title: Expression analysis of LncRNA in Tongue Squamous Cell Carcinoma (TSCC) and matched nonmalignant tissues (NC)

status: Public on Oct 30 2013

city: Beijing

first: Ling-fei

last: Jia

address: 22 Zhongguancun Avenue South, Haidian District

institute: Peking University School and Hospital of Stomatology

summary: Investigation of LncRNA expression level changes in 9 paired of Tongue Squamous Cell Carcinoma specimens

overall_design: LncRNA profiling: TSCC vs NC

first: Guang-yan

last: Yu


title: Altered expression of microRNAs in Tongue squamous cell carcinoma (TSCC) and matched nonmalignant tissues (NC)

country: China

summary: Investigation of microRNA expression level changes in 4 paired of Tongue Squamous Cell Carcinoma specimens

platform_organism:
Homo sapiens
Mus musculus
Rattus norvegicus

overall_design: miRNA profiling: TSCC vs NC


title: Re-establishment of desiccation tolerance in protruded radicles of Medicago truncatula  Wt and abi5 seeds

city: BEAUCOUZE

first: Sandra

last: Pelletier

address: 42, rue Georges Morel - BP 60057

country: France

institute: INRA

summary: Desiccation tolerance (DT) is the capacity to withstand total loss of cellular water. This property is acquired during seed filling and lost just after germination. However, in many species, a germinated seed can regain DT under adverse conditions such as osmotic stress.  We discovered that the germinated seeds of the abscisic acid insensitive 5 (Mtabi5) mutant of Medicago truncatula lost their ability to re-establish DT during osmotic stress.  To characterize the molecular processes that are influenced by MtABI5 during the re-establishment of DT tolerance, a transcriptome analysis was performed on the protruded radicles of germinated Mtabi5 mutants and wilt type before and after an osmotic treatment.

overall_design: Six-condition experiment, R108_T versus R108_P, abi5-1_T versus abi5-1_P,  abi5-2_T versus abi5-2_P. Biological replicates: 9 controls (R108-T, abi5-1_T, abi5-2_T), 9 treatments (R108-P, abi5-1_P, abi5-2_P), independently grown and harvested. One replicate per array.

first: Emmanuel

last: Terrasson

first: Olivier

last: Leprince

first: Julia

last: Buitink


title: Effect of OsHRZ knockdown in rice roots under iron sufficiency and deficiency

status: Public on Oct 17 2013

city: Nonoichi

first: Takanori

last: Kobayashi

state: Ishikawa

address: 1-308 Suematsu

department: Research Institute for Bioresources and Biotechnology

country: Japan

institute: Ishikawa Prefectural University

summary: Transcriptional profiling of rice genes analyzing the effect of knockdown of OsHRZ1 and OsHRZ2 in HRZ2i lines. NT and HRZ2i lines 1, 2 and 3 (2i-1, 2i-2 and 2i-3, respectively) were treated under iron sufficiency for 7 days (+Fe 7d) or under iron deficiency for 1 day (-Fe 1d) or 7 days (-Fe 7d) in hydroponic culture.

overall_design: Comparison between NT and HRZ2i lines at +Fe 7d, -Fe 1d and -Fe 7d. Biological replicates: 2-3 NT replicates, 3 HRZ2i replicates (one each for 2i-1, 2i-2 and 2i-3) for each treatment.

first: Naoko

middle: K

last: Nishizawa


title: affy_tour_2012-02-Study of sunflower seed dormancy by translatome analysis

city: evry

first: caius

last: jose

state: essonne

address: 2 rue gaston cremieux

department: URGV

institute: transcriptomic platform

summary: affy_tour_2012-02 - Identification of transcripts that are addressed to traduction in imbibed seeds in relation with dormancy: comparison of the translatome in Dormant versus Non-Dormant seeds -- At harvest seeds are dormant. They stay dormant if they are stored at -20°C (D) and become non-dormant (ND) if they are stored 2 months at +20°C. Polysomal fractions were purified on sucrose gradients from sunflower axis isolated from dormant and non-dormant seeds imbibed at 10°C during 3h, 15h or 24h. - These fractions allow to identify the transcripts addressed to translation (translatome) during the seed imbibition process (3, 15 and 24h) - The translatome of 2 types of seeds are compared: Dormant vs Non-Dormant at the 3 time points.

overall_design: 18 arrays - SUNFLOWER; time course,treated vs untreated comparison

first: José

last: Caius

first: Hayat

last: Bouteau

first: Sandrine

last: Balzergue

first: Marie-Laure

last: Martin-Magniette


title: Gene expression profiles of unfertilized eggs of Ciona intestinalis

status: Public on Oct 29 2013

city: Kyoto

first: Yutaka

last: Satou

state: Kyoto

address: Kitashirakawa Oiwake-tyo, Sakyo-ku

department: Department of zoology, Graduate School of Science

institute: Kyoto University

summary: The transcriptome of unfertilized eggs of Ciona intestinalis was determined with microarrays.

overall_design: To obtain gene expression profiles of unfertilized eggs, we took 14 biological replicates. For the first through fourth replicates, we also took a technical duplicate. Gene expression profiles of the 8-, 16-, 32-cell embryos were obtained with embryos from the third to fifth animals.

first: Terumi

last: Matsuoka


title: Saos-2 vs. Saos-2-2 cells

status: Public on Oct 11 2013

city: Taipei City

first: Tzu-Hao

last: Cheng

address: No. 155, Sec. 2, Linong St.

department: Institute of Biochemistry and Molecular Biology

country: Taiwan

institute: National Yang-Ming University

summary: Saos-2-2, a TSG101-deficient stable line, was dereived from Saos-2 cells. The goal of this experiment was to determine the effects of TSG101 down-regulation on global gene expression.

overall_design: Saoa-2 and Saos-2-2 samples were labeled with Cys-3 and Cys-5 respectively, and hybrided with microarray simutaneously to differentiate the up- and down-regulated genes.

first: Stanley

middle: N

last: Cohen


title: Caste-specific expression patterns of olfactory related genes in the leaf-cutting ant, Atta vollenweideri

status: Public on Oct 01 2013

city: Jena

first: Heiko

last: Vogel

address: Hans-Knoell-Strasse 8

department: Dpt. of Entomology

country: Germany

institute: Max Planck Institute for Chemical Ecology

summary: To allow estimation of the complexity and gene expression differences of the antennal transcriptome between sexes as well as between castes, microarrays were designed based on an assembly of A. vollenweideri antennal sequence data from all sexes and castes. The microarrays were hybridized with samples generated from the respecitve antennal tissues, with four independent sample pools per sex and caste.

overall_design: Custom 2x105 k Agilent microarrays (Agilent Technologies, Palo Alto, CA) were designed based on the antennal transcriptome data of A.vollenweideri. For all contigs with an identified ORF by automatic annotation, two 60mer oligo probes were designed, with two additional 60mer oligo probes for opposite reading direction for those with unknown ORF, thus resulting in 4 oligo probes per contig. Additionally, we added three 60mer oligo probes for each identified and revised OR coding gene, resulting in a total of 5 oligo probes per OR coding contig. For design and arrangement of the Agilent microarrays, the eArray software (Agilent Technologies, Palo Alto, CA) was used.   For sex- and caste-specific antennal microarray hybridizations, RNA from antennae of 50 (Males) to 300 (Tiny Workers) individuals was pooled per preparation, and four pools (replicates) each were dissected per sex and caste, respectively. Double purified total RNA was added to Agilent Technologies spike-in RNA and labeld using QuickAmp Amplification kit (Agilent Technologies) and the Kreatech ULS Fluorescent Labeling Kit with cyanine 3-CTP dye following the manufacturer´s instructions.  Amplified cRNA samples were used for microarray hybridization, scanned with the Agilent Microarray Scanner and data was extracted from TIFF images with Agilent Feature Extraction software version 9.1. Raw data output files were analyzed using the GeneSpring GX11 and GeneSifter microarray analysis softwares.

first: Sarah

last: Koch

first: Ewald

last: Grosse-Wilde

first: Cristoph

last: Kleineidam


title: HDAC inhibitors attenuate the development of hypersensitivity in models of neuropathic pain [spinal cord tissue]

city: London

first: Franziska

last: Denk

address: Guy's Campus

department: Wolfson SPaRC

country: United Kingdom

institute: King's College London

summary: Histone deacetylase inhibitors (HDACIs) interfere with the epigenetic process of histone acetylation and are known to have analgesic properties in models of chronic inflammatory pain. The aim of this study was to determine whether these compounds could also affect neuropathic pain. Different class I HDACIs were delivered intrathecally into rat spinal cord in models of traumatic nerve injury and antiretroviral drug-induced peripheral neuropathy (stavudine, d4T). Mechanical and thermal hypersensitivity was attenuated by 40% to 50% as a result of HDACI treatment, but only if started before any insult. The drugs globally increased histone acetylation in the spinal cord, but appeared to have no measurable effects in relevant dorsal root ganglia in this treatment paradigm, suggesting that any potential mechanism should be sought in the central nervous system. Microarray analysis of dorsal cord RNA revealed the signature of the specific compound used (MS-275) and suggested that its main effect was mediated through HDAC1. Taken together, these data support a role for histone acetylation in the emergence of neuropathic pain.

overall_design: n = 4, HDACi treated vs. vehicle treated. Ipsilateral dorsal spinal cord tissue after L5 spinal nerve transection, DRG tissue was run in a separate Affymetrix experiment.

first: F

first: W

last: Huang

first: B

last: Sidders

first: A

last: Bithell

first: M

last: Crow

first: J

last: Grist

first: S

last: Sharma

first: D

last: Ziemek

middle: S

last: Rice

first: N

middle: J

last: Buckely

middle: B

last: McMahon


title: in vitro angiogenesis miRNA Array

status: Public on Sep 30 2013

city: Newtown

first: Jennifer

middle: R

last: Gamble

state: NSW

address: Locked Bag No. 6

country: Australia

institute: CENTENARY INSTITUTE

summary:
Angiogenesis is a complex multicellular process requiring the orchestration of many events including migration, alignment, proliferation, lumen formation, remodeling, and maturation. Such complexity indicates that not only individual genes but also entire signaling pathways will be crucial in angiogenesis. To define an angiogenic blueprint of regulated genes, we utilized our well-characterized three-dimensional collagen gel model of in vitro angiogenesis, in which the majority of cells synchronously progress through defined morphological stages culminating in the formation of capillary tubes. We developed a comprehensive three-tiered approach using microarray analysis, which allowed us to identify genes known to be involved in angiogenesis and genes hitherto unlinked to angiogenesis as well as novel genes and has proven especially useful for genes where the magnitude of change is small.
From a screen of miRNAs altered in in vitro angiogenesis we selected a subset that are predicted to target junctional molecules. MiR-27a, was rapidly downregulated upon stimulation of in vitro angiogenesis and its level of expression is reduced in neo-vessels in vivo. The downregulation of miR-27a was essential for angiogenesis since ectopic expression of miR-27a blocked capillary tube formation and angiogenesis. MiR-27a targets the junctional, endothelial specific cadherin, VE-cadherin. Consistent with this, vascular permeability to VEGF in mice is reduced by administration of a general miR-27 inhibitor. To determine that VE-cadherin was the dominant target of miR-27a function we used a novel technology with “Blockmirs”, inhibitors that bind to the miR-27 binding site in VE-cadherin. The Blockmir CD5-2 demonstrated specificity for VE-cadherin and inhibited vascular leak in vitro and in vivo. Furthermore CD5-2 reduced oedema, increased capillary density and potently enhanced recovery form ischemic limb injury in mice. The Blockmir technology offers a refinement in the use of miRNAs especially for therapy. Further, targeting of endothelial junctional molecules by miRNAs has clinical potential especially in diseases associated with vascular leak.

