title: Expression data from two weeks old Arabidopsis wild-type (Columbia-0) and transgenic plant overexpressing NHRGP (at4g16790) plants (OE-N6)

status: Public on Dec 30 2017

city: Guiyang

first: Xiaozhen

last: Huang

state: Guizhou

address: South campus of Guizhou University, Huaxi, Guiyang

country: China

institute: Guizhou University

summary:
Microarray assays can facilitate elucidation of cellular processes and gene network functions in the processes of plant growth and development. To gain further insight into the potential molecular role of the NHRGP gene, we performed Affymetrix whole-genome microarray analysis (http://www.affymetrix.com/) on WT and OE-N6 plants to compare their genome-wide expression profiles.
The differently expressed genes revealed by transcriptional profiling of an HRGP-overexpressing transgenic plant indicate that NHRGP are involved in defense response.

overall_design: Total RNAs were extracted using the Plant RNA Prep Kit (Qiagen, Hilden, Germany) from 2-week-old seedlings of the wild-type and OE-N6 grown on 1/2 MS medium containing 2% sucrose at 22˚C under a 16-h light/8-h dark photoperiod at 100 μmol m–2 s–1. 6μg of total RNA was used to synthesize biotin-labeled cDNA, which was then hybridized with the ATH1 oligonucleotide chips as instructed by the manufacturer (Affymetrix).


title: Systems analysis identifies melanoma-enriched pro-oncogenic networks controlled by the RNA binding protein CELF1

status: Public on Dec 22 2017

city: barcelona

first: BELEN

last: MINANA

state: barcelona

address: dr aiguader 88

department: GENE REGULATION, STEM CELLS AND CANCER

country: Spain

institute: Center for genomic regulation

summary: Melanomas are well-known for their altered mRNA expression profiles. Yet, the specific contribution of mRNA binding proteins (mRBPs) to melanoma development remains unclear. Here we identify a cluster of melanoma-enriched genes under the control of CUGBP Elav-like family member 1 (CELF1). CELF1 was discovered with a distinct prognostic value in melanoma after mining the genomic landscape of the 692 known mRBPs across different cancer types. Genome-wide transcriptomic, proteomic, and RNA-immunoprecipitation studies, together with loss-of-function analyses in cell lines, and histopathological evaluation in clinical biopsies, revealed an intricate repertoire of CELF1-RNA interactors with minimal overlap with other malignancies. This systems approach uncovered the oncogene DEK as an unexpected target and downstream effector of CELF1. Importantly, CELF1 and DEK were found to represent early-induced melanoma genes and adverse indicators of overall patient survival. These results underscore novel roles of CELF1 in melanoma, illustrating tumor type-restricted functions of RBPs in cancer.

overall_design: Three biological replicates were labeled in direct and dye-swap microarray experiments and hybridized onto an Agilent custom splicing-sensitive microarray platform. The pool of melanocytes was compared to cell line SK-Mel-103 (#9) or SK-Mel-19 (#3) respectively.

first: Belén

last: Miñana

first: Metehan

last: Cifdaloz

first: Lisa

last: Osterloh

first: Marisol

last: Soengas

first: Juan

last: Valcárcel


title: MicroRNA expression in male rat hepatocytes and liver sinusoidal endothelial cells (LSECs)

status: Public on Dec 11 2017

city: Kamakura

first: Satoshi

last: Kondo

state: Kanagawa

address: 10-1 tebiro 6-chome

country: Japan

institute: Toray Industries,Inc.

summary: We determined the microRNA expression profiles of the hepatocytes and liver sinusoidal endothelial cells (LSECs) isolated from nontreated rats.

overall_design: MiRNA expression in rat hepatocytes and LSECs was measured.  There were two replicates for each cell type.

first: Shingo

last: Oda

first: Tsuyoshi

last: Yokoi


title: Identification of genes expressed by spinal cord neurons after axotomy and during axon regeneration

status: Public on Dec 10 2017

city: London

first: Lawrence

middle: DF

last: Moon

address: 16 - 18 Newcomen Street

department: Wolfson Centre for Age-Related Diseases

country: United Kingdom

institute: King's College London

summary:
Abstract to follow
Keywords: Regeneration, CNS, neuron, spinal, axon, SCI, axotomy

overall_design:
7 regenerating (Reg), 7 non regenerating (NonReg) and 3 traced, not axotomised (NonAxot) samples of spinal neurons obtained by laser microdissection.

7 rats provided regenerating (Reg) and non-regenerating (NonReg) neurons, allowing within-animal comparison to identify regeneration-associated genes.

3 rats provided traced neurons (NonAxot), allowing between-animal comparison between traced and non-regenerating neurons to identify axotomy-related genes.

Each sample, 1000 laser captured, retrogradely labeled spinal cord neurons.

middle: D

first: Mary

middle: B

last: Bunge

first: Fred

middle: H

last: Gage

first: John

last: Bixby

first: Carol

middle: K

last: Petito

first: Jorge

last: Torres

first: Vance

last: Lemmon

first: Ronald

last: van Kesteren


title: Presenilins mediate endosomal recycling via ARF6 to maintain proper lysosomal clearance

status: Public on Dec 15 2017

city: Leuven

first: Rekin's

last: Janky

address: Herestraat 49 Box 816

department: Nucleomics Core

country: Belgium

institute: VIB

summary: Autophagic and endosomal dysfunctions are prominently observed at preclinical stages of Alzheimer's disease (AD) as well as in presenilin (PSEN) 1-deficient mice and neurons. In the latter, the defects relate to the γ-secretase-independent role of PSEN in lysosomal fusion and organelle turnover. While we demonstrated previously that the impaired capacity of lysosomal fusion is associated with a significant reduction in lysosomal calcium storage/release, the underlying mechanism remained unexplored. Here we demonstrate that PSEN-deficient cells are impaired in endosomal recycling of several cargo proteins reminiscent of clathrin-independent carriers and lipid rafts. This is accompanied by the accumulation of cholesterol in LAMP1-positive organelles. The small GTPase ARF6, an important regulator of lipid raft recycling, fully rescues the endo-lysosomal abnormalities in PSEN-/- cells, suggesting that defective recycling is upstream of lysosomal dysfunction. PSEN-/- cells and neurons present significantly reduced ARF6 expression levels. Importantly, similar decreased ARF6 levels are observed in aging murine neurons and brain and are even more pronounced in AD brains, suggesting a particular vulnerability of ARF6-mediated recycling in the early etiology of AD.

overall_design: 4 cell lines were analyzed from 3 biological replicates. These samples include MEF wild-type, MEF PSEN1&2-/-, MEF PSEN1&2-/- retrovirally transduced with hARF6, and MEF PSEN1&2-/- retrovirally transduced with hPSEN1 D257A/D385A mutant.

first: Katrijn

last: Coen

first: Sebastian

last: Munck

first: Arun

last: Raghunath

first: Tim

last: Raemaekers

first: Wendy

last: Vermeire

middle: S

last: Flannagan

first: Ilse

last: Declerck

first: Veerle

last: Baert

first: Sergio

last: Grinstein

first: Frank

last: Wuytack

first: André

last: Delacourte

last: Rajendran

first: Eeva-Liisa

last: Eskelinen

first: Kris

last: Gevaert

first: Wim

last: Annaert


title: Gene expression changes in neonatal and adult plasmacytoid dendritic cells (pDC) upon TLR7/8 stimulation

status: Public on Dec 21 2017

city: Vancouver

first: Edgardo

last: Fortuno III

state: BC

department: Paediatrics

country: Canada

institute: Child & Family Research Institute - University of British Columbia

summary: We want to define the differences in gene expression changes between neonatal and adult plasmacytoid dendritic cells upon stimulation with TLR7/8.  These differences may point to specific signaling pathways which, in turn, may account for the known differential immune response of babies to vaccination or infection when compared to adults.

overall_design: Total RNA obtained from MACS-purified human pDC (using Miltenyi's Diamond Plasmacytoid Cell Isolation Kit) stimulated with the synthetic TLR7/8 ligand 3M-003 for 1 or 6 hours in vitro compared to unstimulated pDC.


title: Temporal analysis of hippocampal gene co-expression networks in the hyperthermia model of febrile seizures

status: Public on Dec 20 2017

city: São Paulo

first: Hatylas

last: Azevedo

state: Sao Paulo

address: Doutor Arnaldo Avenue, 455

department: Pediatrics

country: Brazil

institute: University of São Paulo

summary: This study sought to investigate temporal changes in hippocampal gene co-expression networks during the development of rats submitted to hyperthermic seizures

overall_design: Total RNA was obtained from the rat ventral hippocampal CA3 region at four time points after HS and then subjected to oligonucleotide microarray profiling. Rat pups (n = 6-8 per group and time period) were divided into two groups: controls (CTRL) and animals submitted to hyperthermia-induced seizures (HS). The temporal endpoints were selected to investigate the acute (P12), latent (P30 and P60) and chronic (P120) stages of the animal model. A weighted gene co-expression network analysis was employed to investigate modules of co-expressed genes, as these genes may be associated to common biological functions. Differentially expressed genes were determined between the hyperthermic seizures group and the normothermic controls for each time interval.

first: Nathalia

last: Khaled

first: Paula

last: Santos

first: Fernanda

last: Bertonha

first: Carlos

middle: A

last: Moreira-Filho


title: Calcium-mediated shaping of naive CD4 T cell phenotype and function

status: Public on Dec 28 2017

city: Paris

first: Franck

last: Letourneur

address: 22 rue mechain

country: France

institute: INSERM

summary: Continuous contact with self-major histocompatibility complex ligands is essential for the survival of naive CD4 T cells. We have previously shown that the resulting tonic TCR signaling also influences their fate upon activation by increasing their ability to differentiate into induced regulatory T cells. To decipher the molecular mechanisms governing this process, microarray data comparing highly (Ly-6C-) and lowly (Ly-6C+) Self-reactive naive CD4 T cells were obtained.

overall_design: CD4 T cells from LNs of C57BL/6 Foxp3-GFP mice were purified by using Dynabeads Untouched Mouse CD4 Cells Kit (Invitrogen). Then, Ly-6C- and Ly-6C+ CD4 TN cells were flow-cytometry sorted as CD4+ CD8α- TCRβ+ GFP- CD25- CD44-/lo cells using a FACS-ARIA3 flow cytometer.

first: Vincent

last: Guichard

first: Nelly

last: Bonilla

first: Aurelie

last: Durand

first: Alexandra

last: Audemard-Verger

first: Thomas

last: Guilbert

first: Bruno

last: Martin

last: Lucas

first: Cedric

last: Auffray


title: Expression analysis of Aedes aegypti starins Moyo-S and Moyo-R in response to different serotypes of dengue virus

city: Columbia

first: Susanta

middle: K.

last: Behura

state: Missouri

address: 920 East Campus Drive

department: Division of Animal Sciences

country: USA

institute: Univeristy of Missouri

summary:
Investigation of whole genome gene expression level changes in Moyo-S and Moyo-R strains of Aedes aegypti after oral infection of serotype 1, serotype 2, serotype 3 and serotype 4 of dengue virus
The Moyo-S is highly suscpetible to dengue infection whereas Moyo-R is refractory to the dengue infection. They have been investigated in our previous studies incluidng Behura et al. (2011). PLoS neglected tropical diseases 5 (11), e1385; and Chauhan et al. (2012). PloS one 7 (10), e47350.

