title: Expression data from yeast exposed to Caspofungin (wild type strain and rlm1, slt2, msn2/4 and bcy1 mutants) and Aminocandin (wild type strain)

city: Madrid

first: Javier

last: Arroyo

state: Madrid

address: Plaza Ramón y Cajal, S/N

department: Facultad de Farmacia, Departamento de Microbiologia II

country: Spain

institute: Universidad Complutense de Madrid

summary: We did transcription profiling on the effect of rlm1 (MAPK Slt2 transcription factor) deletion, slt2 (MAPK of Cell wall intregity pathway) deletion, bcy1 (Regulatory subunit of the cyclic AMP-dependent protein kinase (PKA)) deletion and msn2/4 (Stress-responsive transcriptional activators) deletion in genes involved in Caspofungin response (2 hours of treatment). In addition, we analyzed the genome-wide expression profile of the wild type strain in response to Aminocandin (2 hours of treatment).

platform_organism:
Schizosaccharomyces pombe
Saccharomyces cerevisiae

overall_design: For Caspofungin treatment, six biological samples for wild type strain, three biological samples for rlm1, slt2 and msn2/4 mutants and two biological samples for bcy1 mutant were analyzed . Two biological samples were analyzed for wild type strain in response to Aminocandin. Two microarray experiment were carried out for each biological sample:  1. absence of the drug   2. presence of 15 ng/ml of Caspofungin or Aminocandin for two hours


title: FAS signalling in retroviral neuroinflammation

status: Public on Feb 01 2017

city: Leuven

first: Tim

last: Dierckx

state: Vlaams Brabant

address: Herestraat 49 - 1040

department: Microbiology and Immunology

country: Belgium

institute: KU Leuven

summary: We comprehensively explored Fas expression (protein and mRNA) and function in lymphocyte activation, apoptosis, proliferation and transcriptome, using flow cytometry, [3H]-thymidine incorporation and microarray analysis in PBMC from HTLV-1 Associated Myelopathy/Tropical Spastic Paraparesis (HAM/TSP) patients.

overall_design: A systems analysis of HAM/TSP in vitro gene expression showed that triggering Fas receptor with agonist (but not antagonist) antibody, induces a specific gene set with a central role for NFKB pro-survival signaling (n=3). In addition, ex vivo transcripts significantly correlated to FAS mRNA levels are enriched in proliferative but not apoptotic pathways in HAM/TSP patients (n=6).

first: Johan

last: Van Weyenbergh

first: Wouter

last: Van Delm

first: Soraya

last: Menezes


title: The Legionella pneumophila genome evolved to accommodate multiple regulatory mechanisms controlled by the CsrA-system

status: Public on Jan 26 2017

city: Paris

first: Christophe

last: Rusniok

address: 25, 28 rue du Docteur Roux

department: Genomes et Genetique

country: France

institute: Institut Pasteur

type: Expression profiling by high throughput sequencing

type: Non-coding RNA profiling by high throughput sequencing

summary: The RNA binding protein CsrA is the master regulator of the bi-phasic life cycle of Legionella pneumophila governing virulence expression in this intracellular pathogen. The goal of the study was to use deep sequencing of RNA enriched by co-immunoprecipitation with epitope tagged CsrA to identify CsrA-associated transcripts at the genome level. We found 478 mRNAs or non-coding RNAs to be targets of CsrA. Among those major regulators including FleQ, the regulator of flagella expression, LqsR, the regulator of quorum sensing and RpoS implicated in stress response were identified. The expression of over 40 type IV secreted effector proteins important for intracellular survival and virulence are under the control of CsrA. Combined with transcriptomics, whole shotgun proteomics of a wild type and a CsrA mutant strain and functional analyses of several CsrA-targeted RNAs we identified the first riboswitch in L. pneumophila, a thiamine pyrophosphate riboswitch, and discovered a new mode of regulation by CsrA that allows L. pneumophila to regulate the pentose phosphate pathway and the glycolysis combined or individually although they share genes in a single operon. Our results further underline the indispensable role of CsrA in the life cycle of L. pneumophila and provide new insights into its regulatory roles and mechanisms.

overall_design: For each RIP-seq experiment, epitope-tagged CsrA protein and CsrA without Flag-Tag as negative control was used in parallel to perform the library construction. In total, 5 independent libraries (biological replicates) were executed for both, called IP1, IP2, IP7, IP8 and IP9.

first: Tobias

last: Sahr

first: Francis

last: Impens

first: Giulia

last: Oliva

first: Odile

last: Sismeiro

first: Jean-Yves

last: Coppee

first: Carmen

last: Buchrieser


title: Identification of transcriptome signatures and biomarkers specific for potential developmental toxicants inhibiting human neural crest cell migration

status: Public on Feb 07 2017

city: Cologne

first: Agapios

last: Sachinidis

state: NRW

address: Robert-Kochstr. 39

department: Institute of Neurophysiology

country: Germany

institute: University of Cologne

summary: The in vitro test battery of the European research consortium ESNATS (‘novel stem cell-based test systems’) has been used to screen for potential human developmental toxicants. As part of this effort, the migration of neural crest (MINC) assay has been used to evaluate chemical effects on neural crest function. It identified some drug-like compounds in addition to known environmental toxicants. The hits included the HSP90 inhibitor geldanamycin, the chemotherapeutic arsenic trioxide, the flame-retardant PBDE-99, the pesticide triadimefon and the histone deacetylase inhibitors valproic acid and trichostatin A. Transcriptome changes triggered by these substances in human neural crest cells were recorded and analysed here to answer three questions: (1) can toxicants be individually identified based on their transcript profile; (2) how can the toxicity pattern reflected by transcript changes be compacted/ dimensionality-reduced for practical regulatory use; (3) how can a reduced set of biomarkers be selected for large-scale follow up? Transcript profiling allowed clear separation of different toxicants and the identification of toxicant types in a blinded test study. We also developed a diagrammatic system to visualize and compare toxicity patterns of a group of chemicals by giving a quantitative overview of altered superordinate biological processes (e.g. activation of KEGG pathways or overrepresentation of gene ontology terms). The transcript data were mined for potential markers of toxicity, and 39 transcripts were selected to either indicate general developmental toxicity or distinguish compounds with different modes-of-action in read-across. In summary, we found inclusion of transcriptome data to largely increase the information from the MINC phenotypic test.

overall_design: Human embryonic stem cells (hESC)-derived neural crest cells (NCC) have been treated for 48 hours with non-cytotoxic concentration of different toxicants (Arsenic trioxide, VPA,TSA, Geldanamycin, Triadimefon, PBDE-99, Interferon beta), known to inhibit NCC migration in vitro. Total RNA has been isolated after 48 h treatment and Affymetrix microarray analysis has been performed

first: Giorgia

last: Pallocca

first: Marcel

last: Leist


title: Specific expression of novel long non-coding RNAs in high-hyperdiploid childhood ALL

status: Public on Jan 30 2017

city: Montreal

first: Daniel

last: Sinnett

state: Quebec

address: 3175 Cote-Sainte-Catherine

country: Canada

institute: CHU Sainte-Justine

summary: Pre-B cell childhood acute lymphoblastic leukemia (pre-B cALL) is a heterogeneous disease involving many subtypes typically stratified using a combination of cytogenetic and molecular-based assays. These methods, although widely used rely on the presence of known chromosomal translocations, which is a limiting factor. There is therefore a need for robust, sensitive, and specific molecular biomarkers unaffected by such limitations that would allow better risk stratification and consequently better clinical outcome. In this study we performed a transcriptome analysis of 56 pre-B cALL patients to identify expression signatures in different subtypes. In both protein-coding and long non-coding RNAs (lncRNA), we identified subtype-specific gene signatures distinguishing pre-B cALL subtypes, particularly in t(12;21) and hyperdiploid cases. The genes up-regulated in pre-B cALL subtypes were enriched in bivalent chromatin marks in their promoters. LncRNAs is a new and under-studied class of transcripts. The subtype-specific nature of lncRNAs suggests they may be suitable clinical biomarkers to guide risk stratification and targeted therapies in pre-B cALL patients.

first: Mathieu

last: Lajoie

first: Simon

last: Drouin

first: Maxime

last: Caron

first: Pascal

last: St-Onge

first: Manon

last: Ouimet

first: Romain

last: Gioia

first: Marie-Helene

last: Lafond

first: Ramon

last: Vidal

first: Chantal

last: Richer

first: Karim

last: Oualkacha

first: Arnaud

last: Droit


title: MLL2, but not MLL1, plays a major role to sustain leukemia survival [RNA-seq]

status: Public on Jan 20 2017

city: Sheridan

first: Kenneth

middle: L

last: Jones

state: Wyoming

address: 1309 Coffeen Avenue STE 10090

country: USA

institute: Bioinformatic Solutions LLC

summary: We investigated the effect of Mll1, Mll2 and Mll1;Mll2 deletion on gene expression in MLL-AF9-transformed cells.

overall_design: MLL-AF9 cells transformed from c-Kit-enriched BM cells were treated with ethanol or 100nM 4-OHT for 24 hours. After removing the drug, cells were continued to culture for 2 days and then collected for RNA extraction and RNA-seq.

first: Yufei

last: Chen

first: Patricia

last: Ernst


title: RNA-seq data for bone-marrow-derived macrophages from wildtype and JNK1 knockout mice stimulated with yeast form Candida albicans

status: Public on Jan 18 2017

city: Beijing

first: Xin

last: Lin

address: Haidian Qu Tsinghua yuan

country: China

institute: Tsinghua University

summary: mRNA expression profile for BMDMs from wildtype and JNK1 knockout mice stimulated with yeast form Candida albicans

overall_design: BMDMs from wildtype and JNK1 knockout mice were left untreated or stimulated with yeast form Candida albicans for 24 hour, mRNA of the cells were isolated with TRIZOL and subject to RNA-seq

first: Xueqiang

last: Zhao

first: Yahui

last: Guo

first: Bin

last: Zhang


title: Epigenome analysis of B cell and  B cells infected with Epstein-Barr virus (EBV)

status: Public on Jan 11 2017

first: Rui

address: 52 Fucheng Road

institute: Peking University Cancer Hospital & Institute

summary:
Genome wide DNA methylation profiles of B cell and  B cells infected with EBV (LCLs).
The Illumina Infinium 27k Human DNA methylation Beadchip v1.2 was used to obtain DNA methylation profiles across approximately 27,000 CpGs in B cells and EBV infected B cells. Samples included 8 normal B cells without EBV, 8 normal B cells with EBV.

overall_design: Bisulphite converted DNA from the 16 samples were hybridised to the Illumina Infinium Human MehthylationEPIC BeadChip

first: Zheming

last: Lu


title: MLL2, but not MLL1, plays a major role to sustain leukemia survival [array]

summary:
The MLL1 histone methyltransferase gene undergoes many distinct chromosomal rearrangements to yield poor-prognosis leukemia. The remaining wild-type allele is most commonly, but not always, retained. To what extent the wild-type allele contributes to leukemogenesis is unclear. Here we show using rigorous, independent animal models that endogenous MLL1 is dispensable for MLL-rearranged leukemia. Potential redundancy was addressed by co-deleting the closest paralog, Mll2. Surprisingly, Mll2 deletion alone had a significant impact on survival of MLL-AF9-transformed cells and additional Mll1 loss further reduced viability and proliferation. We show that MLL1/MLL2 collaboration is not through redundancy but regulation of distinct pathways. These findings highlight the relevance of MLL2 as a drug target in MLL-rearranged leukemia and suggest its broader significance in AML.
We used microarray to investigate the effect of Mll1 deletion on gene expression in LSC-enriched MLL-AF9 leukemia cells.

