title: Luteolin attenuates hepatic and adipocyte fibrosis and insulin resistance by targeting toll-like receptors signaling pathway in diet-induced obese mice

status: Public on Mar 06 2018

city: Daegu

first: Myung-Sook

last: Choi

address: 1370, Sankyuk-Dong, Buk-gu

department: Food and Nutrition

institute: Kyungpook National University

summary: The flavonoid luteolin possess a variety of anti-inflammatory properties, but little has known about the detailed mechanisms linked to the anti-metabolic syndrome action of luteolin based on the integration of the transcriptional profile and the phenotype biomarkers. The aim of this study was to investigate the protective role of luteolin on inflammation-mediated metabolic diseases, focusing on its role in modulating toll-like receptor (TLR) signaling pathway triggered up-regulation of pro-inflammatory cytokines. Above all, it provides novel insights into the effect of luteolin on the link among adiposopathy, insulin resistance, hepatic steatosis and fibrosis. C57BL/6J mice were fed a normal, high-fat, and high-fat + 0.005% (w/w) luteolin diet for 16 weeks. In this study, (a) luteolin treatment resulted in an improvement in chronic low-grade inflammation by modulating TLR-signaling pathway resulting in reduced pro-inflammatory cytokines and macrophage accumulation; (b) there is a positive relationship of TLR5, MKK4/7, p38 and JNK-related gene expressions and lipogenesis in luteolin-treated obese mice, which is linked to an attenuation of hepatic lipotoxicity with an increased hepatic anti-oxidant system; (c) luteolin prevented hepatic and adipocyte fibrosis by decreasing ECM accumulation and cathepsin gene expressions; (d) Emr1 and Ccl7 genes, important markers inducing low-grade inflammation, are affected by advancing age as well as body weight, and luteolin treatment normalized those gene expressions; (e) luteolin treatment improved insulin resistance by normalizing pancreatic islet dysfunction, and differentially modulating the plasma GLP-1 and GIP levels. Taken together, luteolin ameliorates the deleterious effects of diet-induced obesity and its comorbidity.

overall_design: Total RNA of adipose tissues was obtained from normal diet, high-fat diet and luteolin added high-fat diet-fed mice and mRNA expression-associated with inflammation was measured.

first: Eun-Young

last: Kwon


title: Physiological concentration changes of intracellular spermine activates DNA methyltransferase 3A and 3B and affects gene methylation

status: Public on Mar 15 2018

city: Saitama

first: Taro

last: Fukui

address: 1-847 Amanuma-cho Omiya-ku

department: Surgery

country: Japan

institute: Jichi Medical University, Saitama Medical Center

type: Methylation profiling by genome tiling array

summary: Polyamines are essential for various cell functions and are produced in most cells, as well as being taken up from extracellular sources. Polyamines, especially spermine, in blood cells increase when polyamines are supplied from the digestive tract. Altered polyamine metabolism has an impact on substrate concentrations and enzyme activities involved in gene methylation, and may affect gene expression. Therefore, we investigated the effect of decreased polyamine synthesis and extracellular spermine supply on substrate concentrations and enzyme activities involved in gene methylation and on changes of methylation in promoter regions using methylation arrays. In Jurkat cells and human mammary epithelial cells, changes in polyamine concentrations differed after polyamine synthesis inhibition. However, S-adenosylmethionine decarboxylase activity and the decarboxylated S-adenosylmethionine to S-adenosyl-L-methionine ratio were decreased by spermine addition in both cells. After inhibiting polyamine synthesis in Jurkat cells by D,L-alpha-difluoromethylornithine, the protein levels of DNA methyltransferase (DNMT) 1, 3A and 3B were not changed, but the activity of the three enzymes markedly decreased. The protein levels of these enzymes were not changed by addition of spermine; however, DNMT 3B was markedly activated and DNMT 3A was also activated. DNMT 1 was not activated. Effects on methylation of promoter regions included significant changes for tumor suppressor genes in response to altered polyamine metabolism. However, no significant changes in methylation status were found on genes of which methylation status and their related protein levels were affected by spermine. When considering these results, there are many genes for which polyamines have an impact on expression via methylation of promoter regions.

overall_design: In order to asess the methylation status under depletion or supplementation of polyamine (Spermine), four DNA samples obtained from Jurkat cells cultured in  were analyzed in four different conditon as follows; Control,   D,L-alpha-difluoromethylornithine (DFMO)(+), Spermine (+), DFMO+Spermine

first: Kuniyasu

last: Soda


title: CHD7 specifies stem cell identity and neurogenic potential in neural progenitors by regulating SOX21 and BRN2 expression in human central nervous system

status: Public on Mar 28 2018

city: Shinjuku-ku

first: Tsukasa

last: Sanosaka

state: Tokyo

address: 35 Shinanomachi

department: Department of Physiology

institute: Keio University School of Medicine

summary: We performed a microarray experiment to analyze the transcriptional profile of human iPSC-derived neural stem/progenitor cells to identify CHD7 target genes

overall_design: AF22 cell were infected with shCTRL, sh410, or sh411 lentivirus to knock down CHD7. After knock down, CHIR was added to induce neuronal differentiation and cultured in N2 medium or N2+B27 medium. Each experiment was duplicated.


title: Genome-wide microRNA analysis of reticulocytes isolated from patients with sickle cell disease

status: Public on Mar 03 2018

city: Augusta

first: Biaoru

last: Li

state: GA

department: Pediatrics

country: USA

institute: MCG

summary: MiRNAs are non-protein-coding small RNA molecules negatively regulating gene through inhibition of mRNA. The characteristics of microRNA expression patterns obtained from sickle cell diseases are not clearly elucidated. In this study, we recruited 12 children and adults suffering from sickle cells diseases with high HbF fetal hemoglobin (HbF) group (6 subjects) and lower HbF (6 subjects). The peripheral blood mononuclear cell (PBMN) were processed using a MACS column with magnetic anti-CD71 antibody to isolate reticulocytes according to the manufacturer’s instructions (Miltenyi Biotec, San Diego, CA). After data normalization, 327 miRNA were identified by PCA (principal component analysis) as differentially expressed in low HbF group compared to high HbF groups.

platform_organism:
Homo sapiens
Mus musculus
Rattus norvegicus

overall_design: Twelve samples were isolated from six sickle cell disease (SCD) patients with high HbF and six with low HbF levels were analyzed. Informed consent was obtained from the subjects and the study was approved by the Institutional Review Boards. Five milliliters of whole-blood were collected from the SCD peripheral blood in EDTA tubes. Following Histopaque separation under centrifuge condition 500g for 30 min, the CD71+ cells located in a layer below peripheral blood mononuclear cell were isolated using a MACS column with magnetic anti-CD71 antibody to isolate reticulocytes according to the manufacturer’s instructions (Miltenyi Biotec, San Diego, CA). Total RNA was extracted from the CD71+ cell by Trizol solution according to the manufacturer’s instructions. After dissolving in 30 μl of RNase free water, the RNA concentration (A260 nm) and purity (A260/280 and A260/230 ratios) were assessed with a ND-1000 spectrophotometer (Thermo Scientific, Wilmington DE) and quality measurement was assayed by Experion equipment (BIO-RAD, Hercules, CA). The RNA was stored at −80°C until further analysis. Subsequently, RNA was isolated from CD71+ cell and used for microRNA Array (Exiqon) containing 1921 human probes for 568 microRNAs mined by two colour data after normalization.

first: B

middle: S

last: Pace

first: C

last: Neunert

first: A

last: Kutlar


title: Low-coverage TAC-seq expression in endometrium

status: Public on Mar 01 2018

city: Tartu

first: Kaarel

last: Krjutskov

state: Tartumaa

address: Teaduspargi tänav 13

country: Estonia

institute: The Competence Centre on Health Technologies

summary: Transcriptomic biomarker detection assay for targeted 57 human uterus endometrium receptivity testing with TAC-seq (targeted allele counting by sequencing).

overall_design: Studied biomarker transcripts were detected by specific 54 bp-long region. Two ligation probes hybridize with target cDNA and ligate. Ligated detector probes are captured, amplified by PCR and sequenced

first: Mariann

last: Koel

first: Priit

last: Paluoja


title: sRNAseq from Arabidopsis leaves non-infected and infected with Turnip mosaic virus (TuMV)

city: Murcia

first: Livia

last: Donaire

state: Murcia

address: Campus de Espinardo

department: Plant Pathology

country: Spain

institute: Centro de Edafología y Biología Aplicada del Segura

type: Non-coding RNA profiling by high throughput sequencing

summary: Sequencing of small RNAs from Arabidopsis leaves non-infected and infected with Turnip mosaic virus at 14 days post inoculation

first: Irene

last: Guzmán-Benito

first: Cesar

last: Llave


title: CRISPR-Cas9 screens in human cells and primary neurons identify modifiers of C9orf72 dipeptide repeat protein toxicity

status: Public on Feb 27 2018

city: Boston

first: Nicholas

middle: J

last: Kramer

state: MA

address: 77 Avenue Louis Pasteur

department: Genetics

institute: Harvard Medical School

type: Expression profiling by high throughput sequencing

summary: Hexanucleotide repeat expansions in the C9orf72 gene are the most common cause of amyotrophic lateral sclerosis and frontotemporal dementia (c9FTD/ALS). The nucleotide repeat expansions are translated into dipeptide repeat (DPR) proteins, which are aggregation-prone and may contribute to neurodegeneration. We used the CRISPR-Cas9 system to perform genome-wide gene knockout screens for suppressors and enhancers of C9orf72 DPR toxicity in human cells. We validated hits by performing secondary CRISPR-Cas9 screens in primary mouse neurons. We uncovered potent modifiers of DPR toxicity whose gene products function in nucleocytoplasmic transport, the endoplasmic reticulum (ER), proteasome, RNA processing pathways, and in chromatin modification. One modifier, TMX2, modulated the ER-stress signature elicited by C9orf72 DPRs in neurons, and improved survival of human induced motor neurons from C9orf72 ALS patients. Together, this work demonstrates the promise of CRISPR-Cas9 screens to define mechanisms of neurodegenerative diseases. This dataset contains the RNA-sequencing data used to support the conclusions from this study.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design:
Differential gene expression derived from RNA-sequencing data, analyzed using DESeq2. 3 independent experiments were performed for this study, each had 6 samples per experiment (3 biological replicate controls and 3 biological replicate experimental conditions).

Experiment #1 = K562 cells treated with 10uM synthetic PR20 peptides compared to untreated controls (samples GSM2934784 - GSM2934789).

Experiment #2 = primary mouse cortical neuron cultures from Cas9+ mice with control sgRNAs or TMX2 targeting sgRNAs, both groups expressing PR50 (samples GSM2934790 - GSM2934795).