overall_design: This is a 12-plex high defination NimbleGen array design. Two strains of Aedes aegypti (Moyo-S and Moyo-R) were investigated afteral orally feeding the females with blood meal contamianted with different serotypes (n =4) of dengue virus. Expression levels of Aedes aegypti genes were measured at two post-infection time points 3hour and 18hour. Uninfected control (blood fed only, no dengue) were prepared for each time point for both Moyo-S and Moyo-R. Each control and test sample was derived from three independent feeding experiments. Hybiridization was done in two batches. In the first batch, 12 sample (4 control and 8 test samples) representing infection material with two serotypes were used. In the second batch, the same procedure was used but for the other two serotypes of dengue virus. Hence, a total of 24 samples were used for hybridization.

first: S

first: D

middle: W

last: Severson


title: microRNA expression in primary murine Alveolar type II cells under Normoxia 21% O2 and Hyperoxia 85% O2 after 6 hours and 24 hours

status: Public on Dec 16 2017

city: Bad Nauheim

first: Rory

last: Morty

address: Parkstr. 1

department: W.G. Kerckhoff-Institut

country: Germany

institute: MPI für Herz- und Lungenforschung

summary: In this study the microRNA expression of primary murine (C57BL/6) lung alveolar type II cells belonging to four different conditions was analyzed. Effects of hyperoxia 24 hours group were compared to the normoxia 24 hours and effects of the hyperoxia 6 hours group were compared to the normoxia 6 hours.

first: Elpidoforos

last: Sakkas

middle: E


title: Breast tumor subtypes correlate with prognosis

status: Public on Dec 31 2017

first: BELEN

last: MINANA

summary:
To advance in our understanding of the biological pathways involved in breast cancer tumor progression we have analyzed a set of breast tumor biopsies in order to identify the genomic pathways in which tumor may develop. With this objective, a cDNA microarray platform containing 800 genes was constructed. These genes were chosen because they are in several representatives signaling pathways, namely estrogen and progesterone receptor related pathways, cell cycle, DNA repair, chromatin remodeling, cell proliferation, apoptosis, cell adhesion, cell invasion and angiogenesis. An analysis of the gene expression profile of a large group of breast tumors was carried out and good correlation with their clinical-histopathological data was obtained. We identified different tumor subclusters with distinctive phenotype characteristics within our population, which later correlated with clinical outcome. The most significant genes able to discriminate between different tumor phenotypes of our training set of samples were determined applying a “Leave-one-out” cross-validation method of statistical analysis called PAM (Prediction analysis of microarrays). The predictor was further tested on a new incoming set of samples where we determined to which subtype of tumor new samples were allocated and predicted outcome was compared to clinical data, showing how some distinct tumor phenotypes correlate with a poor prognosis. Pathway analysis of the most significant genes belonging to each phenotype was performed to elucidate the most representative biological signaling pathways through which tumor progression might elapse.
We constructed a real time expression profiling platform with a selection of the most differentially expressed genes in each subtype, which could be used as a technique to help improve the diagnosis and prognosis of the breast tumor samples of our sample population.

overall_design:
A set of 105 breast tumor tissue samples and 6 from normal breast tissue adjacent to tumors of different individuals were amplified, labeled and hybridized, as described in the methods to our cDNA platform. Universal human reference RNA (UHRR) was used as reference RNA.
Breast tumor samples were labeled with Cy5 and the universal human reference RNA was labeled with Cy3. There are no dye-swaps.

first: Belen

last: Minana


title: Global gene expression analysis of vascular progenitors differentiated from human embryonic stem cells or induced pluripotent stem cells and their corresponding donor starting cells

city: Baltimore

first: Elias

middle: Thomas

last: Zambidis

state: MD

address: 733 N. Broadway

department: Oncology

institute: Johns Hopkins School of Medicine

summary: Global gene expression analysis of CD31+ / CD146 +/- vascular progenitors (VP) derived from (a) human embryonic stem cells (VP-hESC), (b) adult fibroblast derived induced pluripotent stem cells (VP-AdF-iPSC), and (c) stromal primed cord blood CD34+ myeloid progenitor derived iPSC (VP-sp-CB-iPSC), (d) corresponding iPSC, and (e) corresponding starting fibroblasts and myeloid progenitors.

overall_design: Total RNA was harvested from (a) adult fibroblasts, (b) human myeloid progenitors: Non-nucloefected CD34+ CB cells that were expanded with growth factors from Day -3, and co-cultured with bone marrow stromal cells (BMSC) from Day 0 until Day+3. CD45+ myeloid progenitors were FACS-purified on Day +3 (c) FACS-purified CD31+ CD146 +/- vascular progenitors (VP) that were differentiated from human embryonic stem cells (hESC), (d) VP differentiated from low passage stromal-primed 7-factor episomal iPSC derived from growth-factor activated cord blood myeloid progenitors, and (e) VP differentiated from 4 factor viral construct iPSC derived from adult fibroblasts. Illumina HumanHT-12 V4.0 expression beadchips were used for all analyses in this series. Three independent samples of each condition were each run on individual microarrays.

first: Tea

last: Park

first: Jeffrey

last: Huo

first: Ludovic

last: Zimmerlin

first: C

middle: C

last: Talbot

first: Wayne

last: Yu

first: Karan

last: Verma

first: Ann

last: Peters

middle: T


title: PGS: penalized generalized estimating equations with grid search for epigenome-wide multiple measurement study

city: Chicago

first: Yinan

last: Zheng

state: Illinois

address: 680 N Lake Shore Drive, Suite 1400

department: Department of Preventive Medicine

institute: Northwestern University

summary:
Motivation: The need of identifying genetic determinants that disclose the heritability of complex traits as well as pinpoint causative genetic effects in some complex diseases has propelled large-scale, systematic fashion bred epigenome-wide studies. With the very dynamic nature of epigenome and much reduced cost in microarray and sequencing experiments, more and more researchers are now studying epigenomic at multiple time points, i.e. multiple measurement and/or longitudinal study design. However, the popular site-by-site multiple testing as commonly used in genome-wide studies may impair the value of multiple measurements because it leads to underpowered analyses by ignoring the inherent dependent structure, which has called for new methods to address the statistical challenges.
Results: We have proposed a penalized regression model incorporating with grid search method (PGS), for analyzing epigenome-wide multiple measurement data. The development of this analytical framework was motivated by a real-world micro RNA dataset. Comparisons between PGS and the site-by-site testing approach reveal that PGS provides smaller phenotype prediction errors and higher enrichment of phenotype-related biological pathway than the site-by-site testing approach. Our approach is also useful for epigenome-wide data of DNA methylation and histone modifications.

overall_design: The Beijing Truck Driver Air Pollution Study (BTDAS), conducted between June 15 and July 27, 2008, included participants with high exposure to air pollution in Beijing. All participants were examined on two separate examination days with 1-2 week intervals. Detailed study design and data measurements were described previously (Hou, et al., 2011). Lung function was quantified by forced expiratory volume in 1 second (FEV1) on both examination days. Total RNA was extracted from peripheral blood collected from each participant on both examination days.

first: Fei

last: Zhe

first: Wei

last: Zhang

first: Justin

last: Starren

first: Lei

last: Liu

first: Andrea

last: Baccarelli

first: Yi

last: Li

first: Lifang

last: Hou


title: Gene Expression Analysis of Fat Body of Drosophila melnaogaster subjected to Dietary restriction for certain time points

city: Kiel

first: Christine

last: Fink

address: Am Botanischen Garten 1-9

department: Zoological Institute

institute: Kiel University

summary: Dietary restriction is a nutritional intervention that consistently increases life span in animals. To identify alternative, more acceptable nutritional regimes that nevertheless extend life span, we used the fruit fly Drosophila melanogaster as a model. We tested if weekly recurring nutritional regimes composed of phases of ad libitum feeding and dietary restriction can increase life span. Short periods of dietary restriction (up to 2 days) followed by longer ad libitum phases increased life span only marginally, whereas regimes comprising longer contiguous periods (3 days and more) became clearly positive, reaching similar life span extensions as those seen if dietary restriction was applied persistently. Female flies were substantially more responsive to these interventions than males. The finding that a minimal period of 3-4 days of dietary restriction is required to induce robust life span extensions was mirrored by the observation that substantial physiological and transcriptional changes occurred in a similar temporal pattern. Moreover, these dietary restriction induced changes were also detectable after switching to ad libitum feeding. Among the physiological changes induced by these phases of dietary restriction, a reduced metabolic rate and a substantial and long-lasting reduction in insulin signaling were most compelling. Age associated molecular signatures comprising mechanisms that reduce insulin signaling showed up after longer periods of dietary restriction in the fly’s fat body, thus showing how molecular alterations transduce into life span related physiological changes.

overall_design: 6 groups of samples types were included in the experiment: manually isolated fat bodies from a) females subjected to dietary restriction for 1d, b) subjected to dietary restriction for 3d, c) subjected to dietary restriction for 7d and the matching controls subjected to control diets.

first: Thomas

last: Roeder


title: Gene and microRNA expression profiling of patients affected by first acute myocardial infarction (FAMI)

city: Padova

first: Gerolamo

last: Lanfranchi

address: Via U. Bassi, 58/B

department: CRIBI - Biotechnology Center and Biology Department

country: Italy

institute: University of Padova

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: microRNA expression profiling of patients affected by first acute myocardial infarction (FAMI)

summary:
Background: Myocardial infarction (MI) is the single most critical event in coronary disease. Platelets partecipate in processes that precipitate acute MI, lack nuclear DNA but retain megakaryocyte mRNAs, thus their transcriptome could provide information preceding the coronary event. Our aim was to obtain a gene expression atlas of platelets from patients with their very first acute MI (FAMI) in order to identify potential markers of precipitating factors.
Methods and results: Platelets from seventeen FAMI patients and matched controls were collected and RNA and protein were purified. Expression profiles were obtained with genome-wide microarrays. Platelet-specific proteomic analysis was also performed with fluorescent DIGE separation in the same samples. Strong transcriptional down-regulation was observed in patient platelets, whereas more balanced numbers of up and down-represented proteins were found by proteomic analysis.
Conclusions: Platelet transcriptome revealed quantitative differences between FAMI patients and controls. The functional analysis deregulated mRNAs and the integration with proteomic data in platelets may suggest pre-activation of platelets and/or megakaryocytes in FAMI patients before the acute event.

overall_design: miRNA expression profiling was analysed in platelets from 4 patients with their very first acute MI (FAMI) and in 3 controls. We performed miRNA expression profiling from 200 ng of total RNA and following the miRNA Microarray System protocol v. 1.5 (Agilent Technologies).  The level of each miRNA was represented as Ln.

first: Milena

last: Bellin

first: Luisa

last: Nanni

first: Cristiano

last: De Pittà

first: Agnese

last: Viganò

first: Giuliana

last: Vallanti

first: Michele

last: Vasso

first: Diego

last: Vozzi

first: Nicole

last: Cristell

first: Domenico

last: Cianflone

first: Cecilia

last: Gelfi

first: Attilio

last: Maseri


title: Arabidopsis thaliana ecotype Columbia [Col-0]): incubated with yeast (saccharomyces cerevisiae)  vs. Control

city: Brisbane

first: chanyarat

last: Paungfoo-Lonhienne

state: QLD

address: The University of Queensland

department: Science

country: Australia

institute: The University of Queensland

summary: Transcriptional profiling of Arabidopsis incubated with yeast comparing to control (without yeast incubation).

overall_design: Two-condition experiment, yeast vs. Control. Biological replicates: 3 yeast replicates, 3 control replicates.

first: Paungfoo-Lonhienne

last: Chanyarat


title: Gene expression in Klebsiella pneumoniae

status: Public on Dec 25 2017

city: Edinburgh

first: Alasdair

last: Ivens

address: Kings Buildings

institute: Centre for Immunity, Infection and Evolution

summary: Elucidating the RamA Regulon in Klebsiella pneumoniae and the transcriptome profiles of multidrug resistant Klebsiella pneumoniae

platform_organism: Klebsiella pneumoniae subsp. pneumoniae MGH 78578

overall_design: various strains of Klebsiella pneumoniae

first: Thamarai

last: Schneiders


title: Gene expression analysis following 24h- and 48h-siRNA knockdown of transforming growth factor β receptor III (TGFBR3) in human pulmonary arterial smooth muscle cells (hPASMC).

