title: Lack of allergy to timothy grass pollen is not a passive phenomenon but associated with allergen specific modulation of immune reactivity

city: La Jolla

first: Alessandro

last: Sette

address: 9420 Athena Circle

institute: La Jolla Institute for Allergy and Immunology

summary: Timothy grass (TG) pollen is a common seasonal airborne allergen associated with symptoms ranging from mild rhinitis to severe asthma. The aim of this study was to characterize changes in TG-specific T cell responses as a function of seasonality. Peripheral blood mononuclear cells (PBMC) obtained either during the pollen season or out of season, from allergic individuals and non-allergic controls were stimulated either with TG extract or a pool of previously identified immunodominant antigenic regions. PBMC from in season allergic subjects exhibit higher IL-5 and IL-10 responses compared to out of season donors. In the case of non-allergic subjects, as expected we observed lower IL-5 responses and robust production of IFNγ compared to allergic individuals. Strikingly, non-atopic donors exhibited an opposing pattern with decreased immune reactivity in-season. The broad downregulation in non-allergic donors indicates that healthy individuals are not oblivious to allergen exposure but rather react with an active modulation of the responses following the antigenic stimulus provided during the pollen season. Transcriptomic analysis of allergen-specific T cells defined genes modulated in concomitance with allergen exposure and inhibition of responses in non-allergic donors. Magnitude and functionality of T-helper cell responses differ substantially for in season versus out of season in allergic and non-allergic subjects. The results indicate specific and opposing modulation of immune responses following the antigenic stimulation during the pollen season. This seasonal modulation reflects the enactment of specific molecular programs associated with health and allergic disease.

overall_design: 11 allergen-specific T cell RNA samples were analyzed: 5 isolated from PBMC of allergic individuals and 6 from non-allergic individuals (considered as the control group).

first: Denise

last: Hintz

first: Gregory

last: Seumois

first: Amin

last: Gholami

first: Jason

middle: A

last: Greenbaum

first: Jerome

last: Lane

first: Brandie

last: White

first: Bjoern

last: Peters

first: Pandurangan

last: Vijayanand


title: Dicer knockout induced altered miRNA profile

status: Public on Jan 06 2017

city: Suzhou

first: Jianming

last: Li

address: 199 Renai Road

country: China

institute: Soochow University

summary: We detected whole genome microarray expression profiling in three pairs of Dicer knockout coloretal cell lines and their normal controls, including DLD-1, RKO and HCT116.

overall_design: Dicer knockout cell lines were indicated as DLD-1-D, RKO-D and HCT116-D, and their corresponding normal cell lines were referred to DLD-1-C, RKO-C, and HCT116-C.

first: Yao

last: Liu


title: Characterization of gene expression profiles of gastric cancer

status: Public on Dec 31 2016

city: Houston

first: Sangbae

last: Kim

state: TX

address: 1 Baylor plaza

department: HGSC

country: USA

institute: Baylor Colleage of Medicine

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

overall_design: Refer to individual Series


title: Neisseria meningitidis strain MC58 and α522 grown in PPM+ and exposed to human saliva, human whole blood and human cerebrospinal fluid

city: Wuerzburg

first: Biju Joseph

last: Ampattu

address: Josef-Schneider Str 2

department: Department of Microbiology

country: Germany

institute: University of Wuerzburg

summary: Differences in the transcriptional profile of the menigococcal strains MC58 and α710 were compared upon growth in PPM+ and on exposure to human saliva, whole blood and cerebrospinal fluid

overall_design: Common reference design, MC58 and α522 grown in PPM+ and exposed to human saliva, whole blood and cerebrospinal fluid. Aliquots from the individual samples made the common reference pool. Three replicates per array.

first: Biju

last: Joseph

first: Laura

last: Kischkies

first: Matthias

last: Frosh

first: Chrisoph

last: Schoen


title: Response of cauline buds to apical auxin and basal cytokinin treatment

status: Public on Dec 25 2016

city: Cambridge

first: Ottoline

last: Leyser

address: Bateman Street

country: United Kingdom

institute: Sainsbury Laboratory Cambridge University

summary: Identification of genes regulated by apical auxin and basal cytokinin treatment of the nodal stem in cauline buds of Arabidopsis thaliana

overall_design: Three biological replicates each of mock (ethanol control), apical auxin alone and apical auxin plus basal cytokinin

first: Dörte

last: Müller


title: Characterization of gene expression profiles of gastric cancer in Kosin University cohort

summary: Clinical heterogeneity of gastric cancer reflected in unequal outcome of treatment is poorly defined in molecular level, and molecular subtypes and their associated biomarkers have not been established to improve prognostification and treatment of gastric cancer. Using microarray technologies, we analyzed gene expression profiling data from gastric cancer patients and uncovered potential prognostic subtypes and identify gene expression signature associated with prognosis and response to adjuvant chemotherapy.

overall_design: Primary gastric adenocarcinoma  were used for microarray. All the tissues were obtained after curative resection after pathologic confirm Kosin University College of Medicine (Busan, Korea). Microarray experiment and data analysis were done at Department of Systems Biology, MDACC with DNA microarray (Illumina human V3).

first: Ju-Seog

last: Lee

first: Sang-Cheol

last: Oh


title: Seabuckthorn carpenter moth (Eogystia hippophaecolus) Transcriptome or Gene expression

status: Public on Dec 22 2016

city: Beijing

first: Mingming

last: Cui

state: Beijing

address: No. 35 Tsinghua East Road

department: College of Forestry

institute: Beijing Forestry University

type: Expression profiling by high throughput sequencing

summary: By comparing transcriptome profiles for differential gene expression, genes and pathways probably involved in insect cold hardinesswere identified. This dataset provides a global transcriptome data and differential transcriptome comparisons in E. hippophaecolus under cold stress. This may facilitate future genomic studies aimed at improving our understanding of the molecular mechanisms underlying the response of insects to low temperatures.

overall_design: T01 & T02 represent control groups without treatment; T04, T05 & T06 are low temperature treatment groups; T01 & T04 are young larvae; T02 & T05 are middle-aged larvae; T06 is old larvae.

first: Ming

middle: M

first: Shi

middle: X

last: Zong


title: Characterization of gene expression profiles of gastric cancer in the Korea University cohort

overall_design: Primary gastric adenocarcinoma and Surrounding normal fresh frozen tissues were used for microarray. All the tissues were obtained after curative resection after pathologic confirm at Korea University Guro Hospital. Microarray experiment and data analysis were done at Department of Systems Biology, MDACC with DNA microarray (Illumina human V3).


title: 809094 Biomarker Identification in Fracture Healing (experiment #3244 performed 2010 Feb)

status: Public on Jan 05 2017

city: Philadelphia

first: Annamarie

middle: D

last: Horan

state: PA

address: 3737 Market Street, 6th Floor

department: Orthopaedic Surgery

institute: University of Pennsylvania

summary:
The specific genes that distinguish normal fracture healing from abnormal healing or nonunion in humans are unknown.  This study was an exploratory investigation of peripheral blood from 2 acutely injured fracture patients collected over multiple days compared to age and sex matched healthy volunteers.
We used microarrays to do a global comparison between acutely injured (AI) subjects (AIS) vs age and sex matched healthy volunteers (HV).

overall_design: AIS were enrolled into the study upon presentation for fracture care.  Blood was collected into Paxgene blood RNA tubes daily during the inpatient stay.  HV were enrolled in parallel with a one-time blood sample colleciton into Paxgene blood RNA tubes. RNA was extracted from all samples applicable to this experiment.  We explored the data with Partek Genomics suite using all samples at all time points to identify a panel of genes that is differentially expressed across the two groups to enable additional biomaker vetting.

first: Samir

last: Mehta


title: Beta-blocker reverses hypoxia-inducible gene expression

city: Cleveland

first: Hoi I

last: Cheong

address: 9500 Euclid Ave

institute: Cleveland Clinic

summary: To understand the transcripts/ pathways that are impacted by beta-blocker under hypoxia

overall_design: Human endothelial cells are treated with 100uM propranolol (PRO) or diluent alone, and exposed to 2% oxygen (O2) for 24 hours. Normoxic cells served as controls.

first: Hoi

middle: I

first: Serpil

last: Erzurum

first: Bo

last: Hu


city: evry

first: Soubigou-Taconnat

last: Ludivine

address: 2 rue gaston crémieux

department: URGV

country: France

institute: INRA

summary: rs14-01_mitomanip2 - microarray experiment 4 - Mitochondrial transcriptome regulation and coordination with the nucleus - Following a previously established strategy (Val et al., 2011, Nucleic Acids Res. 39, 9262–9274), we express, from an estradiol-inducible nuclear transgene, a trans-cleaving ribozyme directed against the nad9 mitochondrial mRNA and associated as a trailor sequence to a tRNA mimic. The latter serves as a shuttle and ensures mitochondrial uptake of the chimeric RNA through the natural tRNA import pathway. In mitochondria, the ribozyme triggers cleavage and degradation of the target mRNA. The impact of the nad9 mRNA knockdown on the overall plant transcriptome is analyzed over 4 successive days. Control plants express the shuttle RNA combined with a ribozyme that has no specific target in A. thaliana.

overall_design: 10 dye-swap - time course

first: Sandrine

last: Balzergue

first: Ludivine

last: Taconnat

first: André

last: Dietrich

first: Marie-Laure

last: Martin-Magniette


title: Gene expression in limited cutaneous SSc skin

status: Public on Jan 01 2017

city: Lebanon

first: Tammara

last: Wood

state: NH

address: WTRB 674

department: Biomedical Data Science

institute: Dartmouth Medical School

summary: Systemic sclerosis (SSc) is an autoimmune disease characterized by clinical heterogeneity, multi-organ involvement, and complex genetic risk. Here, we report the first multi-tissue meta-analysis of ten independent SSc gene expression datasets. We identify a common immune-fibrotic expression axis across all tissues that is associated with the most severe disease phenotypes. The coexpression patterns conserved across tissues and phenotypes were used to query functional genomic networks, which allowed us to identify common and tissue-specific disease drivers. We find evidence of pro-fibrotic macrophages (MØs) in SSc end-target organs. Prominent genes in the skin functional genomic network are associated with SSc genetic risk and are modulated by immunosuppressive treatment in clinical improvers. These data suggest the interactions between T lymphocytes and MØs are a critical driver of disease and implicate MØs as central to SSc pathogenesis. In total, this study presents a mechanism for fibrosis in SSc end-target tissues, a set of putative therapeutic targets for modulating SSc, and a framework for multi-tissue functional genomic studies of complex human disease.