Experiment #3 = primary mouse cortical neuron cultures treated with a control GFP lentivirus or a lentivirus expressing PR50 (samples GSM2934796 - GSM2934801).

first: Michael

last: Haney

first: Julien

last: Couthouis

middle: C

last: Bassik

first: Aaron

middle: D

last: Gitler


title: ERCC TAC-seq

summary: Targeted assay to detect 22 selected ERCC spike-in mRNA molecules for method sensitivity testing purposes

overall_design: ERCC spike-in cDNA molecules were detected by 54 bp-long specific region. Ligation oligos were hybridized under stringent conditions and therefore ligated. Ligated probes were captured, amplified by PCR and sequenced

last: Krjutshkov


title: Pervasive transcription-dependent chromatin remodeling influences the replication initiation program

status: Public on Feb 24 2018

city: Geneva

last: Soudet

address: 30 quai Ansermet

department: BICEL

country: Switzerland

institute: Université de Genève

type: Genome binding/occupancy profiling by high throughput sequencing

summary: We report here the importance of pervasive transcription in the regulation of replication origins activity in S. cerevisiae. Replication profiles and chromatin profiles were obtained by BrdU-seq and MNase-seq respectively.

overall_design: BrdU-seq was performed 70min after release from G1-phase at 18°C in Nrd1-AA, Nrd1-AA dSet2 and Ysh1-AA strains. MNase-seq was performed after 1h of Rapamycin treatment in Nrd1-AA cells.

first: J

last: Kaur

first: F

last: Stutz


title: 10X single-cell RNASeq profiling of immune infiltrate from Adar1 KO and Wildtype B16 Melanoma

status: Public on Feb 17 2018

first: Kevin

last: Bi

address: 450 Brookline Ave.

department: Pediatric Oncology

institute: Dana-Farber Cancer Institute

summary: Knockout of Adar1 in B16 melanoma results in global reprogramming of the tumor immune microenvironment

overall_design: Profiling of immune infiltrate from 2 Adar1 KO B16 tumors and 2 B16 Wildtype tumors

first: Brian

last: Miller

first: Jeffrey

last: Ishizuka


title: Single cell profiling of the developing mouse brain and spinal cord with split-pool barcoding

status: Public on Feb 21 2018

city: Seattle, WA 98195

first: Alexander

middle: B

last: Rosenberg

state: WA

address: 4000 15th Ave NE

department: Electrical Engineering

institute: University of Washington

summary: To facilitate scalable profiling of single cells, we developed Split Pool Ligation-based Transcriptome sequencing (SPLiT-seq), a single-cell RNA-seq (scRNA-seq) method that labels the cellular origin of RNA through combinatorial barcoding. SPLiT-seq is compatible with fixed cells or nuclei, allows efficient sample multiplexing and requires no customized equipment. We used SPLiT-seq to analyze 156,049 single-nucleus transcriptomes from postnatal day 2 and 11 mouse brains and spinal cords. Over 100 cell types were identified, with gene expression patterns corresponding to cellular function, regional specificity, and stage of differentiation. Pseudotime analysis revealed transcriptional programs driving four developmental lineages, providing a snapshot of early postnatal development in the murine central nervous system. SPLiT-seq provides a path towards comprehensive single-cell transcriptomic analysis of other similarly complex multicellular systems.

overall_design:
Single-cell/nucleus RNA-seq was performed using SPLiT-seq

This code explains how to read the data from the paper into python:
https://gist.github.com/Alex-Rosenberg/5ee8b14ea580144facad9c2b87cebf10

first: Charles

last: Roco


title: Heavy adolescent cannabis consumption produces social and cognitive deficits in adulthood

city: Bonn

first: Joachim

last: Schultze

state: NRW

address: Carl-Troll-Strasse 31

department: Genomics and Immunoregulation

country: Germany

institute: LIMES (Life and Medical Sciences Center Genomics and Immunoregulation)

summary: Population-based studies show cannabis use doubles the risk of developing schizophrenia especially when use occurs in early adolescence (prior to age 15).  However, the cause-and-effect mechanisms are largely unknown. To investigate the effect of cannabis on brain maturation and relation to the development of psychosis-like behaviours in adulthood, we treated young adolescent mice with vehicle or cannabis extract once a day for 2 weeks between postnatal days 14 and 28, and then collected hippocampal tissue for microarray analysis 12 weeks later.  We identify a total of 78 differentially expressed genes (25 upregulated and 53 downregulated; p<0.05, fold change ± 1.2) and validate increases in dopamine D2 receptor (Drd2) and fatty acid amide hydrolase (Faah). Changes in Faah expression were limited to the hippocampus however Drd2 also increased in striatum but not prefrontal cortex or amygdala. When tested in adulthood with a behavioural panel relevant to schizophrenia, cannabis-treated mice displayed lower anxiety in the elevated zero-maze, decreased social preference, increased social novelty preference, mild cognitive impairments in a spatial version of the novel object recognition task and absence of latent inhibition when compared to vehicle controls.  Adolescent treatment with cannabis extract thus lead to long-lasting changes in gene expression within the hippocampus which together result in behavioural deficits consistent with the negative and positive symptoms of schizophrenia.

overall_design: Cannabis extract was obtained from GW Pharmaceuticals (Cambridge, UK) and a dose of 20 mg/kg was administered daily for 14 days to C57BL/6J mice. A 1 mg/mL solution was prepared in vehicle consisting of 50% (v/v) sweet condensed milk containing 10% fat (Baeren Brand, Allgaeuer Alpenmilch GmbH, Muehldorf, Germany) + 0.25% (v/v) olive oil. Extract was first dissolved in 1%(v/v) EtOH at RT for 30 min, after which olive oil was added and samples allowed to dissolve overnight. The EtOH was then evaporated at 70oC and a solution of 50% sweet condensed milk was added to make the final emulsion. Vehicle solutions were made in parallel, omitting the cannabis extract. Pups were habituated to handling on postnatal days 12-13. Pups were then weighed and fed daily by hand using a blunted needle and syringe (not by gavage) from P14 until P28. Average feeding time was between 10-30 minutes per pup. Litters selected for vehicle and cannabis treatment were rotated between dams to minimize maternal care effects. Sires were never housed with pups. Animals were tested concerning behaviour, sucrose preference, elevated zero-maze (EOM), open-field, prepulse inhibition, startle reactivity, latent inhibition, social preference and novelty, Y-maze continuous alternations, novel object recognition, and drug-induced hypermotility. P28 animals were sacrificed 70-80 minutes following the beginning of feeding and in a separate room to that where per os administration took place. Adult animals were sacrificed two weeks following PCP-induced hyperlocomotion to allow sufficient time for drug washout. All mice were anaesthetized with isoflurane until loss of tail-pinch reflex then decapitated and brains removed. Brains were quickly cut into 1mm sections using a mouse brain matrix (Zivic Instruments, Pittsburgh, PA, USA) and sections placed in ice-cold ACSF ((26 mM NaHCO3, 124 mM NaCl, 5 mM KCl, 2 mM CaCl2, 1.3 mM MgCl2, 10 mM D- glucose, 100 U/ml penicillin, and 100 µg/ml streptomycin; all from Sigma-Aldrich). The following regions were dissected using a stereomicroscope: prefrontal cortex, striatum (sometimes further divided into dorsal and ventral regions), hippocampus, and amygdala; then snap frozen in liquid nitrogen and stored at -80oC until further use.

first: S

last: Imbeault

first: A

middle: M

last: Draffehn

middle: L

last: Zimmer


title: DNA methylation signature defines genes modulated by stromal cell contents of human breast tumors [MethylationEPIC]

status: Public on Feb 22 2018

city: Lyon

first: Robert

last: Dante

address: 28, rue Laennec

department: Department of Tumoral Escape

country: France

institute: Cancer Research Center – Lyon

summary: Using genome-wide approaches we have identified groups of genes modulated by CAF-secreted factors from human breast cancer cell lines grown in different CAF-conditioned medium. The genes modulated by CAF secreted factors were characterized by a specific DNA methylation pattern: hypermethylation at transcription start site (TSS) and shore regions. Approximately 60% of them exhibited a methylation-dependent expression level and 20% of them were also dependent on the methyl-CpG-binding protein domain 2. Thus, these specific DNA methylation patterns were linked to an epigenetic control of their expression, upon CAF-secreted factors. We have therefore identified some molecular events defining the responsiveness of groups of genes to stromal cell contents in human breast tumors.

overall_design: SBR3 and AU565 cell lines none treated or treated with CAF-conditionned medium or with Decitabine in duplicate

first: Pauline

last: Mathot

first: Mélodie

last: Grandin

first: Guillaume

last: Devailly

first: Frédérique

last: Souaze

first: Vincent

last: Cahais

first: Sebastian

last: Moran

first: Mario

last: Campone

first: Zdenko

last: Herceg

first: Manel

last: Esteller

first: Philippe

last: Juin

first: Patrick

last: Mehlen


title: Identification of LEC1 binding sites in Arabidopsis seeds during  embryo expansion stage

status: Public on Feb 15 2018

city: guangzhou

first: yilong

last: hu

state: guangdong

address: No.723, xingke road, tianhe district

country: China

institute: south china botanical gardern, chinese academy of science

summary: LEAFY COTYLEDON1 (LEC1), a subunit of the NF-Y CCAAT binding transcription factor, is a key regulator that controls many aspects of seed development including embryo growth and seed storage accumulation. To identified genomic region bound by LEC1 and target genes of LEC1, we expressed a FLAG-tagged form of LEC1 under the control of its native promoter and terminator in lec1-4  mutant seeds. Using an anti-FLAG antibody (Sigma), we performed chromatin immunoprecipitation followed by sequencing (ChIP-Seq) using chromatin isolated from mature stage seeds to identify the genes bound by LEC1. These data reveal that the transcription regulation network of LEC1.

overall_design:
Identification of LEC1 binding sites in arabidopsis seeds at seed mature stages. ChIP and total chromatin controls (input) were were generatedby deep sequencing, with two biological replicates, using Illumina HiSeq 2500.

Please note that the peak files were generated from both ChIP and input samples together and are linked to the correspdonding ChIP sample records.

first: Xingliang

last: hou

first: Yilong

last: Hu


title: Whole methylome analysis of SEM cell lines

status: Public on Feb 12 2018

city: Rostock

first: Catrin

last: Roolf

address: Ernst-Heydemann-Str 6

institute: Rostock university medical center

summary: Genome-wide DNA methylation profiling of human B-ALL cell line SEM after 48 h incubation with DMSO (control), CX-4945 (Silmitasertib), Decitabine (DEC) or combined CX-4945 + DEC treatment. The Infinium MethylationEPIC BeadChip was used to obtain DNA methylation profiles across approximately 866,895 CpG islands.

overall_design: Bisulfite treated DNA of 4 samples was hybridised to the Infinium MethylationEPIC BeadChip

first: Anna

last: Richter

first: Christian

last: Junghanss

first: Mohamed

last: Hamed

first: Yvonne

last: Gladbach

first: Georg

last: Fuellen


title: FHL3 overexpression microarray

status: Public on Feb 02 2018

city: Beijing

first: Wei

last: Han

address: Dongdansantiao 5

institute: CAMS&PUMC

summary: To investigate the target genes of FHL3 in glioma cells, we conducted a gene expression microarray analysis to identify novel FHL3 regulating genes. The FHL3 overexpressed T98G glioma cells l were used as the experiments model. We conservatively established a minimum of 2-fold difference between FHL3 and control group, with an FDR-adjusted P value of less than 0.05, and identified 285 up-regulated and 420 down-regulated genes that met the threshold in all microarray analyses of 3 independent groups.

overall_design: Total RNA from approximately 10e6 T98G cells transfected with vector or FHL3 was extracted using Trizol reagent (Invitrogen). The RNA integrity was measured at an Agilent Bioanalyzer 2100 instrument (Agilent Technologies, Santa Clara, CA). The gene expression microarrays including 3 technical replicates of FHL3 overexpression versus the empty vector were performed at the ShanghaiBio Corporation. We conservatively established at least 2-fold difference, with an FDR-adjusted P value of less than 0.05 as the cut-off values. The biological functions (gene ontology) of the preferential FHL3-regulating genes identified by microarray analysis were determined with the web-based SBC analysis system.


