title: Time course analysis of outer medulla-specific gene expression profiles in the kidneys of Sprague-Dawley rats in a repeated dose study of 2-amino-4-nitrophenol.

status: Public on Sep 27 2016

city: Kitakatsushika-gun

first: Hiroshi

last: Matsumoto

state: Saitama

address: 1600 Shimotakano, Sugito-machi

country: Japan

institute: Chemicals Evaluation and Research Institute, Japan

summary: In the present study, we performed a general toxicity test and a genome-wide gene expression analysis of rat kidney to identify the mechanisms of 2-amino-4-nitrophenol (ANP) -induced chronic renal failure.

overall_design: Experimental design is the two group (control group vs. ANP treated group). The ANP was dissolved in corn oil, and the animals were dosed orally once daily for 28 days.

first: Fumiyo

last: Saito

first: Satsuki

last: Hoshuyama

first: Toshio

last: Kobayashi

first: Masahiro

last: Takeyoshi


title: Rhesus placenta transcriptome in the setting of congenital RhCMV infection

status: Public on Sep 28 2016

city: Durham

first: Cody

middle: Shaw

last: Nelson

state: NC

address: 2 Genome Ct

department: MGM

country: USA

institute: Duke University

summary: Cytomegalovirus (CMV) is the most common congenital infection worldwide, causing deafness and neurodevelopmental delay in infected infants. Preexisting maternal immunity to CMV is known to influence the incidence and severity of congenital infection. To establish the role of maternal antibody in protection against placental CMV transmission, 6 rhesus CMV (RhCMV)-seronegative rhesus monkey dams were CD4+ T cell depleted at the end of the first trimester of pregnancy and treated with either a single dose of standardly-produced hyperimmune globulin (HIG) (n=3) or a dose-optimized regimen of a potently-neutralizing HIG (n=3) prior to IV inoculation with a mixture of RhCMV strains. Passive infusion with HIG provided complete protection against fetal loss (0/6 HIG-treated vs. 5/6 control dams aborted; p=0.015). Furthermore, the dose-optimized, highly-neutralizing HIG product reduced the magnitude and diversity of maternal plasma RhCMV populations and inhibited placental transmission of RhCMV (0/3 transmitted), suggesting that pre-existing highly-neutralizing antibodies are sufficient to prevent congenital CMV infection and disease. In this study, we sought to investigate the placental transcriptome to determine whether: a) RhCMV congenital infection was being controlled at the level of the placenta, b) what genes are up-regulated following RhCMV congenital infection, and c) whether there are any genes associated with protection against viral infection.

overall_design: This study contains 3 groups of monkeys: control, standard HIG-infused, and high-potency HIG-infused. All control animals + 2/3 standard HIG-infused animals had congenitally infected fetuses. Thus, there are 4 independent groups: (1) control + CMV-infected, (2) standard + CMV-infected, (3) standard + not CMV-infected, and (4) high-potency HIG + not CMV-infected. RNA was extracted from sections of fetal placenta for 7 animals in total.

middle: S

first: Kristy

middle: M

last: Bialas

first: Sallie

middle: R

last: Permar


title: Gene expression profiling of generated sunitinib-resistant RCC cell lines

status: Public on Sep 30 2016

city: Shanghai

first: le

last: qu

address: 440 North Chengdu Road

department: Department of Urology

country: China

institute: Second Military Medical University

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

summary: The clinical response to sunitinib in advanced renal-cell carcinoma (RCC) is frequently limited in magnitude and duration due to drug resistance, but the underlying mechanisms remain elusive. To discover mechanisms of resistance, we developed drug-resistant cell lines and have their gene expressions profiled and compared. Results provide insight into the molecular mechanisms underlying sunitinib-resistance.

overall_design: RCC cell lines 786-O and ACHN, which were initially sensitive to Erlotinib treatment, are injected subcutaneously into the flanks of nude mice. Mice were treated with sunitinib orally (40 mg/kg/day) in a standard 4 weeks on, 2 weeks off treatment schedule. After one cycle of treatment, RCC cells dissociated from xenografts were transplanted into secondary mice followed with the same sunitinib-treatment. RCC cells are finally obtained from the 3rd generation xenografts. 7Su3rd is a shortcut of 786-O cells with sunitinib-resistance from the 3rd generation. ACSu3rd is a shortcut of ACHN cells with sunitinib-resistance from the 3rd generation.Gene expression profiles of acquired resistant RCC cells 7Su3rd, ACSu3rd were compared to their parental counterpart 786-O and ACHN, respectively. We designed this experiment to screen for lncRNA which is required for sunitinib-resistance.

first: Le

last: Qu

first: Cheng

last: Chen

first: Linhui

last: Wang

first: Hongyang


title: Gene expression profile of the IL2RG gene depletion in pig spleen

city: Seoul

first: Yun-Jung

last: Choi

address: 120 Neungdon-ro,Gwangjib-gu

department: Animal biotechnology

country: South Korea

institute: KONKUK University

summary: Severe combined immunodeficiency (SCID) occurs in various species, including humans, at a frequency as high as one per 50,000 live births. Generally, SCID can be classified according to the cause of the immunodeficiency, and it includes impaired cytokine-mediated signalling, defective V(D)J recombination, impaired pre-T-cell receptor signalling, and metabolic enzyme deficiencies. Although mice with disrupted SCID-causing genes have provided important insights into the human disease, not all the SCID mice have phenotypes that resemble those in human SCID patients. In humans, most SCID patients are reported to have impaired cytokine-mediated signalling in immune cells. IL2RG is a key component of the immune system, which is associated with the development of X-linked SCID in humans. Despite some phenotypic characterisations and functional studies being performed in SCID animals, little is known about the molecular basis of the different phenotypes of SCID in mouse and pig. In the present experiment, we generated monoallelic IL2RG (mIL2RG+/Δ69-368) KO pigs and investigated patterns of gene expression during their immune development in order to further explore our understanding of immune responses in X-linked SCID.

overall_design: We generated monoallelic IL2RG  KO pigs using TALEN. Three independent experiments were performed at wild spleen and one experiment was performed at  IL2RG KO pigs.

first: Jin-Hoi

last: Kim


title: Gene expression profile of the IL2RG gene depletion in pig spleen and thymus

overall_design: We generated monoallelic IL2RG (mIL2RG+/Δ69-368) KO pigs using TALEN. Two independent experiments were performed at wild thymus and Two experiment was performed at  IL2RG (mIL2RG+/Δ69-368) KO pigs.


title: Gene expression changes of p-nitroanisole-induced in renal cortex of rats

summary: This study is to develop a short term and highly accurate prediction method of renal carcinogenicity based on gene expression profile of rats administrated by carcinogens. We conducted 28 days-repeated dose experiments in male SD rats with p-nitroanisole, and the gene expression profiles of renal cortex were analyzed using custom microarrays.

overall_design: Experimental design is the two group (control group vs. p-nitroanisole treated group). Three biological replicates were performed for each group.


title: Gene expression profile of the IL2RG gene depletion in pig thymus


title: Dynamic Sumoylation of a Conserved Transcription Corepressor Prevents Persistent Inclusion Formation during Hyperosmotic Stress

city: Seattle

first: Maitreya

middle: J.

last: Dunham

state: WA

address: Foege Building, S403B, Box 355065

department: Genome Sciences

institute: University of Washington

summary: Cells are often exposed to physical or chemical stresses that can damage the structures of essential biomolecules. Stress-induced cellular damage can become deleterious if not managed appropriately. Rapid and adaptive responses to stresses are therefore crucial for cell survival. In eukaryotic cells, different stresses trigger post-translational modification of proteins with the small ubiquitin-like modifier SUMO. However, the specific regulatory roles of sumoylation in each stress response are not well understood. Here, we examined the sumoylation events that occur in budding yeast after exposure to hyperosmotic stress. We discovered by proteomic and biochemical analyses that hyperosmotic stress incurs the rapid and transient sumoylation of Cyc8 and Tup1, which together form a conserved transcription corepressor complex that regulates hundreds of genes. Gene expression and cell biological analyses revealed that sumoylation of each protein directs distinct outcomes. In particular, we discovered that Cyc8 sumoylation prevents the persistence of hyperosmotic stress-induced Cyc8-Tup1 inclusions, which involves a glutamine-rich prion domain in Cyc8. We propose that sumoylation protects against persistent inclusion formation during hyperosmotic stress, allowing optimal transcriptional function of the Cyc8-Tup1 complex.

overall_design: This dataset contains gene expression analysis of wild type and mutant yeast strains across a time course (0, 30, or 60 minutes) of hyperosmotic stress (yeast complete+1.2M sorbitol media). We grew biological duplicates (replicates A and B) of four strains expressing different combinations of wild type and sumoylation-deficient Tup1 and Cyc8: wild type, TUP1(K270R), CYC8(K735R,K736R,K738R,K748R), and TUP1(K270R)/CYC8(K735R,K736R,K738R,K748R). The wild type, replicate A, 0 minute sample was labeled with Cy5 and served as a reference for all other replicate A samples; the wild type, replicate B, 0 minute sample was labeled with Cy3 and served as a reference for all other replicate B samples. One array compared the two references to each other.

first: Michelle

last: Oeser

first: Richard

last: Gardner


title: Gene expression changes of 4-hydroxy-m-phenylenediammonium dichloride-induced in renal cortex of rats

first: Hiroshi

last: Matsumoto

summary: This study is to develop a short term and highly accurate prediction method of renal carcinogenicity based on gene expression profile of rats administrated by carcinogens. We conducted 28 days-repeated dose experiments in male SD rats with 4-hydroxy-m-phenylenediammonium dichloride, and the gene expression profiles of renal cortex were analyzed using custom microarrays.

overall_design: Experimental design is the two group (control group vs. 4-hydroxy-m-phenylenediammonium dichloride treated group). Three biological replicates were performed for each group.

first: Fumiyo


title: Gene expression changes of 2-Amino-4-nitrophenol-induced in renal cortex of rats

summary: This study is to develop a short term and highly accurate prediction method of renal carcinogenicity based on gene expression profile of rats administrated by carcinogens. We conducted 28 days-repeated dose experiments in male SD rats with 2-Amino-4-nitrophenol, and the gene expression profiles of renal cortex were analyzed using custom microarrays.

overall_design: Experimental design is the two group (control group vs. 2-Amino-4-nitrophenol treated group). Three biological replicates were performed for each group.

last: Saito


title: Gene expression changes of benzyl acetate-induced in renal cortex of rats

summary: This study is to develop a short term and highly accurate prediction method of renal carcinogenicity based on gene expression profile of rats administrated by carcinogens. We conducted 28 days-repeated dose experiments in male SD rats with benzyl acetate, and the gene expression profiles of renal cortex were analyzed using custom microarrays.

overall_design: Experimental design is the two group (control group vs. benzyl acetate treated group). Three biological replicates were performed for each group.


