title: Identification of hypoxia-regulated genes in the liver of common sole (Solea solea) fed different dietary lipid contents

status: Public on Oct 07 2013

city: Legnaro (PD)

first: Serena

last: Ferraresso

state: Padova

address: Viale dell'Università

department: Dept of Comparative Biomedicine and Food Science

institute: University of Padova

summary: Hepatic transcriptome of sole fed low and high lipid dietary content in the early response to hypoxic stress.

overall_design: Characterization of the hepatic transcriptome of S. solea in order to assess the molecular mechanisms underlying the effects of dietary lipid content on hypoxia tolerance in common sole. S. solea individuals (8 month post-hatching) were fed for two month with commercial diets containing either 11% lipids or 20% lipids. Before hypoxia challenge stress, 38 individuals (19 from each dietary group) were randomly pooled in a single tank (1 m3) and left undisturbed and unfed for 48 h. The hypoxia challenge consisted then in a decrease of water oxygenation from 100 % to 10 % within one hour, followed by a slower descent at 2 % hr-1 to 4%. As fish lost their equilibrium, they were removed and sampled. Thirty six  individuals (18 from each dietary group) were also sampled in normoxic conditions, resulting in 4 experimental groups: Normoxia low-lipid, Normoxia high-lipid, Hypoxia low-lipid, Hypoxia high-lipid. The experimental design was therefore a 2-way full factorial design between two juvenile dietary lipid contents and two oxygen concentration conditions.

first: David

last: Mazurais


title: Gene profile for chemotherapy response in head and neck carcinoma

status: Public on Oct 06 2013

city: Paris

first: Martine

middle: S

last: Aggerbeck

address: 45 rue des Saints Pères

country: France

institute: INSERM

summary: Transcriptional profiling was performed on biopsies from patients with head and neck squamous cell carcinoma that had been treated with cisplatin and 5-fluorouracil to identify genes predictive of response to chemotherapy

overall_design: Two condition experiment, Biopsies from complete clinical responders and from non-responders were compared based upon a common reference using a two color design

first: Aggerbeck

last: Martine

first: Muchielli

last: Marie-Hélène


title: Gene expression profiling of cervical cancer tissues at progressive FIGO defined stages

status: Public on Oct 10 2013

city: Navi Mumbai

first: Rita

last: Mulherkar

state: Maharashtra

address: Kharghar

country: India

institute: Advanced Centre for Treatment, Research and Education in Cancer (ACTREC)

summary: This is a study indented to investigate the alterations in the molecular profile of cervix uteri, as it progresses thorough various FIGO stages of carcinoma, by means of global gene expression profiling, in a cohort of Indian patients. In addition expresion profiles of early and advanced stage cervical cancer were compared to identify biomarkers and therapeutic targets for the advanced stages.

overall_design: Cervical cancer and non-malignant cervical tissues are obtained from consenting patients following hospital ethics committee approved protocols. The samples are profiled against universal Human reference RNA from Stratagene on 19K EST microarrays from Microarray Center, University Health Network, Toronto, Canada. Biological replicates: Normal = 4; Cervical cancer Stage I = 8; Cervical cancer Stage II = 9; Cervical cancer Stage III = 8. One replicate per array.

first: Asha

last: Thomas

first: Chandan

last: Kumar-Sinha

first: Umesh

last: Mahantshetty

first: Shyam

middle: K

last: Shrivastava


title: Deadenylated versus polyadenylated RNAs in bovine immature oocytes

status: Public on Oct 01 2013

city: Quebec

first: maella

last: gohin

state: Qc

address: 2440 Bl. Hochelaga

department: Animal science

country: Canada

institute: Laval University

summary: RNA separation in function of the poly(A) tail length: A- (A≤50) and A150 (A≥150) from 200 immature oocytes (at the germinal vesicle stage, GV) in quadruplicates

overall_design: deadenylated and polyadenylated from each four pools of 200 immature oocytes were hybridized with a 2-color microarray design and one replicate per array.

first: Maella

last: Gohin

first: Eric

last: Fournier

first: Isabelle

last: Dufort

first: Marc-André

last: Sirard


title: Transcriptome analysis of Manila clam (Ruditapes philippinarum) digestive gland after exposure to different concentrations of ibuprofen.

city: Legnaro

first: Massimo

last: Milan

state: PD

address: Viale dell'Università 16

department: Dept. of Department of Public Health, Comparative Pathology,and Veterinary Hygiene

country: Italy

summary: A Ruditapes philippinarum microarray platform was developed to identify digestive gland gene expression profiles in response to 100 µg /l and 1000 µg/l ibuprofen exposure.

overall_design: A comparative analysis of gene expression was conducted in Manila clam R.philippinarum exposed to ibuprofen.Clams were exposed for 1, 3, 5 and 7 days to 0, 100 and 1000 µg IBU/l, and digestive gland gene expression were measured. Gene expression profiling was performed using an Manila clam-specific oligo-DNA microarray of 14,156 probes based on single-colour detection (Cyanine-3 only). Microarrays were scanned with Agilent scanner G2565BA (barcode on the left, DNA on the back surface, scanned through the glass) at a resolution of 5 microns; all slides were scanned twice at two different sensitivity settings (XDRHi 100% and XDRLo 10%); the scanner software created a unique ID for each pair of XDR scans and saved it to both scan image files. Feature Extraction (FE) 9.5 used XDR ID to link the pairs of scans together automatically when extracting data. The signal left after all the FE processing steps have been completed is ProcessedSignal that contains the Multiplicatively Detrended, Background-Subtracted Signal.

first: Milan

last: Massimo

first: Pauletto

last: marianna

first: Matozzo

last: Valerio


title: Light and BcLTF1-dependent gene expression profiles in the phytopathogenic fungus Botrytis cinerea

status: Public on Sep 27 2013

city: Palaiseau

first: Adeline

last: SIMON

address: 22 place de l'agronomie

institute: INRAE

summary: Full transcriptomes of the Botrytis cinerea wild-type strain B0510 and the null-mutant deltaBcLTF1, cultured in continuous darkness or submitted to a light stimulation, were compared to identify light- or/and BcLTF1-dependent genes.

overall_design: The Botrytis cinerea wild-type strain and the null-mutant deltaBcLTF1  were cultured for 52h in continuous darkness ; then, cultures were exposed for 60 min to light before harvest (L) or were harvested after additional 60 min darkness (D). 4 replicates were performed. The 16 total-RNA samples (4 conditions* 4 replicates) were used for hybridization on NimbleGen 4plex gene expression arrays (20,885 gene models from Botrytis cinerea with three 60-mer probes per gene).

first: Julia

last: Schumacher

last: Simon

first: Kim

middle: C

last: Cohrs

first: Muriel

last: Viaud

first: Paul

last: Tudzynski


title: miRNA Expression Profiles in Human AML Samples And in Human and Mouse Blood Cell Lines

city: New Haven

first: Jijun

last: Cheng

state: CT

address: 10 Amistad St.., Rm 214K

department: Genetics

country: USA

institute: Yale University

summary: miRNA expression profiles of a human cohort of 67 cytogenetically normal AML samples, including both TET2 wildtype and TET2 mutants, and human and mouse cell lines comaring control with TET2 overexpression or TET2 knockdown

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus
human gammaherpesvirus 4

overall_design: We profiled the 67 human AML samples together with one biological replicate. Each cell line was grown and treated at the same conditions and triplicacte samples were profiled.

first: Yanwen

last: Guo

first: Jun

last: Lu

first: Suning

last: Chen


title: Perturbation of polyamine catabolism affects normal grape ripening of Trincadeira cultivar

status: Public on Sep 30 2013

city: Lisboa

first: Ana

middle: Margarida

last: Fortes

address: Campus da FCUL

department: Plant Biology

country: Portugal

summary: Grapes (Vitis vinifera L.) are economically the most important fruit crop worldwide. However, the complexity of molecular and biochemical events that lead to ripening of nonclimacteric fruits is not fully understood. In particular the role of polyamines´ catabolism has been little explored.  Ripening of Trincadeira grapes submitted to mock and guazatine treatments, a potent inhibitor of polyamine oxidase activity, was studied taking into account the transcriptional and metabolic profilings complemented with biochemical data. The mRNA expression profiles of one time point (EL 38) corresponding to harvest stage was compared between mock and guazatine treatments using the Affymetrix GrapeGen® genome array containing 23096 probesets corresponding to 18711 unique sequences. A total of 2113 probesets (1877 unigenes) were significantly differentially expressed (1.5 fold) between these samples. These unigenes were assigned to the functional categories of “metabolism”, “regulation overview”, “signaling”, “cellular process”, “transport overview”, “response to stimulus, stress”, “diverse/miscellaneous functions”, “xenoprotein, transposable element”, “development” and “unknown”.  Quantitative RT-PCR validated microarrays results being carried out for seven selected genes and three developmental stages (EL 35, EL 36 and EL 38).   Functional enrichment analysis revealed that genes involved in amino acid, carbohydrate and water transport were more up-regulated in mock treated samples which may suggest that the strong dehydrated phenotype obtained in guazatine treated samples may be due to impaired transport mechanisms. In addition, genes involved in terpenes´ metabolism were differentially expressed between guazatine and mock treated samples. Altogether, the results support an important role of polyamine catabolism in normal grape ripening namely in aroma development and cell expansion.

overall_design: 1 time point in 2010 season at EL 38. 3 biological replicates. 2 treatments

middle: M

first: Patricia

last: Agudelo-Romero


title: Molecular characteristics and metastasis predictor genes of triple-negative breast cancer (II)

status: Public on Jan 02 2014

city: Taipei

first: King-Jen

last: Chang

address: No.1, Changde St., Zhongzheng Dist.

department: Department of Surgery

country: Taiwan

institute: National Taiwan University Hospital

type:
Expression profiling by array
Third-party reanalysis

summary:
This microarray dataset contains 51 triple-negative breast cancers, 25 normal breast tissues, and 106 luminal breast cancers (reanalyzed data from Series GSE24124, GSE9309, and GSE17040).