title: Impact of regulatory variation across human iPSCs and differentiated cells [methylation]

status: Public on Feb 13 2018

city: Chicago

first: Nicholas

middle: E

last: Banovich

state: IL

address: 920 E. 58th Street, CLSC 317

department: Human Genetics

institute: University of Chicago

summary: Induced pluripotent stem cells (iPSCs) are an essential tool for studying cellular differentiation and cell types that are otherwise difficult to access. We investigated the use of iPSCs and iPSC-derived cells to study the impact of genetic variation on gene regulation across different cell types and as models for studies of complex disease. To do so, we established a panel of iPSCs from 58 well-studied Yoruba lymphoblastoid cell lines (LCLs); 14 of these lines were further differentiated into cardiomyocytes. We characterized regulatory variation across individuals and cell types by measuring gene expression levels, chromatin accessibility and DNA methylation. Our analysis focused on a comparison of inter-individual regulatory variation across cell types. While most cell type-specific regulatory quantitative trait loci (QTLs) lie in chromatin that is open only in the affected cell types, we found that 20% of cell type-specific regulatory QTLs are in shared open chromatin. This observation motivated us to develop a deep neural network to predict open chromatin regions from DNA sequence alone. Using this approach, we were able to use the sequences of segregating haplotypes to predict the effects of common SNPs on cell type-specific chromatin accessibility.

overall_design: Bisulfite converted DNA from feeder free iPSCs for meQTL analysis.

first: Yang

middle: I

last: Li

first: Anil

last: Raj

first: Michelle

last: Ward

first: Po-Yuan

last: Tung

first: Jonathan

last: Burnett

first: Marsha

last: Myrthil

first: Samantha

last: Thomas

first: Diego

last: Calderon

first: Peyton

last: Greenside

first: Anshul

last: Kundaje

middle: K

last: Pritchard

first: Yoav

last: Gilad


title: Microarray analysis of microRNAs in CSF and blood of SAH patients

status: Public on Feb 01 2018

city: Kamakura

first: Satoshi

last: Kondo

state: Kanagawa

address: Tebiro 6-10-1

department: New Projects Development Division

institute: Toray Industries,Inc.

summary: The aim of the analysis is to identify changes in the microRNAs expression in early phase after SAH.

overall_design: This study includes one control sample and two SAH samples.

first: Yuchiro

last: Kikkawa

first: Kozue

last: Watanabe

first: Hiroki

last: Kurita

first: Ryota

last: Kurogi


title: Tissue-specific gene expression changes in l(3)mbt mutant ovaries [soma]

city: Paris

first: Remi-Xavier

last: Coux

address: 25 rue du docteur Roux

department: Developmental and Stem Cell Biology dpt

institute: Pasteur Institute

summary: We performed RNAseq on l(3)mbt mutant somatic ovaries to gain a genome-wide view of tissue-specific gene expression changes in L(3)mbt-depleted somatic ovaries.

overall_design: Examination of gene expression changes in mutant and control somatic ovaries.

first: Remi

middle: X

first: Ruth

last: Lehmann


title: Sulfamethoxazole – Trimethoprim represses csgD but 2 maintains virulence genes at 30°C in a clinical 3 Escherichia coli O157:H7 isolate

status: Public on Feb 08 2018

city: Wyndmoor

first: Gaylen

last: Ulrich

state: PA

address: 600 East Mermaid Lane

institute: USDA/ARS/Eastern Regional Research Center

summary: The high frequency of prophage insertions in the mlrA gene of clinical serotype O157:H7  isolates renders such strains deficient in csgD-dependent biofilm formation but prophage  induction may restore certain mlrA properties. In this study we used transcriptomics to  study the effect of high and low sulfamethoxazole–trimethoprim (SMX-TM)  concentrations on prophage induction, biofilm regulation, and virulence gene expression  in strain PA20 under environmental conditions following five-hour and 12-hour  exposures. SMX-TM at a sub-lethal concentration induced strong RecA expression  resulting in concentration- and time-dependent major transcriptional shifts with emphasis  on up-regulation of genes within horizontally-transferred chromosomal regions (HTR).  Neither high or low levels of SMX-TM stimulated csgD expression at either time point,  but both levels resulted in slight suppression. Full expression of Ler-dependent genes  paralleled expression of group 1 pch homologues in the presence of high glrA. Finally,  stx2 expression, which is strongly dependent on prophage induction, was enhanced at 12  hours but suppressed at five hours, in spite of early SOS initiation by the high SMX-TM  concentration. Our findings indicate that, similar to host conditions, exposure to  environmental conditions increased the expression of virulence genes in a clinical isolate  but genes involved in the protective biofilm response were suppressed.

overall_design: We evaluated mRNA expression profile of 2 time points and 3 sulfamethoxazole–trimethoprim (SMX-TM) concentrations

middle: A

last: Uhlich

first: Elisa

last: Andreozzi

first: Bryan

last: Cottrell

first: Erin

middle: R

last: Reichenberger

first: Xinmin

last: Zhang

first: George

last: Paoli


title: RNA-directed DNA methylation involves co-transcriptional small RNA-guided slicing of Pol V transcripts in Arabidopsis.

status: Public on Jan 29 2018

city: Haining

first: Wanlu

last: Liu

state: Zhejiang

address: 718 East Haizhou Rd.,

department: Zhejiang University - University of Edinburgh Institute

institute: Zhejiang University

summary: Small RNAs regulate chromatin modifications such as DNA methylation and gene silencing across eukaryotic genomes. In plants, RNA-directed DNA methylation (RdDM) requires 24-nucleotide (nt) small RNAs (siRNAs) that bind ARGONAUTE4 (AGO4) and target genomic regions for silencing. It also requires non-coding RNAs transcribed by RNA POLYMERASE V (Pol V), that likely serve as scaffolds for binding of AGO4/siRNA complexes. Here we utilized a modified global nuclear run-on (GRO) protocol followed by deep sequencing to capture Pol V nascent transcripts genome-wide.  We uncovered unique characteristics of Pol V RNAs, including a uracil (U) common at position 10.  This uracil was complementary to the 5’ adenine found in many AGO4-bound 24-nt siRNAs and was eliminated in an siRNA-deficient mutant as well as in the ago4/6/9 triple mutant, suggesting that the +10U signature is due to siRNA-mediated co-transcriptional slicing of Pol V transcripts. Expressing wild-type AGO4 in ago4/6/9 was able to restore slicing of Pol V transcripts but a catalytically inactive AGO4 mutant did not correct the slicing defect. We also found that Pol V transcript slicing required the little understood elongation factor SPT5L.  These results highlight the importance of Pol V transcript slicing in RNA-mediated transcriptional gene silencing, which is a conserved process in many eukaryotes.

overall_design: 17 GROseq, 4 small RNAseq


title: Zfp36l1 overexpression/knockdown effect on primary mouse articular chondrocytes

status: Public on Feb 14 2018

city: Gwangju

first: Yoonkyung

last: Won

address: 123 Cheomdangwagiro

country: South Korea

institute: Gwangju Institute of Science and Technology

summary:
Gene expression profiling of primary mouse articular chondrocyte infected with recombinant adenovirus expressing mouse ZFP36 Ring Finger Protein Like 1(Zfp36l1) or recombinant adenovirus expressing mouse small hairpin RNA of Zfp36l1.
In this study, we have attempted to explore the effects of Zfp36l1 gene overexpression or knockdown on mouse transcriptome and have identified numerous genes which are involved in osteoarthritis pathogenesis.

overall_design: Primary mouse articular chondrocytes were isolated from mouse femoral condyles and tibial plateaus cartilage tissue and were infected with null (control) or recombinant adenovirus expressing ZFP36 Ring Finger Protein Like 1 (Ad-Zfp36l1) or small hairpin RNA of Zfp36l1(Ad-shZfp36l1) for 36 hours. At 36 hours post-infection, total RNA was extracted from infected with null control adenovirus (3 biological replicates) or infected with recombinant Ad-Zfp36l1 (3 biological replicates) or recombinant Ad-shZfp36l1 (3 biological replicates) on primary mouse articular chondrocytes and subjected to microarray analysis.

first: Jang-Soo

last: Chun


title: Functional modulation of gene expression by TUC338 during growth of human

status: Public on Jan 24 2018

city: Jacksonville

first: Tushar

last: Patel

state: FL

address: 4500 San Pablo Road

institute: Mayo Clinic

summary: In this study, we have investigated the molecular interactions of an ultraconserved non-coding RNA, TUC338, which is highly upregulated in hepatocellular cancer and implicated in growth regulation. We have identified functional genomic and proteomic determinants of this lncRNA involved in modulation of gene expression.

overall_design: Investigate the molecular interactions of TUC338

first: Hui-Ju

last: Wen

first: Michael

middle: P

last: Walsh

first: Irene

last: Yan

first: Kenji

last: Takahashi

first: Alan

last: Fields


title: Systemic hormonal modulation induces sperm nucleosomal imbalance in rat spermatozoa

status: Public on Jan 25 2018

city: Mumbai

first: N

middle: H

last: Balasinor

state: Maharashtra

address: J. M.  Street,parel

department: Neuroendocrinology

country: India

institute: NIRRH

summary: The male gamete has an immense role in reproduction. Besides contributing one half of the genomic DNA, it contributes important epigenetic information that controls and orchestrates its expression during the early stages of embryo development. Although, DNA methylation is a widely studied epigenetic modification, other epigenetic changes like histone modifications, nucleosome landscape and chromatin compaction are also gaining significant consideration. Sperm chromatin despite being majorly compacted with protamines; strategically retains 2-4% of the genome in nucleosomes. While DNA bases are resilient, epigenetic marks are highly susceptible to reprogramming. Environmental pollutants have been known to affect epigenetic marks and many of those pollutants are known to be xeno-estrogenic. Previous studies using tamoxifen, a Selective Estrogen Receptor Modulator – SERM, has been shown to be associated with post implantation loss and DNA methylation aberration in rats. Also, Cyperoterone acetate (CPA), an antiandrogen, has been shown to induce retention of histone modifications in testis. In this study, we show by MNase-sequencing that systemic hormonal disruption leads to deviation in the nucleosomal localization in spermatozoa at many genes of significance during early embryo development. Thus, environmental pollutants, which are mainly estrogenic or antiandrogenic in nature, may exert epigenetic aberrations in the spermatozoa through hormonal disruption which may lead to severe complications during embryo development or in adult life.

overall_design: Nucleosome profile using MNase-Seq comparing of rat spermatozoa with and without Tamoxifen or Cyperoterone Acetate treatment

first: Mandar

last: Ankolkar

first: Sharvari

last: Deshpande

first: Nafisa


title: TRAF-STOPping atherosclerosis: targeting of CD40-induced TRAF6 signaling in macrophages reduces (established) atherosclerosis

status: Public on Jan 15 2018

city: Amsterdam

first: Perry

last: Moerland

address: Meibergdreef 9

department: Epidemiology and Data Science

country: Netherlands

institute: Amsterdam UMC

summary:
Inhibition of the costimulatory CD40-CD40L receptor/ligand dyad drastically reduces atherosclerosis. However, its long-term blockage can result in immune suppression. We recently identified small molecule inhibitors that block the interaction between CD40 and TNF Receptor Associated Factor (TRAF) 6 (TRAF-STOPs), while leaving CD40-TRAF2/3/5 interactions intact, thereby preserving CD40-mediated immunity. Here we further characterized the working mechanisms of TRAF-STOPs 6877002 and 6860766 in atherogenesis.
Transcriptional profiling in CD40-activated macrophages showed that TRAF-STOP 6877002 had profound effects on the clusters ‘immune responses’ and ‘cell cycle progression’, whereas TRAF-STOP 6860766 only affected ‘immune responses’.