overall_design: Primary MLL-AF9 leukemia mice transformed from Lin-/Sca1+/c-Kit+ (LSK) cells with the genotype of Cre+;Mll1F/+ or Cre+;Mll1F/F were injected with two doses of tamoxifen (TAM) to induce Mll1 deletion. Three days after the last TAM injection, YFP+/Lin-/c-Kit+ leukemia cells were sorted for RNA extraction and microarray.


title: Expression of viral and human microRNAs in blood in The Beijing Truck Driver Air Pollution Study (BTDAS)

status: Public on Feb 09 2017

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: MicroRNAs (miRNAs) are post-transcriptional suppressors of gene expression and potential mediators of environmental effects.  In addition to human miRNAs, viral miRNAs expressed from latent viral sequences are detectable in human cells. We will use this dataset to investigate associations between air pollution exposures and clinical outcomes (such as lung function, blood pressure, etc.)

overall_design:
The Beijing Truck Driver Air Pollution Study (BTDAS), conducted between June 15 and July 27, 2008, included two different groups with high exposure to air pollution: 60 truck drivers and 60 office workers (Baccarelli et al. 2011).  All participants lived in the Beijing metropolitan area and had been working in their current position for at least two years.  No subject was on regular medication, including anti-inflammatory drugs or aspirin, during the course of the study.  We examined each participant on two separate days separated by a one- to two-week interval.  Truck drivers and office workers were similar by age, sex, smoking status, and education.  A self-administered questionnaire was used to collect detailed information on demographics, lifestyle, and other exposures.
--------------------------------------
technical replicate: GSM1540856, GSM1540762
technical replicate: GSM1540857, GSM1540613
technical replicate: GSM1540858, GSM1540854
technical replicate: GSM1540859, GSM1540605
technical replicate: GSM1540860, GSM1540772
technical replicate: GSM1540861, GSM1540648
technical replicate: GSM1540862, GSM1540774
technical replicate: GSM1540863, GSM1540639
technical replicate: GSM1540864, GSM1540792
technical replicate: GSM1540865, GSM1540669
technical replicate: GSM1540866, GSM1540804
technical replicate: GSM1540867, GSM1540665

first: Lifang

last: Hou

first: Andrea

middle: A

last: Baccarelli


title: Novel Non-catalytic Substrate-selective p38α-specific MAPK Inhibitors with Endothelial-Stabilizing and Anti-inflammatory Activity

status: Public on Jan 10 2017

city: Baltimore

first: Theresa

middle: K

last: Hodges

state: MD

address: 801 W. Baltimore Street

department: Institute for Genome Sciences

institute: University of Maryland Baltimore

summary: We developed a novel substrate-selective inhibitor of p38 MAPK, UM101, and compared its effects on TNF-induced gene expression by human lung microvascular endothelial cells (HMVECLs) with the prototypical p38 catalytic inhibitor, SB203580

overall_design: HMVECLs were pretreated with DMSO (vehicle), UM101, or SB203580, then stimulated with TNF for 3h. Total RNA from treated cells and untreated control HMVECLs was isolated, poly(A) mRNA enriched and sequenced using the Illumina HiSeq platform.

first: Jeffrey

middle: D

last: Hasday


title: MicroRNA profiling of gastric cancer

status: Public on Jan 12 2017

city: Krakow

first: Marek

last: Sierżęga

address: Kopernika 40

country: Poland

institute: Jagiellonian University Meical College

summary: The aim of this study was to determine differences in microRNA expression profiles of gastric cancer and adjacent healthy gastric mucosa. Both types of tissue samples were collected during operative procedures of 20 patients. microRNA expression was determined by miRNA microarrays.

platform_organism:
Homo sapiens
Human alphaherpesvirus 1
Human alphaherpesvirus 2
Cytomegalovirus
Lymphocryptovirus
Rhadinovirus
JC polyomavirus
Human immunodeficiency virus 1
Merkel cell polyomavirus
Betapolyomavirus hominis
Betapolyomavirus macacae

overall_design:
Twenty pairs of tissue samples collected from patients diagnosed with gastric cancer. Each pair included resected primary tumor and corresponding healthy gastric mucosa. There were no replicates. Comparative expression analysis was carried out to determine microRNAs up-regulated and down-regulated in cancer tissues compared to healthy mucosa.
Please note that each sample was labeled with both Cy3 and Cy5, resulting in two raw data files per sample ('1_Exiqon_*_S01.txt' for Cy3; '0_Exiqon_*_S01.txt' is for Cy5 data).

last: Sierzega

first: Piotr

last: Kolodziejczyk

first: Jan

last: Kulig


title: The chromatin associated Pf1 protein maintains nucleolar integrity: gene expression from Pf1 +/+ and Pf1-/- mouse embryonic fibroblasts.

city: New York

first: Gregory

last: David

state: NY

address: 550 1st Avenue, MSB417

department: Biochemistry and Molecular Pharmacology

institute: New York University School of Medicine

summary:
Pf1, also known as Phf12 (plant homeodomain (PHD) zinc finger protein 12) is a member of the PHD zinc finger family. Pf1 was first identified in a yeast-two hybrid screen for proteins interacting with the paired amphipathic helix (PAH) 2 domain of mSin3A, and shown to function as a transcriptional repressor . We generated Pf1 knockout mice to define the physiological role of Pf1.
To  identify the molecular mechanisms underlying the cellular defects elicited by genetic inactivation of Pf1, we next examined the impact of a Pf1 deletion on genome-wide transcriptome. RNA extracted from wild-type and Pf1-depleted MEFs was profiled by hybridization to a whole genome microarray.

overall_design: Total RNA from Pf+/+ and Pf1 -/- MEFs at passage 2-3 (Pf+/+ lines 7706-5 and 7706-6 and Pf1 -/- lines 7706-2 and 7706-4) was isolated using Trizol reagent (Thermo Fisher Scientific, Waltham, MA) according to the manufacturers protocol.  The RNA samples were examined on Affymetrix GeneChip Mouse Genome 430A 2.0 Array

first: Richard

last: Graveline

first: Katarzyna

middle: M

last: Marcinkewicz


title: MLL2, but not MLL1, plays a major role to sustain leukemia survival

first: Kenneth

last: Jones

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

overall_design: Refer to individual Series


title: HFF Cells: Control vs. Toxoplasma gondii infected

status: Public on Jan 01 2017

city: Wenzhou

first: liyang

last: huang

institute: Wenzhou Medical College

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

summary: Expression profile microarray of human foreskin fibroblast cell comparing control untreated HFF cell with HFF cell infected with ME49 strain.Study on Toxoplasma gondii infection of HFF cell LncRNAs expression, for further studies on the differential exprssion of LncRNAs in HFF cell against the infection of Toxoplasma gondii research provide the basic function.

overall_design: Two-condition experiment, HFF cell vs Toxoplasma gondii infected HFFcell. Biological replicates: 3 control replicates, 3 infected replicates.

first: Liyang

last: Huang

first: Shaohui

last: Liang


title: Testicular dysgenesis syndrome and long-lasting epigenetic silencing of mouse sperm genes involved in the reproductive system after prenatal exposure to DEHP

status: Public on Jan 09 2017

city: Geneva

first: Ludwig

last: Stenz

address: Rue Michel-Servet 1

department: Department of Genetic Medecine and Development

country: Switzerland

institute: University of Geneva

summary: Prenatal exposure to 300 mg/kg/day of bis(2-ethylhexyl)phthalate (D300) was administered to pregnant mice during embryonic days 9th to 19th, inducing a Testicular Dysgenesis Syndrome (TDS), observed in 100 days old F1 derived C57BL/6J males. A transcriptomic analysis was performed from spermatozoa produced by D300 mice compared with CTL. We used an adapted RNAseq method able to quantify all RNAs molecules independently of the 5’ and 3’ modifications.

overall_design: 5 CTL versus 5 D300.

first: Jessica

last: Escoffier

first: Rita

last: Rahban

first: Serge

last: Nef

first: Ariane

last: Paoloni-Giacobino


title: Transcriptomic response in leaves of two Vitis vinifera L. varieties in field and under greenhouse abiotic stress

city: Lisboa

first: Margarida

last: Rocheta

address: Tapada da ajuda

country: Portugal

institute: Instituto Superior de Agronomia

summary:
Experimental research on the effects of abiotic stress over grapevine has mainly focused on water shortage. The adaptation of plants to stress is a complex response triggered by cascades of molecular networks involved in stress perception, signal transduction, and the expression of specific stress-related genes and metabolites. Approaches such as array-based transcript profiling allow assessing the expression of thousands of genes in control and stress tissues.
Gene expression upon acute (heat and light) and steady (drought) individual stresses and field conditions were compared in two grapevine (Vitis vinifera L.) varieties, Trincadeira (TR) and Touriga Nacional (TN).

overall_design: In the field, only irrigation was used as treatments, thus two treatments were applied: Full irrigated (control) and non irrigated (stress). Irrigation water was applied with drip emitters (4.0 L h-1 for FI) two per vine, positioned 30 cm from the vine trunk. The water was supplied according to the crop’s evapotranspiration (ETc). Samples were taken when the pre dawn leaf water potential was circa -0.7MPa in the NI plants and higher than -0.2MPa in the FI plants. To assess physiological effects of stress treatments: Individual stresses were applied when shoots were 50 to 60 cm high (after circa four months growth). The stresses applied were: W (Water)– stop irrigation until the pre-dawn leaf water potential (Ψw) was -0.9 MPa; L (Light) – 1 hour at 2000µmolm2s-1; H (Heat) – 1 hour at 42ºC

first: João

last: Lucas

first: Miguel

last: Ramos

first: Luisa

last: Carvalho

first: Sara

last: Amâncio


title: Comprehensive miRNA profiling of skeletal muscle and serum in induced and normal mouse muscle atrophy during aging

status: Public on Dec 31 2016

city: Scarsdale

first: Brandon

last: Milholland

state: New York

address: 119B Montgomery Avenue

institute: Albert Einstein College of Medicine

summary: We report comprehensive miRNA expression profiles by miRNA-seq analysis in tibialis anterior muscle and serum of a disuse-induced atrophy model, compared with young (6 months) and old (24 months) mice.

overall_design: RNA-seq of young muscle (n=5), old muscle (n=5), disuse muscle (n=5), young serum (n=5), old serum (n=4) and disuse serum (n=5).

first: Hwa

middle: J

last: Jung

first: Kwang‐Pyo

last: Lee

first: Ki‐Sun

last: Kwon

first: Yousin

last: Suh


title: Iron_deficiency gene expression in Arabidopsis wild type and yellow stripe1-like1/3 (ysl1ysl3) double mutants.

city: Amherst

first: Elsbeth

middle: Lewis

last: Walker

state: Massachusetts

address: 611 North Pleasant St

department: Biology Department

institute: University of Massachusetts

summary: When iron is withdrawn from the growth medium of plants, large changes in gene expression have been observed.  A double mutant with T-DNA insertions in the Arabidopsis yellow stripe1-like1 (At4g24120) and yellow stripe3-like (At5g53550) genes shows strong iron-related phenotypes.  This study is intended to uncover the gene expression changes that occur in leaves and roots of the double mutant compared to wild type plants.