overall_design: A microRNA microarray was performed to investigate miRNAs that were regulated during capillary   tube formation and which could potentially be used as an ‘angiogenic’ miRNA profile. RNA was   isolated from cells harvested at specific time points, previously identified as stages where major   morphological changes are taking place18. These include 0.5 hour (invasion), 3 hours (migration), 6   hours (vacuole coalescence and lumen formation), 12 hours (lumen formation) and 24 hours (tube   maturation).


title: HDAC inhibitors attenuate the development of hypersensitivity in models of neuropathic pain [DRG tissue]

overall_design: n = 4, HDACi treated vs. vehicle treated. Injured ipsilateral DRG after L5 spinal nerve transection. Spinal cord  tissue was run in a separate Affymetrix experiment.


title: leaf transcriptome comparison between wt and pnm1dnls plants-CNRS12-07_PNM1

city: Orsay

first: Stéphanie

last: Pateyron

address: Rue de Noetzlin _ Batiment 630

institute: IPS2_Institute of Plant Sciences Paris-Saclay

summary: rs12-07_pnm1 - leaf transcriptome comparison between wt and pnm1dnls plants - Identification of nuclear genes regulated by PNM1 (At5g60960) in Arabidopsis thaliana. Mature rosettte leaf transcriptomes were compared between WT and PNM1DNLS mutants.

overall_design: 3 dye-swap - normal vs transgenic comparaison

first: Veronique

last: Brunaud

first: MARC

last: GALLAND

first: Philippe

last: Giegé

first: Sandrine

last: Balzergue

first: Marie-Laure

last: Martin-Magniette


title: DNA intermediates of meiotic recombination in synchronous S. pombe at optimal temperature

status: Public on Sep 20 2013

city: San Francisco

first: Kyle

last: Fowler

state: California

address: 600 16th Street

country: USA

institute: University of California San Francisco

type: Genome binding/occupancy profiling by genome tiling array

summary: Crossovers formed by recombination between homologous chromosomes are important for proper homolog segregation during meiosis and for generation of genetic diversity.  Optimal molecular analysis of DNA intermediates of recombination requires synchronous cultures.  We previously described a mutant, pat1-as2, of the fission yeast Schizosaccharomyces pombe that undergoes synchronous meiosis at 25°C when an ATP analog is added to the culture.  Here, we compare recombination intermediates in pat1-as2 at 25°C with those in the widely used pat1-114 temperature-sensitive mutant at 34°C, a temperature higher than optimal.  DNA double-strand breaks at most hotspots are similarly abundant in the two conditions but, remarkably, a few hotspots are distinctly deficient at 25°C.  In both conditions Holliday junctions at DNA break hotspots form more frequently between sister chromatids than between homologs, but a novel species, perhaps arising from invasion by only one end of broken DNA, is more readily observed at 25°C.  Our results confirm the validity of previous assays of recombination intermediates in S. pombe and provide new information on the mechanism of meiotic recombination.

overall_design: DNA double-strand break analysis by immunoprecipation of Rec12-FLAG covalently linked to DNA (without exogenous crosslinking agent used) following meiotic induction via pat1-114 or pat1-as2 alleles

first: Randy

middle: W

last: Hyppa

first: Lubos

last: Cipak

first: Juraj

last: Gregan

first: Gerald

last: Smith


title: Identification of miR-4423 as a Primate-Specific microRNA Highly Expressed in Ciliated Airway Epithelium and Associated with Lung Cancer [Affymetrix]

status: Public on Oct 08 2013

city: Boston

first: Avrum

last: Spira

state: MA

address: 72 East Concord Street, E631

department: Computational Biomedicine

institute: Boston University

summary: Smoking is a significant risk factor for lung cancer, the leading cause of cancer-related deaths worldwide. While microRNAs are regulators of many airway gene-expression changes induced by smoking, their role in modulating changes associated with lung cancer in these cells remains unknown. Here, we use next-generation sequencing of small RNAs in the airway to identify miR-4423 as a novel primate-specific microRNA associated with lung cancer and expressed primarily in mucociliary epithelium. The endogenous expression of miR-4423 increases as bronchial epithelial cells undergo differentiation into mucociliary epithelium in vitro and its overexpression during this process causes an increase in the number of ciliated cells. Furthermore, expression of miR-4423 is reduced in most lung tumors and in cytologically normal epithelium of the mainstem bronchus of smokers with lung cancer. In addition, ectopic expression of miR-4423 in a subset of lung cancer cell lines reduces their anchorage-independent growth and significantly decreases the size of the tumors formed in a mouse xenograft model. Consistent with these phenotypes, overexpression of miR-4423 induces a differentiated-like pattern of airway epithelium gene expression and reverses the expression of many genes that are altered in lung cancer. Together, our results indicate that miR-4423 is a novel regulator of airway epithelium differentiation and that the abrogation of its function contributes to lung carcinogenesis.

overall_design: Small RNA expression was profiled from pooled bronchial airway epithelial cell brushings (n=3 patients/pool) obtained during bronchoscopy from healthy never (NS) and current smokers (S) and smokers with (C) and without (NC) lung cancer. MicroRNA hsa-miR-4423 was over expressed in H1299, Calu6, SW900 and H2170 lung cancer cell lines.

first: Catalina

last: Perdomo

first: Joshua

middle: D

last: Campbell

first: Joseph

last: Gerrein

first: Carmen

last: Tellez

first: Carly

last: Garrison

first: Tonya

middle: C

last: Walser

first: Eduard

last: Drizik

first: Huiqing

last: Si

first: Adam

last: Gower

first: Jessica

last: Vick

first: Christina

last: Anderlind

first: George

last: Jackson

first: Courtney

last: Mankus

first: Frank

last: Schembri

first: Carl

last: O’Hara

first: Brigitte

last: Gomperts

first: Steven

middle: M

last: Dubinett

first: Patrick

last: Hayden

middle: A

last: Belinsky

first: Marc

middle: E

last: Lenburg


title: Transcriptome analysis reveals crosstalk of responsive genes to multiple abiotic stresses in cotton (Gossypium hirsutum L.)

status: Public on Sep 12 2013

first: Weicai

last: Yang

address: No.1 West Beichen Road, Chaoyang District

institute: Institute of Genetics and Developmental Biology, Chinese Academy of Sciences

summary:
Abiotic stress is a major environmental factor that limits cotton growth and yield, moreover, this problem has become more and more serious recently and multiple stresses often occur simultaneously due to the global climate change and environmental pollution.
We used microarrays to analyze the crosstalk of responsive genes to multiple abiotic stresses including ABA,  cold, drought, salinity and alkalinity in cotton.

platform_organism:
Gossypium barbadense
Gossypium hirsutum
Gossypium arboreum
Gossypium raimondii

overall_design: Cotton seedlings with different abiotic stress treatment were selected at 14-day after germination for RNA extraction and hybridization on Affymetrix microarrays. We sought to identify genes involved in diverse stresses including abscisic acid (A), cold (C), drought (M), salinity (N) and alkalinity (P) by comparative microarray analysis (3 biological replicates for each abiotic stress treatment).

first: Yana

last: Zhu

first: Dongqiao

last: Shi

first: Mengbin

last: Ruan

first: Lili

last: Zhang

first: Zhaohong

last: Meng

first: Jie

last: Liu


title: Placental ischemia induces changes in gene expression in chorionic tissue

status: Public on Sep 05 2013

city: Jackson

first: Eric

last: George

state: MS

address: 2500 N. State St

department: Physiology and Biophysics

institute: U of MS Medical Center

summary:
Microarray analysis of differentially expressed genes from rats undergoing placental ischemia versus health controls
Placental ischemia is believed to be an important contributor to human preeclampsia, though the targets induced by the ischemia remain unclear.

overall_design: Chorionic placental tissues from 6 control and 6 placental ischemic reduced uterine perfusion pressure (RUPP) rats were analyzed for gene expression by microarray.

first: Michael

last: Garrett

first: Joey

middle: P

last: Granger


title: Examination of DPY-30, DPY-27, SDC-3, DPY-26, DPY-28, SDC-2, and SUMOylated DPY-27 binding in wild type embryos and smo-1 RNAi treated embryos

status: Public on Aug 31 2013

city: Berkeley

first: Barbara

last: Meyer

state: CA

address: 16 Barker Hall

department: Molecular and Cellular Biology

institute: University of California Berkeley

type: Genome variation profiling by genome tiling array

summary: The essential process of dosage compensation equalizes X-chromosome gene expression between C. elegans XO males and XX hermaphrodites through a dosage compensation complex (DCC) that resembles condensin. The DCC binds to both X chromosomes of hermaphrodites to repress transcription by half. Here we show that post-translational modification by the SUMO conjugation pathway is essential for sex-specific assembly of the DCC onto X. Depletion of the SUMO peptide in vivo severely disrupts binding of particular DCC subunits and causes changes in X-linked gene expression similar to those caused by disrupting genes encoding DCC subunits. Three DCC subunits are themselves SUMOylated, and depletion of SUMO preferentially reduces their binding to X, suggesting that SUMOylation of DCC subunits is essential for robust association with X. DCC SUMOylation is triggered by the signal that initiates DCC assembly onto X. The initial step of assembly--binding of X-targeting factors to recruitment sites on X (rex sites)--is independent of SUMOylation, but robust binding of the complete complex requires SUMOylation. SUMOylated DCC subunits are enriched at rex sites, and SUMOylation enhances interactions between X-targeting factors and condensin subunits that facilitate DCC binding beyond the low level achieved without SUMOylation. DCC subunits also participate in condensin complexes essential for chromosome segregation, but their SUMOylation occurs only in the context of the DCC. Our results reinforce a newly emerging theme in which multiple proteins of a complex are SUMOylated in response to a specific stimulus, leading to accelerated complex formation and enhanced function.

overall_design: ChIP-chip experiments using antibodies against DPY-27, SDC-3, DPY-30, DPY-26, DPY-28 and FLAG-tagged SDC-2 in wild-type and smo-1 RNAi treated  mixed embryos, with IGG controls.  Also, sequential ChIP-chip experiments: (1) ChIP using FLAG antibodies to determine the genome-wide binding sites for SUMOylated proteins, (2) ChIP using FLAG antibodies followed by re-ChIP of eluted protein-chromatin complexes with DPY-27 antibodies to determine genome-wide binding sites for SUMOylated DPY-27 (referred to as DPY-27 re-ChIP experiments), (3) ChIP using FLAG antibodies followed by re-ChIP of eluted protein-chromatin with IGG antibodies to determine background binding (referred to as IGG re-ChIP experiments, and (4) ChIP using DPY-27 antibodies as a control to assess the efficiency of DPY-27 binding and detection in control vs. FLAG-tagged strains.

first: Rebecca

last: Pferdehirt


title: The global gene expression pattern by YDR374C deletion

status: Public on Aug 23 2013

city: Seoul

first: Hyun-Jun

last: Kang

address: 145, Anam-ro, Seongbuk-gu

country: South Korea

institute: Korea University

summary: The Ydr374c is the only protein that has the YTH domain in Saccharomyces cerevisiae. The YTH domain was identified by comparing all known protein sequences with the YT521-B splicing factor, and it is found only in eukaryotes. Recently, it has been reported that the YTH domain conveys RNA-binding ability to a new class of proteins. However, the roles of most YTH family members lacking common sequence motifs outside the YTH domain are unknown. Therefore, to investigate the function of Ydr374c, microarray analysis was performed using the wild-type and YDR374C deletion strains.