overall_design: Gene expression was measured in forearm skin punch biopsies in 10 limited cutaneous systemic sclerosis patients and 5 healthy controls

first: Michael

middle: L

last: Whitfield

first: Christopher

middle: P

last: Denton


title: Response of Streptococcus mutans wild type and lrgAB-deficient strains to environemntal stressors encountered in the oral cavity

status: Public on Dec 20 2016

city: Gainesville

first: SANG-JOON

last: AHN

state: Florida

address: 1395 Center Drive

institute: University of Florida

summary: We assesed the transcriptional response of wild-type and isogenic lrgAB mutant to growth in the presence of three different stress conditions (aerobiosis, high-temperature, and the cell-wall active antibiotic vancomycin) by using RNA-seq

overall_design: Examination of mRNA levels at the mid-exponential phase of growth, in triplicates

first: Sang-Joon

last: Ahn

first: Kelly

middle: C

last: Rice


title: Ubiquitination of the spliceosome auxiliary factor hnRNPA1 by TRAF6 links chronic innate immune signaling with hematopoietic defects and myelodysplasia

city: Columbia

first: Jing

last: Fang

state: SC

address: 715 Sumter Street

department: Drug Discovery and Biomedical Sciences

institute: University of South Carolina

summary: Toll-like receptors (TLR) activation contributes to premalignant hematologic conditions, such as myelodysplastic syndromes (MDS). TRAF6, a TLR effector with ubiquitin (Ub) ligase activity, is overexpressed in MDS hematopoietic stem/progenitor cells (HSPCs). We found that TRAF6 overexpression in mouse HSPC results in impaired hematopoiesis and bone marrow failure. Using a global Ub screen, we identified hnRNPA1, an RNA-binding protein and auxiliary splicing factor, as a substrate of TRAF6. TRAF6 ubiquitination of hnRNPA1 regulated alternative splicing of Arhgap1, which resulted in activation of the GTP-binding Rho family protein Cdc42 and accounted for hematopoietic defects in TRAF6-expressing HSPCs. These results implicate Ub signaling in coordinating RNA processing by TLR pathways during an immune response and in premalignant hematologic diseases, such as MDS.

overall_design: Lineage negative and Sca-1 and c-Kit copositive cells (LSK) that are enriched in hematopoietic stem and progenitor cells (HSPC) were isolated from three TRAF6 transgenic mice (03, 04, 05) and four control littermates (21, 22, 23, 24). RNA was reverse transcribed and labeled, and hybridized onto the GeneChip® Mouse Exon 1.0 ST Arrays. A total of 7 samples were included, and two groups are assigned based on genotype. Comparison comprises mRNA expression profile of TRAF6 transgenic group v.s. wild type group. Exon usage patterns are determined by FIRMA Index with AltAnalyze software.

first: Lyndsey

last: Bolanos

first: Kwangmin

last: Choi

first: Xiaona

last: Liu

first: Susanne

last: Christie

first: Shailaja

last: Akunuru

first: Rupali

last: Kumar

first: Dehua

last: Wang

first: Xiaoting

last: Chen

first: Kenneth

last: Greis

first: Peter

last: Stoilov

first: Marie-Dominique

last: Filippi

first: Jaroslaw

last: Maciejewski

first: Guillermo

last: Garcia-Manero

first: Matthew

middle: T

last: Weirauch

first: Nathan

last: Salamonis

first: Hartmut

last: Geiger

first: Yi

last: Zheng

first: Daniel

last: Starczynowski


title: Comparative transcriptome analysis on alteration of gene expression in ayu (Plecoglossus altivelis) larvae associated with salinity change

city: Ningbo

first: Zhang

last: Hao

address: Fenghua Road No. 818

institute: NINGBO UNIVERSITY

summary: Ayu (Plecoglossus altivelis), an amphidromous fish distributed in East Asia, live in brackish water (BW) during the larval stage and in fresh water (FW) during the adult stage. In this study, we found that ayu larvae of FW acclimation exhibited a slower growth ratio compared with BW acclimation. However, the mechanism underlying FW acclimation on growth suppression is less known. We employed  transcriptome analysis to investigate the differential gene expression of FW acclimation by RNA sequencing. We identified 158 up-regulated and 139 down-regulated transcripts in FW acclimated ayu larvae compared with BW acclimated ones. As determined by Gene Ontology annotation and Kyoto Encyclopedia of Genes and Genomes pathway mapping, functional annotation of the genes covered diverse biological functions and processes. They were involved in in neuroendocrinology, osmotic regulation, energy metabolism, and the cytoskeleton. Transcriptional expression of several differentially expressed genes in response to FW acclimation was further confirmed by real-time quantitative PCR. In accordance with the transcriptome analysis, iodothyronine deiodinase (ID), pro-opiomelanocortin (POMC), betaine--homocysteine S-methyltransferase 1 (BHMT), fructose-bisphosphate aldolase B (aldolase B), tyrosine aminotransferase (TAT), and Na+-K+ ATPase (NKA) were up-regulated after FW acclimation. Furthermore, the mRNA expressions of b-type natriuretic peptide (BNP) and transgelin were down-regulated after FW acclimation. In conclusion, our data indicate that FW acclimation reduces the growth rate of ayu larvae, which may result from the expression alteration of genes related to endocrine hormones, energy metabolism, and direct osmoregulation.

overall_design: Ayu larvae were kept in BW or FW tanks at 20–22 °C in a recirculating system with filtered water after hatching, and fed with commercial pellets once a day. Groups of 20 fish each were subjected to BW (containing 0.17 M NaCl, 10 ppt) in four tanks (BW group) or to FW in the other four tanks (FW group).

first: Xinjiang

last: Lu

first: Jiong


title: Expression data from colon cancer specimens

first: yanyang

last: zhao

address: No. 1 DAHUA Road

institute: The Key Laboratory of Geriatrics, National Institute of Geriatrics, Beijing Hospital, Ministry of Health

summary:
Metastases are responsible for more than 90% of cancer deaths. microRNAs are critical regulators during the metastatic process.
We used microarrays to identify the microRNAs which are implicated in metastasis.

overall_design: Colon cancer and surrounding control tissue specimens were for RNA extraction and hybridization on Affymetrix microarrays.

first: Yanyang

last: Zhao

first: Gang

last: Miao


title: Transcriptome sequence analysis of Phormium tenax under drought stress

status: Public on Dec 17 2016

city: Chengdu

first: Zhenyu

last: Bai

address: 211 Huimin Road, Wenjiang District

institute: Sichuan Agricultural University

summary: To clarify the molecular mechanism of drought resistance in Phormium tenax, transcriptome was sequenced by the Illumina sequencing technology under normal and dry conditions, respectively.  In total, 4,063,419 high quality sequencing contigs, 175,649 transcripts and 75,265 unigenes were obtained in this study. A total of 4,380 genes were differentially expressed, 2,698 of which were finally annotated under drought stress. Differentially expression analysis was also performed upon drought treatment.

overall_design: Transcriptome of two kinds of plant leaves which were treated under normal and drought conditions was sequenced by the Illumina sequencing technology


title: Gene expression profiles of fractionated cells from cirrhotic rat livers

status: Public on Dec 16 2016

city: Dallas

first: Yujin

last: Hoshida

address: 5323 Harry Hines Blvd

institute: University of Texas Southwestern Medical Center

summary: Gene expression profiling was performed in each of hepatocyte fraction and non-parenchymal cell fraction enriched with activated hepatic stellate cells/myofibroblasts from cirrhotic rat livers induced by repeated, low-dose diethylnitrosamine (DEN) treatment.

overall_design: Male Wistar rats received weekly IP injections of diethylnitrosamine (DEN) at 50 mg/kg or vehicle control (PBS) for 18 weeks. Rats were weighed at the end of each week. Animals were sacrificed at 19 weeks after a one-week washout period to eliminate acute effects of DEN. Liver was perfused and hepatocyte and non-parenchymal cell (enriched with hepatic stellate cells) fractions were separated by gradient-based method. Isolated cell fractions were stored at -80°C until RNA extraction. Animals received humane care according to the criteria outlined in the Guide for the Care and Use of Laboratory Animals of the National Academy of Sciences. All animals were maintained in accordance with the institutional guidelines of the Massachusetts General Hospital Subcommittee on Research Animal Care.

first: Bryan

last: Fuchs


title: Selective reactivation of human X-linked genes in female fibroblasts reprogrammed by cell fusion

status: Public on Dec 07 2016

city: London

first: Gopuraja

last: Dharmalingam

address: Faculty of Medicine, Imperial College, Hammersmith Hospital Campus

department: Epigenetics section

institute: MRC London Institute of Medical Sciences

summary: In female mammals, one of the two X chromosomes is silenced as pluripotent cells differentiate. This process, termed X-inactivation, is random and results in mosaic expression of many X-linked genes in female tissues. Although X-inactivation can be reversed in vitro by reprogramming, the extent varies according to species, operator and conditions. Here, we have reprogrammed cloned female human fibroblasts by fusing them with mouse ESCs and examined the kinetics of X-linked gene re-expression. Allele-specific RNA sequencing analysis was used to determine the expression from the inactive X chromosome. This study revealed that a subset of loci within domains prone to escape X-inactivation, or that showed variable expression between somatic clones, were consistently reactivated upon pluripotent reprogramming. This suggests that stochastic events may be stabilised by reprogramming, and conversely, that variable expression is predictive for Xi genes susceptible to re-activation.

sample_organism: Homo sapiens x Mus musculus hybrid cell line

overall_design: We performed RNA-sequencing of two human fibroblast clones derived from TERT-immortalised NHDF17914 (Lonza) and expressing reciprocal X chromosomes  (i.e. clone 12 and 34) before and at 0, 4 and 6 days  after fusion with mouse ESC (E14Tg2a:puroR). Two biological replicates were sequenced for each clone.

first: Irene

last: Cantone


title: Genomic instability during reprogramming by nuclear transfer is DNA replication dependent

city: Morristown

middle: R

last: Treff

state: NJ

address: 111 Madison Ave

department: Molecular Biology

institute: RMA of NJ

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

summary: Somatic cells can be reprogrammed to a pluripotent state by nuclear transfer into oocytes, yet developmental  arrest often occurs. While incomplete transcriptional reprogramming is known to cause developmental failure, reprogramming also involves concurrent changes in gene expression, cell cycle progression and nuclear structure. Here we study cellular reprogramming events in human and mouse nuclear transfer (NT) embryos prior to embryonic genome activation. We show that genetic instability marked by frequent chromosome segregation errors and DNA damage arise prior to, and independent of, transcriptional activity. These errors occur following transition through DNA replication and are repaired by BRCA1. In the absence of mitotic nuclear remodeling, DNA replication is delayed and errors are exacerbated in subsequent mitosis. These results demonstrate that independent of gene expression, cell type-specific features of cell cycle progression constitute a barrier sufficient to prevent the transition from one cell type to another during reprogramming.

overall_design: 16 Samples

first: Gloryn

last: Chia

first: Judith

last: Agudo

first: Mark

middle: V

last: Sauer

first: David

last: Billing

first: Brian

last: Brown

first: Richard

last: Baer

first: Dieter

last: Egli


title: Replication maps of developing C. elegans embryos.

status: Public on Dec 15 2016

city: New York

first: Iestyn

last: Whitehouse

state: New York

address: 1275 York Avenue

institute: Sloan-Kettering Institute

summary: Okazaki fragments were purified and sequenced from C. elegans embryos at various stages of development. The sequencing data was used to map the positions and efficiencies of replication origins.

overall_design: To map the positions of replication origins in C. elegans embryos.

first: Ehsan

last: Pourkarimi


title: RNA-Seq in PWS iPSC-derived neurons

status: Public on Dec 12 2016

first: Lisa

middle: Cole

last: Burnett

state: NY

address: 1150 St Nicholas Avenue

department: Pediatrics, Molecular Genetics

institute: Columbia University

summary: Transcriptional analysis of PWS iPSC-derived neurons compared to unaffected controls

overall_design: 9 unaffected control lines, 2 PWS microdeletion lines, 2 PWS large deletion lines

first: Rudolph

last: Leibel


title: Whole genome-wide transcript profiling to identify differentially expressed genes associated with seed field emergence in two soybean low phytate mutants

status: Public on Dec 05 2016

city: hangzhou

first: fengjie

last: yuan

state: Zhejiang

address: shiqiao road 198

institute: Zhejiang Academy of Agricultural Sciences

summary: Seed germination is important to soybean (Glycine max) growth and development, ultimately affecting soybean yield. A lower seed field emergence has been the main hindrance for breeding soybeans low in phytate. Although this reduction could be overcome by additional breeding and selection, the mechanisms of seed germination in different low phytate mutants remain unknown. In this study, we performed a comparative transcript analysis of two low phytate soybean mutants (TW-1 and TW-1-M), which have the same mutation, a 2 bp deletion in GmMIPS1, but show a significant difference in seed field emergence.