overall_design: or this study, wild type plants were grown with or whithout iron for a period of three days.  In these plants, the levels of iron deficiency chlorosis and the levels of iron are similar to that in the double mutant plants grown with normal iron nutrition. Thus, six samples are compared in this study.  Leaves from wild type plants grown with normal iron nutrition.   Leaves from wild type plants grown without iron for three days. Leaves from ysl1ysl3 double mutant plants grown with normal iron nutrition.   Roots from wild type plants grown with normal iron nutrition.     Roots from wild type plants grown without iron for three days.  Roots from ysl1ysl3 double mutant plants grown with normal iron nutrition. Plants were grown in sterile petri plates containing 1X Murishige and Skoog medium with or without antibiotics.  Plates were placed in an upright position so that the roots grew along the surface rather than inside the agar, which allowed for easy transfer.  Incubator conditions for plate-grown plants were 16 hour light, 8 hour dark at 22C.  After 10 days, plants were moved either to fresh iron containing plates (+Fe samples) or to plates prepared without Fe (-Fe samples).  Growth was continued for 3 days before samples were harvested.  Chlorophyll measurements were made at the time of harvest.


title: Molecular analyses reveal an inflammatory response in the solid component and cystic fluid of human adamantinomatous craniopharyngioma

city: Aurora

first: Andrew

last: Donson

state: CO

department: Pediatrics

institute: CU Anschutz Medical Campus

type:
Expression profiling by array
Third-party reanalysis

summary:
Pediatric adamantinomatous craniopharyngioma (ACP) cyst may be associated with injury to critical neurological structures, such as the hypothalamus, resulting in poor quality of life and shorter lifespan. This work presents evidence that immune actors, both pro-inflammatory and immunomodulatory, and their receptors, are present at unique levels in ACP cyst fluid and tumor tissue, potentially indicating a mechanism underlying cyst growth and tumor invasion of the hypothalamus.
Transcriptomic analysis revealed that ACP, when compared to other pediatric brain tumors and nomral brain, harbored overexpression of a number of inflammatory and immunosuppressive genes.

overall_design: Gene expression profiles were generated from ACP surgical tumor, and surgical tumors of other common pediatric brain tumor types and normal brain samples (n=110) using Affymetrix HG-U133plus2 chips (Platform GPL570).


title: Hyperoxia in FGF10 knock-down mice [Lung]

city: Giessen

first: Jochen

last: Wilhelm

state: Hessen

address: Aulweg 132

department: Institute for Lung Health

institute: Justus-Liebig University Giessen

summary: Our previous data obtained by using immunohistochemistry showed, that Fgf10+/- (50% Fgf10 expression compared to WT) in hyperoxic condition at postnatal day 3 (P3) compared to WT  has less vessel count in the lung and less muscularization of small capillaries in the lung. Furthermore, Fgf10+/- showed a drastic increase in mortality upon hyperoxic lung injury. Main question to be answer by this experiment is as followed: Does Fgf10+/-  mice after hyperoxia from P0-P3 show different expression profiles at P3 compared to WT? To adress this question we harvest lungs at P3 from WT and Fgf10+/- after hyperoxia treatment from P0-P3. For this the mice were sacrificed by Ketamin/ Dormitor ip, lungs were perfused transcardiac with PBS and directly frozen in liquid nitrogen.

overall_design: Two-condition experiment (genotype x treatment): wild-type mice and Fgf10+/- mice are kept in either normoxic or hyperoxic conditions. Sample size: 4 per group (16 total)

first: Chao

last: Cho-Ming

first: Saverio

last: Bellusci


title: Hyperoxia in FGF10 knock-down mice [AEC II cells]

summary: Our previous data obtained by using immunohistochemistry showed, that Fgf10+/- (50% Fgf10 expression compared to WT) in hyperoxic condition at postnatal day 3 (P3) compared to WT  has less vessel count in the lung and less muscularization of small capillaries in the lung. Furthermore, Fgf10+/- showed a drastic increase in mortality upon hyperoxic lung injury. Main question to be answer by this experiment is as followed: Does AEC II from Fgf10+/-  mice in normoxia show different expression profiles at P3 compared to AEC II from WT? To adress this question we harvest lungs at P3 from WT and Fgf10+/- . For this the mice were sacrificed by Ketamin/ Dormitor ip, lungs were perfused transcardiac with PBS and directly frozen in liquid nitrogen.


title: Time course RNA-seq experimant invesitgating two isolates of Puccinia graminis infecting a common wheat host.

city: Manhattan

first: William

middle: Brock

last: Rutter

state: KS

address: 1712 Claflin Road

department: Plant Pathology

institute: Kansas State University

summary: We report a time series RNA-seq experiment involving two isolates of Puccinia graminis separately infecting Triticum aestivum cv. Morocco points post inoculation

overall_design: 3 biological replicates of infected leaf tissue were collected from 5 time points post inoculation plus a mock inoculation as a control

first: Eduard

last: Akhunov


title: Gene expression signatures in GIST-T1 cells transfected with a miR-186 inhibitor molecule

city: Sapporo

first: Hiromu

last: Suzuki

state: Hokkaido

address: S1, W17, Chuo-ku

department: Department of Molecular Biology

country: Japan

institute: Sapporo Medical University

summary: To clarify the role of miR-186 in GIST, we carried out a gene expression microarray analysis using GIST-T1 cells transfected with a miR-186 inhibitor or a negative control. We found that 253 probe sets (229 unique genes) were upregulated (>1.5-fold) by inhibition of miR-186 in GIST-T1 cells.

overall_design: GIST-T1 cells were transfected with a mirVana miR-186 inhibitor  (Thermo Fisher Scientific) or a mirVana miRNA inhibitor Negative Control  (Thermo Fisher Scientific). Forty-eight hours after transfection, total RNA was extracted and gene expression signatures were analyzed.

first: Takeshi

last: Niinuma


title: LLQR E. coli ATCC 25922 vs wild-type E. coli ATCC 25922

city: Seville

first: Jose Manuel

last: Rodriguez Martinez

address: Snchez Pizjuan SN

institute: University of Seville

summary:
Global response to ciprofloxacin in low level quinolone resistant Escherichia coli: a shorter path to survival. Background: Bactericidal activity of quinolones in bacteria has been related to a combination of DNA fragmentation, ROS production and programmed dead cell systems. Subjacent molecular systems responsible for reduction of bactericidal effect in low-level quinolone resistance (LLQR) phenotypes remain to be clarified. To answer this question and to define new possible antimicrobial targets, the transcriptomic profile in isogenic Escherichia coli harbouring quinolone resistance mechanisms in the presence of ciprofloxacin was evaluated.
Materials and methods: E. coli 25922 was used as background strain. Four LLQR isogenic strains were tested for transcriptomic assays: ATCC 25922 (wild-type), EC14 (coding for QnrS1), EC19 (marR deletion and coding for QnrS1) and EC24 (Ser83Leu substitution in GyrA and coding for QnrS1). Cells in exponential phase (DO600=0.4) were exposed to 1 mg/L of ciprofloxacin (breakpoint for reduced susceptibility according to CLSI) during 1 hour and, further, RNA was purified. Gene expression analysis was performed using AGILENT technology. Data obtained for each strain were always normalized to the wild-type E. coli ATCC 25922. Specific ROS modulation targets were validated by genetic and biochemical approach.
Results: A radical differential response to ciprofloxacin in LLQR strains, either up or downregulation, was observed (proportional to the MIC values). Multiple genes implicated in ROS production (related to TCA cycle, aerobic respiration or detoxification systems) were upregulated (sdhC up to 63.5-folds) in LLQR mutants. SOS system components were downregulated (recA up to 30.7-folds). yihE, coding for a protective kinase of programmed cell death, was also upregulated (up to 5.2-folds). SdhC inhibition sensitized LLQR phenotypes (up to Log=2.3 after 24 hours).
Conclusions: At clinical relevant concentration of ciprofloxacin, the pattern of genes expression of critical systems for bacterial survival and mutant development were significantly modified in LLQR phenotypes. This approach allowed validating ROS modulation as an interesting target in terms of bacterial sensitization.

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

overall_design: Two-condition experiment, LLQR E. coli vs wild-type E. coli. Biological replicates: 2 control replicates, 2 replicates for each LLQR strain. E. coli ATCC 25922 (wild-type) and EC14, EC19, EC24 (LLQR) isogenic strains were tested to evaluate the global response to relevant fix concentration of ciprofloxacin (1 mg/L, breakpoint for reduced susceptibility according to CLSI). All of them were susceptible to quinolones according to CLSI breakpoints. Cultures were started from single colonies and grown overnight in 25 ml of LB. These cell were diluted 1:100 and growth to cell concentration of 4x108 cells/ml (OD600 nm=0.4, exponential phase) for treatment. Three biological replicates per genotype were incubated at 1 mg/L of ciprofloxacin during 60 minutes (that means 250xMIC for E. coli ATCC 25922, 8xMIC for EC14, 2xMIC for EC19 and 1xMIC for EC24). Approximately 109 cells (2 ml) were taken for RNA isolation. The pellet was immediately processed. Pellet was pre-incubated in RNAprotect Bacteria Reagent (Qiagen, Hilden, Germany). RNA extraction was performed using the RNeasy Mini Kit (Qiagen, Hilden, Germany). Contaminating DNA was removed from RNA samples with TURBO DNA-free (Ambion, USA). The amount of RNA was measured on the NanoDrop ND-1000 (Thermo Scientific). The integrity of the RNA samples was analyzed with the BioAnalyzer 2100 (Agilent Technologies) using the RNAnano 6000 kit (Agilent Technologies). Labeling, microarray hybridization, scanning, and data processing were performed at the Genomic Unit of the Centro Nacional de Biotecnología (http://wwwuser.cnb.csic.es/~genomica/servicos.htm). Data obtained for each LLQR mutant were always compared to the E. coli ATCC 25922 wild-type strain. FIESTA program was used for analysis (http://bioinfogp.cnb.csic.es) and p-value was determined according to FDR algorithm (p<0.05 was considered significant).

first: Jesús

last: MACHUCA

first: Esther

last: RECACHA

first: Alejandra

last: BRIALES

first: Paula

last: DÍAZ-DE-ALBA

first: J

last: Blazquez

first: Alvaro

last: PASCUAL

first: Jose-Manuel

last: RODRÍGUEZ-MARTÍNEZ


title: RNA-seq to profile the H-NS transcriptome in EHEC O157:H7 strain EDL933

city: Shanghai

first: Baoshan

last: Wan

state: Shanghai

address: Rm 710, Bldg 5, 280 S. Chongqing Rd

department: Department of Microbiology and Immunology

institute: Shanghai Jiao Tong University School of Medicine

summary: In order to define the role of H-NS in regulating gene transcription and further find out the biological significance of this protein in EHEC, we conducted RNA-seq and then analyzed the transcriptome data, using EHEC O157:H7 strain EDL933 and Δhns. A total of 983 genes were found to be regulated by H-NS. 213 and 770 genes exhibited lower and higher transcript levels in Δhns than in WT, respectively. For instance, chemotaxis and flagellar associated genes were down-regulated in Δhns. Besides, 34 genes on virulence plasmid pO157 were down-regulated by H-NS. The outcome of RNA-seq were verified by real time quantitative PCR. As reported in Salmonella Typhimurium, Δhns showed a growth deficiency and altered fitness. We first detected that both stx1 and stx2 in EDL933 were repressed by H-NS. Although no survival difference between EDL933 and Δhns was detected when phagocytized by macrophage, we characterized the higher ability of colonization and in consequence the higher virulence of Δhns to BALB/c mice by experimental analyses than those of WT, especially when intact commensal flora of mice existed. This might indeed help us understand the core role of H-NS in depth.