overall_design: Comparison of gene expression in bone marrow-derived macrophages of C57Bl6 mice (n=3) pre-incubated with vehicle (CTRL) or compound TRAF-STOP 6877002 or TRAF-STOP 6860766 (3 mice/group) for 1 hour and subsequently activated by the agonistic CD40 antibody FGK45.

first: Tom

middle: T

last: Seijkens

first: Claudia

last: vanTiel

first: Esther

last: Lutgens


title: Analysis of the differences in gene expression between wild type and Gpr120 knockout brown adipose tissue

status: Public on Jan 18 2018

city: Coventry

first: Mark

last: Christian

address: Gibbet Hill Road

department: Division of Biomedical Sciences

country: United Kingdom

institute: University of Warwick

summary: The goals were to investigate differences in gene expression between wild type and Gpr120 knockout mouse interscapular brown adipose tissue

overall_design: RNA from wild type (n=6) and Gpr120 knockout (n=5) interscapular brown adipose tissue was extracted. Whole genome expression of wild type and knockout samples were profiled using Illumina MouseWG-6 v2.0 Expression BeadChips.

first: M

last: Schilperoort

first: A

last: van Dam

first: G

last: Hoeke

last: Okolo

last: Hanyaloglu

first: L

last: Dib

first: I

last: Mol

first: Y-W

last: Chan

first: S

last: Damak

first: T

last: Coskun

last: Ulven

last: Kooijman

first: P

last: Rensen


title: Molecular characteristics of the KCNJ5 mutated aldosterone-producing adenomas.

status: Public on Jan 08 2018

city: Setagaya

first: Kazuhiko

last: Nakabayashi

department: Department of Maternal-Fetal Biology

institute: National Research Institute for Child Health and Development

summary: The pathophysiology of aldosterone-producing adenomas (APAs) has been investigated via genetic approaches and the pathogenic significance of a series of somatic mutations, including KCNJ5, has been uncovered. However, how the mutational status of an APA is associated with its molecular characteristics, including its transcriptome and methylome, has not been fully understood. This study was undertaken to explore the molecular characteristics of APAs, specifically focusing on APAs with KCNJ5 mutations as opposed to those without KCNJ5 mutations, by comparing their transcriptome and methylome status. Cortisol-producing adenomas (CPAs) were used as reference. We conducted transcriptome and methylome analyses of 29 APAs with KCNJ5 mutations, 8 APAs without KCNJ5 mutations and 5 CPAs. Genome-wide gene expression and CpG methylation profiles were obtained from RNA and DNA samples extracted from these 42 adrenal tumors. Cluster analysis of the transcriptome and methylome revealed molecular heterogeneity in APAs depending on their mutational status. DNA hypomethylation and gene expression changes in Wnt signaling and inflammatory response pathways were characteristic of APAs with KCNJ5 mutations. Comparisons between transcriptome data from our APAs and that from normal adrenal cortex obtained from the Gene Expression Omnibus suggested similarities between APAs with KCNJ5 mutations and zona glomerulosa. The present study, which is based on transcriptome and methylome analyses, indicates the molecular heterogeneity of APAs depends on their mutational status. Here, we report the unique characteristics of APAs with KCNJ5 mutations.

overall_design: Adrenal tissues were obtained from 37 patients with APAs and 5 patients with CPAs who underwent adrenalectomy at the Tokyo Medical and Dental University Hospital. Gene expression and genome-wide DNA methylation profiles were obtained by RNAseq  and Infinium HumanMethylationEPIC Beadchip (Illumina), respectively.

first: Masanori

last: Murakami

first: Takanobu

last: Yoshimoto

first: Yoshihiro

last: Ogawa


title: A novel genomic signature predicting FDG uptake in diverse metastatic tumors

status: Public on Jan 22 2018

city: Torrevieja

first: Ramon

middle: G

last: Manzano

state: Alicante

address: Partida la Loma s/n

department: Unidad de Consejo Genetico, Plataforma de Oncologia

institute: Hospital Quiron Torrevieja

summary:
Purpose: Building a universal genomic signature predicting the intensity of FDG uptake in diverse metastatic tumors may allow us to understand better the biological processes underlying this phenomenon and their requirements of glucose uptake.
Methods: A balanced training set (n=71) of metastatic tumors including some of the most frequent histologies, with matched PET/CT quantification measurements and whole human genome gene expression microarrays, was used to build the signature. Selection of microarray features was carried out exclusively on the basis of their strong association with FDG uptake (as measured by SUVmean35) by means of univariate linear regression. A thorough bioinformatics study of these genes was performed and multivariable models were built by fitting several state of the art regression techniques to the training set for comparison.
Results: The 909 probes with the strongest association with the SUVmean35 (comprising 742 identifiable genes and 62 probes not matched to a symbol) were used to build the signature. Partial Least Squares using 3 components (PLS-3) was the best performing model in the training dataset cross-validation (Root Mean Square Error, RMSE=0.443) and was validated further in an independent validation dataset (n=13) obtaining a performance within the 95% CI of that obtained in the training dataset (RMSE=0.645). Significantly overrepresented biological processes correlating with the SUVmean35 were identified beyond glycolysis, such as ribosome biogenesis and DNA replication (correlating with a higher SUVmean35), and cytoskeleton reorganization and autophagy (correlating with a lower SUVmean35), among others.
Conclusions: PLS-3 is a signature predicting accurately the intensity of FDG uptake in diverse metastatic tumors. FDG-PET might help in the design of specific targeted therapies directed to counteract the identified malignant biological processes more likely activated in a tumor as inferred from the SUVmean35 and also from its variations in response to antineoplastic treatments.

overall_design: Whole human genome microarrays from biopsies of human metastatic tumors (71 patients) with matched SUVmean35 measurements, this submission includes the 71 patients of the training set used to build the genomic signature predicting FDG uptake in diverse metastatic tumors. This dataset is complemented with a validation set comprised of 13 patients.

first: Elena

last: Martinez Navarro


title: Sequencing of Caenorhabditis elegans wildtype strain (N2) treated with T25B9.1 RNAi for  5 days after L4 larvae stage.

city: Jena

first: JenAge

last: Project

address: Beutenbergstr. 11

institute: Leibniz Institute for Age Research - Fritz Lipmann Institute

summary:
Comparison of gene expression profiles from C. elegans wildtype strain (N2) treated with L4440 and T25B9.1 RNAi for  5 days after L4 larvae stage.

Jena Centre for Systems Biology of Ageing - JenAge (ww.jenage.de)

overall_design: 6 samples in 2 groups:  N2, L4440 5 days (3 Samples); N2, T25B9.1 5 days (3 Samples)

first: Michael

last: Ristow

first: Kim

last: Zarse

first: Rolf

last: Hühne

first: Marco

last: Groth

first: Matthias

last: Platzer


title: A HUS-associated STEC expressing a dicA transcriptional module is related to gene network dysregulation in Caco-2

status: Public on Jan 05 2018

city: Sao Paulo

first: Carlos

middle: Alberto

last: Moreira-Filho

state: SP

address: Av. Dr. Eneas Carvalho de Aguiar 647

department: Departments of Pediatrics

country: Brazil

institute: Faculdade de Medicina da Universidade de Sao Paulo

summary: We conducted comparative gene co-expression network (GCN) analyses of two O113:H21 STEC strains: EH41, reference strain, isolated from hemolytic-uremic syndrome patient in Australia, and Ec472/01, isolated from cattle feces in Brazil. These strains were cultured in fresh or in Caco-2 cell conditioned media. GCN analyses were also accomplished for cultured Caco-2 cells exposed to EH41 or Ec472/01. Differential transcriptome profiles for EH41 and Ec472/01 were not significantly changed by exposure to fresh or Caco-2 conditioned media. Conversely, global gene expression comparison of both strains cultured in conditioned medium revealed a gene set exclusively expressed in EH41, which includes the dicA putative virulence factor regulator. Network analysis showed that this set of genes constitutes an EH41 specific transcriptional module. The GCNs of Caco-2 cells exposed to EH41 or to Ec472/01 presented a major transcriptional module containing many hubs related to inflammatory response that was not found in the GCN of control cells. Moreover, EH41 seems to cause gene network dysregulation in Caco-2. Therefore, EH41 virulence may be derived from its capacity for dysregulating enterocyte genome functioning and its enhanced enteric survival due to slow growth.

sample_organism:
Escherichia coli
Homo sapiens

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

overall_design:
[EH41]: Caco-2 transcriptomic profiles after 3 hrs of interaction with STEC strain EH41 and without interaction (control) were compared in order to identify differentially expressed transcripts
[EC472]: Caco-2 transcriptomic profiles after 3 hrs of interaction with STEC strain EC472/01 and without interaction (control) were compared in order to identify differentially expressed transcripts
[COND]: STEC transcriptomic profiles after 3 hrs incubation in conditioned Caco-2 cell medium: STEC strain EH41 (isolated from patient with HUS) and STEc strain EC472/01 (isolated from cattle) were compared in order to identify differentially expressed transcripts
[FRESH]: STEC transcriptomic profiles after 3 hrs incubation in fresh medium: STEC strain EH41 (isolated from patient with HUS) and STEc strain EC472/01 (isolated from cattle) were compared in order to identify differentially expressed transcripts

first: Silvia

middle: Y

last: Bando

first: Priscila

last: Iamashita

first: Beatriz

last: Guth

first: Luis

middle: F

last: dos Santos

first: André

last: Fujita

first: Cecilia

last: Abe

first: Leandro

last: Ferreira


title: Expression profile of miRNAs in PBMCs infected with PPRV in goat

status: Public on Jan 30 2018

city: Karnal

first: Ravi Kumar

last: Gandham

state: Haryana

address: Makrampur

institute: ICAR-NBAGR

summary: Using high-throughput technology, we aim to identify the expression of miRNAs  for understanding the pathogenesis of PPR.

overall_design: PBMCs were collected after 9 day post infection of  Izatnagar94  PPRV virulent virus infection to identify the global gene expression changes vis - a - vis the control

first: Alok

last: khanduri

first: Aruna

last: Pandey

first: Shikha

last: Saxena

first: Amit

last: Sahu

first: Sajad

last: Wani

first: Waseem

last: Malla

first: Piyali

last: Mondal

first: Raja

middle: i

last: Khan

first: Bina

last: Mishra

first: B

first: A

last: Tiwari

first: Deepak

last: Kumar

first: Aditya

last: Sahoo

first: Ravi


title: Role of skeletal muscle in lung development.

city: Halifax

first: Boris

last: Kablar

state: Nova Scotia

address: 5850 College Street

department: Medical Neuroscience

country: Canada

institute: Dalhousie University

summary:
Skeletal (striated) muscle is one of the four basic tissue types, together with the epithelium, connective and nervous tissues. Lungs, on the other hand, develop from the foregut and among various cell types contain smooth, but not skeletal muscle. Therefore, during earlier stages of development, it is unlikely that skeletal muscle and lung depend on each other. However, during the later stages of development, respiratory muscle, primarily the diaphragm and the intercostal muscles, execute so called fetal breathing-like movements (FBMs), that are essential for lung growth and cell differentiation. In fact, the absence of FBMs results in pulmonary hypoplasia, the most common cause of death in the first week of human neonatal life. Most knowledge on this topic arises from in vivo experiments on larger animals and from various in vitro experiments. In the current era of mouse mutagenesis and functional genomics, it was our goal to develop a mouse model for pulmonary hypoplasia.
We employed various genetically engineered mice lacking different groups of respiratory muscles or lacking all the skeletal muscle and established the criteria for pulmonary hypoplasia in mice, and therefore established a mouse model for this disease. We followed up this discovery with systematic subtractive microarray analysis approach and revealed novel functions in lung development and disease for several molecules. We believe that our approach combines elements of both in vivo and in vitro approaches and allows us to study the function of a series of molecules in the context of lung development and disease and, simultaneously, in the context of lung's dependence on skeletal muscle-executed FBMs.

