title: Gene expression analysis of TIL rich HPV driven head and neck tumours reveals a distinct B-cell signature when compared to HPV independent tumours.

status: Public on Sep 01 2016

city: Southampton

first: Christopher

last: Woelk

state: Hampshire

address: Southampton General Hospital

department: Faculty of Medicine

institute: University of Southampton

summary:
Purpose: Human papilloma virus (HPV) associated head and neck squamous cell carcinoma (HNSCC) has a better prognosis than HPV(-) negative cancer. This may be due, in part, to the higher number of tumour infiltrating lymphocytes (TIL) in HPV(+) tumours. We used RNAseq to evaluate whether these differences in clinical behaviour could be explained simply by a numerical difference in TILs or whether there was a fundamental difference between TILs in these two settings.
Patients and methods: Twenty-three consecutive HNSCC cases with high and moderate TIL density were subjected to RNAseq analysis.  Differentially expressed genes (DEG) between 10 HPV(+) and 13 HPV(-) tumours were identified with EdgeR. Immune subset analysis was performed using, FAIME (Functional Analysis of Individual Microarray Expression) and Immune gene transcript count analysis.
Results: 1634 genes were differentially expressed. There was a dominant immune signature in HPV(+) tumours. After normalizing expression profiles for numerical differences in T cells and B cells, 437 significantly DEGs still remained. A B-cell associated signature emerged, which segregated HPV(+) from HPV(-) cancers  and included CD200, STAG3, GGA2, SPIB and ADAM28. Differential expression of these genes was confirmed  by real-time quantitative PCR and immunohistochemistry.
Conclusion: In our dataset, the difference associated with T-cells between patients with HPV(+) and (-) HNSCC was predominantly numerical. However, when TIL numbers are corrected, a distinct differential B-cell signature was revealed.

overall_design: mRNA profiles of 10 HPV driven (HPV+)  and 13 HPV independant (HPV-) head and neck squamous cell carcinoma (HNSCC) tumours were generated by RNA-Seq, using Illumina HiSeq 2000.

first: Oliver

last: Wood

first: Jeongmin

last: Woo

first: Gregory

last: Seumois

first: Emma

last: King


title: Transcriptome analysis of flower of Arabidopsis accessions

status: Public on Aug 29 2016

city: Potsdam-Golm

first: Takayuki

last: Tohge

address: Am Muehlenberg 1

country: Germany

institute: MPIMP

summary: This work purposed on screening candidates of key genes invovled in the production of phenylacylated flavonol-glycosides

overall_design: 12 samples were used in this experiment


title: Microbiota-derived short-chain fatty acids modulate expression of Campylobacter jejuni determinants required for commensalism and virulence

status: Public on Sep 02 2016

city: Albany

first: Craig

middle: T

last: Parker

state: CA

address: 800 Buchanan St

department: PSM

country: USA

institute: USDA ARS

summary: Campylobacter jejuni effectively promotes commensalism in the intestinal tract of avian hosts and diarrheal disease in humans, yet components of intestinal environments sensed by the bacterium in either host to initiate interactions are mostly unknown. By analyzing a C. jejuni acetogenesis mutant that is defective in both converting acetyl-CoA to acetate and commensal colonization of young chicks, we discovered evidence for C. jejuni sensing spatial gradients of microbiota-derived short-chain fatty acids (SCFAs) and organic acids to modulate expression of determinants required for commensalism. We identified in C. jejuni an SCFA-influenced regulon composed by genes encoding catabolic enzymes and transport systems for amino acids C. jejuni requires for in vivo growth. Expression of these genes was reduced in the acetogenesis mutant, but restored upon supplementation with physiological concentrations of SCFAs such as acetate and butyrate that are present in the lower intestinal tract of avian and human hosts. Conversely, the organic acid lactate, which is abundant in the upper intestinal tract of these hosts where C. jejuni less efficiently colonizes reduced expression of this regulon. We propose a model whereby C. jejuni senses microbiota-produced SCFAs and lactate for spatial orientation in the avian and human host. Sensing these metabolites likely allows C. jejuni to locate preferred niches in the lower intestinal tract and induce expression of factors required for in vivo growth. Our findings provide insights into the types of signals C. jejuni monitors in the avian host for commensalism and likely in the human host to promote diarrheal disease.

overall_design: Two-condition experiment, WT C. jejuni 81-176 SmR  (DRH212) and isogenic ΔCjjptaackA mutant. Biological replicates: 3 81-176 SmR and 3ΔCjjptaackA independently grown to log phase and harvested. Two technical replicates/biological replicate. One replicate per array.   A type 2 gene expression experimental design was used, with fluorescently labeled genomic DNA as a reference channel in each experiment as described by Lucchini, S., et al. 2005.  Infect Immun 73:88-102.

first: P

middle: M

last: Luethy

first: S

last: Huynh

first: D

middle: A

last: Ribardo

middle: E

last: Winter

first: C

middle: R

last: Hendrixson


title: Reduced dosage of β-catenin genetically rescues intracardiac anomalies in a Tbx1 conditional null mouse model of 22q11.2 deletion syndrome

city: Bronx

first: Tingwei

last: Guo

state: NY

address: 1301 Morris Park Avenue, Room 408

department: Genetics

institute: Albert Einstein College of Medicine

summary: Approximately 60-70% of patients with 22q11.2 deletion syndrome (22q11.2DS; velo-cardio-facial syndrome/DiGeorge syndrome) have cardiac outflow tract anomalies including persistent truncus arteriosus (PTA) as the most severe defect. Among the genes in the 22q11.2 region, TBX1, encoding a T-box transcription factor is a major candidate for cardiovascular malformations and its inactivation in mice results in a PTA. To identify novel signaling mechanisms that function downstream, we found that Tbx1 restricts canonical Wnt signaling in the pharyngeal apparatus. To test for tissue specificity within the pharyngeal apparatus, we inactivated Tbx1 in the anterior portion of the secondary heart field (AHF) mesoderm using the Mef2c-AHF-Cre allele and observed a full penetrant PTA (n = 30). Tbx1 promotes progenitor cells but restricts differentiation whereas Wnt signaling, in the AHF, promotes cardiomyocyte differentiation.  To determine whether Tbx1 and canonical Wnt signaling act in opposing pathways, both alleles of Tbx1 and one β-catenin allele were inactivated in the AHF and 85% of them (n = 35) showed partial or complete rescue. The antagonistic function of the two pathways was further confirmed by gene expression profiling, indicating that these two pathways provide a key balance in the AHF to prevent premature differentiation of progenitor cells prior to reaching the cardiac outflow tract.

overall_design: We inactivatedTbx1 and beta-catenin allele to identify function of Tbx1 and beta-catenin in the anterior portion of the secondary heart field (AHF) mesoderm. We also inactivated both alleles of Tbx1 and one β-catenin alleles (rescue design) to determine whether Tbx1 and canonical Wnt signaling act in opposing pathways

first: Bernice

last: Morrow

first: Silvia

last: Racedo


title: MicroRNA expression in control vs. ethanol exposed MCF-7 breast cancer cells in culture

status: Public on Aug 11 2016

city: Torrance

first: Robert

last: Gelfand

address: 1124 W. Carson St

department: surgery

institute: LABiomed at Harbor UCLA,  and Charles Drew Univ

summary: This is the microRNA experiment from the study of ethanol effects on the cultured cell line MCF-7, which is derived from a human malignancy. Cells were cultured in 6 well plates for a period of 4 weeks in the presence or absence of 25 mM ethanol. Cells were washed once with phosphate buffered saline pH 7.4, and RNA was extracted using the Mirvana kit for total RNA extraction. RNA samples were analyzed for microRNA prevalence by LC Sciences of Houston, Tx, USA. The results from 2 separate experiments were normalized and collected as the MultiArray Analysis Data presented here. The miR values are on an arbitrary scale.

overall_design: There are 2 experiments, each containing a control (no ethanol) sample and a sample that was exposed to 25 mM ethanol for 4 weeks.

first: Dolores

last: Vernet

first: Jaydutt

last: Vadgama

first: Nestor

middle: F

last: Gonzalez-Cadavid


title: The effect of ethanol on the cultured human breast cancer line MCF-7

summary: Alcohol consumption is a known risk factor for breast cancer in humans. We used the established breast cancer cell line MCF-7 to analyze the effects of ethanol on gene expression at the RNA level. In addition, we carried out studies on protein levels and the ability of cells to grow in an anchorage independent manner. The DNA microarray results are deposited here. We also provide the results of studies on microRNA levels as a separate data set. Cells grown in culture for 1 to 4 weeks were treated with 0-25 mM ethanol. RNA was extracted using the RNeasy Plus Micro kit and subjected to analysis by DNA microarray, using the Affymetrix human Gene 1.0 ST array (platform GPL19142). RNA samples from different treatments were analysed by the UCLA DNA Core lab. Data were returned as rma values.

overall_design: There are control experiments in which cells were grown without added ethanol, and there are experiments in which cells were grown in the presence of 25 mM ethanol for either 1 week or 4 weeks. One column shows the gene expression values for another cell line MCF12-A, which was established using non-malignant human breast cells and which was grown in the absence of ethanol. In this particular Affymetrix array, most genes are evaluated as a single Probe Set, but there are some which are included in the array as 2 or more Probe Sets.

first: Suren

last: Sarkissyan


title: MCF-7 human breast cancer cells treated with ethanol: DNA microarray expression data and microRNA prevalence data

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

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

overall_design: Refer to individual Series


title: Gene expression profiles of mouse BM LSKs, wild-type as well as Ezh2 KO mouse CML leukemia initiating cells (LICs)

status: Public on Aug 18 2016

city: Boston

first: Huafeng

last: Xie

state: MA

address: 450 Brookline Ave

institute: Dana-Farber Cancer Institute

summary:
Tyrosine kinase inhibitors (TKIs) have revolutionized chronic myelogenous leukemia (CML) management. Disease eradication, however, is hampered by innate resistance of leukemia initiating cells (LICs) to TKI-induced killing, which also provides the basis for subsequent emergence of TKI-resistant mutants. We report that EZH2, the catalytic subunit of Polycomb Repressive Complex 2 (PRC2), is overexpressed in CML LICs, required for colony formation, and survival and cell cycle progression of CML cell lines. A critical role for Ezh2 is supported by genetic studies in a mouse CML model.
Inactivation of Ezh2 in conventional conditional mice and through CRISPR/Cas9-mediated gene editing prevents initiation and maintenance of disease and survival of LICs, irrespective of BCR/ABL1 mutational status, and extends survival. Expression of the Ezh2 homolog Ezh1 is reduced in Ezh2-deficient CML LICs, creating a scenario resembling complete loss of PRC2. EZH2-dependence of CML LICs raises prospects for improved therapy of TKI-resistant CML and/or eradication of disease by addition of EZH2 inhibitors.

overall_design: Bone marrow LSK (Lin-Sca1+Kit+) cells were FACS sorted from 12 weeks old C57/BL6 mice. Wild type and Ezh2 KO CML LICs (GFP+Lin-Sca1+Kit+) were FACS sorted from a retroviral CML mouse model, at 14 days post bone marrow transplantation.  Each sample was double sorted to ensure high purify.

first: Stuart

middle: H

last: Orkin


title: MiR-148a Functions as a Tumor Suppressor by Targeting CCK-BR via Inactivating STAT3 and Akt in Human Gastric Cancer

status: Public on Sep 08 2016

city: Shanghai

first: Beiqin

last: Yu

address: No.197 Ruijin Er Road

department: Ruijin Hospital

country: China

institute: Shanghai Jiao Tong University School of Medicine

summary: To explore the role of miRNAs in gastric cancer, miRNA microarray profiling in 28 pairs of gastric cancer tissues and the matched normal mucosal tissues were performed.