overall_design: RNA sequencing of EHEC O157:H7 strain EDL933 and Δhns in 2 biological repeats.

first: Qiufen

last: Zhang

first: Jing

last: Tao

first: Aiping

last: Zhou

first: Yu-Feng

last: Yao

first: JinJing

last: Ni


title: Role of Alternative splicing in human skeletal muscle and cancer cachexia

city: Edmonton

first: Sambasivarao

last: Damaraju

state: Alberta

address: 11560 University Ave

department: Laboratory medicine and pathology

institute: University of Alberta

summary: Alternative splicing (AS) is a post-transcriptional gene regulatory mechanism that contributes to proteome diversity. Aberrant splicing mechanisms (mutations, polymorphisms, insertion/deletion etc.) contribute to various cancers and muscle related conditions such as Duchenne muscular dystrophy. However, dysregulation of AS in Cancer Cachexia (CC) patients remains unexplored. Our objectives were (i) to profile alternatively spliced genes (ASGs) on a genome-wide scale, and (ii) to identify DE alternatively spliced genes (DASGs) associated with CC. Rectus abdominis muscle biopsies obtained from cancer patients were stratified into cachectic cases (n=21, classified based on International consensus diagnostic framework for CC) and non-cachectic controls (n=19, weight stable cancer patients). Human Transcriptome array 2.0 was used for profiling ASGs using the total RNA isolated from muscle biopsies. Representative DASG signatures were validated using semi-quantitative RT-PCR. We identified 8960 ASGs, of which 922 DASGs (772 up-regulated, 150 down-regulated) were identified at > 1.4 fold-change and p < 0.05. Representative DASGs when validated by semi-quantitative RT-PCR also showed similar trends, confirming the primary findings from the genome-wide arrays. Identified DASGs were associated with myogenesis, adipogenesis, protein ubiquitination and inflammation.  Up to 10% of the DASGs exhibited cassette exon (exon included or skipped) as a predominant form of AS event. We also observed other forms of AS events such as intron retention, alternate promoters. Overall, we have, for the first time conducted global profiling of muscle tissue to identify DASGs associated with CC. The mechanistic roles of the identified DASGs in CC pathophysiology using model systems is warranted, as well as replication of findings in independent cohorts.

overall_design: Identification of Differentially expressed Alternatively spliced genes associated with cancer cachexia

first: Ashok

last: Narasimhan

first: Russell

last: Greiner

first: Oliver

middle: F

last: Bathe

first: Vickie

middle: E

last: Baracos


title: Hyperoxia in FGF10 knock-down mice

first: Jochen

last: Wilhelm


title: Identifying lincRNA as prognostic biomarker for clear cell renal cell carcinoma

city: Stanford

first: Xue

last: Gong

state: CA

institute: Stanford University

summary: RNA sequencing libraries were made for A-498 and 786-O to detect the transcripts regulated by the lincRNA comparing knockdown and the non-targeting control.

overall_design: Two siRNAs were designed, non-target control and the siRNAs were introduced to the cell lines A-498 and 786-O separately by Lipofectamine 2000. After 16 hours total RNA were extracted. Barcoded cDNA libraries were then prepared from total RNA using the Illumina TruSeq RNAseq kit, and sequenced (single-end 36-bp reads) on an Illumina HiSeq instrument.


title: Identification of genes regulated by HSF1-T20A mutant or doxorubicin treatment

city: Ube

first: Eiichi

last: Takaki

state: Yamaguchi

address: minami-kogushi, 1-1-1

institute: Yamaguchi university

summary: To examine whether HSF1-PARP1-PARP13 complex regulates the expression of genes, we performed DNA microarray analysis. We also performed DNA microarray analysis to identify doxorubicin-induced genes,.

overall_design: mRNA levels in HeLa cells with/without HSF1-shRNA and HSF1-knockdown HeLa cells with wild-type HSF1, HSF1-T20A or GFP  were analyzed by DNA microarray analysis using GeneChip human Gene 1.0 ST Array (Affymetrix). mRNA levels in HeLa cells with/without doxorubicin were analyzed by DNA microarray analysis using GeneChip human Gene 1.0 ST Array (Affymetrix).

first: Mitsuaki

last: Fujimoto

first: Akira

last: Nakaki


title: Evaluation of the NUP98-HOXA9 role as oncogenic transcription factor

city: Madrid

first: Ana

last: Del Rio

state: Madrid

address: Calle Melchor Fernandez Almagro 3

institute: CNIO

type: Genome binding/occupancy profiling by high throughput sequencing

summary: To study the oncogenic mechanism triggered by the leukemic fusion protein NUP98-HOXA9, we cloned the cDNA of NUP98-HOXA9 into a retroviral vector (pMSCV-IRES-GFP) and efficiently transduced the HEK293FT human cell line. We performed a ChIP-seq analysis to identify the DNA binding sites of NUP98-HOXA9. These results allowed us to demonstrate that NUP98-HOXA9 regulates the expression of genes involved in the development of Acute Myeloid Leukemia by directly interacting with their enhancer regions. We further investigated the functional contribution to the DNA binding profile of the two moieties that compose the fusion protein. We cloned the coding region of HOXA9 wt and NUP98 wt in the same retroviral vector, established two new cellular models, 293FT-HOXA9 and 293FT-NUP98, and performed separate ChIP-seq analyses. We demonstrated that both moieties contribute importantly to the regulation of the target genes.

overall_design: Identification of NUP98-HOXA9, HOXA9 and NUP98 specific DNA binding sites in human cellular models

first: A

last: Rio-Machin

first: C

last: Cigudosa


title: NUP98-HOXA9 role as oncogenic transcription factor

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


title: Development of NUP98-HOXA9 gene expression signatures

summary: To explore the molecular mechanisms induced by the leukemic fusion protein NUP98-HOXA9, we performed gene expression analysis of human hematopoietic progenitors and primary samples of patients that express NUP98-HOXA9. By combining these data with ChIP-seq results, we observed that the fusion protein is able to both activate and repress the expression of its target genes.

overall_design: Three independent experiments were performed using different clones of the human hematopoietic progenitor model (hHP-NH) and control model (hHP-empty vector). On the other hand, RNA from seven primary samples was analyzed.


title: Transcriptome responses of Lactobacillus acetotolerans F28 to a short and long term ethanol stress

status: Public on Dec 23 2016

city: Beijing

first: xiaoling

last: zhang

address: NO.1 Beichen West Road, Chaoyang District

institute: Institute of microbiology chinese academy of sciences

summary: Exploring the mechanism of ethanol tolerance in  Lactobacillus acetotolerans F28  and finding key genes which maybe participating in protecting cells from damage during ethanol stimulation.

overall_design: Examination of 4 different samples at different time after 12% (v/v) ethonal or water treatment. Every sample was designed for 3 replicates.

first: Xiaopan

last: Yang

first: Kunling

last: Teng

first: Jie

last: Zhang

first: Fangfang

last: Wang

first: Tong

first: Peijie

last: Han

first: Fengyan

last: Bai

first: Jin

last: Zhong


title: Effect of Hsp70 inhibitor JG-98 on gene expression in mouse macrophages

status: Public on Dec 19 2016

city: Boston

first: Boston University

last: Microarray and Sequencing Resource

state: MA

address: 72 East Concord Street, E631

department: Microarray and Sequencing Resource

institute: Boston University

summary: JG-98 reduces migration of macrophages. We assessed how this compound affects expression of genes associated with motility and migration. A number of motility/migration genes were significantly downregulated.

overall_design: Mouse bone marrow macrophages were treated with 0.3 micromole of JG-98 for 16 hours, and RNA was isolated.

first: Michael

last: Sherman


title: Transcriptome Sequencing and Analysis of Three Sheep Intestinal Regions

status: Public on Dec 21 2016

city: Tai’an

first: Chao

last: Tianle

state: Shandong

address: Daizong street, no. 61, 6/5000 Shandong Agricultural University

institute: 6/5000 Shandong Agricultural University

summary: To identify intestinal metabolic related genes and reveal these molecular regulation mechanisms, we sequenced and compared the transcriptomes of mucosal epithelial tissues between cecum, proximal colon and duodenum. A total of 5420 genes constructed by 8055 transcripts were identified as differential expressed genes.

overall_design: Transcriptome comparison of three sheep intestinal regions.

first: Wang

last: Jianmin


title: VEGF promotes RNAPII pausing release through ETS1 to stimulate angiogenesis

city: Minhang

first: bing

address: 800 Dong Chuan Road

department: Shanghai Center for Systems Biomedicine

institute: Shanghai Jiao Tong University

summary: RNA polymerase II (RNAPII) pausing release is a recently recognized checkpoint for transcriptional regulation. The biological roles of RNAPII pausing release and the mechanisms that by which extracellular signals control it are incompletely understood. Here we identify a novel mechanism by which VEGF stimulates RNAPII pausing-release through acetylation of ETS1, a master endothelial cell transcriptional regulator. In endothelial cells (ECs), ETS1 uniquely bound transcribed gene promoters and stimulated their expression by broadly increasing RNA polymerase II (RNAPII) pause release. VEGF enhanced ETS1 chromatin occupancy. Furthermore, VEGF increased ETS1 acetylation, enhancing its binding by BRD4 and thereby stimulating RNAPII pause release. This ETS1-mediated transduction of VEGF signaling to increase RNAPII pausing release was essential for EC angiogenic responses in vitro and in vivo. Together, our results define a new angiogenic pathway in which VEGF enhances ETS1-Brd4 interaction to broadly promote RNAPII pause release and drive angiogenesis.

overall_design: ChiP-seq of ETS1 and Spike-in mRNA seq on HUVEC after VEGF stimulation at 0,1,4,12 hours. ChiP-seq of H3K27ac, H3K27me3, H3K4me1, 2, 3, H3K36me3, c-MYC, RNAPII on HUVEC after VEGF stimulation at 0 hour. ChiP-seq of RNAPII on HUVEC treated with GFP&ETS1 modified RNA, GFP& ETS1 siRNA.  ERCC spike-in RNA-seq of HUVEC treated with GFP&ETS1 modified RNA.

first: Chen-jia

last: Huan

first: Daniel

middle: S

last: Day

first: Yi

last: Fu

first: Ye

last: Sun

first: Shiyan

first: Fang

first: Pengyi

last: Yan

first: Fei

last: Gu

first: Sean

last: Stevens

first: Jonathan

middle: G

last: Seidman

first: Zeguang

first: Peter

last: Park

first: Bing

first: William

middle: T

last: Pu


title: Rheumatoid Arthritis Rat Model Treated with Acupuncture

city: Rome

first: Christine

last: Nardini

address: Via dei Taurini 9

country: Italy

institute: PICB

overall_design: Refer to individual Series


title: Target RNAs of Samd4 identified by RNA IP in mouse osteoblasts

status: Public on Dec 03 2016

first: Ningning

last: Niu

address: 160 Pu Jian Road, Shanghai

department: Clinical Stem Cell Research Center

institute: Shanghai Jiao Tong University School of Medicine Affiliated Renji Hospital

summary: We report the application of RNA immunoprecipitation sequencing technology to identify targets of RNA-binding protein, Samd4, in osteoblasts. By obtaining sequences from immunoprecipitated RNA, we generated several mRNAs which could be bound by Samd4 in mouse osteoblasts.