overall_design: 18 samples were analyzed in this research, and three replicates were included.

first: Fengjie

last: Yuan

first: Danhua

last: Zhu


title: Expression data from Pseudomonas aeruginosa unexposed and exposed to direct current

status: Public on Dec 02 2016

city: Rochester

first: Asha

last: Nair

address: 200 1ST ST SW

institute: Mayo Clinic

summary:
Application of 200 µA of direct current to bacterial biofilms leads to cellular death. We hypothesize that bacterial death is caused, in part, by the generation of reactive oxygen species.
We used microarray analysis to determine the effects at a cellular level following 60 minutes of exposure of bacterial biofilms to 200 µA direct current.

overall_design: Biofilms of Pseudomonas aeruginosa were exposed to either 0 µA or 200 µA of direct current for 60 minutes, RNA was extracted and analyzed using Affymetrix microarray specific for P. aeruginosa

first: Robin

last: Patel

first: Cassandra

last: Brinkman


title: Azacitidine mitigates GvHD via its differential effects on expansion of nTregs in vivo.

status: Public on Dec 23 2016

city: St louis

first: John

middle: F

last: DiPersio

state: MO

address: 660 South Euclid Ave

institute: Washington University

summary: Azacitidine (AzaC) mitigates Graft vs. Host Disease (GVHD) in both murine preclinical transplant models and in human clinical trials while maintaining a robust Graft vs. Leukemia (GVL) effect.  Previous studies have failed to investigate the role of natural Tregs on the mitigation of GVHD by AzaC; instead focusing on the generation of suppressive regulatory T cells (Tregs, CD4+CD25+FOXP3+) through the in vivo conversion of alloreactive donor T effectors (Teff CD4+ CD25-, FOXP3-) and the direct anti-proliferative effects of AzaC on allogeneic T cells. Using B6.Foxp3DTR/GFP mice in which Tregs can be specifically ablated through administration of Diphtheria toxin, we demonstrate that nTregs are required in the donor graft for AzaC to optimally protect against GvHD and that nTregs, unlike T effectors (Teff, CD3+FOXP3-),  are resistant to the anti-proliferative effects of AzaC.   Gene expression analysis identified the potent cell cycle inhibitor, p21, was significantly upregulated in Teff but not nTregs after treatment with AzaC. Furthermore, we demonstrate that Teff cells deficient in p21 are less sensitive to the antiproliferative effects of AzaC.  These results, demonstrate that nTregs are essential for AzaC to fully protect against GvHD and have important clinical implications for future clinical trials testing AzaC as a novel method of GVHD prophylaxis in man.

overall_design:
n=3 per group
nTregs and AzaC generated Tregs, nTregs were purified from the spleens of B6.Foxp3GFP mice and Treg depleted T cells were obtained from B6. Foxp3GFP x B6.CAGDSRED. T Cells were co-cultured at a 1:10 ratio of nTreg to Teff and were activated for 2 days in the presence of anti-CD3/CD28 beads (bead:cell 1:1; Invitrogen) and Xcyte medium supplemented with L-glutamine (4mM), penicillin (100 U/mL), streptomycin (100 µg/mL), and human recombinant IL-2 (hIL-2; 500 U/mL).   The activated T cells were incubated in the presence of AzaC (1µM) (Sigma-Aldrich) or PBS for an additional 2 days.  Cells were sorted using FACS Aria II (BD) to isolate nTreg (CD4+DSRED-FOXP3GFP+), CD4+ Teff (CD4+DSRed+FOXP3GFP-), CD8+ Teff (CD8+DSRed+FOXP3GFP-).

first: Matthew

last: Cooper

first: Darja

last: Karpova

first: Kiran

last: Vij

first: Julie

last: Ritchey

last: Schroeder


title: Development of gene expression signatures for 4 days of waterlogging stress in Arabidopsis thaliana Col-0 plants

status: Public on Dec 01 2016

city: Bangalore

first: Genotypic

last: technology

state: Karnataka

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

country: India

institute: Genotypic Technology

summary: To study the transcriptional changes in waterlogging stress 30 day old Arabidopsis plants were subjected to 4 days of waterlogging stress.  We have employed whole genome microarray expression profiling as a discovery platform to identify genes that behave diferentially to the stress. The information could be used to generate transgenic lines that are resistant to waterlogging stress and can be applied to other closely related species to compromise the crop yeild loss. The transgenic lines contain waterlogging-inducible AP2 family of transcription factor.

overall_design: Agilent one-color experiment; Agilent Whole Genome Arabidopsis 4x44k (AMADID: 021169); Agilent Quick-Amp labeling Kit (p/n5190-0442)

first: Rakesh

middle: K

last: Shukla


title: Universal correction of enzymatic sequence bias

status: Public on Dec 21 2016

city: Charlottesville

first: Michael

last: Guertin

state: Virginia

address: 1340 Jefferson Park Ave

institute: University Of Virginia

type: Genome binding/occupancy profiling by high throughput sequencing

summary: Coupling molecular biology to high throughput sequencing has revolutionized the study of biology. Molecular genomics techniques are continually refined to provide higher resolution mapping of nucleic acid interactions and nucleic acid structure. These assays are converging on single-nucleotide resolution measurements, but the sequence preferences of molecular biology enzymes can interfere with the accurate interpretation of the data. Enzymatic sequence preferences manifest more prominently as the resolution of these assays increase. We developed seqOutBias to seek out enzymatic sequence bias from experimental data and scale individual sequence reads to correct the bias. We show that this software efficiently and successfully corrects the sequence bias resulting from DNase-seq, TACh-seq, ATAC-seq, MNase-seq, and PRO-seq data.

overall_design: Evaluate the sequence bias inherent to ATAC-seq. Genomic DNA is isolated from T lymphoblast cell line. Two biological replicate libraries were prepared and sequenced paired end (2x75).

first: Ninad

last: Walavalkar


title: Genome wide expression profiles of early and late onset breast cancers

status: Public on Nov 21 2016

city: NEW DELHI

first: SUNITA

last: SAXENA

state: NEW DELHI

address: NIP,ICMR,SAFADRJUNG HOSPITAL CAMPUS,NEW DELHI

department: TUMOUR BIOLOGY

institute: NATIONAL INSTITUTE OF PATHOLOGY

summary: Analysis of breast cancer gene expression profiles. The hypothesis tested in the present study was that if differential profiles exsist between early and late onset breast cancer. Results provide important information regarding up- or down-regulated genes playing a mechanistic role in cancer.

overall_design: Breast  tumors were divided into 2 groups based on their age criteria ; Early onset tumors(ET) with age≤ 40yrs and Late onset tumours (LT) with age ≥55 yrs ; Total RNA obtained from the breast tumours were subjected to gene expression profiling, adjacent normal tissues collected from breast cancer patients were used as controls for studying the gene expression profiles of early and late onset tumours

first: Shreshtha

last: Malvia

first: S

last: Bagadi

first: Sunita

last: Saxena


title: Fat body and midgut transcriptome of Wild-type vs. transgenic Aedes aegypti overexpressing JAK/STAT pathway components

status: Public on Nov 26 2016

city: Baltimore

first: George

last: Dimopoulos

state: Maryland

address: 615 N Wolfe St.

department: Molecular Microbiology and Immunology

institute: Johns Hopkins School of Public Health

summary: We have developed genetically modified Ae. aegypti mosquitoes that activate the conserved antiviral JAK/STAT pathway in the fat body tissue, by overexpressing either the receptor Dome or the Janus kinase Hop by the blood feeding-induced vitellogenin (Vg) promoter. Transgene expression inhibits infection with several dengue virus (DENV) serotypes in the midgut as well as systemically and in the salivary glands. The impact of the transgenes Dome and Hop on mosquito longevity was minimal, but it resulted in a compromised fecundity when compared to wild-type mosquitoes. Overexpression of Dome and Hop resulted in profound transcriptome regulation in the fat body tissue as well as the midgut tissue, pinpointing several expression signatures that reflect mechanisms of DENV restriction. Our transcriptome studies and reverse genetic analyses suggested that enrichment of DENV restriction factor and depletion of DENV host factor transcripts likely accounts for the DENV inhibition, and they allowed us to identify novel factors that modulate infection. Interestingly, the fat body-specific activation of the JAK/STAT pathway did not result in any enhanced resistance to Zika virus (ZIKV) or chikungunya virus (CHIKV) infection, thereby indicating a possible specialization of the pathway’s antiviral role.

overall_design: Fat body or midgut of Wild-type (WT, ORLxRock) vs. transgenic (VgHop or VgDome) Aedes aegypti. 4 biological replicates each

first: Natapong

last: Jupatanakul

first: Shuzhen

last: Sim

first: Yesseinia

last: Angleró-Rodríguez

first: Jayme

last: Souza-Neto

first: Suchismita

last: Das

first: Kristin

middle: E

last: Poti

first: Shannan

last: Rossi

first: Nicholas

last: Bergren

first: Nikos

last: Vasilakis


title: Transcriptome changes triggered by the synthetic defense elicitors DPMP in Arabidopsis thaliana

status: Public on Nov 22 2016

city: Riverside

first: Yasemin

last: Bektas

state: CA

address: 2150 Batchelor Hall

department: Botany and Plant Sciences

institute: University of California, Riverside

summary: DPMP (2,4-dichloro-6-{(E)-[(3-methoxyphenyl)imino]methyl}phenol )  is a newly identified synthetic defense elicitor. In order to uncover transcriptional patterns associated with defense activation, we profiled by mRNA-seq responses triggered in 14 d-old plate-grown Arabidopsis seedlings by continuous exposure to  3 µM DPMP or Mock.

overall_design: After Arabidopsis plants were grown for 14 days on ½ MS agar plates containing either 3 µM DPMP  or mock (solvent only), shoot and root tissues were analyzed separately. We performed two independent biological replicates and sequenced the respective libraries using the Illumina HiSeq2500 platform.