title: Gene expression changes of 2,2-bis(bromomethyl)-1,3-propanediol-induced in renal cortex of rats

summary: This study is to develop a short term and highly accurate prediction method of renal carcinogenicity based on gene expression profile of rats administrated by carcinogens. We conducted 28 days-repeated dose experiments in male SD rats with 2,2-bis(bromomethyl)-1,3-propanediol, and the gene expression profiles of renal cortex were analyzed using custom microarrays.

overall_design: Experimental design is the two group (control group vs. 2,2-bis(bromomethyl)-1,3-propanediol treated group). Three biological replicates were performed for each group.


title: miRNA  Expression data from synovium in mouse serum transfer arthritis model (STA) model

city: worcester

first: yukiko

last: maeda

state: massachusetts

address: 364 Plantation Street

department: Medicine

institute: Umass Medical School

summary: To find regulated miRNAs during peak inflammation of rheumatoid arthritis (RA), we have collected synovium from  mouse STA model at day 0  (Non Arthritic) and day 10 (Peak Inflammation). For miRNA profiling, we used high-throughput BioMark Real-Time PCR system (Fluidigm, South San Francisco, CA)

overall_design: We analyzed expression of 750 miRNA in Non-arthritic synovium pooled from 3 mice and Arthritic synovium at peak inflammation pooled from 10 mice. Two biological replicates for each time points. Two technical replicates per sample.

first: Yukiko

last: Maeda

first: Nicholas

middle: H

last: Farina

first: Melissa

last: Matzelle

first: Paul

middle: J

last: Fanning

first: Jane

middle: B

last: Lian

first: Ellen


title: Gene expression changes of carbon tetrachloride-induced in renal cortex of rats

summary: This study is to develop a short term and highly accurate prediction method of renal carcinogenicity based on gene expression profile of rats administrated by carcinogens. We conducted 28 days-repeated dose experiments in male SD rats with carbon tetrachloride, and the gene expression profiles of renal cortex were analyzed using custom microarrays.

first: Masahiro

last: Takeyoshi


title: Gene expression changes of ochratoxin A-induced in renal cortex of rats

summary: This study is to develop a short term and highly accurate prediction method of renal carcinogenicity based on gene expression profile of rats administrated by carcinogens. We conducted 28 days-repeated dose experiments in male SD rats with ochratoxin A, and the gene expression profiles of renal cortex were analyzed using custom microarrays.

overall_design: Experimental design is the two group (control group vs. ochratoxin A treated group). Three biological replicates were performed for each group.


title: Gene expression changes of phenylbutazone-induced in renal cortex of rats

summary: This study is to develop a short term and highly accurate prediction method of renal carcinogenicity based on gene expression profile of rats administrated by carcinogens. We conducted 28 days-repeated dose experiments in male SD rats with phenylbutazone, and the gene expression profiles of renal cortex were analyzed using custom microarrays.

overall_design: Experimental design is the two group (control group vs.phenylbutazone treated group). Three biological replicates were performed for each group.


title: Gene expression changes of 1,2-dibromoethane-induced in renal cortex of rats

summary: This study is to develop a short term and highly accurate prediction method of renal carcinogenicity based on gene expression profile of rats administrated by carcinogens. We conducted 28 days-repeated dose experiments in male SD rats with 1,2-dibromoethane, and the gene expression profiles of renal cortex were analyzed using custom microarrays.

overall_design: Experimental design is the two group (control group vs. 1,2-dibromoethane treated group). Three biological replicates were performed for each group.


title: Gene expression changes of monuron-induced in renal cortex of rats

summary: This study is to develop a short term and highly accurate prediction method of renal carcinogenicity based on gene expression profile of rats administrated by carcinogens. We conducted 28 days-repeated dose experiments in male SD rats with monuron, and the gene expression profiles of renal cortex were analyzed using custom microarrays.

overall_design: Experimental design is the two group (control group vs. monuron treated group). Three biological replicates were performed for each group.


title: Gene expression changes of anthraquinone-induced in renal cortex of rats

summary: This study is to develop a short term and highly accurate prediction method of renal carcinogenicity based on gene expression profile of rats administrated by carcinogens. We conducted 28 days-repeated dose experiments in male SD rats with anthraquinone, and the gene expression profiles of renal cortex were analyzed using custom microarrays.

overall_design: Experimental design is the two group (control group vs. anthraquinone treated group). Three biological replicates were performed for each group.


title: Gene expression changes of 1-amino-2,4-dibromoanthraquinone-induced in renal cortex of rats

summary: This study is to develop a short term and highly accurate prediction method of renal carcinogenicity based on gene expression profile of rats administrated by carcinogens. We conducted 28 days-repeated dose experiments in male SD rats with 1-amino-2,4-dibromoanthraquinone, and the gene expression profiles of renal cortex were analyzed using custom microarrays.

overall_design: Experimental design is the two group (control group vs. 1-amino-2,4-dibromoanthraquinone treated group). Three biological replicates were performed for each group.


title: Gene expression changes of phenolphthalein-induced in renal cortex of rats

summary: This study is to develop a short term and highly accurate prediction method of renal carcinogenicity based on gene expression profile of rats administrated by carcinogens. We conducted 28 days-repeated dose experiments in male SD rats with phenolphthalein, and the gene expression profiles of renal cortex were analyzed using custom microarrays.

overall_design: Experimental design is the two group (control group vs. phenolphthalein treated group). Three biological replicates were performed for each group.


title: Gene expression changes of 1,2,3-trichloropropane-induced in renal cortex of rats

summary: This study is to develop a short term and highly accurate prediction method of renal carcinogenicity based on gene expression profile of rats administrated by carcinogens. We conducted 28 days-repeated dose experiments in male SD rats with 1,2,3-trichloropropane, and the gene expression profiles of renal cortex were analyzed using custom microarrays.

overall_design: Experimental design is the two group (control group vs. 1,2,3-trichloropropane treated group). Three biological replicates were performed for each group.


title: Gene expression changes of N,N'-dinitrosopentamethylenetetramine-induced in renal cortex of rats

summary: This study is to develop a short term and highly accurate prediction method of renal carcinogenicity based on gene expression profile of rats administrated by carcinogens. We conducted 28 days-repeated dose experiments in male SD rats with N,N'-dinitrosopentamethylenetetramine, and the gene expression profiles of renal cortex were analyzed using custom microarrays.

overall_design: Experimental design is the two group (control group vs. N,N'-dinitrosopentamethylenetetramine treated group). Three biological replicates were performed for each group.


title: Gene expression changes of n-nitrosodimethylamine-induced in renal cortex of rats

summary: This study is to develop a short term and highly accurate prediction method of renal carcinogenicity based on gene expression profile of rats administrated by carcinogens. We conducted 28 days-repeated dose experiments in male SD rats with n-nitrosodimethylamine, and the gene expression profiles of renal cortex were analyzed using custom microarrays.

overall_design: Experimental design is the two group (control group vs. n-nitrosodimethylamine treated group). Three biological replicates were performed for each group.


title: Gene expression changes of ethylenediamine dihydrochloride-induced in renal cortex of rats

summary: This study is to develop a short term and highly accurate prediction method of renal carcinogenicity based on gene expression profile of rats administrated by carcinogens. We conducted 28 days-repeated dose experiments in male SD rats with ethylenediamine dihydrochloride, and the gene expression profiles of renal cortex were analyzed using custom microarrays.

overall_design: Experimental design is the two group (control group vs. ethylenediamine dihydrochloride treated group). Three biological replicates were performed for each group.


title: Gene expression changes of nitrilotriacetic acid trisodium monohydrate-induced in renal cortex of rats

summary: This study is to develop a short term and highly accurate prediction method of renal carcinogenicity based on gene expression profile of rats administrated by carcinogens. We conducted 28 days-repeated dose experiments in male SD rats with nitrilotriacetic acid trisodium monohydrate, and the gene expression profiles of renal cortex were analyzed using custom microarrays.

overall_design: Experimental design is the two group (control group vs. nitrilotriacetic acid trisodium monohydrate treated group). Three biological replicates were performed for each group.


title: Gene expression changes of bromodichloromethane-induced in renal cortex of rats

summary: This study is to develop a short term and highly accurate prediction method of renal carcinogenicity based on gene expression profile of rats administrated by carcinogens. We conducted 28 days-repeated dose experiments in male SD rats with bromodichloromethane, and the gene expression profiles of renal cortex were analyzed using custom microarrays.

overall_design: Experimental design is the two group (control group vs. bromodichloromethane treated group). Three biological replicates were performed for each group. Rats were humanely sacrified by bleeding under anesthesia with CO2-O2 (4:1) or isoflurane gas inhalation 24 hr after final administration.


title: Gene expression changes of dipropylene glycol-induced in renal cortex of rats

summary: This study is to develop a short term and highly accurate prediction method of renal carcinogenicity based on gene expression profile of rats administrated by carcinogens. We conducted 28 days-repeated dose experiments in male SD rats with dipropylene glycol, and the gene expression profiles of renal cortex were analyzed using custom microarrays.

overall_design: Experimental design is the two group (control group vs. dipropylene glycol treated group). Three biological replicates were performed for each group.


title: Gene expression changes of chlorothalonil-induced in renal cortex of rats

summary: This study is to develop a short term and highly accurate prediction method of renal carcinogenicity based on gene expression profile of rats administrated by carcinogens. We conducted 28 days-repeated dose experiments in male SD rats with chlorothalonil, and the gene expression profiles of renal cortex were analyzed using custom microarrays.

overall_design: Experimental design is the two group (control group vs.chlorothalonil treated group). Three biological replicates were performed for each group.


title: Initiation of mtDNA transcription is followed by pausing, and diverge across human cell types and during evolution

city: Beer Sheva

first: Dan

last: Mishmar

state: Israel

address: Ben Gurion University of the Negev

department: Life sciences

country: Israel

institute: Ben Gurion University of the Negev

type: Expression profiling by high throughput sequencing

summary: We analyzed nascent mtDNA-encoded RNA transcripts from GRO-seq and PRO-seq experiments in a collection of diverse human cell lines and Metazoan organisms. Accurate detection of human mtDNA transcription initiation sites (TIS) in the heavy and light strands revealed a novel transcription pausing site near the light strand TIS, upstream to the transcription-replication transition region, in conserved sequence block III (CSBIII). The transcription pausing index varied quantitatively among the cell lines. In addition to the human cell lines experiments, our experiments and analysis of non-human organisms enabled detection of previously unknown mtDNA TIS, pausing, and transcription termination sites with unprecedented accuracy. Whereas mammals (chimpanzee, rhesus macaque, rat, and mouse) showed a human-like mtDNA transcription pattern, the invertebrate pattern (Drosophila and C. elegans) profoundly diverged.