overall_design: Twenty-eight pairs of gastric cancer tissues and the matched normal mucosal tissues were performed by human microRNA microarray v.12.0 (Agilent Technologies).

first: Xin

last: Lv

first: Liping

last: Su

first: Jianfang

last: Li

first: Yingyan

first: Qinlong

last: Gu

first: Min

last: Yan

first: Zhenggang

last: Zhu

first: Bingya

last: Liu


title: Dysregulated immune system networks in war veterans with PTSD

status: Public on Aug 26 2016

city: Columbia

first: Mitzi

last: Nagarkatti

state: SC

address: 6439 Garners Ferry Road

department: Pathology Microbiology and Immunology

institute: University of South Carolina School of Medicine

type: Expression profiling by high throughput sequencing

summary:
Purpose: RNA-Seq analysis can help identify large set of differentially expressed genes at a time. We performed RNA-Seq analysis to identify differentially expressed genes in the PBMCs of war veterans suffering from PTSD.
Methods: Total RNA from PBMCs from PTSD +ve and -ve individuals were used for RNA-Seq analysis.
Results: We obtained, on average, ~60 millions reads per sample. More than 70% of the reads were mapped to human genome. Functional analysis of the differentially expressed genes (362) revealed dysregulation in immune system network.
Conclusions: Our present study provides further proof that immune system related genes and pathways are dysregulated in PTSD PBMCs.

overall_design: RNA-Seq was performed with RNA from 5 each control and PTSD individuals. PBMCs collected within one hour of blood draw were used for RNA isolation. 1 ug of total RNA was used for library synthesis and sequenced in a HighSeq 2000 illumina instrument at Tufts University.

first: Marpe

last: Bam

first: Xiaoming

last: Yang


title: Dynamics of the human skeletal muscle transcriptome in response to exercise training - part 2

status: Public on Aug 14 2016

city: Solna

first: Joakim

last: Lundeberg

address: Tomtebodavägen 23A

department: Gene Technology

country: Sweden

institute: KTH-Science for Life Laboratory

summary: In the present study 23 participants completed three months of supervised aerobic exercise training of one leg (training period 1) followed by 9 months of rest before 12 of the participants completed a second exercise training period (training period 2) of three months of both legs. Skeletal muscle biopsies have been collected before and after the training periods. We have compared trained leg with untrained leg and studied gene and isoform expression. Additional samples included in this study has been previously submitted (GEO accession number GSE58387 and GSE60590).

overall_design: Analyze of transcriptome in skeletal muscle biopsy samples in response to exercise training in 23 participants in total (in addition to data previously submitted GEO accession number GSE58387 and GSE60590). Biopsy is collected from skeletal muscle before and after training period.

first: Beata

middle: W

last: Solnestam

first: Maléne

last: Lindholm

first: Stefania

last: Giacomello

first: Mikael

last: Huss

first: Sanela

last: Kjellkvist

first: Carl

middle: J

last: Sundberg


title: Genome-wide analysis of gene expression patterns in human kidney cancer [patients without metastasis]

status: Public on Aug 31 2016

city: Berlin

first: Klaus

last: Jung

address: Schumannstr. 20/21

department: Dept. of Urology

institute: University Hospital Charité

summary: To investigate the mechanisms of ccRCC progression and metastasis, we performed expression profiling of human kidney cancer and benign tissues.

overall_design: mRNA microarray expression analysis was performed by using  28 matched malignant and non-malignant kidney tissue samples from 14 ccRCC patients without diagnosed metastasis.

first: Hellmuth

last: Meyer


title: Salt treatment of PtSnRK2.7 overexpressor

status: Public on Aug 01 2016

city: Ikoma

first: Misato

last: Ohtani

address: 8916-5 Takayama-cho

department: Graduate School of Biological Sciences

country: Japan

institute: NAIST

summary: Subfamily 2 of SNF1-related protein kinase (SnRK2) plays important roles in plant abiotic stress responses as a global positive regulator of abscisic acid signaling. In the genome of the model tree Populus trichocarpa, 12 SnRK2 genes have been identified, and some are upregulated by abiotic stresses. In this study, we heterologously overexpressed the PtSnRK2 genes in Arabidopsis thaliana and found that overexpression of PtSnRK2.5 and PtSnRK2.7 genes enhanced stress tolerance. In the PtSnRK2.5 and PtSnRK2.7 overexpressors, chlorophyll content and root elongation were maintained under salt stress conditions, leading to higher survival rates under salt stress compared with those in the wild type. Transcriptomic analysis revealed that PtSnRK2.7 overexpression affected stress-related metabolic genes, including lipid metabolism and flavonoid metabolism, even under normal growth conditions. However, the stress response genes reported to be upregulated in Arabidopsis SRK2C/SnRK2.6 and wheat SnRK2.8 overexpressors were not changed by PtSnRK2.7 overexpression. Instead, PtSnRK2.7 overexpression widely and largely influenced the transcriptome in response to salt stress; genes related to transport activity, including anion transport-related genes, were characteristically upregulated, and a variety of metabolic genes were specifically downregulated. We also found that the salt stress response genes were greatly upregulated in the PtSnRK2.7 overexpressor. Taken together, poplar subclass 2 PtSnRK2 genes can modulate salt stress tolerance in Arabidopsis, through the activation of cellular signaling pathways in a different manner from that by herbal subclass 2 SnRK2 genes.

overall_design: Total RNAs of the transgenic plants expressing 35S:PtSnRK2.7 treated with or without 200 mM NaCl.  As a control experiment, the wild-type plants were treated similarly. The total RNAs were used for microarray analysis to reveal genes affected by the PtSnRK2.7 overexpression.

first: Xueqing

last: Song

first: Taku

last: Demura

first: Qiang

last: Zhuge


title: Gene expression profiles in wild-type and SUMO knockdown mice after forebrain ischemia

city: Durham

first: Wei

state: NC

address: 303 Research Drive

department: Anesthesiology

institute: Duke University Medical Center

summary:
Transient brain ischemia massively activates global SUMOylation. A large fraction of SUMO targets are nuclear proteins involved in gene expression. However, gene expression profile modulated by ischemia-induced SUMOylation has not been studied.
Using a SUMO knockdown (SUMO-KD) mouse model and microarray technique, we investigated how SUMOylation modulated gene expression after brain ischemia.

overall_design: Wild-type and SUMO-KD mice were subjected to transient forebrain ischemia or sham surgery. The hippocampal CA1 subfield samples collected at 3 hours reperfusion were analyzed using Affymetrix microarrays.

first: Wulf

last: Paschen


title: Genome-wide analysis of gene expression patterns in human kidney cancer [patients with metastasis]

summary: To investigate the mechanisms of kidney tumor progression and metastasis, we performed expression profiling of human kidney cancer and benign tissues.

overall_design: mRNA microarray expression analysis was performed by using  26 matched malignant and non-malignant kidney tissue samples from 13 ccRCC patients with diagnosed metastasis.


title: Real-time quantitative PCR analysis of mice lung tissue after inhalation of S100A8, S100A8 dimer, S100A9 or S100A8/A9 complex in acute lung [S100A8S100A9 LPS induced ALI]

city: UNSW, SYDNEY

first: Kenneth

middle: K

last: Hsu

state: NSW

address: Rm422, 4E, Wallace Wurth Bld,

department: School of Medical Sciences

country: Australia

institute: University of New South Wales

summary:
LPS (10 μg/50 μl PBS; E. coli Serotype 055:B5, Sigma-Aldrich) was administered onto the nares. Baseline levels of genes in mice treated with vehicle (Hanks Balanced Salt solution (HBSS) and PBS),
Intranasal S100s (10 μg/50 μl HBSS) were given 2 h before LPS; control mice received equal volumes of PBS and HBSS. Mice were sacrificed 4 h post LPS inhalation.

overall_design: Expression of inflammatory genes was evaluated with the RT-qPCR array. Relative quantities of mRNA in duplicate samples were obtained using the LightCycler® 480 Software 1.5 and the Efficiency-Method.

first: Yuka

last: Hiroshima


title: Alcohol potentiates the psychostimulant and reinforcing effects of mephedrone in adolescent mice: role of D3 receptors and associated changes in gene expression

city: Barcelona

first: Andrés

middle: Michael

last: Ciudad

state: Barcelona

address: Joan XXIII sn

department: Pharmacology and chemical therapeutics

country: Spain

institute: University of Barcelona

summary: Mephedrone (Meph) is a novel psychostimulant whose recreational consumption is often associated to other drugs, especially alcohol (EtOH). This kind of drug consumption during adolescence is a matter of concern. We studied, in adolescent CD-1 mice, whether low-moderate doses of EtOH could enhance the psychostimulant (locomotor acivity) and reinforcing (conditioned place preference, CPP) effects of mephedrone. Simultaneously we also determined the most relevant transcriptional changes associated to a reinforcing treatment. A single dose of Meph (10 mg/kg, sc) induced an increase of about 100% in locomotor activity, which was a further enhanced by 40% when associated with a dose of EtOH (1 g/kg). The hyperlocomotion was partially antagonized by ketanserin and haloperidol, but only haloperidol blocked the potentiation induced by EtOH.  Furthermore, Meph (25 mg/kg) induced significant positive conditioning, which increased by 70% when administered with 0.75 mg/kg EtOH. Microarray analysis of mRNA extracted from anterior striata of the mice used in CPP experiments reported significant modifications in genes related with neurotransmission and synaptic plasticity, which were further validated by Real-time PCR for all three drug-treated groups.

overall_design: Four groups were compared in the study: adolescent Swiss CD-1 mice treated with saline, ethanol, mephedrone or mephedrone + ethanol during the conditioned place preference (CPP) ten-day procedure, aimed at evaluating reward. Twelve samples are provided, which correspond to triplicates of each treatment group. The samples provided were subsequently normalized and analyzed using the GeneSpring GX 7.3.1 software.

first: A

last: Ciudad-Roberts

first: C


title: Ketamine and Imipramine Reverse Transcriptional Signatures of Susceptibility and Induce Resilience-Specific Gene Expression Profiles

status: Public on Jul 27 2016

city: New York

first: Immanuel

last: Purushothaman

state: New York

address: 1425 Madison Avenue

department: Neuroscience

institute: Icahn School of Medicine at Mount Sinai

summary:
Background: Examining transcriptional regulation by existing antidepressants in key neural circuits implicated in depression, and understanding the relationship to transcriptional mechanisms of susceptibility and natural resilience, may help in the search for new therapeutics. Further, given the heterogeneity of treatment response in human populations, examining both treatment response and non-response is critical.
Methods: We compared the effects of a conventional monoamine-based tricyclic antidepressant, imipramine (14 daily injections), and a rapidly acting, experimental, non-monoamine-based antidepressant, ketamine (single injection), in mice subjected to chronic social defeat stress, a validated model of depression, and used RNA-sequencing to analyze transcriptional profiles associated with susceptibility, resilience and antidepressant response and non-response in prefrontal cortex (PFC), nucleus accumbens, hippocampus, and amygdala.
Results: We identified approximately equal numbers of responder and non-responder mice following ketamine or imipramine treatment. Ketamine induced more expression changes in hippocampus than other brain regions; imipramine induced more expression changes in nucleus accumbens and amygdala. Transcriptional profiles in ketamine and imipramine responders were most similar in PFC, where the least transcriptional regulation occurred for each drug. Non-response reflected both the lack of response-associated gene expression changes and unique gene regulation. In responders, both drugs reversed susceptible associated transcriptional changes as well as induced resilient associated transcription in PFC, with effects varying by drug and brain region studied.
Conclusions: We generated a uniquely large resource of gene expression data in four inter-connected limbic brain regions implicated in depression and its treatment with imipramine or ketamine. Our analyses highlight the PFC as a key site of common transcriptional regulation by both antidepressant drugs and in both reversing susceptibility and inducing resilience associated molecular adaptations. In addition, we found region-specific effects of each drug suggesting both common and unique effects of imipramine versus ketamine.