first: Thomas

last: Eulgem


title: Neurospora crassa transcriptomics reveals oxidative stress and plasma membrane homeostasis biology genes as key targets in response to chitosan

status: Public on Nov 23 2016

city: San Vicente

first: Federico

last: Lopez-Moya

state: Alicante

address: San Vicente Road S/N

department: Marine Science and Applied Biology

country: Spain

institute: University of Alicante

summary:
Purpose: Evaluate and analyze the transcriptional response of N. crassa germinating conidia and determined the main gene functions related with the exposure to chitosan. Identification of main chitosan gene tragets in N. crassa.
Methods: From samples in contact with chitosan for 4, 8 and 16h total RNA was isolated from material using TRIzol reagent. Total RNA was washed and then resuspended. For first strand cDNA synthesis, the fragmented poly (A+) RNA was incubated with random hexamers. Superscript II (200 U; Invitrogen) was added to the first cDNA strand synthesis. End-repair was performed by adding T4 DNA ligase buffer T4 DNA polymerase, Klenow DNA polymerase, T4 PNK. Standard Illumina adapters (FC) were ligated to the cDNA fragments using 2× DNA ligase buffer, 1 µL of adapter oligo mix and DNA ligase. The sample was purified in a 2% low-melting point agarose gel, and a slice of gel containing 200-bp fragments was removed and the DNA purified. A aliquot of purified cDNA library was amplified by PCR using the pfx DNA polymerase with genomic primers 1.1 and 2.1 (Illumina).  All libraries were sequenced on a HiSeq 2000 platform.
Results: A total of 523 N. crassa genes were differentially expressed (log2foldchange ≥ 2; p-value < 0.05) in response to chitosan. Of these, 55.6% (291 genes) were down-regulated and 45.3% (237 genes) up-regulated. This time-course experiment showed a progressive reduction in the number of genes whose expression increased upon exposure to chitosan (142 induced genes at 4h, 119 at 8h and 45 at 16h). In contrast, exposure to chitosan resulted in an increase in the number of genes whose expression levels decreased over time (79, 93 and 207 genes down-regulated at 4, 8 and 16h, respectively). A subset of 22 genes was differentially expressed consistently (log2foldchange ≥ 2; p-value < 0.05) throughout the whole time-course. Expression of 10 N. crassa genes representative of functional categories that were differentially expressed by exposure to chitosan were selected to validate our RNA-seq analysis. Gene expression was evaluated by qRT-PCR following an 8h exposure to chitosan. These genes were involved in the main functions related with the chitosan response. All genes analyzed by qRT-PCR showed an expression pattern consistent with that derived from RNA-seq data analysis.
Conclusions: This work provides the first study of the gene expression response of a filamentous fungus (N. crassa) to chitosan. Transcriptomics revealed oxidoreductase activity, membrane homeostasis and microtubule organization as main gene functions differentially expressed.

overall_design: Transcriptomic response of N. crassa to sub-lethal concentration of chitosan in a time course experiment (4, 8 and 16h)


title: Genome-wide expression profiling of USP9X/Y knockdown in the DU145 cell culture model

city: Belvaux

first: Enrico

last: Glaab

state: Capellen

address: 6, avenue du Swing

country: Luxembourg

institute: University of Luxembourg

summary:
Public transcriptomics studies have shown that several genes display pronounced gender differences in their expression in the human brain, and these differences may influence the clinical manifestations and risk for neuronal disorders. While disease relevant implications have already been proposed for gender differences in hormone levels, life style and genetic diversity, a systems level analysis of brain gene expression disparities between the genders in the context of brain disorders like Alzheimer’s disease (AD) has not yet been conducted.
Here we apply a transcriptome-wide analysis to discover genes with gender-specific expression and significant alterations in public post mortem brain tissue from AD patients compared to unaffected controls. We identify the sex-linked ubiquitin specific peptidase 9 (USP9) as an outstanding candidate gene with one of the largest ratios of male to female median expression levels during adulthood and a highly significant underexpression of the Y-chromosomal form of the gene (USP9Y) in male AD patients compared to controls. Previous studies have shown that USP9 can modulate the phosphorylation of the microtubule-associated protein tau (MAPT), whose dysregulation in AD is thought to play a key role in disease. Here, after observing a high positive correlation between USP9Y and MAPT expression in public transcriptomics data from AD case/control studies, we show that USP9 knockdown results in significantly decreased MAPT expression in the in vitro DU145 cell culture model. From the analysis of transcriptomics data for the knockdown in DU145 cells and prior knowledge from the literature, we derive a model for a USP9-dependent regulatory mechanism modulating MAPT expression via BACH1 and SMAD4. Overall, the combined transcriptomics analyses and identified functional links between USP9 and MAPT suggest USP9 may partially account for gender differences observed in tauopathies and could provide a new target for intervention strategies to modulate MAPT expression and phosphorylation.

overall_design: To assess the biomolecular effects of knocking down USP9 on a transcriptome-wide scale, the human DU145 prostate cancer cell culture model was chosen, after confirming that both USP9X and USP9Y are robustly expressed in this model. ShRNA constructs were then designed for the knockdown of USP9X and USP9X/Y (i.e. targeting USP9X and USP9Y jointly) to infer potential USP9Y-specific gene alterations indirectly by comparing both knockdowns. As readout, microarray expression profiling using the Affymetrix Human Gene 2.0 platform was performed with triplicate samples for each of five considered conditions (USP9X/Y knockdown, USP9X knockdown, scrambled RNA control, transfection reagent control, and unperturbed control).

first: Sandra

last: Köglsberger

first: Julia

last: Forster

first: Paul

last: Antony


title: Genome-wide responses to extracellular actin in Drosophila

status: Public on Nov 15 2016

first: Naren

last: Srinivasan

address: 1 Midland Road

department: Immunobiology Laboratory

institute: The Francis Crick Institute

summary: We report the transcriptional changes in Drosophila after administration of Actin or buffer control

overall_design: Examination of transcriptional responses to actin versus buffer injected flies at 3,6 and 24 hours post injection (each time point includes triplicate samples)

first: Probir

last: Chakravarty

first: Oliver

last: Gordon


title: PRDM14 drives OCT3/4 recruitment via active demethylation in the transition from primed to naïve pluripotency

status: Public on Nov 18 2016

city: Sanda

first: Yoshiyuki

last: Seki

state: hyogo

address: 1, Gakuen Uegahara

department: School of Biological and Environmental Sciences

country: Japan

institute: Kwansei Gakuin University

summary: Primordial germ cells (PGCs) are specified from epiblast cells in mice. Genes associated with naïve pluripotency are transiently repressed in the transition from inner cell mass (ICM) to epiblast cells, followed by their upregulation soon after PGC specification. However, the molecular mechanisms underlying the reactivation of pluripotency genes are poorly characterized. Here, we exploited in vitro differentiation of epiblast-like cells (EpiLCs) from embryonic stem cells (ESCs) to elucidate the molecular and epigenetic functions of PR domain-containing 14 (PRDM14). We found that Prdm14 overexpression in EpiLCs induced their conversion to ESC-like cells even in the absence of leukemia inhibitory factor (LIF). This was impaired by the loss of Kruppel-like factor 2 (Klf2) and ten-eleven translocation (TET) proteins. Furthermore, PRDM14 recruited OCT3/4 to the enhancer regions of naïve pluripotency genes via TET-base excision-repair-mediated demethylation. Our results provide evidence that PRDM14 establishes a transcriptional network for naïve pluripotency via active DNA demethylation.

overall_design: To investigate the function of TET1/TET2 in the transition form primed to naïve pluripotency, we exploited microarray analysis using total mRNA derived from Scramble, Scramble + PRDM14, Tet1/Tet2 KD, Tet1/Tet2 KD + PRDM14 mouse ESCs and EpiLCs.

first: Naoki

last: Okashita

first: Nao

last: Sakashita

first: Osamu

last: Nishimura

first: Mitsutaka

last: Kadota

first: Go

last: Nagamatsu

first: Ayaka

last: Nakajima

first: Yoshiaki

last: Suwa


title: Molecular liver cancer prevention in cirrhosis by organ transcriptome analysis and lysophosphatidic acid pathway inhibition

first: Yujin

last: Hoshida

state: TX

address: 5323 Harry Hines Blvd

institute: University of Texas Southwestern Medical Center

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

sample_organism:
Homo sapiens
Mus musculus
Rattus norvegicus

overall_design: Refer to individual Series


title: TonEBP/NFAT5 regulates inflammatory gene expression in nucleus pulposus cells

status: Public on Nov 08 2016

city: Philadelphia

first: Makarand

last: Risbud

state: PA

address: 1015 Walnut St.

institute: Thomas Jefferson University

summary: RNA sequencing of nucleus pulposus cells transduced with control or TonEBP shRNA and cultured under hypertonic conditions

overall_design: Total mRNA was collected from primary nucleus pulposus cells (both control and TonEBP knockdown cells and subjected to RNA sequencing, n=4 for both experimental groups

first: Johnson

last: Zariel

first: Risbud

last: Makarand


title: Gene expression data from human iPSC differentiated to macrophages and microglia, compared to human blood-derived monocytes and human primary fetal microglia

status: Public on Nov 14 2016

city: Oxford

first: Sally

last: Cowley

address: South Parks Road

department: Sir William Dunn School of Pathology

institute: University of Oxford

summary:
A human Pluripotent Stem Cell microglia model displays a neuronal-co-culture-specific expression profile and inflammatory response  Walther Haenseler, Stephen N. Sansom, Julian Buchrieser, Sarah E. Newey, Craig S. Moore, Francesca J. Nicholls, Satyan Chintawar, Christian Schnell,  Jack P. Antel, Nicholas D. Allen, M. Zameel Cader, Richard Wade-Martins, William S. James, Sally A. Cowley
The aim of the experiment was to compare the gene expression profiles from human iPSC-derived embryonic macrophages (both precursors, mature, and cells cultured in 'microglia medium'), with iPSC-macrophages differentiated to microglia by co-culture with iPSC-derived cortical neurons. They were also compared to human blood-derived monocytes and to human primary fetal microglia.

overall_design: 1 replicate of each of 3 genetic backgrounds for each condition were used. bloodMono were extracted from PBMCs with CD14 MACS beads. iMono were iPSC-derived macrophage precursors, from 3 control lines. iMac were from the same harvest as iMono - cells were set up in macrophage differentiation medium for 2 weeks;  iMGL were as per iMac but cultured in microglia medium; co-iMG (AKA iMG) were as per iMGL but added to SBAD3-01 iPSC-derived cortical neurons, after 2 wks dissociated with accutase and co-iMG were selected with CD11b MACS beads. See manuscript for full cell culture details.  RNA was extracted using an RNeasy kit (Qiagen) for Illumina HT12v4 transcriptome array analysis. fetalMG were human fetal microglia samples (at pre-myelinating gestational ages of fetalMG_1 20, fetalMG_2 23, fetalMG_3 15 weeks) cultured ex vivo in DMEM supplemented with 5% FBS for 5-7 days prior to RNA isolation using standard TrizolTM methods.

first: Walther

last: Haenseler

first: Stephen

middle: N

last: Sansom

first: Julian

last: Buchrieser

first: Sarah

last: Newey

first: Craig

middle: S

last: Moore

first: Francesca

middle: J

last: Nicholls

first: Satyan

last: Chintawar

first: Christian

last: Schnell

first: Jack

last: Antel

first: Nicholas

last: Allen

first: M

middle: Z

last: Cader

first: Richard

last: Wade-Martins

first: William

last: James


title: Transcriptome profiling uncovers potential common mechanisms in fetal trisomies 18 and 21

status: Public on Nov 13 2016

city: Ljubljana

first: Marija

last: Volk

address: slajmerjeva 003

department: Clinical institute of medical genetics

country: Slovenia

institute: UMC ljubljana

summary: Several studies have investigated the gene expression profiles in trisomies 21 and 18 to identify the expression signatures that are characteristic of each of these specific aneuploidy conditions. We hypothesized that the viability of cells with gross genomic imbalances might be associated with the activation of resilience mechanisms that are common to different trisomies and that are reflected by specific shared gene expression patterns. Microarray gene expression analysis of amniocytes from fetuses with trisomy 21 or trisomy 18 was conducted to detect such common expression signatures. Comparative analysis of significantly differentially expressed genes in trisomies 18 and 21 identified 6 dysregulated genes common to both trisomies: OTUD5, ADAMTSL1, TADA2A, PPID, PIAS2, and MAPRE2. These genes are involved in apoptosis, ubiquitination, protein folding, and cell division. Functional analysis demonstrated that both trisomies showed dysregulation of the PI3K/AKT pathway, cell cycle G2/M DNA damage checkpoint regulation, and cell death and survival, as well as inhibition of the upstream regulator TP53. Our data demonstrated that trisomies 18 and 21 share common gene expression signatures, implying that common mechanisms of resilience might be activated in aneuploid cells to resist large genomic imbalances. Studies of other trisomies might further clarify mechanisms activated in trisomy syndromes.