sample_organism:
Caenorhabditis elegans
Drosophila melanogaster
Macaca mulatta
Pan troglodytes
Homo sapiens
Mus musculus
Rattus norvegicus

overall_design:
We re-mapped GRO-seq and PRO-seq data. We calibrated the parameters required to identify sites of transcription initiation, termination and pausing, which was first assigned to human samples but was applied to diverse non-human organisms.
Fastq files of the tested samples were trimmed by Trim-galore to reach a minimum read length of 30 nucleotides.
The trimmed fastq files of the samples were mapped against the entire revised mitochondrial genome using BWA-aln (-q=5, -l=20, -k=2, -t=1). BWA was used to convert SAI into SAM format, which in turn was converted into a BAM file and sorted using Samtools.
Samtools was used to generate VCF files of each sample (mpileup (-uf) command). Then, sample-specific mtDNA sequence was re-constructed for each of the analyzed samples using bcftools call (-c) (Samtools) in combination with vcf2fq from the vcfutils.pl package.
The Fastq files were uniquely re-mapped against the reconstructed sample-specific mtDNA using BWA-aln (-q=5, -l=32, -k=2, -t=1), and BAM files were generated again. Removal of low MAPQ reads was performed using the Samtools ‘view’ command (-F=1804, -q=30)
Coverage per base was calculated for a given sequence interval (separately for each strand) using Bedtolls (version 2.25), by the ‘genomecov’ command ('-d' and '-strand' options).
Since the mtDNA is a circular molecule and some reads may have been erroneously excluded we re-analyzed the Fastq files. To this end we remapped the reads to the sample-specific mtDNA sequence that was rearranged such, that the last 500 nucleotides of the standard mtDNA sequence were cut and pasted at the beginning of the sequence. Mapping was performed and read coverage at the former circle junction of the rearranged sequence was calculated and added to the previous mapping results
Genome build:
Homo sapiens: NC_012920.1; Revised Cambridge Reference Sequence ("rCRS")
Pan troglodytes: NC_001643.1
Macaca mulatta: NC_005943.1
Rattus norvegicus: NC_001665.2
Mus musculus: NC_005089.1
Drosophila melanogaster: NC_024511.2
Caenorhabditis elegans: NC_001328.1

first: Amit

last: Blumberg


title: Identification of ETV6/RUNX1 regulated lncRNAs

status: Public on Sep 26 2016

city: Ghent

first: Farzaneh

last: Ghazavi

address: De Pintelaan 185

department: Center of medical genetics

country: Belgium

institute: Gent university hospital

summary: Overwhelming evidence indicates that long non-coding RNAs have essential roles in tumorigenesis. Nevertheless, their expression and role in pediatric B-cell precursor acute lymphoblastic leukemia has not been extensively explored. Here, we conducted a comprehensive analysis of the long non-coding RNA transcriptome in ETV6/RUNX1 positive BCP-ALL, one of the most frequent subtypes of pediatric leukemia. An ETV6/RUNX1 expression signature was established, consisting of 596 lncRNAs (434 up and 162 down) using expression analysis of a series of primary patient samples. Subsequently, RNA sequencing from BCP-ALL cell lines and shRNA-mediated silencing of ETV6/RUNX1, illustrated that lnc-NKX2-3-1, lnc-TIMM21-5, lnc-ASTN1-1 and lnc-RTN4R-1 are bona fide ETV6/RUNX1 targets and could serve as novel biomarkers of this prevalent subtype of human leukemia.

overall_design: REH cell lines were treated either  with shRNA against ETV6/RUNX1 fusion or with non-targeting shRNA. This was performed for 3 replicates. Expression profiling was performed on three samples with fusion knockdown and three scrambles.

first: Wouter

last: Van Loocke

first: Pieter

last: Van Vlierberghe

first: Barbara

last: De Moerloose

first: Tim

last: Lammens

first: Yves

last: Benoit

first: Frank

last: Speleman


title: Escherichia coli: untreated versus 5-azacytidine-treated expression profiles

status: Public on Sep 24 2016

city: Geneseo

first: Kevin

middle: T

last: Militello

state: New York

address: 1 College Circle

department: Biology

institute: State University of New York at Geneseo

summary:
DNA microarray experiments were used to compare gene expression profiles of untreated and 5-azacytidine treated Escherichia coli at both logarithmic phase and early stationary phase
The goal was to determine the effect of cytosine DNA methylation loss on gene expression (5-azacytidine is a methylation inhibitor)

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

overall_design: Untreated versus 5-azacytidine-treated cells at logarithmic phase and early stationary phase; 5 biological replicates both all experiments


title: Expression data from chicken preadipocytes

city: Harbin

first: Hui

last: Zhang

state: Heilongjiang

address: Mucai street No. 59

department: College of Animal Science and Technology

institute: Northeast Agricultural University

summary:
Gene expression profiles of chicken preadipocytes were constructed using Chicken Genome Arrays to determine the gene expression patterns of preadipocytes derived from two chicken lines divergently selected for abdominal fat content.
Oleate was used as an inducer of preadipocyte differentiation, and the different expressed genes between the normal and oleate treated preadipocyte were analyzed.

overall_design:
Cultured preadipocytes were divided into four groups, including the lean line preadipocytes cultured normally (LC), the fat line preadipocytes cultured normally (FC), the lean line preadipocytes treated with oleate (L) and the fat line preadipocytes treated with oleate (F).
For the lean and fat chicken lines respectively, the abdominal adipose tissues of 15 male birds with 10 day-old were excised and pooled. The pooled abdominal adipose tissues were digested. Digestion was followed by filtration through a 20um screen and centrifugation at 800 g for 10 min at room temperature. This phase allowed the separation of floating adipocytes from the preadipocytes. The preadipocytes were treated with ACK lysis buffer to remove the red blood cells. The preadipocytes at this stage with a high purity were not cultured and a part of the preadipocytes were collected as the 0001 time point. The remaining preadipocytes were seeded at a density of 5x10^4 cells/cm2 in the medium and maintained at 37°C in a humidified, 5% CO2 atmosphere until confluence (3 to 4 d). The preadipocytes were passaged once and harvested when 50% confluent (named as -12h) and 95% confluent (named as 0h). From the 0h time point, the preadipocytes were divided into two groups. The preadipocytes in one group were treated with 160 ug/ml oleate. The preadipocytes in another group were cultured with normal situation as the control. The preadipocytes from the oleate treated and control groups were collected at 12h, 24h, 72h and 120h.


title: Characterizing genetic transitions of copy number alterations and allelic imbalances in metastatic process of the oral tongue carcinoma

status: Public on Sep 23 2016

city: Tokyo

first: Takuma

last: Morita

address: 1-5-45 Yushima, Bunkyo-ku

department: Maxillofacial Surgery

institute: Tokyo Medical and Dental University

summary: Primary tumor heterogeneity can significantly affect the genetic profile of clones at metastatic sites. In order to understand the mechanisms underlying metastasis, we compared the genetic profile of paired primary tumor (PT) and metastatic lymph node (MLN) samples obtained from individual patients.

overall_design: Large-scale genetic profiling was performed on paired PT-MLN tissue samples obtained from 10 oral tongue squamous cell carcinoma (OTSCC) patients using high-density single-nucleotide polymorphism microarrays. We compared the genetic profile of PT and MLN OTSCC samples from the same patient in order to identify common and specific copy number alterations (CNAs) and copy-neutral loss of heterozygosity (CN-LOH).

first: Narikazu

last: Uzawa

first: Kaoru

last: Mogushi

first: Jun

last: Sumino

first: Chieko

last: Michikawa

first: Ken-Ichiro

last: Takahashi

first: Kunihiro

last: Myo

first: Toshiyuki

last: Izumo

first: Kiyoshi

last: Harada


title: Bone marrow mesenchymal cells from Myelodisplastic Syndromes release microvesicles that incorporate into CD34+ cells and may modify their behaviour.

city: Salamanca

first: Beatriz

middle: Roson

last: Burgo

address: Campus Miguel de Unamuno

department: Cancer Research Centre

country: Spain

institute: Consejo Superior de Investigaciones Científicas & Universidad de Salamanca

summary: The secretion of exosomes/ microvesicles (MVs) is a recently described mechanism of intercellular communication that is based on the transfer of bioactive molecules. Our hypothesis was that mesenchymal stromal cells (MSC) from myelodisplastic syndromes (MDS) patients could modify CD34+ hematopoietic progenitor cells (HPC) properties throughout MVs. The latter were isolated from MSC from MDS patients and healthy donors (HD). MVs were purified by ExoQuick-TC exosome precipitation solution or ultracentrifugation and identified by transmission electron microscopy (TEM) and flow cytometry (FC). Their Micro-RNA content was evaluated by microarrays. Incorporation of MVs into CD34+ cells was analyzed by FC and confocal microscopy (CM). Our results showed that MVs displayed the same immunophenotypic pattern and similar morphology. The content of miRNAS in the MVs from MDS and HD was significantly different. Next, MVs incorporation into HPC was observed, being highest after 24 hours of incubation. We demonstrated that MVs could modify the HPC behavior since the incubation of HPC with MVs led to gene expression modification evaluated by RT-PCR and increased cell viability by FC. In summary, we show that BM-MSC produce MVs with different cargo in MDS compared to HD. These structures can incorporate into HPC and modify their properties.

overall_design: In order to study the micro-RNA content of MSC-MVs from both patients and controls, a differential expression analysis of miRNAs was performed. Total RNA from MSC-derived MVs of 8 low-risk MDS and 4 HD were retrotranscribed with Megaplex™ RT Primers pool (Applied Biosystems). 384-well microfluidic cards (TaqMan® MicroRNA Array A) were loaded with retro-transcription product and PCR runs were performed on a 7900HT Fast Real-time PCR system (Applied Biosystems).

first: Sandra

last: Muntión

first: Teresa

middle: L

last: Ramos

first: María

last: Diez-Campelo

last: Roson-Burgo

first: Bruno

last: Paiva

first: María-Eugenia

last: Sarasquete

first: Stefania

last: Bruno

first: Marcos

last: González

first: Jesús

middle: F

last: San Miguel

first: Fermín

last: Sánchez-Guijo

first: María-Consuelo

last: del Cañizo


title: Time course gene expression profile of YPD medium grown Candida albicans mss11 mutant

city: Hsinchu

first: Yu-Ting

last: Chen

address: No.101, Sec. 2, Guang-Fu Rd.

department: Institute of Molecular and Cellular Biology

country: Taiwan

institute: National Tsing Hua University, Taiwan

summary: Candida albicans is an important fungal pathogen in humans. Several virulence factors of C. albicans have been reported, including a morphological transition from yeast to filamentous forms (hyphae and pseudohyphae). Mss11 is a transcriptional activator required for hyphal formation. To reveal the potential target genes of Mss11, DNA microarray analysis was performed to compare wild type and mss11-deleted mutant.

overall_design: 24 arrays was generated from same experiment. Wild type and mss11 mutant cells were incubated in 30 ˚C YPD medium, and were collected at different time points for RNA extraction. The differential expression of wild type and mutant at each time points was performed by 12 arrays including dye swap. The time course gene expression profile of both strain was performed by another 12 arrays.

first: Yu

first: Pei

middle: W

last: Tsai

first: Wen

middle: P

last: Hsieh

first: Chung

middle: Y

last: Lan


title: Aortic microRNA expression in germ-free mice and pathogen-free mice

status: Public on Sep 15 2016

city: Iowa City

first: Ajit

last: Vikram

state: Iowa

address: 431 Newton Rd. 400 EMRB

department: Internal Medicine

institute: University of Iowa

summary: To understand the effect of microbes on microRNAs in aorta, in this study, we examined expression of microRNA in the aorta of male (10 weeks old) germ-free mice and pathogen-free mice (control).