first: Rory

last: Morty

summary: We explored the impact of siRNA-mediated knockdown of the transforming growth factor β receptor III (TGFBR3) on the gene expression in the human pulmonary arterial smooth muscle cells (hPASMC), at 24h and 48h.

overall_design: Human pulmonary arterial smooth muscle cells (hPASMC) in P5 were plated in 6-well plates and transfected with either 200nM siRNA to transforming growth factor β receptor III (TGFBR3) (Santa Cruz Biotechnology) or Scrambled control (Ambion). Total RNA was extracted at 24 and 48h timepoints with peqGOLD TOTAL RNA Kit (VWR).

first: Gero

last: Niess


title: Clinical and molecular characterization of splenic diffuse red pulp lymphomas [Agilent]

status: Public on Dec 23 2017

city: Barcelona

first: Alba

last: Navarro

address: Villaroel, 170

department: Pathology

institute: IDIBAPS - Hospital Clínic

type: Genome variation profiling by genome tiling array

summary: Deep characterization of a large series of splenic diffuse red pulp lymphomas

overall_design: Copy number analysis of Agilent 1*1M arrays was performed for 12 SDRP, with sex-matched control DNAs and without duplicates or dye-swap.

first: Sílvia

last: Beà


title: Gene expression profiling of patients affected by first acute myocardial infarction (FAMI)

first: Gerolamo

last: Lanfranchi

overall_design: We have selected a group of seventeen patients affected by their very first acute myocardial infarction (FAMI), without any sign of previous cardiovascular sufferance. Whole blood was collected within 6 hours from the acute event and freshly purified platelets were used to profile their mRNA population by DNA microarrays. We performed microarray experiments using the CodeLink Expression Bioarray System (GE Healthcare). Total RNA (1.5 µg) was amplified and biotin-labeled using the CodeLink Expression Assay Reagent Kit following the manufacturer’s protocol. Microarray data analysis identified 712 specifically modulated transcripts, out of 17,594, in FAMI patients, compared with normal controls; the majority (666) was down-regulated, and only 46 genes resulted up-regulated. The main result was that all the patients share some common mechanism that leads to a massive and statistical relevant transcript down-regulation.

first: Milena

last: Bellin

first: Luisa

last: Nanni

first: Cristiano

last: De Pittà


title: Single-cell transcriptome analysis of avian neural crest migration reveals signatures of invasion and molecular transitions

status: Public on Dec 19 2017

city: Kansas City

first: Madelaine

last: Gogol

state: MO

address: 1000 E. 50th Street

department: Computational Biology Core

institute: Stowers Institute

type: Expression profiling by high throughput sequencing


title: CUGBP1 dependent whole genome gene expression and alternative splicing in melanoma cell lines

first: Pierre

last: de la Grange

address: 29, rue du Faubourg Saint-Jacques

department: Paris Biotech Santé

institute: GenoSplice technology

summary:
We have identified CUGBP1 dependent regulation of cell cycle and DNA replication/synthesis networks in melanoma cells.
This data set we include gene expression and alternative splicing data of control and CUGBP1 depleted melanoma cell lines (SK-Mel-103 and UACC-62).

overall_design: CUGBP1 was downregulated with shRNA in two melanoma cell lines (SK-Mel-103 and UACC-62). The transcriptome was compared to control infected cells. All experiment was performed in three biological replicates.

first: Metehan

last: Cifdaloz

first: Marisol

last: Soengas


title: ChIP-chip from mouse keratinocytes with Plakoglobin and β-catenin

status: Public on Dec 01 2017

city: Berne

first: Christian

last: Strauss

address: Laengassstrasse 122

country: Switzerland

institute: Institute of Animal Pathology

type: Genome binding/occupancy profiling by array

summary:
Plakoglobin (PG; γ-Catenin, JUP) is a protein with controversial function. First described as a component of intercellular junctions, it has remained unresolved whether this near-ubiquitously expressed protein acts as a genuine transcriptional regulator in adult tissue like its closest relative β-catenin. Here we have mapped the global gene targets of PG by ChIP-chip in differentiating skin keratinocytes. Applying a peak algorithm, over 5’000 high-confidence PG target promoters were identified and 2’000 for β-catenin with an overlap of 38%.
Bioinformatics analyses most significantly associated PG target genes with the Wnt signaling pathway as well as relevant pathways for keratinocyte differentiation. Using a combination of wild-type, PG, β-catenin and PG/β-catenin double null keratinocytes, PG was functionally validated as a LEF/TCF-dependent transcriptional regulator. These data challenge the current understanding of Wnt signaling, one of the most important pathways in tissue homeostasis, by identifying PG as a potent LEF/TCF-dependent transcriptional regulator which functionally overlaps with β-catenin.

overall_design: comparison of Plakoglobin and β-catenin binding to promoters in mouse keratinocytes at the onset of terminal differentiation

first: Eliane

middle: J

last: Müller


title: Microarray expression analysis of transgenic Arabidopsis thaliana

city: Amsterdam

first: Oskar

last: Bruning

address: Science Park 904

department: SILS

country: Netherlands

institute: University of Amsterdam

summary: Comparison of expression differences between Col-0 Arabidopsis thaliana and transgenic plants in the same background carrying three different Fusarium oxysporum effector genes

overall_design: 4 biological replicates of the wildtype Col-0, 4 biological replicates of the 2 independent Avr2 lines, 3 biological replicates of the 2 independent Six6 lines, 4 biological replicates of the single Six8 line were run on microarrays, leaf material was used to isolate RNA

first: Fleur

last: Gawehns

first: Frank

middle: L

last: Takken

first: Hanna

last: Richter


title: Transcriptome-wide microRNA expression of the heart of neonatal rats with polygenic cardiac hypetrophy

city: Melbourne

first: Francine

last: Marques

state: VIC

address: Level 3, 75 Commercial Rd

institute: Baker IDI Heart and Diabetes

summary: Identification of microRNAs differentially expressed between the  neonatal heart of a genetic rat model of cardiac hypertrophy (the Hypertrophic Heart Rat, HHR) and the control (the Normal Heart Rat, NHR) using the Agilent Rat miRNA Microarray Kit Release 16.0.

overall_design: Neonatal (day 2) HHR and age-matched NHR were killed with an overdose of pentobarbitone (Lethobarb). The heart was immediately removed, and the ventricles were dissected from the atriums.  The tissues were first preserved in liquid nitrogen and later transferred to a –80C freezer. Microarrays (one per sample, with no pooling) were performed on 8 neonatal HHR (4 male, 4 female) and 8 neonatal NHR (4 male, 4 female).  After extraction of RNA, cRNA was prepared and arrays performed using Agilent Rat miRNA Microarray Kit Release 16.0 performed at the Ramaciotti Gene Function Analysis facility, University of New South Wales in Sydney, Australia.

middle: Z

first: Claire

last: Curl

first: Paul

last: Lewandowski

first: Lea

last: Delbridge

first: Stephen

last: Harrap

first: Fadi

last: Charchar


title: Liver transcriptional critical balance induced by acetaminophen is prevented by chronic copper loading

city: Rancagua

first: Mauricio

middle: Alejandro

last: Latorre

state: VI

address: Av. Libertador Bernardo OHiggins 611

department: ICI

country: Chile

institute: Universidad de OHiggins

summary: Using a Cebus capucinus model and after chronic copper oral administration, we assessed a global transcriptional liver adaptations induced by acutely challenging the animals with a unique high dose of oral acetaminophen (APAP).

overall_design: Capuchin monkeys fed daily 7.5 mg of Cu/kg for three years (chronic copper protocol) were challenged with a unique dose of 120 mg APAP /kg. Four-condition experiment, control vs. copper, control vs APAP, control vs copper + APAP. Biological replicates: 4 individual monkeys (two channel array, control vs treatmentcontrol). Two technical replicate per array.

first: M

last: Gonzalez


title: Gene expression changes in neonatal and adult myeloid dendritic cells (mDC) upon TLR7/8 stimulation

city: Vancouver

first: Edgardo

last: Fortuno III

institute: Child & Family Research Institute - University of British Columbia

summary: We want to define the differences in gene expression changes between neonatal and adult myeloid dendritic cells upon stimulation with TLR7/8.  These differences may point to specific signaling pathways which, in turn, may account for the known differential immune response of babies to vaccination or infection when compared to adults.

overall_design: Total RNA obtained from MACS-purified human mDC (using Miltenyi's CD1c+ Dendritic Cell Isolation Kit) stimulated with the synthetic TLR7/8 ligand 3M-003 (at final concentration of 5 uM) for 1 or 6 hours in vitro compared to unstimulated mDC.


title: Effect of cardiomyocyte specific KO of AKT1, AKT2, and AKT1 + AKT2  on gene expression profile of the heart

status: Public on Nov 30 2017

city: Duesseldorf

first: Karl

last: Koehrer

address: Universitaetsstr. 1

department: BMFZ

institute: University of Duesseldorf

summary: In the mammalian heart AKT1 and AKT2 are the isoforms of the protein kinase AKT (protein kinase B) which are predominantly expressed. AKT isoforms exert common and specific functions in the field of metabolism, cellular growth, apoptosis and cell migration. To identify specific and common functions of AKT1 and AKT2 isoforms, we generated tamoxifen-inducible, cardiomyocyte-specific AKT1, AKT2, and AKT1+AKT2 double knockout mice (iCMAKT – KO mice).  Inactivation of AKT isoforms was achieved by application of 4-OH-tamoxifen, which activates an OH-Tx inducible cre-recombinase expressed under the control of the αMHC-promoter (αMHC-mercremer). Transgenic mice expressing only the αMHCmercremer construct were also treated with OH-Tx and served as controls. To identify alterations in cardiac gene expression due to AKT deletion we analyzed gene expression profiles of control hearts, iCMAKT1, iCMAKT2 and iCMAKT1+2 hearts.

overall_design: Gene expression of mouse hearts of inducible, cardiomyocyte-specific  AKT1, AKT2 and AKT1+AKT2 KO mice. Mice express a mercremer recombinase under control of the αMHC promotor.  AKT1 and AKT2 genes have loxP-flanked exons6 and7 and exon 5 exon 6 , respectively.  Control mice only express the MHCmercremer  gene. For RNA isolation four hearts of control  control mice, single knockouts and the double KO were used. At age of 3 month  mice were treated with 500µg hydroxytamoxifen (OH-Tx) per day for 5 days to induce the specific KO of AKT alleles in cardiomyocytes. Control mice express the MHCmercremer construct and were treated with OH-Tx equally. For RNA isolation four hearts of control and KO mice were harvested from 3 month old male mice 21 days after induction with OH-Tx. RNA was isolated from heart apex. 3 month old male mice  after 5 injections of 4OH-tamoxifen served as controls.

first: Stefanie

last: Gödecke

first: Finja

last: Möller

first: Andre

last: Heinen

first: René

last: Deenen

last: Köhrer

first: Axel


title: microRNA expression analysis following 24h siRNA knockdown of transforming growth factor β receptor III (TGFBR3) in human pulmonary arterial smooth muscle cells.

first: Rory

last: Morty

summary: We explored the impact of transforming growth factor β receptor III (TGFBR3) knockdown on the microRNA expression in the human pulmonary arterial smooth muscle cells (hPASMC), at 24h timepoint.