overall_design: Whole genome expression profiling was performed on 19 samples; RNA samples of cultivated amniocytes with trisomy 18 and euploid chromosome constitution were hybridized versus pooled reference RNA. Agilent 4x44 two-color Whole Human Genome Expression arrays (GPL6480), which contain 41,001 probes for interrogation of over 19,644 human genes, were used to estimate global transcriptional alterations in trisomy 18 samples.

first: Aleš

last: Maver

first: Alenka

last: Hodžić

first: Luca

last: Lovrečić

first: Borut

last: Peterlin


title: Arraystar lncRNA and mRNA array data for dorsal root ganglia neurons of mice

status: Public on Nov 05 2016

city: Xian

first: Jiaji

last: Lin

address: No. 1. XinSi Road

department: Neurology

institute: Forth Military Medicial University

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

summary: Nerve injury induces long-lasting pathological pain, namely neuropathic pain (NP), which is dysfunction of the whole pain transmission process, including dorsal root ganglia (DRG) in peripheral nerve system (PNS). Melatonin is well known over a long period of time as hormone of circadian rhythm closely related with the various aspects of pain conditions. Melatonin and melatonin related receptors (MTR1A and MTR1B) exerted amazing analgesic effect in many acute and chronic pain experimental studies, including electrically induced pain, thermally induced pain, mechanical induction of pain and chemical induction of pain. However, the anti-nociceptive action of melatonin in NP is still controversial and unclear. In the present study, our research firstly demonstrated the expression of melatonin receptors in the DRGs, and what more interesting is that MTR1A and MTR1B have a completely different cell type location (MTR1A in the satellite cells and MTR1B in the neurons). In order to get a basic glance at the effects of melatonin and MTR1B on the DRG neurons, a microarray analysis is applied to screen the pain related different expression genes in the primary DRGs cultured neurons with treatment of 1mM melatonin, 100μM MTR1B agonist 8-M-PDOT or vehicle (1% ethanol of normal saline). Subsequent examination was performed, and the finding suggested that melatonin suppressed neuropathic pain via MTR1B dependent and independent pathways in dorsal root ganglia neurons. And MTR1B in DRG may be a potential therapeutic target for NP.

overall_design:
Arraystar arrays were performed according to the manufacturer's directions on RNA extracted from primary DRG neurons culture.
The primary DRG neurons were cultured and treated with 1mM melatonin, 100μM MTR1B agonist 8-M-PDOT or vehicle (1% ethanol of normal saline). Total RNA was extracted from each sample using TRizol Reagent according to the protocol from manufacturer. RNA quantity and quality were measured by NanoDrop ND-1000. RNA integrity was assessed by standard denaturing agarose gel electrophoresis. Arraystar Mouse mRNA and ncRNA Microarray V3.0 is applied for the global profiling of mouse lncRNAs and protein-coding transcripts. About 35,923 lncRNAs and 24,881 coding transcripts can be detected by our third-generation mRNA and lncRNA microarray. Differentially expressed genes (DEGs) of 1mM melatonin group (between 1mM melatonin and vehicle treatment) and 100μM 8-M-PDOT group (between 100μM 8-M-PDOT and vehicle treatment) were identified through the random variance model. A p-value was calculated using the paired t-test. The threshold set for up- and down-regulated genes was a fold change ≥ 2.0. The GO and pathway analyses were performed and the pain related GO terms were picked up for subsequent examination.

first: Jia

first: Zhu

middle: Y

last: Li


title: Identification of copy number alterations and the associated genes in oral squamous cell carcinoma

status: Public on Nov 17 2016

city: Kuala Lumpur

first: Rosnah Binti

last: Zain

state: Kuala Lumpur

address: Jalan Lembah Pantai

department: Faculty of Dentistry

country: Malaysia

institute: University of Malaya

summary: Genome-wide profiling of oral squamous cell carcinoma by array-based comparative genomic hybridization

overall_design: 75 gDNA of frozen OSCC tissue (test sample) vs matched gender gDNA blood (reference control)

first: Rosnah

middle: B

first: Vincent-Chong

last: King

first: Iman

last: Salahshourifar


title: Targeting sphingosine kinase by ABC294640 induces KSHV-infected endothelial cell autophagic death

status: Public on Nov 01 2016

city: New Orleans

first: Zhiqiang

last: Qin

state: LA

address: 1700 Tulane Ave

institute: LSUHSC-NO

summary: KSHV is a principal causative agent of Kaposi's Sarcoma (KS). Despite this knowledge about the close relationship between sphingolipid metablism and solid tumors development, the role of  sphingolipid metablism in KSHV-related malignancies remains mostly unclear. We report that targeting sphingosine kinase 2 (SphK2) by a selective inhibitor, ABC294640, significantly induces KSHV+ TIVE-LTC autophagic death. By using microarray analysis, we have identified the global gene profile affected by ABC294640 within KSHV+ TIVE-LTC and several novel “druggable” candidates closely related to cancer cell survival/growth. Finally, we found that targeting TIVE-LTC by ABC294640 effectively  suppressed KSHV tumorigenicity by using a KS-like nude mice model.

overall_design: TIVE-LTC were treated with vehicle control or SphK2 inhibitor ABC294640 (60 µM) for 24 h, and the gene expression signature was compared to respective vehicle controls

first: Lu

last: Dai

first: Amanda

last: Struckhoff

first: Luis

last: Del Valle

first: Charles

middle: D

last: Smith

first: Jovanny

last: Zabaleta

first: Rolf

last: Renne

first: Chris

last: Parsons


title: Gene expression profiles of human hematopoietic progenitors [BLUEPRINT hematopoietic progenitors]

status: Public on Nov 06 2016

city: Vienna

first: Christoph

last: Bock

address: Lazarettgasse 14

country: Austria

institute: CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences

summary: An optimized whole genome bisulfite sequencing protocol (µWGBS, Farlik et al. 2015 Cell Reports) was used to establish DNA methylation profiles of FACS-purified stem and progenitor cells types of the human blood lineage. Most cell types were sorted from the peripheral blood of three donors each (43 donors total) with eight pools of ten cells, two pools of 50 cells, and one pool of 1000 cells. Additionally, two cell types (HSC, MPP) were sorted from bone marrow, fetal liver, and cord blood; single-cell methylome sequencing (scWGBS, Farlik et al. 2015 Cell Reports) was done for selected cell types (HSC, MPP, CMP, GMP, CLP, MLP0); and gene expression profiling using the Smart-seq2 protocol (Picelli et al. 2013 Nature Methods) was done on all stem/progenitor cell types (HSC, MPP, CMP, MEP, GMP, CLP, MLP0, MLP1, MLP2, MLP3).

overall_design:
Gene expression was analyzed for stem/progenitor cell types and terminally differentiated cell types of the human blood lineage (HSC, MPP, CMP, GMP, CLP, MLP0, MLP1, MLP2, MLP3).
--------------------
The raw sequencing data are available from EBI EGA under a data access agreement. Please contact the authors to access the raw data.

first: Matthias

last: Farlik

first: Florian

last: Halbritter

first: Fabian

last: Müller

first: Mattia

last: Frontini


title: Targeted inhibition of platelet-derived growth factor signaling prevents muscle fiber growth during skeletal muscle hypertrophy

status: Public on Oct 25 2016

city: Ann Arbor

first: Christopher

middle: Louis

last: Mendias

state: Michigan

address: 109 Zina Pitcher Place

department: Orthopaedic Surgery

institute: University of Michigan

summary: The platelet-derived growth-factor receptors alpha and beta (PDGFRα and PDGFRβ) mark fibroblasts and pericytes in skeletal muscle, respectively. While the role that these cells play in muscle growth has been evaluated, it was not known whether the receptors that mark these cells play a role in controlling transcriptional and functional changes during skeletal muscle hypertrophy. To evaluate this, we inhibited PDGFR signaling in mice subjected to a synergist ablation muscle growth procedure, and measured changes 3 and 10 days later. The results indicated that PDGF signaling was required for fiber hypertrophy and ECM production that occur during muscle growth.

overall_design: 10 pooled samples total. Equal amounts of RNA isolated from four individual muscles were pooled into a single sample for microarray analysis, and two pooled samples from each group were analyzed. RNA was pooled because gene expression from a pooled sample is similar to the average of the individual samples composing the pooled sample.

first: Kristoffer

last: Sugg

first: Michael

middle: A

last: Korn

first: Dylan

last: Sarver

first: James

last: Markworth

middle: L


title: DNA methylation profiles of human hematopoietic progenitors [BLUEPRINT hematopoietic progenitors]

type: Methylation profiling by high throughput sequencing

overall_design:
DNA methylation was analyzed for stem/progenitor cell types and terminally differentiated cell types of the human blood lineage (HSC, MPP, CMP, MEP, GMP, CLP, MLP0, MLP1, MLP2, MLP3, MK, CD4+ Tcell, CD8+ Tcell, Bcell, NK, Neut, Mono).
--------------------
The raw sequencing data are available from EBI EGA under a data access agreement. Please contact the authors to access the raw data.


title: Expression data from somatic cell nuclear transfer bovine embryo

city: Hohhot

first: Yongchun

last: Zuo

state: Inner Mongolia

address: No.24 Zhaojun Road

department: The Key Laboratory of Mammal Reproductive Biology and Biotechnology Ministry of Education

institute: Research Center for Laboratory Animal Science Inner Mongolia University

summary:
Since the first cloned animal Dolly Sheep was successfully created by using somatic cell nuclear transfer(SCNT) technique. It has become an irreplaceable tool to understand nuclear reprogramming and totipotency and holds huge potentials for regenerative medicine. However, extremely poor development rate of SCNT embryos indicates it is still questionable. The nature of reprogramming oocyte factors and their mechanism of action remain largely unknown.It is evident that the major barrier that hinders the developing iSCNT embryo mainly appears at the time of embryonic genome activation (EGA), which primarily occurs at the eight-cell stage in mammalian. The interspecies somatic cell nuclear transfer (iSCNT) is desired model for nuclear reprogramming research and a powerful tool for discovering the master genome activation genes. In this study, a valuable transcriptome recourse of iSCNT embryos was established, which derived from more than 2000 clone embryos of four different inter-family donor cells. Based on weighted gene co-expression network (WGCNA) approach, we provide an extensive transcriptome analysis of differentially expressed genes(DEG) for iSCNT embryos. The total gene expression patterns of different iSCNT embryos were discussed. 26 cell-specific modules with were identified, and those module significance and GO enriched categories were analyzed. The regulatory pathways of reprogramming barriers were further enriched. As master genome trigger genes, the transcripts related to TFIID subunit, RNA polymerase and Mediator were incomplete activated in iSCNT embryos. This indicated that pioneer factors, present in the cytoplasm of the oocyte, were failed to bind the sequence target on the heterology nuclear genome. This genomic incompatibility between the nuclear donor cell and the cytoplast may be as a major contributing factor causes the developmental failure of iSCNT cloned embryos.
This study demonstrates that the iSCNT embryos undergoes only partial or incomplete reprogramming at eight-cell stage in mammalian. Our results offered convincing evidence that the  abnormal expression of key master pathways may be caused the embryo developmental block of cloning embryo. This work will contribute to a better understanding of the molecular interaction between nuclear–cytoplasmic interaction and provides insight into the molecular determinants of nuclear reprogramming, human embryonic stem cell (hESC)-based therapies and rescuing highly endangered species.

