title: Role of endogenous type I Interferon  in spontaneous, Her2/Neu oncogene-driven carcinogenesis

status: Public on May 22 2018

city: Rome

first: Luciano

last: Castiello

address: Viale Regina Elena 291

country: Italy

institute: Istituto Pasteur Italia - Fondazione Cenci Bolognetti

summary: Type I Interferons (IFN-I) are anti-viral and immuno-modulating cytokines involved in many steps across tumor initiation and progression. IFN-I act directly on tumor cells inhibiting cell growth and indirectly by activating immune cells to mount antitumor response. To understand the role of endogenous IFN-I in spontaneous, oncogene-driven carcinogenesis, we characterized tumors arising in Her2/neu transgenic (neuT) mice carrying a non-functional mutation in the IFN-I receptor (IFNAR1), thus being unresponsive to this family of cytokines.  Compared to parental neu+/-mice (neuT mice), IFNAR1-/- neu+/- mice (IFNAR-neuT mice) showed earlier onset and increased tumor multiplicity with marked vascularization. Of note, IFNAR-neuT tumors specifically exhibited  deregulation of genes having adverse prognostic value in  breast cancer patients, including breast cancer stem cells (BCSC) marker aldehyde dehydrogenase-1A1 (ALDH1A1). An increased amount of BCSC was observed in IFNAR-neuT tumors, as assessed by ALDH1A1 enzymatic activity, clonogenic assay and tumorigenic capacity. In vitro exposure of neuT+ mammospheres and  cell lines to anti-IFN-I antibodies resulted in increased frequency of ALDH+ cells, suggesting that IFN-I  control  stemness in tumor cells. Altogether, these results reveal an essential role of IFN-I in NeuT-driven spontaneous carcinogenesis through intrinsic control of BCSC.

overall_design: 30 samples of mouse mammary glands, belonging to 4 groups: Wild-type, IFNAR1-/-, Her2/Neu+, and Her2/Neu+/IFNAR1-/-. Samples were cohybridized with Universal Reference Mouse RNA

first: Eleonora

last: Aricò

first: Paola

last: Sestili

first: Filippo

last: Belardelli

first: Enrico

last: Proietti

first: Giovanna

last: Schiavoni

first: Domenica

last: Monque

first: Antonella

last: Sistigu

first: Rosanna

last: Dattilo

first: Fiorella

last: Ciaffoni

first: Mauro

last: Biffoni

first: Maria

last: Ferrantini

first: Manuela

last: Iezzi

first: Federica

last: Moschella

first: Alessi

last: Lamolinara

first: Ann

last: Zeuner

first: Anna

middle: M

last: Pacca

first: Daniele

last: Macchia


title: Ago2-RIP-chip in Dicer WT and KO macrophages

status: Public on May 23 2018

city: Munich

first: Andreas

last: Schober

state: Bavaria

address: Pettenkoferstr. 9

department: Institute for Cardiovascular Prevention

country: Germany

institute: Ludwig-Maximilians-University

summary: To determine the spectrum of miRNA targets regulated following Dicer deletion, we performed argonaute 2 (AGO2)-RNA Immunoprecipitation (RIP)-microarray in bone marrow-derived macrophages (BMDMs) from LysM-Cre/Dicerflox/flox/Apoe–/– and LysM-Cre/Dicerwt/wt/Apoe–/– mice. This analysis combined with miRNA profiling in Dicer wild type (WT) and knockout (KO) BMDMs may help to identify the miRNA targets regulated by Dicer deletion.

overall_design: Bone marrow cells were harvested from femora of 6-8 week old male LysM-Cre/Dicerflox/flox/Apoe–/– or LysM-Cre/Dicerwt/wt/Apoe–/– mice, re-suspended in DMEM-F12/10% FCS/10% L929-conditioned medium, and cultured for 7 days to differentiate into primary macrophages. RNA was isolated before and after AGO2-RIP or IgG control-RIP using Trizol.

first: Yuanyuan

last: Wei


title: Systems analysis of phosphate-limitation induced lipid accumulation by the oleaginous yeast Rhodosporidium toruloides

status: Public on May 31 2018

city: Dalian

first: Wang

middle: Ya

address: 457 Zhongshan Road

country: China

institute: Dalian Institute of Chemical Physics

type: Expression profiling by high throughput sequencing

summary: Lipid accumulation by oleaginous microorganisms is of great scientific interest and biotechnological potential. While nitrogen limitation has been routinely employed, low-cost raw materials usually contain rich nitrogenous components, thus preventing from efficient lipid production. Inorganic phosphate (Pi) limitation has been found sufficient to promote conversion of sugars into lipids, yet the molecular basis of cellular response to Pi-limitation and concurrent lipid accumulation remains elusive. Here we performed multi-omic analyses of the oleaginous yeast Rhodosporidium toruloides to shield lights on Pi-limitation induced lipid accumulation. Samples were prepared under Pi-limited as well as Pi-replete chemostat conditions, and subjected to analysis at the transcriptomic, proteomic and metabolomic level. In total, 7970 genes, 4212 proteins and 123 metabolites were identified. Results showed that Pi-limitation facilitates up-regulation of Pi-associated metabolism, RNA degradation and triacylglycerol biosynthesis, while down-regulation of ribosome biosynthesis and tricarboxylic acid cycle. Pi-limitation leads to de-phosphorylation of adenosine monophosphate, the allosteric activator of isocitrate dehydrogenase key to lipid biosynthesis. It was found that NADPH, the key cofactor for fatty acid biosynthesis, is limited due to reduced flux through the pentose phosphate pathway and transhydrogenation cycle, and that this can be overcomed by overexpression of an endogenous malic enzyme. These phenomena are found distinctive from those under nitrogen-limitation. The information greatly enriches our understanding on microbial oleaginicity and Pi-related metabolism. Importantly, systems data may facilitate designing advanced cell factories for production of lipids and related oleochemicals.

overall_design: Rhodosporidium toruloides was prepared under Pi-limited as well as Pi-replete chemostat conditions, and subjected to analysis at the transcriptomic, proteomic and metabolomic level

first: Yanan

last: Wang

first: Zongbao

middle: K

last: Zhao


title: Study of the function of AtOXR2 in stress response by transcriptional profiling of Arabidopsis thaliana with incresed expression of AtOXR2 (oeOXR2 plants)

city: Santa Fe

first: Elina

last: WELCHEN

state: Santa Fe

address: Colectora Ruta Nac. Nº168 km. 0

country: Argentina

institute: Instituto de Agrobiotecnologia del Litoral

summary: Analysis of transcriptional profiling of Arabidopsis Col-0 leaves from wild-type and plants with incresed levels of AtOXR2 (oeOXR2 plants)

overall_design: Two-condition experiment, Control vs. Overexpressed plants. Biological replicates: 2 control, 2 overexpressed plants

first: Wlechen

last: Elina

first: Colombatti

last: Francisco


title: MicroRNA (miRNA) expression profiling of blood leukocytes of Parkinson's disease (PD) patients pre- and post-deep brain stimulation treatment and of healthy control volunteers

city: London

first: Lilach

last: Soreq

address: Queen Square

department: Molecular  Neuroscience

country: United Kingdom

institute: UCL

summary: Parkinson's disease (PD) is a prevalent, multifaceted neurodegenerative disease caused by mostly unknown factors. MicroRNAs (miRNAs) are small (~21 nucleotides long) RNAs that regulate up to hundreds of target genes. To study the role of miRNAs in PD and following surgical brain electrical stimulation treatment response, the expression profiling of miRNAs in peripheral blood leukocyte cells of PD patients pre- deep brain stimulation (DBS) and post-DBS both on electrical stimulation, and following a short one-hour electrical stimulation cessation, as well as of healthy control volunteers, were examined.

overall_design: Total RNA was extracted from the blood leukocytes of 3 PD patients in three states: pre-DBS, post-DBS on electrical stimulation and following one hour off electrical stimulation, and of 3 healthy control volunteers. miRNA expression was examined.

first: Hagai

last: Bergman

first: Zvi

last: Israel

first: Hermona


title: The modulation of acetic acid pathway genes in Arabidopsis produces drought-stress tolerant plants

city: Yokohama-Shi, Tsurumi Ku

first: Khurram

last: Bashir

state: Kanagawa

address: 1-7-22 Suehiro-cho

department: Center for Sustainable Resource Science

country: Japan

institute: RIKEN

summary: Gene expression profiles of  control and drought-stressed shoots of WT and pTSPO-PDC1-5 was performed using the custom microarray Agilent-034592

overall_design: WT and transgenic seeds were sown in trays containing Dio propagation mix no. 2 professional soil (Dio Chemicals, Japan) and germinated and grown at 22°C under a 16 h light/8 h dark cycle, and a 60 µmol m−2 s−1 photon flux density. Two weeks after germination, plants were subjected to drought treatment by removing excess water from the trays and ceasing any subsequent watering. Shoot samples were collected 11 days after drought stress treatment. Plants not subjected to drought stress treatment were used as control. Samples were immediately frozen in liquid nitrogen and stored at -80 degrees until RNA extraction.

first: Sultana

last: Rasheed

first: Jong-Myong

last: Kim

first: Marina

last: Ando

first: Maho

last: Tanaka

first: Motoaki

last: Seki


title: A map of the PGC-1α- and NT-PGC-1α-regulated transcriptional network in brown adipose tissue [ChIP-Seq]

city: Baton Rouge

first: Ji Suk

last: Chang

state: LA

address: 6400 Perkins Rd.

department: Gene Regulation and Metabolism

country: USA

institute: Pennington Biomedical Research Center

type: Genome binding/occupancy profiling by high throughput sequencing

summary: Transcriptional coactivator PGC-1α and its splice variant NT-PGC-1α play crucial roles in regulating cold-induced thermogenesis in brown adipose tissue (BAT). PGC-1α and NT-PGC-1α are highly induced by cold in BAT and subsequently bind to and coactivate many different transcription factors to regulate expression of genes involved in mitochondrial biogenesis, fatty acid oxidation, respiration and thermogenesis. To identify the complete repertoire of PGC-1α and NT-PGC-1α target genes in BAT, we analyzed genome-wide DNA-binding and gene expression profiles. We find that PGC-1α-/NT-PGC-1α binding broadly associates with cold-mediated transcriptional activation. In addition to their known target genes in mitochondrial biogenesis, fatty acid oxidation, respiration and thermogenesis, PGC-1α and NT-PGC-1α target to a broad spectrum of genes involved in diverse biological pathways including ubiquitin-dependent protein catabolism, ribonucleoprotein complex biosynthesis, phospholipid biosynthesis, angiogenesis, glycogen metabolism, phosphorylation, and autophagy. Our findings expand the number of genes and biological pathways that may be regulated by PGC-1α and NT-PGC-1α and provide further insight into the transcriptional regulatory network in which PGC-1α and NT-PGC-1α coordinate a comprehensive transcriptional response in BAT in response to cold.