overall_design: Examination of Samd4-binding RNAs in osteoblasts.

first: Niu

last: Ningning

first: Yang

last: Qin


title: Genome-wide analysis of long non-coding RNA (lncRNA) profiles in leg muscle of Xinghua Chickens.

status: Public on Dec 13 2016

city: Guangzhou

first: Zhenhui

last: Li

address: Tianhe District Wushan road

institute: South China Agricultural University

summary: We have used RNA-seq to examine long non-coding RNA (lncRNA) and mRNA from rRNA depleted in  chicken leg musle of three different development stages (11 embryo age, 16 embryo age, and 1 days post hatch). Our study reveals the prevalence of lncRNA in chicken, and has identified lncRNA differentially abundant in different stage of embryonic skeletal muscle, suggesting its important functions during poultry muscle development.

overall_design: To assess lncRNA and mRNA expression during chicken skeletal muscle development, we sequenced and analyzed leg musle at 11 embryo age, 16 embryo age, and 1 days post hatch.

first: Hongjia

last: Ouyang

first: Qinghua

last: Nie


title: Expression analysis of novel and known antifungal drugs using S. cerevisiae as a model

status: Public on Dec 30 2016

city: Torino

first: Irene

last: Stefanini

address: via Accademia Albertina

institute: University of Turin

summary: A systematic approach allowing the identification of the molecular way of action of novel potential drugs still represents the golden-tool for drug-discovery researchers. While high-throughput screening technologies of large libraries is now well established, the assessment of the drug targets and mechanism of action is still under development. Taking advantage of the yeast model Saccharomyces cerevisiae, we herein applied BarSeq, a Next Generation Sequencing based method to the analysis of both haploinsufficiency and homozygous fitness effects of a novel antifungal drug compared to the well-known antifungal, ketoconazole. Integrative bioinformatic analysis of BarSeq, whole genome expression analysis and classical biological assays identified the target and cell pathways affected by the novel antifungal. Confirmation of the effects observed in the yeast model as well as in pathogenic fungi further demonstrated the reliability of the multi-sided approach and the novelty of the targets and mode of action of the new class of molecules studied that thus represent a valuable source of novel antifungals.

overall_design: Two-condition experiments, drug vs. DMSO-treated S. cerevisiae cells. Analyzed drugs: two concentrations of ketoconazole (2.5 uM and 50 uM) and one concentration of the novel proposed antifungal 089. Biological replicates: 3 control replicates for each experiment.

first: Lisa

last: Rizzetto

first: Damariz

last: Rivero

first: Duccio

last: Cavalieri


title: Gene expression in the brains of different strains of laboratory mice upon intranasal infection with vaccine strain (TC83) of Venezuelan equine encephalitis virus

status: Public on Dec 10 2016

city: Galveston

first: Slobodan

last: Paessler

state: TX

address: 301 University Blvd

department: Pathology

institute: UTMB

summary:
Differing from other experimental models, intranasal infection with vaccine strain of Venezuelan equine encephalitis virus, VEEV, (TC83) caused high titer infection in the brain and 90–100% mortality in the C3H/HeN murine model. Intranasal infection with VEEV (TC83) caused persistent viral infection in the brains of mice without functional αβ T-cells (αβ-TCR -/-). While wild-type C57BL/6 mice clear infectious virus in the brain by 13 dpi, αβ-TCR -/- maintain infectious virus in the brain to 92 dpi.
To better characterize the susceptibility to disease development in different strains of mice, we have analyzed the gene transcriptomes in the brains of infected mice.

overall_design: Using Affymetrix microarray analysis of brain homogenates, we compared the transcriptional profiles of mock-infected to VEEV (TC83)-infected C3H/HeN mice and we contrasted the transcriptional responses of VEEV (TC83)-infected relative mock-infected αβ-TCR -/- and wild-type C57BL6/J mice at the peak of acute disease associated with uniform high viral load in the brain and significant clinical symptoms, six days post-infection.

first: Olga

last: Kolokoltsova

first: Katherine

last: Taylor

first: Allison

last: Poussard

first: Jennifer

last: Smith

first: D

last: Estes


title: Affymetrix Chip Data of the Transcriptome of the Rheumatoid Arthritis Rat Model Treated with Acupuncture (Affymetrix, mRNA, batch 2)

first: Christine

last: Nardini

summary: We report the application of Affymetrix technology for high-throughput profiling of the transcriptome of the rheumatoid arthritis (RA) rat model induced by collagen type II (CIA),  with acupuncture and Methotrexate+acupuncture treatment, as well as epidermal needle manipulation on healthy rat model.

overall_design: The experiment was designed as 3 arms: epidermal needle manipulation on healthy rat model (HAP) and RA (rheumatoid arthritis) rat model (AP), and Methotrexate injection accompanied with epidermal needle manipulation (MTXAP). Whole blood sampling was carried out before any therapy in RA (RA_T0) and healthy rats (NORA_T0) rats, and after 34 days of therapeutic treatments for any group (AP, HAP and MTXAP). From all the 14 blood collected samples (three replicates for each group, for each timepoint), PBMC (Peripheral Blood mononuclear Cells) were isolated and total RNA extracted. Finally, purified RNA were analyzed using Affymetrix microarray technology (rat230 2.0, ~31,000 probe sets, ~ 30,000 transcripts and variants from over 28,000 well-substantiated rat genes).

first: Valentina

last: Devescovi

first: Yuanhua

last: Liu


title: Developmental hotspots drive transcriptional variability and convergence in the Drosophila olfactory system

status: Public on Dec 01 2016

city: Durham

first: Jia Wern

last: Pan

state: NC

address: French Family Science Center, Science Drive

department: Biology

institute: Duke University

summary: The goal of this study was to identify the preponderance of developmental hotspots in the Drosophila olfactory system. Using RNASeq-derived transcriptome profiles of the developing and adult antennae for six different Drosophila species, we show that a few highly variable transcription factors may drive, likely in a combinatorial fashion, high variability in a few select olfactory receptor neuron (ORN) developmental lineages (i.e. developmental hotspots) in an otherwise mostly conserved background. Furthermore, the high variability of these few ORN lineages leads to a correspondingly high probability that they will recruited during the adaptation of the Drosophila olfactory system to specific ecological pressures, one potential example being the remarkably convergent antennal transcriptome profiles in two Drosophila species that have independently evolved the ability to specialize on specific host plants.

sample_organism:
Drosophila ananassae
Drosophila erecta
Drosophila sechellia
Drosophila simulans
Drosophila virilis

overall_design: mRNA profiles from antenna and antennal discs across 4 developmental time points for 6 Drosophila species

first: Jia

middle: W

first: Qingyun

first: Alicia

last: Brandt

first: Sumie

last: Okuwa

first: Corbin

last: Jones

first: Pelin

middle: C

last: Volkan


title: Inference of cell-type composition from human brain transcriptomic datasets illuminates the effects of age, manner of death, dissection, and psychiatric diagnosis

status: Public on Dec 20 2016

city: Ann Arbor

first: Megan

middle: Hastings

last: Hagenauer

state: MI

address: 205 Zina Pitcher Pl.

department: MBNI

institute: University of Michigan

summary: Most neuroscientists would agree that psychiatric illness is unlikely to arise from pathological changes that occur uniformly across all cells in a given brain region. Despite this fact, the majority of transcriptomic analyses of the human brain to date are conducted using macro-dissected tissue due to the difficulty of conducting single-cell level analyses on donated post-mortem brains. To address this issue statistically, we compiled a database of several thousand transcripts that were specifically-enriched in one of 10 primary brain cell types identified in published single cell type transcriptomic experiments. Using this database, we predicted the relative cell type composition for 157 human dorsolateral prefrontal cortex samples using Affymetrix microarray data collected by the Pritzker Neuropsychiatric Consortium, as well as for 841 samples spanning 160 brain regions included in an Agilent microarray dataset collected by the Allen Brain Atlas. These predictions were generated by averaging normalized expression levels across the transcripts specific to each primary cell type to create a “cell type index”. Using this method, we determined that the expression of cell type specific transcripts identified by different experiments, methodologies, and species clustered into three main cell type groups: neurons, oligodendrocytes, and astrocytes/support cells. Overall, the principal components of variation in the data were largely explained by the neuron to glia ratio of the samples. When comparing across brain regions, we were able to easily capture canonical cell type signatures – increased endothelial cells and vasculature in the choroid plexus, oligodendrocytes in the corpus callosum, astrocytes in the central glial substance, neurons and immature cells in the dentate gyrus, and oligodendrocytes and interneurons in the globus pallidus. The relative balance of these cell types was influenced by a variety of demographic, pre- and post-mortem variables. Age and prolonged anaerobic conditions around the time of death were associated with decreased neuronal content and increased astrocytic and endothelial content in the tissue, replicating the known higher vulnerability of neurons to aging and adverse conditions, and illustrating the proliferation of vasculature in a hypoxic environment. We also found that the red blood cell content was reduced in individuals who died in a manner that involved systemic blood loss. Finally, statistically accounting for cell type improved both the sensitivity and interpretability of diagnosis effects within the data. We were able to observe a decrease in astrocytic content in subjects with Major Depressive Disorder, mirroring what had been previously observed morphometrically. By including a set of “cell type indices” in a larger model examining the relationship between gene expression and neuropsychiatric illness, we were able to successfully detect almost twice as many genes with previously identified relationships to bipolar disorder and schizophrenia than using traditional analysis methods.

overall_design:
Sample collection, including human subject recruitment and characterization, tissue dissection, and RNA extraction, was described previously (see Evans 2003 Neurobiol Dis 14:240-250, Vawter 2003 Neuropsychopharm 29: 373-384, Li 2004 Biol Psychiatry 55:346-352, Li 2013 PNAS 110: 9950-9955). The original sample size included dorsolateral prefrontal cortex (DLPFC) tissue from 172 subjects. We ran each sample on at least two microarrays (chip count=367) using the Affymetrix U133-A or U133Plus-v2 GeneChips, however, we only used the U133A part of the U133Plus-v2 GeneChip in our analysis and also 4  samples have been excluded by quality filtering. We applied RMA (Robust Multi-array Analysis) (see Irizarry 2003 Biostatistics 4:249-264, Irizarry 2003 Nucleic Acids Res 31:e15) to summarize probe set expression levels, using a custom Chip Definition File, resulting in expression data for 11,911 ENTREZ transcripts. All downstream analyses were performed in R. Details of the data processing, including data cleaning and normalization, are located in the Supplementary Materials for Li 2013 PNAS 110: 9950-9955 and Hagenauer et al. (submitted).