sample_organism:
Bos taurus
Pantholops hodgsonii
Procapra przewalskii

overall_design: In this study, the Affymetrix gene chip bovine genome array was used for gene array analysis. The Affymetrix Gene Chip Bovine Genome array contains 24,027 probe sets corresponding to approximately 23,000 transcripts including assemblies from ~19,000 UniGene clusters. The arrays images were first quantified using Gene Chip Operating Software (GCOS, Affymetrix). Samples are divided into two groups, one is embryos, another is the somatic cells. In embryos group, we collected two biological replicates of bovine oocytes, contains 1150 oocytes (BMII, ID-1) and 1000 occytes (BMII, ID-2) respectively; Two biological replicates of bovine-bovine intraspecies cloned embryos (BBNT), replicates contain 309(ID-3) and 552(ID-4) BBNT embryos; 527(ID-5) Przewalski's gazelle –Bovine  interspecies nuclear transfer 8- to 16-cell stage embryos (PBNT) , 521(ID-6) Yak-Bovine interspecies nuclear transfer 8- to 16-cell stage embryos ,515(ID-7) Tibetan–bovine interspecies nuclear transfer 8- to 16-cell stage embryos (TBNT). In somatic cell group, we collected two biological replicates Luxi cattle somatic cells (LC, ID- 8,9), Mongolia cattle somatic cells(MC, ID-10,11) , Yak somatic cells(YC, ID-13,14) and Tibetan somatic cells(TC, ID-15,16) respectively. In addition, we also collected Holstein somatic cells (HC, ID-12) and three replicates Przewalski’s gazelle somatic cells(PC, ID-17,18,19)


title: A small molecule inhibitor of iron-sulfur cluster assembly is toxic to Staphylococcus aureus in an Sae-dependent manner

status: Public on Oct 20 2016

city: Rochester

first: Paul

last: Dunman

state: NY

address: 601 Elmwood Avenue

department: Microbiology and Immunology

institute: University of Rochester

summary:
VU0038882 ('882) is a small molecule compound with antistaphylococcal activity and increased activity toward the organism during anaerobic growth conditions.
The mechanism of action of '882 is hypothesized to be saeRS dependent
S. aureus Affymetrix GeneChips were used to compare the S. aureus expression properties of wild type and isogenic ΔsaeRS mutant cells in response to '882 challenge during anaerobic growth conditions.
Significant differences were observed between the expression properties of '882 treated S. aureus wild type and saeRS mutant cells in comparison to '882 vehicle (DMSO) treated cells.

overall_design: S. aureus strain Newman (wild type) or an isogenic saeRA mutant (ΔsaeRS) were grown in laboratory medium to exponential phase during anaerobic growth conditions, treated with DMSO or '882 for 10 min, total bacterial RNA was isolated, labeled and applied to Affymetrix GeneChips.  We sought to determine whether the transcriptional profiles of S. aureus wild type and saeRS mutant cells differed in response to '882.

middle: M

first: Eric

last: Skaar


title: Long non-coding RNA produced by RNA polymerase V determines boundaries of heterochromatin

status: Public on Oct 24 2016

first: Andrzej

middle: T

last: Wierzbicki

address: 830 N. University

department: Molecular, Cellular, and Developmental Biology

summary: We report genome-wide detection of long noncoding RNA (lncRNA) generate by Pol V in transcriptional gene silencing in Arabidopsis thaliana. We further show that most of these transcripts are bound by AGO4.

overall_design:
RNA immunoprecipitation followed by high-throughput sequencing (RIP-seq)
RNA immunoprecipitation with an anti-AGO4 antibody was performed in one biological replicate and included Col-0, nrpe1, and ago4-1; RNA immunoprecipitation with an anti-NRPE1 (largest subunit of Pol V) was performed in two replicates; replicate 1 included Col-0 and nrpe1, replicated two included Col-0, nrpe1, ago4-1, and idn2-1

first: Gudrun

last: Böhmdorfer

first: Shriya

last: Sethuraman

first: M

last: Rowley

first: Michał

last: Krzysztoń

middle: H

last: Rothi

first: Lilia

last: Bouzit


title: RNA-seq analysis of in vivo- and in vitro-produced mouse oocytes

status: Public on Oct 17 2016

city: Fukuoka

first: Nobuhiko

last: Hamazaki

state: Fukuoka

address: Maidashi 3-1-1, Higashi-ku,

department: Department of Developmental Stem Cell Biology

institute: Kyushu University

summary: The female germline undergoes a unique line of differentiation processes that endows totipotency to the egg. During these processes, biologically significant events such as meiosis and oocyte growth are controlled in an orderly manner, with any disorder causing infertility and developmental arrest of the next generation. Reconstitution in vitro of the entire process of oogenesis from pluripotent stem cells is a key achievement in stem cell biology and regenerative medicine, but a robust and reproducible culture system has not been established. Here, we report successful reconstitution in vitro throughout the entire process of oogenesis from pluripotent stem cells, yielding in vitro-produced eggs that gave rise to healthy pups. Moreover, the pluripotent stem lines were re-derived from the in vitro-generated eggs, thereby reconstituting one generation on a dish. This culture system will provide a unique platform for elucidating the molecular mechanisms underlying totipotency and could open an avenue to producing vast numbers of eggs in vitro.

overall_design: The transcriptomes of ES cells (ESCs), primordial germ cell-like cells at day 6 of differentiation (PGCLCs_d6), PGCLCs aggregated with gonadal somatic cells (PGCLCs_agg3), in vitro-produced primary oocytes in secondary follicles (vitro_2nd_fol_oocyte) and MII oocytes (vitro MII oocytes) are determined by RNA-seq analysis. For comparison, the transcriptomes of E12.5 PGCs (vivo_E12.5_PGCs), P8 primary oocytes (vivo_2nd_fol._oocyte) and MII oocytes (vivo_MII_oocyte) in vivo are also determined. Biologically triplicated (rep1-3) or duplicated (rep1-2) samples are sequnced simultaneously.

first: Katsuhiko

last: Hayashi


title: Epigenetic Effects of Maternal Obesity on Wharton's Jelly (WJ) Mesenchymal Stromal Cells (MSCs): Implications For Cellular Therapy. (methylation study)

status: Public on Oct 16 2016

city: Paris

first: Pierre

last: de la Grange

address: 29, rue du Faubourg Saint-Jacques

department: Paris Biotech Santé

institute: GenoSplice technology

summary:
7 WJ-MSC lines from non-obese BMI <25 kg/m2 were compared with 7 WJ-MSC lines obese BMI >30 kg/m2.  No template was used as a negative control
Triplicates for each line were analyses for epigenome-wide methylation (>480,000 CpG sites) using Infinium Human Methylation 450 BeadChip Kit (Illumina).

overall_design: Bisulphite converted DNA (500 ng/sample) from the 15 samples (triplicates from 14 lines + 3 repiclates from no template samples) were hybridised to the Infinium Human Methylation 450 BeadChip Kit (Illumina)

first: Dusko

last: Ilic

first: Heba

last: Badraiq


title: A single bout of cryotherapy does not alter the transcriptome of metabolome of human skeletal muscle

first: Christopher

last: Mendias

summary: Cryotherapy is a commonly used therapeutic modality for skeletal muscle injuries in sports medicine. Despite the widespread use of this modality, there is little known about the biochemical effects of cryotherapy in skeletal muscle tissue of humans. The purpose of this study was to determine the effect of cryotherapy on the transcriptome of human skeletal muscle. Using a paired design, 8 healthy male subjects (age 24.7±4.5 years, BMI 22.2±1.6) received ice-cup massage or sham cup massage over a 45 cm2 area on each thigh for 15 min. Two hours after application, bilateral biopsies were taken at a depth of 2 cm from the vastus lateralis in the center of the ice or sham area. Muscle biopsies were from each leg were then subjected to microarray analysis.

overall_design: Each of the 8 healthy male subjects received ice-cup and sham application over a 45 cm2 area on separate thighs for 15 min. Bilateral biopsies were taken from the Vastus Lateralis in the center of the ice or sham area 2 hours after application. Differences between groups were tested using t-tests corrected for multiple comparisons.

middle: C

last: Sarver

first: Kristoffer

last: Sugg

first: Nate

middle: P

last: Disser

first: Elizabeth

middle: R

last: Sibilsky Enselman

first: Tariq

last: Awan


title: Expression data from MDA-MB-231 cells treated with dinaciclib

status: Public on Oct 18 2016

city: Boston

first: Shawn

last: Johnson

state: MA

address: 450 Brookline Avenue, Mayer Rm 434

department: Medical Oncology

institute: Dana-Farber Cancer Institute

summary:
Dinaciclib potently inhibits CDK12, resulting in decreased mRNA from many genes associated with DNA damage signaling and repair.
We used microarrays to assess changes in global mRNA levels following dinaciclib treatment in breast cancer cells

overall_design: MDA-MB-231 cells were treated for 12 hours with dinaciclib before cells were trypsinized and treated with trizol for mRNA extraction


title: Genome-wide methylation analysis of DNMT3B gene isoforms revealed specific methylation profiles in breast cell lines

status: Public on Oct 31 2016

city: quebec

first: Francine

last: Durocher

state: quebec

address: 2705, Laurier Blvd

department: Molecular Medicine

country: Canada

institute: CHU de Quebec Research Centre

type: Methylation profiling by genome tiling array

summary: Both DNA methylation and alternative splicing represent mechanisms closely involved in regulation of gene expression and are well known to be involved in cancer susceptibility and development.   Human DNA methylation is introduced into DNA by enzymes of the DNA cytosine methyltransferases family, which includes DNMT3B. The DNMT3B protein allows a de novo DNA methylation activity, which is a key mechanism involved in the transformation of normal cell into cancer cell. The DNMT3B3 isoform is overexpressed in cancerous tissues and tumor cell lines, and could act as a dominant negative factor. This isoform was found to be highly expressed in our cohort of non-BRCA1/2 families. Using Infinium Human Methylation 450 BeadChips, we undertook the characterization of the specific methylation profile associated with this DNMT3B3 isoform and its DNMT3B2 wild type counterpart in ER/PR-positive and –negative breast cancer cell lines.  A large spectrum of DNMT3B3/DNMT3B2 expression ratio values was observed in cancer and non-cancerous cell lines. Based on their methylation profiles, hierarchical clustering of parental cell lines revealed clustering of cells based on their ER/PR status. Overexpression of DNMT3B3 triggered methylation changes of thousands of CpG sites in MCF7, T-47D, MDA-MB-231 and MCF10A cells. These methylated loci were distributed in similar proportion over the 22 autosomal chromosomes and genomic locations such as promoter, gene body or intergenic regions. Pathways associated with genes containing these differentially methylated CpG sites were also determined regarding their enrichment. Moreover, based on the trend of methylation changes, the results suggest an anti-proliferative effect of the DNMT3B3 isoform through negative effect on its wild-type isoform counterpart DNMT3B2.   To our knowledge, this study represents the first exhaustive analysis describing specific methylation profile triggered by modulated expression of DNMT3B isoforms and revealed specific genes and pathways, which could significantly regulate cell growth and proliferation as well as other biological and molecular mechanisms.