overall_design: Examination of genome-wide PGC-1α/NT-PGC-1α binding sites in brown adipose tissue

first: JiSuk

first: Sujoy

last: Ghosh

first: Susan

last: Newman

first: Michael

last: Salbaum


title: Spatial regulation of transcription and histone occupancy by histone chaperones FACT and Spt6

status: Public on May 21 2018

city: Rochester

first: Chhabi

last: Govind

state: mi

address: 333 Science and Engineering Building

department: Biological Sciences

institute: Oakland University

type: Genome binding/occupancy profiling by genome tiling array

summary:
The FACT complex and Spt6 are conserved histone chaperones that are recruited to the open reading frames of transcribed genes. In this study, we provide evidence that FACT interaction with acetylated H3 tail is important for its localization to the coding sequences. Pol II CTD kinase Kin28 additionally stimulates FACT recruitment to a subset of genes. Pol II occupancies in the 5’ ends of transcribed genes are greatly reduced on depleting FACT, whereas reduced occupancies at the 3’ ends were observed upon Spt6 depletion indicating that these factors modulate Pol II progression through distinct regions of transcribed coding sequences. While FACT is largely responsible for reassembling histones, we uncover a role for Spt6 in promoting histone eviction in addition to widely-accepted role for Spt6 in histone reassembly. Consistent with their localization in the coding regions, simultaneously impairing FACT and Spt6 function severely dampens histone eviction and impairs transcription genome-wide.
ChIP-chip experiments to measure Spt16 occupancies in WT and kin28as mutant, as well Rpb3 and histone H3 occupancies in undepleted or depleted cells for Spt16 and Spt6, and also in the strain lacking Spt6 tandem SH2 domain

overall_design: The WT and mutant strains were grown in Synthetic complete and cells were induced for Gcn4 by treating with Sulfometuron methyl for 30 minutes and processed for chromatin immunoprecipitation using antibodies again Myc, Rpb3 or histone H3.

middle: k


title: Gene expression in alveolar macrophages between bleomycin–treated wild-type and S1pr2-/- mice.

status: Public on May 30 2018

city: Kanazawa

first: Takumi

last: Nishiuchi

address: 13-1 Takaramachi

institute: Kanazawa University

summary: We compared mRNA expression in alveolar macrophages between bleomycin–treated wild-type and S1pr2-/- mice, using DNA microarray analysis. In S1pr2-/- macrophages, 398 genes showed decreases to less than 50% of the levels in wild-type macrophages. In contrast, 122 genes showed more than 2.0-fold increases in S1pr2-/- macrophages compared with wild-type macrophages. The downregulated genes in S1pr2-/- mice included the following potentially fibrosis–related genes: profibrotic cytokines, chemokines, and the markers characteristic of classically activated (M1) and alternatively activated (M2) macrophages.

overall_design: BALF cells from wild-type and S1pr2-/- mice on day 22 after bleomycin administration were collected and analyzed.  Two independent experiments were performed.

first: Yoh

last: Takuwa

first: Yasuo

last: Okamoto


title: Gene expression profiling of vein graft restenosis

city: Nanchang

first: Qun

last: Wang

state: Jiangxi Province

address: No.461, Bayi Road,

institute: First Affiliated Hospital of Nanchang University

summary: Occlusive artery disease (CAD) is the leading cause of death worldwide. Bypass graft surgery remains the prevalently performed treatments for occlusive arterial disease, and veins are the most frequently used conduits for surgical revascularization. However, clinical efficacy is highly affected by the long-term potency rates of vein grafts, and no optimal treatments are available for prevention of vein graft restenosis (VGR) until today. Therefore, it is urgent to improve the understanding of molecular mechanisms involved in mediating VGR, and thereby provide potential potent therapeutic targets for prevention of vein graft failure. In this study, we aim to explore potential crucial genes and pathways associated with VGR and provide valid biological information for further investigation of VGR.

overall_design: A total of 16 samples were used in this study, including, 6 samples(A1,A2, A3, A4, A5, A6) that are vein grafts removed 1 day after surgery, 6 samples (C1, C2, C3, C4, C5, C6) that are vein grafts removed in 7 days after surgery group, and 4 samples (O1, O2, O3, O4) that are vein grafts obtained from sham surgery group.


title: Gene signature of young, replicative and TNF-α-induced premature senescent of human microvascular endothelial cells-lung (HMVEC-L)

city: KUALA LUMPUR

first: Pooi-Fong

last: Wong

address: Faculty of Medicine

department: Pharmacology

country: Malaysia

institute: University of malaya

summary: Despite the fact that miRNAs have been extensively investigated for their involvement in diseases, senescence as well as inflammation, miRNAs involved in TNF-α- induced premature senescence remain to be uncovered. Hence, the present study aims to identify unique miRNAs and their respective signaling pathways in TNF-α-induced senescence in lung microvascular endothelial cells and novel targets for prevention or protection against premature senescence and endothelial hyperpermeability.  Gene profiling was established using the same RNA input as that used for miRNA profiing. We have employed Agilent Whole Human Genome microarray platform  to evaluate the expressions of 19,596 human genes.

overall_design: Gene expression profiles were established for young, replicative and TNF-α-induced premature senescent of HMVEC-L.

first: Hui-Lan

last: Jong

first: Mohd

middle: R

last: Mustafa

first: Sazaly

last: AbuBakar


title: Human CRC cells (Caco2 and SW480): AURKA siRNA vs non targeted siRNA

city: Amsterdam

first: Beatriz

last: Carvalho

address: Plesmanlaan 121

country: Netherlands

institute: NKI

summary: Transcriptional profiling of Caco2 and SW480 CRC cells transfected with AURKA siRNA or a control (non-targeted) siRNA. Caco2 and SW480 both have a gain of chromosomal arm 20q, where the AURKA gene is located. The goal was to determine the effects of AURKA knock-down on global gene expression.

overall_design: Two-condition experimental design: AURKA siRNA vs control (non-targeted) siRNA. Total number of samples: two transfected samples and two control samples (Caco2 and SW480 CRC cell lines). Two biological replicates were performed for each sample.

first: Marianne

last: Tijssen

first: Anke

middle: H

last: Sillars-Hardebol

first: Linda

middle: J

last: Bosch

first: Annika

last: Jacobsen

first: Remond

last: Fijneman

first: Gerrit

middle: A

last: Meijer


title: Cestode Antigens Block LPS-induced Inflammatory Mediators and Condition Macrophages to Educate Anti-colitic T Cells

city: Calgary

first: Jose

middle: L

last: Reyes

state: Alberta

address: 3330 Hospital Dr. NW

department: Physiology and Pharmacology

country: Canada

institute: The University of Calgary

summary: We tested the ability of rat worm Hymenolepis diminuta parasite crude antigens (HdAg) to induce a regulatory-associated program in bone-marrow derived macrophages (BMMs). Also, we compared gene expression profile of BMMs exposed to HdAg with those exposed to IL-4 which elicits a well-known alternative program.

overall_design: Macrophages were grown from bone marrow precursors incubated with M-CSF for 7 days. Mature macrophages were exposed for 20 hr to IL-4 (ng/ml), H. diminuta antigens (100ug/ml) or H. diminuta antigens plus anti-IL-10 blocking antibody (5ug/ml) and mRNA collected. Next,10ng of mRNA from each group were hybridized overnight following manufacturer`s instructions and gene expression was compared to unstimulated macrophages.

first: Fernando

last: Lopes

first: Matthew

last: Workentine

first: Markus

last: Geuking

first: Derek

last: McKay


title: Gene expression analysis during time dependent Cry toxin exposure in Achaea janata larva.

status: Public on May 26 2018

city: Hyderabad

first: Aparna

middle: Dutta

last: Gupta

state: Telangana

address: S-41, Department of Animal Biology, School of Life Sciences, University of Hyderabad

department: Department of Animal Biology

country: India

institute: University of Hyderabad

summary: Bacillus thuringiensis Cry toxin is used for insect pest management. When susceptible insect larvae ingest the Bt toxin it shows various physiological and cellular changes. We have employed Agilent One Color matrix based microarray to check the mid-gut gene expression upon Cry toxin exposure in Achaea janata (Castor semilooper). Microarray analysis shows significant variation in gene expression upon Cry toxin exposure.

overall_design: Agilent Custom Castor semilooper Gene Expression 8X60K (AMADID: 84278) designed by Genotypic Technology Private Limited , Labeling kit: Agilent Quick-Amp labeling Kit (p/n5190-0442)

first: Narender

last: Dhania

first: Vinod

last: Chauhan

last: Chaitanya

last: Dutta-Gupta


title: Persistent ER stress in maize seedlings engages ZmIRE1 in a multiphasic process that transitions from prosurvival activities to cell death [ChIP-Seq]

city: Ames

first: Andrew

last: Severin

email: severin@iastate.edu, csiva@iastate.edu

state: IA

address: 2200 Osborn Drive

department: Office of Biotechnology

institute: Iowa State University

summary: GFP-tagged nuclear localized versions of Zmbzip60 & Zmbzip91 were overexpressed & pulled downed with GFP Ab to look for promoter binding elements

overall_design: Each sample was collected in three biological replicates

first: Renu

last: Srivastava

first: Zhaoxia

last: Li

first: Giulia

last: Russo

first: Jie

last: Tang

first: Ran

last: Bi

first: Usha

last: Muppirala

first: Sivanandan

last: Chudalayandi

first: Mingze

last: He

first: Sam

last: Vaitkevicius

first: Carolyn

last: Lawrence-Dill

first: Peng

last: Liu

first: Ann

last: Stapleton

first: Diane

last: Bassham

first: Federica

last: Brandizzi

first: Stephen

last: Howell


title: Genome-wide analysis of Vibrio cholerae cytolysin (VCC) in T84 monolayer cells

status: Public on May 25 2018

city: Umeå

first: Aziz

last: Bitar

address: Umeå University

country: Sweden

institute: Umeå University

summary: Non-toxic cocentrations of VCC induces upregulation of inflammatory genes in T84 monolayer cells

overall_design: Stimulation with VCC was done from the apical side of polarized tight monolayers of T84 cells by replacing the LB medium in the upper chamber with 0.5 mL challenge medium containing 160 ng/ml (VCC). Experimental control was done with challenge LB medium only. The challenge was done under aerobic condition and at 37°C for 5 hours. Total RNA was extracted from T84 polarized tight monolayers by using the Qiagen RNeasy Mini Kit according to the manufacturer's instructions and dissolved in RNase-free water containing Promega rRNasin ribonuclease inhibitor. Quality control was performed with Agilent 2100 Bioanalyser and NanoDrop.

first: Marie-Louise

last: Hammarström


title: Persistent ER stress in maize seedlings engages ZmIRE1 in a multiphasic process that transitions from prosurvival activities to cell death [RNA-Seq]

first: Andrew

last: Severin

summary: We tracked the gene expression events following treatment of maize seedlings with the endoplasmic reticulum (ER) stress agent tunicamycin. ER stress elicits the unfolded protein response (UPR) and when plants are faced with persistent stress, the UPR transitions from an adaptive or cell survival phase to programmed cell death.

overall_design: Each sample was collected in 3 biological replicates and two technical replicates.

first: Renu

last: Srivastava


title: miRNA expression profile in aortas from LysM-Cre/Dicerflox/flox/Apoe–/– mice compared with LysM-Cre/Dicerwt/wt/Apoe–/– mice fed with high-fat diet for 12 weeks

first: Andreas

last: Schober

summary: The global change of the miRNA expression profile during atherosclerosis is due to the infiltration of different types of leukocytes into the arterial vessel wall in addition to disease-specific regulation in vascular cells. Monocyte-derived macrophage accumulation in the subintimal region is critical in the formation of atherosclerotic plaques. However, the role of Dicer, the key enzyme for miRNA biogenesis, during the development of atherosclerosis is currently unknown. To detect the effect of Dicer on miRNA expression in lesional macrophages, the comparison of the miRNA expression profiles was performed in aortas from Apoe deficient mice with or without a myeloid cell-specific knockout of Dicer after 12-week high-fat diet (HFD) programme. This screening combined with functional study may help to identify the crucial miRNAs that play a role in the macrophage function during atherogenesis.

overall_design: LysM-Cre/Dicerflox/flox/Apoe–/– and LysM-Cre/Dicerwt/wt/Apoe–/– littermates (6–8 weeks) were fed a high-fat diet comprising 21% crude fat for 12 weeks. The aortas were harvested after in situ perfusion with RNAlater. Total RNA was isolated using mirVana microRNA Isolation Kit.

first: Yuanyuan

last: Wei


title: A map of the PGC-1α- and NT-PGC-1α-regulated transcriptional network in brown adipose tissue

first: Ji Suk

last: Chang

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

overall_design: Refer to individual Series


title: Comparative analysis of gene expression in tomato leaves during mild and severe potato spindle tuber viroid infection.

status: Public on May 29 2018

city: Warszawa

first: Aneta

last: Więsyk

address: Pawinskiego 5a

country: Poland

institute: Institute of Biochemistry and Biophysics, PAS

summary: We employed microarray analysis to observe dynamic changes of gene expression profiles in response to mild and severe potato spindle tuber (PSTVd) infection in the leaves of tomato cv ‘Rutgers’.

overall_design: Solanum lycopersicum cv 'Rutgers' was infected with mild (M) and severe (S23) PSTVd isolates. Leaf samples were collected at four phases of disease: i) symptomless – 8 days post inoculation (dpi); ii) early stage of symptoms -17 dpi; iii) full spectrum of symptoms – 24 dpi; iiii) recovery - 49 dpi. Three independent biological replicates of PSTVd-M, PSTVd-S23 and pUC9 (control) were analised at every time point but two replicates of PSTVd-M at 8dpi. Totally 35 samples of RNA were analysed.

first: Anna

last: Góra-Sochacka

last: Fogtman


title: Global expression of Sebacous Gland carcinoma [miRNA]

city: Whitechapel

first: John

last: Bladen

address: 4 Newark Street

department: Blizard Institute

institute: QMUL

summary:
Samples were taken from patients undergoing cancer excision for pagetoid (wide) sebaceous gland carcinoma (SGC) and different individuals undergoing excision for nodular (local) SGC.
Diifferent individuals who did not have cancer as Control samples, specifically their tarsal plate, were also taken.

overall_design:
Pagetoid SGC vs Nodular SGC vs normal eyelid control.