Please note that [1] the data from the control subjects was previously uploaded to GEO as part of GSE45642 (GSM1124358-GSM1124518) [2] the original raw data for the 'DLPFC_Male_Control_r_p_UCDavis_10622' (GSM2431810) sample is unavailable and thus, the annotated version CEL file is provided.

middle: H

first: Jun

middle: Z

last: Li

first: David

last: Walsh

first: Cortney

last: Turner

first: William

last: Bunney

first: Richard

last: Myers

first: Jack

last: Barchas

first: Alan

last: Schatzberg

first: Stanley

last: Watson

first: Huda

last: Akil


title: Recurrent involvement of DPP9 in gene fusions in serous ovarian carcinoma

city: Oslo

first: Marianne

middle: Lislerud

last: Smebye

address: Postboks 4953 Nydalen

country: Norway

institute: Oslo University Hospital

summary: We have looked for fusion genes in ovarian carcinomas. We combined previously known genomic aberrations, detected by karyotyping, and gene expression analysis. We found recurrent DPP9 gene expression deregulation with matching translocations. In additon, candidate fusion partner genes from the exon-level expression analysis were ranked according to deviating expression compared to the median of the sample set. The results were collated with data obtained from the RNA-seq analysis.

overall_design: We analyzed 19 previously karyotyped ovarian carcinomas (18 of the serous histotype and one undifferentiated) using exon-level gene expression microarrays (Affymetrix Human Exon 1.0 ST platform) to identify aberrantly expressed genes possibly involved in gene fusion events. In addition, some of the samples were analyzed by RNA-sequencing.

middle: L

first: Antonio

last: Agostini

first: Bjarne

last: Johannessen

first: Jim

last: Thorsen

first: Ben

last: Davidson

first: Claes

last: Tropé

first: Sverre

last: Heim

first: Rolf

middle: I

last: Skotheim

first: Francesca

last: Micci


title: Genome profiling of free circulating tumor DNA by oncoscan and comparison to profiles in tumor biopsies evaluated by cytoscan

status: Public on Nov 30 2016

city: Copenhagen

first: Olga

last: Østrup

address: Blegdamsvej 9

department: Genomic Medicine

country: Denmark

institute: Copenhagen University Hospital (Rigshospitalet)

summary: Genomic profiles of tumor DNA obtained from biopsies were systematically compared to corresponding samples of circulating cell free tumor DNA. The aim was to investigate correspondance between numerical, segmental and focal aberrations, as well as precision in detection and resolution of oncoscan array performance on cfDNA.

overall_design: tumor DNA from biopsies was analyzed for genomic aberrations by CytoScan HD and cfDNA from blood by OncoScan.

first: Lise

middle: B

last: Ahlborn

first: Finn

last: Nielsen


title: The footprint of the aging stroma in older breast cancer patients.

status: Public on Nov 26 2016

city: Brussel

first: Yacine

last: Bareche

address: Rue Héger-Bordetstraat 1

institute: Jules Bordet Institute

summary:
Background: Tumoral masses are not only composed of malignant cells, but also enclose a more or less ample stromal micromilieu, which has been shown to influence the cancer cell behaviour. As aging induces accumulation of senescent cells in the body, this micromilieu is thought to be different in cancers occurring in old patients compared to the younger counterparts. More specifically, senescence-related fibroblastic features, such as the Senescence Associated Secretory Profile (SASP) and the induction of Autophagy, are suspected to stimulate tumor growth and progression.
Methods: We compared gene expression profiles in stromal fields of breast carcinomas by performing laser capture microdissection of the cancer-associated stroma from 8 old (≥80 years at diagnosis) and 9 young (< 45 years at diagnosis) triple negative breast cancer patients. Gene expression data were obtained by microarray analysis (Affymetrix). Differential gene expression and Gene Set Enrichment Analysis (GSEA) were performed.
Results: Differential gene expression analysis showed higher growth-, dedifferentiation- and migration- promoting gene expression in the stromal samples of older vs younger patients. GSEA confirmed the presence of a SASP, as well as the presence of Autophagy in the stroma of older patients.
Conclusion: We provide the first evidence in humans that older age at diagnosis is associated with a different stromal micromilieu in breast cancers. The SASP and the presence of Autophagy appear to be important age-induced stromal features.

overall_design: Gene expression data were generated from micro-dissected stromal tissue.

first: Barbara

last: Brouwers

first: Debora

last: Fumagalli

first: Sylvain

last: Brohee

first: Sigrid

last: Hatse

first: Olivier

last: Govaere

first: Giuseppe

last: Floris

first: Kathleen

last: Van den Eynde

first: Patrick

last: Schöffski

first: Ann

last: Smeets

first: Diether

last: Lambrechts

first: Christos

last: Sotiriou

first: Hans

last: Wildiers


title: To find out microRNA contribute to the development of gallbladder cancer

status: Public on Nov 18 2016

city: Shanghai

first: Huaifeng

last: Li

address: NO.1665, kongjiang road, Shanghai, China

department: general surgery

institute: Xinhua hospital affiliated to Shanghai jiaotong university, school of medicine

summary: MicroRNAs (miRNAs) play a critical role in the progression of cancer. However, little is known on the miRNAs expression profiles of gallbladder cancer.We performed this microarray to identify miRNAs associated with gallbladder cancer.

overall_design: 4 pairs of  gallbladder cancer tissues and paired normal gallbladder tissues were collected after colecystectomy.

first: Ying-bin

last: Liu

first: Yi-jun

last: Shu

first: Run-Fa

last: Bao

first: Lin

last: Jiang

first: Wei

last: Gong

first: Xiang-song

last: Wu

first: Mao-lan

first: Xu-an

last: Wang

first: Yi-jian

last: Zhang


title: Determining Prostate Cancer Aggressiveness Utilizing a Novel DNA Methylation Approach

city: Los Angeles

first: Kamilla

last: Mundbjerg

address: 1441 Eastlake Ave

department: Norris Comprehensive Cancer Center

institute: USC Keck School of Medicine

type: Methylation profiling by genome tiling array

summary: The clinical management of prostate cancer is challenging and currently relies primarily on staging, histological grading, and tumor size. In this study, we take advantage of the propensity of prostate cancer to be multifocal and categorize aggressiveness of individual prostate cancer foci based on DNA methylation patterns in primary and metastatic tumors.

overall_design: Bisulfite converted DNA from 92 samples was hybridized to the Illumina Infinium 450k Human Methylation Beadchip

first: Gangning

last: Liang


title: Genetic and mechanistic diversity of piRNA 3' end formation

status: Public on Nov 16 2016

city: Vienna

first: Jakob

last: Schnabl

state: Vienna

address: Dr. Bohr-Gasse 3

country: Austria

institute: IMBA - Institute of Molecular Biotechnology

summary: Small regulatory RNAs guide Argonaute (Ago) proteins in a sequence-specific manner to their targets and therefore have important roles in eukaryotic gene silencing. Of the three small RNA classes, microRNAs and short interfering RNAs are processed from double-stranded precursors into defined 21- to 23-mers by Dicer, an endoribonuclease with intrinsic ruler function. PIWI- interacting RNAs (piRNAs)—the 22–30-nt-long guides for PIWI- clade Ago proteins that silence transposons in animal gonads— are generated independently of Dicer from single-stranded precursors. piRNA 5′ ends are defined either by Zucchini, the Drosophila homologue of mitoPLD—a mitochondria-anchored endonuclease, or by piRNA-guided target cleavage. Formation of piRNA 3′ ends is poorly understood. Here we report that two genetically and mechanistically distinct pathways generate piRNA 3′ ends in Drosophila. The initiating nucleases are either Zucchini or the PIWI-clade proteins Aubergine (Aub)/Ago3. While Zucchini- mediated cleavages directly define mature piRNA 3′ ends, Aub/ Ago3-mediated cleavages liberate pre-piRNAs that require extensive resection by the 3′-to-5′ exoribonuclease Nibbler (Drosophila homologue of Mut-7). The relative activity of these two pathways dictates the extent to which piRNAs are directed to cytoplasmic or nuclear PIWI-clade proteins and thereby sets the balance between post-transcriptional and transcriptional silencing. Notably, loss of both Zucchini and Nibbler reveals a minimal, Argonaute-driven small RNA biogenesis pathway in which piRNA 5′ and 3′ ends are directly produced by closely spaced Aub/Ago3-mediated cleavage events. Our data reveal a coherent model for piRNA biogenesis, and should aid the mechanistic dissection of the processes that govern piRNA 3′-end formation.

overall_design: This study aims at understanding how piRNA 3' ends are formed in Drosophila and what the role of the exonuclease Nibbler is in their formation.

first: Rippei

last: Hayashi

first: Dominik

last: Handler

first: Fabio

last: Mohn

first: Stefan

last: Ameres

first: Julius

last: Brennecke


title: Digital Gene Expression (DGE) Analysis of Human Umbilical Vein Endothelial Cells (HUVECs) At 24 Hours Post Hantaavirus Infection

status: Public on Nov 17 2016

city: Xi’an

first: Hong-Wei

last: Ma

state: Shaanxi

address: 169 Changle West Road

department: Department of Microbiology

institute: Fourth Military Medical University

summary: Hantavirus infection causing zoonotic diseases with a high mortality rate in humans has long been a global public health concern. Over the past decades, accumulating evidences suggest that long noncoding RNAs (lncRNAs) play key regulatory roles in innate immunity. However, the involvement of host lncRNAs in hantaviral control remains uncharacterized. To explore the potential role of long non-coding RNAs in host innate immune responses, DGE analysis of HUVECs for whole genome profiling was performed at 24 hours post HTNV infection.

overall_design: RNA isolated from HUVECs, which were either mock infected or treated with live or Co60-inactivated HTNV at MOI 1 for 24 hours, was sequenced on an Illumina Platform. More than 3.4 million reads per sample were obtained. One sample in the Mock, HTNV infection or Co60-inactivated HTNV infection group were collected for DGE. No replicates were applied in each group.

last: Ye

first: Fang-Lin


title: Inefficient DNA repair is an aging-related modifier of Parkinson disease

status: Public on Nov 13 2016

city: Maastricht

first: Kasper

last: Derks

state: Limburg

address: P. Debyelaan 25

department: Clinical Genetics

country: Netherlands

institute: Maastricht University Medical Center

summary: The underlying relation between Parkinson disease (PD) etiopathology and its major risk factor, aging, is largely unknown. The nature of the specific age-related mechanisms promoting PD onset is experimentally difficult to elucidate because aging is a highly complex process contributed by multiple factors. Recent evidence, however, established a strong and causative link between genome stability and aging. To investigate a possible nexus between DNA damage accumulation, aging, and PD we examined DNA repair pathways associated with aging in laboratory animal models and human cases. We demonstrate that dermal fibroblasts from PD patients display flawed nucleotide excision repair (NER) capacity and that NER-defective mice exhibit typical PD-like pathological alterations, including decreased dopaminergic innervation in the striatum, increased phospho-synuclein levels, and defects in mitochondrial respiration. NER mouse mutants are also more sensitive to the prototypical PD toxin MPTP and their transcriptomic landscape shares important similarities with that of PD patients. Overall, our results demonstrate that specific defects in DNA repair impact the dopaminergic system, are associated with human PD pathology, and might therefore constitute a novel risk factor for PD by affecting the aging process.

overall_design: In total 8 samples were analyzed, 4 controls and 4 Ercc1 mutants.

first: Sara

last: Sepe

first: Chiara

last: Milanese

first: Sylvia

last: Gabriels

first: Cesar

last: Payan-Gomez

first: Wilfred

last: van Ijcken

first: Yvonne

middle: M

last: Rijksen

first: Alex

last: Nigg

first: Sandra

last: Moreno

first: Silvia

last: Cerri

last: Blandini

first: Jan

last: Hoeijmakers

first: Pier

last: Mastroberardino


title: Expression data from CD34+ CML cells

status: Public on Nov 11 2016

city: Glasgow

first: Lisa

last: Hopcroft

address: Paul O'Gorman Leukaemia Research Centre

country: United Kingdom

institute: University of Glasgow

summary: We used microarrays to assess differential gene expression between treatment arms.