overall_design: Mouse embryos were obtained at E18.5 for RNA extraction and hybridization on Affymetrix microarrays.

first: Mark

last: Baguma-Nibasheka

first: Dijana

last: Gugic

first: Mirna

last: Saraga-Babic


title: Biological characteristics of gene expression features in pancreatic cancer cell induced by proton and x-ray irradiation IV

status: Public on Dec 30 2017

city: Kanazawa

first: Yoshio

last: Sakai

state: Ishikawa

address: 13-1 Takara-machi

department: Department of Gastroenterology

institute: Kanazawa University

summary: The aim of the study is to disclose the distinct alteration of biological characteristics of gene expression features in pancreas cancer cell, MIAPaCa-2, irradiated by proton and x-ray. The survived MIAPaCa-2 cells after irradiation with proton and x-ray were isolated and gene expression profiles were analyzed.

overall_design: MIAPaCa-2 cells after x-ray irradiation were expanded. The expanded cells were either re-irradiated by proton with 8 Gy (n=4) or not irradiated (n=4). After 4 hours, RNA was extracted, followed by gene expression analysis.

first: Haruo

last: Fujinaga

first: Tatsuya

last: Yamashita

first: Kuniaki

last: Arai

first: Takeshi

last: Terashima

first: Takuya

last: Komura

first: Akihiro

last: Seki

first: Kazunori

last: Kawaguchi

first: Alessandro

last: Nasti

first: Keiko

last: Yoshida

first: Takashi

last: Wada

first: Kazutaka

last: Yamamoto

first: Kyo

last: Kume

last: Hasegawa

first: Takushi

last: Takata

first: Masao

last: Honda

first: Shuichi

last: Kaneko


title: Biological characteristics of gene expression features in pancreatic cancer cell induced by proton and x-ray irradiation III

last: Sakai

overall_design: MIAPaCa-2 cells after proton irradiation were expanded. The expanded cells were either re-irradiated by proton with 8 Gy (n=5) or not irradiated (n=5). After 4 hours, RNA was extracted, followed by gene expression analysis.


title: Biological characteristics of gene expression features in pancreatic cancer cell induced by proton and x-ray irradiation

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

overall_design: Refer to individual Series


title: Biological characteristics of gene expression features in pancreatic cancer cell induced by proton and x-ray irradiation II

overall_design: MIAPaCa-2 cells were irradiated with proton or X-ray with 8 Gy dose in vitro. After 7 to 17 days, the colonies with survival cells were picked up and expanded.   RNA was isolated from each expanded surviving cells (proton-irradiated surviving cells: n =5, X-ray-irradiated surviving cells: n=4) , followed by gene expression analysis.

last: Fujinaga


title: Biological characteristics of gene expression features in pancreatic cancer cell induced by proton and x-ray irradiation I

overall_design: MIAPaCa-2 cells were  irradiated with proton or x-ray with 2 Gy or 8 Gy. After 3 h or 12 h of irradiation, RNA was isolated and gene expression profile was examined by DNA microarray for a total of 8 specific conditions (n=1) plus control (n=1).

last: Yamashita


title: MicroRNA Expression Analysis of Advanced Colorectal Cancer Reveals a microRNA Signature with Prognostic and Predictive Value

status: Public on Dec 16 2017

city: Guangzhou

first: Zhaolei

last: Zeng

address: No. 651 Dong Feng Road East

department: Cancer Center

institute: Sun Yat-sen University

summary: We performed a prospective cohort study in patients with advanced CRC to identify a miRNA signature that could predict the benefit of receiving first-line chemotherapy for these patients.

overall_design: Twenty-one paired tumours and adjacent normal tissues were collected from patients with advanced CRC and analysed by miRNA microarrays.

first: Zhao-lei

first: Jia-huan

last: Lu

first: Zhi-xiang

last: Zuo

first: Rui-hua

last: Xu


title: Gene expression comparison in control and DEK oncogene depleted human melanoma cell lines

status: Public on Dec 21 2017

city: Madrid

first: Metehan

last: Cifdaloz

state: Comunidad de Madrid

address: C/ Melchor Fernández Almagro, 3

department: Molecular Oncology Program

institute: CNIO

summary: Gene expression SK-Mel-103 melanoma cell line to find genes controled by DEK oncogene

overall_design: Three biological replicates were labeled  and hybridized onto Agilent-014850 platform.

first: Lisa

last: Osterloh

first: Marisol

last: Soengas


title: Gene expression profiling of LMC and MMC motor neurons in SMA mice

status: Public on Dec 12 2017

city: New York

first: George

middle: Z

last: Mentis

state: NY

address: 630 W 168th Street

department: Dept of Pathology&Cell Biology

institute: Columbia University

summary: Spinal muscular atrophy (SMA) is a neurodegenerative disease which exhibits selective motor neuron death caused by a ubiquitous deficiency of the survival motor neuron (SMN) protein.  It remains unclear how the ubiquitous reduction of SMN lead to death in selective motor neuron pools. Medial motor neuron columns (MMC) are vulnerable, whereas lateral motor columns (LMC) are resistant to motor neuron death in SMA. Here we performed microarray and pathway analysis comparing cholera toxin subunit B (CTb) labeled vulnerable MMC and resistant LMC of pre-symptomatic SMA with corresponding motor neuron columns of control mice to identify pathways involved in selective motor neuron death in SMA. WT is FVB. SMN is Delta7 (SMNΔ7;SMN2;Smn-) on a FVB background.

overall_design: 8 different groups (WT and SMA medial motor columns (MMC),WT and SMA lateral motor columns (LMC), WT and SMA DRG (Dorsal Root Ganglion) and WT and SMA Raphe. 3 biological replicates per group.

first: Christian

last: Simon

first: Yan

last: Dai

first: Charalampia

last: Koutsioumpa

first: John

last: Pagiazitis

first: Joshua

last: Calif

first: Meaghan

last: Van Alstyne

first: Xiaojian

last: Wang

first: Joe

last: Rabinowitz

first: Livio

last: Pellizzoni

first: Christopher

last: Henderson


title: Selection of well-tolerated GalNAc-conjugated siRNAs by screening for RNAi-mediated off-target effects in rodent toxicity studies

status: Public on Jan 11 2018

city: Cambridge

first: Joseph

last: Barry

state: MA

address: 300 Third Street #3

institute: Alnylam Pharmaceuticals

summary: Small interfering RNAs (siRNAs) conjugated to a trivalent N-acetylgalactosamine (GalNAc) ligand are being evaluated in investigational clinical studies for a variety of indications. The typical development candidate selection process includes evaluation of the most active compounds for toxicity in rats at pharmacologically-exaggerated doses. The subset of GalNAc-siRNAs that show rat hepatotoxicity is not advanced to clinical development.  Potential mechanisms of hepatotoxicity include toxicities associated with the intracellular accumulation of oligonucleotides and their metabolites, RNA interference (RNAi)-mediated hybridization-based off-target effects, and/or perturbation of endogenous RNAi pathways. Here we show that rodent hepatotoxicity observed at supratherapeutic exposures can be largely attributed to RNAi-mediated off-target effects, but not chemical modifications or the perturbation of RNAi pathways. Furthermore, these off-target effects can be mitigated by modulating seed-pairing using a thermally destabilizing chemical modification, which significantly improves the safety profile of a GalNAc-siRNA in rat and may minimize the occurrence of hepatotoxic siRNAs across species.

overall_design:
RNASeq analysis of hepatotoxicity
Rat livers were collected 24 h post-50 mg/kg single dose of GalNAc-siRNAs and snap-frozen. Rat hepatocytes (BioreclamationIVT) were transfected with 10 nM GalNAc-siRNAs using Lipofectamine RNAiMAX (Thermo Fisher Scientific) according to manufacturer’s instructions, and harvested 24 h post-transfection. Rat hepatocytes were not tested for mycoplasma contamination. RNA extracted with the miRNeasy kit (Qiagen) was used for cDNA library preparation with the TruSeq Stranded Total RNA Library Prep Kit (Illumina) and sequenced on the HiSeq or NextSeq500 sequencers (Illumina), all according to manufacturers’ instructions. Raw RNAseq reads were filtered with minimal mean quality scores of 25 and minimal remaining length of 36, using fastq-mcf. Filtered reads were aligned to the Rattus norvegicus genome (Rnor_6.0) using STAR (ultrafast universal RNA-seq aligner) with default parameters. Uniquely aligned reads were counted by featureCounts. Differential gene expression analysis was performed by the R package DESeq2.The open source DESeq2 R package was used for the RNAseq data analysis.

first: Maja

middle: M

last: Janas

first: Mark

last: Schegel

first: Carole

last: Harbison

first: Vedat

middle: O

last: Yilmaz

first: Yongfeng

last: Jiang

first: Rubina

last: Parmar

first: Ivan

last: Zlatev

first: Adam

last: Castoreno

first: Huilei

first: Svetlana

last: Shulga-Morskaya

first: Kallanthottathil

last: Rajeev

first: Muthiah

last: Manoharan

first: Natalie

middle: D

last: Keirstead

first: Martin

last: Maier

first: Vasant

last: Jadhav


title: Genome wide gene expression analysis of differential fetal cotyledons

first: Syed

middle: Azmal

last: Ali

address: G.T. Road, ABTC, Proteomics and Cell Biology Lab

department: Animal Biotechnology

institute: National Dairy Research Institute

summary: In an attempt to unveil the molecular mechanisms of fetal-maternal interactions during early pregnancy, we have performed the pregnancy induced gene expression analysis in the gravid uteri of fetal cotyledons using the Affymetrix GeneChip Genome Array. In this study, we have performed the microarray analysis of the RNA isolated from fetal cotyledon tissue of Bubalus bubalis on less than 45 day of pregnancy. We have identified total of 8587 differentially expressed genes with significance p ≤ 0.05 in four biological replicates.  Bioinformatics analysis of microarray data reveal the cluster of genes involved at the placentome level for various functions such as fetus attachment, transport of nutrition, and immune response. Interestingly, we have identified multiple isoforms of pregnancy associated glycoproteins (PAGs) which were highly up regulated with average fold change of 472.93 in pregnant buffaloes.  It was observed the genes responsible for increased immune response were down regulated, suggesting an immune suppressive environment which is required to adapt the semiallogenic fetus for successful pregnancy. We have identified the genes and pathways involved during embryo development and the cluster of genes involved in fetal-maternal interaction, attachment, nourishment of fetus, and immune response. The present study will provide future directions for developing pregnancy diagnosis kit in livestock which is highly necessary for increasing the reproductive efficiency of buffaloes.