Nanostring technology carried out at UCL Genomics, UCL GOS Institute of Child Health, 30 Guilford Street, London WC1N 1EH

first: Jun

last: Wang

first: Ajanthah

last: Sangaralingam


title: miRNA expression profiles in Dicer WT and KO bone marrow-derived macrophages

city: Munich

address: Pettenkoferstr. 9

institute: Ludwig-Maximilians-University

summary: The global change of the miRNA expression profile during atherosclerosis is due to the infiltration of different types of leukocytes into the arterial vessel wall in addition to disease-specific regulation in vascular cells. Monocyte-derived macrophage accumulation in the subintimal region is critical in the formation of atherosclerotic plaques. However, the role of Dicer, the key enzyme for miRNA biogenesis, during the development of atherosclerosis is currently unknown. To detect the effect of Dicer on miRNA expression in macrophages, the comparison of the miRNA expression profiles was performed in bone marrow-derived macrophages (BMDMs) from LysM-Cre/Dicerflox/flox/Apoe–/– and LysM-Cre/Dicerwt/wt/Apoe–/– mice. This screening combined with miRNA profiling in atherosclerotic aortas may help to identify the crucial miRNAs that play a role in the macrophage function during atherogenesis.

overall_design: Bone marrow cells were harvested from femora of 6-8 week old male LysM-Cre/Dicerflox/flox/Apoe–/– or LysM-Cre/Dicerwt/wt/Apoe–/– mice (3 mice per group), re-suspended in DMEM-F12/10% FCS/10% L929-conditioned medium, and cultured for 7 days to differentiate into primary macrophages. Total RNA was isolated using mirVana microRNA Isolation Kit.


title: Intestinal necrotizing enterocolitis triggers hippocampal gene expression and neuronal differentiation in preterm neonates

city: Copenhagen

first: Xiaoyu

last: Pan

address: Dyrlægevej 68

country: Denmark

institute: University of Copenhagen

summary: Necrotizing enterocolitis (NEC) is an acute gut inflammatory disorder that mainly affects preterm neonates. A large proportion of NEC survivors develop neuronal deficits later in life, however the effect of early stages of NEC on the developing brain is unknown. Using preterm pigs as a NEC-sensitive animal model, we profiled the hippocampal gene expression in response to severe NEC lesions. The NEC-induced differentially expressed genes (DEGs) in the hippocampus segregated the piglets suffering from small intestinal NEC (Si-NEC) from those showing NEC lesions only in the colon (Co-NEC). Only when NEC lesions were observed in the small intestine, did piglets show reduced physical activity together with up-regulation of hippocampal genes related to inflammation and hypoxia, which was further verified by qPCR. Cluster analyses revealed key hippocampal NEC–related DEGs for Si-NEC (23 genes, including S100A8, PDK4, EDN1, IER3, Opalin, TXNIP) and Co-NEC (3 genes: GSTM3, TF, and S100A1). Both NEC phenotypes showed only two down-regulated DEGs (TMEM 167, HBB) and were devoid of any histological signs of microglia activation. Cerebrospinal fluid (CSF) from NEC-positive pigs contained elevated levels of several inflammatory proteins and in vitro exposure of immature hippocampal neurons to NEC-related CSF promoted neuritogenesis. Further in vitro experiments with neurite outgrowth indicated that VEGF, CINC-3, S100A9 and S100A8/S100A9 may play a role in NEC effects on hippocampal development. In conclusion, NEC lesions, especially when involving the small intestine, alter hippocampal gene expression with potential neuroinflammation and effects on neural circuit formation. Our results demonstrated that gut lesions affect the immature brain at early stages of disease progression. Thus, supportive care is important for preterm infants experienced with NEC to lessen possible later neurological dysfunctions.

overall_design: Examination of hippocampal transcriptome in NEC (n=5 and 6 for colon-NEC and small intestine-NEC, respectively) and healthy preterm neonates (n=5).

first: Jing

last: Sun

first: Line

last: Christiansen

first: Xiaolong

last: Yuan

first: Kerstin

last: Skovgaard

first: Yanqi

last: Li

first: Dereck

last: Chatterton

first: Sanne

middle: S

last: Kaalund

first: Fei

last: Gao

first: Per

middle: T

last: Sangild

first: Stanislava

last: Pankratova


title: Epigenetic signature of extended critical period learning

city: Chicago

first: Sarah

middle: E

last: London

state: IL

address: 940 E 57th Street

institute: University of Chicago

summary: We used a combination of ChIPseq, RNAseq, bioinformatic analysis, and molecular biology in the auditory forebrain, a brain area required for tutor song memorization to elucidate the role epigenetics plays in song learning. These  analyses revealed thousands of genes were differentially marked by PTMs under these two conditions, indicating greater transcription in the birds with extended learning.

overall_design: H3K4me3, H3K27me3, H3K9me3 and Pol II ChIP-seq was performed on p65 Tutor and Isolate and p32 Zebra Finch Songbird

first: S

first: T

last: Kelly


title: A map of the PGC-1α- and NT-PGC-1α-regulated transcriptional network in brown adipose tissue [SAGE]

first: Ji Suk

last: Chang

summary: Transcriptional coactivator PGC-1α and its splice variant NT-PGC-1α play crucial roles in regulating cold-induced thermogenesis in brown adipose tissue (BAT). PGC-1α and NT-PGC-1α are highly induced by cold in BAT and subsequently bind to and coactivate many different transcription factors to regulate expression of genes involved in mitochondrial biogenesis, fatty acid oxidation, respiration and thermogenesis. To identify the complete repertoire of PGC-1α and NT-PGC-1α target genes in BAT, we analyzed genome-wide DNA-binding and gene expression profiles. We find that PGC-1α-/NT-PGC-1α binding broadly associates with cold-mediated transcriptional activation. In addition to their known target genes in mitochondrial biogenesis, fatty acid oxidation, respiration and thermogenesis, PGC-1α and NT-PGC-1α target to a broad spectrum of genes involved in diverse biological pathways including ubiquitin-dependent protein catabolism, ribonucleoprotein complex biosynthesis, phospholipid biosynthesis, angiogenesis, glycogen metabolism, phosphorylation, and autophagy. Our findings expand the number of genes and biological pathways that may be regulated by PGC-1α and NT-PGC-1α and provide further insight into the transcriptional regulatory network in which PGC-1α and NT-PGC-1α coordinate a comprehensive transcriptional response in BAT in response to cold.

overall_design: Examination of brown adipose tissue mRNA profiles of mice housed at 28°C or exposed to 4°C for 6h

first: JiSuk

first: Sujoy

last: Ghosh

first: Susan

last: Newman

first: Michael

last: Salbaum


title: Unwavering Pathobiology of Volumetric Muscle Loss Injury

city: Lexington

first: Darrell

middle: Orlyn

last: Ricke

state: MA

address: 244 Wood Street

department: Group 48 Bioengineering Systems & Technology

institute: MIT Lincoln Laboratory

summary: Volumetric muscle loss (VML) resulting from extremity trauma presents chronic and persistent functional deficits which ultimately manifest disability. Acellular biological scaffolds, or decellularized extracellular matrices (ECMs), embody an ideal treatment platform due to their current clinical use for soft tissue repair, off-the-shelf availability, and zero autogenous donor tissue burden. ECMs have been reported to promote functional skeletal muscle tissue remodeling in small and large animal models of VML injury, and this conclusion was reached in a recent clinical trial that enrolled 13 patients. However, numerous other pre-clinical reports have not observed ECM-mediated skeletal muscle regeneration. The current study was designed to reconcile these discrepancies. The capacity of ECMs to orchestrate functional muscle tissue remodeling was interrogated in a porcine VML injury model using unbiased assessments of muscle tissue regeneration and functional recovery. Here, we show that VML injury incites an overwhelming inflammatory and fibrotic response that leads to expansive fibrous tissue deposition and chronic functional deficits, which ECM repair does not augment.

overall_design: RNA-Seq time couse of muscle volumetric muscle loss injury healing with controls

middle: O

first: Carlos

last: Aguilar


title: Next Generation Sequencing Facilitates Quantitative Analysis of H5N1 Wild Type and NS1-truncated Lung Transcriptomes in SPF chickens

city: Yangzhou

first: Shaohua

last: Shi

state: Jiangsu

address: 48 East Wenhui Road

department: College of Veterinary Medicine

institute: Yangzhou University

summary: H5N1 highly pathogenic avian influenza (HPAI) has raised global concern for causing huge economic losses in poultry industry. By using reversal genetic technical, we have rescued a H5 wild-type virus rS and its NS1-truncated virus S-NS99, harboring only 99 amino acids in the amino terminus of NS1. We then used a high-throughput RNA-seq method to analyze host and pathogen transcriptomes in the lungs of chickens infected with rS and S-NS99. Sequenced numbers of viral transcripts and expression levels of host immune-related genes at 1 day post infection (dpi) were higher in rS-infected than S-NS99-infected chickens. The numbers of immune response of rS-infected chickens by Gene Ontology (GO) enrichment were higher than S-NS99-infected chickens. KEGG pathway analysis revealed rS infection could provoke significantly stronger immune response than S-NS99. Collectively, our data provide new insight into the underlying mechanisms of the diﬀerential length NS1 of avian influenza viruses.

overall_design: Lung mRNA profiles of SPF chickens infected with NS-truncated H5N1 AIV and wild type were generated by deep sequencing using HiSeq 2500 Sequencing System.

first: Shi

last: Shaohua

first: Peng

last: Daxin


title: Copy number variation in ex vivo P. falciparum from High vs Low transmission areas in east Africa

first: Margaret

middle: Jane

last: Mackinnon

country: Australia

summary: The aim of this study was to describe gene copy number variation in Plasmodium falciparum parasites sourced from high vs. low malaria transmission settings in east Africa in order to test the hypothesis that malaria parasites are locally adapted to their environment.  In three separate experiments, parasites from ‘High’ vs. ‘Low’ transmission populations were taken from non-immune children and evaluated for copy number variants by microarray against a reference genome. Two of these population comparisons were geographic in nature while the third was temporal, i.e., before and after a marked decline in malaria. This study is described in Simam et al. 2018 BMC Genomics.