overall_design: For the microarray analysis, wild-type and YDR374C deletion strains were cultured in SD medium and harvested at the mid-exponential phase (OD600=0.7), and total RNA was extracted.

first: Cheol-Won

last: Yun


title: A genome-wide analysis of open chromatin in human epididymis epithelial cells reveals novel candidate regulatory elements for male infertility [Transcriptome data]

status: Public on Sep 06 2013

city: Cleveland

first: Ann

last: Harris

state: OH

address: 10900 Euclid Avenue

institute: Case Western Reserve University Medical School

summary: The epithelium lining the epididymis has a pivotal role in ensuring a luminal environment that can support normal sperm maturation. Many of the individual genes that encode proteins involved in establishing the epididymal luminal fluid are well characterized. They include ion channels, ion exchangers, transporters and solute carriers. However, the molecular mechanisms that coordinate expression of these genes and modulate their activities in response to biological stimuli are less well understood. To identify cis-regulatory elements for genes expressed in human epididymis epithelial cells we generated genome-wide maps of open chromatin by DNase-seq. This analysis identified 33,542 epididymis-selective DNase I hypersensitive sites (DHS), which were not evident in five cell types of different lineages. Identification of genes with epididymis-selective DHS at their promoters revealed gene pathways that are active in immature epididymis epithelial cells. These include processes correlating with epithelial function and also others with specific roles in the epididymis including retinol metabolism and ascorbate and aldarate metabolism. Peaks of epididymis-selective chromatin were seen in the androgen receptor gene and the cystic fibrosis transmembrane conductance regulator (CFTR) gene, which has a critical role in regulating ion transport across the epididymis epithelium. In silico prediction of transcription factor binding sites that were over-represented in epididymis-selective DHS identified epithelial transcription factors including ELF5 and ELF3, the androgen receptor, Pax2 and Sox9, as components of epididymis transcriptional networks. Active genes, which are targets of each transcription factor, reveal important biological processes in the epididymis epithelium.

overall_design:
HEE cells were cultured as described previously (Harris and Coleman 1989). RNA was isolated by Trizol extraction from three primary cultures of HEE cells. Total RNA was purified by Millipore Microcon YM-100 filter centrifugation and shipped to MoGene, MO, for gene expression analysis on Nimblegen 4 x 72K HG18 60mer arrays.

This submission represents transcriptome component of study.

first: Jared

last: Bischof

first: Austin

last: Gillen

first: Lingyun

last: Song

first: Nehal

last: Gosalia

first: Darin

last: London

first: Terrence

last: Furey

first: Gregory

last: Crawford


title: Stressor  mRNA expression profiling of three different stressors in the water flea Daphnia magna

status: Public on Sep 01 2013

city: Leuven

first: Mieke

last: Jansen

address: Ch. Deberiotstraat 32

department: Biology

country: Belgium

institute: KULeuven

summary: Microarray analyses were used to evaluate patterns of gene transcription following exposure of the waterflea Daphnia magna to two natural and one anthropogenic stressor. cDNA microarrays compiled of three life stage specific and three stressor-specific EST libraries, yielding 1734 different EST sequences, were used. We exposed the water flea Daphnia magna to three stressors known to exert strong selection in natural populations of this species i.e. a sublethal concentration of the pesticide carbaryl, infective spores of the endoparasite Pasteuria ramosa, and fish predation risk mimicked by exposure to fish kairomones. A total of 148 gene fragments were differentially expressed compared to the control. Most gene fragments were downregulated under stress (82.4% downregulation compared to 17.6% upregulation) irrespective of the treatment. In approximately 5% of the cases up- or downregulation depended on stressor identity. Based on a PCA, we could identify two different groups within our exposure treatments: small and big gene expression differences compared to the control condition. The treatments parasite 96h exposure, carbaryl 144h of exposure and fish 144h of exposure are combined in the high stress group.

overall_design:
26 samples x 2 biological replicates were analysed in a carriage wheel design (Khanin & Wit, 2005; Knapen et al., 2009) with a reference sample composed of a clutch of non-exposed D. magna that were collected at different time points ranging from 0-24h until three weeks old.

The 26 samples included: 4 treatments (control, carbaryl, fish and parasite exposure) x three time points (48h, 96h and 144h) x 2 replicates + 2 start samples (non-exposed individuals younger than 24h old). This led to 52 different microarray hybridizations: 26 hybridizations for the inner part of the wheel, where every sample is hybridized against the reference, and another 26 for the outer part. Color flip experiments were incorporated per sample to fulfill the conditions of technical replicates on the level of labelling; every stressor-time combination was included at least once in red and once in green. One hybridization in the outer part of the wheel had technical problems, and is not included here.

first: Lucia

last: Vergauwen

first: Tine

last: Vandenbrouck

first: Dries

last: Knapen

first: Nathalie

last: Dom

first: Katina

middle: I

last: Spanier

first: Anke

last: Cielen

first: Luc

last: De Meester


title: H4K16 acetylation marks active genes and enhancers of embryonic stem cells, but does not alter chromatin compaction [NimbleGen array]

city: Edinburgh

first: Gillian

last: Taylor

address: MRC HGU Crewe Road South

institute: IGMM

summary: We report that acetylation of H4K16 is a new marker of active enhancers and that some enhancers are marked by H3K4me1, MOF and H4K16ac but not by acetylated H3K27 or p300, suggesting that they are novel p300-independent regulatory elements.

overall_design: ChIP on chip over neuronal and control genes for H4K16ac in undifferentiated 46c (sox1-gfp) ES cells and for 5 day differentiated FACS sorted Neural Progenitor Cells differentiated with NB27 and Neuro2 medium supplements

first: Ragnhild

last: Eskeland

first: Betül

last: Hekimoglu-Balkan

first: Madapura

last: Pradeepa

first: Wendy

last: Bickmore


title: HDAC inhibitors attenuate the development of hypersensitivity in models of neuropathic pain

first: Franziska

last: Denk

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

overall_design: Refer to individual Series


title: Long noncoding RNAs are dysregulated in malignant pleural mesothelioma

status: Public on Aug 22 2013

city: Concord

first: Casey

last: Wright

address: Gate 3, Hospital Road

institute: ADRI

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

summary: Malignant Pleural Mesothelioma (MPM) is an aggressive cancer that is often diagnosed at an advanced stage and is characterized by a long latency period (20-40 years between initial exposure and diagnosis) and prior exposure to asbestos. Currently accurate diagnosis of MPM is difficult due to the lack of sensitive biomarkers, and despite minor improvements in treatment, median survival rates do not exceed 12 months. Accumulating evidence suggests that aberrant expression of long non-coding RNAs (lncRNAs) play an important functional role in cancer biology. LncRNAs are a class of recently discovered non-protein coding RNAs >200 nucleotides in length with a role in regulating transcription. Here we used NCode long noncoding microarrays to identify differentially expressed lncRNAs potentially involved in MPM pathogenesis. High priority candidate lncRNAs were selected on the basis of statistical (P<0.05) and biological significance (>3-fold difference). Expression levels of 9 candidate lncRNAs were technically validated using RT-qPCR, and biologically validated in three independent test sets: (1) 57 archived MPM tissues obtained from extrapleural pneumonectomy patients, (2) 15 cryopreserved MPM and 3 benign pleura, and (3) an extended panel of 10 MPM cell lines. RT-qPCR analysis demonstrated consistent up-regulation of these lncRNAs in independent datasets. ROC curve analysis showed that two candidates were able to separate benign pleura and MPM with high sensitivity and specificity, and were associated with nodal metastases and survival following induction chemotherapy. These results suggest that lncRNAs have potential to serve as biomarkers in MPM.

overall_design: To identify mRNA and lncRNA biomarkers associated with malignant pleural mesothelioma (MPM), we performed gene expression array analysis on 4 MPM cell lines (H28, MM05, MSTO-211H, H226) compared to the immortalised mesothelial line (MeT-5A). All cell lines were profiled in duplicate. Synthesis of the labelled first strand cDNA was conducted using the Superscript Plus Direct cDNA labeling system with starting material of 10ug total RNA. The labeled dNTP mix was added to the reaction to generate labeled second strand cDNA. Following the hydrolysis reaction, single-stranded cDNA was purified using low elution volume spin cartridges included in the purification module. Samples were labelled using Alexa Fluor 555 dyes. Samples were then hybridised to NCode Long Noncoding RNA Microarrays. Slides were scanned using an Agilent Scanner. Genes differentially expressed between Met-5A and the MPM cell lines were identified on the basis of P-value and fold change.

first: Michaela

last: Kirschner

first: Yuen

middle: Y

last: Cheng

first: Kenneth

last: O'Byrne

first: Steven

middle: G

last: Gray

first: Karin

last: Schlech

first: Mir

last: Hoda

first: Sonja

last: Klebe

first: Brian

last: McCaughan

first: Nico

last: van Zandwijk

first: Glen

last: Reid


title: Sequences tags  expressed  in ovules of Arabidopsis thaliana using Massively Parallel Signature Sequencing (MPSS)

status: Public on Aug 21 2013

city: Irapuato

first: Alma

last: Armenta

address: Km 9.6 Libramiento Norte Carretera León

country: Mexico

institute: CINVESTAV

summary: We report the use of MPSS data to compare transcripts expressed in wild-type and sporocyteless mutant ovules

overall_design: All MPSS libraries were performed as described by Meyers et al (Nature Biotechnol. 2004 Aug;22(8):1006-11. Epub 2004 Jul 11.)

first: Jean-Philippe

last: Vielle-Calzada

first: Blake

last: Meyers


title: Inhibition of phosphodiesterase-4 promotes oligodendrocyte precursor cell differentiation and enhances CNS remyelination

status: Public on Aug 29 2013

city: Cambridge

first: Szymon

last: Myrta

address: West Forvie Building, Robinson Way

department: Clinical Neurosciences

institute: University of Cambridge

type:
Expression profiling by array
Third-party reanalysis

summary: We used transcription-profiling to identify mitogen-activated protein kinase (Mapk) signaling as an important regulator involved in the differentiation of oligodendrocyte progenitor cells (OPCs) into oligodendrocytes. We show in tissue culture that activation of Mapk signaling by elevation of intracellular levels of cAMP using administration of either dibutyryl-cAMP or inhibitors of the cAMP-hydrolyzing enzyme phosphodiesterase-4 (Pde4) enhances OPC differentiation. Finally, we demonstrate that systemic delivery of a Pde4 inhibitor leads to enhanced differentiation of OPCs within focal areas of toxin-induced demyelination and a consequent acceleration of remyelination.

overall_design:
Study was conducted to identify the genes that are differentialy regulated during early time point of OPC differentiation.

This study includes reanalyzed data from the following 6 Samples available in GSE24821: [i] 5 days post lesion (dpl) laser captured caudal cerebellar peduncle (CCP) replicates 1-3 (GSM610956-GSM610958), and [ii] 14 dpl laser captured CCP replicates 1-3 (GSM610959-GSM610961).