Keywords: Expression profiling by array

overall_design: Specimens of breast cancer tissue were collected and snap-frozen from breast cancer patients who had surgery between 1995 and 2008 at National Taiwan University Hospital (NTUH, Taipei, Taiwan). Clinicopathological information was obtained for all breast cancer patients along with informed consent. The AJCC/UICC TNM system was used for breast cancer staging classification.

first: Wen-Hung

last: Kuo


title: Long non-coding RNAs expression study of a Rett syndrome mouse model

status: Public on Oct 03 2013

city: L'Hospitalet de Llobregat

first: Manel

last: Esteller

state: Barcelona

address: Hospital Duran i Reynals Av. Gran Via s/n km, 2.7

department: PEBC

country: Spain

institute: IDIBELL

summary: In order to identify some lncRNA potentially involved in Rett syndrome we performed a mouse lncRNA expression microarray on whole brain samples coming from wild-type and MeCP2 Knock-out littermates. We found 2 lncRNAs directly bound by MeCP2 and upregulated in KO samples. We then focused on AK081227 because it overlaps with Gabrr2. The expression of this GABA receptor and the overlapping AK081227 are inversely correlated in thalamus, suggesting the long non-coding is regulating his own host.

overall_design: Whole brain total RNA was extracted from two Wild type mice (P60) and two MeCP2 KO littermates (P60)

first: Paolo

last: Petazzi


title: Evaluation of different responses of the intestinal microbiota to a TNF-α mediated pro-inflammatory stimulus by the HTF-Microbi.Array

status: Public on Sep 26 2013

city: Bologna

first: Simone

last: Rampelli

address: Via Belmeloro 6

institute: University of Bologna

summary:
We developed a non-invasive ex vivo HT29 cell-based minimal model to fingerprint the mucosa-associated microbiota fraction in humans.
HT29 cell-associated fractions were characterized by the universal phylogenetic array platform HTF-Microbi.Array, both in presence or in absence of a TNF-α-mediated pro-inflammatory stimulus.

overall_design: A high taxonomical level fingerprint profiling of the mucosa-associated microbiota was performed on a group of 12 breast-fed infants and 6 adults (used as controls). Relative abundance of the bacterial species was assessed by using a so-called HTF-Microbi.Array, based on a ligation detection reaction (LDR) - Univerasal array (UA) assay, capable of correctly identify up to 31 intestinal bacterial groups, covering up to 95% of the human gut microbiota

first: Manuela

last: Centanni

first: Silvia

last: Turroni

first: Clarissa

last: Consolandi

first: Clelia

last: Peano

first: Marco

last: Severgnini

first: Elena

last: Biagi

first: Giada

last: Caredda

first: Gianluca

last: De Bellis

first: Patrizia

last: Brigidi

last: Candela


title: The Gene Expression Profile of Peripheral Blood Mononuclear Cells from EV71-Infected Rhesus Neonates

status: Public on Sep 24 2013

city: Kunming

first: Ying

last: Zhang

state: Yunnan

address: 935 Jiaoling Rd.

country: China

institute: Institute of Medical Biology, Chinese Academy of Medicine Science

summary: To study the gene expression during EV71 infection, we have employed whole Rhesus Monkey genome microarray expression profiling as a discovery platform to identify genes with the potential to distinguish infection process. Rhesus monkey peripheral blood from the experiment or control donors was isolated, extracted the RNA and screened by microarray. The results indicated that the expression levels of more than 500 functional genes associated with multiple pathways were modulated. To confirm the results of the microarray analysis, 25 individual genes were random selected and were analyzed using real-time RT-PCR amplification. The expression levels of genes associated with immune inflammatory responses were up-regulated during the period from day 4 to 10 post-infection. The expressions of two genes (TAC1 and IL17A), which play major roles in inflammatory reactions, were remarkably up-regulated during the infection period.

overall_design: Enterovirus 71 infection induced gene expression in rhesus monkey peripheral blood mononuclear cells was measured at 4, 7 and 10 days after viral infection.  Three samples from two experiment donors and one control donor were performed at each time (4, 7 or 10 days). To exclude the individual difference, mix the two experiment samples at each time, and mix the three control samples.

first: Erxia

last: Yang

first: Qihan

last: Li


title: Gene expression of the mouse choroid plexus epithelium (CPE)

city: Amsterdam

first: Sarah

last: Janssen

address: Meibergdreef 47

department: Ophthalmogenetics

country: Netherlands

institute: Netherlands Institute for Neuroscience

summary: We investigated the gene expression of the mouse CPE. We isolated CPE cells from three mouse brains with laser dissection microscopy. Next, we performed RNA isolation, amplification, labeling and hybridization against 44k Agilent microarrays.

overall_design: We performed the microarrays against a common reference sample, which was mouse RPE/choroid RNA. We performed 3 mouse CPE replicates from 3 different mouse from the same strain, namely C57BL/6 .

middle: F

first: Arthur

middle: A

last: Bergen


title: Fsh controls gene expression in fish both independently of and through steroid mediation

status: Public on Sep 23 2013

city: Rennes

first: Elisabeth

last: Sambroni

address: Bat 16A Campus de Beaulieu

department: PHASE

institute: INRA

summary:
We recently demonstrated that Fsh modifies in vitro the testicular transcriptome of rainbow trout at early stages of spermatogenesis. Some of the regulated genes were found related to pathways highly relevant for the testicular functions i.e. spermatogenesis and steroidogenesis. Unlike in mammals, in fish both gonadotropins are able to efficiently stimulate the steroidogenesis, likely through a direct interaction with their cognate receptors present on the Leydig cells.
In this context, we wondered whether the effects of Fsh on the tubular compartment were mediated through the production of steroids. To address this issue we performed in vitro incubations of testis explants in the presence of Fsh alone or in combination with an inhibitor of the steroidogenesis, the trilostane. Trilostane significantly reduced or suppressed the response to Fsh of many genes showing that important aspects of the Fsh action on fish testis is indirect and requires the production of steroids. Interestingly, most of the genes regulated in response to Fsh through the steroid mediation were similarly regulated by Lh and many were also found regulated by androgen treatment. On the other hand, for many other genes the response to Fsh was not affected in the presence of trilostane. A majority of those genes were also preferentially regulated by Fsh, as compared to Lh, suggesting that specific regulatory effects of Fsh were independent of steroid production. Finally antagonistic effects between Fsh and steroids were found, in particular for genes encoding clue factors of steroidogenesis or for genes of the Igf system that tended to be inhibited by androgens.

overall_design: Testes were collected from all-male population rainbow trout at early stages of spermatogenesis.Testes were chopped in small pieces, in sterile conditions and then pooled and mixed. Testis fragments were randomly distributed (60-80 mg per well) on Nunc polycarbonate membrane inserts in 24-well plates filled with 300 µL of modified L15 culture medium supplemented with 2% Ultroser SF. Incubation were performed in six replicates for 96 hours, at 12°C, in the absence or presence of purified trout Fsh alone (500 ng/mL) or in combination with 10 µg/mL trilostane, an inhibitor of 3 beta-hydroxysteroid dehydrogenase. A pre-incubation with trilostane was done for 1 hour before adding Fsh.

first: Jean-Jacques

last: Lareyre

first: Florence

last: Le Gac


title: Characterization of Gene Expression in Rice Shoot and Root

status: Public on Sep 14 2013

city: Hsinchu

first: Jia-Shing

last: Chen

address: 6F, No 6, Technology Road 5

institute: Phalanx biotech Group

summary: The rice OneArray® 60-mer, oligonucleotide microarray consists of a total of 21,179 probes covering 20,806 genes of japonica and 13,683 genes of indica. Through a validation study, total RNA isolated from rice shoots and roots were used for comparison of gene expression profiles via microarray examination. A list of significantly differentially expressed genes was generated; 438 shoot-specific genes were identified among 3,138 up-regulated genes, and 463 root-specific genes were found among 3,845 down-regulated genes.

overall_design: The Phalanx microarray platform is based upon the hybridization of a single labeled sample (derived from RNA), followed by one-channel detection. The intensity of the hybridization signal is used to determine target concentration. In order to validate the technical quality of each probe in our arrays, we carried out 10 independent hybridizations on samples representing two different rice tissues – root and shoot.  To examine the gene expression profiles between rice root and shoot development, total RNA extracted from rice root and shoot were processed on the rice OneArray® microarray following the standard protocol using five arrays for each tissue type. Raw expression data from 10 microarrays (e.g. 5 arrays × 2 tissues) were normalized and Pearson’s correlation coefficients were calculated for the data sets of hybridization signal intensities.

first: Shang-Chi

last: Lin

first: Chia-Ying

first: Yen-Ting

last: Hsieh

first: Ping-Hui

last: Pai

first: L

first: Shengwan

last: Lee


title: Gene expression analysis of yehUT two component regulatory system

status: Public on Sep 17 2013

city: Hinxton

first: Vanessa

middle: Kuan

last: Wong

state: Cambridgeshire

address: Wellcome Trust Genome Campus

department: Microbial Pathogenesis

country: United Kingdom

institute: Wellcome Trust Sanger Institute

summary: Part of a study to characterise the two component regulatory system yehUT of  Salmonella enterica serovar Salmonella Typhi and Typhimurium.

platform_organism: Salmonella enterica subsp. enterica serovar Typhimurium str. SL1344

overall_design: 24 Samples examined, 12 of strain Salmonella Typhi BRD948 and 12 of strain Salmonella Typhimurium ST4/74.


title: DNA methylation profiles across different brain regions in healthy mice

status: Public on Sep 16 2013

first: Manel

last: Esteller

type: Methylation profiling by genome tiling array

summary: Genome wide DNA methylation profiling of normal and disease samples from different mice models. A custom Illumina Golden Gate DNA methylation Beadchip was used to obtain DNA methylation profiles across approximately 800 CpGs.

overall_design: Bisulphite converted DNA from the 66 samples were hybridised to the Illumina custom golden gate DNA methylation array.

first: Jose

middle: V

last: Sanchez-Mut


title: Dynamic profile of gene expression in rice flag leaf under high temperature

status: Public on Sep 10 2013

city: Changsha

first: Xianwen

state: Hunan

address: 1 Nongda Road, Furong District

institute: Hunan Agricultural University

summary: To comprehend the gene expression profile in rice flag leaf under high temperature, Agilent 4×44k rice oligo microarray experiments were carried out using rice flag leaf of reproductive stage at 0 min, 20 min, 60 min, 2 hr, 4 hr, and 8 hr after the treatment of 40 degree centigrade, and the significantly expressed genes mainly involved in transcriptional regulation, transport, protein binding, antioxidant, and stress response were identified. Among them, the predominant transcription factor gene families were Hsf, NAC, AP2/ERF, WRKY, MYB, and C2H2. KMC analysis discovered the time-dependent gene expression pattern under heat. The metabolism pathway analysis demonstrated that, under heat treatment, glycolysis and ubiquitin-proteasome was enhanced, and TCA, gluconeogenesis, the secondary metabolism and light-reaction in the photosystem was dramatically repressed, which revealed the great importance of maintaining primary metabolism and protein homeostasis in response to heat in rice flag leaf.

overall_design: Heat shock induced gene expression in rice flag leaf of reproductive stage was measured at 0 min, 20 min, 60 min, 2 hr, 4 hr, and 8 hr after the treatment of 40 degree centigrade in plant growth chamber. Two independent replicate experiments were performed at each time point.

first: Jiaping

first: Ailing

last: Liu

first: Jie

last: Zou

first: Xinbo


title: Epigenetic Basis of Regeneration: Analysis of Genomic DNA Methylation Profiles in the MRL/MpJ mouse

status: Public on Aug 20 2013

city: Gdansk

first: Pawel

last: Sachadyn

address: Narutowicza 11/12

department: Microbiology

country: Poland

institute: Gdansk University of Technology

summary: Epigenetic regulation plays essential role in cell differentiation and dedifferentiation, which are the intrinsic processes involved in regeneration. In order to investigate the epigenetic basis of regeneration capacity, we choose DNA methylation as one of the most important epigenetic mechanisms and the MRL/MpJ mouse as a model of mammalian regeneration reported to exhibit enhanced regeneration response in different organs. We report the comparative analysis of genomic DNA methylation profiles of the MRL/MpJ and the control C57BL/6J mouse. Methylated DNA immunoprecipitation (MeDIP) followed by microarray analysis using Nimblegen “3x720K CpG Island Plus RefSeq Promoter” platform were applied in order to carry out genome-wide DNA methylation profiling covering 20,404 promoter regions. We identified hundreds of hypo- and hypermethylated genes and CpG islands in heart, liver and spleen, and 37 of them in the three tissues. Decreased inter-tissue diversification and the shift of DNA methylation balance upstream the genes distinguish the genomic methylation patterns of the MRL/MpJ mouse from the C57BL/6J. Homeobox genes and a number of other genes involved in embryonic morphogenesis are significantly over-represented among the genes hypomethylated in the MRL/MpJ mouse. These findings indicate that epigenetic patterning might be a likely molecular basis of regeneration capability in the MRL/MpJ mouse.