overall_design: Organism : Bos taurus, Agilent Bovine Gene Expression  8x60k Array (AMADID: 029411) designed by Genotypic Technology Private Limited

last: Azmal Ali


title: mRNA expression from wild type and gp130F/F mice antrum at 4 weeks of age in specific pathogen free (SPF) and germ free (GF) conditions

status: Public on Dec 01 2017

city: Chapel Hill

first: Di

last: Wu

state: North Carolina

address: 385 S. Columbia Street, CB#7455

institute: University of North Carolina

summary:
The role of microbe in promoting the initiation of gastric cancer (GC), the third most lethal cancer worldwide, are ill-defined. Here, we found that tumor size and weight in gp130F/F mouse stomach at condition were significantly reduced compared to those of at SPF condition. To investigate the underlying mechanism and how host genes were regulated in the presence/absence of microbe, arrays were performed in stomach tissue from gp130F/F and WT at 4 week old at SPF and GF conditions.
The onset of gastric inflammation-associated adenomatous hyperplasia in gp130F/F mice occurs at ~6 weeks of age, with established intestinal-type tumors (3 months of age) progressively growing until a maximum size is reached at 6 months of age, with some evidence of carcinoma in situ. Since this phenotype histologically mimics early stage human GC, we therefore utilized gp130F/F mice as a model to identify miRNAs involved in the initiating molecular events leading to early stage GC. For this purpose, we performed miRNA microarrays on mouse gastric antrum tissue from gp130F/F and sex-matched littermate wild-type (gp130+/+) control mice aged 4 weeks; this age was chosen since antrum tissue from 4 week old (wo) gp130F/F mice is devoid of any histological signs of inflammation or hyperplasia, and is thus comparable to wild-type gastric antrum tissue.

overall_design: Total RNA from 4 week old mouse antrum samples was subjected to an illumina array platform. The raw data was normalized using neqc. We included BL6 samples for data normalization, but not for comparisons between sample groups.

first: Patrick

last: Tan

first: Liang

last: Yu

first: Brendan

middle: J

last: Jenkins


title: Identification of a signal transducer and activator of transcription 3-regulated microRNA-200 family signature with prognostic potential in early gastric cancer

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

platform_organism:
Mus musculus
synthetic construct


title: CapG a putative oncogen affects gene expression in breast cancer cells

status: Public on Nov 30 2017

city: Duesseldorf

first: Karl

last: Koehrer

address: Universitaetsstr. 1

department: BMFZ

institute: University of Duesseldorf

summary: The transition from ductal carcinoma in situ (DCIS) to invasive ductal carcinoma (IDC) is an important step during breast tumorgenesis. Understanding its molecular changes may uncover both novel preventive and therapeutic strategies and may help to identify high-risk DCIS that progress to IDC. The mechanisms are unknown and the role of CapG in the nucleus is an enigma. Here, we tested the association between clinicopathological CapG expression in tumor samples and used a cell culture model to test the hypothesis that CapG affects gene expression. Breast cancer samples were analyzed by reverse transcriptase – real time PCR (RT-qPCR). We used microarray analysis to study the transcriptome of the cell culture model and validated changes in gene expression in laser capture micro-dissected formalin-fixed paraffin-embedded (FFPE) invasive ductal carcinoma (IDC) and ductal carcinoma in situ (DCIS), respectively. We were able to associate increased CapG expression with an invasive breast cancer phenotype. In 28.2% of breast cancer samples CapG expression in breast cancer samples revealed in 28.2% a very high CapG expression and statistical significant association (p<0.05) to positive metastasis status (M1) and negative ER status (ER-). In case of CapG overexpression microarray analyses generated a list of differential expressed genes and revealed enhanced expression levels of GPNMB, NRP1, LOXL2, TRIM47 and COL16A1, while ZDHHC11, KIAA1467 were down-regulated. We show here for the first time an effect on the transcriptome by experimental modification of CapG expression. Concluding, CapG is involved in tumor progression.

overall_design: CapG expression was modifed in two different breast cancer cell lines (MDA-MB-231 and BT-20), either knock-down (MDA-MB-231) or overexpression (BT-20). Untreated cell lines served as controls. Four independent experiments for each condition were performed.

first: Neumann

last: Martin

first: Schultz

last: Silke

first: Neves

last: Rui

first: Sotlar

last: Karl

first: Schleithoff

last: Carolin

first: Deenen

last: René

first: Fleisch

last: Markus

first: Fehm

last: Tanja

first: Neubauer

last: Hans

first: Niederacher

last: Dieter


title: Differential genomic-methylation profile of U937 cells transduced with WT/mutant-DNMT3A

city: TauYau

first: Yun-Shien

last: Lee

state: Taiwan

address: TauYau

department: Dept. Biotechnology

country: Taiwan

institute: Ming Chuan Univ

summary:
DNA methyltransferase 3A (DNMT3A) gene is mutated in various myeloid neoplasms including acute myeloid leukemia (AML), especially at the Arg882 and associated with inferior outcomes. Despite the current progress of functional role of DNMT3A mutations, the molecular pathogenesis of myeloid malignancies remains poorly understood. The mechanisms of AML transformation and functional role of DNMT3A mutations through its target genes in the leukemogenesis remain to be explored. Here we wished to perform the differential genomic-methylation profile in U937 cells over-expressed with DNMT3A-Arg882His/Cys (R882H/C) mutations including DNMT3A-WT and vector using Illumina MethylationEPIC BeadChip microarray.
Results: Differential genomic-methylation assess identified both hypo- and hypermethylation features in different regions throughout the whole genome of DNMT3A mutants-transduced U937 cells.

overall_design: Genomic methylation profiling of U937 cells  with empty vector, or overexpression of wildtype DNMT3A, DNMT3A mutant R882C or DNMT3A mutant R882H.

first: Rabindranath

last: Bera

first: Lee-Yung

last: Shih

first: Ming-Chun

last: Chiu

first: Ying-Jung

last: Huang

first: Der-Cherng

last: Liang


title: Tissue microRNA signatures to predict breast cancer recurrence in young women aged under 35 years old

status: Public on Nov 22 2017

city: Tokyo

first: AI

last: Mitsuhashi

address: 5-1-1, Tsukiji, Chuo-ku

institute: National Cancer Center Research Institute

summary: Identification for microRNA signatures to predict breast cancer recurrence in young women were performed through expression profiling of a total 2565 miRNAs in 45 samples diagnosed as invasive ducatal carcinoma of no special type (NST) cases which had been consecutively operated on within a defined short period of time.

overall_design: In the study presented here, a consecutively operated, well-defined cohorts of 45 primary breast cancer cases were used to acquire expression profiles of a total of 2,565 microRNAs. Cases were analyzed according to the recurrence status in first 5 years after curative surgery.

first: Ai

last: Mitsuhashi-Hironaka

first: Juntaro

last: Matsuzaki

first: Ryou-u

last: Takahashi

first: Masayuki

last: Yoshida

first: Yutaka

last: Nezu

first: Yusuke

last: Yamamoto

first: Sho

last: Shiino

first: Takayuki

last: Kinoshita

first: Toshikazu

last: Ushijima

first: Nobuyoshi

last: Hiraoka

first: Chikako

last: Shimizu

first: Kenji

last: Tamura

first: Takahiro

last: Ochiya


title: p52 transgenic expression with or without LPS in mouse lungs

city: Nashville

first: Timothy

middle: S.

last: Blackwell

state: TN

department: Department of Cancer Biology

institute: Vanderbilt University

summary:
To understand the mechanism by which p52 expression augments tumorigenesis, gene expression microarray analysis was performed using mRNA isolated from lungs of CCSP-p52 and WT mice on dox for 1 week to identify genes with altered expression in CCSP-p52 mice. The microarray dataset includes eight samples, with two replicates for each combination of two factors (p52 and LPS).Since samples with and without LPS stimulation were processed and microarray profiled at the same time, we assumed the random data variations were similar across all samples and built a linear model across the eight samples accounting for both p52 and LPS experimental factors.  The coefficient (estimated log fold change) and p-value associated with the p52 factor were retrieved for the selection of differentially expressed genes. When selecting top-ranking p52-induced genes, only probe sets mapping to known genes and having positive expression changes were considered.
While the used microarrays were Affymetrix Mouse Gene 1.0 ST arrays, in the later step of probe set annotation we used annotation table associated with Mouse Gene 1.1 ST (GPL11533 table). The Robust Multichip Average method implemented in R package “oligo” (v1.28.3) was employed to normalize imported raw data. Probe sets interrogating control, unmapped, or intron sequences were ignored, leaving 79% of probe sets for a differential expression analysis. Linear models and empirical Bayes methods implemented in R package “limma” (v3.20.8) were applied to estimate log fold changes and p-values for the p52-vs-WT effect.

overall_design: CCSP-p52 transgenic mice generated from CCSP-tTS/(tet-O)7-FLAG-p52 founder lines were targeted mice. Age- and sex-matched genotype-negative littermate controls were designated as WT mice. Transgene expression was activated by administering 2 g/L dox (Sigma) along with 2% sucrose in drinking water. The lungs of CCSP-p52 and WT mice on dox for 1 week and mice on dox for 1 week 48 hours after intratracheal LPS administration were harvested, and three mice were pooled for each of samples. For half samples, LPS (Lipopolysaccharide) was adminstered. As a result, a total of 8 samples (2 WT dox only, 2 WT with LPS, 2 CCSP-p52 dox only, 2 CCSP-p52 with LPS) were microarray profiled.

first: Jamie

last: Saxon

first: Hui

last: Yu


title: Molecular heterogeneity of NK/T-cell lymphoma

status: Public on Nov 25 2017

city: Singapore

first: Siok-Bian

last: Ng

address: National University Hospital, 5 Lower Kent Ridge Road, Main Building, level 3

department: Department of Pathology

country: Singapore

institute: National University Health System, Singapore

type:
Expression profiling by array
Non-coding RNA profiling by array
Genome variation profiling by SNP array

platform_organism:
Homo sapiens
synthetic construct


title: Molecular heterogeneity of NK/T-cell lymphoma (expression)

summary: To investigate if biologically distinct subsets exists in extranodal NK/T-cell lymphoma (NKTL), we performed unsupervised integrative analyses of gene expression profiling (GEP), miRNA profiling, and copy number aberration (CNA) on 66 cases of NKTL from diverse anatomical sites. This series is the GEP data.

overall_design: Unsupervised analysis of FFPE NKTL samples.

first: Tae-Hoon

last: Chung


title: Transcriptomic analysis of murine microglia from embryonic development to adulthood

status: Public on Nov 21 2017

first: jinmiao

last: chen

address: 8A Biomedical Grove, #04-06 Immunos

institute: Singapore Immunology Network

summary: Microarray analysis of murine microglia from different stages of development was performed. Results showed that different phases of microglia development had different group of genes up-regulated for specific functions.

overall_design: RNA was extracted from microglia/progenitors from E10.5 embryos to adult mice. Gene expression analysis was done to observe DEGs and differential pathway analysis.

first: Guillaume

last: Hoeffel

first: Donovan

last: Low

first: Florent

last: Ginhoux


title: Reprogramming lineage committed cells into iMSC-LC

city: Sydney

first: Ashwin

last: Unnikrishnan

state: NSW

address: Room 217, Level 2, Adult Cancer Program, Lowy Cancer Research Centre, University of New South Wales

department: Lowy Cancer Research Centre

country: Australia

institute: University of New South Wales

summary: Genome-wide gene expression comparision between mesenchymal stem cells, lineage differentiated cells and reprogrammed cells.

overall_design: Total RNA obtained from MSCs, lineage differentiated cells and reprogrammed cells.

first: Vashe

last: Chandrakanthan

first: John

middle: E

last: Pimanda


title: Mapping alterations spatially and temporally during early stages of breast tumourigenesis [expression]

status: Public on Nov 02 2017

city: Toronto

first: Susan

last: Done

state: Ontario

address: 200 Elizabeth St. Rm 11E-228

department: Laboratory Medicine and Pathobiology

institute: University of Toronto

summary: Identifying genomic alterations that precede tumourigenesis of breast tumours will allow us to better understand tumour development and heterogeneity. In particular, by obtaining and profiling normal-epithelium samples at various distances from the tumour, we can draft both a spatial and temporal map of the genomic events and transcriptomic alterations that occur along the mammary duct (leading up to and including the tumour).