overall_design: Human pulmonary arterial smooth muscle cells (hPASMC) in P2 were plated in 6-well plates and transfected with 200nM siRNA to transforming growth factor β receptor III (TGFBR3) (Santa Cruz Biotechnology) or Scrambled control (Ambion). Total RNA was extracted at 24h with miRNeasy Mini Kit (Qiagen) following the manufacturer’s instructions.

first: Gero

last: Niess


title: Excessive UBE3A dosage impairs fine-tuning of retinoid acid signaling in autism spectrum disorders

city: Shanghai

first: Ronggui

last: Hu

state: Shanghai

address: Room 405, New Biochemistry Building, 320 Yue-yang Road, Shanghai, China

institute: Institute of Biochemsitry and Cell Biology

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

summary: The autism spectrum disorders (ASD) are a collection of disorders with heterogeneous etiology, exhibiting common traits including impaired social interactions and communications, repetitive behaviors. 15q11-q13 copy number variations (CNV) were found in 1-3% of ASD cases; of which the detailed mechanism of the major contributor UBE3A gene acted still remained elusive. Here we identified a key enzyme in RA synthesis, negatively regulated in ubiquitination-dependent mode promoted by UBE3A. Our data provide evidences linking UBE3A hyperactivity with ASD phenotypes, with implications for understanding ASD etiology and providing potential interventions in ASD clinical therapy.

overall_design: To identify whether CNV variations existed within different patients diagnosed with ASD, genomic DNA were extracted from three patient blood samples and investigated using Human660W-Quad Beadchip assay.

first: Hui

last: Guo

first: Kun

last: Xia

first: Xingxing

last: Xu


title: Study of knock-in mice expressing the co-Factor FOG-2 that can not bind pRb

status: Public on Dec 02 2017

city: Paris

first: Franck

last: Letourneur

address: 22 rue mechain

institute: INSERM

summary: Expression data using microarrays in proliferating Wt and FOG-2 Rb-  E14.5 MEF cells

overall_design: Wt and FOG-2 Rb- MEF were collected at early proliferation stage before differentiation

first: O

last: Goupille

first: T

last: Penglong

first: Z

last: Kadri

last: Granger-Locatelli

first: R

last: Denis

first: S

last: Luquet

first: C

last: Badoual

last: Fucharoen

first: L

last: Maouche-Chrétien

first: P

last: Leboulch

last: Chrétien


title: Transcript profiling in rice stem base of wild type and crown root less 1 mutant after auxin treatment

city: Montpellier

first: Pascal

last: Gantet

address: Avenue Agropolis

department: IRD

institute: Université Montpellier 2

summary:
Lateral Organ Boundary Domain (LBD) transcription factors are specific of plants and are involved in the control of development. One LBD clade is related to the control of root development (Coudert et al., 2013, Mol. Biol. Evol. 30, 569-572). Belonging to this clade, CROWN ROOT LESS 1 controls the initiation of crown roots in rice and its expression is induced by auxin (Inukai Plant Cell, 17, 1387-1396, Liu et al., 2005, Plant J., 43, 47-56). The aim of this study was to identify CRL1-dependant auxin responsive genes.
Transcriptome analysis in wild-type and crl1 mutant stem bases after exogenous auxin treatment of plantlets revealed 126 CRL1-dependant auxin responsive genes including a large part of genes encoding proteins involved in signal transduction pathways that may be related to cell division, expansion and differentiation, and root development.

overall_design: 8 days old seedlings cultivated in vitro of wild type or crl1 mutant were treated by auxin. Transcriptome profiling were conducted just before, 2h and 4h after auxin treatment to identify CRL1-dependant auxin responsive genes. Two independent repetitions of the experiment were done.

first: Van

last: Le

first: Martial

last: Pré


title: Gene expression analysis following 6h-, 12h-, 18h- and 24h-siRNA knockdown of transforming growth factor β receptor III (TGFBR3) in human pulmonary arterial smooth muscle cells (hPASMC).

city: Bad Nauheim

first: Rory

last: Morty

address: Parkstr. 1

institute: MPI für Herz- und Lungenforschung

summary: We explored the impact of transforming growth factor β receptor III (TGFBR3) knockdown on the gene expression in the human pulmonary arterial smooth muscle cells (hPASMC), following 6h, 12h, 18h and 24h.

overall_design: Human pulmonary arterial smooth muscle cells (hPASMC) in P4 were plated in 6-well plates and transfected with either 200nM siRNA to transforming growth factor β receptor III (TGFBR3) (Santa Cruz Biotechnology) or Scrambled control (Ambion). Total RNA was extracted at 6, 12, 18 and 24h timepoint with peqGOLD TOTAL RNA Kit (VWR).

first: Gero

last: Niess


title: 16MB binding of STAT1 and IRF1 transcription factors in IFNg treated and untreated HeLa cells using NimbleGen array

city: Toronto

first: Rod

last: Bremner

state: ON

address: 600 University Ave

department: Lunenfeld-Tanenbaum Research Institute

institute: Mount Sinai Hospital

type: Genome binding/occupancy profiling by genome tiling array

summary: Analysis of STAT1 and IRF1 binding in IFNg treated and untreated HeLa cells for 6 hours was done using 50mer oligonucleotide probes at 30bp intervals tiling over non-repetitive 16MB gene locus (HG17).

overall_design: Three replicates for each marker at each state.

last: Xu

last: Yu

first: K

last: Huang


title: Leukocyte gene regulation and patterns of natural language use.

status: Public on Dec 05 2017

city: Los Angeles

first: Steve

last: Cole

state: CA

address: 11-934 Factor Bldg, UCLA

department: Medicine

institute: UCLA School of Medicine

summary: Analysis of transcript abundance estimates as a function of demographic, psychometric, and language use features.

overall_design: Gene expression profiling was conducted on peripheral blood samples collected from healthy adults in the Atlanta metropolitan area.  In addition to background characteristics (age, sex, race/ethnicity, body mass index/BMI, smoking history), participants were also assessed for patterns of natural language use (using the electronically activated recorder system with data processing by Linguistic Inquiry and Word Count software; Mehl, MR, et al. (2001) The Electronically Activated Recorder (EAR): a device for sampling naturalistic daily activities and conversations Behavior Research Methods, Instruments, & Computers 33, 517-523; Pennebaker, JW, Booth, RJ & Francis, ME (2007) Linguistic Inquiry and Word Count: LIWC 2007, www.liwc.net) and self-report psychometric measures of stress (Cohen, S, Kessler, RC & Underwood Gordon, L (1995) Perceived Stress Scale. In Measuring stress:  A guide for health and social scientists (Oxford University Press, New York)), anxiety (Beck, AT, Epstein, N, Brown, G & Steer, RA (1988) An inventory for measuring clinical anxiety: Psychometric properties Journal of Consulting and Clinical Psychology 56, 893-897), depression (Beck, A, Steer, R & Brown, G (1996) Beck Depression Inventory - Second Edition manual (Psychological Corporation, San Antonio TX)) and loneliness (Russell, D, Peplau, LA & Cutrona, CE (1980) The revised UCLA Loneliness Scale: concurrent and discriminant validity evidence J Pers Soc Psychol. 39, 472-80).  Analyses also controlled for variations in the prevalence of distinct leukocyte subsets as indicated by the relative abundance of mRNA encoding CD3D, CD4, CD8A, CD19, CD56/NCAM1, CD16/FCGR3A, and CD14 (each standardized to mean=0/standard deviation=1 for analysis). Derived language metrics include total words spoken (WordCount); average sentence length (WordsPerSentence); frequency of recorded samples in which particpants were talking and were alone; the relative prevalence of 8 general categories of function words (adverbs, articles, auxiliary verbs, conjunctions, negations, prepositions, quantifiers, and impersonal pronouns) and 5 sub-categories of personal pronouns (1st person singular (i), 1st person plural (we), 2nd person singular (you), 3rd person singular (shehe), and 3rd person plural (they)); and the categorical-dynamic index (CDI; Pennebaker, JW, et al. (2014) When small words foretell academic success: the case of college admissions essays, PLoS One 9, e115844).   Higher values of each scale score indicate greater levels of stress, anxiety, etc.  Dichotomous variables were coded 0=no/absent and 1=yes/present.  Valid gene expression data are available for 143 participants.


title: Molecular characterisation of High Beta Carotene (HBC) Mutant

city: Bangalore

first: Genotypic

last: technology

state: Karnataka

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

country: India

institute: Genotypic Technology

summary: The High-β-Carotene (HBC) mutant identified from EMS mutagenized population of cultivar Arka Vikas and the biochemical studies revealed that mutant fruits contain four times higher level of β-Carotene in comparison to Wild type (cv. Arka Vikas). We have developed whole genome microarray expression profiling as a discovery platform to identify differentially expressed genes in fruits containing High-β-Carotene mutant in comparison to Wild type (cv. Arka Vikas). Tomato fruit tissue samples from different stages of fruit ripening like Mature green, Breaker, Turning and Ripening stages of High-β-Carotene (HBC) mutant and Wild type (cv. Arka VIkas) were used for microarray gene expression analysis. Carotenoid pathway analysis of both mutant and wild type reveals that the high expression of chromoplast specific lycopene- β-cyclase gene in the HBC mutant, which is involved in the conversion of lycopene to β-carotene, but in wild type the expression of this gene, was low. Four genes (PSY, PDS, CRTISO, CYCB) of the carotenoid pathway was quantified in the same RNA samples by real-time PCR, confirming that the variation of the gene expression in HBC mutant.

overall_design: Organism : Solanum lycopersicum, Agilent Tomato Gene Expression  8x60k Array (AMADID: 065951) designed by Geotypic Technology Private limited

middle: O

last: Basha

first: N

last: Rajesh


title: MicroRNA expression profiling for coronary artery calcification in Indian chronic kidney disease patients

summary: Our study investigates the expression profilling of miRNAs in the pathogenesis of coronary artery calcification in chronic kidney disease patients and identify alter miRNA gene expression which will gives a unique platform for new drug discovery

overall_design: Organism : Homo sapiens, Agilent Custom Human Gene Expression  8x60k Array (AMADID: 046064) designed  by Genotypic Technology Private Limited.

first: Kumaresan

last: Ramanathan

first: Giri

last: Padmanabhan

first: Bhooma

last: Vijayaraghavan

first: Nathiya

last: Shanmugam

first: Antony

last: Arockiam

first: Sridharan

last: Jeyamohan


title: Transcriptomic profile of pfd4 plants under low temperatures

city: Boston

first: Carlos

last: Perea Resa

address: 185 Cambridge St

institute: MGH-HMS

summary: Transcriptional profiling of two-old week pfd4/Col-0 (WT) plants in response to low temperatures

overall_design: Comparison between total RNA from two-old-week pfd4 and Col-0/wt plants in response to 4C for 24h

last: Perea-Resa

first: Miguel

last: Rodriguez-Milla

first: Elisa

last: Iniesto

first: Vicente

last: Rubio

first: Julio

last: Salinas


title: LncRNA profile study reveals massive lncRNAs associated with lentoid body differentiation derived from human iPSCs

city: Hangzhou

first: Qiuli

last: FU

state: Zhejiang

address: Jiefang road 88#

institute: Zhejiang University

summary: LBs were derived from human-induced pluripotent stem cells (iPSCs) using the fried egg method. The transcriptome of LBs vs iPSCs was examined through microarray analysis.

overall_design: Two condition experiment, human iPSCs (D0) vs LBs on D28/D29. Biological replicates:3 iPSCs, 3 LBs, independently grown and harvest.

first: Zhenwei

last: QIN

first: Ke

last: YAO


title: miRNA expression data from fractionated SH-SY5Y cells

city: Callaghan

first: Murray

last: Cairns

state: NSW

address: University Drive

institute: University of Newcastle

summary:
miRNA activity is typically associated with the cytoplasm, but a growing body of evidence suggests non-canonical roles for miRNA in the nucleus. We study miRNA dynamics in neurons and wanted to investigate this possibility in a human neuronal model.
We used microarrays to investigate the miRNA composition of the nuclear and cytoplasmic compartments of undifferentiated SH-SY5Y cells.