For the reanalyzed data, raw data files were background-corrected, normalized and summarized using the RMA algorithm as implemented in the R statistical programming environment (http://www.r-project.org). Differential expression between sample groups was assessed using the moderated t-test as implemented in the limma package for the Bioconductor suite of R bioinformatics software (http://bioconductor.org). In order to correct for hypothesis testing on such a scale, P-values relating to differential expression were corrected for multiple testing using FDR correction. Differential expression across sample groups was deemed significant at an FDR of 5% (q < 0.05).
The processed data for the reanalyzed dataset is linked below as supplementary file 'GSE50042_reanalyzed_Samples.txt'. The processed data for Samples GSM1213100-GSM1213114 is linked below as supplementary file 'GSE50042_processed_data.txt'.

first: Yasir

last: Syed

first: Alexandra

last: Baer

first: Matthias

last: Hofer

first: Ginez

last: González

first: Jon

last: Rundle

first: Jeffrey

last: Huang

first: Chao

last: Zhao

first: Moritz

last: Rossner

first: Matthew

last: Trotter

first: Gert

last: Lubec

first: Robin

last: Franklin

first: Mark

last: Kotter


status: Public on Aug 27 2013

first: Jennifer

middle: L

last: Bowen

address: 100 Morrissey Blvd

institute: University of Massachusetts Boston

summary:
Increasing atmospheric CO2 concentrations are causing decreased pH over vast expanses of the ocean. This decreasing pH may alter biogeochemical cycling of carbon and nitrogen via the microbial process of nitrification, a key process that couples these cycles in the ocean, but which is often sensitive to acidic conditions.  Recent reports indicate a decrease in oceanic nitrification rates under experimentally lowered pH.  How composition and abundance of ammonia oxidizing bacteria (AOB) and archaea (AOA) assemblages respond to decreasing oceanic pH, however, is unknown.  We sampled microbes from two different acidification experiments and used a combination of qPCR and functional gene microarrays for the ammonia monooxygenase gene (amoA) to assess how acidification alters the structure of ammonia oxidizer assemblages.  We show that despite widely different experimental conditions, acidification consistently altered the community composition of AOB by increasing the relative abundance of taxa related to the Nitrosomonas ureae clade.  In one experiment this increase was sufficient to cause an increase in the overall abundance of AOB.  There were no systematic shifts in the community structure or abundance of AOA in either experiment.  These different responses to acidification underscore the important role of microbial community structure in the resiliency of marine ecosystems.
SUBMITTER_CITATION:
Title:  Acidification alters the composition of ammonia oxidizing microbial assemblages in marine mesocosms
Journal:  Marine Ecology Progress Series
Issue: 492
Pages: 1-8
DOI:  10.3354/meps 10526
Authors:
Jennifer L Bowen
Patrick J Kearns
Michael Holcomb
Bess B Ward

sample_organism:
synthetic construct
environmental samples
environmental samples
environmental samples
environmental samples
environmental samples
environmental samples

overall_design: amoA gene diversity from two ocean acidification experiments, Monterey Bay experiment (two time points, ambient and acidified) and Vineyard Sound experiment (ambient and acifidied, with and without nutrients) examined with 2 two-color arrays (Cy3 and Cy5): the universal standard 20-mer oligo is printed to the slide with a 70-mer oligo (an archetype).  Environmental DNA sequences (fluoresced with Cy3) within 15% of the 70-mer conjugated to a 20-mer oligo (fluoresced with Cy5) complementary to the universal standard will bind to the oligo probes on the array.  Signal is the ratio of Cy3 to Cy5.

first: Patrick

last: Kearns

first: Michael

last: Holcomb

first: Bess

last: Ward


title: Applied Biosystems Human TaqMan Low Density Array (TLDA) in plasma samples from HCC cases and controls

city: New York

first: Jing

last: Shen

address: 650 W. 168th St. Black Building Rm.1608

institute: Columbia University

summary: MicroRNAs (miRNAs) are abundant in the circulation and play a central role in diverse biological processes; they may be useful for early diagnosis of hepatocellular carcinoma (HCC). We conducted a two-phase, case-control study (20 pairs for the discovery set and 49 pairs for the validation set) to test the hypothesis that genome-wide dysregulation of circulating miRNAs differentiate HCC cases from controls. Taqman low density arrays were used to examine genome-wide miRNA expression for the discovery set, and quantitative RT-PCR was used to validate candidate miRNAs for both discovery and validation sets. Sixty-six miRNAs were found to be significantly over-expressed in plasma of HCC cases compared to controls after adjusting for false discovery rate (p<0.05). A volcano plot indicated that 7 miRNAs had greater than 2-fold case-control differences with p<0.01. Four significant miRNAs (miR-150, miR-30c, miR-483-5p and miR-520b) detectable in all samples with varied expression levels were further validated in a validation set. MiR-483-5p was statistically significantly over-expressed in HCC cases compared with controls (3.20 vs. 0.82, p<0.0001). HCC risk factors and clinic-pathological characteristics did not influence miR-483-5p expression. The combination of plasma miR-483-5p level and HCV status can significantly differentiate HCC cases from controls with an AUC of 0.908 (p<0.0001). The sensitivity and specificity were, respectively, 75.5% and 89.8%. These preliminary results suggest the importance of dysregulated circulating miR-483-5p as a potential HCC biomarker. Confirmation of aberrant expression of miR-483-5p in a large prospective HCC study will provide support for its application to HCC detection.

overall_design: A hospital-based HCC case-control study including 20 HCC patients and 20 controls is conducted in Columbia University Medical Center (CUMC), which is approved by the Institutional Review Board. Cases were newly diagnosed HCC patients who were treated in the Hepatobiliary Oncology Clinics, CUMC, and examined pathologically. Controls were recruited from volunteers through the Research Recruitment and Minority Outreach (RRMO) core of Herbert Irving Comprehensive Cancer Center (HICCC). Flyers were placed at strategic locations around CUMC where hospital visitors and employees frequent or were handed out at inreach events at the hospital or at outreach events in the community. Interested participants were directed to contact the trained recruitment staff from the RRMO and given further information about participation. Interested participants were excluded from the control group if diagnosed for any kind of cancer or liver disease. Eligible controls were asked to fill out the same demographic and epidemiological questionnaire as HCC cases. In the current study, controls were matched with HCC cases on age (±5 yrs), gender (male/female) and ethnicities (Caucasian/Hispanic/African-American/Asian).


title: Transcriptional profiling of Escherichia coli after addition of CORM-3 and iCORM-3 to aerobically and anaerobically growing cells

city: Sheffield

first: Robert

last: Poole

state: South Yorkshire

address: Firth Court, Western Bank

department: Molecular Biology & Biotechnology

institute: University of Sheffield

summary:
Escherichia coli strain MG1655 was grown in a New Brunswick Scientific Bioflow III Biofermentor under continuous culture (chemostat) conditions. Cells were grown in defined media containing 2 mM glycerol as the sole and limiting source of energy and carbon. The working volume was 200 ml, and the dilution rate 0.2 h-1. For aerobic growth, the air-flow rate was 0.1 l/min, and the dissolved oxygen tension was maintained at ~7% air saturation by measuring oxygen dissolved in the culture using a Broadley James D140 OxyProbe® electrode. For anaerobic growth, cells are grown on 100 % nitrogen gas bubbled at 0.1 l/min Cells were grown as above to steady-state, At steady-state, CORM-3 or iCORM-3 was added to the chemostat culture at a final concentration of 40 uM.
Samples were taken immediately prior to the addition of CORM-3 or iCORM-3 and over a time course of 2.5, 5, 10, 20, 40 and 80 min exposure to (i)CORM-3 for subsequent analysis using microarrays. Cells were harvested directly into phenol:ethanol to stabilize RNA, and total RNA was purified using Qiagen’s RNeasy Mini kit as recommended by the suppliers.

overall_design: Time course experiment with samples taken immediately prior to or 2.5, 5, 10, 20, 40 or 80 minutes after addition of either 40uM CORM-3 or iCORM-3 under either 0 or 100 % perceived aerobiosis. 2 biological repeats were performed for each condition with 2 technical (dye swap) repeats per biological repeat.

first: Samantha

last: McLean

middle: K


title: Gain and loss of H4K16 acetylation during ES cell differentiation [NimbleGen ChIP-chip]

first: Gillian

last: Taylor

summary: H4K16ac is gained on hox loci and lost on pluripotency genes upon differentiation

overall_design: ChIP on chip over hox loxi and pluripotency genes for H4K16ac in undifferentiated ES cells and after 3 days of retinoic acid treatment

first: Ragnhild

last: Eskeland

first: Madapura

last: Pradeepa

first: Wendy

last: Bickmore


title: Comparative Analysis of Seed Transcriptomes of Ambient Ozone-Fumigated Two Different Rice Cultivars

status: Public on Aug 20 2013

city: Tsukuba

first: RANDEEP

last: RAKWAL

state: Ibaraki

address: 1-1-1 Tennodai

department: Institute of Health and Sport Sciences

institute: University of Tsukuba

summary: High ozone (O3) concentration causes serious damages in plant productivity. Climate models forecast that ground O3 level in the future will reach phytotoxic range, resulting in crop yield losses. With an ultimate goal to screen molecular factors to minimize losses of crop production by the rise of O3 level, we have started an investigation on effects of O3 on rice using rice DNA chip. Herein, we have utilized the samples of dry mature rice seeds harvested in an ozone-sensitive rice cultivar (Oryza sativa L. indica cv. Takanari) and a tolerant cultivar (Oryza sativa L. japonica cv. Koshihikari) which were fumigated with ambient air (mean O3: 32.7 ppb) in small open-top chambers (OTCs). First, we extracted total RNA from dry mature rice seeds of Takanari and Koshihikari using a modified protocol based on cethyltrimethylammonium bromide extraction buffer and phenol-chloroform-isoamylalcohol treatment. Furthermore, to perform microarray analysis using the Agilent 4x44 rice DNA Chip and the dye-swap method, we designed a balanced block design comparing seeds in an ambient air-fumigated rice cultivar and those in a filtered air-fumigated rice cultivar. Direct comparison of Koshihikari and Takanari O3 transcriptomes in seeds of rice plants fumigated with ambient O3 in OTCs successfully showed that genes encoding proteins involved in jasmonic acid, GABA biosynthesis, cell wall and membrane modification, starch mobilization, and secondary metabolite biosynthesis are differently regulated in an O3-sensitive cv. Takanari and a tolerant cv. Koshihikari.

overall_design: Comparison between O. sativa L. indica cv. Takanari and japonica cv. Koshihikari grown under ozone for their lifetime was performed. Controls were plants grown under filtered air. Three biological replicates (4 plants in each biological replicate in each small open top chamber - seed; pooled) were used, and dye-swaped.