overall_design: 183 parasite isolates samples were analysed.  These derived from children below 13 years of age with three or fewer previous clinical episodes of malaria who were diagnosed with uncomplicated P. falciparum malaria at hospitals and dispensaries in western Kenya (2008, Kisumu), coastal Kenya (Kilifi, in 1994-1996 and in 2010-2012) and eastern Sudan (2007) which have long-term high, medium and low malaria transmission intensities, respectively.   DNA material was collected from each sample immediately ex vivo, i.e., without further replication cycles in in vitro culture.

first: Joan

last: Simam

first: Martin

last: Rono


title: Young, replicative and TNF-a-induced premature senescent of human microvascular endothelial cells-lung (HMVEC-L)

first: Pooi-Fong

last: Wong

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


title: Ago2-RIP-chip and miRNA expression profile in Dicer WT and KO macrophages from bone marrow or aorta

first: Andreas

last: Schober

type:
Expression profiling by RT-PCR
Other


title: miRNA signature of young, replicative and TNF-α-induced premature senescent of human microvascular endothelial cells-lung (HMVEC-L)

summary: Despite the fact that miRNAs have been extensively investigated for their involvement in diseases, senescence as well as inflammation, miRNAs involved in TNF-α- induced premature senescence remain to be uncovered. Hence, the present study aims to identify unique miRNAs and their respective signaling pathways in TNF-α-induced senescence in lung microvascular endothelial cells and novel targets for prevention or protection against premature senescence and endothelial hyperpermeability.  We have employed Agilent Human MicroRNAs microarray platform  to evaluate the expressions of 866 human miRNAs and 89 human viral miRNAs, based on Sanger miRNA database release 12.0.

overall_design: miRNA expression profiles were established for young, replicative and TNF-α-induced premature senescent of HMVEC-L.

first: Hui-Lan

last: Jong

first: Mohd

last: Mustafa

first: Sazaly

last: AbuBakar


title: Analysis of gene expression change between Ishikawa-02 SC and Ishikawa-02 shSOX2

status: Public on May 18 2018

city: Hsinchu

first: Ming-Han

last: Kuo

address: No. 101, Section 2, Kuang-Fu Road, Hsinchu, Taiwan 30013, R.O.C.

country: Taiwan

institute: National Tsing Hua University

summary: We collected total RNA from both Ishikawa-02 SC and Ishikawa-02 shSOX2 and examined mRNA expression profile, comprehensively.

overall_design:
Ishikawa-02 cells transduced with lentiviral particles encoding scramble control (SC) or shSOX2.
[contributor] Yu-Ting Chou's lab at National Tsing Hua University

first: Chang-Jung

last: Lee


title: Bioactive compound from marine sponge-derived Streptomyces sp. SBT348 inhibits staphylococcal growth and biofilm formation

status: Public on May 17 2018

city: Würzburg

first: Richa

last: Bharti

address: Josef-Schneider-Straße 2 / Bau D15

department: IMIB,Core Unit Systemmedizin

institute: University of Wuerzburg

summary: Staphylococcus epidermidis, the common inhabitant of human skin and mucosal surfaces has emerged as an important pathogen in patients receiving surgical implants and medical devices.  Entering the body via surgical sites and colonizing the medical devices through formation of multi-layered biofilms it leads to refractory and persistent device-related infections (DRIs). Staphylococcal proportions within biofilms are more tolerant to antibiotics and immune responses, and thus are hard-to-treat. The consequent morbidity and mortality, and economic losses in health care systems has strongly necessitated the need for development of new anti-bacterial and anti-biofilm based therapeutics. In this study, we describe the biological activity of a marine sponge-derived Streptomyces sp. SBT348 extract in restraining staphylococcal growth and biofilm formation on polystyrene, glass, medically relevant titan metal and silicone surfaces. A bio-assay guided fractionation was performed to isolate the active compound (C3) from the crude SBT348 extract. Our results demonstrated that C3 effectively inhibits the growth (MIC: 31.25 µg/ml) and biofilm formation (sub-MIC range: 1.95-<31.25 µg/ml) of S. epidermidis RP62A in vitro. Chemical characterization of C3 by heat and enzyme treatments, and High-Resolution Fourier Transform Mass Spectrometry (HRMS) revealed its heat-stable and non-proteinaceous nature, and high molecular weight (1258. 3257 Da).  Cytotoxicity profiling of C3 in vitro on mouse fibroblast (NIH/3T3) and macrophage (J774.1) cell lines, and in vivo on the greater wax moth larvae Galleria melonella revealed its non-toxic nature at the effective dose. Transcriptome analysis of C3 treated-S. epidermidis RP62A has further unmasked the negative effect of C3 on central metabolism (carbon, amino acid and protein, lipids, nucleotide and energy) suggesting its mode of action. Taken together, these findings suggest that C3 could be possibly used as antibacterial and antibiofilm coatings on medically-relevant surfaces and prevent the relapsing staphylococcal DRIs.

overall_design: Examination of transcriptome of S. epidermidis RP62A treated with the bioactive compound C3 (62.5 µg/ml) at 20 min and 3 h time point

first: Srikkanth

last: Balasubramanian

first: Tobias

last: Oelschlaeger


title: The early expansion of a defective NKG2Apos/CD56dim/CD16neg NK cell subset represents a therapeutic target in haploidentical HSCT

city: Rozzano, Milan

first: Emilia Maria Cristina

last: Mazza

address: Via Alessandro Manzoni, 56

institute: Humanitas Clinical and Research Center

summary: Natural Killer (NK) cells are the first lymphocyte population to reconstitute early after non myelo-ablative and T cell-replete haploidentical hematopoietic stem cell transplantations (h-HSCTs) with post-transplant infusion of cyclophosphamide. The present study characterizes the transient and predominant expansion starting from the 2nd week after h-HSCT of a donor-derived unconventional subset of CD56dim/CD16neg (uCD56dim) NK cells expressing remarkable high levels of NKG2A and low levels of NKp46. Both transcription and phenotypic profiles indicated that uCD56dim NK cells are a distinct NK cell subpopulation with features of late differentiation, yet retaining proliferative capability and functional plasticity to generate conventional CD56bright/CD16pos NK cells in response to IL-15 plus IL-18. uCD56dim NK cells represent by far the largest NK cell subset detectable in the following 7 weeks after h-HSCT and they also express high levels of the activating receptors NKGD and NKp30 as well as of the lytic granules Granzyme-B and Perforin. Nonetheless, uCD56dim NK cells displayed a defective cytotoxicity that could be reversed by blocking the inhibitory receptor CD94/NKG2A. These data open new important perspectives to better understand the ontogenesis/homeostasis of human NK cells and to develop a novel immune-therapeutic approach by targeting the inhibitory NKG2A check point, thus enhancing NK cell alloreactivity early after h-HSCT.

overall_design: FACS-sorted NK cell subsets from the peripheral blood of healthy donors and their h-HSCT recipients were seeded at 0.1 x 106 cells/ml and cultured in presence of 30 U/ml rhIL-15 (Miltenyi) and 100 ng/ml rhIL-18 (MBL International Corporation) for 14 days. NK cell proliferation was determined by the analysis of 5-(and 6)-carboxyfluorescein diacetate succinimidyl ester (CFSE; Life Technologies) dilution. Before stimulation, cells were stained with 2 M CFSE for 7 min at 37C and then washed in FBS and medium.

first: Alessandra

last: Roberto

first: Clara

last: Di Vito

first: Emilia

first: Silvio

last: Bicciato

first: Enrico

last: Lugli

first: Domenico

last: Mavilio


title: Transcriptome response to the Deepwater Horizon oil spill identifies novel candidate genes for oil tolerance in natural populations of the foundation plant Spartina alterniflora

status: Public on May 19 2018

city: Durham

first: Mariano

last: Alvarez

state: NC

address: 2916 Bivins Road

department: Biology

institute: Duke University

summary: Genome-wide expression assay of S. alterniflora individuals from populations (4 from Louisiana, 2 from Mississippi) either exposed or unexposed to the Deepwater Horizon oil spill

overall_design: 9 individuals at each populations were pooled randomly into 3 replicate RNA pools per population, then converted to cDNA and hybridized to a custom 1-color 4x44k Agilent microarray

first: Julie

last: Ferreira de Carvalho

first: Armel

last: Salmon

first: Malika

last: Ainouche

first: Armand

last: Cavé-Radet

first: Abdelhak

last: El Amrani

first: Tammy

last: Foster

first: Sydney

last: Moyer

first: Christina

last: Richards


title: Dissecting acid stress response in Rhizobium tropici CIAT 899

city: Cuernavaca

first: Luis

middle: Fernando

last: Lozano

state: Morelos

address: Av. Universidad 2001

country: Mexico

institute: Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México

summary: Rhizobium tropici CIAT899 is a nodule-forming α-proteobacterium displaying intrinsic resistance to several abiotic stress conditions such as low soil pH and high temperatures, which are common in tropical environments. It is a good competitor for Phaseolus vulgaris (common bean) nodule occupancy at low pH values, however little is known about the genetic or physiological basis of acid tolerance about gene expression under acidic conditions. To identify genes responding to pH stress we studied the transcriptomes of cells grown under different pH conditions. RNA was extracted from cells grown for several generations in minimal medium at 6.8 or 4.5 (adapted cells). In addition, we acid-shocked cells pre-grown at pH 6.8 for 45 minutes at pH 4.5. Transcriptomes were determined by RNA-Seq. From a total of 6289 protein-coding genes, 383 were found to be differentially expressed under acidic conditions versus control, among which 351 were induced and 32 repressed; only 11 genes were induced upon acid shock. The acid stress response of R. tropici CIAT899 is versatile: we found genes encoding response regulators and membrane transporters, but also enzymes involved in amino acid and carbohydrate metabolism and proton extrusion. Our findings enhance our understanding of the core genes that are important during the acid stress response in R. tropici.

overall_design:
Bacterial strains and culture conditions. Rhizobium tropici CIAT899 was routinely grown in TY medium (Beringer, 1974) or the minimal medium described by Kingsley and Bohlool (1992), adjusted to pH 6.8 (MM- buffered to pH 6.8 with 20 mM N-(2-Hydroxyethyl)piperazine-N′-(2-ethanesulfonic acid) Hepes)) or to pH 4.5 (MAM- buffered to pH 4.5 with 25 mM Homopiperazine-N,N’-bis-2[ethanesulfonic] acid [Homopipes]; Research organics, Cleveland, OH, U.S.A.) at 30° C. MM and MAM were solidified with 0.8% gelrite (Carl Roth GmbH, Karlsruhe, Germany). Antibiotics were added at the following final concentrations (µg/mL): kanamycin (Km) 50; carbenicillin (Cb) 100; tetracycline (Tc) 10 and nalidixic acid (Nal) 20, if not indicated otherwise.
RNA isolation. R. tropici CIAT899 was pre-grown in TY medium, then cultured in MM (control pH 6.8) (sample AR) or MAM (pH 4.5) (sample BR) until an OD60 of 0.6-0.7. For acid shock treatment cells were cultured in MM medium to mid-log phase, then washed with MAM and incubated another 45 minutes in MAM (pH 4.5) (sample CR). Cultures were harvested by centrifugation and the pellets were immediately frozen in liquid nitrogen. Total RNA was prepared using the RNeasy mini kit (QIAGEN, Hildesheim, Germany) with some modifications. Pellets were resuspended in RLT buffer, with lysozyme (20 mg per mL; QIAGEN, Hildesheim, Germany) containing Zirconium Oxide Beads (0.5 mm, Next Advance). Cells were disrupted using the Bullet Blender Tissue Homogenizer (Next-Advance) in impact-resistant 2 mL tubes. Genomic DNA was digested with RNase free DNase (QIAGEN, Hildesheim, Germany) for 20 minutes at room temperature. Final RNA concentrations were determined using a NanoDrop (Thermo Scientific). The typical OD260 to OD280 ratio of RNA samples was approximately 2.0. The integrity of RNA samples was verified using a TapeStation 2200 instrument (Agilent Technologies) and the RNA integrity number (RINe) was determined.
RNA-seq and data analysis. RNA-Seq libraries were prepared using the TruSeq RNA sample Prep kit (Illumina) and sequenced (150 nt per read) by HiSeq 2500 instrument (Illumina) at the Beijing Genomics Institute (BGI, China). For the analysis of RNA-Seq data, Bowtie2 was used to align raw reads to the R. tropici CIAT 899 genome (Genbank entry U00096.2) and samtools was used to obtain BAM files. Differentially expressed genes (DEGs) were obtained via NOISeq 2.14.1 Bioconductor package using local fit and betaPrior parameter set to False. NOISeq implements differential expression analysis based on the Negative Binomial distribution. A false discovery rate (FDR) threshold of 0.95 was set for DEG calling. Sample clustering and principal component analyses were performed upon variance stabilizing transformation of expression data (NOISeq package). Transcripts were called as differentially expressed when the FDR-Log2FC adjusted p values were below 0.05 and fold-changes over 2 (Tarasona et al., 2011, Tarasona et al., 2015).