overall_design: SH-SY5Y cultures at 80% confluence were collected by trypsinisation, and the nuclear and cytoplasmic fractions separated by hypotonic lysis.

first: B

last: Goldie

first: C

last: Fitzsimmons

first: J

last: Weidenhofer

middle: R

last: Atkins

first: D

last: Wang

first: M


title: Mislocalization of the cell polarity protein Scribble (Scrib) induces SPARC secretion in hepatocellular carcinoma

city: Mannheim

first: Carsten

last: Sticht

address: Theodor-Kutzer-Ufer

department: ZMF

institute: University Heidelberg

summary: Cell polarity is crucial for the maintenance of epithelial cell function and its loss may have an im-portant role in the development and progression of cancer. We here show that overexpression and cytoplasmic enrichment of the baso-lateral polarity complex protein Scribble (Scrib) correlates with poor prognosis of hepatocellular cancer (HCC) patients. Expression of the cytoplasmic ScribP305L in hepatocellular cells induces epithelial to mesenchymal transition (EMT) and supports HCC cell invasion in comparison to cells expressing membrane-localized ScribWT. ScribP305L induces AKT signalling through destabilization of the phosphatases phosphatase and tensin homolog (PTEN) and PH domain and leucine rich repeat protein phosphatase 1 (PHLPP1). Moreover, cytoplasmic ScribP305L stimulates the expression of secreted protein acidic and cysteine rich (SPARC) de-pending on the AP1 constituents ATF2 and JunB, which drives HCC cell invasiveness. In vivo, combined hydrodynamic delivery of ScribP305L but not ScribWT and c-MYC initiates tumour for-mation in hepatocytes and cytoplasmic Scrib correlates with AKT phosphorylation, and AP1 ex-pression in human HCC tissues. Together, overexpression and mislocalization of Scrib represents an early event involved in the initiation and progression of liver cancer.

overall_design: Triplicates of three cell lines were compared: untrasfected HepG2, HepG2 cell expressing wildtype Scribbel and HepG2 cell expressing mutated Scribble.

first: Kai

last: Breuhahn

first: Shan

last: Wan


title: Effect of cardiomyocyte specific KO of  AKT1 + AKT2  on gene expression profile of the heart

first: Karl

last: Koehrer

summary: In the mammalian heart AKT1 and AKT2 are the isoforms of the protein kinase AKT (protein kinase B) which are predominantly expressed. AKT isoforms exert common and specific functions in the field of metabolism, cellular growth, apoptosis and cell migration. To identify specific and  common functions of AKT1 and AKT2 isoforms, we generated tamoxifen-inducible, cardiomyocyte-specific  AKT1+AKT2 double knockout mice (iCMAKT – KO mice).  Inactivation of AKT isoforms was achieved by application of 4-OH-tamoxifen, which activates an OH-Tx inducible cre-recombinase expressed under the control of the αMHC-promoter (αMHC-mercremer). Transgenic mice expressing only the αMHCmercremer construct were also treated with OH-Tx and served as controls. To identify alterations in cardiac gene expression due to AKT deletion we analyzed gene expression profiles of control hearts and iCMAKT1+2 hearts.

overall_design: Gene expression of mouse hearts of inducible, cardiomyocyte-specific  AKT1+AKT2 KO mice. Mice express a mercremer recombinase under control of the αMHC promotor.  AKT1 and AKT2 genes have loxP-flanked exons6 and7 and exon 5 exon 6 , respectively.  Control mice only express the MHCmercremer  gene. For RNA isolation four hearts of control  control mice and three double KO were used. At age of 3 month  mice were treated with 500µg hydroxytamoxifen (OH-Tx) per day for 5 days to induce the specific KO of AKT alleles in cardiomyocytes. Control mice express the MHCmercremer construct and were treated with OH-Tx equally. For RNA isolation four hearts of control and KO mice were harvested from 3 month old male mice 10 days after induction with OH-Tx. RNA was isolated from heart apex. 3 month old male mice  after 5 injections of 4OH-tamoxifen served as controls.

first: Stefanie

last: Gödecke

first: Finja

last: Möller

first: Andre

last: Heinen

first: René

last: Deenen

last: Köhrer

first: Axel


title: Transcriptome profiling of OsbZIP48 rice transgenics

status: Public on Oct 11 2017

city: New Delhi

first: Jitendra

middle: Paul

last: Khurana

address: Benito Juarez Road

department: Department of Plant Molecular Biology

institute: University of Delhi South Campus

summary: Rice transgenic plants of the bZIP encoding gene, OsbZIP48, in the Pusa Basmati 1 (PB1) variety have been found to display differences in the total height. In order to elucidate changes at the transcriptome level, microarray of the  10-day-old seedlings of over-expresseion (OE) and knock-down (KD) lines along with vector control (VC) were carried out.

overall_design: Seedlings of OsbZIP48-OE, OsbZIP48-KD and VC  grown for seven days at 28±1oC in light. RNA from the whole seedlings were extracted from each sample and hybridized on rice Affymetrix microarrays. Two biological replicates of each sample were used for microarray analysis. Overall, ten samples were analyzed representing the transgenic lines and vector control constructs.

first: Naini

last: Burman

first: Akanksha

last: Bhatnagar

middle: P


title: Cartilage microRNA dysregulation during the onset and progression of mouse osteoarthritis is independent of aggrecanolysis and overlaps with candidates from end-stage human disease [miRNA]

first: John

last: Bateman

address: Flemington Road

department: Skeletal Biology

institute: Murdoch Childrens Research Institute

summary: The purpose of this study is to characterize the expression profile of microRNAs and their target mRNAs in cartilage and subchondral bone (SCB) in a mouse model of post-traumatic osteoarthritis (OA).

overall_design: OA was induced in adult male C57BL6 mice by destabilization of the medial meniscus (DMM). RNA from medial tibial cartilage and SCB of DMM and sham-operated mice was isolated by laser micro-dissection at 1 and 6 weeks post-surgery (n=3-4/time point/group). Expression profiling was performed using Agilent microarrays. Joint pathology was scored histologically.

first: Louise

middle: H

last: Kung

first: Varshini

last: Ravi

first: Lynn

last: Rowley

first: Constanza

last: Angelucci

first: Amanda

last: Fosang

first: Katrina

middle: M

last: Bell

first: Christopher

middle: B

last: Little

middle: F


title: Genome wide transcriptional changes during peach fruit development

city: Padova

first: Gerolamo

last: Lanfranchi

address: Via U. Bassi, 58/B

institute: University of Padova

summary: Fleshy fruit help in reproduction by developing structures that, reached a given maturity stage, become attractive to animals that, feeding on them, spread the contained seeds in the environment. According to the species, seed development can be at the same pace with the pericarp, or be ready for dispersion before or after the ripening of the fruit. In peach, seed and mesocarp maturation are on pace in mid-season cultivars, while in early ripening ones the seed is not mature at ripening, with the endosperm not yet fully reabsorbed. On the contrary, slow ripening genotypes show the opposite, i.e. a mature seed in a fruit unable to fully ripen. To gain insights on the molecular control of peach fruit development and ripening and on the interactions between the seed and the mesocarp, genome wide transcriptional changes of the two fruit parts have been investigated throughout development from flower anthesis up to commercial ripening in the mid-season cultivar Fantasia. Besides flower, six time points encompassing the four fruit developmental stages were investigated.

overall_design: The dataset consists of thirteen samples (flower, seed at six time points, mesocarp at the same six time points), each with three biological replicates (repA, repB, repC). The experiment is a developmental series, with expression time course analyzed within a single tissue (either seed or mesocarp), excluding, beside flower, data of the other tissue. Gene enrichment analysis has been conducted on genes differentially expressed between following stages of the same tissue. Expression of differentially expressed genes in one tissue have been examined in the other tissue to asses the tissue specificity vs the stage specificity of the regulation.

first: Valerio

last: Zaffolon

first: Alice

last: Tadiello

first: Angela

last: Rasori

first: Claudio

last: Forcato

first: Nicola

last: Vitulo

first: Stefano

last: Cagnin

first: Angelo

last: Ramina

last: Bonghi

first: Livio

last: Trainotti


title: cDNA expression profiling of 4T1 breast cancer cells isolated from tumor-draining lymph node (4T1LN) or primary tumors (4T1PT)

status: Public on Sep 10 2017

city: Taipei

first: Shih-Chia

last: Huang

address: 128 Academia Road, Section 2, Nankang

country: Taiwan

institute: Academia Sinica

summary: Investigating the gene expression profile changes between 4T1LN and 4T1PT.

overall_design: Balb/c mice were injected with 4T1 cells at both site of 4th mammary fat pad. Three weeks later, mice were sacrificed and primary tumors and inguinal tumor-draining lymph nodes were harvested. Primary tumors from both 4th fat pads were excised, minced with scissors, and then digested in collagenase type I (150 U⁄ ml) plus hyaluronidase (50 U/ml) for 16 hr at humidified 37 °C incubator supplemented with 5% CO2. Inguinal tumor-draining LNs were excised and dissociated by mechanical disruption. Tissues were dissociated by 100 μm cell strainers from BD Biosciences (San Jose, CA, USA) and maintained in complete RPMI 1640 medium containing 60 μM 6-thioguanine (Sigma-Aldrich, St. Louis, MO, USA) and seeded into 10 cm dishes. After 10-14 days, cells were harvested and stained with APC-conjugated rat anti-mouse CD24 (#101814, Biolegend, San Diego, CA, USA) and PE-conjugated hamster anti-mouse CD29 antibodies (#102208, Biolegend, San Diego, CA, USA) for 30 mins at 4℃. The CD24+CD29+ 4T1 cell population was sorted on a FACS Aria II cell sorter. CD24+CD29+ 4T1 cell sorted from Inguinal tumor-draining LNs called 4T1LN cells, CD24+CD29+ 4T1 cell sorted from primary tumors called 4T1PT cells.

first: Shih

first: Wen

last: Lee


title: Gene expression profiles of denervation in prostate cells

city: Houston

first: Chad

last: Creighton

state: TX

address: One Baylor Plaza, Mail Stop: BCM305

department: Biostatistics, Ducan Cancer Center

institute: Baylor College of Medicine

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

sample_organism:
Homo sapiens
Rattus norvegicus

platform_organism:
Homo sapiens
Rattus norvegicus

overall_design: Refer to individual Series


title: Gene expression profile of Samd7 KO retina at P12

status: Public on Sep 05 2017

city: Suita

first: Takahisa

last: Furukawa

state: Osaka

address: 6-2-4 Furuedai

department: Developmental Biology

institute: Osaka Bioscience Institute

summary: To analyze the expression profile in the Samd7 KO retina, we performed a microarray analysis using wild-type and Samd7 KO retina at P12.

overall_design: We performed a microarray analysis using wild-type and Samd7 KO retina at P12, and compared the expression profiles.

first: Yoshihiro

last: Omori


title: Expression data from melanoma cancer cell line CHL-1 after Bromodomain and extra terminal domain inhibitor BAY 1238097 treatment

status: Public on Oct 31 2017

city: Berlin

first: Ralf

last: Lesche

address: Muellerstr 178

institute: Bayer Pharma AG

summary:
Bromodomain and extra terminal domain (BET) inhibtion reduces occupancy of BET-family at promoter and enhancer sites. This finally leads to genome wide changes in the transcription of specific genes.
We used microarray profiling to investigate the changes made by BET inhibitor BAY 1238097, trying to identify the underlying changes of gene regulation that lead to sensitivity.