overall_design: mRNA profiles of susceptibility to chronic social defeat stress as well as treatment response were generated across 4 separate brain regions, with a sample size of 3-5 per group.

first: Rosemary

middle: C

last: Bagot

first: Hannah

last: Cates

first: Eric

last: Nestler


title: Genome-wide analysis of gene expression patterns in human kidney cancer

first: Klaus


title: Real-time quantitative PCR analysis of mice lung tissue [S100A9 time course]

summary: Recombinant-murine S100A9 were used at 10 mg/50 ml in Hanks Balanced Salt solution (HBSS) or control HBSS administered onto the nares of BALB/C mice. To assess direct effects, mice were sacrificed 1, 4, 6, or 12 h post-inhalation of S100A9. Because S100A9 is reported to initiate proinflammatory responses by ligating TLR4 and/or RAGE, a quantitative PCR array was developed to analyze 49 genes, selected to reflect potential acute inflammatory changes induced by ligation of these receptors.


title: Murine chondrocytes cells：stiff gel vs. the soft gel

status: Public on Jul 26 2016

city: beijing

first: YAN

last: ZU

address: tsinghua university

institute: TSINGHUA

summary: Transcriptional profiling of mouse chondrocytes cells comparing control untreated chondrocytes cells with chondrocytes cells plated in stiff and soft ECM. Goal was to determine the effects of ECM stiffness on  gene expression.

overall_design: Three-condition experiment: normal, stiff ECM, soft ECM. Biological replicates: 3 normal replicates, 3 stiff ECM replicates, 3 soft ECM replicates.

first: Jing

last: Du

first: Yan

last: Zu


title: Effect of erythropoietin (EPO) and leukemia-inhibitory factor (LIF) on gene expression profiling in differentiating rat CG4-EPOR oligodendrocytes

status: Public on Jul 22 2016

city: Brighton

first: Pietro

last: Ghezzi

address: BSMS Teaching Building

country: United Kingdom

institute: Brighton & Sussex Medical School

summary: Analysis of the gene expression profile in differentiating rat CG4-EPOR oligodendrocytes treated with EPO, LIF or their combination for 1h or 20h

overall_design: Gene expression was measured undifferentiated CG4-EPOR cells and in differentiating cells at 1h and 20h in 5 conditions: control, EPO 10ng/ml, LIF 0.2ng/ml, LIF 10ng/ml, EPO 10ng/ml+LIF 10ng/ml); 3 or 4 replicates.

first: Manuela

last: Mengozzi

first: Georgina

last: Gyetvai


title: Homeobox protein NKX2-3 modulates lymphocyte dynamics and promotes B-cell lymphomagenesis

city: Pamplona

first: Victor

last: Segura

state: Navarra

address: Avda. Pío XII, 55

department: Unit of Proteomics, Genomics and Bioinformatics

institute: FIMA

summary: Molecular cloning of a t(10;14)(q24;q32) from a B-cell lymphoma showed a recurrent breakpoint in homeobox NKX2-3 gene, which was highly expressed in comparison to non-expressing mature B lymphocytes. Epigenetically-mediated NKX2-3 over-expression was selectively found in patients with splenic marginal-zone lymphoma, MALT lymphoma and extranodal diffuse large-cell lymphoma. In young mice, restricted expression of NKX2-3 to lymphocytes activated multiple integrins (LFA-1, VLA-4, MAC-1), adhesion molecules (ICAM-1, MadCAM-1, L-selectin) and the chemokine receptor CXCR4 that enhanced their homing and migration to splenic tissues, whereby they were retained, progressively accumulating to form non-clonal tumors. At 18 months, B cells acquired genomic rearrangements and generated clonal B-cell lymphomas mirroring the spectrum of human NKX2-3-expressing tumors. Mouse and human lymphomas displaying NKX2-3 expression shared histopahological, genomic and molecular features, including canonical NF-KB activation. NF-KB inhibition reduced tumorigenecity of NKX2-3-positive lymphomas. Our study reveals that oncogenic NKX2-3 promotes B-cell lymphomagenesis by disturbing lymphocyte dynamics.

overall_design: Comparisson of global gene expression profiling between Emu-NKX2-3 transgenes mice and wild type mice.

first: Eloy

last: Robles

first: Jose

last: Martinez-Climent


title: Adaptation of the Kinome Promotes Resistance to BET Bromodomain Inhibitors in Ovarian Cancer

status: Public on Jul 21 2016

city: PHILADELPHIA

first: yuesheng

last: Li

state: PA

address: 333 Cottman Ave.

department: Genomic Facility

institute: Fox Chase Cancer Center

summary: Small molecule BET bromodomain inhibitors (BETi) are actively being pursued in clinical trials for the treatment of a variety of cancers, however, the mechanisms of resistance to targeted BET protein inhibitors remain poorly understood. Using a novel mass spectrometry approach that globally measures kinase signaling at the proteomic level, we evaluated the response of the kinome to targeted BET inhibitor treatment in a panel of BRD4-dependent ovarian carcinoma (OC) cell lines. Despite initial inhibitory effects of BETi, OC cells acquired resistance following sustained treatment with the BETi, JQ1. Through application of Multiplexed Inhibitor Beads (MIBs) and mass spectrometry, we demonstrate that BETi resistance is mediated by adaptive kinome reprogramming, where activation of compensatory pro-survival kinase networks overcomes BET protein inhibition. Furthermore, drug combinations blocking these kinases may prevent or delay the development of drug resistance and enhance the efficacy of BET inhibitor therapy.

overall_design: RNAseq was employed to identify changes in kinase RNA expression following short term (48h) or chronic (JQ1R) JQ1 treatment in three different ovarian cancer cell lines.

first: James

middle: S

last: Duncan

first: Kelly

first: Alison

last: Kurimchak

first: Yuesheng


title: Glomerular Transcriptome Profiling Comparing DBA/2 and C57BL/6 mice

city: Stanford

first: Vivek

last: Bhalla

address: 777 Welch Road, Suite DE

institute: Stanford University School of Medicine

summary: Comparing glomerular gene expression level between mice with different susceptibilities to diabetic nephropathy, DBA/2 (susceptible) and C57BL/6 (resistant) mice, respectively. The hypothesis is that differential expression of glomerular genes regulate susceptibility to diabetic nephropathy. The results show immune related genes. Thus, glomerular inflammation may increase susceptibility to diabetic nephropathy in mice.

overall_design: RNA isolated from kidney glomeruli of DBA/2 and C57BL/6 mice, with or without 4 weeks diabetes induced by streptozotocin.

first: Xiaoyi

last: Zheng

first: Fariborz

last: Soroush

first: Jin

last: Long

first: Evan

last: Hall

first: Puneeth

last: Adishesha

first: Sanchita

last: Bhattacharaya

first: Mohammad

last: Kiani


title: The gene expression profile of Bacillus subtilis response to the high-temperature fermentation

status: Public on Jul 18 2016

city: Nanjing

first: weiying

last: wang

address: 1 Wenyuan Road

department: College of Life Sciences

institute: Nanjing Normal University

summary: High-temperature fermentation of the Bacillus subtilis isolated from the black part of maotai Daqu. Studying on the gene expression profile using microarray for analyzing the connection between metabolites and the maotai flavor substances. 84 differential expressed genes were obtained, including 40 up-regulated genes and 44 down-regulated genes.The differentially expressed genes involved in the metabolic pathways were just only KBL (glycine C - acetyltransferase) and ripA (bifunctional 3, 4 - dihydroxy - 4-2 - butanone phosphate synthase), up-regulated 2.9 and 2.9 times respectively, and their catalytic reaction prodction of aminobutyric acid and dihydroxy ethyl ketone  phosphate, respectively. They may be further derived into alcohol and ketone flavoring substances.  However, a large number of differential expressed genes was related to sporulation, such as ybaN (polysaccharide deacetylase) and rapA (aspartic acid phosphatase), they were up-regulated 17.5 times and down-regulated 112.5 times. YbaN is closely related to the formation of spore cortex and high temperature group spore cortex obvious thickening by TEM. RapA is signaling molecules to restrain spore formation, its lower expression can promote the sporulation in group A. Formation and release of peptidoglycan and the DPA (2, 6 - Pyridinedicarboxylic acid) of spore cortex during theseveral rounds of low temperature to high temperature circulation fermentation may be the main source of furan and pyranand  nitrogen heterocyclic compounds  in maotai flavor substances . In this paper, the formation of high-temperature fermentation Bacillus subtilis spores is closely related to the generation of maotai flavor substances.

overall_design: There are total of eight samples. It divided two groups, set as group A (High temperature fermentation) and B (normal temperature fermentation, continuous 37C). There are four replicates for each group.

first: Weiying

last: Wang

first: Bin

last: Lian


title: Transcriptome Sequencing of Adipose-Derived Mesechymal Stromal Cells

status: Public on Jul 13 2016

city: Rochester

first: Asha

last: Nair

address: 200 1ST ST SW

institute: Mayo Clinic

summary: We performed RNA-sequencing to determine the abundance of all RNA transcripts expressed by adipose-derived mesenchymal stromal cells (AMSC) under proliferating and confluent conditions.

overall_design: AMSCs were plated at 3,000 cells/cm2 in growth media and incubated at 37°C, 5% CO2. Proliferating samples were harvested when cells were 70% confluent, and confluent samples were collected at 100% confluence. Following RNA extraction, RNA-sequencing was performed to evaluate differential transcript abundence between proliferating and confluent samples.

first: Andre

last: van Wijnen


title: Mechanisms of nickel toxicity in bacteria

status: Public on Jul 01 2016

city: Villeurbanne

first: Agnès

last: Rodrigue

address: 10 rue Dubois

country: France

institute: INSA Lyon CNRS

summary: We report the effects of a nickel stress on the transcriptome of Escherichia coli coli cells, evaluated by RNA-Seq experiments

overall_design: Comparison between wild type E. coli grown in miminal media in the presence or not of 50 µM NiCl2 during 10 min - 2 conditions compared with 3 replicates each

first: Manon

last: Gault


title: Single-cell measurements of osteolineage cells within the bone marrow cell niche

city: Boston

first: Peter

last: Kharchenko

address: 10 Shattuck St.

department: DBMI

institute: Harvard Medical School

summary: We report an approach biased only by the anatomic proximity of hematopoietic stem/progenitor cells (HSPC) to a putative niche cell as the criterion for molecular analysis. Comparative RNA-Seq profiling of single mesenchymal cells immediately proximal to transplanted HSPCs and those located further away revealed that HSPC-proximal cells have a distinct genome-wide transcriptional signature, highly enriched for genes previously implicated in HSPC niche function.

overall_design: RNA-seq samples.