first: Julio

last: Guerrero-Castro

first: Christian

last: Sohlenkamp


title: A capsular polysaccharide-specific antibody alters Streptococcus pneumoniae gene expression during nasopharyngeal colonization of mice

city: Bronx

first: Liise-anne

last: Pirofski

state: New York

address: 1300 Morris Park Ave

department: Medicine - Infectious Diseases

institute: Albert Einstein College of Medicine

summary: The effects of serotype 3-specific monoclonal antibodies on S. pneumoniae gene expression during nasopharyngeal colonization of mice were tested via RNA-seq.

overall_design: Mice were treated with mAbs 1E2, 7A9, 31B12, or PBS, and infected with ST3 S. pneumoniae 2 hours later.  Nasopharyngeal lavage fluid was collected 24 hrs post-infection to analyze bacterial gene expression by RNA-seq.

first: Christopher

last: Doyle

first: Jee-Young

last: Moon

first: Johanna

middle: P

last: Daily

first: Tao

last: Wang


title: Schwann cell precursor mRNA in normal culture conditions

status: Public on May 15 2018

city: Kamakura

first: Satoshi

last: Kondo

address: 10-1 tebiro 6-chome

institute: Toray Industries,Inc.

summary: Schwann cell precursor mRNA are carried out in RNAome analyses

overall_design: Schwann cell precursor mRNA are carried out in 3D gene microarray analyses

first: Yuki

last: Miyamoto

first: Junji

last: Yamauchi


title: Exon Level Expression Profiling: a Novel Unbiased Transcriptome

status: Public on May 14 2018

city: Nagoya

first: Mikako

last: Ito

address: 65 Tsurumai, Showa-ku

institute: Nagoya University Graduate School of Medicine

summary: Transcriptome analysis of RNA samples from Sfpq gene targeted mouse brains

overall_design: We analyzed mRNA expression in cerebral cortices from 3 control, 3 Sfpq+/- and 3 Sfpq-/- E13.5 mice embryos using the Affymetrix Mouse Exon 1.0 ST platform. Array data was processed by Affymetrix Exon Array Computational Tool. No techinical replicates were performed.

first: Akihide

last: Takeuchi

first: Kei

last: Iida

first: Kensuke

last: Ninomiya

first: Takaya

last: Abe

first: Hiroshi

last: Kiyonari

first: Kinji

last: Ohno

first: Masatoshi

last: Hagiwara


title: Transcriptome analysis for leaf morphology in Brassica rapa

city: Daejeon

first: Yoonkang

last: Hur

address: 99 Daehak-ro, Yuseong-gu

country: South Korea

institute: Chungnam National University

summary: Among Brassica rapa, rapid cycling Brassica rapa and Brassica rapa inbred line Kenshin showed contrasting leaf morphology. To identify genes associated with leaf morphology, four distinct F2 progeny of RcBr X Kenshin cross and their parents were selected. Leaf samples were collected from 6 materials, isolated total RNA, and subjected to newly developved 135K microarray. Experiments were performed with three or two biologic

overall_design: A total of 6 chips were used for the microarray experiment.   Experiments were performed with three or two biological replicates.


title: Effect of luxS gene mutation on Streptococcus pneumonaie biofilm gene expression

city: Seoul

first: Mukesh

middle: Kumar

last: Yadav

state: Seoul

department: Institute for Medical Device Clinical Trials

institute: Korea University

summary: Streptococcus pneumoniae is opportunistic bacteria cause’s acute otitis media (AOM) in children. It colonizes the nasopharynx in the form of biofilms, and these biofilms act as reservoir, and are vital for pneumococcal infections. The pneumococcal biofilms are regulated by LuxS/AI-2 media quorum sensing. In this study, we confirmed the role of LuxS/AI-2 for in vitro formation of biofilms, assessed the effects of the absence of LuxS/AI-2 signaling, for pneumococcal middle ear infection and identified global genes regulated by LuxS/AI-2 during formation of pneumococcal biofilms. In the cDNA-microarray analysis, 117 genes were differentially expressed in D39 luxS mutant when compared with D39 wild type. Among the 66 genes encoding putative proteins and previously characterized proteins, 60 were significantly down-regulated and 6 were significantly up-regulated. The functional annotation revealed that genes involve in DNA replication and repair, ATP synthesis, capsule biosynthesis, cell division and cell cycle, signal transduction, transcription regulation, competence, virulence, and carbohydrate metabolism were down-regulated in the absence of LuxS/AI-2.

overall_design: The in vitro biofilm formation ability of S. pneumoniae D39 wild type and an isogenic luxS strain were evaluated using a static microtiter plate assay as described previously. Briefly, the pneumococcal strains were grown on BAP overnight, and a single colony from the plate was transferred to BHI broth and grown to mid-exponential phase. These log-phase cells were diluted 1:200, and 1 mL of this cell suspension was seeded into 24-well polystyrene flat-bottom microtiter plates (BD Falcon, Sparks, MD, USA) and incubated at 37°C for various times. After incubation, the planktonic cells and medium were removed, and the biofilms remaining in the wells were washed twice with PBS. Global gene expression of S. pneumoniae D39 wild type and D39luxS biofilms was analyzed by cDNA-microarray. For the experiment, S. pneumoniae D39 wild type and D39luxS biofilms were grown in a 24-well plate for 18 h as described above. The biofilms were washed twice with PBS, scraped, and suspended in PBS. Then, the biofilm cells were pelleted by centrifugation and treated with 100 µL of lysozyme (3 mg/mL in TE; Sigma-Aldrich, St. Louis, MO, USA) for 4 min to lyse the cells. Total RNA was extracted using the RNeasy Total RNA Isolation System Kit (Qiagen, Valencia, CA, USA) according to the manufacturer’s instructions. Contaminating DNA was removed by on-column RNase-free DNase (Qiagen) treatment for 10 min at 20–25°C. The quantity and quality of total RNA was detected using a Nano-drop, and the integrity of RNA was assessed with a Bioanalyzer 2100 (Agilent, Palo Alto, CA, USA). RNA probe synthesis and hybridization were performed using the Agilent Low Input Quick Amp WT Labeling Kit according to the manufacturer’s protocol. Briefly, 200 ng of total biofilm RNA were mixed with WT primer mix, and the samples were incubated at 65°C for 10 min. Then, cDNA master mix was prepared with 5× first strand buffer, 0.1M DTT, 10mM dNTP mix, and RNase Block Mix (AffinityScript) and added to the RNA + WT primer reaction. The samples were incubated at 40°C for 2 h, and then RT and dsDNA synthesis were terminated by incubation at 70°C for 15 min. The transcription master mix was prepared according to the manufacturer’s protocol (5× Transcription buffer, 0.1M DTT, NTP mix, T7-RNA polymerase Blend, and Cyanine 5-CTP in nuclease-free water). Transcription of dsDNA was performed by adding transcription master mix to the dsDNA reaction samples and incubating the mix at 40°C for 2 h. Amplified and labeled cRNA was purified on an RNase mini column (Qiagen) according to the manufacturer’s protocol. The labeled cRNA target was quantified using an ND-1000 spectrophotometer (NanoDrop Technologies, Inc., Wilmington, DE, USA).   After checking the labeling efficiency of the cyanine 5-labeled cRNA target, the cRNA was fragmented by adding 10× blocking agent and 25× fragmentation buffer and incubating at 60°C for 30 min. The fragmented cRNA was resuspended in 2× hybridization buffer and directly pipetted onto an assembled S.pneumoniae_6x7k V2 Microarray (Mycroarray.com). The arrays were hybridized at 57°C for 17 h in an Agilent Hybridization oven. The hybridized microarrays were washed according to the manufacturer’s washing protocol (Agilent Technology). After an overnight incubation at 42°C, the slide was washed twice with washing solution 1 (containing 2× SSC, 0.1% SDS) for 5 min at 42°C, washed once with washing solution 2 (containing 0.1× SSC and 0.1% SDS) for 10 min at room temperature, and finally washed four times with 0.1× SSC for 1 min at room temperature. The slide was dried by centrifugation at 650 rpm for 5 min. The hybridization image on the slide was scanned with a 4000B apparatus (Axon Instruments, Union City, CA, USA).  The hybridization image was analyzed with GenePix Pro 3.0 software (Axon Instruments, Union City, CA, USA) to obtain the gene expression ratios in D39 wild type and D39luxS biofilms. The microarray data were analyzed with Genowiz 4.0TM (Ocimum Biosolutions, Hyderabad, India), and normalized with Global LOWESS. The cutoffs for up-regulated and down-regulated genes were +2-fold and -2-fold, respectively. The microarray experiment was performed with three biological replicates. Statistical significance was calculated by Student’s t-test, and P value less than 0.05 was considered significant. STRING version 10.5 (https://string-db.org) was used for the functional annotation, and the UniProtKB database(http://www.uniprot.org/uniprot/P0A4M0) was used to search for clusters of biological processes in the gene ontology database within the two sets of differentially expressed genes (D39luxS mutant and D39 wild type). Microarray data has been deposited in NCBI's Gene Expression Omnibus (GEO) database (http://www.ncbi.nlm.nih.gov/geo/info/linking.html) and are accessible through GEO Series accession number.

first: Jae-Jun

last: Song


title: Tissue-specific orchestration of nutrient dependent responses in D. melanogaster

status: Public on May 20 2018

city: Novato

first: Pankaj

last: Kapahi

state: CA

address: 8001 Redwood Blvd

institute: Buck Institute for Research on Aging

summary:
Dietary restriction (DR) is a robust intervention to slow aging, but how individual tissues respond to DR is largely unknown. We developed a translating ribosome affinity purification method in Drosophila (Fly-TRAP) and investigated mRNA translational profiles of seven primary tissues upon DR.
Here we demonstrate that DR alters the mRNA translation expression of proteins genes involved in tissue structural integrity, metabolism, and signal communication in a tissue-specific and coordinated manner. DR enhances the expression of mitochondrial genes in some tissues but decreases in others. Genes involved in mRNA translation were increased specifically in the gut and fat body. A key finding from the study was that DR upregulates several neuroendocrine factors and their corresponding receptors in specific peripheral tissues. Additionally, several a list of secreted factors was in non-neuronal tissues were increased upon changed in response to DR, some of which affected longevity. These results suggest that DR enhances tissue-tissue communication to leading to a longer lifespan and improved tissue homeostasis.

overall_design: 82 experimental samples were analyzed using Nimblegen oligo microarrays. Cy3 single color array were used for both AL and DR samples.