overall_design: CHL-1 cells were treated with BAY 1238097 a potent and selective Bromodomain and extra terminal domain (BET) inhibitor before RNA extraction and hybridization on Affymetrix microarrays. We wanted to investigate the transcriptional changes after BET bromodomain inhibtion in the BAY 1238097-sensitive CHL-1 melanoma cell line. Cells were treated with 75 nM (IC50) or 468 nM (IC90) of BAY 1238097 for 4h and 24h to look at dose-dependent changes on transcriptional level.

first: Olaf

last: Klingbeil

first: Bernard

last: Haendler


title: Transcription of Nearly All Yeast RNA Polymerase II-Transcribed Genes Is Dependent on Transcription Factor TFIID

status: Public on Sep 15 2017

city: Illkirch

first: Didier

last: Devys

address: 1 rue Laurent Fries / BP 10142

institute: Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC)

summary:
RNA Pol II transcription has been implied to be either regulated by the general transcription factor TFIID or the co-activator SAGA. Also, this dominancy of either SAGA or TFIID might be according to the existance, or not, of a TATA consensus sequence.
We used microarrays to analyse newly-synthesized RNA in two mutants that allow conditional nuclear depletion of Taf4 or Taf5 to reevaluate whether some genes are more affected than others.

platform_organism:
Schizosaccharomyces pombe
Saccharomyces cerevisiae

overall_design: The genotype of yeast strains was modified to allow nuclear depletion of either Taf4 or Taf5. Taf4 (or Taf5) was depleted from the nucleus by adding either 5uM rapamycin to the cells. To the control cultures only DMSO was added (in these cells Tafs are not depleted from the nucleus and thus were used as the control samples). Newly synthesized mRNA were labeled using 4tU labeling 30 min after the addition of rapamycin. Labeling occured for 6 min. mRNA levels and synthesis rates were measured using Affymetrix GeneChip Yeast Genome 2.0 Array.

first: Linda

last: Warfield

first: Srinivas

last: Ramachandran

first: Tiago

last: Baptista

first: Laszlo

last: Tora

first: Steven

last: Hahn


title: Expression data of J3T-1 and J3T-2 glioma

status: Public on Oct 01 2017

city: Okayama

last: Otani

address: 2-5-1 Shikata, kita-ku

department: Neurological Surgery

institute: Okayama University

summary:
We established two novel glioma subclones those showed different invasive and angiogenic phenotypes. J3T-1 demonstrates robust angiogenesis and perivascular invasion. J3T-2 demonstrates diffuse invasion along white matter tracts.
We used microarrays to show the difference of gene expression that contribute to the difference of phenotype.

overall_design: J3T-1 and J3T-2 were derived from the same parental canine glioma cell. These cell lines have similar genetic backgrounds but have different phenotypes of invasion and angiogenesis. We investigated each one of them.

first: Tomotsugu

last: Ichikawa

first: Satoshi

last: Inoue


title: Affymetrix OncoScan data for IDH and TP53 mutant gliomas

status: Public on Sep 01 2017

city: Toyoake

first: Shunsuke

last: Nakae

state: Aichi

address: 1-98 Dengakubakubo Kutsukakecho

institute: human

summary: IDH and TP53 mutant gliomas are high recurrent tumor, and thus we aimed to detect malignant and recurent factors in this genetic type of gliomas

overall_design: OncoScan arrays were performed for two set, i.e., primary and recurrent tumors, of IDH and TP53 mutant gliomas.

first: Fujiko

last: Sueishi


title: Transcriptomic changes of Campylobacter jejuni subsp. jejuni strain 81116 in water

city: St-Anne-de-Bellevue

first: Sebastien

last: Faucher

state: QC

address: 21,111 Lakeshore

department: Natural Resource Sciences

institute: McGill University

summary:
Campylobacter jejuni is the leading cause of campylobacteriosis in the developed world. Although most cases are caused by consumption of contaminated meat, a significant proportion is caused by consumption of contaminated water. Some C. jejuni isolates are better than others at surviving in water, which suggests that these strains are better adapted to transmission by water than others.
The aim of this study is to investigate this phenomenon further. CFU counts and viability assays showed that strain 81116 survives better than strain 81-176 in a defined freshwater medium at 4°C. Comparative transcriptomic profiling using microarray revealed that these strains respond differently to water. This series presents the transcriptome of strain 81116 in water.

sample_organism: Campylobacter jejuni subsp. jejuni 81116

overall_design: Campylobacter jejuni was first cultured on TSA-Blood plate at 42 °C for 2 days. C. jejuni was suspended in 100 ml of Fraquil or Brucella broth at an OD600 of 1 in triplicates and washed three times with either Fraquil or Brucella broth. The suspensions were then incubated at 4°C for 4h. RNA was extractedl, labelled, and hybridized on microarrays, with labeled gDNA as reference channel.

first: Hana

last: Trigui

first: Kristen

last: Lee

first: Alexandre

last: Thibodeau

first: Simon

last: Lévesque

first: Philippe

last: Fravalo

first: Ann

last: Letellier


title: Seasonal changes of gene expression of eyes in Medaka fish (Oryzias latipes)

city: Fuchu-shi

first: Tsuyoshi

last: Shimmura

state: Tokyo

address: 3-8-1 Harumi-cho

institute: Tokyo University of Agriculture and Technology

summary: To examine the seasonal adaptation, we compared the gene expression of eyes between SL (short-day and low-temperature conditions: 10 h light/14 h dark and 8 °C) and LD (long-day and warm-temperature conditions: 14 h light/10 h dark and 26 °C) conditions in Medaka fish (Oryzias latipes).

overall_design: The gene expression of eyes was measured at 16 hours after light onset (zeitgeber time: ZT16) on days 0, 1, 2, 3, 5, 7, and 14 after transfer from SL to LD conditions. For each time point, cRNAs prepared from pooled eyes (n=3) were hybridized to duplicate sets of microarrays.

first: Takashi

last: Yoshimura


title: Effect of Imatinib (1microM, 24 hours) on the microRNA repertoire of chronic myeloid leukemia cell line K562

city: BORDEAUX

first: Bruno

last: CARDINAUD

address: 146 rue Leo Saignat

department: INSERM U1035

institute: Bordeaux University

summary: Using a microarray-based miRNA profiling, we found in a model of chronic myeloid leukemia (CML) that the activity of the oncoprotein BCR-ABL1 regulates the expression of miR-21, a "onco-microRNA" known to be overexpressed in numerous cancers. This relies on the phosphorylation status of STAT5, a transcription factor known to be activated by the kinase activity of BCR-ABL1. Mir-21 regulates the expression of PDCD4 (programmed cell death protein 4), a tumor suppressor identified here through a proteomics approach

overall_design: The microRNA repertoire of K562 cells having been either not treated (n=3) or treated (n=3) with the tyrosine kinase inhibitor Imatinib (1microM, 24h) was studied using Agilent microRNA V2 microarrays

last: Cardinaud


title: HCT116 gene expression analysis upon CAF stimulation

status: Public on Aug 31 2017

city: paris

first: danijela

last: matic vignjevic

address: 12 rue Lhomond

institute: institut curie

summary: HCT116 colon carcinoma cells invade more the basement membrane when carcinoma-associated fibroblasts (CAFs) are present. In order to identify if CAFs induce an invasive phenotype to HCT116 cells, and therefore regulate genes expression related to invasion, we compared gene expression of HCT116 cells cultured alone or in the presence of CAFs.

overall_design: HCT116 cells were cultured with or without CAFs and were later collected and subjected to the gene expression analysis

first: Danijela

last: Vignjevic

first: Alexandros

last: Glentis

first: David

last: Gentien


title: A miRNA-based signature associated to relapse in pediatric t(8;21)RUNX1-RUNX1T1

status: Public on Sep 14 2017

first: Matteo

last: Zampini

state: PD

address: corso stati uniti 4

institute: Istituto di Ricerca Pediatrica (IRP)  Città della Speranza

summary: We performed genome wide miRNA expression analysis to investigate the ability of miRNAs in predicting leukemia relapse from 33 t(8;21) pediatric AMLs at diagnosis divided into a training and a validation cohort. COX regression analysis and ROC curves were used to identify a powerful miRNA signature able to predict relapse in t(8;21) AML patients.  miRNA profiling showed that patients with high- or low- risk of relapse had different expression profiles.  We support the role of microRNAs in modulating the prognosis of t(8;21)-AML and the use of a miRNA expression signature at diagnosis  to better define standard risk cases in pediatric AML.

overall_design: 260 ng of bone marrow RNA from 33 patients with de novo AML harboring t(8;21) pediatric AML at diagnosis were hybridized on Affymetrix GeneChip® miRNA 4.0 arrays for high throughput detection. Class comparisons between different patient subgroups (Relapsed vs No Relapsed) were performed. Moreover,  6 matched relapse specimens were hybridized on Affymetrix GeneChip® miRNA 4.0 arrays and analyzed.

first: M

last: Pigazzi


title: Myc target gene, long intergenic noncoding RNA, Linc00176 in hepatocellular carcinoma regulates cell cycle and cell survival by titrating tumor suppressor microRNAs.

status: Public on Sep 07 2017

city: Hannover

first: Doan Duy Hai

last: Tran

state: Niedersachsen

address: Carl-Neubergsstr. 1

department: Institut of physiological Chemistry

institute: Hannover Medical School

summary: Hepatocellular carcinoma (HCC) is a frequent form of cancer with a poor prognosis and with limited possibilities for medical intervention. Recent evidence has accumulated that long noncoding RNAs (lncRNAs) are important regulators of disease processes including cancer. Chromatin remodeling in cancer cells may result in an unusual expression of lncRNAs and indeed it has been shown that more than 7000 unannotated lncRNAs are expressed in HCCs. We identified a novel long intergenic noncoding RNA, Linc00176, that plays a role in proliferation and survival of HCC. Linc00176 regulates expression of more than 200 genes by the sponge function for tumor suppressor miRNAs, miR-9 and miR-185. Linc00176 is expressed at a high level only in HCC, and is activated by Myc, Max and AP-4 transcription regulators. Myc also upregulates miR-9 and miR-185. In Linc00176-depleted HCC, these miRNAs were released from Linc00176 and downregulated their target mRNAs. Thus, depletion of Linc00176 disrupted the cell cycle and induced necroptosis in HCC via released tumor suppressor miRNAs. These data indicate that atypically expressed lncRNAs may be useful targets for cancer therapy.

overall_design: In one dual-color microarray hybridization, mRNA expression changes after depletion of Linc00176

first: D

middle: D

first: T

last: Tamura


title: Cardiotrophin 1 stimulates beneficial myogenic and vascular remodeling in the heart

city: Ottawa

first: Theodore

last: Perkins

address: 501 Smyth Rd.

department: Cellular and Molecular Medicine

institute: Ottawa Hospital Research Institute

summary: Primary neonatal cardiomyocytes treated with human cardiotrophin 1 (hCT1) or control (Ctrl) for 24 hours

overall_design: This data set contains 3 replicates each for hCT1 and Ctrl

first: Lynn

middle: A

last: Megeney

first: Mohammad

last: Abdul-Ghani


title: Expression data from peripheral whole blood of non-IBD controls, CD and UC patients

status: Public on Sep 11 2017

city: Barcelona

first: Azucena

last: Salas

address: Rosselló, 149-153

department: Gastroenterology

institute: IDIBAPS

summary:
Ulcerative colitis (UC) is a chronic inflammatory disease of the colon with preiods of active disease followed by remission.
We performed a whole-genome transcriptional analysis of peripheral whole blood (PAXgene tubes) from patients with endoscopically active and inactive UC and CD, as well as non-inflammatory controls.