overall_design: For each cell line treatment, between 3 and 6 replicates have been performed. Cell line treatments include negative controls such as untreated, scramble shRNA-transduced+empty vector-transfected as well as empty vector-transfected only.  A total of 94 samples have been analyzed which include all appropriate treatments in 7 different cell lines namely MCF7, T-47D, CAMA1, ZR-75-1, MDA-231, BT549 and MCF10A. The main goal was to generate extreme (low and high) gene expression ratios of DNMT3B3/DNMT3B2 in each cell line.

first: Karine

middle: V

last: Plourde

first: Yvan

last: Labrie

first: Frederic

last: Guenard


title: Transcriptional response of P. aeruginosa PA1 to bacteriophage PaP1 infection

status: Public on Oct 19 2016

city: ChongQing

first: Xia

last: Zhao

address: Shapingba

institute: Third military medical school

summary: Explore the genome-scale phage-host interactions across different developmental infection stages

platform_organism:
Pseudomonas aeruginosa PAO1
Pseudomonas phage PaP1

overall_design: Samples were taken from the PA1 Lysates infected with phage PaP1 at four internal time (0, 5, 15 and 45min). Three independent experiments were performed at each time point.

first: Shuai

last: Le


title: The kinetics of ethylene-regulated changes in the root transcriptome

status: Public on Oct 01 2016

city: WINSTON SALEM

first: Gloria

middle: Kressin

last: Muday

state: North Carolina

address: 1834 Wake Forest Road

department: Biology

institute: Wake Forest University

summary:
Ethylene-dependent gene expression was assayed by treating with 1 uM ACC, an ethylene precursor, or a control treatment to Arabidopsis seedlings by transferring 6 day old Arabidopsis grown on a a nylon mesh to fresh ACC-containing or control media
Seedling roots were harvested 0, .5, 1, 2, 4, 8, 12, and 24 hours after treatment and the resultant RNA was used for microarray analysis to determine the kinetic profiles of auxin-responsive gene expression

overall_design: 8 timepoints after control or ACC treatment done in triplicate

first: Alexandria

middle: F

last: Harkey

first: Amy

last: Olex

middle: K

first: Jacquelyn

last: Fetrow


title: Gene expression of breast cancer cell lines treated with conditioned medium derived from NAF and CAF

city: Milan

first: Matteo

last: Dugo

address: via Olgettina 60

department: Department of Medical Oncology

country: Italy

institute: IRCCS Ospedale San Raffaele

summary: We treated nine lines of breast cancer cells with conditioned medium derived from NAF and CAF to study the paracrine interaction beetween stroma and tumor. Gene expression profiles for breast cancer cell lines are reported after 72h of treatment with conditioned medium derived from NAF and CAF or with control media.

overall_design: Biological triplicates for NAF, CAF and CTR treated cells were generated by independent treatments and total RNA extractions.

first: Giuseppe

last: Merlino

first: Francesca

last: D'aiuto

first: Vera

last: Cappelletti

first: Maria Grazia

last: Daidone


title: The destiny of the resistance/susceptibility against GCRV has been congenitally destined by epigenetic mechanism in CIK cells [miRNA-seq]

status: Public on Sep 28 2016

city: Shanghai

first: Ze-Guang

last: Han

address: 800 Dongchuan Road

department: Shanghai Center for Systems Biomedicine

institute: Shanghai Jiao Tong University

type: Non-coding RNA profiling by high throughput sequencing

summary: In this study, the resistant and susceptible monoclonal CIK cell lines were first established which would be the ponderable research models for the nosogenesis mechanism of the hemorrhagic disease. C1 (CIK cells), R2 (resistant cells) and S3 (susceptible cells) samples were carried out RNA-Seq, MeDIP-Seq and small RNA-Seq by the next-generation sequencing strategy, bioinformatics analysis as well as experimental verification. It was discovered that the aboriginality of CIK cells were gravitated to the susceptible trait. And the discrepancies between resistance and susceptibility against GCRV could primarily attribute to antioxidant activity, cell killing activity and cell proliferation regulation. Here we comprehensively present the profiling and characteristics of DNA methylation and microRNA in the resistant and susceptible CIK cells and proposed that high mCHH methylation distribution might be a characteristic modulator in C. idella. What’s more, a series of genes modulated by DNA methylation or microRNA were designated as potential biomarkers for the resistance breeding. This study laid the foundation and opened novel avenues for nosogenesis research on hemorragic disease of C. idella.

overall_design: C1 (CIK cells), R2 (resistant cells) and S3 (susceptible cells) samples were carried out RNA-Seq, MeDIP-Seq and small RNA-Seq by the next-generation sequencing strategy.

first: Jianguo

last: Su

first: Xueying

last: Shang


title: The destiny of the resistance/susceptibility against GCRV has been congenitally destined by epigenetic mechanism in CIK cells [RNA-seq]


title: The destiny of the resistance/susceptibility against GCRV has been congenitally destined by epigenetic mechanism in CIK cells

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

overall_design: Refer to individual Series


title: Different toxicity mechanisms for citrinin and ochratoxin A revealed by transcriptomic analysis in yeast

city: Valencia

first: Markus

last: Proft

address: Jaime Roig 11

institute: Inst. Biomedicina Valencia IBV CSIC

summary: The aim of this study was to reveal the genomic response of yeast cells to the related mycotoxins citrinin (CIT) and ochratoxin A (OTA). Both mycotoxins can be produced by the same filamentous fungi and co-contaminate the same foodstuff. However, it is not known whether CIT and OTA share the same toxicity mechanisms or not. We performed transcriptomic profiling experiments using microarray hybridization of a pdr5 mutant strain exposed separately to CIT or OTA and exposed to a combination of both toxins. A yeast pdr5 mutant was used, because it is significantly sensitized to both toxins. We find that CIT and OTA cause the rapid activation of largely non-overlapping gene sets. The most prominent functional group of CIT-activated genes corresponds to the cellular response to oxidative stress, while OTA-activated genes belong predominantly to  single organism developmental processes and meiosis/sporulation. The combined exposure of CIT and OTA revealed a mixed response of functional gene groups. Our results demonstrate that CIT and OTA have distinguishable and independent biological effects with oxidative stress being a hallmark for CIT toxicity and the deregulation of developmental genes being the principal feature for OTA toxicity.

overall_design: Gene expression in yeast cells was measured under four conditions: control, citrinin (200ppm), ochratoxin A(200ppm), and a combination of both mycotoxins (100ppm of each). Samples were taken at 30 (ochratoxin A and combined treatment) and 60 min (control and citrinin).  Four replicates were performed for each condition.

first: Amparo

last: Pascual-Ahuir

first: Elena

last: Vanacloig-Pedros


title: Genome-wide expression profiles during the post-eclosion and pre-vitellogenic stages of adult female Culex quinquefasciatus

status: Public on Sep 26 2016

city: Auburn

first: Nannan

last: Liu

state: AL

address: 301 Funchess Hall

department: Entomology

institute: Auburn University

summary: The Southern house mosquito, Culex quinquefasciatus, is an anautogenous mosquito species that requires a blood meal in order to provision the eggs. Following the eclosion of the adults from the pupal stage, adult female mosquitoes require a period of time for mating and development before they are competent to take a blood meal. In order to better understand the genes involved in preparing the females to take a blood meal, populations of non-blooded adult female Cx. quinquefasciatus were collected from even-aged populations and used for RNA Seq analysis. A total of seven post-eclosion time points were selected (2, 12, 24, 36, 48, 60, and 72 hours), which spanned the pre-blood feeding time period and the time period during which the females were competent for the acquisition of the blood meal. Overall, the majority of differentially-expressed genes were identified between the 2 and 12h time points with most genes reaching stable expression after 36h. This study identified the global changes in gene expression profiles over time as the females become competent to acquire the blood meal.

overall_design: Time series analysis of gene expression in Cx. quinquefasciatus using RNASeq. Data were analysed using the Tophat-Cufflinks-Cuffdiff pipeline from the Center for Bioinformatics and Computational Biology, Univ. Maryland College Park.

first: Lee

last: Zhang


title: KRas targeting by clinically significant miR-193a-3p inhibits mutant KRas lung cancer growth, circulating tumor cells and metastasis in vivo

status: Public on Sep 18 2016

city: Houston

last: Seviour

institute: UT MD Anderson Cancer Center

summary: Ras family oncogenes are mutated in approximately 30% of human cancers and cause resistance to multiple treatment modalities.  While identifying methods to directly target mutant KRas have been challenging, targeting regulators of KRas may be beneficial.  Using a systems approach of integrating a genome-wide miRNA screen with patient data of a phospho-proteomic signature of the KRas downstream pathway, we identified miR-193a-3p as a potent tumor suppressor capable of reversing KRas-related signaling, whereby the 3’UTR of KRas is directly targeted via two miR-193a-3p binding sites.  Mechanistic studies revealed that miR-193a-3p inhibited the KRas protein signature, KRas downstream transcriptomic network, proliferation, induced a G1 arrest, and reduced colony formation in 3D cultures through direct targeting of KRas. An ex vivo lung cancer model showed that miR-193a-3p significantly reduced the viability of circulating tumor cells as well as decreased metastasis.  In vivo studies revealed that miR-193a-3p significantly reduced tumor growth as well as metastasis of a KRas-mutant lung cancer xenograft model.

overall_design: Total RNA extracted 48 hours after transfection with either control (NT) or miR-193a-3p, with 3 replicates per condition

middle: G

first: Vasuda

last: Sehgal

first: Dhruva

last: Mishra

first: Rajesha

last: Rupaimoole

first: Cristian

last: Rodriguez-Aguayo

first: Gabriel

last: Lopez-Berestein

first: Ju-Seog

last: Lee

first: Anil

last: Sook

first: Min

last: Kim

first: Gordon

last: Mills

first: Prahlad

last: Ram


title: RNA-seq analysis of gene transcripts during callus formation  from the basal part of young rice leaf explants

status: Public on Sep 14 2016

first: Lin

last: XU

address: 300 Fenglin Road

department: Chinese Academy of Sciences

institute: Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences

summary: To explore the molecular mechanism that confers the ability to regenerate on certain tissues in rice, we performed an RNA-seq experiment during callus formation from the basal part of young leaf explants about 7 mm in length.The 1727 genes are significantly highly upregulated in 2 DAC and 1839 genes in 5 DAC on Callus Induced Medium as compared to that of 0 DAC based on the following criteria: fc>10 and P value <0.05.

overall_design: Total RNA obtained from the base region（2 mm) of 7 mm rice leaf explants at time 0, 2 DAC and 5 DAC on Callus Induced Medium.

first: Guifang

first: Wu

first: Meifang

last: Qi

first: Jian

last: Xu


title: Profiling of gut gene expression in Cry1Ab-resistant and susceptible strains of Ostrinia nubilalis reveals possible adaptations of resistant larvae to transgenic Cry1Ab corn

city: Stoneville

first: JIANXIU

last: YAO

state: Mississippi

address: 141 Experiment station Rd

institute: USDA-ARS

summary: We revealed a total of 398 gut genes differentially expressed (i.e., either up- or down-regulated genes with expression ratio ≥2.0) in S-strain larvae, while only 264 gut genes differentially expressed in R-strain larvae after fed transgenic corn leaves. Although the percentages of down-regulated genes among the total number of differentially expressed genes (199 genes or 50% in S-strain; 119 genes or 45% in R-strain) were similar between the R and S-strains, the expression ratios of down-regulated genes were much higher in S-strain than in R-strain. These results imply that R-strain larvae had an increased ability to deal with transgenic corn as compared with S-strain larvae. We also revealed that 17 and 9 significantly up- or down-regulated gut genes from S- and R-strain larvae, respectively, including serine proteases (trypsins and chymotrypsins) and aminopeptidases.

overall_design: Trangenic corn induced gene expression was measured in O. nubilalis resistant and susceptible strains' gut at 6-hrs after transgenic corn feeding.  Three independent experiments were performed using three insect gut samples ,and each sample was from five insects' gut pooled.

first: Jianxiu

last: Yao

first: Kun

middle: Y

last: Zhu


title: Widespread downregulation of cardiac mitochondrial and sarcomeric genes in patients with sepsis

status: Public on Sep 22 2016

city: Indianapolis

first: Scot

middle: J

last: Matkovich

state: IN

address: Lilly Corporate Center

institute: Eli Lilly and Company

summary: The mechanism(s) for septic cardiomyopathy in humans is not known. To address this, we performed transcriptional profiling of hearts from patients who died from sepsis, in comparison to non-failing human donor hearts that could not be transplanted for technical reasons.

overall_design:
20 sepsis patients, 11 ischemic heart disease (IHD), 9 nonischemic dilated cardiomyopathy (DCM), 11 non-failing donors.