overall_design: We assessed global expression of microRNAs in the thoracic aorta of germ-free mice (n = 3) and pathogen-free mice (n = 3) using the Nanosting nCounter assay.

first: Kaikobad

last: Irani


title: Lnc-RNA expression pattern in ETV6/RUNX1-driven b-cell precursor acute lymphoblastic leukemia (BCP-ALL)

first: Farzaneh

last: Ghazavi

overall_design: Gene expression profiling of 64 BCP-ALL patient samples

first: Wouter

last: Van Loocke

first: Pieter

last: Van Vlierberghe

first: Barbara

last: De Moerloose

first: Tim

last: Lammens

first: Yves

last: Benoit

first: Frank

last: Speleman


title: UNCOVERING VULVAR CARCINOMA: AN INTEGRATIVE APPROACH [CGH]

city: Sao Paulo

first: Fabio

middle: Albuquerque

last: Marchi

address: Av Dr Arnaldo

department: CTO

country: Brazil

institute: ICESP

summary: Array-based comparative genomic hybridization (array CGH) analyses was used to analyze 17 VSCC samples from untreated patients. The data were validated using quantitative PCR.

overall_design: Experiment condition, 17 VSCC DNA samples obtained from untreated patients were labeled with Cy3 and commercial reference samples (Promega) were labled with Cy5. Samples Cy3 and Cy5 were mixed and hybridized at slide glasses Agilent 8x60 platform.

middle: A

first: Andre

last: Lavorato


title: A. lyrata transcriptomic responses against salt stress

status: Public on Sep 14 2016

city: Kolkata

first: Malay

last: Das

state: West Bengal

address: 86/1 College Street

department: Biological Sciences

country: India

institute: Presidency University

summary: Using A. lyratamicroarray platform the transcriptomic response of shoot tissues was characterized at two different time points- 3h and 27h after 250mM and 500mM of NaCl treatments.

overall_design: Six weeks old, soil grown Arabidopsis lyrata, ssp. lyrata plants were treated either with 250 or 500 mM NaCl solution by flush flooding, while the control group was watered.

first: Georg

last: Haberer

first: Anton

last: Schäffner


title: A. thaliana transcriptomic responses against salt stress

summary: Using A. thaliana microarray platform the transcriptomic response of shoot tissues was characterized at two different time points- 3h and 27h after 250mM and 500mM of NaCl treatments.

overall_design: Four weeks old, soil grown Arabidopsis thaliana, Col 0 plants were treated either with 250 or 500 mM NaCl solution by flush flooding, while the control group was watered.


title: A. lyrata transcriptomic responses against UV-B stress

summary: By using A. lyrata microarray platform, the transcriptomic response of shoot tissues was characterized at 4h and 8h post exposure to UV-B radiation at wavelength of 300 nm..

overall_design: Six weeks old Arabidopsis lyrata ssp. lyrata rosettes were exposed to UV-B radiation in the environmental chamber of Helmholtz Zentrum, Muenchen and tissues were harvested at 4h and 8h post-exposure time points.


title: A. thaliana transcriptomic responses against UV-B stress

summary: By using A. thaliana microarray platform, the transcriptomic response of shoot tissues was characterized at 4h and 8h post exposure to UV-B radiation at wavelength of 300 nm..

overall_design: Four weeks old Arabidopsis thaliana, Col 0 rosettes were exposed to UV-B radiation in the environmental chamber of Helmholtz Zentrum, Muenchen and tissues were harvested at 4h and 8h post-exposure time points.


title: A. lyrata ssp. lyrata root and flower-bud transcriptomes

summary: Using A. lyrata microarray platform the root and flower bud specific gene expression was characterized.

overall_design: Roots and flower-buds from 6 weeks old A. lyrata plants grown hydroponically on a raft were harvested and used as biological tissues for total RNA extraction. Tissues harvested from 8-10 plants were pooled together and were defined as a biological replicate.


title: The CpxRA two-component system promotes intracellular survival and is a key regulator of virulence factors in Legionella pneumophila

status: Public on Sep 16 2016

city: St-Anne-de-Bellevue

first: Sebastien

last: Faucher

state: QC

address: 21,111 Lakeshore

department: Natural Resource Sciences

country: Canada

institute: McGill University

summary:
The bacterium Legionella pneumophila is capable of intracellular replication within freshwater protozoa as well as human alveolar macrophages, the latter of which results in the serious pneumonia Legionnaires’ disease. A primary factor involved in these host cell interactions is the Dot/Icm Type IV secretion system that is responsible for translocating effector proteins needed to establish and maintain the bacterial replicative niche. Several regulatory factors have been identified to control the expression of the Dot/Icm system and effectors, one of which is the CpxRA two-component system, suggesting essentiality for virulence. However, studies elsewhere have shown that L. pneumophila strains harboring mutated cpxRA genes have minimal to no impact on L. pneumophila intracellular growth in protozoa and macrophages.
In this study, we generated L. pneumophila cpxR, cpxA, and cpxRA in-frame null mutant strains to further delineate the role of the CpxRA system in bacterial survival and virulence. Surprisingly, we found that cpxR and cpxRA are essential for intracellular replication within Acanthamoeba castellanii, but not in U937 macrophage-like cells. Transcriptome analysis revealed that CpxRA regulates a large number of virulence-associated proteins including a number of Dot/Icm effectors as well as 14 Type II secreted substrates. Furthermore, the cpxR and cpxRA mutants were more sodium resistant than wildtype, and cpxRA expression reaches maximal levels during post-exponential phase. Taken together, our findings suggest the CpxRA system is a key contributor to L. pneumophila virulence via virulence factor regulation.

platform_organism: Legionella pneumophila subsp. pneumophila str. Philadelphia 1

overall_design: Legionella pneumophila Philadelphia-1 strains Lp02 and isogenic mutant ΔcpxRA were grown in BYE broth at 37°C to exponential phase (E) and post-exponential phase (PE).

first: Jennifer

last: Tanner

first: Laam

last: Li

first: Ann

middle: C

last: Brassinga


title: A Comprehensive Hybridization Model Allows Whole HERV Transcriptome Profiling Using High Density Microarray

status: Public on Sep 21 2016

city: Pierre Bénite

first: Jeremie

middle: FC

last: Becker

address: Centre Hospitalier Lyon Sud, Bâtiment 3F

department: Medical diagnostic Discovery department

country: France

institute: bioMérieux

summary:
Human endogenous retroviruses (HERVs) have received much attention for their implications in the etiology of many human diseases and their profound effect on evolution. Notably, recent studies have highlighted associations between HERVs expression and cancers [1], autoimmunity [2] and neurological [3] conditions. Their repetitive nature makes their study particularly challenging, where expression studies have largely focused on individual loci [4] or general trends within families [5, 6, 7]. To refine our understanding of HERVs activity, we introduce here a new microarray, HERV-V3, that offers an almost complete coverage of HERVs and their ancestors (mammalian apparent LTR-retrotransposons, MALRs) at the locus level.
This was made possible by the careful detection and annotation of genomic HERVs/MALRs sequences as well as the development of a new hybridization model, allowing the optimization of probe performances and the control of cross-reactions. Although no gold standard in HERVs measurement exists to validate the array, HERV-V3 analytical performances were comparable to commercial Affymetrix arrays, and for a selection of tissue/pathological specific loci, the patterns of expression found on HERV-V3 were consistent with those reported in the literature.

overall_design: HERV-V3 technical performances were evaluated on the MAQC samples, composed of two independent samples (A, Stratagene Universal RNA, and B, Ambion Human Brain RNA) from which two titration samples were generated (C and D, consisting of 3:1 and 1:3 ratios of A to B, respectively). Each sample was performed in technical triplicate.  The biological validation was performed on three different tissues (colon, placenta and prostate) and two primary human cell lines (OSCAR and EBJ14).

first: Philippe

last: Perot

first: Valerie

last: Cheynet

first: Guy

last: Oriol

first: Nathalie

last: Mugnier

first: Jean-Baptiste

last: Veyrieras

first: François

last: Mallet


title: A. lyrata ssp. lyrata transcriptomic responses against drought stress

summary: Using A. lyrata microarray platform the transcriptomic response of shoot tissues was characterized at two different time points- 8d and 11d after withdrawal of regular water application..

overall_design: Five weeks old Arabidopsis lyrata ssp. lyrata plants were stopped watering for the treatment groups, while the control group was watered on regular intervals. Samples for early time points were harvested at 8 days after drought treatment began, while samples for late time-point was harvested after 11 days.


title: miRNAs:Biomarkers of Storage Lesions of RBC.

city: Guangzhou

first: xie

middle: xu

last: hong

address: Guangzhou First People's Hospital,NO.1.Panfu Road

department: Department of Blood Transfusion

institute: Guangzhou First People's Hospital

summary: Investigation of  miRNA expression level changes in RBCs stored for 20 days, RBCs stored for 20 days with 1uM SNP, compared to healthy,male type O donors, and to explore the mechanism of storage lesions of RBC.

platform_organism:
Homo sapiens
Mus musculus
Rattus norvegicus

overall_design: In this study, nine samples from three healthy, male type O donors, three donors whose RBCs stored for 20 days, and three donors whose RBCs stored for 20 days with 1uM SNP were used to acquire the miRNA expression profiling, and to explore the mechanism of storage lesions of RBC.

first: Yaming

last: Wei

first: Xuhong

last: Xie


title: Genome-wide analysis of pediatric-type follicular lymphoma reveals a low genetic complexity and recurrent alterations of TNFRSF14 gene

city: Barcelona

first: Itziar

last: Salaverria

address: Rossello 153

institute: Hospital Clínic

summary: Pediatric-type follicular lymphoma (PTFL) is a variant of FL with distinctive clinico-pathological features. Patients are predominantly young males presenting with localized lymphadenopathy; the tumor shows high grade cytology and lacks both BCL2 expression and t(14;18) translocation. The genetic alterations involved in the pathogenesis of PTFL are not known.