overall_design: Dataset consisting of 9 patients with breast cancer, from which multiple normal epithelium samples were obtained from along the duct leading to the tumour,  one sample from the contralateral duct, and a sample from the tumor itself

first: Moustafa

last: Abdalla


title: Mapping alterations spatially and temporally during early stages of breast tumourigenesis

type: Genome variation profiling by genome tiling array

overall_design: Refer to individual Series


title: ZIC2 Is Required For Nodal Expression And The Establishment Of Left-Sided Identity

status: Public on Oct 31 2017

city: liverpool

first: Iain

last: Dykes

state: Select...

address: James Parson Bl, Byrom Street,

department: Pharmacy & Biomolecular science

institute: Liverpool John Moores University

summary: The purpose of this study was to identify putative downstream targets of the transcription factor ZIC2 in the mouse embryo. The results indicate loss of NODAL pathway expression, consistent with the observed phenotype of right isomerism in heart, lungs and viscera.

overall_design: Total RNA obtained from wildtype whole embryos at day E8.0-E8.5 was compared to that from mutant Zic2 iso/iso embryos

first: Shoumo

last: Bhattacharya


title: Gene expression data from Phase 2 of the SAMARA study (Supporting a Multi-disciplinary Approach to Researching Atherosclerosis)

status: Public on Nov 01 2017

first: Jonathan

middle: C

last: Schisler

state: NC

address: MBRB, Rm 2340C

department: McAllister Heart Institute

institute: The University of North Carolina at Chapel Hill

summary: Our goal was to measure molecular phenotypes associated with coronary atherosclerosis severity in a geriatric cohort.

overall_design:
We utilized a “sample x reference” experimental design strategy in which RNA extracted from human peripheral blood mononuclear cells was hybridized to the microarray slide in the presence of labeled Universal Human Reference RNA (UHRR, Stratagene, LaJolla, CA). A total of 143 subjects were used in this analysis. Briefly, five hundred nanograms of total RNA were used for gene expression profiling following reverse transcription and T-7 polymerase-mediated amplification/labeling with Cyanine-5 CTP. Labeled subject cRNA was co-hybridized to Agilent G4112F Whole Human Genome 4x44K oligonucleotide arrays with equimolar amounts of Cyanine-3 labeled UHRR. Slides were hybridized, washed, and scanned on an Axon 4000b microarray scanner. The data were processed using Feature Extraction (v9.5.1.1, Agilent) and imported into GeneSpring (v13, Agilent).
The sample titles are composed using the following scheme: ID_gender_ancestry_ObsCad_CadClass_CXCL5rank

first: Eleanor

last: Hiliard

first: Cam

last: Patterson


title: Clinical Evidence Supports a Protective Role for CXCL5 in Coronary Artery Disease Progression in the Elderly

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

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


title: Post-transcriptional Gene Silencing Mediated by microRNAs is Controlled by Nucleoplasmic Sfpq [Agilent]

status: Public on Oct 20 2017

city: Nice

first: Silvia

last: Bottini

address: 299, chemin de la ginestiere

summary: There is a growing body of evidence about the presence and the activity of the miRISC in the nucleus of mammalian cells. Here, we show by quantitative proteomic analysis that Ago2 interacts with nucleoplasmic Sfpq in a RNA-dependent fashion. By HITS-CLIP and transcriptomic analyses, we demonstrated that Sfpq directly controls the miRNA targeting of a subset of crucial miRNA-target mRNAs when it binds locally. Sfpq modulates miRNA targeting in both nucleoplasm and cytoplasm, indicating a nucleoplasmic imprinting of Sfpq-target mRNAs that influence miRNA targeting in both cellular compartments. Mechanistically, Sfpq binds to a sizeable set of long 3’UTR forming long aggregates to optimize miRNA position/recruitment to selected binding sites, as we show for Lin28A mRNA. These results extend the miRNA-mediated post-transcriptional gene silencing into the nucleoplasm and indicate that an unique Sfpq-dependent post-transcriptional strategy for controlling both nuclear and cytoplasmic gene expression takes place in cells during physio-pathological events.

overall_design: Agilent one-color microarray of P19 cells in control, let-7a overexpression, SFPQ knockdown, let-7a overexpression and SFPQ knockdown. Four replicates for each condition.

first: Nedra

last: Hamouda-Tekaya

first: Raphael

last: Mategot

first: Laure-Emmanuelle

last: Zaragosi

first: Stephane

last: Audebert

first: Valerie

last: Grandjean

first: Claire

last: Mauduit

first: Mohamed

last: Benahmed

first: Pascal

last: Barbry

first: Emanuela

last: Repetto

first: Michele

last: Trabucchi


title: DNA methylation signatures of illicit drug injection and hepatitis C are associated with HIV frailty II

status: Public on Nov 17 2017

city: New Haven

first: Ke

last: Xu

address: 300 George St.

department: department of psychiatry

institute: Yale University

summary: This dataset is used as replication set for Illumina 450k. Genome wide DNA methylation profiling of IDU+/HCV+ and IDV-/HCV- individuals for DNA samples extracted from peripheral blood. The Illumina Infinium Human DNA methylation 450 Beadchip was used to obtain DNA methylation profiles across approximately 480,000 CpGs. Samples included 216 IDU+/HCV+ and 170 IDU-/HCV- individuals. The goal was to identify genome-wide differentially methylated CpG sites between IDU+/HCV+ and IDU-/HCV- samples.

overall_design: Bisulfite converted DNA from the 405 DNA samples were hybridized to the Illumina Infinium MethylationEPIC Beadchip. The samples were extracted from whole blood. The subjects including 100 IDU+/HCV+ and 305 IDU-/HCV- were recruited from the Veteran Aging Cohort Study. All subjects were inform consented and the study protocol was approved by Connecticut Veteran Affair Healthcare System IRB and Yale Human Research Protection Program at Yale University.

first: Xinyu

last: Zhang

first: Amy

last: Justice


title: Expression of villi-specific genes reveals the novel prognostic biomarkers in human various cancers

city: Beijing

first: tao

middle: bo

last: zhang

address: No. 17 South Panjiayuan, Chaoyang District

institute: Cancer Hospital

summary: The relationship between oncogenesis and embryo development are surprised similarity,  early placental villi development from 6 weeks to 10 weeks of pregnancy were profiled using microarrays. Through comparative villi and mature placenta data, we identified villi-specific genes that were highly expressed in villus. The large fraction of villi-specific genes dysregulated in transcriptional level across tumors and most of villi-specific genes up-regulated in human cancers. Then by the GO enrichment results, we selected 5 immune-related genes, 6 proliferation-related genes, 8 focal adhesion-related genes that were found to have reported with genomic alterations. The expression of three group genes predicted poor prognosis of a subset of tumors. Our strategy provided a fresh idea for discovering the novel prognostic biomarkers of tumors.

overall_design: There are 44 samples, including 36 villus samples and 8  Postpartum placental samples. Gene expression profiling analysis of these samples was performed using Agilent 4x44K human whole genome gene expression microarray.

first: Botao

first: Xuexin

last: Yu

first: Shujun

last: Cheng


title: miR-7 as novel predictive epigenetic biomarker for platinum-resistance in cancer

status: Public on Oct 05 2017

first: Carlos

last: Rodriguez Antolin

address: Paseo de la Castellana

department: Genetics

institute: Hospital La Paz Institute for Health Research

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


title: Genome-wide analysis of mRNA expression in control and ChRO1 depleted C2C12 (Myoblasts and Myotubes)

status: Public on Sep 28 2017

city: Suwon

first: Jinyoung

last: Park

address: Seobu-ro 2066, Jangan-gu

institute: Sungkyunkwan University

summary:
The novel lncRNA ChRO1 (Chromatin ReOrganization associated lncRNA 1) which we discovered seems to be involved in myogenesis by association with heterochromatin reorganization during muscle differentiation. We wanted to identify which genes are influenced by ChRO1 depletion in muscle differentiation.
Analysis of the function of ChRO1 during myogenesis in gene expression level. The hypothesis in present study was that ChRO1 promotes myogenesis. Results provide important information that ChRO1 is involved in expression of various myogenic genes.

overall_design: mRNA obtained from wild-type myoblasts and myotubes (Scr_MB,Scr_MT), and ChRO1 depleted myoblasts and myotubes (sh#1_MB,sh#1_MT)

first: Eun-Jung

last: Cho


title: miR-7 as novel predictive epigenetic biomarker for platinum-resistance in cancer (gene expression)

summary: Background. One of the major limitations associated to the platinum use is the resistance that almost invariably will progress in lung and ovarian cancers. In the current study, we sought to identify epigenetically regulated miRNAs as novel biomarkers of platinum-resistance in those tumor types. Methods. We combined transcriptomic data from miRNA and mRNA under the influence of an epigenetic reactivation treatment, followed by qRT-PCR and epigenteic validations for an accurate candidate selection in 23 human cancer cell lines. Functional analysis were performed to study their biological and therapeutic implications, that were further tested in 257 primary samples obtained from lung and ovarian tumors. Results. We identified a group of 9 miRNAs belonging to the CM19 cluster and 7 potential miRNA-targets potentially involved in resistance development, in both tumor types. Deregulation of miR-7, -132, -335 and -148a may be a common event in the development of CDDP-resistance. miR-7 presented specific methylation in the resistant subtypes and its reexpression, decreased cell viability, suggesting a possible cell sensitization to cisplatin. Our translational approach indicated that miR-7 methylation is a frequent event that may play an important role in the early establishment of NSCLC tumorigenesis, and seems to play an additional platinum-predictive role in ovarian cancer.  Conclusions. miR-7 is a novel potential epigenetic biomarker tool for the selection of ovarian cancer patients with higher risk to earlier relapse and worst response to platinum-based chemotherapy. Funding. FIS (ISCIII): PI12/00386, PI13/01450, PI15/00186, and FEDER/FSE (Una manera de hacer Europa).

overall_design: Total RNA from Sensitive (S), Resistant (R) and Resistant under epigenetic reactivation treatment cells (RT) was extracted, by the guanidine thiocyanate method using TRIZOL reagent (Invitrogen, CA) and purified with miRNeasy mini kit (Quiagen, CA), combined with DNAsa treatment. Labelled cDNA from the 12 cell lines was hybridized by duplicate into Agilent platformsfor mRNA microarrays “Agilent Whole Human Genome Microarray (4x44K)”.

first: O

last: Vera

first: J

last: Jimenez

last: Pernía

first: C

last: Rodriguez-Antolin

first: F

last: Sánchez Cabo

last: Soto

first: R

last: Rosas

last: Rodriguez

first: S

last: Lopez-Magallon

first: I

last: Esteban

first: A

last: Dopazo

last: Rojo

last: Belda

last: Alvarez

last: Benitez

last: Perona

last: De Castro

last: Ibanez de Cáceres


title: Novel data integration approaches identify concordant and discordant immune responses between mice and humans [human cells]

status: Public on Sep 21 2017

city: Berlin

first: Teresa

last: Domaszewska

state: Berlin

address: Virchovweg 12

department: Immunology

institute: Max Planck Institute for Infection Biology

summary: We have conducted experiments to compare transcriptional response to tuberculosis (TB) in THP1 cells in time points 1hr,6hr and 24hr after infection.

overall_design: We infected THP1 cells with Mycobacterium tuberculosis, extracted total RNA at time points 1hr, 6hr and 24hr after infection and performed microarray experiments. We performed 5 experiments including 9 infected and 9 control (uninfected) samples (time points 6h and 24h) and 15 infected and 14 control samples in time points 6h and before infection.