first: Lev

last: Silberstein

middle: V

first: David

last: Scadden


title: Nutrigenomic effects of glucosinolates on liver, muscle and distal kidney of Atlantic salmon

city: Aas

first: Aleksei

last: Krasnov

address: Osloveien 1

department: Fish Health

country: Norway

institute: Nofima AS

summary: Glucosinolates (GLs) present in plants from the Brassica family hold promise in the biological control of the skin parasite salmon louse (Lepeophtheirus salmonis) in farmed Atlantic salmon. We recently reported significantly reduced lice infestation in fish fed GLs. However, their wider application requires better knowledge of GLs’ actions, including positive and adverse effects that may occur under the overexposure. Microarray analyses performed in the liver, muscle and distal kidney of salmon under high dose of GLs suggested massive tissue remodeling and reduction of cellular proliferation in skeletal muscle and liver. In the distal kidney, gene expression profiles induced under the high dose of GLs pointed to activation of anti-fibrotic responses. At the same time, prevalent activation of genes from the Phase-2 detoxification pathways could be considered part of beneficial effects. Multiple gene expression evidence suggested GLs-mediated iron/heme withdrawal response, including increase in heme degradation in muscle (up-regulation of heme oxygenase-1), decrease of its synthesis in liver (down-regulation of porphobilinogen deaminase) and increase in iron sequestration from blood (hepatic induction of hepcidin-1 and renal induction of intracellular storage protein ferritin). This could be beneficial upon encounter with the parasite, which depends on the provision of iron/heme by the host.

platform_organism:
Oncorhynchus mykiss
Salmo salar

overall_design: Atlantic salmon received control feed and feed with 13% of the GL-containing raw ingredient during three weeks. Microarray analyses were performed in distal kidney, liver and muscle.

first: Helle

last: Jodaa Holm

first: Stanko

last: Skugor


title: Apical complex protein Pals1 is required to maintain cerebellar progenitor cells in a proliferative state

status: Public on Jun 30 2016

city: Houston

first: Sangbae

last: Kim

state: TX

address: 1 Baylor plaza

department: HGSC

institute: Baylor Colleage of Medicine

summary: Through their biased localization and function within the cell, polarity complex proteins are necessary to establish the cellular asymmetry required for tissue organization. Well-characterized germinal zones, mitogenic signals, and cell types make the cerebellum an excellent model for addressing the critical function of polarity complex proteins in the generation and organization of neural tissues. Deleting apical polarity complex protein Pals1 in the developing cerebellum results in a remarkably undersized cerebellum with disrupted layers in poorly formed folia and strikingly reduced granule cell production. We demonstrate that Pals1 is not only essential for cerebellum organogenesis, but also for preventing premature differentiation and thus maintaining progenitor pools in cerebellar germinal zones, including cerebellar granule neuron precursors (CGNP) in the external granule layer (EGL). In the Pals1 mutants, expression of genes that regulate cell cycle were diminished, correlating with the loss of proliferating population of germinal zones. Furthermore, enhanced Shh signaling through activated Smoothened (Smo) cannot overcome impaired cerebellar cell generation, arguing for an epistatic role of Pals1 in proliferation capacity.  Our study identifies Pals1 as a new intrinsic factor that regulates the generation of cerebellar cells and Pals1 deficiency as a potential inhibitor of overactive mitogenic signaling.

overall_design: Two groups of samples are included:  mRNA obtained from 4 WT and 4 CKO animals at E17.5. hGFAP-Cre mice was used to delete Pals1 from most cerebellar neurons and glia (termed Pals1 CKO). Pals1fl/fl and hGFAP-Cre (Zhuo et al., 2001) were bred for generation of CKO.

first: Jun-Young

last: Park

first: Lucinda

last: Hughes

first: Ju-Seog

last: Lee

first: Seonhee


title: Gene expression analysis of control and Tbx20 mutant Tie2Cre lineage from E12.5 hearts

city: Utrecht

first: Cornelis

middle: J.

last: Boogerd

address: Uppsalalaan 8

department: Developmental Biology and Stem Cell Research

country: Netherlands

institute: Hubrecht Institute

summary:
To investigate roles for Tbx20 in endocardium, we ablated Tbx20 utilizing Tie2Cre.  Tie2Cre;Tbx20 mutants died at E14, exhibiting defects in multiple aspects of cardiac septation. Although endocardial cells lacking Tbx20 were able to undergo endothelial-to-mesenchymal transition, cushion mesenchymal cells lacking Tbx20 did not disperse normally. Non-cell autonomous roles of endocardial Tbx20 were also revealed, as evidenced by decreased myocardialization of outflow tract and failure of dorsal mesenchymal protrusion formation in mutants. To examine how ablation of Tbx20 in endocardial lineages affected gene expression, we performed global gene expression analysis on purified endocardial lineages. E12.5 hearts were dissociated, and Tie2Cre;RosatdTom lineage traced cells of controls and mutants were isolated by fluorescence activated cell sorting (FACS), after exclusion of blood cells (Ter119+, CD41+ and/or CD45+).  Mutant endocardial lineages exhibited decreased expression of genes associated with extracellular matrix and cell migration.
E12.5 hearts were dissociated, and Tie2Cre;RosatdTom lineage traced cells of controls and mutants were isolated by fluorescence activated cell sorting (FACS), after exclusion of blood cells (Ter119+, CD41+ and/or CD45+).

overall_design: FACS sorted Tie2Cre lineage from E12.5 hearts: Tie2Cre;Tbx20 +/loxP Control hearts versus Tie2Cre;Tbx20 loxP/- mutant hearts


title: Dehydration impaired normal renal development in infant mice

city: Seoul

first: Chong-Su

address: Gwanak-ro 1, Gwanak-gu

department: Food and nutrition

country: South Korea

institute: Seoul national university

summary: The kidney is a major organ in which fluid balance and waste excretion is regulated. To obtain mature functions of the kidney, normal renal developmental processes need to be preceded. Comprehensive genetic programs underlying renal development during prenatal life have been widely studied. However, postnatal renal development, from infancy to juvenile period, have not been studied yet. Here, we investigated if structural and functional kidney development was still undergoing in early life by analyzing renal transcriptional networks of infant (4 weeks old) and juvenile (7 weeks old) mice. We further examined the effects of dehydration on kidney development. Kidneys at 4 weeks and 7 weeks old showed significantly distinctive functional network of genes. Gene sets related to cell cycle regulators and immature glomerular barrier integrity (COL4A1, COL4A2) were enriched in infantile kidneys while genes associated with ion transport and drug metabolism (CYP450 family) were shown in juvenile kidneys. Dehydration during infancy suppressed renal growth by interrupting SHH signaling pathway which targets cell cycle regulators. Importantly, disruption of developmental program ultimately led to long-term alterations in renal filtration function, by causing a decline in glomerular filtration barrier integrity. Taken together, we provide meaningful perspectives of renal development in infancy which suggests molecular and physiological background why infants are more vulnerable to dehydration than adults. These results provide new insights into the systemic effects of dehydration on renal development and may propose possible markers for clinical application in pediatric dehydration.

overall_design: Total RNA obtained from isolated kidneys subjected to water restriction for 1 week (RES 1W, 4-week-old) and 4 weeks (RES 4W, 7-week-old), and each group was compared to control group; CON 1W (4-week-old), CON 4W (7-week-old) respectively.

first: Dong-Mi

last: Shin


title: Real-time quantitative PCR analysis of mice lung tissue [S100A8 time course]

first: Kenneth

last: Hsu

summary: Recombinant-murine S100A8 were used at 10 mg/50 ml in Hanks Balanced Salt solution (HBSS) or control HBSS administered onto the nares of BALB/C mice. To assess direct effects, mice were sacrificed 1, 4, 6, or 12 h post-inhalation of S100A8. Because S100A8 is reported to initiate proinflammatory responses by ligating TLR4 and/or RAGE, a quantitative PCR array was developed to analyze 49 genes, selected to reflect potential acute inflammatory changes induced by ligation of these receptors.

first: Yuka

last: Hiroshima


title: Locally adapted populations of a copepod species exhibit starkly different gene expression responses to different thermal environments

status: Public on Jul 25 2016

city: La Jolla

first: Thiago

middle: Ghirello

last: Lima

state: California

address: 9500 Gilman Drive #0202

institute: Scripps Institution of Oceanography

summary: This study aimed at measuring transcriptome-wide gene expression in four populations of the copepod T. californicus. Populations were exposed to two different thermal regime, a variable 20-28 degree and a constant 20 degree followed by a one-time stress at 28 degrees. RNA was extracted at 20 and 28 degrees for all populations from all thermal regimes. Transcriptome-wide gene expression was measured, and differentially expressed genes were determined for all populations for the different temperature combinations. The results show that each populations responds to the changes in temperature in a drastically different manner (in terms of gene expression), which can have implications regarding the way these and other organisms will respond to climate change.

overall_design: Two southern and two northern populations of Tigriopus californicus were exposed to a variable 20-28 degree and a constant 20 degree  followed by a one-time stress at 28 degrees. RNA was extracted at 20 and 28 degrees for all  populations from all thermal regimes. mRNA profiles were generated by 100bp single end sequencing in the Illumina HiSeq 2000 and 2500, with one replicate per population per treatment.

middle: G

first: Christopher

last: Willett


title: Exposure of bovine oocytes and embryos to elevated non-esterified fatty acid concentrations: integration of epigenetic and transcriptomic signatures in resultant blastocysts [gene expression]

status: Public on Jun 28 2016

city: Wilrijk

first: Karolien

middle: LJ

last: Desmet

state: Antwerpen

address: Universiteitsplein 1

department: Veterinary Sciences

country: Belgium

institute: University of Antwerp

summary: Metabolic stress associated with negative energy balance in high producing dairy cattle and obesity in women is a risk factor for decreased fertility. Non-esterified fatty acids (NEFA) are involved in this pathogenesis as they jeopardize oocyte and embryo development. Growing evidence indicates that maternal metabolic disorders can disturb epigenetic programming, and more specifically DNA methylation, in the offspring. Final oocyte maturation and early embryo development coincide with specific methylation changes and both time periods are sensitive to adverse environments. Therefore, we investigated whether elevated NEFA concentrations affect the establishment and maintenance of DNA methylation patterns in oocytes and embryos and subsequently alter transcriptomic profiles and developmental competence of the resultant blastocysts. To do this, bovine oocytes and embryos were exposed to different NEFA concentrations in two separate experiments. In the first experiment, oocytes were matured in vitro for 24 hours in medium containing: 1) physiological (“BASAL”) concentrations of oleic (OA), palmitic (PA) and stearic (SA) or 2) elevated (pathophysiological or “HIGH COMBI”) concentrations of OA, PA and SA. In the second experiment, zygotes were cultivated in vitro for 6.5 days under BASAL or HIGH COMBI conditions. The developmental competence was evaluated by assessing cleavage and blastocyst rate. Overall gene expression and DNA methylation of resultant blastocysts were analyzed using microarray techniques. Data regarding DNA methylation were re-evaluated by pyrosequencing. HIGH COMBI-exposed oocytes and embryos displayed a lower competence to develop into blastocysts compared to their BASAL-exposed counterparts (19.3 % compared to 23.2 % and 18.2 % compared to 25.3 %, respectively) (P < 0.05). HIGH COMBI-exposed oocytes and embryos resulted in blastocysts with altered DNA methylation profiles and transcriptomic fingerprints, compared to BASAL-exposed counterparts. Differences in gene expression and methylation were more pronounced after exposure during culture compared to maturation suggesting that zygotes are more susceptible to an adverse environment. Main gene networks affected were related to lipid and carbohydrate metabolism, cell death, immune response and metabolic disorders. This may offer clues regarding the high rate of embryonic loss and metabolic diseases during later stages of life observed in offspring from mothers displaying lipolytic disorders.

overall_design: The effect of elevated NEFA exposure during embryo culture (6.5 days) on gene expression was evaluated by exposing embryos to the BASAL or HIGH COMBI conditions. A total of 1412 oocytes were used, equally distributed between treatments in 4 replicates. Resultant day 7.5 blastocysts were snap frozen for subsequent transcriptome analysis (80 blastocysts in each experiments, equally collected between treatments in 4 replicates).