overall_design: genome-wide DNA methylation profiling in the heart, liver, and spleen tissues of MRL/MpJ and C57BL/6J mouse

first: B

last: Górnikiewicz

first: A

last: Ronowicz

first: J

last: Podolak

first: P

last: Madanecki

last: Stanislawska-Sachadyn


title: A Unifying Model for Molecular Determinants of the Pre-selection Vβ Repertoire [ChIP-chip]

status: Public on Aug 14 2013

first: Eugene

last: Oltz

state: MO

address: 660 S Euclid Avenue

department: Pathology and Immunology

institute: Washington Univeristy in St.Louis

type: Genome binding/occupancy profiling by genome tiling array

summary:
Chip-chip from pro-T(DN) cells from Rag1KO mice for H3K27ac, P300 and FAIRE
The primary antigen receptor repertoire is sculpted by the process of V(D)J recombination, which must strike a balance between diversification and favoring gene segments with specialized functions. The precise determinants of how often gene segments are chosen to complete variable region coding exons remain elusive. We have quantified Vβ usage in the pre-selection Tcrb repertoire and report relative contributions of 14 distinct features in shaping their recombination efficiencies, including transcription, chromatin environment, spatial proximity to their DβJβ targets, and quality of recombinase recognition elements. Computational analyses provide a unifying model, revealing a minimal set of eight parameters that are predictive of Vβusage, dominated by chromatin modifications associated with transcription, but largely independent of the precise spatial proximity to DβJβclusters.

overall_design: Rag1KO DN epigenetic landscape at Tcrb

first: Suhasni

last: Gopalakrishnan

first: Alexander

last: Predeus

first: Maxim

last: Artyomov


title: Gene expression analysis of wild type Pectobacteriumwasabie SCC3193 wildtype compared to a SCC3193 inactivation mutant of RsmA, inactivation mutant of ExpA and an ExpA RsmA double inactivation mutant.

status: Public on Sep 01 2013

city: Helsinki

first: Martin

last: Broberg

address: Viikinkaari 5D

department: Biosciences

country: Finland

institute: University of Helsinki

summary: The phytopathogen Pectobacterium wasabiae SCC3193 is a model for research on virulence regulation in soft rot pathogens. Two proteins acting as global regulators of the expression on genes involved in virulence in SCC3193 are ExpA, a DNA binding transcriptional regulator, and RsmA, an RNA binding post transcriptional regulator. Studies of related enterobacterial phytopathogens suggest that homologues of ExpA (GacA) affect gene expression partly by modulating RsmA-like protein activity. However, the exact extent of this regulon overlap has not been mapped. To elucidate the role of RsmA in ExpA controlled gene expression goes through RsmA in P. wasabiae we performed a gene expression microarray analysis of the wild type strain, an expA mutant, an rsmA mutant, and an expA rsmA double mutant. The microarray-based data of various virulence related genes was confirmed through quantitative RT-PCR. Subsequently, assays were made to link observed transcriptomic differences to changes in growth rate, PCWDE production, and virulence in planta between the four strains. We could conclude that the majority of ExpA regulation seems routed via RsmA modulation. However we could identify genes involved in electron transport, oligogalacturonide transport and metabolism, which ExpA seems to influence independently of RsmA, directly or indirectly.

overall_design: Gene expression analysis from P. wasabie SCC3193 wildtype, SCC3193 rsmA mutant, SCC3193 expA mutant and SCC3193 expA rsmA double mutant was performed on RNA samples extraxcted from the strains at late-logarithmic (late-log) and early stationary (stat) growth phase. Strains were grown in liquid hrp inducing minimal medium cultures supplemented with 0.4% polygalacturonic acid at 200 rpm shaking and 28 degrees celsius. Three biological replicates were used from each strain at each growth phase point.

first: Gir-Won

first: Johanna

last: Nykyri

first: Yong-Hwan

first: Tapio

last: Palva

first: Minna

last: Pirhonen


title: Cool-responsive change in the rice anther transcriptome

status: Public on Aug 06 2013

city: Sapporo

first: Yuji

last: Kishima

address: Kita-ku Kita 9 Nishi 9 W105

country: Japan

institute: Hokkaido University

summary: The genome-wide transcriptome analyses using microarray probes containing genes and repeat sequences have been performed to examine response to the low-temperature in rice. We have particularly focused on the rice anther at the booting stage, since the low-temperature at this stage resulted in pollen abortion. The results demonstrated that the low-temperature stress caused genome-wide changes of transcriptional activities not only in genes, but also in repeat sequences of the rice anther. The degrees of the temperature responsive changes varied among the rice strains.

overall_design: The five rice strains exposed to the low temperature at 12°C for four days, were used for the microarray analyses. RNA was extracted from the anthers one day (C1), three days (C3) and five days (C5: this is one day after completion of the cool treatment) after the cool treatment and non-treated anthers (C0) with three biological replicates.

first: Seiya

last: Ishiguro


title: DELLA targets in proliferating leaf tissue

status: Public on Aug 01 2013

city: Gent

first: Hannes

last: Claeys

address: Technologiepark 927

department: Plant Systems Biology

country: Belgium

institute: VIB-UGent

summary: Transcriptome changes 1h or 4h following DELLA stabilisation in microdissected fully proliferating Arabidopsis leaves

overall_design: 35S::gai-GR plants (Claeys et al., 2012) were grown on meshes overlaying 1/2 MS medium for 9 days, and were then transferred to plates containing 5 µM dexamethasone or DMSO (mock). Samples were obtained from three independent experiments and from multiple plates within the experiment. Whole seedlings were harvested rapidly in an excess of RNAlater® solution (Ambion) and, after overnight storage at 4°C, the third leaf was dissected from 128 plants under a binocular microscope on a cooling plate with precision microscissors. Dissected leaves were transferred to a new tube, frozen in liquid nitrogen, and ground with a Retsch machine and 3-mm metal balls. RNA was extracted with TriZol (Invitrogen) and further purified with the RNeasy Mini Kit (Qiagen). DNA digestion was done on columns with RNase-free DNase I (Roche). One µg of pure RNA samples were hybridized to Affymetrix ATH1 arrays at the VIB Microarray Facility (Leuven, Belgium).

first: Aleksandra

last: Skirycz

first: Stefanie

last: De Bodt

first: Dirk

last: Inzé


title: Dissecting the grey zone between follicular lymphoma and nodal marginal zone lymphoma using morphological and genetic features

status: Public on Jul 16 2013

first: Daoud

last: Sie

address: De Boelelaan 1117

department: Pathology

institute: Vrije Universiteit Medical Center

type: Genome variation profiling by genome tiling array

summary:
Nodal marginal zone lymphoma is a poorly defined entity in the WHO classification, largely based on criteria by exclusion and the diagnosis often remains subjective. Follicular Lymphoma lacking t(14;18), have similar characteristics which results in a major potential diagnostic overlap which this study aims to dissect.
Four subgroups of lymphoma samples (n=56) were analyzed with high-resolution arrayCGH; Nodal marginal zone lymphoma, t(14;18)-negative Follicular Lymphoma, localized t(14:18)-positive Follicular Lymphoma and disseminated t(14;18)-positive Follicular Lymphoma.
Gains on chromosomes 7, 8 and 12 were observed in all subgroups. The mean number of aberrations was higher in disseminated t(14;18)-positive Follicular Lymphoma compared to localized t(14:18)-positive Follicular Lymphoma (p<0.01) and the majority of alterations in localized t(14:18)-positive Follicular Lymphoma were also found in disseminated t(14;18)-positive Follicular Lymphoma. Nodal marginal zone lymphoma was marked by 3q gains with amplifications of four genes. A different overall pattern of aberrations was seen in t(14;18)-negative Follicular Lymphoma compared to t(14;18)-positive Follicular Lymphoma. t(14;18)-negative Follicular Lymphoma is marked by specific (focal) gains on chromosome 3 as observed in Nodal marginal zone lymphoma.
Our results support the notion that localized t(14:18)-positive Follicular Lymphoma represents an early phase of disseminated t(14;18)-positive Follicular Lymphoma. t(14;18)-negative Follicular Lymphoma bears aberrations that are more alike Nodal marginal zone lymphoma, suggesting a relation between these groups.

overall_design: Four subgroups of follicular lymphoma were analyzed: NMZL (n=14), t-FL (n=12), LOC t+FL (n=16), DIS t+FL (n=14).

first: Oscar

last: Krijgsman

first: Patricia

last: Gonzalez

first: Olga

last: Balagué Ponz

first: Marit

last: Roemer

last: Slot

first: Annegien

last: Broeks

first: Linde

last: Braaf

first: Ron

last: Kerkhoven

first: Freek

last: Bot

first: Krijn

last: van Groningen

first: Max

last: Beijert

first: Bauke

last: Ylstra

first: Daphne

last: de Jong


title: Genome-wide analyses of Fusarium fujikuroi reveal complex regulation of secondary metabolism and new metabolites

status: Public on Jul 01 2013

city: Freising

first: Ulrich

last: Guldener

state: Bavaria

address: Maximus-von-Imhof-Forum 3

department: Chair of genome-oriented bioinformatics

country: Germany

institute: Technische Universität München

summary:
Investigation of whole genome gene expression of the Fusarium fujikuroi wild type IMI58289 under gibberellin-inducing and -repressing conditions.