overall_design: The aim of this study was to perform a complete genetic characterization of PTFL. Forty-two cases (40 males and 2 females; mean age: 16 years, range 5-31) with consensus diagnosis were analyzed by fluorescence in situ hybridization, copy number (CN) array and targeted sequencing analyses of genes associated with FL pathogenesis

first: Janine

last: Schmidt

first: Leticia

last: Quintanilla-Martinez


title: Expression data from camptothecin-treated rat primary motor neurons

status: Public on Sep 20 2016

city: Philadelphia

first: Matthew

middle: E R

last: Butchbach

state: PA

address: 1020 Locust St

institute: Thomas Jefferson University

summary: Topoisomerase 1 (TOP1) poisons like camptothecin (CPT), which are used as chemotherapeutic agents in cancer, elicit DNA damage in quiescient neurons. In this study, we examined the effects of CPT and actinomycin D (ActD) on neuronal cells. Motor (MNs) and cortical (CNs) neurons were more susceptible to the toxic effects of CPT and ActD than fibroblasts. MNs and CNs exhibited a delayed DNA damage response—increase in nuclear γ-H2AX foci—relative to fibroblasts. Neuronal cells expressed higher levels of Top1 mRNA than fibroblasts which could explain their enhanced vulnerability to CPT and ActD toxicity. Microarray analysis was performed to identify differentially regulated transcripts in MNs treated with CPT for 2 hours. Many immediate-early genes including Fos and Egr-1 were upregulated in CPT-treated MNs. Fos mRNA levels were elevated in all cells types treated with CPT; Egr-1 transcript levels, however, were reduced in CPT-treated fibroblasts even though they were elevated in treated MNs and CNs. Pathway and network analysis of the differentially expressed transcripts revealed activation of ERK and JNK signaling cascades in CPT-treated MNs. In conclusion, MNs were more vulnerable than fibroblasts to the damaging effects of TOP1 poisons and they elicit a unique intracellular response to CPT treatment.

overall_design: DIV2 rat primary motor neuron cultures (n=3/treatment) were treated with either 1 microM camptothecin (cpt) or DMSO for 2 hours. Total RNA was isolated from each sample, labeled with biotin and then hybridized on Affymetrix GeneChip Rat Gene 1.0ST arrays.

middle: E


title: Serum miRNA expression profiles in suckling piglets and weaning piglets

city: Hangzhou

first: Xin

last: Tao

address: Shiqiao Road 145

institute: Zhejiang Academy of Agricultural Sciences

summary: MicroRNAs (miRNAs) in serum are very stable and specific. Moreover, serum miRNAs are non-destructive and convenient. Studies have shown that the changes of serum miRNAs are closely relative to the pathological stresses and diseases. Our previous studies suggested that weaning stress induced the abnormal miRNA transcriptome in the intestine of piglets. In this project, we will further screen serum miRNA expression in piglets induced by weaning stress using miRNA microarray. Microarrays containing 422 porcine unique miRNA probes were employed to identify differences in the expression patterns of the miRNA between weaning piglets at 4 d after weaning and suckling piglets at the same days old. A total of 115 differentally expressed miRNAs were found,therein 63 miRNAs upregulated and 52 miRNA downregulated; 64 miRNAs are statistically significant but have low signals (signal < 500);122 miRNAs are not statistically significant (p > 0.01); the remaining 132 miRNAs have not detected signals.

overall_design: In the study presented here, two treatements from weaning piglets at 4 d after weaning and from sucking piglets on the same days as the weaning piglets. For each treatment, 4 biological total RNA samples were pooled with equal contribution.

first: Ziwei

last: Xu

first: Xiaoming

last: Men


title: Effects of digested onion extracts on intestinal gene expression: an interspecies comparison using different intestine models

city: Lelystad

first: Marcel

last: Hulst

state: Flevoland

address: Edelhertweg 15

department: Livestock research

country: Netherlands

institute: Animal Sciences Group

summary: Applicability of in vitro (human Caco-2 cells) and ex vivo intestine models (rat precision cut intestine slices and the pig in-situ small intestinal segment perfusion (SISP) technique) to study the effect of food compounds. In vitro digested yellow (YOd) and white onion extracts (WOd) were used as model food compounds and transcriptomics was applied to obtain more insight into which extent mode of actions depend on the model.

overall_design:
Within eight male piglets (5 week-old, 8.2 kg) five paired SISP segments were prepared at 31-58% along the total length of small intestine (jejunum). At t = 0 segments were filled with 20 ml of Saline control solution (S), 20 ml onion digest (YOd or WOd), or 20 ml control digest (Sd). After 30 min, perfusion (2 ml/15 min) was started simultaneously for all segments for a period of 6 h. Perfusion was stopped and for preparation of mucosal scrapings 10 cm of the caudal part of each segment was dissected and directly frozen in liquid nitrogen and stored at -80°C. In the first 4 piglets (number 1-4), YOd and Sd samples were distributed over a pair of segments, and over the piglets according to a Latin-square design. In the second 4 piglets (number 5-8) WOd and Sd samples were distributed over segments and piglets in the same manner as in piglets 1-4.
jejunum pig, host-feed interaction

middle: M

first: Jan

last: van der Meulen

first: Arjan

last: Hoekman

first: Mari

last: Smits


title: Identification of miRNAs associated with dark-induced senescence in Arabidopsis

status: Public on Sep 19 2016

first: Xunyan

last: Liu

address: Xuelin street 16#, Xiasha,

institute: Hangzhou Normal University

summary: To find the miRNAs that may be involved in dark-induced leaf senescence, we identified miRNAs by microarray platform using Arabidopsis thaliana leaves from both whole darkened plants (DPs) and individually darkened leaves (IDLs). Control, IDLs and DPs were treated for 2, 4 or 6 d in the same climate chambers (16 h light/8 h dark, 250 mmol m-2 s-1).

overall_design: 7 samples were analyzed, namely the control, DP-2, DP-4, DP-6, IDL-2, IDL-4 and IDL-6. DP means Arabidopsis thaliana leaves from both whole darkened plant. And IDL means that leaves were covered by a black plastic bag and aluminum foil to reduce heat, whereas the rest of the plant remained in light. Every sample was collected in 28 plants from the 6th to 10th rosettes.

first: Xiaoying

last: Huo

first: Chao

last: Wang

first: Yibo

last: Teng


title: Overexpression of the primary sigma factor gene sigA improved carotenoid production by Corynebacterium glutamicum: application to production of β-carotene and the non-native linear C50 carotenoid bisanhydrobacterioruberin

city: Bielefeld

first: Hironori

last: Taniguchi

country: Germany

institute: Bielefeld University

summary: Corynebacterium glutamicum shows yellow pigmentation due to biosynthesis of the C50 carotenoid decaprenoxanthin and its glycosides. This bacterium has been engineered for production of various non-native cyclic C40 and C50 carotenoids such as β-carotene, astaxanthin or sarcinaxanthin. In this study, the effect of modulating gene expression more broadly by overexpression of sigma factor genes on carotenoid production by C. glutamicum was characterized. Overexpression of the primary sigma factor gene sigA improved lycopene production by recombinant C. glutamicum up to eight fold. In C. glutamicum wild type, overexpression of sigA led to two fold increased accumulation of the native carotenoid decaprenoxanthin in the stationary growth phase. Under these conditions, genes related to thiamine synthesis and aromatic compound degradation showed increased RNA levels and addition of thiamine and the aromatic iron chelator protocatechuic acid to the culture medium enhanced carotenoid production when sigA was overexpressed. Deletion of the gene for the alternative sigma factor SigB, which is expected to replace SigA in RNA polymerase holoenzymes during transition to the stationary growth phase, also increased carotenoid production. The strategy of sigA overexpression could be successfully transferred to production of the non-native carotenoids β-carotene and bisanhydrobacterioruberin. Production of the latter is the first demonstration that C. glutamicum may accumulate a non-native linear C50 carotenoid instead of the native cyclic C50 carotenoid decaprenoxanthin.

overall_design: Differential expresssion under sigA overexpression was evaluated at two different growth stages (8 hours and 24 hours after inoculation), comparing with the empty vector control.

first: Nadja

last: Henke

first: Sabine

last: Heider

first: Volker

last: Wendisch


title: Transcriptomic Analysis of Persistent Infection with Foot-and-Mouth Disease Virus in Cattle Suggests Impairment of Apoptosis and Cell-Mediated Immunity in the Nasopharynx

city: Orient

first: James

middle: J.

last: Zhu

state: NY

department: Foreign Animal Disease Research Unit

institute: USDA-ARS

summary: In order to investigate the mechanisms of persistent foot-and-mouth disease virus (FMDV) infection in cattle, transcriptome alterations associated with the FMDV carrier state were characterized using a bovine whole-transcriptome microarray. Eighteen cattle (8 vaccinated with a recombinant FMDV A vaccine, 10 non-vaccinated) were challenged with FMDV A24 Cruzeiro, and the gene expression profiles of nasopharyngeal tissues collected between 21 and 35 days after challenge were compared between 11 persistently infected carriers and 7 non-carriers. Carriers and non-carriers were further compared to 2 naïve animals that had been neither vaccinated nor challenged. At a controlled false-discovery rate of 10% and a minimum difference in expression of 50%, 648 genes were differentially expressed between FMDV carriers and non-carriers, and most (467) had higher expression in carriers. Among these, genes associated with cellular proliferation and the immune response – such as chemokines, cytokines and genes regulating T and B cells – were significantly overrepresented. Differential gene expression was significantly correlated between non-vaccinated and vaccinated animals (biological correlation +0.97), indicating a similar transcriptome profile across these groups. Genes related to prostaglandin E2 production and type 2 immune polarization, as well as to the induction of regulatory T cells and T-cell exhaustion were overexpressed in carriers. In contrast, tissues from non-carrier animals expressed higher levels of complement regulators and pro-apoptotic genes that could promote virus clearance. Based on these findings, we propose that FMDV persistence in nasopharyngeal tissues of cattle is maintained by an impairment of apoptosis and the local suppression of cell-mediated antiviral immunity by inducible regulatory T cells.

platform_organism:
Bos taurus
Foot-and-mouth disease virus
Human adenovirus 5

overall_design: Samples of nasopharyngeal epithelium from 20 Holstein cattle (11 persistently FMDV-infected carriers, 7 non-carriers, 2 naïve animals) were labeled with Cy3 and Cy5 and hybridized to paired 4x45K arrays in a dye-swap arrangement.  However, the numbers of FMDV carriers, non-carriers and controls were different, precluding a fully connected dye-swap design. A separate-channel approach using a common correlation model (Smyth and Altman, 2013,  BMC Bioinformatics 14:165, doi: 10.1186/1471-2105-14-165) was used instead.

first: Michael

last: Eschbaumer

first: Carolina

last: Stenfeldt

first: George

middle: R

last: Smoliga

first: Juan

last: Pacheco

first: Luis

last: Rodriguez

first: Robert

last: Li

first: Jonathan

last: Arzt


title: Genomic copy-number aberrations in ductal carcinomas in situ with and without invasive components

city: Otsu

first: Mina

last: Kitamura

state: Shiga

address: Seta, Tsukinowa-cho

department: Pathology

institute: Shiga University of Medical Science

type: Genome variation profiling by genome tiling array

summary: In the breast, the reduction of invasive ductal carcinoma (IDC) seems to be smaller than expected from an increasing number of ductal carcinoma in situ (DCIS) detection in screening programs, suggesting that some DCIS lesions remain dormant and take a very long time for progression to IDC. However, the progression risk of individual DCIS and papilloma to IDC largely remain unassessable. To tackle this problem, we applied array-based comparative genomic hybridization to DCIS, IDC and papilloma lesions. We confirmed the presence of chromosomal copy-number alterations (CNAs) reported previously in breast cancers and the absence of chromosomal CNAs in the papillomas examined. These findings suggest that gene CNA profile is a good lineage marker for prediction of progression risk of individual tumors and that tumor progression within each lineage is driven by epigenetic rather than genetic alterations.