overall_design: Ulcerative colitis and Crohn's Disease patients as well as non-inflammatory controls were collected for whole blood RNA extraction and hybridization on Affymetrix microarrays.  All patients had undergone clinical and endoscopic evaluations at the time of sample collection. Disease activity was assessed using the endoscopic scores. For UC, active disease was defined as a endoscopic Mayo sub score >=1 and inactive disease as a endoscopic Mayo sub score =0. For CD, active disease was defined as a partial CDEIS >3.5 and inactive disease as a partial CDEIS <=3.5 (where partial CDEIS corresponds to the CDEIS from the worst segment). Finally, a total of 97 blood samples were analyzed: 22 healthy controls, 8 inactive UC, 17 active UC, 9 inactive CD and 41 active CD. As two batches were processed, 4 samples were analyzed in both batches in order to control the batch effect.

first: Núria

last: Planell


title: Expression data generated by full-length and truncated syndecan-1 overexpression in B6FS fibrosarcoma cell line

city: Huddinge

first: Tünde

last: Szatmári

state: Stockholm

address: F42 Karolinska Universitetssjukhuset

department: Laboratory Medicine

country: Sweden

institute: Karolinska Institute

summary:
To dissect the functions of syndecan-1 in the nucleus, and separate them from functions related to the cell-surface, we transfected fibrosarcoma cells with two constructs: one encoding the full-length syndecan-1, which translocates to the nucleus and another encoding syndecan-1 lacking the RMKKK nuclear localization signal with hampered nuclear translocation.
Using this model system, we combined global transcriptomic and proteomic approaches in order to disclose the molecular mechanisms governing the nuclear translocation and its related functions. Our analysis identified several genes and pathways related to the nuclear compartment TGF-β pathway was activated by nuclear syndecan-1 and three genes were significantly altered by NLS deletion: NEK11 , DOCK8 , and EGR-1 as potential candidates coupled to syndecan-1 in the nucleus.

overall_design: Gene expression profiles (Human Gene 1.1 ST) of fibrosarcoma cells were studied in cells overexpressing full length syndecan-1 (N=3), syndecan-1 lacking its NLS (N=3) and empty vector control cells (N=3)

first: F

last: Mundt

last: Brodin

first: K

last: Dobra


title: Gene expression changes following knockdown or overexpression of HHEX/PRH

status: Public on Aug 14 2017

city: Birmingham

first: John

last: Halsall

address: Medical School, Vincent Drive

department: Cancer and Genomic Sciences

institute: University of Birmingham

summary: Breast tumours progress from hyperplasia to ductal carcinoma in situ (DCIS) and invasive breast carcinoma (IBC). PRH/HHEX (Proline Rich Homeodomain/Haematopoietically expressed homeobox) is a transcription factor that displays both tumour suppressor and oncogenic activity in different disease contexts however, the role of PRH in breast cancer is poorly understood. To determine the consequences of PRH loss of function in breast cancer cells we generated inducible PRH depletion in MCF-7 cells. We show that PRH depletion results in increased MCF-7 cell proliferation in part at least due to increased vascular endothelial growth factor signaling. Moreover we demonstrate that PRH depletion increases the formation of breast cancer cells with cancer stem cell-like properties. Finally, and in keeping with these findings, we show that PRH over-expression inhibits the growth of mammary tumours in mice.  Collectively these data indicate that PRH plays a tumour suppressive role in the breast and they provide an explanation for the finding that low PRH mRNA levels are associated with a poor prognosis in breast cancer.

overall_design: A 12 array study in which Proline-Rich Homeodomain protein (PRH/HHEX) is either knocked down or overexpressed in MCF7 cells. In the knockdown experiment there are 3 scrambled shRNA control replicates and 3 PRH shRNA replicates. In the overexpression experiment there are 3 empty vector transfected control replicates and 3 PRH transfected overexpression replicates.

first: Rachael

last: Kershaw

first: Padma-Sheela

last: Jayaraman


title: Expression data from P8 mouse postnatal retina with various Rb mutant conditions

city: Toronto

first: Sean

last: McCurdy

address: 27 King's College Circle

department: Laboratory Medicine and Pathobiology

institute: University of Toronto

summary: Mouse retinal samples  were collected at postnatal day 8 (P8). Each contain different perturbations in retinoblastoma (RB) gene function in order to evaluate the dependency of CDK2 on the RB-E2F axis.

overall_design: Murine retina with different RB family perturbations were collected at P8. RNA from each sample was isolated then hybridized on Affymetrix microarray. Each n represents a biological replicate.

first: Rod

last: Bremner

first: Marek

last: Pacal


title: Expression data from rice lamina joint development

status: Public on Aug 29 2017

city: Shanghai

first: Hong-Wei

last: Xue

address: 300 Fenglin Road

country: China

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

summary:
Identification of factors regulating leaf inclination reveal a complex regulatory network of lamina joint development, however, the dynamic transcriptional programming of it remain to be elucidated.
We used microarrays to detail the global gene expression profiles at different developmental stages of lamina joint and identified distinct classes of differentially expressed genes during this process, characterized the regulating factors of rice lamina joint development.

overall_design: Four developmental stages (stage 2, 4, 5, 6) of lamina joints of last leaf, last second leaf and last third leaf were selected. 0.5cm adjacent part of lamina joint of the last third leaf was harvested as leaf control at stage 4. Totally thirteen samples were collected and each sample has two biological replicates.

first: Hongwei

first: Lijuan

last: Zhou


title: Specific macronutrients exert unique influences on the adipose-liver axis to promote hepatic steatosis in mice

city: San Francisco

first: Caroline

last: Duwaerts

address: 1001 Potrero Ave - Building 40 - Room 4102

department: Medicine-GI

institute: UCSF

summary: Testing the effect of specific macronutrient combinations on mouse metabolism in vivo, we determined that diets pairing starch as carbohydrate with oleate as fat (42%:42% kcal) induced significant white adipose tissue pathology and hepatic steatosis compared to other isocaloric combinations.

overall_design: C3H/HeOuJ mice were borken into 5 experimental groups fed 42% of calories as CHO:42% of calories as FAT and 1 control chow group.  Diets are as follows: custom DYETS#D511341  Starch/oleate, custom DYETS#D511344 sucrose/oleate, custom DYETS#D511343 starch/palmitate, custom DYETS#D511342 sucrose/palmitate, Tekland TD.95217 Adjusted Fat Diet (Western Diet), and PicoDiets #5053 Chow - Fed for 6months.  Epididymal white adipose tissue was homogenized and analyzed with NanoString nCounter® Mouse Immunology panel for gene expression levels

first: Jacquelyn

last: Maher


title: A synthetic DNA-binding inhibitor of SOX2 guided human induced pluripotent stem cells to differentiate into cardiac mesoderm

status: Public on Aug 01 2017

city: Kyoto

first: Junichi

last: Taniguchi

address: Kitashirakawa-Oiwakecho, Sakyo-Ku

department: Department of Chemistry, Graduate School of Science

country: Japan

institute: Kyoto University

summary: Targeted differentiation of human induced pluripotent stem cells (hiPSCs) using only chemicals is proclaimed to have value-added clinical potential in the regeneration of complex cell types like cardiomyocytes. Despite the availability of several small molecule inhibitors capable of modulating specific receptor-ligand interaction or enzymatic activity, no bioactive synthetic DNA-binding inhibitor targeting key cell fate-controlling gene like SOX2 is available yet. Herein, we demonstrate a novel DNA-based chemical approach to guide hiPSCs differentiation using pyrrole-imidazole polyamides (PIPs), which are sequence-selective DNA-binding synthetic molecules. Harnessing the knowledge about key transcriptional changes associated with cardiomyocyte induction, we developed a PIP termed SOX-L targeting 5′-CTTTGTT-3′ sequence and demonstrate the inhibition of SOX2-DNA interaction and mesoderm induction of hiPSCs. Genome-wide gene analyses revealed that SOX-L remarkably specified cardiac mesoderm by triggering targeted alteration in SOX2-associated gene regulatory networks. Also, employment of SOX-L along with a Wnt inhibitor successfully generated spontaneously contracting cardiomyocytes to validate our concept that DNA-binding inhibitors like PIPs could be used for directed differentiation of hiPSCs. Because PIPs could be fine-tuned to target specific DNA sequences, our DNA-based approach could be expanded to directly target and distinctively regulate key transcription factor associated with the desired cell type.

overall_design: Genome-wide gene expression change in 201B7 by treatment of PIP SOX-L were examined.

first: Hiroshi

last: Sugiyama


title: Differential activation of human ILC2s by IL-25 and IL-33

city: Leicester

first: David

middle: John

last: Cousins

address: NIHR BRC Respiratory, Glenfield Hospital

department: Respiratory Sciences

country: United Kingdom

institute: University of Leicester

summary: The epithelial cell derived cytokines IL-25 and IL-33 can both activate type 2 innate lymphoid cells (ILC2s). It is not known whether the actions of these cytokines on ILC2s are similar or divergent. To investigate this we performed in vitro culture of human ILC2s with a variety of cytokine combinations including IL-2, IL-7, IL-25 and IL-33. Transcriptome profiling of these different condtions allowed us to assess the impact on gene expression of the different treatments. The results show that IL-25 and IL-33 promote divergent gene expression programs indicating that differential expression of these cytokines can cause diverse ILC2 effector function.

overall_design: Human ILC2s were cultured for 7 days in the presence of 6 different cytokine combinations. Three biological replicates.

first: Batika

last: Rana


title: Global transcriptome profiling identifies KLF15 and SLC25A10 as regulators of adipocytes insulin sensitivity in obese women [siRNA]

status: Public on Jun 29 2017

city: Stockholm

first: Ingrid

last: Dahlman

address: Karolinska Huddinge

institute: Karolinska

summary:
The aim of this study was to identify new genes controlling insulin sensitivity in adipocytes from obese women with either insulin-resistant (OIR) or -sensitive (OIS) adipocytes.
432 genes were differentially expressed between the OIR and OIS group (FDR <5%). These genes are enriched in pathways related to glucose and amino acid metabolism, cellular respiration, and insulin signaling. Two IR-associated genes, KLF15 and SLC25A10, were selected for functional evaluation.

overall_design: Insulin sensitivity was determined by measuring lipogenesis in isolated adipocytes from abdominal subcutaneous white adipose tissue (WAT). Knockdown of KLF15 and SLC25A10 genes using siRNA inhibited insulin-stimulated lipogenesis in in vitro differentiated primary adipocytes. Transcriptome profiling of siRNA treated cells suggested that KLF15 controlled insulin stimulated lipogenesis by influencing expression of PPARG, PXMP2, AQP7, LPL and genes in the mitochondrial respiratory chain. Knockdown of SLC25A10 had modest impact on the transcriptome. Significance analysis of microarrays (SAM) was use to compare the difference in gene expression between groups.


title: Quorum Sensing/Quorum Quenching in Acinetobacter baumannii clinical strains

status: Public on Jun 12 2017

city: A Coruña

first: Maria

last: Tomas-Carmona

address: As Xubias, 84

department: Microbiology Department

country: Spain

institute: Instituto de Investigación Biomédica de A Coruña (INIBIC) / Complexo Hospitalario Universitario de A Coruña (CHUAC)

summary: We worked with microarrys analysis in presence of 3-oxo-C12-HSL molecule to analyze the profile of the genes implicated in the Quorum Quenching network in A.baumannii clinical strains. Interestingly, only 13 genes were overexpressed under 3-oxo-C12-HSL molecule being the most level a gene which encodes an Alpha/beta hydrolase enzyme (5.01). The 46.15% of the genes overexpressed were implicated in the synthesis of the acyl-homoserine lactones (AHLs).