first: Kyoungwon

last: Cho

first: Junko

last: Shibato

first: Akihiro

last: Kubo

first: Yoshihisa

last: Kohno

first: Kouji

last: Satoh

first: Shoshi

last: Kikuchi

first: Abhijit

last: Sarkar

first: Ganesh

last: Agrawal

first: Randeep

last: Rakwal


title: Maize kernels: Non Inoculated vs. Inoculated with Fusarium verticillioides

status: Public on Aug 17 2013

city: Rosario

first: Valeria

middle: Alina

last: Campos Bermudez

address: Suipacha 531

country: Argentina

institute: CEFOBI

summary: Fusarium verticillioides is a detrimental fungus that can contaminate maize grains with mycotoxins that are harmful to human and animal health. Breeding and growing resistant genotypes is one alternative to reduce contamination and subsequent production of mycotoxins by this fungus. However, little is known about the resistant mechanism relevant to breeding in this pathosystem. Therefore, our aim was to identify genes and metabolites that may be related to Fusarium ear rot resistance using resistant and susceptible maize inbreds. Kernels of the resistant inbred showed significantly reduced disease severity, and reduced levels of total fumonisin and ergosterol content compared with the susceptible one. Gene expression data were obtained from microarray hybridizations using F. verticillioides inoculated and non inoculated maize kernels. Differentially expressed sequences were identified and classified into 36 functional categories. Most of the differentially expressed genes were assigned to the categories “protein, RNA, DNA, stress, transport, signaling and cell metabolism”. These genes encode for PR proteins, detoxification and primary metabolism enzymes. Fungal inoculation did not produce considerable changes in gene expression and metabolites in the resistant L4637 inbred, probably due to a preformed or constitutive resistance mechanism. Defense-related genes were induced or repressed in kernels of the susceptible inbred L4674, responding specifically to the pathogen infection. The qRT-PCR in infected silks showed that glucanase, lipid transfer, xylanase inhibitor, PR1 and 26S proteosome transcripts had higher expression ratios in the susceptible line compared to the resistant one in response to fungal infection. Through this study, a global view of differential genes expressed and metabolites concentration during resistance and susceptibility to F. verticillioides inoculation has been obtained, giving additional information about the mechanisms and pathways conferring resistance to this important disease in maize.

overall_design:
Global view of differential genes expressed during resistance and susceptibility to F. verticillioides inoculation.
Two maize inbred lines : one resistant (L4637) and one susceptible (L4674) to F. verticillioides infection. Two-condition experiment, Inoculated (I) vs. non-inoculated (NI) lines. Biological replicates: 3 . One replicate per array.

last: Campos-Bermudez

first: Carolina

last: Fauguel


title: Epigenetic changes in Down syndrome leukemogenesis

status: Public on Aug 19 2013

city: Miami

first: Maria

middle: Eugenia

last: Figueroa

state: FL

address: 1501 NW 10th Ave, BRB 709A, Locator code C227

department: Human Genetics

institute: University of Miiami

type: Methylation profiling by genome tiling array

summary: Acute megakaryoblastic leukemia (AMKL) is more frequently seen in Down syndrome patients, where it is often preceded by a transient myeloproliferative disorder (DS-TMD). The development of DS-TMD and DS-AMKL require not only the presence of the trisomy 21 but also that of GATA1 mutations. However, despite extensive studies into the genetics of DS-AMKL, not much is known about the epigenetic deregulation associated with this disease. In order to understand how epigenetic changes at the DNA methylation level contribute to DS leukemogenesis we performed DNA methylation profiling at different stages of development of this disease and analyzed the dynamics of epigenetic reprogramming. Early genome-wide epigenetic changes can be detected in trisomy 21 fetal liver mononuclear cells, even prior to the development of hematological abnormalities. These early changes are characterized by marked loss of DNA methylation at genes associated with regulation of key developmental processes. This first wave of aberrant DNA hypomethylation is followed by a second wave of epigenetic reprogramming detected in blast cells from DS-TMD and DS-AMKL, characterized by gains of methylation. This second wave of hypermethylation targets a distinct set of genes, preferentially affecting genes involved in hematopoiesis and regulation of cell growth and proliferation.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: DNA methylation profiles obtained at different stages of the development of Down syndrome AMKL and from CD41+ cells from partial trisomic mice

first: John

last: Crispino


title: Genome-wide effects of Spt6 on RNA pol II and Histone H3 occupancy in budding yeast (ChIP-Chip)

status: Public on Aug 16 2013

city: Aurora

first: David

middle: L.

last: Bentley

state: CO

department: Biochemistry and Mol. Genetics

institute: U. Colorado School of Medicine

summary: whole genome analysis of RNA pol II and histone H3 in WT and Spt6-depleted cells using a tetracycline regulated ts degron mutant, spt6-td.

overall_design: ChiP-ChIP using ligation-mediated PCR amplified material hybridized to Nimblegen 385K arrays 50mers median probe spacing 32 bp cat. No. C4214-00-01

first: Hyunmin

last: Kim

last: Benltey


title: Effects of Diet on Resource Utilization by a Model Human Gut Microbiota Containing Bacteroides cellulosilyticus WH2, a Symbiont with an Extensive Glycobiome (GeneChip)

city: Saint Louis

first: Nathan

last: McNulty

state: MO

address: 4444 Forest Park Ave. (5th Floor)

department: Center for Genome Sciences and Systems Biology

institute: Washington University School of Medicine

summary: The human gut microbiota is an important metabolic organ, yet little is known about how its individual species interact, establish dominant positions, and respond to changes in environmental factors such as diet. In this study, gnotobiotic mice were colonized with an artificial microbiota comprising 12 sequenced human gut bacterial species and fed oscillating diets of disparate composition. Rapid, reproducible, and reversible changes in the structure of this assemblage were observed. Time-series microbial RNA-Seq analyses revealed staggered functional responses to diet shifts throughout the assemblage that were heavily focused on carbohydrate and amino acid metabolism. High-resolution shotgun metaproteomics confirmed many of these responses at a protein level. One member, Bacteroides cellulosilyticus WH2, proved exceptionally fit regardless of diet. Its genome encoded more carbohydrate active enzymes than any previously sequenced member of the Bacteroidetes. Transcriptional profiling indicated that B. cellulosilyticus WH2 is an adaptive forager that tailors its versatile carbohydrate utilization strategy to available dietary polysaccharides, with a strong emphasis on plant-derived xylans abundant in dietary staples like cereal grains. Two highly expressed, diet-specific polysaccharide utilization loci (PULs) in B. cellulosilyticus WH2 were identified, one with characteristics of xylan utilization systems. Introduction of a B. cellulosilyticus WH2 library comprising >90,000 isogenic transposon mutants into gnotobiotic mice, along with the other artificial community members, confirmed that these loci represent critical diet-specific fitness determinants. Carbohydrates that trigger dramatic increases in expression of these two loci and many of the organism’s 111 other predicted PULs were identified by RNA-Seq during in vitro growth on 31 distinct carbohydrate substrates, allowing us to better interpret in vivo RNA-Seq and proteomics data. These results offer insight into how gut microbes adapt to dietary perturbations at both a community level and from the perspective of a well-adapted symbiont with exceptional saccharolytic capabilities, and illustrate the value of artificial communities.

sample_organism:
Bacteroides thetaiotaomicron VPI-5482
Bacteroides sp. WH2
Blautia obeum ATCC 29174
Dorea longicatena DSM 13814
[Clostridium] scindens ATCC 35704
Bacteroides ovatus ATCC 8483
Bacteroides uniformis ATCC 8492
Bacteroides caccae ATCC 43185
Collinsella aerofaciens ATCC 25986
Thomasclavelia spiroformis DSM 1552
Phocaeicola vulgatus ATCC 8482
Parabacteroides distasonis ATCC 8503

platform_organism:
Bacteroides thetaiotaomicron VPI-5482
Bacteroides sp. WH2
Blautia obeum ATCC 29174
[Ruminococcus] torques ATCC 27756
Dorea longicatena DSM 13814
[Clostridium] scindens ATCC 35704
Bacteroides ovatus ATCC 8483
Bacteroides uniformis ATCC 8492
Faecalibacterium prausnitzii M21/2
Bacteroides caccae ATCC 43185
Collinsella aerofaciens ATCC 25986
Thomasclavelia spiroformis DSM 1552
Phocaeicola vulgatus ATCC 8482
Parabacteroides distasonis ATCC 8503
Agathobacter rectalis ATCC 33656

overall_design: An artificial community of 12 human gut bacterial species was introduced into germ-free male C57BL/6J mice at 10-12 weeks of age. Mice were split into two treatment groups, with each treatment group receiving an oscillating diet regimen in which animals were switched between a low fat, high plant polysaccharide (LF/HPP) diet and a high fat, high sugar (HF/HS) diet at two week intervals. One group was started on the LF/HPP diet, was switched to the HF/HS diet, and was then switched back to the LF/HPP diet. The other group was started on the HF/HS diet, was switched to the LF/HPP diet, and was then switched back to the HF/HS diet. Cecal contents were collected from each animal at the time of sacrifice which corresponded to the end of each treatment group's third diet phase. Separate gene expression profiles for each of the 12 species in the artificial community were generated for each sample using a series of custom mask files. 14 total samples (7 from animals consuming the LF/HPP diet at the time of sacrifice, 7 from animals consuming the HF/HS diet at the time of sacrifice). 12 gene expression profiles per sample (1/species).


title: Transcriptome comparison of the wild type strain Azoarcus sp. BH72  with that of nifLA knockout strain under nitrogen fixing condition

status: Public on Aug 15 2013

city: Bremen

first: Barbara

last: Reinhold-Hurek

department: Microbe-Plant-Interactions

institute: University Bremen

summary: Azoarcus sp. BH72 is known to express nitrogenase genes endophytically in  rice seedlings in gnotobiotic culture. Availability of fixed nitrogen is one of the important signals regulating the transcription of nitrogenase genes and hence nitrogen fixing activity. NifA is the essential transcription activator of nif genes. RNA isolated from the nifA knockout mutant of strain BH72 was compared with the transcriptome of  wild type under nitrogen fixing condition using a global genome wide microarray approach and the differences in the gene expression profile were monitered.

overall_design: RNA isolated from wild type strain BH72  and  nifLA mutant strain BHLAO  grown respectively under microaerobic nitrogen fixing condition with glutamate as poor nitrogen source  was used for two color whole genome microarray approach


title: Transcriptional profiling of nitrogen fixation and the role of NifA in the diazotrophic endophyte Azoarcus sp. strain BH72


title: Relationship between Differential Hepatic microRNA Expression and Decreased Hepatic Cytochrome P450 3A Activity in Cirrhosis

city: PHILADELPHIA

first: Chirayu

middle: Pankaj

last: Goswami

state: PA

address: 110 S 11TH STREET

department: MOLECULAR DIAGNOSTIC LABORATORY

institute: THOMAS JEFFERSON UNIVERSITY HOSPITAL

summary:
Background and Aim: Liver cirrhosis is associated with decreased hepatic cytochrome  P4503A (CYP3A) activity but the pathogenesis of this phenomenon is not well  elucidated. In this study, we examined if certain microRNAs (miRNA) are associated  with decreased hepatic CYP3A activity in cirrhosis.
Hepatic CYP3A activity and miRNA microarray expression profiles were  measured in cirrhotic (n=22) and normal (n=12) liver tissue. Hepatic CYP3A activity  was measured via midazolam hydroxylation in human liver microsomes. Additionally,  hepatic CYP3A4 protein concentration and the expression of CYP3A4 mRNA were  measured. Analyses were conducted to identify miRNAs which were differentially  expressed between two groups but also were significantly associated with lower  hepatic CYP3A activity.