overall_design: Array-based Comparative Genomic Hybridization. Cases include 33 invasive ductal carcinomas, 24 ductal carcinomas in situ and 12 papillomas. IDC samples include 26 ductal components, 30 invasive components and 7 metastatic axillary lymph nodes. There are 26 DCIS samples because two DCIS cases were sampled from two different ductal areas.


title: The genetic basis of adaptation to climatic stress in Siberian indigenous populations

city: Tucson

first: Tatiana

middle: M.

last: Karafet

state: AZ

address: BSW #246, 1041 E Lowell Str.

department: ARL

institute: University of Arizona

summary: Affymetrix single nucleotide polymorphism (SNP) array data were used to study genes that underlie human adaptation to climatic stress, with a focus on genetic changes that lead to long-term cold tolerance. Siberia provides the best opportunity to investigate the genetic mechanisms of cold resistance because of the long-term ancestry of indigenous populations in some of the coldest climates on earth. While much of northern Europe was under ice throughout the last glacial period, Siberia remained relatively ice free, and archaeological evidence suggests that people inhabited this region for more than 40,000 years. We gathered SNP data from ~200 individuals from 15 indigenous Siberian populations that inhabit a range of arctic climates and compare their patterns of genetic variation with those from other world populations from warmer climates.Particular attention is paid to regions containing genes that have been previously implicated in cold adaptation or that function in known pathways connected to energy metabolism or cold adapted phenotypes (e.g., those involved in basal metabolic rate and brown adipose tissue function).

overall_design: 651 samples from 40 populations has been genotyped using the Affymetrix platform Axiom_GW_Hu_SNP.r2

first: Brian

last: Hallmark

first: Olga

middle: V

last: Savina

last: Hammer


title: A. thaliana root and flower-bud transcriptomes

first: Malay

last: Das

summary: Using A. thaliana microarray platform the root and flower bud specific gene expression was characterized.

overall_design: Roots and flower-buds from 6 weeks old A. thaliana plants grown hydroponically on a raft were harvested and used as biological tissues for total RNA extraction. Tissues harvested from 8-10 plants were pooled together and were defined as a biological replicate.

first: Georg

last: Haberer

first: Anton

last: Schäffner


title: T cell cancer therapy requires CD40-CD40L activation of TNFα-iNOS-producing dendritic cells

city: Padova

first: Silvio

last: Bicciato

address: via U. Bassi 59/b

department: Molecular Medicine

country: Italy

institute: University of Padova

summary: The effectiveness of new cancer therapies such as checkpoint blockade and adoptive cell transfer of activated anti-tumor T cells requires overcoming immunosuppressive tumor microenvironments. We found that the activation of tumor-infiltrating myeloid cells to produce local nitric oxide is a prerequisite for adoptively transferred CD8+ cytotoxic T cells to destroy tumors. These myeloid cells are phenotypically similar to ‘Tip-DCs’ or nitric oxide- and TNFα-producing dendritic cells. The nitric oxide-dependent killing was tempered by coincident arginase 1 expression, which competes with iNOS for arginine, the substrate for nitric oxide production. Depletion of immunosuppressive CSF-1R-dependent arginase 1+ myeloid cells enhanced nitric oxide-dependent tumor killing. Tumor killing via iNOS was independent of the microbiota but dependent on the CD40-CD40L pathway and, in part, lymphotoxin alpha. We extended our findings in mice to uncover a strong correlation between iNOS, CD40 and TNF expression and survival in colorectal cancer patients. Our results identify a network of anti-tumor targets to boost the efficacy of cancer immunotherapies.

overall_design: EG7 tumor was injected in C57BL/6 and after 7 days of tumor growth mice were treated with adoptive  CD8+ T cells specific to recognize  OVA antigen. After 3 days mice were sacrified and tumor masses used to isolate cells.CD11b+NO+Ly6C+Ly6G- live cells were FACS sorted from tumor masses pooled from 12 mice for each sample. 3 samples from 3 different experiments were obtained.

first: Ilaria

last: Marigo

first: Serena

last: Zilio

first: Emilia

last: Mazza

first: Vincenzo

last: Bronte


title: Utility of circulating serum miRNAs as biomarkers of early cartilage degeneration in animal models of post-traumatic osteoarthritis and inflammatory arthritis

status: Public on Sep 11 2016

city: Melbourne

first: John

last: Bateman

address: Flemington Road

department: Skeletal Biology

country: Australia

institute: Murdoch Childrens Research Institute

summary: The purpose of this study was to identify potential serum microRNA (miRNA) biomarkers of cartilage degeneration comparing preclinical mouse models of post-traumatic osteoarthritis and inflammatory arthritis.

overall_design: Cartilage degeneration was induced in one knee of 10-12 week old male C57BL6 mice by surgical destabilization of the medial meniscus (DMM) or intra-articular injection of methylated-bovine-serum-albumin (AIA), with sham-operated or saline-injected control animals (n=6/treatment/time). Total serum RNA and knee joints were isolated at 1, 4 and 16 weeks post-induction. Cartilage degeneration was scored histologically. Serum miRNA expression profiling was performed using Agilent microarrays and validated by quantitative PCR.

first: Louise

middle: H

last: Kung

first: Sanaa

last: Zaki

first: Varshini

last: Ravi

first: Lynn

last: Rowley

first: Katrina

last: Bell

first: Christopher

middle: B

last: Little

first: Margaret

last: Smith


title: SNP microarry analysis of primary and first recurrent pediatric ependymoma

city: Aurora

first: Ichiro

last: Nakachi

state: CO

address: 12700 East 19th Avenue, RC2 9th floor

department: Division of Pulmonary Sciences and Critical Care Medicine, Department of Medicine

institute: University of Colorado Denver

summary: We compared genomic characteristics of primary and first recurrent pediatric ependymoma to identify sub-group specific differences.

overall_design: We investigated 11 matched pairs of primary and first recurrent pediatric ependymoma using Illumina HumanOmni2.5 SNP microarray. Seven of these were paired with matched reference blood DNA and analyzed.  Primary samples are denoted by _1; first recurrent samples are denoted by _2; germline DNA is denoted by _G.

first: Lindsey

last: Hoffman

first: Andrew

last: Donson

first: Nicholas

last: Foreman


title: Mouse tumors: Chaos3 Mammary Tumors (MTs) vs. Controls

city: Ithaca

last: Schimenti

address: College of Veterinary Medicine T9014A

department: Biomedical Scinces

institute: Cornell University

summary:
CNV profiling of tumors obtained from our Chaos3 mouse model for spontaneous breast cancer.
The goal of this experiment was to determine copy number variations that were specific to MTs derived from this mouse model, when comapared to non-MTs.

overall_design: 15 tumor samples (12 MTs and 3 non-MTs) were analyzed against reference wild-type DNAs from C57Bl/6J and C3HeB/FeJ

first: Nithya

last: Kartha


title: A. thaliana transcriptomic responses against drought stress

first: Malay

last: Das

institute: Presidency University

summary: Using A. thaliana microarray platform the transcriptomic response of shoot tissues was characterized at two different time points- 8d and 11d after withdrawal of regular water application..

overall_design: Three weeks old Arabidopsis thaliana, Col0 plants were stopped watering for the treatment groups, while the control group was watered on regular intervals. Samples for early time points were harvested at 8 days after drought treatment began, while samples for late time-point was harvested after 11 days.

first: Georg

last: Haberer

first: Anton

last: Schäffner


title: MicroRNA expression profiling in gastric cancers plasmas

status: Public on Sep 13 2016

first: Yejia

last: Cui

address: NO1 Panfu Road

summary: To investigate miRNA expression profiles between gastric cancers plasma and healthy controls plasma,screening the microRNAs that can serve as plasma biomarkers for the early diagnosis of gastric cancer by miRNA array.

overall_design: miRCURY™ LNA expression array was used to investigate the differences of miRNA expression profiles in 5 gastric cancers plasma and 3 healthy controls,the miRNA array contains 3100 capture probes, covering all human, mouse and rat microRNAs annotated in miRBase 18.0.


title: Shewanella piezotolerans WP3 wild-type strain high hydrostatic pressure for 120 min

status: Public on Sep 10 2016

city: Shanghai

first: Huahua

last: Jian

address: No.800 Dongchuan Road

institute: Shanghai Jiao Tong University

summary: The WP3 strains was cultured at 20°C/0.1 MPa, and then was incubated at high hydrostatic pressure (HHP, 50 MPa) for 120 min. The transcriptional profiles after and before HHP shock were compared.

overall_design: Three biological replicates sample and 6 technical replicates for each experiment

first: Shengkang

last: Li

first: Fengping

last: Wang


title: Shewanella piezotolerans WP3 wild-type strain high hydrostatic pressure for 30 min

summary: The WP3 strains was cultured at 20°C/0.1 MPa, and then was incubated at high hydrostatic pressure (HHP, 50 MPa) for 30 min. The transcriptional profiles after and before HHP shock were compared.


title: Shewanella piezotolerans WP3 wild-type strain cold shock for 60 min

summary: The WP3 strains was cultured at 20°C and cold shocked at 0°C for 60 min. The transcriptional profiles after and before cold shock were compared.


title: Shewanella piezotolerans WP3 wild-type strain cold shock for 30 min

summary: The WP3 strains was cultured at 20°C and cold shocked at 0°C for 30 min. The transcriptional profiles after and before cold shock were compared.

overall_design: Three biological replicate samples and 6 technical replicates for each experiment


title: Murine 3T3-F442A Cells: Control vs. Growth hormone

city: Jinan

first: Yuchao

last: Zhang

address: 44 Wenhua Road West

institute: Shandong University

summary: Growth hormone-treated mouse 3T3-F442A adipocytes  comparing control untreated F442A cells.

overall_design: Two-condition experiment, GH vs. Con cells.  One replicate per array.  Note that these mouse samples were hybridized to a rat microarray.

first: Yuantao

last: Liu

first: Xiangdong


title: MiR-196b is epigenetically silenced during the pre-malignant stage of lung carcinogenesis

status: Public on Sep 09 2016

city: Albuquerque

first: Carmen

last: Tellez

state: NM

address: 2425 Ridgecrest Dr. SE

institute: Lovelace Respiratory Research Institute

summary:
MicroRNA silencing by promoter hypermethylation may represent a mechanism by which lung cancer develops and progresses, but the microRNAs involved during malignant transformation are unknown. We previously established a model of pre-malignant lung cancer wherein we treated human bronchial epithelial cells (HBEC) with low doses of tobacco carcinogens. Here, we demonstrate that next-generation sequencing of carcinogen-transformed HBECs treated with the demethylating agent 5-aza-2'deoxycytidine revealed miR-196b and miR-34c-5p to be epigenetic targets. Bisulfite sequencing confirmed dense promoter hypermethylation indicative of silencing in multiple malignant cell lines and primary tumors. Chromatin immunoprecipitation studies further demonstrated an enrichment in repressive histone marks on the miR-196b promoter during HBEC transformation. Restoration of miR-196b expression by transfecting transformed HBECs with specific mimics led to cell cycle arrest mediated in part through transcriptional regulation of the FOS oncogene, and miR-196b re-expression also significantly reduced the growth of tumor xenografts. Luciferase assays demonstrated that forced expression of miR-196b inhibited the FOS promoter and AP-1 reporter activity. Finally, a case-control study revealed that methylation of miR-196b in sputum was strongly associated with lung cancer (OR = 4.7, p<0.001). Collectively, these studies highlight miR-196b as a tumor suppressor whose silencing early in lung carcinogenesis may provide a selective growth advantage to pre-malignant cells. Targeted delivery of miR-196b could therefore serve as a preventive or therapeutic strategy for the management of lung cancer.
HBEC2MBT and H1975 were transiently transfected with a miR-196b mimic and subjected to array-based genome-wide gene expression profiling 48 hours post transfection.