overall_design: The arrays were designed (Bioarray Genetic Diagnosis, Alicante) using eArray (Agilent) from the complete genome of A. baumannii strain (Ab ST-2 clon_2010). Experiments were performed from three biological replicates of RNA treated with DNAse obtained from a culture in exponential average phase (optical density at 600 nm of 0.6) in the presence of 3-oxo-C12- HSL at a final concentration of 10 uM. As a negative control (RNA untreated) RNA was used with dimethyl sulfoxide (DMSO, a solvent of said acyl homoserine lactone). The RNA samples were quantified in a NanoDrop ND-1000 Spectrophotometer (NanoDrop Technologies). Quality and integrity analysis of the samples was carried out in an Agilent 2100 Bioanalyzer with the RNA 6000 Nano reagents and the RNA Nano Chips (Agilent Technologies).

first: M

last: Lopez

first: E

last: Gato

first: L

last: Blasco

last: Fernandez-Garcia

first: G

last: Bou

last: Tomas


title: Transcriptomic changes in signet ring cell colorectal cancer

status: Public on Jul 21 2017

city: Cambridge

first: Muhammad

middle: Abdullah

last: Alvi

address: Addenbrooke's site

institute: University of Cambridge

summary: Data used to look for gene expression changes correlating with DNA methylation in signet ring cell colorectal cancer.

overall_design: Looking for gene expression changes in 10 normal-tumour matched and another 16 tumour only samples (test cohort).

first: Manuel

last: Salto-Tellez


title: Expression data from NB4 control shRNA cells and NB4 TRIB3 shRNA cells

status: Public on May 12 2017

city: Beijing

first: Ke

last: Li

state: Xicheng

address: Nanwei street A2

department: pharmacology

institute: IMM

summary:
To identify the top 20 up-regulated genes in NB4 TRIB3 shRNA cells in comparison with NB4 control shRNA cells, we examined the microarray gene expression profile of these groups above.
Despite the fact that combined therapy of all-trans retinoic acid (ATRA) with arsenic trioxide (ATO) or chemotherapy dramatically improves the prognosis of patients with acute promyelocytic leukemia (APL), these regimens can cause systemic infections and secondary leukemias. Here we report that expression of the pseudokinase Tribble 3 (TRIB3) associates positively with APL progression and therapeutic resistance. The elevated TRIB3 expression promotes APL by interacting with PML-RARa and suppressing its sumoylation, ubiquitylation and degradation. This represses PML nuclear body assembly, p53-mediated senescence, cell differentiation, and supports cellular self-renewal. Genetically inhibiting Trib3 expression or disturbing the TRIB3/PML-RARa interaction produces potent therapeutic efficacy against APL and has synergic anti-APL effects when used in combination with ATRA or ATO by promoting PML-RARa degradation and PML expression. Our study provides new insight into APL pathogenesis and a new therapeutic option against APL.

overall_design: Total RNA of NB4 control shRNA and NB4 TRIB3 shRNA was obtained, and RNA quantity and quality were measured by NanoDrop ND-1000. RNA microarrays were performed.


title: Precipitation of mRNAs by Ago2 and phosphorylation mutants

status: Public on Jun 22 2017

city: Regensburg

first: Gunter

last: Meister

state: Bayern

address: Am Biopark9

department: Institute of Biochemistry, Genetics and Microbiology

institute: University of Regensburg

summary:
Argonaute (Ago) proteins associate with microRNAs (miRNAs), which guide them to complementary target mRNAs resulting in gene silencing.
RNA coimmunoprecipitations (RIP) were performed with Ago2 and Ago2 mutants. The precipitated mRNAs were analyzed using one Affymetrix microarrays to compare the mRNA preciptation rates of mutants vs Ago2 wild type.

overall_design:
HEK293 cells were transfected with plasmids expressing tagged h.s. Ago2 (wild type) or tagged h.s. Ago2 mutants Ago2_824-34A (Phos3A), Ago2_824-34E(Phos3E) and Ago2-Y529E(529E). Following RIP, mRNA was extracted and hybridized to Affymetrix microarrays.
The Input Samples and the IP samples underwent separate VSN ERCC normalization.

first: Daniela

last: Zeitler

first: Johannes

last: Danner

first: Nicholas

last: Strieder


title: Global transcriptome profiling identifies KLF15 and SLC25A10 as regulators of adipocytes insulin sensitivity in obese women

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

overall_design: Refer to individual Series


title: Antisecretory Factor Reduces Tumor Pressure and Exhibits Anti-Tumor Activity in Human Glioblastoma

status: Public on May 01 2017

last: Quigley

address: 1450 Third St. Room 207

department: Helen Diller Comprehensive Cancer Center

summary: Glioblastoma (GBM) is among the most aggressive cancers and progresses with developing high interstitial fluid pressure (IFP). Increased IFP is a barrier to drug uptake, but the relationship between mechanical/osmotic stresses and tumor biology remains unclear. Blocking shrinkage-sensitive sodium-potassium-chloride co-transporter 1 (NKKC1) with its inhibitor bumetanide hinders proliferation and invasion of GBM cells. However, its clinical application is limited by poor brain penetration and adverse-effects. We found that compression promotes GBM cell proliferation, an effect antagonized by either bumetanide or antisecretory factor (AF), an antisecretory protein with a proved safety in humans. AF and bumetanide inhibited osmotic adaptation of cultured GBM cells in a similar manner. Using a telemetry-based approach, AF administration reduced IFP in patient-derived GBM xenografts, decreased tumor growth, increased cellular uptake of chemotherapeutics, and promoted temozolomide-sensitivity in GBM xenografts. In conclusion, AF therapy represents a novel pressure-reducing strategy with anti-tumor activity to safely improve the outcome of GBM patients.

overall_design: 16 samples, no replicates, 4 treatment conditions, derived from 4 individual patients

first: Anders

middle: I

last: Persson


title: Rice Gene Network Inferred from Expression Profiling of Plants Carrying Xa3/Xa26.

status: Public on Jun 13 2017

city: WUHAN

first: hanming

last: hong

address: SHIZHISHAN

institute: NCPGR

summary:
Japonica rice (Oryza sativa ssp. japonica) variety Mudanjiang 8 (MDJ8) is the wild-type and is susceptible to Xoo. Transgenic rice line Rb49 carries the MR gene Xa3/Xa26, which is driven by its native promoter with the genetic background of MDJ8, and this line is resistant to certain strains (including strain PXO61) of Xoo. Although many studies on Xa3/Xa26-mediated resistace to rice Xoo have been published, the molecular mechanism of this major resistance gene remains poorly understood. Here, we use affymetrix microarray technology to analyze the regulated network mediated by Xa3/Xa26
We used microarrays to study the gene expression network mediated by Xa3/Xa26. Plants were inoculated with the Xoo strain PXO61 at the four-leaf to five-leaf stage by the leaf-clipping method. Control rice plants were inoculated with water (mock inoculation). Samples were collected before inoculation (ck) and at 2, 4, and 24 hours after PXO61 or mock inoculation from Rb49 and MDJ8. Leaf fragments approximately 2 cm in length that were immediately next to the inoculation site were collected.

overall_design: Rice leaves collected at different time points post mock or PXO61 treatments were selected  for RNA extraction and hybridization on Affymetrix microarrays. We sought to obtain the regulated network mediated by Xa3/Xa26.

first: Hanming

last: Hong

first: Yanyan

last: Liu

first: Haitao

last: Zhang

first: Jinghua

last: Xiao

first: Xianghua

first: Shiping

last: Wang


title: DNA methylation analysis of bull semen according to peripubertal age (10vs16 mo)

status: Public on Apr 08 2017

city: Québec City

first: Marc-André

last: Sirard

state: Quebec

address: Offfice 2732, 2440 Hochelaga Blvd.

department: Sciences Animales

country: Canada

institute: Université Laval

type: Methylation profiling by genome tiling array

summary: The DNA methylation pattern in spermatozoa of bulls at different age was investigated. Spermatozoa collected from 4 different bulls at 10 and 16 month each. Genome-wide DNA methylation analysis was performed by micro array using EDMA platform.

overall_design: Two condition experiment,  4 bulls, all collected at 10 and 16 months old

first: Simon

last: Lambert

first: Patrick

last: Blondin

first: Christian

last: Vigneault

first: Rémi

last: Labrecque


title: Methylation pattern analysis of bull semen at 10,12 and 16 months old


title: Cluster regulation of RUNX family by "gene switch" triggers a profound tumor regression of diverse origins.

status: Public on Mar 26 2017

first: Junichi

last: Taniguchi

summary: Although Runt-related transcription factor 1 (RUNX1) has been generally considered to be a tumor suppressor, a growing body of evidence strongly suggests its pro-oncogenic property in acute myeloid leukemia (AML), Here we demonstrate that anti-leukemic effect mediated by RUNX1 depletion is highly dependent on a functional p53-mediated cell death pathway. Based on our present findings, anti-tumor effect elicited by RUNX1 silencing was compensated by the other RUNX family members such as RUNX2 and RUNX3, and a simultaneous attenuation of whole RUNX family members as a cluster displayed a much stronger anti-tumor effect relative to their individual suppression. Notably, switching off RUNX cluster utilizing the novel alkylating agent-conjugated pyrrole-imidazole (PI) polyamides, which specifically bound to the consensus RUNX-binding sequences, was highly effective against leukemia as well as dismal-prognostic solid tumors arising from diverse origins in vivo without any significant adverse events. Together, this work identifies the crucial role of RUNX cluster in the maintenance and the progression of cancer cells, and the indicated gene switch technology-dependent its modulation would be a novel strategy to control malignancies.

overall_design: Genome-wide gene expression change by knockdown of RUNX family genes or alkylating PIP conjugates were examined.

first: Ken

last: Morita

first: Hiroshi

last: Sugiyama

first: Yasuhiko

last: Kamikubo


title: circRNA expression in HCC and matched non-tumor tissues

status: Public on Apr 04 2017

city: HANGZHOU

first: DAN

last: HAN

state: ZHEJIANG

address: 866 YUHANGTANG ROAD

department: MEDICAL COLLEGE

institute: ZHEJIANG UNIVERSITY

summary: To determine the circRNA expression profile in HCC and matched non-tumor tissues, we used circRNA microArray analysis form Arraystar to examine the expression of circRNAs in HCC and matched non-tumor tissues.

overall_design: Hepar tissues from HCC surgery were distributed into two experimental groups: normal tissue group and tumor tissue group, then perform circRNAs chips by Arraystar Human circRNAs chip (Arraystar)

first: Dan

last: Han

first: Xuetao

last: Cao


title: The drought-responsive gene expression in rice panicle

status: Public on Jun 14 2017

first: haibin

last: wei

address: 294 Taiyuan Road

department: Institute for Nutritional Sciences

institute: Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences

summary: The young panicles 2 cm length were used for expression analysis in well watered control and drought stressed treatment. The panicle samples from biological replicates of six rice varieties were obtained in three independent experiments. The expression profiles were generated using Affymetrix rice genome arrays.

overall_design: In this study, six rice varieties were grown in cement enclosed plots. Water was drained for drought stress in the plots at later tillering stage and allowed to dry. The young panicles (2 cm in length) at the onset of the panicle differentiation were sampled and harvested to microarray experiments.

first: Shunwu

last: Yu

first: Chen

last: Chen


title: Transcriptomics analysis of Hirschsprung’s disease

status: Public on Mar 22 2017

city: Nanjing

first: yankai

last: xia

state: Jiangsu

address: 101Longmian Avenue, Jiangning District

institute: Nanjing Medical University

summary: A total of 3 pooled control and 3 pooled case colon samples were analyzed.

overall_design: case vs. control

first: Yankai

last: Xia

first: Weibing

last: Tang

first: Minjian