overall_design: Liver tissue was collected from individuals with established cirrhosis who were awaiting liver transplantation (n=22) at the time of their liver transplantation procedure in the operating room. Normal liver tissue (n=12) was obtained from patients undergoing liver resection for metastatic/benign liver lesions with no underlying chronic liver disease

first: Raj

last: Vuppalanchi

first: Liang

last: Tiebing

first: Rohit

last: Nalamasu

first: Lang

last: Li

last: Jones

first: Rongrong

last: Wei

first: Wanqing

last: Liu

first: Naga

last: Chalasani


title: HuR and miR-1192 regulate myogenesis by modulating the translation of HMGB1 mRNA

status: Public on Aug 14 2013

city: Montreal

first: Imed

last: Gallouzi

state: QC

address: 3655 Promenade Sir William Osler

department: Biochemistry

country: Canada

institute: McGill University

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


title: HuR and miR-1192 regulate myogenesis by modulating the translation of HMGB1 mRNA (mRNA)

summary: Upon muscle injury the high mobility group box 1 (HMGB1) protein is up-regulated and secreted to initiate reparative responses. Here we show that HMGB1 controls myogenesis both in vitro and in vivo, during development and after adult muscle injury. HMGB1 expression in muscle cells is regulated at the translational level: the miRNA miR-1192 inhibits HMGB1 translation and the RNA-binding protein HuR promotes it. HuR binds to a cis-element, HuRBS, located in the 3'UTR of the HMGB1 transcript, and at the same time miR-1192 is recruited to an adjacent seed element. The binding of HuR to the HuRBS prevents the recruitment of Argonaute 2 (Ago2), overriding miR-1192-mediated translation inhibition.  Depleting HuR reduces myoblast fusion and silencing miR-1192 re-establishes the fusion potential of HuR-depleted cells. We propose that HuR promotes the commitment of myoblasts to myogenesis by enhancing the translation of HMGB1 and suppressing the translation inhibition mediated by miR-1192.

overall_design: RNA content was extracted following immunoprecipitation of HuR using a monoclonal antibody (3A2) and the levels of mRNA were compared to an IgG control in order to determine which transcripts were enriched in the HuR ribonucleoprotein complex.

first: Virginie

last: Dormoy-Raclet

first: Anne

last: Cammas

last: Celona

first: Xian

last: Lian

first: Kate

last: van der Giessen

first: Marija

last: Zivojnovic

first: Silvia

last: Brunelli

first: Francesca

last: Riuzzi

first: Guglielmo

last: Sorci

first: Brain

middle: T

last: Wilhelm

first: Sergio

last: Di Marco

first: Rosario

last: Donato

first: Marco

last: Bianchi


title: Gene regulation in LPS-induced PTB in E15.5 C57BL/6 mice

city: Queens

first: Sandra

middle: Eve

last: Reznik

state: NY

address: 8000 Utopia Parkway

department: Pharmaceutical Sciences

institute: St. John's University

summary: Multiple molecular pathways affected in LPS-triggered PTB with IL-beta major node

overall_design: LPS-induced mice (n=5) paired individually with pooled reference sample of negative controls (n=12)

first: Chih-Hung

last: Chen

first: Haoting

last: Yen

first: Aldo

last: Massimi

first: Ekaterina

last: Milova


title: The roles of IRF-3 and IRF-7 in innate antiviral immunity against dengue virus

city: La Jolla

first: Hui-Wen

address: 9420 Athena Circle

institute: La Jolla Institute for Allergy and Immunology

summary: We investigated the roles of IRF-3 and IRF-7 in innate antiviral immunity against dengue virus (DENV). Double-deficient Irf-3-/-7-/- mice infected with the DENV2 strain S221 possessed 1,000-150,000 fold higher levels of viral RNA than wild-type and single-deficient mice 24 hours after infection; however, they remained resistant to lethal infection. IFN-α/β was induced similarly in wild-type and Irf-3-/- mice post DENV infection, whereas in the Irf-7-/- and Irf-3-/-7-/- mice, significantly low levels of IFN-α/β expression was observed within 24 hours post-infection. IFN-stimulated gene (ISG) induction was also delayed in Irf-3-/-7-/- mice relative to wild-type and single-deficient mice. In particular, Cxcl10 and Ifnα2 were rapidly induced independently of both IRF-3 and IRF-7 in the Irf-3-/-7-/- mice with DENV infection. Higher levels of serum IFN-γ, IL-6, CXCL10, IL-8, IL-12 p70, and TNF were also observed in Irf-3-/-7-/- mice 24 hours after infection, at which time point viral titers peaked and started to be cleared. Antibody-mediated blockade experiments revealed that IFN-γ, CXCL10, and CXCR3 function to restrict DENV replication in Irf-3-/-7-/- mice. Additionally, the ISGs Cxcl10, Ifit1, Ifit3, and Mx2 can be induced via an IRF-3- and IRF-7-independent pathway that does not involve IFN-γ signaling for protection against DENV. Collectively, these results demonstrate that IRF-3 and IRF-7 are redundant, albeit IRF-7 plays a more important role than IRF-3 in inducing the initial IFN-α/β response; only the combined actions of IRF-3 and IRF-7 are necessary for efficient control of early DENV infection; and the late, IRF-3- and IRF-7-independent pathway contributes to anti-DENV immunity.

overall_design: To identify the antiviral genes that are controlled by IRF-3 and IRF-7 signaling during DENV infection, we examined a panel of ISG expression in the spleens of wild-type, Irf-3-/-, Irf-7-/- and Irf-3-/-7-/- mice at 12 or 24 hours after DENV infection using a quantitative PCR array kit. The fold changes in expression of 55 genes from infected mice were normalized to that of strain-matched naïve mice.

first: Kevin

last: King

first: Jui

last: Tu

first: Marisa

last: Sanchez

first: Andrew

middle: D

last: Luster

first: Sujan

last: Shresta


title: Cisplatin sensitivity in nasopharyngeal carcinoma cells (NPC)

status: Public on Aug 13 2013

city: Grand Rapids

first: Sok Kean

last: Khoo

state: MI

address: 333 Bostwick NE

institute: Van Andel Institute

summary: Transcriptional profiling of cisplatin sensitive NPCs

overall_design: 6-condition experiment, CNE2 vs. S16  cells at 0, 2 or 8 hr treatment. Biological replicates: 2 for each control (0 hr), 2 for each treatment (2 hr and 8 hr), independently grown and harvested, dye-swapped.

first: Ran-Yi

last: Lui

first: Zizheng

last: Dong

first: Jianguo

last: Liu

first: Ling

last: Zhou

first: Wenlin

last: Huang

first: Sok

first: Zhongfa

last: Zhang

first: David

last: Petillo

first: Bin

last: Teh

first: Chao-Nan

last: Qian

first: Jian-Ting


title: B lymphocyte activation induces DNA methylation reprogramming and establishes a common epigenetic signature in memory B and plasma cell compartments

city: Research Triangle Park

first: Deepak

last: Mav

state: NC

address: 2 Davis Drive

institute: Sciome LLC

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

overall_design: Refer to individual Series


title: B lymphocyte activation induces DNA methylation reprogramming and establishes a common epigenetic signature in memory B and plasma cell compartments [gene expression profiling]

summary:
DNA methylation profiling of human B cell populations representing a developmental series before and after immune activation.
The B cells are derived from inflamed tonsils.  The B cells were already activated in vivo in patients, therefore there was no need to stimulate the B cells after isolation.
Gene expression profiling was also performed from the same samples.

overall_design:
Four B cell subsets:  Naïve, germinal center B cells (GC), memory B cells, and plasma cells (PC) were purified by FACS ex vivo from tonsils of 8 human subjects.  Methylated CpG island Recovery assay (MIRA) was utilized to enrich for methylated DNA fragments from each sample for microarray analysis.  RNA was copurified from the same cell samples for gene expression profiling on microarray.
*** This Series reports gene expression profiling data. ***

first: Anne

last: Lai

first: Ruchir

last: Shah

first: Cissy

last: Geigerman

first: Steve

last: Sobol

last: Jaye

first: Paul

last: Wade

first: Sara

last: Grimm


title: HuR and miR-1192 regulate myogenesis by modulating the translation of HMGB1 mRNA (miRNA)

first: Imed

last: Gallouzi

first: Virginie

last: Dormoy-Raclet

last: Cammas

first: Barbara

last: Celona

first: Xian

last: Lian

first: Kate

last: van der Giessen

first: Marija

last: Zivojnovic

first: Silvia

last: Brunelli

first: Francesca

last: Riuzzi

first: Guglielmo

last: Sorci

first: Brain

last: Wilhelm

first: Sergio

last: Di Marco

first: Rosario

last: Donato

first: Marco

last: Bianchi


title: Bacteria- and IMD Pathway-Independent Immune Defenses against Plasmodium falciparum in Anopheles gambiae

status: Public on Aug 10 2013

city: Baltimore

first: George

last: Dimopoulos

state: MD

address: 615 N. Wolfe Street

department: Molecular Microbiology and Immunology

institute: Johns Hopkins School of Public Health

summary: The mosquito Anopheles gambiae uses its innate immune system to control bacterial and Plasmodium infection of its midgut tissue. The activation of potent IMD pathway-mediated anti-Plasmodium falciparum defenses is dependent on the presence of the midgut microbiota, which activate this defense system upon parasite infection through a peptidoglycan recognition protein, PGRPLC. We employed transcriptomic and reverse genetic analyses to compare the P. falciparum infection-responsive transcriptomes of septic and aseptic mosquitoes and to determine whether bacteria-independent anti-Plasmodium defenses exist. To examine the impact of P. falciparum infection on the mosquito midgut and carcass transcriptomes in the presence or absence of midgut bacteria, we used A. gambiae whole genome microarrays to compare the mRNA abundance of P. falciparum-infected and -naïve mosquitoes of antibiotic- and non-antibiotic treated cohorts. P. falciparum infection induced changes in the abundance of as many as 2,183 and 2,429 transcripts in whole mosquitoes belonging to a variety of functional groups in aseptic and septic mosquitoes. Ultimately, we were interested in identifying the genes involved in bacteria-independent anti-Plasmodium responses, and therefore we focused on transcripts displaying increased abundance in the parasite-infected aseptic midguts, placing a particular emphasis on those with predicted immune functions. Because of the central role of serine protease cascades in regulating insect immune defenses, we focused the remainder of our analysis on a clip-domain serine protease C2 (CLIPC2, AGAP004317) and a serine protease inhibitor 7 (SRPN7, AGAP007693) that were specifically upregulated in the parasite-infected, aseptic mosquito midgut. We showed that SRPN7 negatively and CLIPC2 positively regulate the anti-Plasmodium defense, independently of the midgut-associated bacteria. Co-silencing assays suggested that these two genes may function together in a signaling cascade. Neither gene was regulated, nor modulated, by infection with the rodent malaria parasite Plasmodium berghei, suggesting that SRPN7 and CLIPC2 are components of a defense system with preferential activity towards P. falciparum. Further analysis using RNA interference determined that these genes do not regulate the anti-Plasmodium defense mediated by the IMD pathway, and both factors act as agonists of the endogenous midgut microbiota, further demonstrating the lack of functional relatedness between these genes and the bacteria-dependent activation of the IMD pathway. This is the first study confirming the existence of a bacteria-independent, anti-P. falciparum defense.

overall_design: Aseptic and septic midguts and carcasses from P. falciparum-infected A. gambiae vs aseptic and septic midguts and carcasses from uninfected, blood-fed A. gambiae. 3 biological replicates and 1 pseudo-replicate per each array.

