarray experiments.

first: Hung-Ming

last: Lam

first: Jing

last: Chen

first: Bin

last: Ouyang

first: Shuk-mei

last: Ho