Fusarium fujikuroi is a biotechnologically important fungus due to its almost unique ability to produce gibberellic acids (GAs), a family of phytohormones. The fungus was already described about 100 years ago as the causative agent of Bakanae (foolish seedling) disease of rice. Beside GAs, the fungus is known to produce some pigments and mycotoxins, but for only eight products the biosynthetic genes are known. Here we present a high-quality genome sequence of the first member of the Gibberella fujikuroi species complex (GFC), that allowed de novo genome assembly with 12 scaffolds corresponding to the 12 chromosomes. In this work, we focused on identification of all potential secondary metabolism-related gene clusters and their regulation in response to nitrogen availability by transcriptome, proteome, HPLC-FLPC and ChIP-seq analyses. We show that most of the cluster genes are regulated in a nitrogen-dependent manner, and that expression profiles fit to proteome and ChIP-seq data for some but not all clusters. Comparison with genomes of all available Fusarium species, including the recently sequenced F. mangiferae and F. circinatum, showed only a small number of common gene clusters and provides new insights into the divergence of secondary metabolism in the genus Fusarium. Phylogenetic analyses suggest that some gene clusters were acquired by horizontal gene transfer, while others were present in ancient Fusarim species and have evolved differently by gene duplications and losses. One PKS and one NRPS gene cluster are unique for F. fujikuroi. Their products were identified by combining overexpression of cluster genes with HPLC-FLPC -based product analyses. In planta, expression studies suggest a specific role of the PKS19 product in rice infection. Our results indicate that comparative genomics together with the used genome-wide experimental approaches is a powerful tool to uncover new secondary metabolites and to understand their regulation on the transcript, protein and epigenetic levels.

overall_design: In this study, we hybridized in total 15 microarrays using total RNA recovered from wild-type cultures of F. fujikuroi IMI58289. Two cultures were grown on a 6 mM Gln medium. Additionally, two technical replicates were created. Four cultures were grown on a 60 mM Gln medium. Again, two technical replicates were created. On a 6 mM NO3 medium, three cultures were grown, and two cultures on a 120 mM NO3 medium, with no technical replicates. Each chip measures the expression level of 14,397 genes from F. fujikuroi IMI58289 with eight 60-mer probes.

first: Philipp

last: Wiemann

first: Christian

last: Sieber

first: Lena

last: Studt

first: Caroline

last: Michielse

last: Güldener

first: Bettina

last: Tudzynski


title: A novel methyl-binding domain protein enrichment method for identifying genome-wide tissue-specific DNA methylation from nanogram DNA samples

status: Public on Jun 10 2013

city: Baltimore

first: Verity

middle: Frances

last: Oliver

state: MD

address: 400 North Broadway, Smith 3001P

department: Ophthalmology

institute: Johns Hopkins University

summary:
Growing evidence suggests that DNA methylation plays a role in tissue-specific differentiation. Current approaches to methylome analysis using MBD-enrichment are restricted to large (≥1 µg) DNA samples, limiting the analysis of small tissue samples. Here we present a technique which enables characterization of genome wide tissue-specific methylation patterns from nanogram quantities of DNA.
We have developed a methodology utilizing MBD2b/MBD3L1-enrichment for methylated DNA, kinase pre-treated ligation-mediated PCR amplification (MeKL) and hybridization to the comprehensive high-throughput array for relative methylation (CHARM) customized NimbleGen 2.1M mouse tiling arrays (Feinberg_MM8_Me_HX1), which we termed MeKL-chip. The kinase-modification in combination with the addition of PEG have increased the ligation-mediated PCR amplification over 20-fold, enabling >400-fold amplification of starting DNA.  We have shown that MeKL-chip can be applied to as little as 20 ng DNA, enabling comprehensive analysis of small DNA samples. Applying MeKL-chip to the mouse retina (a limited tissue source) and brain, 2498 tissue-specific differentially methylated regions (T-DMRs) were characterized.  The top five T-DMRs (Rgs20, Hes2, Nfic, Cckbr and Six3os1) were validated by pyrosequencing.   MeKL-chip enables genome-wide methylation analysis of nanogram quantities of DNA with a wide range of observed-to-expected CpG ratios due to the binding properties of the MBD2b/MBD3L1 protein complex. This methodology enabled the first analysis of genome-wide methylation in the mouse retina, characterizing novel T-DMRs.

overall_design: MBD-enrichment was performed on 3 x retina  and 3 x brain DNA samples from adult C57BL/6J mice on varied DNA quantities (250, 50, 25 and 10 ng). Samples were amplified using a modified ligation-mediated PCR and hybridized to custom NimbleGen 2.1M mouse arrays (Feinberg_MM8_Me_HX1)

first: Jun

last: Wan

first: Saurabh

last: Agarwal

first: Donald

middle: J

last: Zack

first: Jiang

last: Qian

first: Shannath

middle: L

last: Merbs


title: Small nucleolar RNAs and small Cajal body-specific RNAs show distinct transcriptional profiles in the context of the molecular heterogeneity of multiple myeloma.

status: Public on Jun 25 2013

city: MILAN

first: Luca

last: Agnelli

address: Venezian 1

department: Department of Advanced Diagnostics

institute: IRCCS Istituto Nazionale dei Tumori

summary: Small nucleolar RNAs (snoRNAs) and small Cajal body-specific RNAs (scaRNAs) are non-coding RNAs involved in the maturation of other RNA molecules and generally located in the introns of host genes. It is now emerging that altered sno/scaRNAs expression may play a pathological role in cancer. This study elucidates the patterns of sno/scaRNAs expression in multiple myeloma (MM), by profiling puri?ed malignant plasma cells from 55 MMs, 8 secondary plasma cell leukemias (sPCL) and 4 normal controls. Overall, a global sno/scaRNAs down-regulation was found in MMs and at more extent in sPCLs compared to normal plasma cells. Whereas SCARNA22 resulted the only sno/scaRNA characterizing the TC4 MM, TC2 group displayed a distinct sno/scaRNA signature overexpressing members of SNORD115 and SNORD116 families located in a region finely regulated by imprinting mechanism at 15q11. However, the imprinting center resulted overall hypomethylated in MMs independently of the SNORD115 and SNORD116 expression levels. Finally, integrative analyses with available gene expression and genome-wide data revealed the occurrence of significant sno/scaRNAs/host genes co-expression and the putative influence of allelic imbalances on specific snoRNAs expression. Our data extend the current view of sno/scaRNAs deregulation in cancer and add novel information into the bio-molecular complexity of plasma cell dyscrasias.

overall_design: This series of microarray experiments contains the gene expression profiles of purified plasma cells (PCs) obtained from 55 multiple myeloma (MM) and 8 secondary plasma cell leukemia (sPCL) at diagnosis. PCs were purified from bone marrow samples using CD138 immunomagnetic microbeads according to the manufacturer's instructions (MidiMACS system, Miltenyi Biotec); the purity of the positively selected PCs was assessed by morphology and flow cytometry and was > 90% in all cases. 5.5 micrograms of single-stranded DNA target obtained from 100 ng of purified total RNA was fragmented and then labeled using the WT Terminal Labeling Kit according to the standard Affymetrix protocol (GeneChip® Whole Transcript (WT) Sense Target Labeling Assay Manual). The fragmented labeled single-stranded DNA target was hybridized for 16 hours and 30 minutes at 45°C on GeneChip® Gene 1.0 ST array according to the standard Affymetrix protocol. Washing and scanning were performed using GeneChip System of Affymetrix (GeneChip Hybridization Oven 640, GeneChip Fluidics Station 450 and GeneChip Scanner 7G). The raw intensity expression values were processed by Robust Multi-array Average (RMA) complete procedure with the re-mapped Chip Definition Files (CDF) from BrainArray libraries version 15.0.0 available at http://brainarray.mbni.med.umich.edu/Brainarray/Database/CustomCDF/15.0.0/entrezg.asp.

first: D

last: Ronchetti

first: K

last: Todoerti

first: G

last: Tuana

first: L

last: Mosca

first: M

last: Lionetti

first: S

last: Fabris

first: E

last: Bonaparte

last: Miozzo

last: Ferrarini

first: P

last: Tassone

first: A

last: Neri


title: Identification of genes

status: Public on May 30 2013

city: aas

first: Fabian

last: Grammes

address: Arboretvn. 2

department: CIGENE

country: Norway

institute: Norwegian University of Life Sciences

summary: Identifying genes that show differential expression by comparing Atlantic salmon fed with different diets to the negative control group (FM).

platform_organism:
Oncorhynchus mykiss
Salmo salar

overall_design: Comparing gene expression of the distal intestine from Atlantic salmon receiving different diets, totally 57 arrays.

first: Felipe

last: Reveco

first: Odd-Helge

last: Romarheim

first: Thor

last: Landsverk

first: Liv-Trunn

last: Mydland

first: Margareth

last: Øverland


title: Anaerobic oxidation of benzene by Geobacter metallireducens

status: Public on Apr 30 2013

city: Amherst

first: Tian

last: Zhang

state: MA

address: 639 North Pleasant St.

institute: University of Massachusetts

summary: Anaerobic activation of benzene is expected to represent a novel biochemistry of environmental significance but research into the mechanisms has been stymied by a lack of a genetically tractable pure culture which unequivocally does not use molecular oxygen to activate benzene. Geobacter metallireducens grew in a medium in which benzene was the sole electron donor and Fe(III) was the sole electron acceptor with a stoichiometry of benzene loss and Fe(III) reduction consistent with benzene oxidation to carbon dioxide coupled with Fe(III) reduction. Phenol labeled with 18O was produced when the medium was labeled with H218O, as expected for a true anaerobic conversion of benzene to phenol.  Gene expression patterns indicated that benzene was metabolized through a phenol intermediate rather than benzoate or toluene. Deletion of ppcB, which encodes a subunit of the phenylphosphate carboxylase, an enzyme required for phenol metabolism, inhibited metabolism of benzene.  Deleting genes specific for benzoate or toluene metabolism did not.  Comparison of gene expression patterns in cells grown on benzene versus cells grown on phenol revealed genes specifically expressed in benzene-grown cells.  Deletion of one of these, Gmet_3376, inhibited anaerobic benzene oxidation, but not the metabolism of phenol, benzoate, or toluene.  The availability of a genetically tractable pure culture that can anaerobically convert benzene to phenol with oxygen derived from water should significantly accelerate elucidation of the mechanisms by which benzene can be activated in the absence of molecular oxygen.

overall_design:
Total RNA from
three separate cultures of G. metallireducens grown with 250 µM benzene
three separate cultures of G. metallireducens grown with 500 µM phenol
three separate cultures of G. metallireducens grown with 1 mM benzoate
three separate cultures of G. metallireducens grown with 500 µM toluene
three separate cultures of G. metallireducens grown with 10 mM acetate
were used to study
[1] Anaerobic oxidation of benzene by G. metallireducens (Benzene vs. acetate, Benzene vs. benzoate, Benzene vs. phenol, Benzene vs. toluene)
[2] Anaerobic oxidation of benzoate by G. metallireducens (Benzoate vs. acetate)
[3] Anaerobic oxidation of phenol by G. metallireducens (Phenol vs. acetate)
[4] Anaerobic oxidation of toluene by G. metallireducens (Toluene vs. acetate)

Each chip measures the expression level of 3,627 genes from G. metallireducens DSM 7210 with nine 45-60-mer probe pairs (PM/MM) per gene, with three-fold technical redundancy.

first: Pier-Luc

last: Tremblay

first: Jessica

last: Smith

first: Derek

last: Lovley


title: Transcriptomes of developing rice ovules

status: Public on Feb 15 2013

city: Mishima

first: Nori

last: Kurata

state: Shizuoka

address: 1111 Yata

institute: National Institute of Genetics

summary:
We aimed to reveal transitions of gene expression profile in developing female gametophytes of rice in this study. The developmental process of rice female gametophyte, from megaspore mother cell at pre-meiotic stage to mature embryo sac, was separated into six stages. Developing ovules at each stage were separated from surrounding sporophyte tissues and collected using LMD. RNA samples extracted from them were subjected to microarray analysis.
Dynamic gene expression profiles during female gametogenesis were revealed. Comparison of transcriptome in developing female gametophytes with those of male gametophyes revealed both conserved and diverged features between male and female gametogenesis. A lot of characteristic genes, such as a subset of transposable elements, auxin responsive genes and transcription factor genes, which showed dynamic expression profiles during female gametogenesis, were identified in this study. We believe that our transcriptome data will serve as a backbone of further focused biological analysis to understand the molecular basis in female gametogenesis of plant.

overall_design: Gene expression profiles of developing ovules were analyzed according to stage progression. Three or four biological replicates were prepared for each stage, and a total of nineteen samples were analyzed.