middle: L

first: Veerle

last: Van Hoeck

first: Dominic

last: Gagné

first: Eric

last: Fournier

first: Avinash

last: Thakur

first: Alan

last: O'Doherty

first: Colum

middle: P

last: Walsh

first: Marc-André

last: Sirard

first: Peter

last: Bols

first: Jo

last: Leroy


title: Exposure of bovine oocytes and embryos to elevated non-esterified fatty acid concentrations: integration of epigenetic and transcriptomic signatures in resultant blastocysts [DNA methylation]

type: Methylation profiling by genome tiling array

overall_design: Two experiments were set up to characterize the epigenomic profile of the resultant day 7.5 blastocysts. In the first (in vitro maturation or IVM) experiment, the effect of elevated NEFA exposure during oocyte maturation (24 h) on DNA methylation profiles was evaluated by exposing oocytes to the BASAL or HIGH COMBI conditions. In the second (in vitro culture or IVC) experiment, the effect of elevated NEFA exposure during embryo culture (6.5 days) on DNA methylation marks was evaluated by exposing embryos to the BASAL or HIGH COMBI conditions. A total of 1039 and 1412 oocytes were used in the IVM and IVC experiment, respectively, equally distributed between treatments in 4 replicates. Resultant day 7.5 blastocysts were snap frozen for subsequent DNA methylation analysis (80 blastocysts in each experiments, equally collected between treatments in 4 replicates).

middle: M

middle: E


title: Ridaforolimus (MK-8669) synergizes with Dalotuzumab (MK-0646) in hormone-sensitive breast cancer

first: Marc

middle: A

last: Becker

state: MN

address: 200 First St SW

department: Medical Oncology

summary: Introduction: Mammalian target of rapamycin (mTOR) represents a key downstream intermediate for a myriad of oncogenic receptor tyrosine kinases. In the case of the insulin-like growth factor (IGF) pathway, the mTOR complex (mTORC1) mediates IGF-1 receptor (IGF-1R)-induced estrogen receptor alpha (ERα) phosphorylation/activation and leads to increased proliferation and growth in breast cancer cells. As a result, the prevalence of mTOR inhibitors combined with hormonal therapy has increased in recent years. Conversely, activated mTORC1 provides negative feedback regulation of IGF signaling via insulin receptor substrate (IRS)-1/2 serine phosphorylation and subsequent proteasomal degradation. Thus, the IGF pathway may provide escape (e.g. de novo or acquired resistance) from mTORC1 inhibitors. It is therefore plausible that combined inhibition of mTORC1 and IGF-1R for select subsets of ER-positive breast cancer patients presents as a viable therapeutic option.   Methods: Using hormone-sensitive breast cancer cells stably transfected with the aromatase gene (MCF-7/AC-1), works presented herein describe the in vitro and in vivo antitumor efficacy of the following compounds: dalotuzumab (DALO; “MK-0646”; anti-IGF-1R antibody), ridaforolimus (RIDA; “MK-8669”; mTORC1 small molecule inhibitor) and letrozole (“LET”, aromatase inhibitor).   Results: With the exception of MK-0646, all single agent and combination treatment arms effectively inhibited xenograft tumor growth, albeit to varying degrees. Correlative tissue analyses revealed MK-0646 alone and in combination with LET induced insulin receptor alpha A (InsR-A) isoform upregulation (both mRNA and protein expression), thereby further supporting a triple therapy approach.   Conclusion: These data provide preclinical rationalization towards the combined triple therapy of LET plus MK-0646 plus MK-8669 as an efficacious anti-tumor strategy for ER-positive breast tumors.

overall_design: 46 samples, 28 days post treatment

first: Paul

last: Haluska


title: Transcriptomic and Epigenetic Signatures of Mouse Cardiac Progenitor Cells

status: Public on Jul 24 2016

city: Honolulu

first: Yiqiang

last: Zhang

state: HI

address: 651 Ilalo St BSB-311D

department: Anatomy, Biochemistry and Physiology

institute: University of Hawaii Manoa

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

overall_design: Refer to individual Series


title: Exposure of bovine oocytes and embryos to elevated non-esterified fatty acid concentrations: integration of epigenetic and transcriptomic signatures in resultant blastocysts


title: MicroRNA expression proﬁling in GC-2 cells following 50 Hz ELF-EMF

city: Chongqing

first: Jin-yi

last: liu

address: gaotanyan street

department: College of Preventive Medicine

institute: Third Military Medical University

summary:
Aberrant miRNA expression has been related to the development of human germ cell tumors, but little is known about effect of ELF-EMFs on miRNA expression. ELF-EMFs may epigenetically modify cells, which may account for the adverse effects of ELF-EMFs on the male reproductive system.
To identify miRNAs that were differentially expressed between the sham and ELF-EMF exposure groups, we performed an Affymetrix microarray analysis to establish the miRNA expression profiles.

overall_design: Mouse spermatocyte-derived GC-2 cells were intermittently exposed to a 50 Hz ELF-EMF for 72 h (5 min on/10 min off) at magnetic field intensities of 1 mT and 3 mT. miRNA expression was profiled using Affymetrix Mouse Genechip miRNA 3.0 arrays.

last: Liu

first: Yong


title: miRNA expression profile analysis in myelodysplastic syndromes

city: Shanghai

first: Feng

last: Xu

state: Shanghai

address: 600 Yishan Road

department: Hematology

institute: Shanghai Jiaotong University Affiliated Sixth People's Hospital

summary:
The miRNA-related signaling pathways in MDS could be screened using high throughput bioinformatics analysis based on the miRNAs expression profile network.
Here, we tried to identify the miRNAs-regulated pathways through a miRNA microarray in CD34+ cells from MDS patients.

overall_design: miRNA expression profile analysis was performed in 12 MDS patients and 6 normal controls using GeneChip® miRNA 3.0 Array, and diffirential miRNAs were identified.

first: Xiao

last: Li


title: Gene expression profile analysis in myelodysplastic syndromes

summary:
The pathogenesis-related signaling pathways in MDS could be screened using high throughput bioinformatics analysis based on the gene expression profile network.
Here, we tried to identify the mRNAs-regulated pathways through a mRNA microarray in CD34+ cells from MDS patients.

overall_design: Gene expression profile analysis was performed in 12 MDS patients and 6 normal controls using GeneChip® PrimeView™ Human Gene Expression Array, and diffirential genes were identified.


title: The WOPR protein Ros1 is a master regulator of sporogenesis and effector gene expression in the maize pathogen Ustilago maydis [RNA-Seq]

status: Public on Jun 24 2016

city: Marburg

first: Marie

last: Tollot

state: Hessen

address: Karl-von-Frisch-Strasse 10

department: Organismic Interactions

institute: MPI Marburg

summary:
Goals: characterization of the transcription factor Ros1 in Ustilago maydis
Methods: generation of deletion mutants, microscopic observations, ectopic expression of ros1, identification of Ros1 regulated genes by RNAseq and ChIP sequencing
Results:  Ros1 is not involved in plant colonization but is essential to trigger sporogenesis during late stages of infection. Premature expression of ros1 revealed that Ros1 counteracts the b-dependent filamentation program and induces morphological alterations resembling the early steps of sporogenesis. Transcriptional profiling and ChIP seq analyses revealed that Ros1 affects the expression of about 30 % of all U. maydis genes with 40% being direct targets. Cell wall remodeling and plasma membrane modifications are among the processes affected by Ros1 dependent regulation. Interestingly a large number of b-dependent genes including transcription factors and effector genes involved in biotrophy establishment were downregulated by Ros1 while a subset of novel “late effectors” were upregulated. Taken together our results indicate that Ros1 is a master regulator of sporogenesis in U. maydis and that the switch to sporogenesis is accompanied by the differential regulation of 75% of the effector genes.

overall_design: Two samples corresponding to plant material infected with either U. maydis wild type strains FB1 x FB2 or the ros1 deletion strains FB1Dros1 x FB2Dros1 were analyzed in triplicate.

first: Daniela

last: Assmann

first: Christian

first: Janine

last: Altmüller

first: Julien

middle: Y

last: Dutheil

first: Carl-Eric

last: Wegner

first: Regine

last: Kahmann


title: Characteristic expression of  MSX1, MSX2, TBX2, and ENTPD1 in dental pulp cells

status: Public on Jun 20 2016

city: Hiroshima

first: katsumi

last: Fujimoto

address: 1-2-3 Kasumi, Minami-ku

institute: Hiroshima University

summary:
Dental pulp cells (DPCs) are a promising source of transplantable cells in regenerative medicine. However, DPCs have not been fully characterized at the molecular level. The purpose of this study was to distinguish DPCs from various source-derived mesenchymal stem cells, fibroblasts, and other cells by the expression of several DPC-characteristic genes. DPCs were isolated from human pulp tissues by the explant method, or the enzyme digestion method, and maintained with media containing 10% serum or 7.5% platelet-rich plasma. RNA was isolated from the cells and from dental pulp tissue specimens. The mRNA levels were determined by DNA microarray and quantitative real-time PCR analyses.
The msh homeobox1 (MSX1), msh homeobox 2 (MSX2), T-box 2 (TBX2), and ectonucleoside triphosphate diphosphohydrolase 1 (ENTPD1) mRNA levels in DPCs were higher than the levels found in the following cells: mesenchymal stem cells, derived from bone marrow, synovium, and adipose tissue; and in cells such as fibroblasts, osteoblasts, adipocytes, and chondrocytes. The enhanced expression in DPCs was consistently observed irrespective of donor age, tooth type, and culture medium. Moreover, these genes were expressed at high levels in dental pulp tissue in vivo. We conclude that this gene set may be useful in the identification and characterization of DPCs in basic studies and pulp cell-based regeneration therapy.

overall_design: Dental pulp cells were isolated by the explant outgrowth method (Calcified tissue international (2000) 66:129-138.) from healthy teeth according to protocol approved by ethical authorities at Hiroshima University.  Human skin fibroblasts were obtained from Kurabo (Osaka, Japan). Human gingival fibroblasts were isolated as described previously (Journal of periodontal research (2003) 38: 242-246.). Bone marrow-derived MSCs (BM-MSCs) were isolated13 from Hiroshima University with informed consent, or were obtained from Cambrex Bio Science Walkersville, Inc. (Walkersville, MD) and PromoCell Co., Ltd. (Heidelberg, Germany). Osteoarthritis and rheumatoid arthritis synovium-derived MSCs, and adipose tissue-derived MSCs, were obtained from Cell Applications Inc. (San Diego, CA) and Zen-Bio Inc. (Research Triangle Park, NC). Osteoblasts, adipocytes, and chondrocytes, which were derived from BM-MSC, were cultured with appropriate differentiation-inducing media for 28 days (Genes to cells (2009)14:407-424).  Cells were cultured under similar conditions using the same batch of FBS. These cells were expanded with FGF-2 to maintain their multipotent nature throughout several mitotic divisions. We removed FGF-2 from the culture medium 72 h before the isolation of RNA to decrease a direct effect of the growth factor on gene expression. The total RNA was isolated, 24 h after the cultures reached confluency, using TRIzol (Life Technologies, Japan) and an RNeasy Mini Kit (Qiagen, Chatsworth, CA).  DNA microarray analysis was performed by KURABO GeneChip Custom Analysis Service with Human Genome U133 Plus 2.0 chips(Affymetrix. Inc., Santa Clara, CA). The CHP data (Microarray Suite version 5.0, Scaling Factor = 1, Normalization Value = 1, Detection Call a1 = 0.05, a2 = 0.065, Tau = 0.015, Affymetrix Inc.) were standardized by the global median normalization method using GeneSpring (Silicon Genetics, Redwood City, CA). The normalization was limited by flag values, and the median was calculated using the genes that exceeded the Present or Marginal flag restriction.