overall_design: Total RNA was isolated with TRIzol from transiently transfected cell lines 48 hours post transfection and subjected to bead array

middle: S

first: Daniel

last: Juri

first: Kieu

last: Do

first: Maria

last: Picchi

first: Teresa

first: Gang

first: Avrum

last: Spira

first: Steven

last: Belinsky


title: Shewanella piezotolerans WP3 wild-type strain cold shock for 90 min

summary: The WP3 strains was cultured at 20°C and cold shocked at 0°C for 90 min. The transcriptional profiles after and before cold shock were compared.


title: ADTRP siRNA Microarray Data in HepG2 Cell Line

status: Public on Sep 07 2016

city: Cleveland

first: QING

middle: K

last: WANG

state: Ohio

address: 9500 Euclid Ave

department: Molecular Cardiology

institute: Cleveland Clinic

summary:
Coronary artery disease (CAD) and its complication myocardial infarction (MI) are the leading cause of death worldwide.Our genome-wide association studies (GWAS) in the Chinese population identified a genomic variant, rs6903956, in intron 1 of the C6orf105 gene (later named as ADTRP) as a significant risk factor for CAD and MI. Based on itscell membrane localization and its function on regulation of TFPI, we hypothesize that ADTRP acts as a cell signaling molecule that affects function and expression of many downstream genes/proteins. We performed global gene expression profiling in cells with knockdown of ADTRP expression to identify other downstream targets of ADTRP.
To identify other downstream targets of ADTRP, we performed global gene expression profiling in cells with knockdown of ADTRP expression.  Because ADTRP downstream genes include those involved in cell cycle regulation and apoptosis as well as multiple histone genes, we carried out cellular studies on cell cycle, cell proliferation and apoptosis to further characterize the function of ADTRP.

overall_design: Global gene expression of ADTRP siRNA sampels and negative controls were profiled by Affymetrix GeneChip PrimeView arrays in HepG2 cells,  top downstream genes with differntial expression levels were selected for validation in HepG2, HUVEC, and EAhy926 endothelial cells. Because ADTRP downstream genes include those involved in cell cycle regulation and apoptosis as well as multiple histone genes, we carried out cellular studies on cell cycle, cell proliferation and apoptosis to further characterize the function of ADTRP.

first: Qing

first: Chuyan

last: Luo

first: Subo

last: Qin

first: Qiuyun

last: Chen


title: Genome-wide profiling of C. elegans gonadal RNA

city: Basel

first: Rafal

last: Ciosk

state: Schweiz

address: Maulbeerstrasse 66

country: Switzerland

institute: Friedrich Miescher Institute

type: Expression profiling by genome tiling array

summary: To better understand the role of Notch signaling in germline biology, we analyzed GLP-1/Notch- and PRC2-dependent changes in gene expression in C. elegans.

overall_design: We isolated RNA from dissected gonads and analysed the expression changes.

first: Irene

last: Kalchhauser

first: Balazs

last: Hargitai

first: Stephane

last: Thiry

first: Erik

last: Cabuy

first: Tim

last: Roloff

first: Edward

last: Oakeley

first: Dimosthenis

last: Gaidatzis


title: Lifespan extension by diet restriction in DNA repair deficient progeroid Ercc1Δ/- mice [miRNA]

city: Bilthoven

first: Jeroen

last: Pennings

address: A. van Leeuwenhoeklaan 9

institute: Natl. Inst. Public Health & Environment

summary: DNA repair-deficient Ercc1Δ/- mice show premature cell death, senescence and numerous accelerated aging features limiting lifespan to 4-6 month. Simultaneously they exhibit a ‘survival response’, which suppresses growth and enhances maintenance, resembling the anti-aging response induced by dietary restriction (DR). Here we report that subjecting these progeroid, dwarf mutants to actual dietary restriction (DR) resulted in the largest lifespan increase recorded in mammals. Thirty percent DR tripled median and maximal remaining lifespan, and drastically retarded numerous aspects of accelerated aging, e.g. DR animals retained 50% more neurons and maintained full motoric function. The DR response in Ercc1Δ/- mice resembled DR in wild type animals including reduced insulin signaling. Interestingly, ad libitum Ercc1Δ/- liver expression profiles showed preferential extinction of expression of long genes, consistent with genome-wide accumulation of stochastic, transcription-blocking lesions, which affect long genes more than short ones. DR largely prevented this decline of transcriptional output, indicating that DR prolongs genome function. Our findings strengthen the link between DNA damage and aging, establish Ercc1Δ/- mice as powerful model for identifying interventions to promote healthy aging, reveal untapped potential for reducing endogenous damage, provide new venues for understanding the molecular mechanism of DR, and suggest a counterintuitive DR-like therapy for human progeroid genome instability syndromes and DR-like interventions for preventing neurodegenerative diseases.

overall_design: 20 samples (4 groups with 5 replicates each) in a common reference design

first: Martijn

last: Dollé

first: Akos

last: Gyenis

first: Wilbert

last: Vermeij


title: Skeletal muscle derived stem cell implantation therapy in a rat model of erectile dysfunction

city: Torrance

first: Robert

last: Gelfand

state: CA

address: 1124 W. Carson St

department: surgery

institute: LABiomed at Harbor UCLA,  and Charles Drew Univ

summary:
Muscle derived stem cells were isolated from Zucker Obese rats and implanted into the penises of diabetic rats. Rats were analyzed for potential therapeutic benefit.
The skeletal muscle derived stem cells were grown in culture and analyzed by DNA microarray analysis for gene expression.

overall_design: RNA was isolated using the RNeasy Plus Micro kit and tested using the Affymetrix rat gene 1.0 ST microarray (GPL6247).

first: Istvan

last: Kovanesc

first: Dolores

last: Vernet

first: Maryam

last: Masouminia

first: Leila

last: Loni

first: James

last: Aboagye

last: Tsao

first: Jacob

last: Rajfer

first: Nestor

middle: F

last: Gonzalez-Cadavid


title: Effect of fipronil on the thyroid gland transcriptome in the rat

city: Villenave d'Ornon

first: Pascal

middle: GP

last: Martin

address: 71 avenue Edouard Bourlaux

department: UMR1332 BFP

institute: INRAE

summary: Fipronil is a widely-used broad-spectrum phenylpyrazole insecticide. It has been shown that fipronil increases the hepatic metabolism of thyroid hormone in the rat, which may induce compensatory mechanisms at the level of the thyroid gland itself. Here, we studied the effect of fipronil on the transcriptome of the thyroid gland in the rat. Adult (2- to 3-month-old) female Wistar rats were treated per os with fipronil (3 mg/kg) or the vehicle alone for 14 days. The transcriptome of their thyroid gland was analyzed using Agilent 4x44K microarrays.

overall_design: Thyroid gland gene expression was measured from female Wistar rats treated with vehicle (n = 10) or fipronil (n = 10) using a dye switch design.

middle: G

first: Julien

last: Leghait

first: Frédéric

last: Lasserre

first: Arnaud

last: Polizzi

first: Catherine

last: Viguié

first: Thierry

last: Pineau


title: RPF-1 transcription factor coordinates expression of developmental genes in inducible HEK293/RPF-1 stable transfectants

status: Public on Sep 06 2016

city: Milan

first: Loris

last: De Cecco

address: via Venezian 1

institute: IRCSS Istituto Nazionale Tumori

summary:
RPF-1, a transcription factors encoded by POU6F2 gene, appears to be expressed in the developing nervous system and embryonic kidney. We generated a stable HEK/RPF-1 transfectant expressing the protein in a tetracycline (Tet)-dependent induction and addressed the whole transcriptome regulated by RPF-1. We detected a gross alteration of gene expression that is consistent with its occupancy at proximal promoters, and gel retardation assay and promoter-reporter activity, addressing a few target genes, indicated a dependence by RPF-1 of transcriptional response. GO analysis supports a role for this factor in the genetic programs guiding early differentiation of embryonic kidney and neuronal fate.     RPF-1, a transcription factors encoded by POU6F2 gene, appears to be expressed in the developing nervous system and embryonic kidney. We generated a stable HEK/RPF-1 transfectant expressing the protein in a tetracycline (Tet)-dependent induction and addressed the whole transcriptome regulated by RPF-1. We detected a gross alteration of gene expression that is consistent with its occupancy at proximal promoters, and gel retardation assay and promoter-reporter activity, addressing a few target genes, indicated a dependence by RPF-1 of transcriptional response. GO analysis supports a role for this factor in the genetic programs guiding early differentiation of embryonic kidney and neuronal fate.
Gene array analysis shows that RPF-1 transcription factor modify the transcriptome of HEK293 cells by regulating a genetic program endowed with developmental programs

overall_design: Comparison of HEK293 cells induced for RPF-1 expression (Tet-) over uninduced control (Tet+) and Mock cells. RPF-1 cDNA was inserted into the pTRE2puro vector to generate stable Tet-inducible KEK293 transfectants. Upon Tet removal from the medium, HEK/RPF-1 transfectants expressed the transcription factor RPF-1.  Cells were then seeded in 10 cm dishes, cultured for 48 h either in complete medium supplemented with Tet (+) or in Tet-depleted medium (-), harvested, and spun down before RNA isolation. Comparative analysis between HEK/RPF-1 induced (Tet-) and uninduced (Tet+) transfectants allowed us to identify genes transcriptionally regulated by RPF-1. Residual effects on gene expression due to Tet supplementation into culture media was ruled out by comparison with the Mock transfectant.

first: L

first: A

last: Fiorino


title: Real-time quantitative PCR analysis of serum miRNA in response to ionizing radiation in mice

city: Lanzhou

first: Wenjun

last: Wei

address: 509 Nanchang Road

institute: Institute of Modern Physics, Chinese Academy of Sciences

summary: Kunming mice were total body irradiated by 0.5Gy and 2Gy carbon ions radaition. After 24 hours, blood was collected and serum was isolated. Total RNA of serum sample was extracted by miRNeasy Serum/Plasma Kit (Qiagen, Germany). Then, miRCURY LNA™ Universal RT microRNA PCR, Ready-to-Use Mouse&Rat Panel I V3 (Exiqon, Denmark) containing 384 assays was performed to profile miRNAs differential expression in these serum sample.