first: Takahiko

last: Kubo

first: Masahiro

last: Fujita

first: Hirokazu

last: Takahashi

first: Mikio

last: Nakazono

first: Nobuhiro

last: Tsutsumi


title: Identification of molecular key determinants of the Mycobacterium abscessus smooth and rough morphotypes through transcriptome analyses

status: Public on May 15 2013

city: Paris

first: Alexandre

last: Pawlik

address: 28 rue du Dr. Roux

country: France

institute: Institut Pasteur

summary: In this study, we were interested to get deeper insights into the molecular mechanisms that govern the formation and selection of the different colony morphologies in Mycobacterium abscessus strains, including the potential reversibility of the rough (R) phenotype into a smooth (S) phenotype. We used next generation sequencing (NGS) and micro-array / RNAseq approaches to determine the genome sequences and transcriptomic profiles of three isogenic S/R strain couples of M. abscessus. One clinical isolate strain named CF and two collection strains referred as 19977-AT and 19977-IP.

overall_design: To perform the transcriptomic comparison of the rough variant versus the smooth variant for each M. abscessus strain, a customized micro-array has been manufactured by Agilent (8 x 15k format). The design of oligonucleotides covering all protein coding sequences was done using OligoArray version 2.1 on the basis of the 4920 predicted coding sequences composing the entire M. abscessus genome. The experimental data for each of the 3 strains consisted of 6 hybridizations (3 biological replicates with dye-swap).

first: Marie-Agnés

last: Dillies

first: Jean-Yves

last: Coppée

first: Roland

last: Brosch

first: Jean-Louis

last: Herrmann


title: EMPV1 technical repeat

status: Public on Feb 25 2013

city: Madison

first: chi

last: zhou

state: WI

address: 202 S. Park Street, PAB1, Meriter Hospital

department: Department of OB/Gyn

institute: University of Wisconsin-Madison

summary: 2-4-8 cell porcine embryo technical repeat dye-swap for Agilent EMPV1 (4x44k Format)

first: Chi

last: Zhou


title: Genome-wide analysis of dexamethasone-responsive gene expression in mouse triceps surae muscle

status: Public on Feb 12 2013

city: Davis

first: J.

middle: David

last: Furlow

state: CA

address: One Shields Avenue

institute: UC Davis

summary: Analysis of dexamethasone-regulation of muscle mass at gene expression level. The hypothesis tested in the present study was that the presence of MuRF1 contributes to the extent of gene expression changes observed in specific sets of genes during a challenge leading to muscle atrophy. Results provide important information on the response of triceps surae muscle to synthetic glucocorticoid treatment, such as specific cell signaling and metabolic enzyme genes, that may be influenced by MuRF1 during atrophy.

overall_design: Total RNA obtained from isolated triceps surae muscle subjected to 3 or 14 days dexamethasone treatment compated to untreated littermate control muscles.

first: David

first: Monica

last: Watson

last: Waddell

first: Eric

last: Neff

first: Leslie

last: Baehr

first: Adam

middle: P

last: Ross

first: Sue

last: Bodine


title: Heme-based respiration of Leuconostoc gasicomitatum

status: Public on Feb 08 2013

first: Elina

last: Jääskeläinen

address: P.O. Box 66 (Agnes Sjöbergin katu 2)

department: Food Hygiene and Environmental Health

institute: University of helsinki

summary: Transcriptonal profiling of Leuconostoc gasicomitatum LMG18811T (wild type)  grown in MRS medium with or without heme. Mutant LMG18811T::pSIP1333A (mutating cydB gene which is essential in the respiratory chain) grown in MRS with or without heme. Comparing mutant and wildtype with and without heme.

overall_design: Two-condition experiments with wild type and cydB mutant. 1) wild type with heme vs wild type without heme (HVV), 2) wild type with heme vs mutant with heme (HMHV) 3) mutant with heme vs mutant without heme (MHM) 4) wildtype without heme vs mutant without heme (MV).


title: LGR5 positivity defines stem-like cells in colorectal cancer [aCGH]

status: Public on May 07 2013

city: Bethesda

first: Yue

last: Hu

address: 50 South Drive, Bldg. 50, Rm. 1408

department: Genetic

institute: NCI

summary: Lgr5-EGFP-IRES-Cre-ERT2 mice were exposed to azoxymethane/dextrane sodium sulfate (AOM/DSS) which induces inflammation-driven colon tumors. Tumors were then flow-sorted into fractions of epithelial cells that expressed high or low levels of Lgr5. To exclude that transcriptional differences between Lgr5 high and low mouse colon tumor cells were imposed by distinct patterns of chromosomal aberrations in the two cell fractions, we also performed array comparative genomic hybridization (aCGH) from these tumors. All eight analyzed tumors were chromosomally stable, and thus, no difference between Lgr5 high and low cells could be detected.

overall_design: AOM/DSS-induced mouse colon tumors were flow-sorted into Lgr5 high and low cells before aCGH was performed. Biological replicates: 8. Two CGH array platforms.

first: Daniela

middle: D

last: Hirsch

first: Timo

last: Gaiser

first: Thomas

last: Ried


title: Effect of overexpression of a nitrate-inducible GARP-type transcriptional repressor NIGT1 in rice

status: Public on Jan 03 2013

city: Bunkoy-ku

first: Shuichi

last: Yanagisawa

state: Tokyo

address: Yayoi 1-1-1

department: Biotechnology Research Center

institute: The University of Tokyo

summary: Nitrogen is the most important macronutrient in plants and its supply induces responses in gene expression, metabolism and developmental processes. However, the molecular mechanisms underlying the nitrogen responses remain poorly understood. Here we show that the supply of nitrate but not ammonium immediately induces the expression of a transcriptional repressor gene in rice, designated NIGT1 (Nitrate-Inducible, GARP-type Transcriptional Repressor 1). The results of DNA-binding site selection experiments and electrophoretic mobility shift assays indicated that NIGT1 binds to DNA containing either of two consensus sequences, GAATC and GAATATTC. In transient reporter assays, NIGT1 was found to repress transcription from the promoters containing the identified NIGT1-binding sequences in vivo. Furthermore, NIGT1 repressed the activity of its own promoter, suggesting an auto-repression mechanism. Consistently, nitrate-induced NIGT1 expression was found to be downregulated after a transient peak during nitrate treatment, and the nitrate-induced expression of NIGT1 decreased in transgenic rice plants in which this gene was constitutively overexpressed. Furthermore, the chlorophyll content that could be a marker of nitrogen utilization was found to be decreased in NIGT1 overexpressors of rice grown with nitrate medium but not with ammonium medium. Thus, we propose NIGT1 as a nitrate-inducible and auto-repressible transcriptional repressor that may play a role in the nitrogen response in rice. Taken together with the fact that the NIGT1-binding sites are conserved in promoter sequences of Arabidopsis NIGT1 homologs, our findings imply the presence of a time-dependent complex system for nitrate-responsive transcriptional regulation that is conserved in both monocots and dicots.

overall_design: Nitrate-induced gene expression in rice shoots was monitored 2 hours after the treatment with 10 mM potassium nitrate in the NIGT1-overexpressing lines and vector control lines.

first: Naoya

last: Sawaki


title: Molecular Subtypes in Head and Neck Cancer [expression]

status: Public on Mar 01 2013

city: Chapel Hill

first: Vonn

last: Walter

state: NC

address: CB#7295, School of Medicine

institute: Lineberger Comprehensive Cancer Center

summary: Head and neck squamous cell carcinoma (HNSCC) is a heterogeneous disease whose underlying etiology has not been explained by traditional prognostic factors such as tumor site, stage, or histology. Although previous studies have shown that molecular subtypes of HNSCC exist, the benefit of such a classification scheme has not been fully realized. We show that molecular subtypes of HNSCC exist; that these subtypes have distinct patterns of chromosomal gain and loss, some of which affect canonical oncogenes and tumor suppressors; and that the subtypes are biologically and clinically relevant. These subtypes provide new insight into HNSCC etiology, as well as a valuable method for classifying HNSCC tumors.

overall_design: A total of 163 samples were considered. Quality control procedures were applied to microarray probe-level intensity files. A total of 138 tumor arrays remained after removing low-quality arrays, duplicate arrays, and arrays from non-HNSCC samples. The normexp background correction and loess normalization procedures were applied to the probe-level data. After log transformation, probes were matched to a common gene database to produce expression values for 15595 genes.


title: Peri-pubertal gonadotropin-releasing hormone agonist treatment affects sex-biased gene expression of amygdala in sheep

status: Public on May 31 2013

city: Oslo

first: Syed

last: Nuruddin

address: Ullevalsveien 72

department: Production animal clinical sciences

institute: Norwegian school of veterinary science

summary:
Background: The exact nature of the interrelationship between pubertal brain development and hormones involvement has always attracted wide interest. Brain structural changes that occur during the pubertal developmental process mainly appear in the regions most closely linked with emotion, motivation and cognitive functions. Using a sheep model, we have previously shown that peri-pubertal pharmacological blockade of gonadotropin-releasing hormone (GnRH) receptors results in increased sex-differences in cognitive executive function and emotional control, as well as in a sex- and side-specific gene expression pattern of hippocampal genes associated with synaptic plasticity and endocrine signaling. In this study, we explore the effects of this treatment regime on the amygdalar gene expression profile.

Methods: The study was conducted with 30 same-sex twin lambs (14 female and 16 male), half of which were treated with the GnRH agonist (GnRHa) goserelin acetate every 4th week, beginning before puberty, until 50 weeks of age. The gene expression profiles of left and right amygdala samples from all 30 animals were measured by using ovine 8 X 15 K Agilent microarrays. Furthermore, differential expression of a selected number of genes was confirmed by qRT-PCR (Quantitative real time PCR). Networking analyses and Gene Ontology (GO) Term analyses were performed with the Ingenuity Pathway Analysis (IPA), version 7.5 DAVID (Database for Annotation, Visualization and integrated Discovery) software packages respectively.

Results: GnRHa treatment was associated with significant sex- and hemisphere-specific differential expression of genes. Interestingly, genome-wide transcription showed a set of 438 (p value <0.05) genes in female treated left and 46 (p value <0.0.5) genes in females treated right amygdala were differentially expressed but not in any treatment group of male animals.