first: B

middle: J

last: Blumberg

first: S

last: Trop

last: Das

first: G


title: Gene expression in the blood of Live Attenuated Rev-Independent Nef¯SIV  infected Rhesus macaques during acute infection

status: Public on Aug 09 2013

city: Atlanta

first: Siddappa

last: Byrareddy

address: 101 Woodruff circle

department: Pathology & Laboratory Medicine

institute: Emory Univeristy

summary: Rhesus macaques (RMs) inoculated with live-attenuated Rev-Independent Nef¯ simian immunodeficiency virus (Rev-Ind Nef¯SIV) as adults or neonates controlled viremia to undetectable levels and showed no signs of immunodeficiency over 6-8 years of follow-up.  We tested the capacity of this live-attenuated virus to protect RMs against pathogenic, heterologous SIVsmE660 challenges

overall_design:
Blood
PBMC
Time after SIV infection: 2 weeks post SIV infection
Infection:Rev-Ind Nef¯SIV

first: Ruth

last: Ruprecht


title: N-acetylglucosamine (GlcNAc) Triggers a Rapid, Temperature-Responsive Morphogenetic Program in Thermally Dimorphic Fungi

status: Public on Aug 12 2013

city: San Francisco

first: Mark

last: Voorhies

address: 513 Parnassus, S472

department: Microbiology and Immunology

institute: University of California

summary: Thermally dimorphic human fungal pathogens undergo a reversible program of cellular differentiation in response to their environment that is essential for infectivity and pathogenicity. In the soil, these organisms grow as highly polarized, multicellular hyphal filaments that produce infectious particles. When inhaled by a mammalian host, these cells switch to a unicellular yeast form that causes disease even in healthy hosts. Temperature is considered to be the primary environmental cue that promotes reversible cellular differentiation; however, a shift to a lower temperature in vitro induces filamentous growth in an inefficient and asynchronous manner. In a search for other signals that regulate morphogenesis, we considered the monosaccharide N-acetylglucosamine (GlcNAc), which is a major component of microbial cell walls and is ubiquitous in the environment. GlcNAc was a potent and specific inducer of the yeast-to-filament transition in two thermally dimorphic fungi, Histoplasma capsulatum and Blastomyces dermatitidis. Micromolar concentrations of GlcNAc induced a robust morphological transition of H. capsulatum after temperature shift, indicating that fungal cells sense GlcNAc to promote filamentation. The synchronous morphologic transition stimulated by low temperature and GlcNAc allowed us to examine the temporal regulation of the transcriptome during morphogenesis to reveal candidate genes involved in establishing the filamentous growth program. Through this analysis, we identified two genes encoding GlcNAc transporters, NGT1 and NGT2, that were necessary for H. capsulatum cells to robustly filament in response to GlcNAc. Unexpectedly, NGT1 and NGT2 were important for efficient H. capsulatum yeast-to-filament conversion in standard glucose medium, suggesting that Ngt1 and Ngt2 monitor endogenous levels of GlcNAc to control multicellular filamentous growth in response to temperature. Overall, our work indicates that GlcNAc functions as a highly conserved cue of morphogenesis in fungi, which further enhances the significance of this ubiquitous sugar in cellular signaling in eukaryotes.

overall_design:
For each time-course sample, cDNA was coupled
to Cy5 and a reference cDNA pool was made by combining RNA from t = 0 and
all late time course samples, which was coupled to Cy3. For end point
microarray experiments (i.e., established yeast samples compared to
established filamentous samples), G217B yeast cDNA was coupled to Cy5 and
filament cDNA was coupled to Cy3.

first: Sarah

last: Gilmore

first: Shamoon

last: Naseem

first: James

middle: B

last: Konopka

first: Anita

last: Sil


title: B lymphocyte activation induces DNA methylation reprogramming and establishes a common epigenetic signature in memory B and plasma cell compartments [DNA methylation profiling]

first: Deepak

last: Mav

summary:
DNA methylation profiling of human B cell populations representing a developmental series before and after immune activation. The B cells are derived from inflamed tonsils.  The B cells were already activated in vivo in patients, therefore there was no need to stimulate the B cells after isolation.
Gene expression profiling was also performed from the same samples.

overall_design:
Four B cell subsets:  Naïve, germinal center B cells (GC), memory B cells, and plasma cells (PC) were purified by FACS ex vivo from tonsils of 8 human subjects.  Methylated CpG island Recovery assay (MIRA) was utilized to enrich for methylated DNA fragments from each sample for microarray analysis.
*** This Series reports DNA methylation profiling data. ***

first: Anne

last: Lai

first: Ruchir

last: Shah

first: Cissy

last: Geigerman

first: Steve

last: Sobol

first: David

last: Jaye

first: Paul

middle: A

last: Wade

first: Sara

last: Grimm


title: Global Analysis of de novo Transcription Following Biosynthetic Labeling in a Dinoflagellate, Karenia brevis

status: Public on Aug 01 2013

city: Charleston

first: Frances

middle: M

last: Van Dolah

state: SC

address: 219 Fort Johnson Rd

institute: Marine Biotoxins Program, NOAA Center for Coastal Environmental Health and Biomolecular Research

summary: Dinoflagellates possess many physiological processes that appear to be under post-transcriptional control.  However, the extent to which their genes are regulated post-transcriptionally remains unresolved.  To gain insight into role of de novo transcription in dinoflagellates, we biosynthetically labeled RNA with 4-thiouracil to isolate newly transcribed RNA in Karenia brevis.  These isolated fractions were then used for analysis of global de novo transcription by hybridization to a K. brevis microarray.  As previous microarray studies indicated that transcripts for pentatricopeptide repeat (PPR) proteins rapidly increased in response to nutrient addition, we queried the newly synthesized RNA pools at 1 and 4 h following nitrate addition to N-depleted cultures.  Transcriptome-wide there was little evidence of changes in the rate of de novo transcription during the first 4 h, relative to that in N-depleted cells, and no evidence for increased PPR protein transcription.  These results lend support to the growing consensus of post-transcriptional control of gene expression in dinoflagellates.

overall_design: Cultures were acclimated to 10 µM nitrate for a minimum of two months during which time cultures were transferred weekly in log phase.  For addition experiments, nutrient replete and N-limited 1 L cultures were grown to stationary phase (Day 9).  Using sodium nitrate, 155 µM NO3 was added to stationary phase cultures.  Cultures  were exposed to 0.2 mM 4-thiouracil for 1 h to biosynthetically label newly transcribed RNA during the first hour post-N-addition (n=3) or during the fourth hour post-N-addition (n=3).  N-limited cultures (n=3) were also exposed to 0.2 mM 4-thiouracil for 1 h to biosynthetically label newly transcribed RNA.  Cultures were harvested after 1 h exposure to 4-thiouracil and total RNA extracted.   Following extraction, RNA was biotinylated to allow for purification of the thiolated newly synthesized RNA from the total RNA pool using streptavidin coated magnetic beads.  The newly transcribed RNA from each culture was independently labeled and hybridized to microarrys in a one color format.  Based on the appearance of bioanlayzer profiles newly synthesized RNA was treated as mRNA in the labeling protocol.

first: Jeanine

middle: S

last: Morey


title: Gene expression arrays of cardiomyocyte ribosome-associated RNAs during zebrafish heart regeneration

city: Durham

first: Kenneth

middle: Daniel

last: Poss

address: 349 Nanaline Duke Building, Box 3709,  Duke University Medical Center

department: Cell Biology

institute: Duke University, HHMI

summary: A transgenic line cmlc2:TRAP was made to express EGFP-fused ribosomal protein L10a (EGFP-L10a) in zebrafish cardiomyocytes. Then ribosome-associated RNAs were immuoprecipitated from uninjured and injured adult cmlc2:TRAP fish to determine the differential expression changes during zebrafish heart regeneration.

overall_design: A nine chip study with cardiomyocyte ribosome associated RNAs  purified from three separate isolation of uninjured adult cmlc2:TRAP fish hearts, three separate isolation of 1 day post amupation (dpa) adult cmlc2:TRAP fish hearts, and three separate isolation of 7 dpa adult cmlc2:TRAP fish hearts.


title: Global Analysis of mRNA Half-lives Following Biosynthetic Labeling in a Dinoflagellate, Karenia brevis

summary: Dinoflagellates possess many physiological processes that appear to be under post-transcriptional control.  However, the extent to which their genes are regulated post-transcriptionally remains unresolved.  To gain insight into the role of differential mRNA stability in dinoflagellates, we biosynthetically labeled RNA with 4-thiouracil to isolate newly transcribed and pre-existing RNA pools in Karenia brevis.  These isolated fractions were then used for analysis of global mRNA stability by hybridization to a K. brevis microarray.  Global K. brevis mRNA half-lives were calculated from the ratio of newly transcribed/pre-existing RNA for 7086 array features using the online software HALO (Half-life Organizer).  Overall, mRNA half-lives were substantially longer than reported in other organisms studied at the global level, ranging from 42 minutes to greater than 3 days, with a median of 33 hours.  Thirteen percent of messages showed a half-life of 3 days, demonstrating their stability throughtout the course of the cell cycle and divison.  Consistent with well-documented trends observed in other organisms, housekeeping processes, including energy metabolism and transport, were significantly enriched in the most highly stable messages.  Shorter-lived transcripts included a higher proportion of transcriptional regulation, stress response, and other response/regulatory processes.

overall_design: Log phase cultures (n=6) were exposed to 0.2 mM 4-thiouracil for 2h to biosynthetically label newly transcribed RNA and total RNA was extracted.  Following extraction, RNA was biotinylated to allow for purification of the thiolated newly synthesized RNA from the total RNA pool using streptavidin coated magnetic beads.  From each replicate 3 pools of RNA, total RNA, pre-exisiting RNA, and newly synthesized RNA, were Cy3 labeled and hybridized to microarrys in a one color format.  Based on the appearance of bioanlayzer profiles, total and pre-existing RNA were treated as total RNA, while newly synthesized RNA was treated as mRNA in the labeling protocol.


title: In silico nano-dissection: defining cell type specificity at transcriptional level in human disease (tubulointerstitium)

status: Public on Aug 06 2013

city: Ann Arbor

first: Viji

last: Nair

address: 1152 West Medical Centre Dr.

institute: University of Michigan

summary:
To identify genes with cell-lineage-specific expression not accessible by experimental micro-dissection, we developed a genome-scale iterative method, in-silico nano-dissection, which leverages high-throughput functional-genomics data from tissue homogenates using a machine-learning framework.
This study applied nano-dissection to chronic kidney disease and identified transcripts specific to podocytes, key cells in the glomerular filter responsible for hereditary proteinuric syndromes and acquired CKD. In-silico prediction accuracy exceeded predictions derived from fluorescence-tagged-murine podocytes, identified genes recently implicated in hereditary glomerular disease and predicted genes significantly correlated with kidney function. The nano-dissection method is broadly applicable to define lineage specificity in many functional and disease contexts.

overall_design: We applied a machine-learning framework on high-throughput gene expression data from human kidney biopsy tissue homogenates and predict novel podocyte-specific genes. The prediction was validated by Human Protein Atlas at protein level. Prediction accuracy was compared with predictions derived from experimental approach using fluorescence-tagged-murine podocytes.

first: Wenjun

last: Ju

first: Casey

last: Greene

first: Felix

last: Eichinger

first: Jeffery

last: Hodgin

first: Markus

last: Bitzer

first: Young-suk

last: Lee

first: Qian

last: Zhu

first: Masami

last: Kehata

first: Min

last: Li

first: Maria

middle: P

last: Rastaldi

first: Clemens

last: Cohen

first: Olga

last: Troyanskaya

first: Matthias

last: Kretzler


title: In silico nano-dissection: defining cell type specificity at transcriptional level in human disease


title: Streptococcus pneumoniae D39 spxB- mutant vs. D39 wild-type

status: Public on Aug 08 2013

city: Groningen

first: Jetta

last: Bijlsma

address: Hanzeplein 1

department: Medical Microbiology

country: Netherlands

institute: University Medical Center Groningen

summary: Comparison of the Streptococcus pneumoniae D39 spxB- mutant vs D39. For DNA microarray analysis, D39 wild-type and two independently obtained D39spxB- mutants were grown as four, two and two biological replicates, respectively, in Glc-M17 under semi-aerobic conditions and harvested at an OD595 of approximately 0.25 (mid-exponential). The RNA of both D39spxB- strains was compared to D39 and the combined data was analyzed. All other procedures regarding microarray analyses were done as described before. A gene was considered differentially expressed when the fold change was ≥ 2, ≤ 0.5, with a Bayes p ≤ 0.00001 and when at least 7 measurements were available.