first: Sakiko

last: Fujii

first: Katsumi

first: Noriko

last: Goto

first: Masami

last: Kanawa

first: Takeshi

last: Kawamoto

first: Haiou

last: Pan

first: Petcharin

last: Srivatanakul

first: Waralak

last: Rakdang

first: Juthamas

last: Pornprasitwech

first: Tania

last: Saskianti

first: Ketut

last: Suardita

first: Fusanori

last: Nishimura

first: Yukio

last: Kato


title: The WOPR protein Ros1 is a master regulator of sporogenesis and effector gene expression in the maize pathogen Ustilago maydis

first: Marie

last: Tollot

type: Genome binding/occupancy profiling by high throughput sequencing


title: Gene expression changes in dorsal dermal fibroblasts after beta-catenin deletion in vivo

status: Public on Jun 16 2016

city: Cleveland

first: Radhika

middle: Paresh

last: Atit

state: Ohio

address: 2074 Adelbert Road, Millis 316

department: Biology

institute: Case Western Reserve University

summary:
Goal of this study was to examine gene expression changes upon conditional deletion of beta-catenin at E10.5 in dermal fibroblasts.
Method:  Skin tissues were treated in 0/25% trypsin for 15 min at 37 degrees C to obtain single cells for FACS sorting and collected in RNA later. RNA was extracted with Karcturus pico pure kit. The RT and amplification was done using Nugen's ovation RNA-seq system V2.  Libraries for sequencing were prepared with Illumina TruSeq kit. Transcriptome of  FACS sorted E13.5 Engrailed1; RRYFP lineage-marked dorsal dermal fibroblasts was generated next-gen sequencing, in triplicate, using Illumina HiSeq machine. The sequence reads that passed quality filters were analyzed by TopHat followed by Cufflinks. qRT–PCR validation was performed using TaqMan and SYBR Green assays
Results: We mapped about 33-49 million sequence reads per sample and obtained 76-79% of uniquely mapped percentage.  We assembled the reads to the mouse ref genome (build mm10).

overall_design: E13.5 dermal fibroblast mRNA profiles from En1;RRYFP (n=2) and En1Cre;RRYFP;beta-catenin flox/del (n=3) embryos (from three different litters) were generated by deep sequencing using Illumina Hi Seq


title: Expression profile of long non-coding RNAs in human earlobe keloids

status: Public on Jun 14 2016

city: Wuhan

first: Guozheng

last: Xu

state: Hubei

address: 627 Wuluo Street

department: Department of Neurosurgery

institute: Wuhan General Hospital of Guangzhou Military Command of Chinese PLA

summary:
Microarray analysis was used to determine the expression profiles of lncRNAs and mRNAs between 3 pairs of earlobe keloid and normal specimens.
Results provide insight into involement of lncRNAs in the pathological process of earlobe keloid formation.

first: Liang

last: Guo

first: Kai

first: Hongbo

last: Yan

first: Haifeng

last: Feng

first: Linlin

last: Chai


title: The WOPR protein Ros1 is a master regulator of sporogenesis and effector gene expression in the maize pathogen Ustilago maydis [ChIP-Seq]

overall_design: 4 samples were analyzed in triplicate. The first two samples correspond to input and output DNA obtained from ChIP carried out on plant material infected with U. maydis strains expressing  Ros1 with an HA tag. The other two other samples correspond to input and output DNA from ChIP carried out on plant material infected with U. maydis strains expressing Ros1 without a tag (control samples).

first: Daniela

last: Assmann

first: Christian

last: Becker

first: Janine

last: Altmüller

first: Julien

last: Dutheil

first: Carl-Eric

last: Wegner

first: Regine

last: Kahmann


title: Early response of human monocyte-derived macrophages (MDM) to HIV-1

status: Public on Jun 10 2016

city: Paris

first: Santy

last: Marques-Ladeira

state: Ile de France

address: 12, rue Lhomond

institute: Institut Curie

summary: Human MDM were exposed to VSVG-pseudotyped HIV-1 NL-AD8 for 8h, 24h, and with HIV-1 + AZT for 24h

overall_design: MDM from 3 healthy blood donors were differentiated for 7 days, exposed or not to HIV-1 +/- AZT for 8h and 24h before being lysed. RNA was extracted, reverse-transcribed, hybridized on 2.1 ST microarrays to analyse the early transcriptomic response of MDM to infection.

first: Bruna

last: Cunha de Alencar

first: Marion

last: Desdouits

first: Jérémie

last: Decalf

first: Philippe

last: Benaroch


title: Sheep milk transcriptome

status: Public on Jun 07 2016

city: Leon

first: Juan-Jose

last: Arranz

state: Leon

address: Campus de Vegazana

department: Produccion animal

institute: Universidad de Leon

summary: This study presents a dynamic characterization of the sheep milk transcriptome aiming at achieving a better understanding of the sheep lactating mammary gland. Transcriptome sequencing (RNA-seq) was performed on total RNA extracted from milk somatic cells from ewes on days 10, 50, 120 and 150 after lambing. The experiment was performed in Spanish Churra and Assaf breeds, which differ in their milk production traits. Nearly 67% of the annotated genes in the reference genome (Oar_v3.1) were expressed in ovine milk somatic cells. For the two breeds and across the four lactation stages studied, the most highly expressed genes encoded caseins and whey proteins. We detected differentially expressed genes (DEGs) across lactation points, with the largest differences being found, between day 10 and day 150. Upregulated GO terms at late lactation stages were linked mainly to developmental processes linked to extracellular matrix remodeling. A total of 256 annotated DEGs were detected in the Assaf and Churra comparison. Some genes selectively upregulated in the Churra breed grouped under the endopeptidase and channel activity GO terms. These genes could be related to the higher cheese yield of this breed. Overall, this study provides the first integrated overview on sheep milk gene expression.

overall_design: A total of eight healthy sheep were selected to be included in the experiment, four Assaf and four Churra ewes. 32 Milk Somatic Cells (MSCs) samples were collected on days 10, 50, 120 and 150 after lambing. In each time point 4 biological replicates from each breed were collected unless on day 120 that only three biological replicates from each breed were sequenced.

first: Juan

middle: J

first: Aroa

last: Suárez-Vega

first: Beatriz

last: Gutiérrez-Gil

first: Gwenola

last: Tosser-Klopp

first: Christophe

last: Klopp


title: elli-1 gene expression array

status: Public on Jun 08 2016

city: Salisbury Cove

first: Dustin

middle: Lynn

last: Updike

state: ME

address: 159 Old Bar Harbor Rd.

institute: Mount Desert Island Biological Laboratory

summary: Germ cells contain non-membrane bound cytoplasmic organelles that help maintain germline integrity.  In C. elegans they are called P granules; without them, the germline undergoes partial masculinization or aberrant differentiation.  One key P-granule component is the Argonaute CSR-1, a small-RNA binding protein that antagonizes accumulation of sperm-specific transcripts in developing oocytes.  Loss of CSR-1 or components of its pathway results in a very specific, enlarged P-granule phenotype.  In a forward screen to identify mutants with abnormal P granules, ten alleles were recovered with csr-1 P-granule phenotypes, eight of which contain mutations in known CSR-1 pathway components (csr-1, ego-1, ekl-1, and drh-3).  The remaining two alleles are in a novel gene now called elli-1 (enlarged germline granules).  ELLI-1 is first expressed in primordial germ cells during mid-embryogenesis and continues to be expressed in the adult germline.  While ELLI-1 forms cytoplasmic aggregates, they occasionally dock, but do not co-localize with P granules.  Instead, the majority of ELLI-1 aggregates accumulate in the shared germline cytoplasm.  In elli-1 mutants, several genes that promote RNAi and P-granule accumulation are upregulated, and embryonic lethality, sterility, and RNAi resistance in a hypomorphic drh-3 allele is enhanced.  Like mutations in other CSR-1 pathway components, elli-1 is an enhancer of glp-1 sterility, suggesting that ELLI-1 functions with the CSR-1 pathway to modulate RNAi activity, P-granule accumulation, and post-transcriptional expression in the germline.

overall_design: Four RNA samples from strain DUP9 elli-1(sam3) were compared to four RNA samples from strain DUP17 (control).

first: Karolina

last: Andralojc


title: MicroRNAs defining side population of human malignant mesothelioma cell lines identified by microarray analysis

status: Public on Jun 15 2016

first: Myung-Chul

last: Kim

address: 1 Gwanak-ro, Gwanak-gu

department: deparment of clinical pathology

institute: College of Veterinary Medicine, Seoul National University

summary:
Intratumoral heterogeneity is a major barrier against effective cancer therapy. Human malignant mesothelioma (HMM) that is closely associated with asbestos exposure is extremely heterogeneous in morphology and molecular phenotype. Contrast to genetic mutations, the role of epigenetic modifications in the generation and maintenance of heterogeneous populations in cancers remains largely undetermined.
The present study was performed to investigate underlying molecular mechanisms for the emergence of intratumoral heterogeneity by identifying the global microRNA expression profile of distinct subpopulations of MS1 cell line, a HMM cell line. More aggressive cancer cells could be enriched by side population (SP) assay in HMM [20]. The sorted SP and NSP subpopulations were subjected to the microarray analysis of miRNA expression to investigate differentially altered miRNA genes defining tumor heterogeneity in HMM. Total RNAs were isolated from the sorted subpopulations of HMM cells, SP and non-SP fractions. The expression profile of miRNAs was evaluated using Affymetrix GeneChip miRNA Arrays. After data extraction and normalization, the microRNAs defining the cell subpopulations were determined using bioinformatics softwares. A total of 95 miRNAs including 42 up-regulated and 53 down-regulated were identified based on the criteria of 2 fold difference and a p-value < 0.05. Functional ontology of the dysregulated miRNAs revealed that a large number of target genes were categorized into the regulation of various cellular processes, including cell proliferation, programmed cell death, cell migration, cellular response to stress, and stem cell maintenance. The data show that  microRNAs are significantly involved in  the generation and maintenance of intratumoral heterogeneity and their regulation could be an effective strategy  to eradicate a more aggressive cancer cell subpopulation.
This is the first to report the profile of miRNA expression in CSCs in HMM by using side population assay assisted with flow cytometry. It will be valuable to understand the regulatory function of HMM CSC miRNAs in generation and maintenance of intratumoral heterogeneity.

overall_design: Total RNAs were isolated from the sorted subpopulations of HMM cells, SP and non-SP fractions. (no replicates)

first: Na-yon

first: Hang-ah

first: Uree

last: Seo

first: Yongbaek


title: Identification of Multiple Proteins Coupling Transcriptional Regulation to Genome Stability in Arabidopsis thaliana

status: Public on Jun 01 2016

city: Seattle

first: Christopher

middle: Joel

last: Hale

state: WA

address: 1959 NE Pacific St., HSC H-458

department: Pathology

institute: University of Washington

type: Methylation profiling by high throughput sequencing

summary: Eukaryotic genomes are heavily regulated by epigenetic marks that often act to modulate the transcriptional control of genetic elements. In Arabidopsis thaliana the ATXR5 and ATXR6 histone methyltransferases, and their cognate H3K27 monomethylation mark, act in transcriptional silencing while also maintaining genome stability by preventing generation of excess DNA corresponding to pericentromeric heterochromatin. In this study we characterize the atxr5 atxr6 transcriptome and its relationship to the DNA damage response which suggests that the atxr5 atxr6 transcriptional defects may be epistatic to the genome instability defects in the mutants. In addition we isolate several factors that modulate both the transcriptional and genomic instability phenotypes of atxr5 atxr6 mutants, which suggest a mechanism for atxr5 atxr6-induced extra DNA involving conflicts between the replicative and transcriptional processes in the cell.