overall_design: CD34+ CML cells treated for 16hrs with imatinib, dasatinib, BMS214662 and BMS225975.

first: Mhairi

last: Copland


title: C. saccharolyticus transcriptomes reveal consequences of chemical pre-treatment and genetic modification of lignocellulose

status: Public on Nov 23 2016

city: Raleigh

first: Robert

last: Kelly

address: Campus Box 7905

department: Chemical and Biomolecular Engineering

institute: North Carolina State University

summary: The genome of the lignocellulose-degrading, extremely thermophilic bacterium Caldicellulosiruptor saccharolyticus encodes genes comprising clusters of glycoside hydrolases, ABC transporters and metabolic enzymes that are transcriptionally responsive to carbohydrates. Transcriptomic and biosolubilization analyses were used to determine if C. saccharolyticus could be deployed as a probe to assess the characteristics of plant biomass feedstocks and efficacy of pre-treatment methods, as these both relate to deconstruction strategies for biofuels production. Based on the response of C. saccharolyticus to plant cell wall polysaccharides, genomic loci were identified that reflected the availability of cellulose, glucomannan, pectin and xylan in biomass to microbial degradation. Furthermore, these loci were useful in assessing how various plant biomass feedstocks (genetically and chemically modified Populus sp., unpretreated Populus sp., and chemically modified switchgrass) were amenable C. saccharolyticus solubilization.

overall_design: Three independant 4-slide loop designs were used with a total of ten treatments. Biological repeats were harvested for each treatment. Loop #1 consists of plant model polysaccharides: crystalline cellulose (Avicel), mannan (konjac glucomannan), xylan (birchwood) and pectin. Loop #2 consists of comically pretreated and genetically modified plant biomass: Populus trichopcarpa (unpretreated), dilute acid pretreated switchgrass, dilute pretreated Populus trichocarpa x deltoides and genetically modified, lignin-reduced P. trichocarpa (as4CL1). Loop #3 consists of genetically modified P. trichocarpa: P. trichocarpa (unpretreated), and two variants of cellulose-reduced P. trichocarpa (7-1 and 7-2). Each condition was labeled with cy3 and cy5 dyes.

last: Blumer-Schuette

first: Jeffrey

middle: V

last: Zurawski

first: Jonathan

last: Conway

first: Piyum

last: Khatibi

first: Derrick

last: Lewis

first: Quanzi

last: Li

first: Vincent

last: Chiang


title: Differential gene expression analysis of WT and p190-B-/- HSC after bone marrow transplantation

status: Public on Nov 14 2016

city: Cincinnati

first: Marie-Dominique

last: Filippi

state: OH

address: 3333 Burnet Av

department: Experimental Hematology and Cancer Biology

institute: Cincinnati Children's Research Foundation

summary: The overall goals are these experiments are to identify genes and pathways that are critical for hematopoietic stem cell functions during bone marrow regeneration after transplantation. We have found that loss of expression of p190-B RhoGAP, a negative regulator of RhoGTPase, enhances HSC long-term engraftment. Hence, we used microarray analysis to compare gene exprssion profile of WT and p190-B-/- HSC after transplantation.

overall_design: Expression profiles of mRNA in HSCs from WT and p190-B-/- transplanted mice

first: Ashwini

last: Hinge

first: Bruce

last: Aronow


title: Gene expression analysis in Plaa+/+ and PlaaG23V/G23V cerebellum/caudal brain

status: Public on Nov 05 2016

city: Edinburgh

first: Emma

middle: A

last: Hall

state: Midlothian

address: Western General Hospital, Crewe Road

department: University of Edinburgh

institute: MRC HGU, IGMM

summary: Mice homozygous for p. Gly23Val substitution in Phospholipase A2 Activating Protein (PLAA: PlaaG23V/G23V) display muscle weakness, cerebellar atazia and tremor.  To investigate the molecular mechanism for these phenotypes we dissected the caudal region of the brain including the cerebellum and hind brain from three wild type (Plaa+/+) and three mutant (PlaaG23V/G23V) mice, extracted RNA and performed gene-level microarray analysis

overall_design: We analysed RNA extracted from the caudal brain of three wild type (Plaa+/+) and three mutant (PlaaG23V/G23V) mice

first: Peter

last: Budd

first: Pleasantine

last: Mill


title: Small molecules modulate chromatin accessibility to promote NEUROG2-mediated fibroblast-to-neuron reprogramming [RNA-seq]

status: Public on Nov 09 2016

city: Dallas

first: Derek

middle: K

last: Smith

state: Texas

address: 5323 Harry Hines Blvd, NA5.202

department: Molecular Biology

institute: The University of Texas Southwestern Medical Center

summary: Pro-neural transcription factors and small molecules can induce the transdifferentiation of fibroblasts into functional neurons; however, a molecular mechanism detailing the immediate-early events that catalyze this conversion has not been well defined. We previously demonstrated that NEUROG2, forskolin (F), and dorsomorphin (D) can induce functional neurons with high-efficiency. Here, we used this model to define the genetic and epigenetic events that initiate an acquisition of neuronal identity. We demonstrate that NEUROG2 is a pioneer factor, FD enhances both genome-wide NEUROG2 chromatin occupancy and H3K27 acetylation, and synergistic transcription by these factors is essential to successful reprogramming. CREB1, activated by FD, promotes neuron survival and acts with NEUROG2 to upregulate SOX4, which co-activates NEUROD1 and NEUROD4. In addition to this hierarchical function, SOX4 targets SWI/SNF subunits and SOX4 knockdown results in extensive loss of open chromatin and abolishes reprogramming. Applying these insights, adult human glioblastoma and skin fibroblast reprogramming was improved using SOX4, SMARCA4, and chromatin modifying chemicals.

overall_design: Total RNA (36 datasets: Time course analysis of changes in gene expression using MRC-5 fibroblasts, MRC-5 fibroblasts transduced with NEUROG2-encoding lentivirus, and MRC-5 fibroblasts transduced with NEUROG2-encoding lentivirus exposed to forskolin and dorsomorphin)

first: Chun-Li

last: Zhang


title: Small molecules modulate chromatin accessibility to promote NEUROG2-mediated fibroblast-to-neuron reprogramming

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

overall_design: Refer to individual Series


title: FOXK2 ChIP sequencing in non-treated MCF-7 cells

status: Public on Nov 08 2016

city: Hangzhou

first: Xinhua

last: Liu

state: Zhejiang

address: NO.2318, Yuhangtang road

department: School of Basic Medicine

institute: Hangzhou Normal University

summary: Although clinically associated with severe intellectual disability, West syndrome, Dandy-Walker malformation, and syndactyly, the biological function of FOXK2 remains poorly explored. Here we report that FOXK2 acts as a transcription repressor. Strikingly, FOXK2 interacts with multiple transcription corepressor complexes including NCoR/SMRT, SIN3A, NuRD, and REST/CoREST. FOXK2 assembles these transcription programs to repress a cohort of genes including HIF1 and EZH2 and to regulate several signaling pathways including the hypoxic response that is critically implicated in tumor development and progression. We showed that FOXK2 inhibits the proliferation and invasion of breast cancer cells in vitro and suppresses the growth and metastasis of breast cancer in vivo. Interestingly, FOXK2 is transactivated by ERand transrepressed via reciprocal successive feedback by HIF1/EZH2. Significantly, the expression of FOXK2 is progressively lost during breast cancer progression, leading to elevated expression of EZH2, an eminent feature of aggressive breast cancer. Indeed, the expression of FOXK2 is inversely correlated with that of EZH2 and HIF1in breast carcinomas, and low FOXK2 expression is strongly correlated with higher histologic grades, positive lymph nodes, and ER/PR/Her2 status, all indicators of poor prognosis. Our experiments revealed that FOXK2 is massively involved in transcription repression, providing a molecular basis for the understanding of the mechanistic action of FOXK2. Our study identified the ER-FOXK2-HIF1/EZH2 axis in breast cancer progression, supporting the pursuit of these molecules as therapeutic targets for breast cancer intervention.

overall_design: Examination of FOXK2 target genes in MCF-7 cells

first: Lin

last: Shan

first: Xing

last: Zhou


title: Identification of ciprofloxacin helper drug targets by RNA-seq

status: Public on Nov 04 2016

first: Rasmus

middle: Nielsen

last: Klitgaard

address: Ole Maaløes vej 5, Building 4 2nd floor

department: Department of biology

institute: University of Copenhagen

summary: The aim of this study was to identify genes that can be targeted by helper drugs to counteract resistance towards ciprofloxacin (CIP). In order to reveal the impact of ciprofloxacin on the transcriptome, differential gene-expression analysis by RNA-seq was performed on the multidrug resistant E. coli strain ST131, treated with a clinically relevant concentration of ciprofloxacin (2 µg/mL).

overall_design: E. coli ST131 UR40 was treated with ciprofloxacin (2µg/mL) and samples were taken at time points 0 min, 30 min and 90min.


title: Dissecting Gene Expression Changes Accompanying a Euploid-Aneuploid Phenotypic Switch

status: Public on Nov 01 2016

city: Seattle

first: Aimee

last: Dudley

state: Washington

address: 720 Broadway

institute: PNDRI

summary:
Purpose:To dissect the mechanisms underlying altered gene expression in aneuploids, we measured transcript abundance in colonies of haploid yeast strain F45 and derived strains, including strains disomic for chromosomes XV and XVI, using RNA-seq. F45 colonies display complex “fluffy” morphologies, while the disomic colonies are smooth, resembling laboratory strains
Methods: RNA-seq analysis was carried out on RNA isolated from fully developed S. cerevisiae colonies, grown on solid medium for four days, either in triplicate or quadruplicate. Stranded, paired-end sequencing was carried out in two batches. In the first batch 2x51 bp sequencing was carried out on an Illumina Hiseq2000 and in the second batch 2x75 bp sequencing was carried out on an Illumina NextSeq.  Readpairs were aligned using Bowtie2 (version 2.1.0)with the parameters [-N 1 -I 50 -X 450 -p 6 --reorder -x -S] and allowing 1 mismatch per read. Differential transcription was detected and quantified using EdgeR (v. 3.6.8)
Results: Our two disomes displayed similar transcriptional profiles, a phenomenon not driven by their shared smooth colony morphology nor specified purely by the karyotype. Surprisingly, the environmental stress response (ESR) was induced in euploid F45, relative to the two disomes, rather than vice-versa. We also identified genes whose expression reflected a non-linear interaction between the copy number of a transcriptional regulatory gene on chromosome XVI, DIG1, and the copy number of other chromosome XVI genes. DIG1 and the remaining chromosome XVI genes also demonstrated distinct contributions to the effect of the chromosome XVI disome on ESR gene expression.
Conclusions: Expression changes in aneuploids reflect a mixture of effects shared between different aneuploidies, including stress responses, and effects unique to perturbing the copy number of particular chromosomes, including non-linear copy number interactions between genes. The balance between these two phenomena is likely to be genotype and environment specific.

overall_design: mRNA profiles of 4 day old haploid F45 colonies, and colonies derived from F45 were generated by deep sequencing, in triplicate or quadruplicate, using Illumina Hiseq2000 or Illumina Nextseq sequencing.