first: Guiping

last: Du

first: Patrick

middle: W

last: Li

first: Kazutaka

last: Akagi

first: Christopher

last: Nelson

first: Subhash

middle: D

last: Katewa

first: Robi

last: Tacutu

first: Artem

last: Zykovich

first: Simon

last: Melov

first: Sean

last: Mooney

first: João

last: de Magalhães

first: Rachel

middle: B

last: Brem


title: Unilateral mastication induced alternations of microRNAs expression profiling in synovium of rat temporomandibular joint

status: Public on May 16 2018

city: Hangzhou

first: YU

last: ZHAO

address: Yuhangtang Road 388#

institute: College of Pharmeceutical Sciences

summary: The present study investigated the alterations of miRNA expression profiling in synovium of temporomandibular joint(TMJ) in a rat model of experimental unilateral mastication. The synovium tissue of TMJ condyles from rats with 4- and 8-weeks unilateral mastication were harvested to extract miRNA for profiling holistic expression alternations. A total of 20 differentially expressed miRNAs were identified. Except for 3 miRNAs with uncertain function, those miRNAs are associated with cell proliferation, invasion, and osteoblast differentiation process.

overall_design: The miRNA expression profiling of synovial tissue in in bilateral condyles of rats with experimental tooth loss for 4- and 8-weeks was compared to that from sham-operated control. (n=4)

first: Mengjie

last: Wu

first: Yiqun

last: Zhou


title: Comparison of oligodendrocyte miRNAs in normal and differentiated conditions in culture

first: Satoshi

last: Kondo

summary: Oligodendrocyte miRNAs in normal and differentiated conditions are compared.

overall_design: Oligodendrocyte miRNAs in normal and differentiated conditions are isolated and compared.

first: Yuki

last: Miyamoto

first: Junji

last: Yamauchi


title: Cis-regulatory divergence of eloF drives reproductive isolation in Drosophila

city: Stanford

first: Peter

middle: Acuña

last: Combs

address: Gilbert Rm 309, 371 Serra Mall

institute: Stanford University

summary: The differential production of pheromones is a major barrier to mating between species in Drosophila. Individuals from morphologically similar sister species can produce different sets of cuticular hydrocarbons that allow potential mates to identify them as a suitable partner. In order to elucidate cis-regulatory mechanisms behind speciation, we looked for allele-specific expression in hydrocarbon-producing oenocytes from F1 hybrids of the sister species D. simulans and D. sechellia. By focusing on cis-regulatory changes specific to female oenocytes, we rapidly identified a small number of candidate genes. Oour RNA-seq approach proved to be far more efficient than QTL mapping in identifying candidate genes, and it can be used to pinpoint the genetic basis for a wide range of traits differing due to cis-regulatory divergence between any interfertile species.

sample_organism: Drosophila sechellia x Drosophila simulans

overall_design: mRNA profiles of male and female oenocytes and fat bodies were generated from F1 hybrid D. sechellia x D. simulans flies, by deep sequencing, in duplicate, using Illumina HiSeq 2000

first: Joshua

last: Krupp

first: Neil

last: Khosla

first: Dmitri

last: Petrov

first: Joel

last: Levine

first: Hunter

last: Fraser


title: Y79 Rb Cell line: CD133 positive vs CD133 negative cancer stem like cells

city: Basel

first: Ravi Kiran Reddy

last: KALATHUR

state: Basel

address: Mattenstrasse 28

department: Departement Biomedizin

country: Switzerland

institute: University of Basel

summary: Gene expression and pathway analysis of sorted CD133 negative and CD133 positive population

overall_design: Two color experiment (CD133 negative population (Cy5) Vs CD133 positive population (Cy3)

first: Murali

middle: M

last: Balla

first: Imran

last: Khan

first: Ravi

last: Kiran

first: Reddy

last: Kalathur

first: Geeta

middle: K

last: Vemuganti

first: P

last: Kondiah


title: Ezh2 is essential for activation-induced CD8+ T cell cycle progression via repressing Cdkn1a and Cdkn2c expression

status: Public on May 11 2018

city: Baltimore

first: Minoru

last: Ko

state: MD

address: 251 Bayview Blvd, Suite 100, 10C

department: National Institute on Aging

institute: NIH

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

overall_design: Refer to individual Series


title: miRNA expression signatures of acne inversa (AI) patients with NCSTN mutations and healthy individuals

city: Nanjing

first: Yanyan

last: He

address: Jiangwangmiao Street

department: Institute of Dermatology

country: China

institute: hinese Academy of Medical Sciences and Peking Union Medical College

summary: To elucidate the relationship between NCSTN mutations and familial AI pathogenesis by investigating differential miRNA expression, we have employed miRNA microarray profiling as a discovery platform to identify miRNA with the potential to be involved in familial AI pathogenesis. Skin biopsies were obtained from the lesions of AI patients with NCSTN mutations . Control skin tissues were obtained from healthy individuals undergoing cosmetic surgery procedures

overall_design: Two groups, AI patients with NCSTN mutations vs. healthy individuals. Each group contains 5 samples.


title: Transcriptomic analyses of gastrointestinal function in the “dwarf” and “medium” forms of Sthenoteuthis oualaniensis during sexual maturation

city: Guangzhou

first: Lulu

last: Yan

state: Guangdong

address: No. 231 Xingang West Road

institute: South China Sea Fisheries Research Institute, CAFS

summary: Sthenoteuthis oualaniensis (SA) is an important squid species in the South China Sea. Based on SA samples collected in 2016, SA was divided into the “dwarf” form (DF) and “medium” form (MF). To understand the changes in gastrointestinal function in SA during sexual maturation, we undertook transcriptomic analyses of the stomach and intestine tissues of the DF and MF of SA using the deep-sequencing platform Illumina HiSeq™. We exploited a high-throughput method to delineate differentially expressed genes (DEGs) in the DF and MF of SA. A total of 135,464 unigenes (68627 unigenes of the DG and 66837 unigenes of the MF) were generated. We identified 7965 and 4051 relative DEGs in the intestine and stomach tissue of the mature DF of SA compared with those of the immature DF of SA; and 22138 and 18460 DEGs in the intestine and stomach of the mature MF of SA compared with those of the immature MF of SA. Functional categorization and pathway analyses of these DEGs with regard to the metabolism of differentially expressed genes were noted. This work is the first to identify a set of genes associated with gastrointestinal function during the sexual maturation of SA.

overall_design: Intestinal and stomach tissues were sampled from three mature dwarf form (DF) SAs, three immature DF SAs, three mature medium form (MF) SAs, and three immature MF SAs, respectively.

first: Chao

last: Zhao

first: Jun

last: Zhang

first: Lihua

last: Qiu

first: Zuozhi

last: Chen


title: Transposon-associated epigenetic silencing during Pleurotus ostreatus life cycle

city: Pamplona

first: Raul

last: Castanera

address: Campus Arrosadia, DPTO Producción Agraria

country: Spain

institute: Public University of Navarre

type: Methylation profiling by high throughput sequencing

type: Non-coding RNA profiling by high throughput sequencing

summary: In this study, we analyzed the genome-wide epigenetic and transcriptional patterns of the white-rot basidiomycete Pleurotus ostreatus throughout its life cycle. Our results performed by using high-throughput sequencing analyses revealed that strain-specific DNA methylation profiles are primarily involved in the repression of transposon activity, and suggest that 21 nt small RNAs play a key role in transposon silencing.Furthermore, we provide evidence that transposon-associated DNA methylation, but not sRNA production, is directly involved in the silencing of genes surrounded by transposons. Finally, we identified key genes activated in the fruiting process through the comparative analysis of transcriptomes.

overall_design: Examination of mRNA-seq, smallRNAseq and Bisulfite-seq in six samples of Pleurotus ostreatus, using three biological replicates

first: Alessandra

last: Borgognone

first: Raúl

first: Marco

last: Morselli

first: Leticia

last: López-Varas

first: Liudmilla

last: Rubbi

first: Antonio

middle: G

last: Pisabarro

first: Matteo

last: Pellegrini

first: Lucía

last: Ramírez


title: Molecular characterization of pyrethroid resistance in the olive fruit fly Bactrocera oleae

status: Public on May 12 2018

city: Gent

first: Nicky

last: Wybouw

address: Coupure Links 653

department: Department of Crop Protection

country: Belgium

institute: University of Ghent

summary:
Α reduction of pyrethroid efficacy has been recently recorded in the olive fruit fly Bactrocera oleae, the most destructive insect pest of olives worldwide.
We analyzed the transcriptomic differences between two highly pyrethroid resistant populations versus a relatively susceptible field population and two laboratory strains to gain more insight into the molecular mechanism of resistance.
A large number of genes was found to be significantly differentially transcribed across the pairwise comparisons between resistant and susceptible insect populations. Interestingly, gene set analysis revealed that genes of the ‘electron carrier activity’ GO group were  enriched in one specific pairwise transcriptomic comparison. As P450 monooxygenase enzymes are typically associated with this Molecular Function GO-group, this might reflect a P450-mediated resistance mechanism.
These results suggest that transcriptional induction of the CYP6 P450s might be an important mechanism of pyrethroid resistance in B. oleae and pave the way for the development of synergists and molecular diagnostics for insecticide resistance management.

overall_design: Four biological replicates from the B. olaea population LAB, AN12, AN14, and FOK14 (each consisting of 10 pooled one-to-three days old females) were collected. In total, three major comparisons were performed; AN12 vs HYB, AN14 vs LAB, and AN14 vs FOK14.

first: Nena

last: Pavlidi

first: Anastasia

last: Kampouraki

first: Vasilis

last: Tseliou

first: Wannes

last: Dermauw

first: Emmanouil

last: Roditakis

first: Ralf

last: Nauen

first: Thomas

last: van Leeuwen

first: John

last: Vontas


title: Expression data from WT (Pparafl/fl) mice and hepatocyte-specific PPARα disruption (Ppara△Hep) mice liver tissue at 12 hours after PHx or Sham operation

status: Public on May 10 2018

city: Beijing

first: Guomin

last: Xie

address: fengtai youanmen

institute: University

summary:
PPARα act as the master of lipid metabolism in liver, however, the changes of its target genes after PHx and the effects of PPARα on regenerative genes were unknown. At 12 to 24 hours after PHx, the mice develope marked steatosis, therefore the time point of 12 hour after PHx was choosen to perform microarray analysis.
We used microarray to detail the gene expression of WT (Pparafl/fl) mice and hepatocyte-specific PPARα disruption (Ppara△Hep)  mice liver tissue at 12 hour after PHx or Sham operation

overall_design: The time points of 12 hour after PHx or Sham operation were choosed  for RNA extraction and hybridization on Affymetrix microarrays. The mice were devided into four groups: 1. Pparafl/fl mice at 12 hours after Sham operation, 2.Pparafl/fl mice at 12 hours after PHx operation, 3. Ppara△Hep mice at 12 hours after Sham operation,  3. Ppara△Hep mice at 12 hours after PHx operation.