overall_design: One condition design comparision of two strains including a dye swap.

first: Oscar

last: Kuipers

first: Jolanda

last: Neef

first: Vahid

middle: F

last: Andisi

first: Henrik

last: Gradstedt

first: Sandra

last: Carvalho

first: Ana

middle: R

last: Neves


title: A gDNA microarray for genotyping Salvia species

status: Public on Jul 31 2013

city: Bundoora

first: Nitin

last: Mantri

state: Victoria

address: Plenty Road

department: School of Science

institute: RMIT University

summary: Salvia is an important genus from the Lamiaceae with approximately 1000 species distributed globally. Several Salvia species are commercially important because of their medicinal and culinary properties. We report the construction of the first fingerprinting array for Salvia species enriched with polymorphic and divergent DNA sequences and demonstrate the potential of this array for fingerprinting several economically important members of this genus.

sample_organism: Salvia officinalis subsp. lavandulifolia

overall_design: In order to generate the Salvia Subtracted Diversity Array (SDA), a Suppression Subtractive Hybridization (SSH) was performed between a pool of ten Salvia species and a pool of non-angiosperm and angiosperms (excluding the Lamiaceae) to selectively isolate Salvia-specific sequences. A total of 285 subtracted genomic DNA (gDNA) fragments were amplified and arrayed. DNA fingerprints were obtained for fifteen Salvia genotypes including three that were not part of the original subtraction pool. Hierarchical cluster analysis indicated that the Salvia-specific SDA was capable of differentiating closely related species of S. officinalis and S. miltiorrhiza and was also able to reveal genetic relationships consistent with geographical origins. Species-specific features were also found for S. elegans, S. officinalis, S. sclarea, S. przewalskii and S. runcinata.

first: Alexandra

last: Olarte

first: Edwin

last: Pang


title: Chromosome conformation capture-on-chip of dexamethasone synchronized cells at several circadian times

city: Irvine

first: Paolo

last: Sassone-Corsi

address: 340 Sprague Hall

department: Center for Epigenetics and Metabolism. Dept. Biological Chemistry

summary: The spatial organization of genes in the interphase nucleus plays an important role in establishment and regulation of gene expression. The circadian expressed and clock controlled genes represent about 10% of the transcripts in the mammalian cells, however the role of genome topology in the expression of genes in a circadian manner remains to be elucidated. In this study we investigated the characteristics and dynamics of the genomic loci that contact the clock controlled gene Dbp during the circadian cycle. To do so, we combined genome-wide interaction profiling by chromosome conformation capture-on-chip (4C) technology with analyses of circadian gene expression in synchronized mouse embryonic fibroblasts (MEFs). This approach allowed us to elucidate the three-dimensional organization of the genome during the circadian cycle around the clock controlled gene Dbp, paralleling its circadian expression. We found that the Dbp genomic environment remains largely similar during the circadian cycle. However, specific DNA regions change their frequency of interaction with Dbp as the circadian cycle progresses, delineating a Dbp circadian interactome. These specific changes are not present in Bmal1-/- MEF, suggesting that the clock machinery is implicated in shaping the genomic landscape around the Dbp locus. The Dbp interactome is enriched in DNA elements related to the clock system (E boxes). We found a spatial clustering of functionally related genes. The Dbp circadian interactome contains a subset of circadian genes whose expression closely parallels that for Dbp. Taken together, our results indicate that the Dbp subnuclear environment is organized to privilege the clock directed gene expression program.

overall_design:
Wild type mouse embryonic fibroblasts at the circadian times (CT) 22, 26, 30, 34 and 46.
Bmal1-/- mouse embrionic fibroblasts at CT 22 and CT 34
Biological replicate using an independent line of wild type mouse embrionic fibroblast at CT 22 and CT 34
This submission represents the chromosome conformation capture-on-chip component of the overall study

first: Lorena

last: Aguilar-Arnal


title: Real-time quantitative PCR analysis of mouse mature CD4SP thymocytes

status: Public on Jul 27 2013

city: Bethesda

first: Jung-Hyun

last: Park

address: 10 Center Dr

department: EIB

institute: NIH/NCI

summary: RNA was isolated with the RNeasy kit (Qiagen) from electronically sorted mature CD4SP thymocytes. RNA was reverse transcribed into cDNA by oligo(dT) priming with the QuantiTect Reverse transcription kit (Qiagen). The expression of 84 key genes involved in apoptosis, or programmed cell death was performed with mouse apoptosis RT2ProfilerTM PCR array system (PAMM-012 E; SABiosciences). PCR Array data were analyzed by the Ct data analysis method.

overall_design: qPCR gene expression profiling.  CD4SP thymocytes from WT and Ik7Tg mice were used.

first: Changwan

last: Hong


title: Real-time quantitative PCR analysis of mouse immature CD4SP thymocytes

summary: RNA was isolated with the RNeasy kit (Qiagen) from electronically sorted immature CD4SP thymocytes. RNA was reverse transcribed into cDNA by oligo(dT) priming with the QuantiTect Reverse transcription kit (Qiagen). The expression of 84 key genes involved in apoptosis, or programmed cell death was performed with mouse apoptosis RT2ProfilerTM PCR array system (PAMM-012 E; SABiosciences). PCR Array data were analyzed by the Ct data analysis method.

last: park


title: Gene expression-based, inflammatory response prediction by bronchial epithelial cell line treated with signal peptide of eosinophil cationic protein

status: Public on Jul 20 2013

city: Taichung Ciy

first: Hao-Teng

last: Chang

address: No.91, Hsueh-shih Rd. N. Dist.

institute: China Medical University

summary: Background Eosinophil cationic protein is a clinical asthma biomarker that would be released into blood, especially gathered in bronchia. The signal peptide of eosinophil cationic protein (ECPsp) plays an important role in translocating ECP to the extracellular space. We previously reported that ECPsp inhibits microbial growth and regulates the expression of mammalian genes encoding tumor growth factor-a (TGF-a) and epidermal growth factor receptor (EGFR). Results In the present study, we first generated a DNA microarray dataset, which showed that ECPsp upregulated proinflammatory molecules, including chemokines, interferon-induced molecules, and Toll-like receptors. The levels of mRNAs encoding CCL5, CXCL10, CXCL11, CXCL16, STAT1, and STAT2 were increased in the presence of ECPsp by 2.07-, 4.21-, 7.52-, 2.6-, 3.58-, and 1.67-fold, respectively. We then generated a functional linkage network by integrating the microarray dataset with the pathway database of Kyoto Encyclopedia of Genes and Genomes. This revealed that STAT1[/2], an important transcriptional factor that regulates cytokine expression and release, served as a hub to connect the pathways of cytokine stimulation (TGF-a and EGFR pathways) and inflammatory responses. Furthermore, integrating TGF-a and EGFR with the functional linkage network indicated that STAT1 served as a hub that connects two functional clusters, including (1) cell proliferation and survival, and (2) inflammation. Finally, we found that conditioned medium in which cells that express ECPsp had been cultured could chemoattract macrophages. Therefore, we hypothesize that ECPsp may regulate the migration of macrophages in vivo. Conclusion The increased expression and release of various cytokines triggered by ECPsp may attract macrophages to bronchia to purge damaged cells. Our approach, involving experimental and computational systems biology, predicts pathways and potential biological functions for further characterization of this novel function of ECPsp under inflammatory conditions.

overall_design: The control group of this study is Beas-2B cells treated with pEGFP-C1, and the experiment group is the same cell line treated with pEGFPN1-ECPsp. Each group was conducted by two biological repeats and two technical repeats were done in DNA microarray analyses. On the microarray chip, 29,187 probes correspond to the annotated genes in the RefSeq v38 and Ensembl v56 databases. Furthermore, 1,088 control probes are also included for monitoring the sample quality and the hybridization process.

first: Yu-Shu

last: Liu

first: Pei-Wen

last: Tsai

first: Tan-chi

last: Fan

first: Yong

last: Wang

first: Chia-Hung

last: Hsieh

first: Margaret

first: Tun-Wen

last: Pai

first: Chien-Fu

last: Huang

first: Chung-Yu

last: Lan


title: Real-time quantitative PCR analysis of mouse total CD4SP thymocytes

summary: RNA was isolated with the RNeasy kit (Qiagen) from electronically sorted total CD4SP thymocytes. RNA was reverse transcribed into cDNA by oligo(dT) priming with the QuantiTect Reverse transcription kit (Qiagen). The expression of 84 key genes involved in apoptosis, or programmed cell death was performed with mouse apoptosis RT2ProfilerTM PCR array system (PAMM-012 E; SABiosciences). PCR Array data were analyzed by the Ct data analysis method.


title: The Microbial Gene Diversity along an Elevation Gradient of the Tibetan Grassland

status: Public on Jul 13 2013

city: Beijing

first: Gao

last: Ying

address: Qinghua East Street

institute: Tsinghua University

summary: Tibet is one of the most threatened regions by climate warming, thus understanding how its microbial communities function may be of high importance for predicting microbial responses to climate changes. Here, we report a study to profile soil microbial structural genes, which infers functional roles of microbial communities, along four sites/elevations of a Tibetan mountainous grassland, aiming to explore potential microbial responses to climate changes via a strategy of space-for-time substitution. Using a microarray-based metagenomics tool named GeoChip 4.0, we showed that microbial communities were distinct for most but not all of the sites. Substantial variations were apparent in stress, N and C cycling genes, but they were in line with the functional roles of these genes. Cold shock genes were more abundant at higher elevations. Also, gdh converting ammonium into urea was more abundant at higher elevations while ureC converting urea into ammonium was less abundant, which was consistent with soil ammonium contents. Significant correlations were observed between N-cycling genes (ureC, gdh and amoA) and nitrous oxide flux, suggesting that they contributed to community metabolism. Lastly, we found by CCA, Mantel tests and the similarity tests that soil pH, temperature, NH4+–N and vegetation diversity accounted for the majority (81.4%) of microbial community variations, suggesting that these four attributes were major factors affecting soil microbial communities. Based on these observations, we predict that climate changes in the Tibetan grasslands are very likely to change soil microbial community functional structure, with particular impacts on microbial N cycling genes and consequently microbe-mediated soil N dynamics.

overall_design: Twelve samples were collected from four elevations (3200, 3400, 3600 and 3800 m) along a Tibetan grassland; Three replicates in every elevation

first: Yunfeng

last: Yang

first: Ying

last: Gao


title: Transcriptome changes following castration of Korean cattle bulls in longissimus dorsi muscle

status: Public on Jun 30 2013

city: Gwangju

first: Myunggi

last: Baik

address: 77 yongbong-ro buk-gu

institute: chonnam university

summary: Transcripome of longissimus dorsi muscle was compared between Korean cattle bulls and steers by using a customized bovine Combimatrix microarray containing 10,199 genes.

overall_design: A customized bovine Combimatrix microarray containing 10,199 genes were constructed, and transcripome of longissimus dorsi muscle was compared between Korean cattle bulls (3 bulls) and steers (3 high-marbled and 3 low-marbled steers) by using the microarray hybridzation.

first: Jinjong

last: Bong