Conclusion: Our results indicate that GnRH directly and/or indirectly is involved in the regulation of sex- and side-specific differential expression of genes in amygdala. Hence, this finding should be considered when long-term peri-pubertal GnRHa treatment is used in children.

overall_design: GnRHa-treated and untreated animals. This submission includes a total 56 samples for 8 groups (male control left and right amygdala, female control left and right amygdala, male treated left and right amygdala, and female treated left and right amygdala), with 7 biological replicates each group (n=7). Four male samples had poor RNA quality and are not included here. Dye-swaps were performed.

first: Brynildsrud

middle: O

last: Brønstad


title: Genome-wide analysis of denervation and dexamethasone-responsive gene expression in mouse triceps surae muscle

first: J.

last: Furlow

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

overall_design: Refer to individual Series


title: Dynamic profile of gene expression in rice panicle under high temperature

status: Public on Nov 28 2012

city: Changsha

first: Xianwen

last: Zhang

address: 1 Nongda Road, Furong District

institute: Hunan Agricultural University

summary: To comprehend the profile of rice gene expression at reproductive stage under high temperature, Agilent 4×44k rice oligo microarray experiments were carried out using rice panicle of developmental stage 7-9 at 0min, 20min, 1hr, 2hr, 4hr, and 8hr after the treatment of 40 degree centigrade, and the significantly expressed genes mainly involved in transcriptional regulation, transport, cellular homeostasis, and stress response were identified. Among them, the predominant transcription factor gene families were Hsf, NAC, AP2/ERF, WRKY, MYB, and C2H2. KMC analysis discovered the time-dependent gene expression pattern under heat. The results of motif co-occurrence on the promoters of genes from an early up-regulated cluster showed the important roles of GCC box, HSE, ABRE, and CE3, and unraveled the possible cross-talk mechanism during heating. The response model central to ROS combined with transcriptome data indicated the great importance to maintain ROS balance in heat response in rice panicle and the wide existing of cross-talks.

overall_design: Heat shock induced gene expression in rice panicle of developmental stage 7-9 was measured at 0min, 20min, 1hr, 2hr, 4hr, and 8hr after the treatment of 40 degree centigrade in plant growth chamber. Two independent replicate experiments were performed at each time point.

first: Jiaping

last: Li

first: Ailing

last: Liu

first: Jie

last: Zou

first: Xiaoyun

last: Zhou

first: Jianhua

last: Xiang

first: Wirat

last: Rerksiri

first: Yan

last: Peng

first: Xingyao

last: Xiong

first: Xinbo

last: Chen


title: Expression data of multiple sclerosis patients receiving glatiramer acetate therapy [U133 Plus 2.0]

status: Public on Dec 07 2012

city: Rostock

first: Michael

last: Hecker

address: Gehlsheimer Str. 20

department: Department of Neurology

institute: University of Rostock

summary: The purpose of this study was to analyze the transcriptional effects induced by glatiramer acetate treatment (GA; Copaxone, 20 mg injected subcutaneously once daily) in blood monocytes of patients with relapsing-remitting form of multiple sclerosis (MS). By using Affymetrix DNA microarrays, we obtained genome-wide expression profiles of monocytes from 8 MS patients within the first two months of GA administration.

overall_design: EDTA blood samples were taken from all patients immediately before first and second GA injection as well as after 1 week, 1 month and 2 months. Total RNA of CD14+ monocytes isolated by magnetic-activated cell sorting (MACS) from each sample was extracted, labeled and hybridized to Affymetrix Human Genome U133 Plus 2.0 arrays to quantify the mRNA levels. This GEO entry provides the U133 Plus 2.0 microarray data.

first: Dirk

last: Koczan

first: Robert

middle: H

last: Goertsches

first: Uwe

last: Zettl


title: The effects of a probiotic yeast on the bacterial diversity and population structure in the rumen of cattle.

status: Public on Jan 01 2013

city: Aberystwyth

first: Eric

last: PINLOCHE

address: Cledwyn Building

institute: IBERS

summary: SARST-V1 method was used to asses the effect of live yeast on the microbial population of the rumen of cows fed an acidogenic diet

overall_design: 3 cows were used in 3 by 3 latin-square design with 3 periods. In each period animals received either 0.5g/d of yeast, 5g/d of yeast or none. Rumen microbiota was analysed using the SARST-V1 method for each period.

first: E

last: Pinloche

first: J

last: Marden

last: Auclair

first: C

last: Bayourthe

last: Newbold


title: Combinatorial targeting of glycolysis and oxidative phosphorylation suppresses tumor growth and metastases.

status: Public on Dec 31 2012

city: Houston

first: Sangbae

last: Kim

state: TX

address: 1 Baylor plaza

department: HGSC

institute: Baylor Colleage of Medicine

summary: The Warburg effect, consisting of increased glucose uptake and glycolysis, provides metabolic energy as well as cellular building blocks for tumor growth. Inhibition of the Warburg effect with 2-deoxyglucose (2DG) has been explored in clinical trials with limited efficacy. Blockage of glycolysis can induce autopahgy resulting in alternative energy generation through oxidative phosphorylation providing a potential bypass of the effects of inhibition of glycolysis. Here in we demonstrate that activation of AMPK, as a consequence of energetic stress, induces mitochondrial energy production potentially bypassing the effects of glycolysis inhibition. We thus combined blockage of glycolysis by 2DG with inhibition of the electron transfer complex I (ETC1) in the mitochondria with the clinically applicable antidiabetic drug metformin. The combination resulted in activation of AMPK and autopahgy that however rendered eventual depletion of ATP and cell death. Furthermore, combined inhibition of glycolysis and mitochondrial respiration inhibited tumor growth and markedly decreased metastatic capacity in vivo. In order to understand the mechanism of these metabolic inhibitors, we performed whole genome transcriptional analysis.

overall_design: Human SK-4 esophageal cancer cell lines were treated  with 5 different treatment groups [2 deoxy glucose (4mM), Metformin (5mM), AICAR (2mM), 2 deoxy glucose (4mM) plus Metformin (5mM) and 2 deoxy glucose (4mM) plus AICAR (2mM)] with non treated control groups for 12 hrs. Each groups was quadruplicated. Microarray experiments and data analysis were done at Dept. of Systems Biology, MDACC (Houston, USA)

first: Jae-Ho

last: Cheong

first: EunSung

last: Park

first: Gordon

middle: B

last: Mills


title: Genome-wide analysis of denervation induced gene expression in mouse triceps surae muscle

first: J.

last: Furlow

summary: Analysis of denervation induced regulation of muscle mass at gene expression level. The hypothesis tested in the present study was that the presence of MuRF1 contributes to the extent of gene expression changes observed in specific sets of genes during a challenge leading to muscle atrophy. Results provide important information on the response of triceps surae muscle to sciatic nerve resection (denervation), such as specific structural, metabolic, and neuromuscular junction associated genes, that may be influenced by MuRF1 during atrophy.

overall_design: Total RNA obtained from isolated triceps surae muscle subjected to 3 or 14 days post-denervation compared to nonsurgically treated littermate control muscles.

first: David

first: Monica

last: Watson

middle: S

last: Waddell

last: Neff

first: Leslie

last: Baehr

first: Adam

last: Ross

first: Sue

last: Bodine


title: Mice Lacking a Myc Enhancer Element that Includes Human SNP rs6983267 Are Resistant to Intestinal Tumors

status: Public on Nov 02 2012

city: Stockholm

first: Martin

last: Enge

address: CCK, Z4

department: Dep of Oncology-Pathology

country: Sweden

institute: Karolinska Institute

summary: Multiple cancer-associated single nucleotide polymorphisms (SNPs) have been mapped to conserved sequences within a 500 kilobase region upstream of the MYC oncogene on human chromosome 8q24. These SNPs may affect cancer development through altered regulation of MYC expression, but this hypothesis has been difficult to confirm. We generated mice deficient in Myc-335, a putative MYC regulatory element that contains rs6983267, a SNP accounting for more human cancer- related morbidity than any other genetic variant or mutation. In Myc-335 null mice, Myc transcripts were expressed in the intestinal crypts in a pattern similar to that in wild-type mice but at modestly reduced levels. The mutant mice displayed no overt phenotype but were markedly resistant to intestinal tumorigenesis induced by the APCmin mutation. These results establish that a cancer-associated SNP identified in human genome-wide association studies has a functional effect in vivo.

overall_design:
Exon-array analysis of mouse colon tissues from Myc-335 null and wild-type mouse (both mice are male and from the same litter).

Related ChIP-seq data available in Short Read Archive, Accession ERP001919


title: Transcriptional changes in response to oxidative stress in combination with temperature extremes in rice

status: Public on Dec 26 2012

city: New Delhi

first: Anil

last: Grover

state: Delhi

address: Benito Juarez Road

department: Plant Molecular Biology

country: India

institute: University of Delhi South Campus

summary: Genome wide expression profiles of 10-day-old seedlings in response to prior exposure with OS followed by heat stress or cold stress as well simultaneous exposure to OS along with HS/CS was done to study the transcriptional changes in response to combination of stresses.

overall_design: 10-day old rice seedlings were used for experiments. Transcript profiling was done in 10-day old rice seedling following oxidative Stress prior to High Temperature Stress (PO_HS) or Low Temperature Stress (PO_CS) and Oxidative Stress during High Temperature Stress (DO_HS)/ during Low temperature stress (DO_CS). Unstressed seedlings were used as control. For each condition, three biological replicates were processed in a similar manner for the microarray analysis.

first: Dheeraj

last: Mittal


title: Sheep skin lymph  CD103 and CD11b -type DC in vitro response to Canine Adenovirus vector

status: Public on Nov 30 2012

city: Illkirch

first: Doulaye

last: Dembele

address: 1 rue Laurent Fries

department: Biopuces

institute: IGBMC

summary: Transcriptomic profiling of sheep skin lymph DC subsets after 16h in vitro culture in medium or stimulated by non replicative Canine Adenovirus serotype 2

overall_design: Reference design: total enriched lymph dendritic cells- Biological replicates: 4 sheep (70958, 50274, 30066, 11261)- Samples: FACS sorted CD103 -type and CD11b type cultured in medium or with CAV2

first: I

last: Schwartz-Cornil


title: Transcriptome and signalling response to As stress

status: Public on Oct 21 2012

city: Tainan

first: Tsai-Lien

last: Huang

state: Taiwan

address: No.1, University Raod,

department: Life Sciences

institute: National Cheng Kung University

summary:
Arsenic (As) is considered as the most common toxic metalloid, but its molecular mode of action is not well understood. In this study, we demonstrated that As(V) induced intracellular ROS production and Ca2+ accumulation in rice roots. To understand the molecular basis of plant cell responses to As better, we have undertaken a large-scale analysis of the rice transcriptome during As(V) stress. Up-regulated genes were enriched in transcripts involved in abiotic stress, chemical detoxification pathways, secondary metabolic process, transcription regulation and protein degradation while down-regulated genes were enriched in transcripts involved in secondary cell wall biogenesis, cell cycle and oligopeptide transporter.
Molecular mechanisms for the As(V) in rice roots

overall_design: Comparison of mock control and rice seedlings treated with 25 μM As(V); Biological replicates: 3 control replicates, 3 As(V)-treated replicates.

first: Hao-Jen


title: Regulation of neurogenin-dependent gene expression by geminin

status: Public on Dec 06 2012

city: Saint Louis

first: Kristen

last: Kroll

address: 320 McDonnell Sciences/660 S. Euclid Ave.

department: Developmental Biology

institute: Washington University School of Medicine

summary:
Transcriptional targets of neurogenin (Ngnr1) were identified by over-expression of an inducible form of neurogenin in Xenopus ectodermal explants. The effects of co-expressing the nucleoprotein geminin on Ngnr1-dependent target gene transactivation were defined.