first: Aijuan

last: Qu


title: Ezh2 is essential for activation-induced CD8+ T cell cycle progression via repressing Cdkn1a and Cdkn2c expression (Part I)

first: Minoru

last: Ko

summary: Transition from resting to cell cycle in response to antigenic stimulation is an essential step for naïve CD8+ T cells to differentiate to effector and memory cells. Leaving the resting state requires dramatic changes of chromatin status in the key cell cycle inhibitors but the details of these concerted events are not fully elucidated. Here, we showed that Ehz2, an enzymatic component of polycomb repressive complex 2 (PRC2) catalyzing the trimethylation of lysine 27 on histone 3 (H3K27me3), regulates activation induced naïve CD8+ T cells proliferation and apoptosis. When Ezh2 was deleted during thymocyte development (Ezh2fl/flCD4Cre+ mice), naive CD8+ T cells displayed impaired proliferation and increased apoptosis in response to antigen stimulation. However, naive CD8+ T cells only had impaired proliferation but no increased apoptosis when Ezh2 was deleted after activation (Ezh2fl/flGzmBCre+ mice), suggesting cell cycle and apoptosis are temporally separable events controlled by Ezh2. We then showed that deletion of Ezh2 resulted in the increased expression of cyclin-dependent kinase inhibitors Cdkn2a (p16 and Arf) and Cdkn1c (p57) in activated naïve CD8+ T cells as the consequence of reduced levels of H3K27me3 in these two gene loci. Finally, with real time imaging, we observed prolonged cell division times of naïve CD8+ T cells in the absence of Ezh2 post in vitro stimulation. Together, these findings reveal that repression of Cdkn2a and Cdkn1c by Ezh2 plays an essential role in permission of activation-induced CD8+ T cell proliferation.

overall_design: Ezh2 regulates H3K27me3 ofCdkn1candCdkn2alocus.To understand how early the changes in expression of cell cycle related-genes happens in the absence of Ezh2, we included four additional early time points (2, 4, 6, and 8 hours after stimulation) during the course of 72 hours after anti-CD3/CD28 stimulation. Ezh2 mRNA levels were increased at 8 hours, peaked around 48-72 hours after stimulation (Fig. 5A). We then compared expressions of 12 cell-cycle regulators and found thatCdkn1c(p57) was dramatically increased at 2 hours and peaked at 4 hours (>2 folds higher in Ezh2 deficient CD8+T cells than in WT CD8+T cells) after stimulation (Figure 5A). ForCdkn2family, expression ofCdkn2aV1 (Arf)andCdkn2aV2 (p16), key regulators for apoptosis and cell cycle, respectively, were increased in Ezh2 deficient naïve CD8+T cells compared to WT naïve CD8+T cells from 8 to 72 hours after stimulation

first: Guobing

last: Chen

first: Nan-ping

last: Weng


title: Ezh2 is essential for activation-induced CD8+ T cell cycle progression via repressing Cdkn1a and Cdkn2c expression (Part II)

overall_design: To understand how Ezh2, an enzymatic component of polycomb repressive complex 2 (PRC2) catalyzing the trimethylation of lysine 27 on histone 3 (H3K27me3), regulates activation induced naïve CD8+ T cells proliferation and apoptosis. We used Ezh2fl/flCD4Cre+ mice to analyze naive CD8+ T cells proliferation and function during immune response. We analyzed cell cycle progression, apoptosis,  global gene expression, and histone H3K27me3 in specific cell cycle regulators in naive CD8 T cells .


title: OsPRR37 confers an expanded regulation of the diurnal rhythms of the transcriptome and photoperiodic flowering pathways in rice

city: Wuhan

first: Chuan

last: Liu

state: Hubei

address: Luojiashan

department: College of Life Sciences

institute: Wuhan University

summary: The circadian clock enables organisms to rapidly adapt to the ever-changing environmental conditions that are caused by daily light/dark cycles. Circadian clock genes universally affect key agricultural traits, particularly flowering time. Here, we show that OsPRR37, a circadian clock gene, delays rice flowering time in an expression level-dependent manner. Using high-throughput mRNA sequencing on an OsPRR37 overexpressing transgenic line (OsPRR37-OE5) and the recipient parent Guangluai4 that contains the loss-of-function Osprr37, we identify 14,992 genes that display diurnal rhythms, which account for 52.9% of the transcriptome. Overexpressing OsPRR37 weakens the transcriptomic rhythms and alters the phases of rhythmic genes. In total, 3,210 differentially expressed genes (DEGs) are identified, among which 1,863 rhythmic DEGs show a correlation between the change of absolute amplitudes and the mean expression levels. We further reveal that OsPRR37 functions as a transcriptional repressor to repress the expression levels and amplitudes of day-phased clock genes. More importantly, OsPRR37 confers expanded regulation on the evening-phased rhythmic DEGs by repressing the morning-phased rhythmic DEGs. Further study shows that OsPRR37 expands its regulation on flowering pathways by repressing Ehd1. Thus, our results demonstrate an expanded regulation mechanism of the circadian clock on the diurnal rhythms of the transcriptome.

overall_design: Totally 36 samples were analyzed by using Illumina HiSeq2500, in which 18 for GL and 18 for OsPRR37-OE5. The precise sampling times were set as 4:00, 8:00, 12:00, 16:00, 20:00, and 0:00 over a single day with three biological repeats for each time point.

first: Daichang

last: Yang


title: miRNA expression signatures of the skin tissue of NcstnΔKC mice and normal mice

first: Yanyan

last: He

summary: We constructed keratinocyte-specific Ncstn-knockout mice to investigate the role of NCSTN in the pathogenesis of human AI.

overall_design: Two groups, NcstnΔKC mice vs. normal mice. Each group contains 4 samples.


title: Epigenomics of Phaseolus vulgaris

city: Athens

first: Robert

middle: J

last: Schmitz

state: GA

address: B416 Davison Life Sciences

department: Genetics

institute: University of Georgia

summary: Cytosine methylation is a base modification that is often used by genomes to store information that is stably inherited through mitotic cell divisions. Most cytosine DNA methylation is stable throughout different cell types or by exposure to different environmental conditions in plant genomes. Here, we profile the epigenomes of ~100 Phaseolus vulgaris lines to explore the extent of natural epigenomic variation. We also use these data to determine the extent to which DNA methylation variants are linked to genetic variations.

overall_design: 92 MethylC-seq, 100 RNA-seq  and 100 smallRNA-seq for Phaseolus vulgaris

first: Scott

middle: A

last: Jackson


title: Gene expression profiling from Al treatment in rice root tips

first: Gezi

last: Li

address: #866,Yuhangtang Road

institute: Zhejiang University

summary:
The root tip of rice before or after Al stress have been used. And some gense were regulated in this stress.
We used microarrays to detail the  global programme of gene expression underlying Al stress and identified distinct classes of up-regulated genes during this process.

overall_design: Root tips were selected for RNA extraction and hybridization on Affymetrix microarrays. We sought to obtain homogeneous populations of root in order to increase the temporal resolution of expression profiles. To that end, we labled different treatments, i.e. before Al treatment (Control, three repeat were C1, C2, and C3, respectively), after 6 h Al treatment (Treatment,three repeat were T1, T2, and T3, reapectively).

first: Wei

last: Fan


title: Establishment and characterization of prostate cancer organoids [array]

city: Bethesda

first: Adam

middle: G.

last: Sowalsky

address: 37 Convent Drive Building 37 Room 1062B

department: Genitourinary Malignancies Branch

institute: National Cancer Institute

summary:
Prostate cancer translational research has been hampered by the lack of comprehensive and tractable models that represent the genomic landscape of clinical disease.
Metastatic castrate-resistant prostate cancer (mCRPC) patient derived xenografts (PDXs) recapitulate the genetic and phenotypic diversity of the disease.
We sought to establish a representative, preclinical platform of PDX-derived organoids that is experimentally facile for high throughput and mechanistic analysis.

overall_design:
To investigate the effects of organoid establishment on clonal selection and drift, we assessed somatic copy number alteration in DNA derived from PDX and multiple generations of organoid from the same individual.

The raw data is being submitted to dbGaP study phs001587 due to patient privacy concerns.

NIH grant(s):
ZIA BC011782 Mechanisms of Pathogenesis in Patient Derived Organoid Models of Prostate Cancer NATIONAL CANCER INSTITUTE KATHLEEN SIEBENLIST
ZIA BC011679 Mechanisms Driving Evolution of Aggressive Prostate Cancer NATIONAL CANCER INSTITUTE ADAM SOWALSKY

first: Michael

middle: L

last: Beshiri

first: Eva

last: Corey

first: Kathleen

last: Kelly


title: Presence of aggregates of smooth endoplasmic reticulum in MII oocytes affects oocyte development competence: a molecular-based evidence

city: Genova

first: Sara

last: Stigliani

address: largo R Benzi 10

country: Italy

institute: IRCCS AOU San Martino-IST

summary: The oocytes presenting SERa are considered dysmorphic and have been associated with reduced embryological outcome and an increased risk of congenital anomalies. Therefore, in 2011 the Alpha/ESHRE Consensus strongly recommended not to inseminate MII oocytes displaying SERa (SERa+). Not all Centers follow this recommendation and some Authors reported that SERa+ can lead to healthy newborns. Moreover, no experimental data about the effect of SERa presence on the oocyte molecular status are available. To date the question whether or not SERa+ oocytes should be discarded as well as the opportunity to review or not the ESHRE consensus are still open for debate.   This study included 28 women, < 38 years aged, without any ovarian pathology, undergoing IVF treatment. Supernumerary MII oocytes with no sign of morphological alterations and SERa+ oocytes were donated after written informed consent. A total of 31 oocytes without SERa (SERa-) and 24 SERa+ oocytes were analyzed. Pools of ≈10 oocytes for both group were prepared. Total RNA was extracted from each pool, amplified, labelled and hybridized on oligonucleotide microarrays. Analyses were performed by R software using the limma package. The expression profiles of SERa+ oocytes significantly differed from those of SERa- oocytes in 488 probe sets corresponding to 102 down-regulated and 283 up-regulated unique transcripts. Gene Ontology analysis by DAVID bioinformatics resource disclosed that three main biological processes were significantly down-regulated in SERa+ oocytes respect to SERa- oocytes: i) genes involved in cell and mitotic nuclear division, spindle assembly, chromosome partition and G2/M transition of mitotic cell cycle; ii) organization of cytoskeleton and microtubules; iii) mitochondrial structure and activity. Among the transcripts up-regulated in SERa+ oocytes, the most significantly (P= 0.002) enriched GO term was “GoLoco motif” including RAP1GAP, GPSM3, and GPSM1 genes.  Data validation in a larger cohort of samples would be beneficial, although we applied stringent criteria for gene selection (fold-change >3 or <1/3 and FDR<0.1). Surveys on clinical outcomes, malformation rates, and follow-up of babies born after transfer of embryos from SERa+ oocytes are necessary. For the first time we provide information on molecular status of SERa+ oocytes, highlighting possible correlations among presence of SERa, altered oocyte physiology and reduced developmental competence. Based on our findings, we believe that it is far too early for an eventual revision of the 2011 Alpha/ESHRE Consensus on the issue and presence of SERa should be still a “red flag” in clinical IVF practices.

overall_design: This study included 28 women undergoing IVF treatment, < 38 years aged, without any ovarian pathology. Surplus MII oocytes were donated after written informed consent. A total of 31 normal oocytes and 24 oocytes with SERa were analyzed.

first: Paola

last: Scaruffi

first: Stefano

last: Moretti


title: Transcriptomic Analysis of Arabidopsis plants treated with Histone Deacetylase inhibitors, Ky-9 and Ky-72

status: Public on May 09 2018

city: Lubbock

first: chien

middle: Van

last: ha

state: TX

address: 1006 Carton Avenue, Box 43135

department: IGCAST

country: USA

institute: texas tech university

summary: To analyze the molecular function of HDAC inhibitors in salt stress responses in Arabidopsis, we conducted microarray analysis using 4-day-old plants, which were treated with 1 μM Ky-9 or Ky-72 or water for 24 h, and then treated with or without 100 mM NaCl for 2 h

overall_design: Microarray analysis was conducted using HDAC inhibitors-treated and non-treated plants subjected to non-stress and salt-stress condition for 2 h.