first: Lisa

last: Scheuermann

first: Anca

last: Dorhoi

first: Karin

last: Hahnke

first: Hans

last: Mollenkopf

first: January

last: Weiner


title: Novel data integration approaches identify concordant and discordant immune responses between mice and humans


title: Genome-wide DNA methylation profiling in nine HMECs

status: Public on Sep 13 2017

city: daejeon

first: Jonglyul

last: Park

address: 52, Eoeun-dong, Yuseong-gu

department: Medical genomics

institute: Korea Research Institute of Bioscience and Biotechnology

summary: Genome wide DNA methylation profiling of nine breast HMECs samples (184AA3, 184AA2, 184AA4, 184A1, 184D, 184BE1, 184B5, 184B5ME, 184FMY2). The Illumina Infinium 850k Human DNA methylation Beadchip was used to obtain DNA methylation profiles across approximately 850,000 CpGs in nine breast HMECs samples.

overall_design: Bisulphite converted DNA from the nine samples were hybridised to the Illumina Infinium 850k Human Methylation Beadchip

first: Yong

middle: S

last: Lee

first: Seon

last: Kim


title: Whole transcriptomic analysis of B16 tumor environment 14 days after tumor inoculation in the absence of regulatory T cells (Treg)

status: Public on Aug 31 2017

city: Farmington

first: Djamel

last: Nehar-Belaid

state: CONNECTICUT

address: 10 discovery drive

institute: THE JACKSON LABORATORY

summary: Analysis of weakly immunogenic, B16 tumor environment at gene expression level after Treg depletion

overall_design: Total RNA obtained from Treg-depleted tumor environment (PC61 group) was compared with PBS-treated tumor environment (PBS group)

last: NEHAR-BELAID

first: Phuong

last: Pham Hang

first: David

last: KLATZMANN


title: EMT blockage is required for mouse naïve pluripotent stem cell derivation

status: Public on Oct 02 2017

city: Tehran

first: Ali

last: Sharifi-Zarchi

address: Royan Institute, Bani Hashem Sq.

country: Iran

institute: Royan Institute for Stem Cell Biology and Technology

summary: Pluripotency is the differentiation capacity of particular cells exhibited in the early embryo in vivo and embryonic stem (ES) cells have been shown to originate from the inner cell mass (ICM) of an E3.5 blastocyst. Although the potential for ES cells to differentiate into the three germ layers is equated to ICM cells, they differ in the ability to maintain the capacity for self-renewal.  Despite several studies on the maintenance of ES cells in the ground state of pluripotency, the precise mechanism of conversion from the ICM to the ES cell remains unclear. Here , we have examined the cell characteristics and expression profile within the intermediate stages of ES cell derivation from the ICM. Gene clustering and ontology (GO) analyses showed a significant change in the expression of epigenetic modifiers and DNA methylation-related genes in the intermediate stages. We have proposed that an epithelial-to-mesenchymal transition (EMT) blockage is required during derivation of mouse ES cells from E3.5 blastocysts. This study suggests a novel mechanistic insight into ES cell derivation and provides a time-course transcriptome profiling resource for the dissection of gene regulatory networks that underlie the transition from ICM to ES cells.

overall_design: For the first microarray analysis, Blastocyst-outgrowths were collected on days-3, -5, -7, and -9 from seeded E3.5 blastocysts as well as from isolated ICMs and ES cells, in three biological replicates. Between 20 to 30 outgrowths were picked and pooled for each biological replicate.  For the second microarray analysis, we collected new samples in a time resolution experiment that included ICM-outgrowths on days-0.5, -1, -2, -3, -5 and ES cells that were in passages -2, -4, and-15. In addition, we collected ICM-outgrowths cultivated in N2B27 supplemented with SB431542 on days -1 (D1-SB) and -3 (D3-SB) as the negative control. Between 30 to 40 ICM-outgrowths were picked and pooled in two biological replicates.

first: Mehdi

last: Totonchi

first: Seyedeh-Nafiseh

last: Hassani

first: Natalia

last: Tapia

first: Kenjiro

last: Adachi

first: Boris

last: Greber

first: Julia

last: Arand

first: Davood

last: Sabour

first: Marcos

last: Araúzo-Bravo

first: Mohammad

last: Pakzad

first: Jörn

last: Walter

first: Hamid

last: Gourabi

middle: R

last: Schöler

first: Hossein

last: Baharvand


title: Transcriptomic profiles of blood in murine polymicrobial sepsis

status: Public on Sep 01 2017

city: Jena

first: S.

last: Lambeck

address: Erlanger Allee 101

institute: JUH

summary:
Transcriptional effects in circulating leukocytes from mice challenged to peritoneal contamination and infection (PCI) compared to sham (vehicle control).
We gratefully acknowledge the BMBF grant for the Center for Sepsis Control and Care (CSCC) for this study

overall_design: Time resolved murine PCI challenge groups x four replicates, Sham control x three replicates

first: M

last: Weber

first: S

last: Lindig


title: Disturbed flow promotes arterial stiffening through thrombospondin-1 (TSP-1) signaling pathways

city: Atlanta

first: Sandeep

last: Kumar

state: GA

address: 1760 Haygood Dr.

department: Biomedical Engineering

country: USA

institute: Emory University

summary:
Arterial stiffness is a prevalent, independent cardiovascular risk factor, but the underlying mechanisms are not well understood. Wall shear stress and shear-sensitive genes may promote arterial stiffening through clinically important signaling pathways. Our goal was to identify how disturbed blood flow leads to arterial stiffness using the mouse partial carotid ligation model.
Here we used our in vivo partial carotid ligation model to induce d-flow in the LCA while the contralateral RCA continues to experience stable laminar flow using the C57BL/6x129SvEv mice, TSP-1 knockout (KO), and C57Bl/6J mice. We compared these to aged (80 week) mice which had increased arterial stiffness due to aging. Changes in gene expression were identified using microarrays that were performed on the endothelial-enriched RNA isolated from the carotids exposed to stable flow (RCA) and compared to disturbed flow (LCA). Arterial stiffness was determined ex vivo by biaxial mechanical testing and in vivo by ultrasound techniques. Myointimal hyperplasia and immunohistochemistry were performed in sectioned carotid arteries. In vitro testing of signaling pathways utilized oscillatory and laminar wall shear stress. Human arteries were tested ex vivo to validate critical results found in the animal model.

overall_design: Endothelial-enriched RNA was isolated from WT carotids exposed to stable flow or disturbed flow. Three replicates each.

first: Luke

last: Brewster

first: Chan

middle: W

last: Kim

first: Dong

last: Kang

first: Hanjoong

last: Jo


title: Tracking the molecular patterns of a common response across tissues in murine sepsis to refine treatment strategies

summary: Transcriptional effects in liver, lung, spleen and blood samples from mice challenged to Sham and Sepsis by Peritoneal Contamination and Infection (PCI) were monitored after 6 and 24 hours

overall_design: 4 Tissues x 2 Time Resolved Treatment Groups x 4 Replicates, 4 Tissues x Sham Control x 3 Replicates

last: Bauer


title: Glutamine supplementation suppresses herpes simplex virus reactivation

status: Public on Aug 30 2017

city: Bethesda

first: Timothy

middle: G

last: Myers

state: MD

address: 50 South Drive, Room 5509

department: Research Technologies Branch

institute: National Institute of Allergy and Infectious Diseases


title: Glutamine supplementation suppresses herpes simplex virus reactivation III

summary: Chronic viral infections are difficult to treat and new approaches, particularly those involving enhancing immune responses are needed.  Herpes simplex virus (HSV) establishes latency, reactivates frequently, and breakthrough reactivation can occur despite suppressive antiviral therapy.  Virus-specific T cells are important to control HSV, and activated T cells require increased metabolism of glutamine for their proliferation.  We found that treatment of HSV-1 latently infected mice and HSV-2 infected guinea pigs with supplemental oral glutamine reduced virus reactivation.  Transcriptome analysis of mice treated with glutamine showed that several interferon (IFN)-γ inducible genes were upregulated.  Unlike wild-type mice, supplemental glutamine was ineffective in reducing the rate of HSV-1 reactivation in IFN-γ knock-out mice.  Mice treated with glutamine had higher numbers of HSV-specific IFN-γ producing CD8 T cells in latently infected ganglia.  Thus, glutamine may enhance the IFN-γ-associated immune response and reduce the rate of reactivation of latent virus infection.

overall_design: RNA from HSV-1 latently infected  trigeminal ganglia of mice receiving dietary supplement of glutamine (test) were compared to those that received supplemental glycine (control); 9 arrays for each condition including 1 technical replicate. Each independent RNA sample was composed of 4 Tg organs from two mice pooled.

first: Kening

last: Wang

first: Yo

last: Hoshino

first: Kennichi

last: Dowdell

first: Marta

last: Bosch-Marce

first: Mayra

last: Sarmiento

first: Lesley

last: Pesnicak

first: Philip

last: Krause

first: Jeffrey

middle: I

last: Cohen


title: Glutamine supplementation suppresses herpes simplex virus reactivation II

overall_design: RNA from HSV-1 latently infected  trigeminal ganglia of mice receiving dietary supplement of glutamine (test) were compared to those that received supplemental glycine (control); 9 arrays for each condition including 2 technical replicate glycine and one technical replicate for glutamine. Each independent RNA sample was composed of 4 Tg organs from two mice pooled.


title: Gene expression profiling of gastric early-stage carcinoma and precancerous lesions

status: Public on Aug 29 2017

first: Xue

last: Xu

state: Beijing

address: ShuaiFuYuan 1

institute: Chinese Academy of Medical Sciences & Peking Union Medical College

summary: To investigated the molecular distinction and functional correlation among different histopathological types of gastric neoplasia, the whole genome expression profiling of gastric early-stage carcinoma(EGC) and high-grade and low-grade intraepithelial neoplasia (HGIN and LGIN) were explored. This research will provide biological evidence for the clinical application in different gastric early-stage neoplasia.

overall_design: Human gastric tissue samples were collected for the microarray research, which included 19 LGIN, 20 HGIN, 19 EGC and 19 chronic gastritis tissue samples. EGC are confined to mucosa or submucosa by surgery or ESD(Endoscopic Submucosal Dissection).

first: Lin

last: Feng

first: Shujun

last: Cheng

first: Xinghua

last: Lu


title: Gene expression profiling of cardiomyocyte-enriched populations isolated from mice subject  to transverse aortic constriction (TAC) and treated with BIX-01294 for 1 week

city: Rozzano

first: Simone

last: Serio

state: Milano

address: Via Alessandro Manzoni, 56

department: Cardiovascular Medicine

country: Italy

institute: Humanitas Research Hospital

summary: The role of the histone mehyltrasferase G9a (also known as Ehmt2) in cardiac hypertrophy has not been studied extensively. To address how G9a promotes cardiac hypertrophy, we assessed the gene expression signature defined by G9a in cardiomyocytes (CM) of mice subject to transverse aortic constriction (TAC) for 1 wk, a surgical procedure that causes cardiac hypertrophy following the induction of pressure overload. To this end, we compared the expression profiles of CMs isolated from mice treated with the G9a inhibitor BIX-01294 and control groups (untreated and DMSO-treated mice at baseline and after TAC). The expression profiles were defined by Illumina arrays  .

overall_design: Profiling of the transcriptome of cardiomyocyte-enriched populations isolated from mice subject at transverse aortic constriction (TAC) and treated with BIX-01294 for 1 week. Two biological replicates were profiled for each cell type.

first: Roberto

last: Papait

first: Gianluigi

last: Condorelli