overall_design: PolyA RNA sequencing (RNA-seq), whole-genome resequencing (DNA-seq), and whole-genome bisulfite sequencing (methyl-seq) was performed on Arabidospsis thaliana mutant and wildtype plants.  DNA-seq was used to characterize DNA copy number and map EMS-induced mutations, RNA-seq was used to quantify transcript abundance and map EMS-induced mutations, and methyl-seq was used to assess DNA methylation. Details of the relationship between samples in this series and figures in the associated manuscript can be found in Supplemental Table 4 of the associated manuscript. Unless otherwise noted in the description all lines are ecotype Columbia, and all genotypes should be assumed homozygous unless otherwise indicated with a '/'.


title: Adenovirus Serotype 5 Vectors Trigger IL-27-Dependent Inhibitory CD4+ T Cell Responses

city: Oxford

first: Nicholas

last: Provine

state: Oxfordshire

address: John Radcliffe Hospital

department: NDM - Experimental Medicine

institute: University of Oxford

summary:
Viral vectors are attractive vaccine platforms that elicit robust innate and adaptive immune responses; however, viral vector vaccine candidates vary greatly in their ability to induce protective immunity.
Ad5 vectors elicit robust CD8+ T cell responses but typically characterized by an exhausted phenotype.
The mechanisms by which Ad5 vectors induce dysfunctional CD8+ T cells have not been fully elucidated.
Here we demonstrate that Ad5 vectors, but not Ad26 vectors, elicit exhausted antigen-specific IL-10+PD1+ CD4+ T cells with a dysfunctional transcriptional profile, and these cells effectively suppress CD8+ T cells responses in vivo.
Induction of inhibitory CD4+ T cells by Ad5 vectors was associated with increased IL-27 expression, and IL-27 blockade improved CD4+ T cell polyfunctionality.
Together our data highlight a novel role for IL-27 in regulating responses to viral vector vaccines.

overall_design: Splenic CD45.2+ OT-II TCR-Tg CD4 T cells from CD45.1+ B6 mice immunized with Ad5-OVA or Ad26-OVA were purified by FACS on day 10 post-immunization

first: Rafael

last: Larocca

first: Dan

middle: H

last: Barouch


title: Expression data from Arabidopsis thaliana root and piriformaspora indica  during log and short term interaction

status: Public on May 30 2016

city: Jena

first: khabat

last: vahabi

state: Deutschland

address: Dornburger Straße 159

department: plant physiology

institute: Friedrich-Schiller-Universität

summary:
Piriformospora indica, an endophytic fungus of Sebacinales, colonizes the roots of many plant species including Arabidopsis thaliana. The symbiotic interaction promotes plant per-formance, growth and resistance/tolerance against abiotic and biotic stress. We demonstrate that exudated compounds from the fungus activate stress and defense responses in the Arabidopsis roots and shoots before the two partners are in physical contact. They induce stomata closure, stimulate reactive oxygen species (ROS) production, stress-related phytohormone accumulation and activate defense and stress genes in the roots and/or shoots. Once a physical contact is established, the stomata re-open, ROS and phytohormone levels decline, and the gene expression pattern indicates a shift from defense to mutualistic interaction.
We propose that exudated compounds from P. indica induce stress and defense responses in the host. Root colonization results in the downregulation of defense responses and the activation of genes involved in promoting plant growth, metabolism and performance.

overall_design: Twelve day-old (48 h cold treatment and 10 days of illumination) Arabidopsis seedlings of equal sizes were selected for co-cultivation experiments. They were transferred to PNM plates with a nylone membrane on the top (Johnson et al. 2011) and exposed to a fungal plug 5 mm in diameter or a KM plug of the same size without fungal hyphae (control). The plugs were placed 3 cm away from the closest root part . The light intensity (80 ± 5 μmol m-2 sec-1) was checked every third day to ensure that both P. indica- and mock-treated seedlings receive equal amounts of light.

first: Khabat

last: Vahabi


title: Mouse embryonic fibroblasts (MEFs) : AK156230 knockdown cells vs control cells

status: Public on May 25 2016

city: Dongguan

first: Yu-ning

last: Chen

address: Xin Cheng Avenue 1#, Songshan Lake

institute: Guangdong Medical University

summary: mRNAs expression profile of  MEFs comparing AK156230 knockdown cells with control cells. The microarray with coverage of 45038 mouse mRNAs.

overall_design: In the study presented here, AK156230 knockdown MEFs and control MEFs were selected for RNA extraction and hybridization on Affymetrix microarrays.

first: Meng-yun

last: Cai

first: Shun

last: Xu

first: Mei

last: Meng

first: Xingcong

last: Ren

first: Jay

middle: W

last: Yang

first: Yu-qi

last: Dong

first: Xinguang

last: Liu

first: Jin-Ming

first: Xing-dong

last: Xiong


title: Transcriptomics of Neisseria gonorrhoeae

status: Public on May 24 2016

city: Kingston upon Thames

first: Lori

last: Snyder

address: Penrhyn Road

department: School of Life Sciences, Pharmacy, and Chemistry

institute: Kingston University

summary: The overall goals and objectives of this study are to investigate the transcriptomics of Neisseria gonorrhoeae using RNA-seq. This work will look at gene expression, start points of transcription, transcriptional termination, and differences between these in different conditions and between strains and growing cultures over time.

overall_design: The starting baseline for this study is Neisseria gonorrhoeae strain NCCP11945, minimally passaged since it was genome sequenced, grown at 37C in 5% CO2. All other experiments would be based off of this, both in terms of number of samples and replicates.

first: Sabrina

middle: B

last: Roberts


title: LECT2 effect on the bone marrow cells of mice

status: Public on May 20 2016

city: Ningbo

first: Zhang

last: Hao

address: Fenghua Road No. 818

institute: NINGBO UNIVERSITY

summary: Hematopoietic stem cell (HSC) is under dynamic controlled in the bone marrow to differentiate into cells of all lineages that constitute the blood. The bone marrow niches form a specific microenvironment to maintain and regulate HSC. However, the mechanisms that the effect of cytokines from blood on HSC function still remain largely unknown. Leukocyte chemotactic factor 2 (LECT2), a liver-derived cytokine, is involved in many immune dysfunctions, such as sepsis, cancer and diabetes. Here we showed that LECT2 affected the gene expression of bone marrow cells in mice. Especially, we found that LECT2 treatment for 3 and 5 days led to the down-regulation of cytokines such as, TNF, IL-6, IL-1β, CXCL10, CCL4, CCL3 et al. Moreover, the functions and mechanisms for LECT2 regulated HSC in bone marrow is still needed further investigation.

overall_design: Recombinant LECT2 was subcutaneously injected at a dose of 300 μg/kg body weight (once a day for 0, 3, or 5 days) in mice. The bone marrow cells were flushed out from femur, tibia, pelvis, and humerous in PBS.

first: Jiong

first: Xinjiang

last: Lu


title: Arabidopsis lyrata gene annotation using RNA-sequencing data

status: Public on May 17 2016

city: Olomouc - Holice

first: Ales

last: Pecinka

address: Slechtitelu 31

department: Centre of Plant Structural and Functional Genomics

country: Czech Republic

institute: Institute of Experimental Botany

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

sample_organism:
Arabidopsis thaliana
Arabidopsis lyrata subsp. lyrata

overall_design: Refer to individual Series


title: Circulating microRNAs: Association with lung function in asthma

status: Public on Jun 09 2016

city: Boston

first: Alvin

middle: T.

last: Kho

state: MA

address: 320 Longwood Avenue

department: Informatics Program

institute: Boston Children's Hospital

summary: Blood serum from 160 Childhood Asthma Management Program (CAMP) subjects were microRNA profiles with 13 subjects profiled twice. Each subject has diverse clinical phenotypes notably spirometry related phenotypes.

overall_design: Least squares linear regression was applied with subject phenotypes as the dependent variable, and microRNA Ct values (data matrix quantile normalized) as the independent variable to identify significant associations between subject phenotype and microRNA abundance.

middle: T

first: Sunita

last: Sharma

first: Joshua

middle: S

last: Davis

first: Joseph

last: Spina

first: Dagnie

last: Howard

first: Kevin

last: McEnroy

first: Kip

last: Moore

first: Jody

last: Sylvia

first: Scott

last: Weiss

first: Kelan

last: Tantisira


title: Gene expression profile of F4/80+ cells isolated from tumors implanted in wild type and St2-/- mouse

status: Public on May 03 2016

city: Stockholm

first: Hiromasa

last: Morikawa

state: Stockholms

address: Karolinska University Hospital, L8:05

department: Medicine

institute: Karolinska Institutet

summary: We report a novel mechanism of the interaction between perivascular cell and TAMs in promoting metastasis through the IL-33-ST2-dependent pathway. IL-33 was the highest up-regulated gene through activation of SOX7 transcription factor in PDGF-BB-stimulated pericytes. Gain- and loss-of-function experiments validate that IL-33 promotes metastasis through recruitment of TAMs. Il33-/- deficient mice showed impaired TAM recruitment and metastasis. Pharmacological inhibition of the IL-33-ST2 signalling by a soluble ST2 significantly inhibited TAMs and metastasis. Genetic deletion of host IL-33 in mice also blocked PDGF-BB-induced TAM recruitment and metastasis. High IL-33 in human cancers correlated with poor survival prognosis. These findings shed novel mechanisms of tumour stroma in promoting metastasis and have therapeutic implications for cancer therapy.

overall_design: F4/80+ cells are isolated from tumors implanted in wild type and St2-/- mouse (n=3 samples/group)

first: Yunlong

last: Yang

first: Yihai

last: Cao


title: SpermBase - A database for sperm-borne RNA contents

status: Public on May 07 2016

city: reno

first: Wei

last: Yan

state: NV

address: 1664 N. Virginia Street

department: Physiology

institute: University of Nevada

type: Non-coding RNA profiling by high throughput sequencing

summary:
Purpose: Sperm-borne RNA are particularly sensitive to degradation and methodology-induced bias, thus necessitating the use of a consistent, effective RNA extraction protocol for inter-species comparisons. To this end, we established SpermBase, an RNA expression database consisting of small and large RNA expression data obtained using consistent methodologies.
Methods: Total RNA was extracted from total sperm and sperm head samples using an RNA extraction protocol that required only slight, species-specific alterations at the lysis stage. Total RNA was subjected to either RNA-Seq (large RNA) or sncRNA-Seq (small RNA).
Results: By using a consistent methodology, we were able to perform a cross-species analysis on the conserved features of large and small sperm-borne RNAs. We identified conserved features in both populations of RNAs in the four mammalian species (i.e., mouse, rabbit, rat, and human) surveyed.
Conclusions: Our study demonstrates an effective, near-universal approach to the study of sperm-borne RNAs, and identifies conserved characteristics in the large and small RNA populations of mammalian sperm.

sample_organism:
Homo sapiens
Oryctolagus cuniculus
Mus musculus
Rattus norvegicus

overall_design: Total RNA was extracted from total sperm and sperm head samples and subjected to sncRNA-Seq or RNA-Seq.