The additional de-identified, clinical data for GSM2109161-66, GSM2109168-79 (total 18 samples) is provided in the 'Clinical_metadata.xls' (as a series supplementary file).

first: Bernard

last: Brownstein

first: Richard

middle: S

last: Hotchkiss

first: Douglas

last: Mann


title: Global transcriptional profiling of Ustilago bromivora during axenic growth and pathogenic development

status: Public on Nov 03 2016

city: Vienna

first: Angelika

middle: B

last: Czedik-Eysenberg

address: Dr-Bohr-Gasse 3

institute: Gregor-Mendel-Institute

summary: To provide insights into expression patterns of the genes encoding putatively secreted proteins in U. bromivora during saprophytic growth and in planta, we conducted RNA-seq analyses. To this end, we isolated RNA from axenic U. bromivora UB1 culture and from stems of twelve day old B. hybridum Bd28 plants that were spore-inoculated with U. bromivora. Among the 6756 transcripts found to be expressed in our dataset, 493 were significantly upregulated in planta compared to axenic culture (logFC > 2, adjusted p-value < 0.1), while 1138 transcripts were significantly downregulated. Notably, transcripts predicted to encode secreted proteins are significantly enriched among the upregulated transcripts compared to all annotated genes.

overall_design: RNA-seq analysis of axenically grown Ustilago bromivora UB1 and Brachypodium hybridum Bd28 infected with Ustilago bromivora spores (twelve days after planting of infected caryopses) using Illumina NGS. The study was performed in triplicates.

first: Franziska

last: Rabe

first: Heinz

last: Ekker

first: Armin

last: Djamei


title: Bevacizumab-resistant HT-29 tumors vs untreated control

status: Public on Sep 08 2016

city: Chiba

first: Yukie

last: Yoshii

address: Anagawa 4-9-1, Inage

institute: National Institute of Radiological Sciences

summary: Gene expression of bevacizumab-resistant HT-29 tumors vs untreated control

overall_design: Sample tissues were immediately frozen by liquid nitrogen after isolation. Total RNAs were extracted from samples with a PureLink RNA Mini Kit (Life Technologies). The integrity of total RNAs was evaluated using an Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA, USA). Low Input Quick Amp Labeling Kit, one-color (Agilent Technologies) was used to prepare Cy3-labelled target cRNA according to the manufacturer's instructions. Labeled cRNAs were hybridized with a SurePrint G3 Human GE 8×60K Microarrays (Agilent Technologies). Three separate hybridizations were performed for each sample. Array images were captured using a DNA Microarray Scanner (Agilent Technologies), and data were analyzed using Feature Extraction Software (Agilent Technologies) to obtain background-corrected signal intensities. Data were further analyzed with GeneSpring GX Software (Version 11.0, Agilent Technologies). After data filtering, mRNAs differentially expressed in target cells versus controls were assessed by Fisher’s exact test, followed by multiple corrections using the Benjamini and Hochberg false discovery rate (FDR) method. Gene sets with a FDR q-value < 0.05 were considered to be significant.


title: Characterization of Type I Interferon pathway during Hepatic   Differentiation of Human Pluripotent Stem Cells and hepatitis C virus   infection

city: Los Angeles

first: Wolf

last: Wiedemeyer

state: California

address: 8700 Beverly Blvd.

department: BMS

institute: Cedars-Sinai

summary: Pluripotent stem cells are being actively studied as a cell source for regenerating damaged liver.   For long term survival of engrafting cells in the body, not only do the cells have to execute liverspecific  function but also withstand the physical strains and invading pathogens. The cellular  innate immune system orchestrated by the interferon (IFN) pathway provides the first line of  defense against pathogens. The objective of this study is to assess the innate immune function  as well as to systematically profile the IFN-induced genes during hepatic differentiation of  pluripotent stem cells. To address this objective, we derived endodermal cells (day 5 postdifferentiation),  hepatoblast (day 15) and immature hepatocytes (day 21) from human embryonic  stem cells (hESC). Day 5, 15 and 21 cells were stimulated with IFN-α and subjected to IFN  pathway analysis. Transcriptome analysis was carried out by RNA sequencing. The results  showed that the IFN-α treatment activated STAT-JAK pathway in differentiating cells.  Transcriptome analysis indicated stage specific expression of classical and non-classical IFNstimulated  genes (ISGs). Subsequent validation confirmed the expression of novel ISGs  including RASGRP3, CLMP and TRANK1 by differentiated hepatocytes upon IFN treatment.  Hepatitis C virus replication in hESC-derived hepatic cells induced the expression of ISGs –  LAMP3, ETV7, RASGRP3, and TRANK1. The hESC-derived hepatic cells contain intact innate  system and can recognize invading pathogens. Besides assessing the tissue-specific functions  for cell therapy applications, it may also be important to test the innate immune function of  engrafting cells to ensure adequate defense against infections and improve graft survival.

overall_design: 12 samples total, 4 samples in each time point (day 5, day 15, day 21).  Each group of 4 within each time point has 2 control and 2 treatment samples in which the cells were stimulated with human interferon-alpha A (R and D Systems) at a concentration of 5000 IU for 6 hours.

first: Joseph

middle: I

last: Irudayam

first: Deisy

last: Contreras

first: Lindsay

last: Spurka

first: Aparna

last: Subramanian

first: Jenieke

last: Allen

first: Songyang

last: Ren

first: Vidhya

last: Kanagavel

first: Quoclinh

last: Nguyen

first: Arunachalam

last: Ramaiah

first: Kalidas

last: Ramamoorthy

first: Samuel

middle: W

last: French

first: Andrew

last: Klein

first: Vincent

last: Funari

first: Vaithilingaraja

last: Arumugaswami


title: Pho and Ph, H3K27me3 and Engrailed ChIP-seq data in PRE-deleted third instar Drosophila larval brains and disks and 4C-seq data in the third instar larval brains and disks

status: Public on Sep 24 2016

city: North Bethesda

first: sandip

last: de

state: MD

address: 6 center drive

department: rm 3B-331, bldg 6B

institute: NICHD/NIH

summary: Genome-wide binding profile of PcG proteins- Pho and Ph, H3K27me3 and Engrailed in Drosophila third instar larval brains and disks, in duplicate, using Illumina HiSeq 2500. The sequence reads that passed quality filters were analyzed.

overall_design: Drosophila third instar larval brains and disks were dissected and fixed with 2% HCHO before sonication. After sonication, chromatin immunoprecipitation was carried out.

first: Sandip

last: De

first: Harold

last: Smith

first: Judith

last: Kassis


title: Characterization of Two Novel Ependymoma Cell Lines with Chromosome 1q gain derived from Posterior Fossa Tumors of Childhood

status: Public on Sep 09 2016

city: Aurora

middle: M

last: Donson

state: CO

department: Pediatrics

institute: CU Anschutz Medical Campus

summary:
Introduction: Ependymoma (EPN) studies have revealed certain genetic markers, such as gain of chromosome 1q (1q+), as indicators of poor survival and high rate of recurrence. Development of novel therapeutics for EPN has been hampered by a lack of in vivo and in vivo models. We describe two unique 1q+ cell lines (811 and 928) derived from two children with metastatic, recurrent EPN. Both cell lines were characterized using histological, karyotypic and transcriptomic methods
Transcriptomic analysis revealed that both lines, when cultured in 3D format, clustered closer to primary EPN tumors than monolayer format and with better fidelity of EPN-specific transcripts, namely those related to cilia function. Additionally, 3D culture histology revealed striking ependymal rosette formation, similar to primary tumors. Transcriptional enrichment of extracellular matrix, however, was a common signature of EPN primary tumor and cell lines in both monolayer and 3D formats.

overall_design: Gene expression profiles were generated from cell cultures, surgical tumor and normal brain samples (n=110) using Affymetrix HG-U133plus2 chips (Platform GPL570).


title: m6A RNA methylation promotes XIST-mediated transcriptional repression

status: Public on Sep 07 2016

city: New York

first: Deepak

last: Patil

address: 1300 York Avenue, LC-523, Box 70

department: Pharmacology

institute: Weill Cornell Medical College

summary: XIST is a long non-coding RNA (lncRNA) that mediates transcriptional silencing of X chromosome genes. Here we show that XIST is highly methylated with at least 78 N6-methyladenosine (m6A) residues, a reversible base modification whose function in lncRNAs is unknown. We show that m6A formation in XIST, as well as cellular mRNAs, is mediated by RBM15 and its paralog RBM15B, which bind the m6A-methylation complex and recruit it to specific sites in RNA. This results in methylation of adenosines in adjacent m6A consensus motifs. Furthermore, knockdown of RBM15 and RBM15B, or knockdown of the m6A methyltransferase METTL3 impairs XIST-mediated gene silencing. A systematic comparison of m6A-binding proteins shows that YTHDC1 preferentially recognizes m6A in XIST and is required for XIST function. Additionally, artificial tethering of YTHDC1 to XIST rescues XIST-mediated silencing upon loss of m6A. These data reveal a pathway of m6A formation and recognition required for XIST-mediated transcriptional repression.

overall_design: Three to four biological HEK293T replicates were used to perform iCLIP of endogenous YTH proteins, RBM15, and RBM15B. Crosslinking induced truncations were identified using CIMS-CITS pipeline.

first: Chun-Kan

last: Chen

first: Brian

last: Pickering

first: Amy

last: Chow

first: Constanza

last: Jackson

first: Mitchell

last: Guttman

first: Samie

last: Jaffrey


title: Ovol2 expression in germ cells

status: Public on Aug 31 2016

city: Tsukuba

first: Kuniya

last: Abe

state: Ibaraki

address: 3-1-1 Koyadai

department: BioResource Center

institute: RIKEN

summary: To analyze gene expression patterns of mouse Ovo-like gene family genes, global gene expression profiles of ES cells and germ cells were determined by Agilent microarray.

overall_design: ES cells were cultured as undifferentiated state on feeder layers. For harvesting the ES cells, the stem cells were separated from feeder cells, and RNA was extracted from the ESCs. Embryonic germ cells were isolated from Oct4-GFP mice by FACS and RNAs were extracted from purified germ cells.


title: The destiny of the resistance/susceptibility against GCRV has been congenitally destined by epigenetic mechanism in CIK cells (MeDIP-seq)

first: Ze-Guang

last: Han

first: Jianguo

last: Su

first: Xueying

last: Shang