first: Huong

last: Nguyen

first: Kaori

last: Sako

first: Akihiro

last: Matsui

first: Minoru

last: Ueda

first: Maho

last: Tanaka

last: Ito

first: Norikazu

last: Nishino

last: Yoshida

first: Motoaki

last: Seki


title: AMPKα2 knockout mice and usage of alternative transcription start sites

city: Pullman

first: Zhihua

last: Jiang

state: WA

address: Veterinary and Biomedical Research Building, Room 151

department: Animal Science

institute: Washington State University

summary: Role of alternative transcription start sites in muscle growth and development remains largely undetermined.  Our WTSS-seq (whole transcriptome start site sequencing) approach to capture 5'-end of RNAs clearly revealed alternative transcription start  events responsible for  increased muscle mass in AMPK α2 knockout mice.

overall_design: Total RNA samples obtained from muscle tissue of knockout (KO) and wild-type (WT) mice were used to construct WTSS-seq libraries. Four WTSS-seq libraries, including two AMPK α2 KO mice and two AMPK α2 WT mice were involved in this submission.

first: Xiang

last: Zhou

first: Shuwen

last: Zhang

first: Jennifer

last: Michal

first: Yangzi

first: Min

last: Du


title: Fire ant alate virgin and de-alate mated queen brain transcriptomes

city: College Station

first: Cecilia

last: Tamborindeguy

address: Heep Center

institute: Texas A&M University

summary: Transcriptomes of dissected brains from  alate virgin and de-alate mated queens from polygyne fire ants were analyzed and compared. Four replicates of each condition were obtained. Thirteen genes were upregulated in mated queen brain and nine were downregulated.  We found that for four differentially expressed genes in brain selected for qPCR analyses, changes in gene expression were most likely driven by the changes in physiological state (i.e. age, nutritional status or dominance rank) or in social environment (released from influence of primer pheromone).

overall_design: Fire ant brain mRNA profiles of de-alate mated and alate virgin queens were generated by deep sequencing of four replicates per condition, using Illumina.

first: Travis

last: Caulkins

first: Meir-Er

last: Chen

first: Arinder

last: Arora

first: Chloe

last: Hawkings

first: Patricia

middle: V

last: Pietrantonio


title: Expression data of mRNA from wild-type A549 cells and microRNA-203 knockout A549 cells during H5N1 infections

first: Sen

address: East Street of Fengtai

institute: State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology

summary: MicroRNA-203 was up-regulated markedly upon H5N1 virus infection. To identify the potential target genes of miR-203, we constructed a miR-203 knockout A549 cell line. Then wild-type and miR-203 knockout A549 cells were mock-infected or infected with H5N1 virus for 48h. The Agilent Whole Human Genome Oligo Microarray was performed to analyze the mRNA expression profiling. Meanwhile, the online tool TargetScanHuman (http://www.targetscan.org/vert_71/) was used to predict biological targets of miR-203. We combined the predicted genes with the genes differentially expressed in wild-type and miR-203 knockout A549 cells, and preliminarily identified some candidate mRNAs. Then more experiments were performed to further verify these target genes, such as dual-luciferase reporter assay, quantitative real-time PCR or Western blot analysis.

overall_design: Wild-type A549 cells and microRNA-203 knockout A549 cells were un-infected, mock-infected or infected with H5N1 virus for 48h to measure the gene expression.

first: Yi

last: Hu


title: Expression of genes in THP-1 macrophages in response to C. glabrata wt, Cgvps34Δ and Cgyps(1-11)Δ cells.

city: Bangalore

first: Genotypic

last: technology

state: Karnataka

address: 259, Apoorva 4th cross,80 feet Road,RMV 2ND STAGE

institute: Genotypic Technology

summary: To understand the host response of C. glabrata, we have employed the whole genome microarray expression profiling  to identify the differentially regulated genes. For this, differentiated THP-1 cells were infected with C. glabrata wt, Cgvps34Δ and Cgyps(1-11)Δ cells for 6 h. Uninfected THP-1 cells, treated with PBS were taken as control. Total RNA was extracted using TriZol Reagent followed by ethonol precipitation. The experiments were performed in biological duplicate.

overall_design: Organism : Homo sapiens, Agilent's Human Gene Expression  8x60k Array (AMADID: 039494), Experiments were done in biological duplicates.

first: Rupinder

last: Kaur

first: Vandana

last: Sharma

first: Mubashshir

last: Rasheed


title: Shoot responses to different nitrate supply to roots in wild-type and genotypes affected for cytokinin biosynthesis and transport

city: Montpellier

first: Sandrine

last: Ruffel

address: 2 Place Viala

department: Montpellier University

country: France

institute: INRA

summary:
Plants face temporal and spatial variation in nitrogen (N) availability. This includes heterogeneity in soil nitrate (NO3-) content. To face these constraints, plants modify their gene expression and physiological processes to optimize N acquisition. This plasticity relies on a complex long-distance root-shoot-root signaling network that remains poorly understood. We previously showed that cytokinin (CK) biosynthesis is required to trigger systemic N signaling. Here, we performed split-root experiments and used a combination of CK-related mutant analyses, hormone profiling, transcriptomic analysis, NO3- uptake assays, and root growth measurements to gain insight into systemic N signaling in Arabidopsis thaliana. By comparing wild-type plants and mutants affected in CK biosynthesis and ABCG14-dependent root-to-shoot translocation of CK, we revealed an important role for active trans-Zeatin (tZ) in systemic N signaling. Both rapid sentinel gene regulation and long-term functional acclimation to heterogeneous NO3- supply, including NO3- transport and root growth regulation, are likely mediated by the integration of tZ content in shoots. Furthermore, shoot transcriptome profiling revealed that glutamate/glutamine metabolism is likely a target of tZ root-to-shoot translocation, prompting an interesting hypothesis regarding shoot-to-root communication. Finally, this study highlights tZ-independent pathways regulating gene expression in shoots as well as NO3- uptake activity in response to total N-deprivation.
We used microarrays to detail transcriptional reprogramming occurring in shoots in response to heterogeneous nitrate supply compared to homogeneous nitrate supply in wild-type Arabidopsis thaliana plants and in two mutants affected in cytokinin biosynthesis and transport.

overall_design: Plants were grown in homogeneous medium containing sufficient nitrogen and the root system was divided in two parts (around day 14 after germination). The plants were transferred in split-root plates (around Day 18) containing 1mM KNO3 on both sides of the plates (C.KNO3) or in heterogeneous media containing 1mM KNO3 on one side and 1mM KCl on the other side (Split). Plants (Col-0, ipt3,5,7 and abcg14) were collected 24hours after the beginning of the treatment. This experiment has been replicated 4 times (4 independent experiments) and in each experiment three plants have been pooled in one sample.

first: Arthur

last: Poitout


title: Expression profilings of fission yeast strains (NETSEQ data set)

status: Public on May 08 2018

first: Shiv

last: Grewal

address: NCI bldg 37 Rm 6068 9000 Rockville Pike

department: LBMB

institute: NCI

summary: Native elongation transcript sequencing in wild-type and clr4∆ grown at 18°C.

first: Pamela

middle: S

last: Gallagher

first: David

last: Wheeler

first: Gobi

last: Thillainadesan

first: Jothy

last: Dhakshnamoorthy

first: Vanivilasini

last: Balachandran

first: Christopher

last: Wellman

middle: I


title: An intermittent caloric restriction / medium fat diet protects liver from the progression of non-alcoholic fatty liver disease in C57BL/6J mice

city: Wageningen

first: Guido

last: Hooiveld

address: HELIX, Stippeneng 4

department: Div. Human Nutrition & Health

country: Netherlands

institute: Wageningen University

summary:
Background & Aims: In this study, we investigated metabolic and molecular effects of weekly intervening 30% calorie restriction on long term natural progression of non-alcoholic fatty liver disease (NAFLD), which was induced by a medium fat diet.
Methods: Male C57BL/6J mice of 9 weeks old received either (1) a control (C), (2) a calorie restricted (CR), (3) a medium fat (MF; 25%fat) or (4) an intermittent diet (ID), a weekly alternating diet consisting of calorie restriction and medium fat diet ad libitum until sacrifice at the age of 12 months. Various metabolic and molecular features of the liver were examined.
Results: The ID regimen improved the status of a range of metabolic parameters and showed no progression to NAFLD: proper glucose tolerance, low hepatic triglyceride content, low plasma alanine aminotransferase and no abnormalities in its liver morphological features; similarly to that of CR. In contrast, the metabolic parameters in a number of the C and MF animals indicated development of NAFLD and hepatic fibrosis, which was positively correlated with body weight. Despite the metabolic phenotypes similarity, the liver gene expression profile of ID-fed mice did not reflect that of CR mice and resembled more to C and MF-fed mice with similar low body weight.
Conclusions: Our study reveals that ID is beneficial for metabolic health and prevents the development of NAFLD in mice, with a gene expression profile similar to C and MF diet in a body weight-dependent manner.

overall_design: Male C57BL/6J mice were divided to 4 dietary intervention groups: Control (AIN-93W), 30% calorie restriction (CR; AIN-93W-CR), medium fat (MF; AIN-93W-MF; 25% energy from fat) and intermittent diet (ID; weekly alternating diet between AIN-93W-MF ad lib and 40% CR of AIN-93W). We treated the mice with either solvent (mock treatment) or PPARa agonist, Wy-14,643 (Wy treatment), 6 hours prior to sacrifice. The mock- and Wy-treatment were applied to body weight-matched mice within each diet group. We performed various measurements on metabolic parameters and gene expression analysis. We made a selection of animals for the microarray analysis: from each diet group we took 4 animals with lowest and highest body weight, both the mock- and Wy-treated animals.

first: Fenni

last: Rusli

first: Arantza

last: Zubia

first: Carolien

last: Lute

first: Mark

last: Boekschoten

first: Michael

last: Müller

first: Wilma

last: Steegenga


title: Identification of PPARG regulated genes in human GM-CSF-primed monocyte-derived macrophages

city: Madrid

first: Amaya

last: Puig

state: Madrid

address: Dr. Esquerdo 46

department: Immunology

institute: Hospital Gregorio Marañón

summary: Identification of PPARG regulated genes in human GM-CSF polarized monocyte-derived macrophages by siRNA knock-down approaches.

overall_design: Human peripheral blood monocytes from three independent healthy donors (1, 2 and 3) were isolated by anti-CD14-labeled magnetic microbeads. CD14+ monocytes were cultured for 7 days in RPMI 10% FCS containing GM-CSF (M1). After 7 days, M1 cells were transfected with 50 nM siRNA for PPARG (siPPARG) or siRNA with a scramble sequence (siControl) from Ambion, for 48 hours.Total RNA from each condition was extracted and purified using the RNA isolation kit (Macheray-Nagel). Labelled RNA was used as hybridization probes on human Agilent-072363 SurePrint G3 Human Gene Expression v3 8x60K (G4851C). All experimental procedures were performed following manufacturer instructions. Microarrays were scanned on an Agilent G2539A scanner. Scanned images and raw data were pre-processed with GeneSpring GX (Agilent).

first: Angel

last: Corbí

first: Concha

last: Nieto Mazarrón

last: Puig-Kröger


title: Variation of mRNA and lncRNA expression after using AMD3100 in rat chronic allograft nephropathy model.

first: Hao

last: Tang

address: Capital Medical University Beijing Chaoyang Hospital

department: Department of Urology

institute: Institute of Urology, Capital Medical University.

summary: To investigate the variation of mRNA and lncRNA expression after using AMD3100 in rat chronic allograft nephropathy model (CAN) model, we have employed mRNA and lncRNA microarray expression profiling as a discovery platform to identify genes with the potential. CAN rat models were established using male Fisher 344 to Lewis rats. Rats in the experimental group(n=3) were treated with AMD3100 (1 mg/kg/day subcutaneously, 0–12 weeks), rats in the control group(n=3) were treated with saline. The kidney grafts were harvested 12 weeks after modeling for microarray analysis.

overall_design: AMD3100 induced gene expression in kidneys of rat CAN model was measured at 12 weeks after kidney transplantation.

first: Yue

last: Xu