overall_design: miRNA qRT-PCR expression profling. The relative miRNA expression levels of serum samples from mice exposed to 0.5Gy and 2Gy carbon ions radaition were compared with control group (0Gy, sham-exposed at the same conditions). Each treatment has three independent samples.

first: Jufang

last: Wang


title: ChIP-chip from HEK293-RPF-1 stable transfectants expressing the HA-tagged RPF-1 transcription factor

city: Milano

first: gabriele

last: bucci

state: MI

address: via olgettina 58

department: CTGB

institute: IRCCS Ospedale San Raffaele

type: Genome binding/occupancy profiling by high throughput sequencing

summary:
RPF-1 binds promoters of genes modulated by its induction in HEK/RPF-1 transfectant
Chromatin IP (ChIP) combined to chromatin array analysis (ChIP-chip) shows that RPF-1 transcription factor bind to promoter elements of genes repressed or activated by RPF-1 expression

overall_design: Comparison of cells induced for RPF-1 expression (Tet-) over uninduced control cells (Tet+)

first: Antonio

first: Gabriele

last: Bucci


title: Global miRNA expression in small bowel neuroendocrine tumors (SBNET) and their lymph node/liver metastases

status: Public on Sep 05 2016

city: London

first: Andrea

last: Frilling

address: Du Cane Road

department: Department of Surgery and Cancer, Hammersmith Campus

country: United Kingdom

institute: Imperial College London

summary: miRNA profiling study revealing novel miRNAs deregulated in SBNET compared to normal small bowel and identifying miRNA that are differentially regulated with disease progression. These have the potential to be used in the future for patient stratification and treatment response monitoring.

overall_design:
Dataset 1
Matched samples from 15 SBNET patients (47 samples) were used to determine a miRNA profile for SBNET and identify potential markers of disease progression. Patient numbers: 1-15.
Dataset 2
A second dataset of miRNA expression data (43 samples) containing an increased number of liver metastases, as well as SBNET and lymph node metastases. Patient numbers: B9-B140, controls: C1, C2.

first: Helen

middle: C

last: Miller

first: Adam

last: Frampton

first: Anna

last: Malczewska

first: Silvia

last: Ottaviani

first: Euan

middle: A

last: Stronach

first: Rashpal

last: Flora

first: Daniel

last: Kaemmerer

first: Gerd

last: Schwach

first: Roswitha

last: Pfragner

first: Omar

last: Faiz

first: Beata

last: Kos-Kudła

first: George

last: Hanna

first: Justin

last: Stebbing

first: Leandro

last: Castellano


title: RNA expression data from primary neuroblastoma tumors

status: Public on Sep 08 2016

city: Heidelberg

first: Maral

last: Saadati

address: Im Neuenheimer Feld 280

department: Biostatistics

institute: German Cancer Research Center

summary: RNA expression profiles of 105 primary neuroblastomas derived from customized 4 x 44k oligonucleotide microarrays (Agilent Technologies). These profiles are part of an integrative study combining genomewide epigenetic profiles with transcriptome data of the same neuroblastoma cohort. Tumors were derived from 40 low-risk, 9 intermediate-risk and 56 high-risk patients.

overall_design: Transcription profiles of 105 primary neuroblastomas derived from customized 4 x 44k oligonucleotide microarrays (Agilent Technologies)

first: Kai

middle: O

last: Henrich

first: Sebastian

last: Bender

first: Moritz

last: Gartlgruber

first: Chunxuan

last: Shao

first: Carl

last: Herrmann

first: Martha

last: Parzonka

last: Dreidax

first: Matthias

last: Fischer

first: David

middle: J

last: Duffy

first: Peter

last: Schmezer

first: Christoph

last: Plass

first: Thomas

last: Höfer

first: Axel

last: Benner

first: Stefan

last: Pfister

first: Frank

last: Westermann


title: Gene profiling of primary chicken embryo fibroblasts (CEFs) grown under the conditions of contact-inhibition, serum starvation, or both in comparison to normal cycling cells

city: Hamilton

first: Bart

middle: Michal

last: Maslikowski

state: Ontario

address: 1280 Main St. West

department: Biology

institute: McMaster University

summary: To investigate the differences of expression patterns in primary chicken embryo fibroblasts (CEFs) under conditions of contact-inhibition and serum starvation, we undertook a gene profiling study to characterize the transcriptomes of CEFs grown under conditions of contact inhibition, serum starvation or both, in relation to normal growing (cycling) cells.

overall_design: Primary chicken embryo fibroblasts (CEFs) were grown under conditions of contact inhibition, serum starvation or both, and compared in relation to normal growing (cycling) cells. All experimental groups consisted of three biological replicates except for the contact-inhibited group, which was conducted in quadruplicate.

first: Michael

last: Erb

first: Dora

last: Camacho

first: Wenli

last: Xie

last: Maślikowski

first: Ben

last: Fielding

first: Romita

last: Ghosh

first: Flore-Anne

last: Poujade

first: Mohammad

last: Athar

first: Samantha

last: Assee

first: Mantella

last: Laura-Eve

first: Pierre

last: Bédard


title: Comparison of miRNA from healthy donors versus Rheumatoid arthritis patients

city: Montpellier

first: Florence

last: Apparailly

address: CHU Saint Eloi, 80 rue Augustin Fliche

institute: INSERM

summary: miRNA differential expression in Rheumatoid arthritis(RA) blood: Microarray analysis of miRNAs in blood from RA and healthy donors.

overall_design: Total RNA was extracted from blood samples from 8 RA patients and 8 healthy donors and pooled for miRNA microarray analysis. RNA quality control, labeling, hybridization, and scanning were performed by LC Sciences (Houston, TX) using the latest probe content in the Sanger miRBase (Sanger miRBase 11.0). Preliminary statistical analysis was performed by LC sciences on raw data normalized by the locally weighted regression method on the background-subtracted data.

first: Isabelle

last: Duroux-Richard


title: Integrated mRNA and miRNA expression profiling in blood reveals candidate biomarkers associated with endurance exercise in horse (mRNA)

status: Public on Sep 04 2016

city: jouy en josas

first: Nuria

last: Mach

address: Domaine de Vilvert

institute: INRA

summary: The adaptive response to extreme endurance exercise might involve transcriptional and translational regulation by microRNAs (miRNAs). Therefore, the aim of this study was to define an integrative analysis of blood transcriptome and miRNome in horses before and after a long endurance ride (160 km) using equine microarrays. A total of 2,453 genes and 162 miRNAs were found to be differentially expressed (DEG) between animals at rest and after the endurance ride. To gain understanding of the biological functions regulated by the differentially expressed miRNA, we used a hypergeometric test analysis. Notably, we detected 42 differentially expressed miRNAs that putatively regulate a total of 350 depleted DEGs, involved in glucose metabolism, fatty acid oxidation, mitochondrion biogenesis, and immune response pathways. Graphical Gaussian models in an independent validation set of animals confirmed that 4 miRNAs could be strong candidate regulatory molecules for endurance exercise adaptation. This study represents, to the best of our knowledge, the first integrated comprehensive overview of the miRNA-mRNA co-regulation networks that may play a central role in controlling post-transcriptomic regulations during endurance exercise in horses.

overall_design: Sixty-one Arabian or half-breed Arabian horses (20 females and 41 geldings) aged 10 ± 2 years (±SEM) were recruited on voluntary basis of the owner on three 160 km endurance rides.

first: Núria

first: Sandra

last: Plancade

first: Jerôme

last: Lecardonnel

first: Alicja

last: Pacholewska

first: Julie

last: Rivière

first: Marco

last: Moroldo

first: Anne

last: Vaiman

first: Caroline

last: Morgenthaler

first: Marine

last: Beinat

first: Alizée

last: Nevot

first: Céline

last: Robert

first: Eric

last: Barrey


title: Integrated mRNA and miRNA expression profiling in blood reveals candidate biomarkers associated with endurance exercise in horse (miRNA)


title: Integrated mRNA and miRNA expression profiling in blood reveals candidate biomarkers associated with endurance exercise in horse

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

overall_design: Refer to individual Series


title: Promoter array characterization of AR binding sites

status: Public on Sep 02 2016

city: Bangalore

first: Genotypic

last: technology

state: Karnataka

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

institute: Genotypic Technology

type: Genome binding/occupancy profiling by genome tiling array

summary: To find novel targets regulated by AR upon DHT stimaulation at 24 hours of time point

overall_design: Agilent two-color ChIP on chip  experiment, Organism: Homo sapiens  , Agilent 2X400K Human Promoter array (AMADID: G4874A_27954)

first: Jatin

last: Mehta

first: Sunita

last: Saxena


title: The analysis of differential gene expression after remote ischemic preconditioning of renal ischemia reperfusion injury

city: Seoul

first: Young Eun

last: Yoon

address: yonsei-ro 50-1

department: Urology

institute: Yonsei University

summary: To investigate the mechanism by which ischemic preconditioning (IPC) produces tissue tolerance to renal ischemia reperfusion injury in a pig model

overall_design:
15 female Yorkshire pigs were divided into three groups:
1: no IPC and 90 minutes warm ischemia;
2: remote IPC with an early window followed by 90 min warm ischemia;
3: remote IPC with a late window followed by warm ischemia 24 hrs later.
Kidney tissues were obtained after 72 hours.

first: W

last: Han

first: Y

middle: E


title: The gene expression analysis of human astrocyte exposure to anti-suprabasin antibody: identification of a novel antibody for neuropsychiatric systemic lupus erythematosus

status: Public on Sep 01 2016

city: Izumo

first: Kunihiro

last: Ichinose

address: 89-1 Enya-cho

department: Department of Rheumatology

country: Japan

institute: Shimane University Faculty of Medicine

summary: [Objectives]: Neuropsychiatric systemic lupus erythematosus (NPSLE) is often difficult to diagnose and distinguish from those of other diseases, because no specific antibodies have yet been detected.  [Methods]: We developed a novel proteomic strategy for identifying and profiling antigens in immune complexes (ICs) in the cerebrospinal fluid (CSF) of 26 NPSLE patients. We performed in vitro experiments using astrocytes and analyzed functional change by microarray.  [Results]: We identified ICs of suprabasin (SBSN), a molecule which is thought to play a role in epidermal differentiation. Microarray data showed that the senescence and autophagy pathways were significantly changed in astrocytes with anti-SBSN antibody exposure compared to normal immunoglobulin G (IgG) exposure.  [Conclusions]: These findings indicate that SBSN could be a novel autoantibody for the evaluation of suspected NPSLE, and may help elucidate the pathogenesis underlying this disease.

overall_design: The cultured human astrocyte exposed to non IgG, control rabbit IgG and anti suprabasin antibodies with or without lipopolysaccharide (1μg/ml) for 24 h were collected for RNA isolation. We divided into the following 6 samples, Non IgG LPS(-), Non IgG LPS(+), Norm IgG LPS(-), Norm IgG LPS(+), SBSN LPS(-) and SBSN IgG LPS(+).

first: Kaname

last: Ohyama

first: Naotaka

last: Kuroda

first: Atsushi

last: Kawakami