Regulating the transition from lineage-restricted progenitors to terminally differentiated cells is a central aspect of nervous system development. Here, we investigated the role of the nucleoprotein geminin in regulating neurogenesis at a mechanistic level during both Xenopus primary neurogenesis and mammalian neuronal differentiation in vitro. The latter work utilized both neural cells derived from embryonic stem and embryonal carcinoma cells in vitro and neural stem cells from mouse forebrain. In all of these contexts, geminin antagonized the ability of neural bHLH transcription factors to activate transcriptional programs promoting neurogenesis. Furthermore, geminin promoted a bivalent chromatin state, characterized by the presence of both activating and repressive histone modifications, at genes encoding transcription factors that promote neurogenesis. This epigenetic state restrains the expression of genes that regulate commitment of undifferentiated stem and neuronal precursor cells to neuronal lineages. Geminin is highly expressed in undifferentiated neuronal precursor cells but is downregulated prior to differentiation. Therefore, these data support a model whereby geminin promotes the neuronal precursor cell state by modulating both the epigenetic status and expression of genes encoding neurogenesis-promoting factors. Additional developmental signals acting in these cells can then control their transition toward terminal neuronal or glial differentiation during mammalian neurogenesis.

overall_design: A dexamethasone-inducible (GR ligand binding domain fused) form of Xenopus neurogenin-related 1, NgnrGR, was over-expressed in Xenopus embryonic ectodermal explants, in the presence or absence of over-expressed geminin. Induction of Ngnr1 activity was used to define direct targets as previously described (EMBO J. 26(24): 5093-5108). The ability of geminin to suppress Ngnr1-dependent transactivation of its target gene programs was determined.

first: Jong

middle: W

last: Lim


title: Inositol regulation with Cryptococcus neoformans JEC21 70-mer whole genome array

status: Public on Sep 29 2012

city: Newark

first: Chaoyang

last: Xue

state: NJ

address: 225 Warren Street

institute: University of Medicine and Dentistry of New Jersey

summary: Cryptococcus neoformans is the most common cause of fungal meningitis, with high mortality and morbidity. The reason for the frequent occurrence of Cryptococcus infection in the central nervous system (CNS) is poorly understood. In this study, we find that inositol plays an important role in the transversal of Cryptococcus across the blood-brain barrier (BBB) both in an in vitro human BBB model and in vivo animal models. The inositol stimulation of BBB crossing is dependent upon fungal inositol transporters. The upregulation of genes involved in the inositol catabolism pathway is evident in a microarray analysis. The expression of CPS1, a gene encoding the hyaluronic acid synthase in Cryptococcus, is also upregulated by the inositol treatment. The production of hyaluronic acid increased in cells treated with inositol, which leads to the enhanced binding ability of Cryptococcus cells to the human brain microvascular endothelial cells (HBMECs) constituting the BBB. Overall, our studies provide a mechanism for inositol-dependent Cryptococcus transversal of the BBB, supporting our hypothesis that host inositol utilization by the fungus contributes to Cryptococcus CNS infection.

overall_design: To understand the effect of inositol on gene expression profiles during cell development, microarray experiments were performed to monitor the genes regulated by inositol. H99 overnight culture was washed with dH2O once, and cells were inoculated on SD medium with or without inositol. Cells were collected from SD plates 24 hr post-inoculation, washed with dH2O, and total RNA was purified. Total RNAs were extracted using Trizol Reagents (Invitrogen) and purified using the Qiagen RNeasy cleanup kit (Qiagen). Cy3 and Cy5-labeled cDNA were generated by incorporating amino-allyl-dUTP during reverse transcription of 5 µg of total RNA as described previously and competitively hybridized to a JEC21 whole-genome array generated previously at Washington University in Saint Louis. After hybridization, arrays were scanned with a GenePix 4000B scanner (Axon Instruments, http://www.axon.com) and analyzed by using GenePix Pro version 4.0 and BRB array tools (developed by Richard Simon and Amy Peng Lam at the National Cancer Institute; http://linus.nci.nih.gov/BRB-ArrayTools.html)

first: Tong-Bao

last: Liu

first: Yina

last: Wang


title: MicroRNA signature in murine atherosclerosis

city: Munich

first: Andreas

last: Schober

address: Pettenkoferstr. 9

department: Institute for Cardiovascular Prevention

institute: Ludwig-Maximilians-University


title: Major functional transcriptome of an inferred center regulator of an ER(-) breast cancer model system

status: Public on Sep 25 2012

city: Taipei

first: Fon-Jou

last: Hsieh

address: No. 7, Chung-Shan South Rd

department: Department of obstetrics and gynecology

institute: National Taiwan University

summary: We aimed to find clinically relevant gene activities ruled by the signal transducer and activator of transcription 3 (STAT3) proteins in an ER(-) breast cancer population via network approach. STAT3 is negatively associated with both lymph nodal category and stage. MYC is a component of STAT3 network. MYC and STAT3 may co-regulate gene expressions for Warburg effect, stem cell like phenotype, cell proliferation and angiogenesis. We identified a STAT3 network in silico showing its ability in predicting its target gene expressions primarily for specific tumor subtype, tumor progression, treatment options and prognostic features. The aberrant expressions of MYC and STAT3 are enriched in triple negatives (TN). They promote histological grade, vascularity, metastasis and tumor anti-apoptotic activities. VEGFA, STAT3, FOXM1 and METAP2 are druggable targets. High levels of METAP2, MMP7, IGF2 and IGF2R are unfavorable prognostic factors. STAT3 is an inferred center regulator at early cancer development predominantly in TN.

overall_design: 91 specimens of primary infiltrating ductal carcinoma of breast (IDC) included triple negatives(48/91), ERBB2+(29/91),ER(-)PR(+)HER(-)(5/91), ER(-)PR(+)HER(+)(6/91) and ER(-) but HER(?)(3/91). Five specimens for metaplastic carcinoma of breast (MCB) were included. Seven non-tumor samples were surgically taken from breast tissue adjacent to some of 91 ER(-) IDC breast tumors as a control in this study.

first: Li-Yu

first: Li-Yun

last: Chang

first: Wen-Hung

last: Kuo

first: Hsiao-Lin

last: Hwa

first: Yi-Shing

last: Lin

first: Shiu-Feng

first: Chiung-Nien

last: Chen

first: King-Jen


title: SRL1 encodes a putative GPI-anchored protein and modulates rice leaf rolling by regulating the differentiation of bulliform cells

status: Public on Sep 05 2012

city: Shanghai

first: Jingjing

last: Xiang

state: Shanghai

address: 300 Fenglin Road

institute: Institute of Plant Physiol & Ecology, Chinese Academy of Sciences

summary: To identify genes involved in the differentiation of bulliform cells,  genome-wide analysis of gene expression profiles was performed in cells to be differentiated into bulliform cells in srl1-1 but epidermal cells in Nip.

overall_design: The seedlings of Nip and srl1-1 were fixed at 5 DAG (day after germination), and cells to be differentiated into bulliform cells in srl1-1 but epidermal cells in Nip were isolated by LCM (laser capture microdissection). Then total RNA were extracted from two independent biological replicates.

first: Jing-Jing

first: Hong-Wei


title: microRNA Expression based, Effects of Chronic Intermittent Ethanol paradigm on mouse brain

status: Public on Dec 31 2013

city: Austin

first: Giorgio

last: Gorini

address: 2500 Speedway A4800

department: Waggoner Center for Alcohol and Addiction Research

institute: The University of Texas at Austin

summary: We analyzed cerebral cortices (CTX) and midbrains (MB) from male C57BL/6J mice subjected to a CIE, 2BC paradigm, which induces heavy drinking and represents one of the best available animal models for alcohol dependence and relapse drinking.

overall_design: Samples from CTX and MB of 21 mice: 7 Naïve, 7 Air-2BC, and 7 CIE-2BC. One channel was used for the actual sample, the second channel was used fot Internal QC Reference.

first: Yury

last: Nunez

first: Roy

last: Mayfield


title: The molecular response of Clostridium thermocellum ATCC 27405 to ethanol shock

status: Public on Aug 16 2012

city: Golden

first: Shihui

last: YANG

state: CO

address: 1617 Cole Blvd

department: National Bioenergy Center

institute: National Renewable Energy Lab

summary: Clostridium thermocellum is a Gram-positive, anaerobic, thermophilic bacterium that ferments cellulose into ethanol. It is a candidate industrial consolidated bioprocess (CBP) biocatalyst for lignocellulosic bioethanol production. However, C. thermocellum is relatively sensitive to ethanol compared to yeast. Previous studies have investigated the membrane and protein composition of wild-type and ethanol tolerant strains, but relatively little is known about the genome changes associated with the ethanol tolerant C. thermocellum strain. In this study, C. thermocellum cultures were grown to mid-exponential phase and then either shocked with the supplementation of ethanol to a final concentration of 3.95 g/L (equal to 0.5% [v/v]) or were untreated. Samples were taken pre-shock and 2, 12, 30, 60, 120, 240 min post-shock for multiple systems biology analyses.  The addition of ethanol dramatically reduced the C. thermocellum growth and the final cell density was approximately half of the control fermentations, with concomitant reductions in substrate consumption in the treated cultures. The response of C. thermocellum to ethanol was dynamic and involved more than six hundred genes that were significantly and differentially expressed between the different conditions over time and every functional category was represented. Cellobiose was accumulated within the ethanol-shocked C. thermocellum cells, as well as the sugar phosphates such as fructose-6-P and cellobiose-6-P. The comparison and correlation among intracellular metabolites, proteomic and transcriptomics profiles as well as the ethanol effects on cellulosome, hydrogenase glycolysis and nitrogen metabolism are discussed, which led us to propose that C. thermocellum may utilize the nitrogen metabolism to bypass the arrested carbon metabolism in responding to ethanol stress shock, and the nitrogen metabolic pathway and redox balance may be the key target for improving ethanol tolerance and production in C. thermocellum.

overall_design: A thirty array study using total RNA recovered from wild-type cultures of Clostridium thermocellum at different time points of 0, 12, 30, 60, 120, and 240 min post-inoculation with 3.95 g/L [0.5% (v/v)] treatment compred to that of control without ethanol supplementation. Two biological replicates for treatment and control condition.

last: Yang

first: Richard

last: Giannone

first: Timothy

last: Tschaplinski

first: Zamin

first: Nancy

last: Engle

first: Dice

last: Lezlee

first: Miguel

last: Rodriguez

first: Robert

last: Hettich

first: Martin

last: Keller

first: Steven

last: Brown


title: Microarray development for the Grooved carpet shell clam, Ruditapes decussatus: Functional approach to host parasite interaction

status: Public on Aug 01 2012

city: Legnaro

first: Massimo

last: Milan

state: PD

address: Viale dell'Università 16

department: Dept. of Department of Public Health, Comparative Pathology,and Veterinary Hygiene

country: Italy

institute: University of Padova

summary: An R.decussatus microarray platform was developed to to profile gene expression in R. decussatus heavy infected by Perkinsus olseni

overall_design: A comparative analysis of gene expression was conducted between Grooved carpet shell clam R. decussatus individuals for non infected and infected by Perkinsus olseni clam gills. Gene expression profiling was performed using an R.decussatus oligo-DNA microarray of 43,758 probes based on single-colour detection (Cyanine-3 only). Microarrays were scanned with Agilent scanner G2565BA at a resolution of 5 microns; all slides were scanned twice at two different sensitivity settings (XDRHi 100% and XDRLo 10%); the scanner software created a unique ID for each pair of XDR scans and saved it to both scan image files. Feature Extraction (FE) 9.5 used XDR ID to link the pairs of scans together automatically when extracting data. The signal left after all the FE processing steps have been completed is ProcessedSignal that contains the Multiplicatively Detrended, Background-Subtracted Signal.