first: Andrew

last: Schuster

first: Chong

last: Tang

first: Tian

last: Yu


title: DNA methylation analysis of paediatric pilocytic and diffuse astrocytomas

status: Public on May 10 2016

city: London

first: Denise

last: Sheer

address: Blizard Institute, 4 Newark Street

department: Neuroscience & Trauma

institute: Barts & The London School of Medicine & Dentistry

summary: Paediatric low-grade gliomas (LGGs) account for about a third of all brain tumours in children. We conducted a detailed study of DNA methylation to improve our understanding of the biology of pilocytic and diffuse astrocytomas. Comparisons were performed between tumours and normal brain controls from matching location, and between pilocytic and diffuse astrocytomas. Pilocytic astrocytomas were found to have a distinctive signature involving 315 CpG sites, with the majority of the sites (312 CpG sites) hypomethylated in pilocytic astrocytomas. Additionally many of the sites were located within annotated enhancers. The distinct signature in pilocytic astrocytomas was not present in diffuse astrocytomas or in published profiles of other brain tumours and normal brain tissue. On further analysis of the 315 CpG sites, the AP-1 transcription factor complex was predicted to bind within 200bp of a subset of teh 315 differentially methylated CpG sites. We also observed up-regulation of the AP-1 factors, FOS and FOSL1 in pilocytic astrocytomas. Our findings highlight novel epigenetic differences between pilocytic and diffuse astrocytomas, in addition to well-described alterations involving BRAF, MYB and FGFR1.

overall_design: Genomic DNA from frozen tumour material was bisulphite converted and analysed using Illumina Infinium HumanMethylation 450K arrays. Pre-processing was performed using genome studio. Statistical approaches were used to identify differential methylation patterns between 17 pilocytic astrocytoma, 10 diffuse astrocytoma  and normal brain controls (1 foetal brain, 1 adult brain, 1 foetal cerebellum, 1 foetal frontal lobe and ReN VM Neural Stem Cell-line).

first: Jennie

middle: N

last: Jeyapalan

first: Gabriel

last: Doctor

first: Tania

last: Jones

first: Samuel

last: Alberman

first: Alexander

last: Tep

first: Chirag

last: Haria

first: Ed

middle: C

last: Schwalbe

first: Isabel

last: Morley

first: Alfred

last: Hill

first: Magdalena

last: LeCain

first: Diego

last: Ottaviani

first: Steven

last: Clifford

first: Ibrahim

last: Qaddoumi

first: Ruth

middle: G

last: Tatevossian

first: David

last: Ellison


title: Transcriptomic profilling of sweet basil (Ocimum basilicum) downy mildew (Peronospora belbahrii) infection

status: Public on Apr 30 2016

city: Xi'an

first: Li

last: Guo

state: Shaanxi

address: 28 Xianning West Road

institute: Xi'an Jiao Tong University

summary: Applying a metatranscriptomic analysis pipeline (Guo et al. 2016 Frontiers in Plant Science), we are the first to analyze the host-pathogen metatranscriptome of the basil downy mildew system. RNA-sequencing technology was utilized to gain access to the full array of expressed transcripts from both O. basilicum and P. belbahrii. This RNA-seq workflow has allowed us to identity nearly 3,000 candidate P. belbahrii genes expressed in planta, as well as 1,267 and 2,798 candidate O. basilicum genes induced or suppressed respectively under P. belbahrii infection (five days post inoculation). Up-regulated candidate genes are highly enriched for biological processes such as biotic and abiotic stress responses whereas down-regulated genes are enriched for metabolism and photosynthesis, suggesting that basil plants actively respond to pathogen infection with transcriptome reprogramming.

sample_organism:
Ocimum basilicum
Peronospora belbahrii

platform_organism:
Ocimum basilicum
Peronospora belbahrii

overall_design: RNAseq data were generated from O. basilicum plants either uninfected or infected with P. belbahrii at 5 days post inoculation.

first: Li-Jun

last: Ma


title: Role of MPL expression in determining heterogeneity of leukemia-initiating capacity of chronic myelogenous leukemia stem cells

city: Duarte

first: Xiwei

last: Wu

state: CA

address: 1500 E Duarte Rd

department: Molecular and Cellular Biology

institute: Beckman Research Institute

summary: Using a CML mouse model, we identified differences in gene expression between leukemic compared with non-leukemic LTHSC, including increased expression of the thrombopoietin (THPO) receptor MPL. LTHSC expressing high levels of MPL showed enhanced JAK/STAT signaling and proliferation in response to THPO in vitro, and increased leukemogenic capacity in vivo compared to LTHSC with low MPL expression. Although both G0 and S-phase subpopulations were increased in MPL expressing LTHSC, LSC capacity was restricted to quiescent cells. Inhibition of MPL expression in CML LTHSC resulted in reduced THPO-induced JAK/STAT signaling and leukemogenic potential. Similar observations were made with LTHSC from CML patients. MPL expressing LTHSC demonstrated reduced sensitivity to BCR-ABL TKI treatment but demonstrated increased sensitivity to JAK inhibitors. Our studies identify MPL expression levels as a key determinant of heterogeneous leukemia-initiating capacity and drug sensitivity of CML LTHSC, and suggest that MPL-expressing CML stem cells are critical targets for therapy.

overall_design: To evaluate heterogeneity in LSC potential, donor LTHSC from SCL-tTA/BCR-ABL mice (200 cells/mouse) were transplanted into a cohort of congenic FVBN mice. Recipient mice were followed for engraftment of donor CML cells and development of CML. LTHSCs  were isolated from leukemic and non-leukemic recipient mice and global gene expression was analyzed using RNA-Seq.

first: Ravi

last: Bhatia

first: Bin

last: Zhang


title: A simple screening approach to prioritize genes for functional analysis identifies a role for IRF7 in the control of RSV disease.

first: Myrsini

last: Kaforou

address: Norfolk Place

institute: Imperial College London

summary: Genome-wide analysis of transcriptional profiles in children <17 years of age with RSV infection and healthy controls

overall_design: Patients with RSV were recruited at or after presentation to hospital. Main inclusion criteria were presence of illness of sufficient severity to warrant blood tests for clinical reasons, in child aged <17 years. All patients had an illness consistent with RSV infection, with microbiological findings to match. Blood was collected into PAX gene tubes (PreAnalytiX). Total RNA integrity was assessed using an Agilent 2100 Bioanalyzer (Agilent, Palo Alto, CA). Labeled cRNA was hybridized to Illumina Human HT-12 v4 Beadchips. Numbers of arrays analysed were as follows: RSV infection (n=27), Healthy controls (n=52).

first: J

last: Herberg

first: M

last: Levin

first: V

last: Wright


title: Gene expression data from epididymal fat of A/J mouse and A/J-12SM consomic mouse

city: Nagoya

first: Misato

last: Kobayashi

state: Aichi

address: Furo-cho, Chikusa-ku

department: Graduate School of Bioagricultural Sciences

institute: Nagoya University

summary:
SMXA-5 mouse shows a high-fat induced fatty liver. The QTL for fatty liver was mapped on mouse chromosome 12, designated as Fl1sa. The liver weight and liver triglyceride content of A/J-12SM consomic mouse was lower than that of A/J mouse.
In contrast, the epididymal fat weight tended to be higher in A/J-12SM consomic mouse than that in A/J. We compared the epididymal fat's gene expressions between A/J mouse and A/J-12SM consomic mouse.

overall_design: Total RNA of male A/J mice and A/J-12SM consomic mice fed a high-fat diet for 7 weeks were extracted from epididymal fat of three mice. The RNAs form three mice were pooled and hybridized on one Affymetrix microarry.

first: Miyako

last: Suzuki

first: Atsushi

last: Murai

first: Fumihiko

last: Horio


title: Analysis of gene expression patterns of Arabidopsis roots grown in methyl jasmonate (MeJA), cytokinin (CK), MeJA/CK- treated conditions

status: Public on Jul 30 2016

city: Seoul

first: TAEYOUNG

last: UM

address: Daehak-dong, Gwanak-gu

department: College of Agriculture Sciences

institute: SEOUL NATIONAL UNIVERSITY

summary: Purpose: Understanding of MeJA, CK effect on regulation of gene expression patterns in Arabidopsis roots

overall_design: Total mRNA was extracted from 7-day-old Arabidopsis roots grown in MeJA (10uM), CK (50nM) and MeJA/CK-treated conditions. To generate cDNA libraries with TruSeq RNA library kit, 1 μg of total RNA was used. This step consisted of polyA-selected RNA extraction, RNA fragmentation, random hexamer primed reverse transcription and 100 nt paired-end sequencing by Illumina HiSeq2000. 4,403 genes satisfying |fold change|≥2 in at least one data set were collected.

first: Geupil

last: Jang

first: Sun

last: Chang

first: Tae

last: Um

first: Yang

middle: D

last: Choi


title: Associations with early life socio-economic position in adult DNA methylation

city: Montreal

first: Moshe

last: Szyf

state: Quebec

address: McIntyre Medical Building, 3655 Promenade Sir William Osler, Room 1309

department: Pharmacology

country: Canada

institute: McGill University

summary:
Comparison of whole blood DNA methylation in 45 year-old humans with low and high childhood and adulthood socio-economic position

Background: Disadvantaged socio-economic position (SEP) in childhood is associated with increased adult mortality and morbidity. We aimed to establish whether childhood SEP was associated with differential methylation of adult DNA.

Methods: Forty adult males from the 1958 British Birth Cohort Study were selected from SEP extremes in both early childhood and mid-adulthood. We performed genome-wide methylation analysis on blood DNA taken at 45y using MeDIP (methylated DNA immunoprecipitation).  We mapped in triplicate the methylation state of promoters of ~20,000 genes and 400 microRNAs. Probe methylation scores were averaged across triplicates and differential methylation between groups of individuals was determined. Differentially methylated promoter sites of selected genes were validated using pyrosequencing of bisulfite-converted DNA.

Results: 9,112 variably methylated probes (from N=223,359 on the microarray) corresponded to 6,176 gene promoters with at least one variable probe. Unsupervised hierarchical clustering of probes obtained from the 500 most variable promoters revealed a cluster enriched with high SEP individuals confirming that SEP differences contribute to overall epigenetic variation. Methylation levels for 1252 gene promoters were associated with childhood SEP vs 545 promoters for adulthood SEP. Functionally, associations with childhood SEP appear in promoters of genes enriched in key cell signalling pathways.  The differentially methylated promoters associated with SEP cluster in megabase-sized regions of the genome.

Conclusions: Adult blood DNA methylation profiles show more associations with childhood SEP than adult SEP. Organization of these associations across the genome suggests a well-defined epigenetic pattern linked to early socio-economic environment.

overall_design: Forty adult males from the 1958 British Birth Cohort Study were selected from SEP extremes in both early childhood and mid-adulthood. We performed genome-wide methylation analysis on blood DNA taken at 45y using MeDIP (methylated DNA immunoprecipitation) with custom-designed microarrays.  Probes on the microarrays were selected to tile from -1000bp to +250bp of each transcription start site.  Methylation profiles were generated in triplicate.

first: Nada

last: Borghol

first: Matthew

last: Suderman

first: Wendy

last: McArdle

first: Ariane

last: Racine

first: Michael

last: Hallett

first: Marcus

last: Pembrey

first: Clyde

last: Hertzman

first: Chris

last: Power


title: Differential gene expression profiling of resting Vs proliferating Treg cells from NOD mice G-BMDC-T-cell co-cultures

status: Public on May 04 2016

city: Chiciago

first: Prabhakaran

last: Kumar

state: Illinois

address: 835 S Wolcott Ave.

department: Microbiology and Immunology

institute: UIC

summary:
Resting and proliferating Treg cells from NOD mice G-BMDC-Treg co-cultures were sorted out and anlyzed for differential gene expresion pattern.
Proliferating Treg cells had increased expression of )X40, Notch and IL-2R related genes inaddition to Foxp3 and its functional partners genes.

overall_design: Resting Vs prolifrating Treg cells.

first: Palash

last: Bhattacharya

first: Khaled

last: Alharshwi

first: Alejandra

last: Malinelerana

first: Bellur

last: Prabhakar