first: Luca

last: Bargelloni

first: Ricardo

last: Leite


title: WRKY type transcription factor OsWRKY28 overexpression effect on rice leaves 48 h after Magnaporthe Oryzae infection

status: Public on Sep 30 2012

city: Tokyo

first: Kazunori

last: Okada

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

institute: The University of Tokyo

summary: Analysis of transgenic rice overexpressing OsWRKY28, a WRKY type transcription factor. Results provide insight into the role of OsWRKY28 in the defense signaling against rice blast fungus.

overall_design: Expression profiling in wild-type and OsWRKY28 overexpressing rice leaves infected with or without Magnaporthe Oryzae was analyzed using one-color method with three biological replicates.

first: Koji

last: Miyamoto

first: Takafumi

last: Shimizu

first: Tetsuya

last: Chujo

first: Takeo

last: Shimogawa

first: Eiichi

last: Minami

first: Hisakazu

last: Yamane

first: Hideaki

last: Nojiri


title: Estrogen modulates hepatic gene expression and survival of rainbow trout infected with pathogenic bacteria Yersinia ruckeri.

status: Public on Jun 17 2012

city: Aas

first: Aleksei

last: Krasnov

address: Osloveien 1

department: Fish Health

institute: Nofima AS

summary: Juvenile rainbow trout were exposed to two different concentrations of 17β-estradiol (E2) (2 or 20 mg/kg feed), and then infected with three concentrations of Yersinia ruckeri, a bacterial pathogen causing massive losses in wild and farmed salmonid populations. Infection with Y. ruckeri caused mortality of trout, and this effect was significantly enhanced by simultaneous exposure to high E2 dose. Analysis of hepatic gene expression profiles revealed complex regulations of pathways involved in immune responses, stress responses and detoxicification pathways. E2 markedly reduced expression of several genes implicated in xenobiotic metabolism. The results suggest that the interaction between pathogen and E2 interfered with the fish’s capability of clearing toxic compounds. The findings of the current study add to our understanding of multiple exposure responses in fish.

overall_design: Microarray analyses compared 3 groups of pathogen infected fish: no estrogen treatment (NE2), low (LE2) and high (HE2) doses of hormone

first: Michael

last: Wenger


title: miRNA profiling of infiltrating glioma cells

status: Public on May 04 2012

city: Regensburg

first: Sabit

last: Delic

address: Franz-Josef-Strauss-Allee 11

department: Department of Neuropathology

institute: University Hospital Regensburg

summary:
Diffusely infiltrative growth of human astrocytic gliomas is one of the major obstacles to successful tumor therapy. Thorough insights into the miRNAs inolved in regulating glioma cell invasion thus appear of major relevance for the development of novel and advanced therapies.
miRNA expression profiling on microdissected human tumor biopsy specimens was performed to identify differentially expressed miRNAs in invading glioblastoma cells in vivo.

overall_design: miRNA was extracted from the infiltrative rim (INF) as well as from the central tumor areas (CEN) of 7 patients with malignant glioma. The Micro Fluidic Card System (Applied Biosystems) was used according to the manufacturer’s protocol for miRNA expression profiling.

first: Markus

last: Riemenschneider


title: Construction of Reusable Plasmid Libraries for Strain Construction

city: College Station

first: James

last: Winkler

address: 3122 TAMU

country: USA

institute: Texas A&M University

summary: Test whether it is possible to conjugate a whole plasmid library into a recipient strain without loss of fidelity (as judged by aCGH analysis)

sample_organism:
Escherichia coli
Escherichia coli BW25113

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

overall_design: Donor and Recipient Libraries are compared with array CGH to detect copy number differences, a simple selection experiment is also performed

first: Katy

middle: C

last: Kao


title: Let-7b regulates skeletal muscle growth, development and fat deposition in deletion-type dwarf chickens (7-week-old chickens)

status: Public on Apr 18 2012

city: Guangzhou

first: Hongmei

last: Li

address: Guangzhou tianhe wushan street

institute: south china agricultural university

summary: A deletion mutation in the growth hormone receptor (GHR) gene results in the inhibition of skeletal muscle growth and fat deposition in dwarf chickens. In this study, microarray techniques were used to detect the miRNA and mRNA expression profiles of 14-day-old embryo and 7-week-old chicken skeletal muscle of deletion-type dwarf chickens and normal-type chickens. Skeletal muscle tissues of Dwarf recessive White Rock chickens and normal recessive White Rock chickens were used to make the microarray assay. Results show the expression of miR-1623 and miR-181b in 14-day-old embryos and of let-7b and miR-128 in 7-week-old chickens. let-7b was the only miRNA found to be completely complementary to its target in the 3'UTR of GHR and inhibited GHR gene expression. KEGG (Kyoto Encyclopaedia of Genes and Genomes) pathway analysis and RT-PCR verified that there were three main signalling pathways regulating the skeletal muscle growth and fat deposition of chickens influenced by the let-7b-regulated GHR gene. The suppression of the cytokine signalling 3 (SOCS3) gene was found to be involved in the signalling pathway of adipocytokines. We found that let-7b is the critical miRNA involved in the regulation of the GHR gene. SOCS3 plays a critical role in the network regulating skeletal muscle growth and fat deposition via let-7b-mediated GHR gene expression.

overall_design:
Two groups were analyzed in the array assay: one group consisted of normal recessive White Rock 7-week-old chicken leg muscle tissues, and the other group consisted of dwarf recessive White Rock 7-week-old chicken leg muscle tissues. The control samples were labeled as A1b, A2b, A3b, and the dwarf chicken samples were labeled as B1b, B2b, and B3b. 9 total chickens per breed, 3 chickens used per breed for each sample. 523 mature miRNA sequences were assembled and integrated into the LC miRNA microarray design, and different expression miRNAs were measured on the 7000HT Fast Real-Time PCR system.
REPLACE
This submission represents the miRNA profiling component of the study.

first: Shumao

last: Lin

first: Xiquan

last: Zhang


title: Let-7b regulates skeletal muscle growth, development and fat deposition in deletion-type dwarf chickens

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

overall_design: Refer to individual Series


title: Global gene expression analysis of the OsDIS1 overexpression plants under normal and drought stress conditions

status: Public on Jan 01 2012

city: Changsha

first: Joseph

last: Ning

state: Hunan

address: No.1 Nongda Road，Furong District

institute: Hunan Agricultural Univrsity

summary: To identify genes involved in the OsDIS1-mediated drought-responsive pathway, we performed microarray analysis of the OsDIS1 overexpression and wild-type plants under both normal and drought stress conditions using the Agilent rice Genechip. Seven-day-old plants of the OsDIS1 overexpression line 9-4-2 as well as the wild-type plants were used in the drought treatment. OsLEA3 was used as a positive control for the drought treatment. Genes with more than two-fold changes in the overexpression plants compared with the wild-type plants were selected. The expression pattern of some differentially expressed genes was further confirmed by real-time PCR.

overall_design: The OsDIS1 overexpression 9-4-2 plants and the wild-type plants were cultured on 1/2 MS medium plus 3% sucrose for seven days. About half of the plants were sampled as the untreated control for RNA isolation, and the rest were transferred with 1/2 MS medium onto filter papers to induce drought stress. When the leaves of the OsDIS1 overexpression plants began to show drought stress phenotypes, we collected leaves for RNA isolation. OsLEA3 was used as a positive control for the drought treatment.

first: Yuese

first: Guoliang

last: Wang

first: Qi

last: Xie


title: OsMADS29 regulates the degradation of the nucellus and the nucellar projection during rice seed development

status: Public on Apr 05 2012

city: shanghai

first: linlin

last: yin

address: 300 fenglin road

institute: SIPPE

summary: To identify the downstream genes of OsMADS29, a genome-wide analysis of the gene expression profiles in the nucellar projection cells of ZH11 and A-OsMADS29 was performed. Hybridization with the microarray and subsequent analysis showed that a total of 1318 genes displayed altered expression (at least 2-fold) under suppressed OsMADS29 expression. Among the altered genes, 492 were up-regulated, and 826 were down-regulated.

overall_design: The ZH11 and A-OsMADS29 (line2 and line14) were growth in the same condition.Then maternal nucellar projection cells of their seeds at 3 DAF (day after flowering) were fixed and obtained by LCM (laser capture microdissection), and total RNA was extracted and amplified from two independent biological samples.

first: Lin

last: Yin

first: Hong

last: Xue


title: Let-7b regulates skeletal muscle growth, development and fat deposition in deletion-type dwarf chickens (14-day-old embryos)

overall_design:
Two groups were analyzed in the array assay: one group consisted of normal recessive White Rock 14-day-old embryo leg muscle tissues, and the other group consisted of dwarf recessive White Rock 14-day-old embryo leg muscle tissues. The control samples were labeled as A1, A2, A3, and the dwarf chicken samples were labeled as B1, B2, and B3. 9 total embryos per breed, 3 embryos used per breed for each sample. 523 mature miRNA sequences were assembled and integrated into the LC miRNA microarray design, and different expression miRNAs were measured on the 7000HT Fast Real-Time PCR system.

This submission represents the miRNA profiling component of the study.


title: Transcriptomic analysis of milk somatic cells in mastitis resistant and susceptible sheep upon challenge with Staphylococcus epidermidis and Staphylococcus aureus

status: Public on Oct 01 2011

city: CASTANET TOLOSAN CEDEX

first: Cécile

last: Bonnefont

address: Auzeville B.P. 52627

institute: INRA

summary: Staphylococci are major pathogens in humans and animals and emerging antibiotic-resistant strains have further increased the importance of this health issue. The existence of a genetic basis of host response to bacterial infections has been widely documented but the underlying mechanisms and genes are still largely unknown. Previously, two divergent lines of sheep selected on their milk somatic cell count called high and low SCS lines, have been showed to be respectively more and less susceptible to intra mammary infections (IMI). Transcriptional profiling of milk somatic cells (MSC) of high and low SCS sheep infected successively by S. epidermidis and S. aureus was performed to provide enhanced knowledge about the genetic basis of differential host response to IMI with Staphylococci. Gene expression in MSC of high and low SCS sheep collected 12h post-challenge was performed on a 15K gene ovine oligoarray (Agilent). MSC were mainly neutrophils. The high number of differentially expressed genes between the two bacterial strains indicated, among others, increased number of T-cells in MSC after S. aureus, compared to S. epidermidis challenge. Differential regulation of 366 genes between resistant and susceptible animals was largely associated with immune and inflammatory response (including pathogen recognition TLR2 pathway and cell migration), signal transduction, cell proliferation and apoptosis. Close biological connection between most of differentially expressed genes into Ingenuity Pathway Analysis networks further indicated consistency between the genes that were differentially-expressed between resistant and susceptible animals. Gene profiling in high and low SCS sheep provided strong candidates for biological pathway and gene underlying genetically determined resistance and susceptibility towards Staphylococci infections opening new fields for further investigation.  Keywords: Staphylococcus epidermidis, Staphylococcus aureus, milk somatic cells, mammalian, transcriptome, immunity, mastitis

overall_design: 22 samples in a two-colour dye-swap experimental design

first: CMD

first: M

last: Toufeer

first: E

last: Foulon

first: C

last: Caubet

first: MR

last: Aurel

first: CR

last: Granié

first: G

last: Foucras

first: R

last: Rupp