first: Gareth

last: Cromie

first: Zhihao

last: Tan

first: Michelle

last: Hays

first: Eric

last: Jeffery


title: Small molecules modulate chromatin accessibility to promote NEUROG2-mediated fibroblast-to-neuron reprogramming [ChIP-Seq]

overall_design: Histone 3 lysine 27 acetylation (3 input datasets, 6 immunoprecipitation datasets), histone 3 lysine 27 methylation (3 input datasets, 6 immunoprecipitation datasets), NEUROG2 (6 input datasets, 12 immunoprecipitation datasets), and SOX4 (1 input dataset, 3 immunoprecipitation datasets)


title: Change of metabolite profiles and gene transcription in subjects with high T2D risk by low ambulatory activity

city: Pierre Bénite

first: emmanuelle

last: meugnier

address: Cens Eli Bat 2 D- Hopital Lyon Sud

overall_design: We analyzed from sedentary and obese subjects by NMR lipoproteins, apolipoproteins, mono- and polyunsaturated fatty acids, gluconeogenic substrates, amino acids and glycoproteins, known to be related to T2D risks, and studied their associations with  amounts and intensities of accelerometer recorded physical activities

first: Karl

last: Herzig

first: Emmanuelle

last: Meugnier

first: Hubert

last: Vidal


title: Small molecules modulate chromatin accessibility to promote NEUROG2-mediated fibroblast-to-neuron reprogramming [ATAC-seq]

overall_design: ATAC-seq (4 datasets)

first: Smith

last: Derek K.

first: Zhang

last: Chun-Li


title: Expression data from C57BL/6 mouse bone-marrow derived macrophages

city: Boston

first: Boston University

last: Microarray and Sequencing Resource

address: 72 East Concord Street, E631

department: Microarray and Sequencing Resource

institute: Boston University

summary:
Given the dearth of new antibiotics, host-directed therapies (HDTs) are especially desirable. Since IFN-gamma (IFNγ) plays a central role in host resistance to intracellular bacteria, including Mycobacterium tuberculosis, we searched for small molecules to augment the IFNγ response in macrophages. Using a novel screen we identified a compound belonging to the rocaglate family(CMLD009433) that synergize with a sub-threshold concentration of IFNγ to enhance macrophage activation.
We used microarrays to detail the global programme of gene expression mediated by the rocaglate CMLD009433(C9433) and identified upregulation of several important regulatory genes important for host defense.

overall_design: Bone marrow derived macrophages from C57BL/6 mouse treated with 0.2U/ml IFNγ in presence and absence of of CMLD009433(C9433) were selected for RNA extraction and hybridization on Affymetrix microarrays.

first: Bidisha

last: Bhattacharya

first: Igor

last: Kramnik


title: RNA-seq analysis of mRNAs immunoprecipitated by wild-type (WT) or phospho-mimetic (S200D) FLAG-LIN28A in PA1 cells

status: Public on Oct 28 2016

first: Areum

last: Han

address: Karp Family Building, 7th Floor. 300 Longwood Ave.

institute: Boston Children's Hospital

summary: To explore the effect of LIN28 (S200) phosphorylation on LIN28's association with mRNAs on a transcriptome-wide scale, we performed mRNA-seq on RNAs immunoprecipitated (RIP-seq) by wild-type (WT) or phospho-mimetic (S200D) LIN28 in PA1 cells.

overall_design: Examination of mRNAs immunoprecipitated by wild-type and phospho-mimetic (S200D) FLAG-LIN28 (in triplicate)

first: Kaloyan

last: Tsanov

first: Daniel

middle: S

last: Pearson

first: George

middle: Q

last: Daley


title: Screening and functional investigation of miRNAs regulating milk fat metabolism in dairy goat mammary gland

status: Public on Oct 21 2016

city: Xi'an

first: Zhi

last: Chen

state: Select a State or Province

address: 22 Xinong Road, Yangling

department: Shaanxi Key Laboratory of Molecular Biology for Agriculture

institute: College of Animal Science and Technology, Northwest A&F University,  China

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

summary: Fat metabolism is a complicated process regulated by a series of factors. microRNAs (miRNAs) are a class of negative regulator of proteins and play crucial roles in many biological processes, including fat metabolism. Although there have been some researches indicating that miRNAs could influence the milk fat metabolism through targeting some factors, little is known about the effect of miRNAs on goat milk fat metabolism. Here we utilized an improved miRNA detection assay, S-Poly(T), to profile the expression of miRNAs in the goat mammary gland in early-lactation and dry-lactation. Overall, we found 146 miRNAs expression changed between early-lactation and dry-lactation, with 81 up-regulation and 65 down-regulation, among which the miR-27a, miR-200a and miR-200c have been reported to be involved in the milk fat metabolism process.

overall_design: To investigate the connection between the miRNA regulation and this physiological process in a more comprehensive way, here we profiled the differential miRNAs expression between early-lactation and dry-lactation in goat mammary gland with S-Poly(T) real method, including 267 Capra hircus primary miRNAs and 793 Bos taurus primary miRNAs from miRBase (http://www.mirbase.org/) and the new discovered miRNAs by Solexa sequencing. As Capra hircus and Bos taurus share high sequence homology with each other, some raw data or referenced data are overlapping. We have marked out the overlapping data, and details can be found in the additional materials (S1-first screening). All the miRNAs with four-fold change and p-value smaller than 0.05 were chosen as candidates.

first: Jun

last: Luo

first: Chen

last: Zhi


title: miRNA expression profiling of alcohol exposure in Drosophila melanogaster

status: Public on Oct 26 2016

city: San Juan

first: Alfredo

last: Ghezzi

state: Puerto Rico

address: PO box 23360

department: Department of Biology

institute: University of Puerto Rico, Rio Piedras

summary: We sequenced microRNA from heads of two D. melanogaster populations: an ethanol treated group (30 minutes after sedation with ethanol saturated vapor), and an age-matched untreated control group; and calculated differential microRNA expression between the two groups.

overall_design: Examination of microRNA levels in heads of D. melanogaster adult females after ethanol exposure using next generation sequencing (NGS)

first: Andrzej

last: Pietrzykowski


title: RNA-seq analysis of mRNAs immunoprecipitated by wild-type (WT) or phospho-null (S200A) FLAG-LIN28A in HeLa cells

summary: To explore the effect of LIN28 (S200) phosphorylation on LIN28's association with mRNAs on a transcriptome-wide scale, we performed mRNA-seq on RNAs immunoprecipitated (RIP-seq) by wild-type (WT) or phospho-null (S200A) LIN28 in HeLa cells.

overall_design: Examination of mRNAs immunoprecipitated by wild-type and phospho-null (S200A) FLAG-LIN28 (in triplicate)


title: gene expression level study of nurse like cells (NLC) derived from CLL cancer patients in homosapiens.

status: Public on Oct 12 2016

city: Toulouse

first: Mary

last: Poupot

address: avenue Hubert Curien

institute: Inserm U1037

summary:
NLC are generated from the in vitro culture of PBMC from CLL patients. These NLC derived from the differentiation of blood monocytes in contact with blood leukemic cells,
We used microarrays to detail the global programme of NLC gene expression compared to monocytes gene expression.

overall_design: 19 NLC were purified from cultures of PBMC from 19 untreated patients for RNA extraction and hybridization on Affymetrix microarrays.

first: Loïc

last: Ysebaert

first: Frédéric

last: Boissard


title: Transcriptome assessment of the Pompe (Gaa-/-) mouse cervical cord confirms widespread neuropathology.

status: Public on Oct 11 2016

summary:
The only FDA approved therapy for Pompe is directed at correcting skeletal and cardiac muscle pathology, however, clinical and animal model data show strong histological evidence for a neurological disease component. While neuronal cell death and neuroinflammation are prominent in many lysosomal disorders, these processes have not been evaluated in Pompe disease.  There is also no information available regarding the impact of Pompe disease on the fundamental pathways associated with synaptic communication.
We used microarrays to gain insight regarding pathogenetic signaling pathways that might contribute to neuropathology in  Pompe (Gaa-/-) mice.

overall_design: To test whether systemic absence of GAA protein activated signalling pathways associated with neuropathology, genomic data (Affymetrix Mouse Gene Array 2.0ST) from the mid-cervical spinal cord in 6-and 16-mo old Pompe (Gaa-/-) were evaluated.

first: Sara

last: Turner

first: David

last: Fuller


title: RNA-seq analysis of mRNAs immunoprecipitated by wild-type (WT), phospho-mimetic (S200D), or phospho-null (S200A) FLAG-LIN28A


title: Microarray for Gramella flava JLT2011

status: Public on Nov 19 2016

city: Xiamen

first: Kai

last: Tang

address: Zhourong quan BLV 3-313, Xiamen University, Xianan, Xiamen

institute: Xiamen University

summary: mRNA in Gramella flava JLT2011 during different treatments

overall_design: mRNA  in Gramella flava JLT2011  at the expotential phase during different treatments

first: Yingfan

last: Lin

first: Yu


title: Global gene expression profiling and antibiotic susceptibility after repeated exposure to the carbon monoxide-releasing molecule-2 (CORM-2) in multidrug-resistant ESBL-producing uropathogenic Escherichia coli

status: Public on Oct 06 2016

city: Örebro

first: Robert

last: Kruse

address: S grevrosengatan

department: Medical Sciences

country: Sweden

institute: Örebro University

summary:
Treatment of urinary tract infections is today a challenge due to the increasing prevalence of multidrug-resistant ESBL-producing uropathogenic Escherichia coli (UPEC). There is an urgent need for new treatment strategies for multidrug-resistant UPEC and preferably with targets that have low potential for development of resistance. Carbon monoxide-releasing molecules (CORMs) are novel and potent antibacterial agents.
The present study examines the transcriptomic targets of CORM-2 in a multidrug-resistant ESBL-producing UPEC isolate (ESBL7) in response to a single exposure to CORM-2 and after repeated exposure to CORM-2. The bacterial viability and minimal inhibitory concentration (MIC) were also examined after repeated exposure to CORM-2. Microarray analysis revealed that a wide range of processes were affected by CORM-2, including a general trend of down-regulation in energy metabolism and biosynthesis pathways and up-regulation of the SOS response and DNA repair. Several genes involved in virulence (ibpB), antibiotic resistance (marAB, mdtABC) and biofilm formation (bhsA, yfgF) were up-regulated, while some genes involved in virulence (kpsC, fepCEG, entABE), antibiotic resistance (evgA) and biofilm formation (artIP) were down-regulated. Repeated exposure to CORM-2 did not alter the gene expression patterns, the growth inhibitory response to CORM-2 or the MIC values for CORM-2, cefotaxime, ciprofloxacin and trimethoprim.

overall_design: ESBL7 from the original isolate, or isolates pre-exposed 20 times to CORM-2 (250 µM) or vehicle (2.5% DMSO) for 4 hours at 37 °C, were used to inoculate MS-medium followed by exposure to CORM-2 (250 µM) or vehicle for 30 min at 37 °C. Microarray were performed on first exposure to sub-inhibitory levels of CORM-2 (250 µM), first exposure to vehicle (2.5% DMSO), pre-exposed 20 times to CORM-2 respectively pre-exposed 20 times to vehicle. Four independent experiments were included in each group.

first: Charlotte

last: Bang

first: Isak

last: Demirel

first: Katarina

last: Persson


title: Microarray Expression Analysis of Circular RNAs in Pancreatic Ductal Adenocarcinoma

status: Public on Oct 07 2016

city: ChongQing

first: ShiXiang

last: Guo

state: ChongQing

address: GaoTanYan street No.29，ShaPingBa district

department: Southwest hospital，Third Military Medical University

institute: institute of Hepatopancreatobiliary Surgery

summary: To investigate the expression profile of circular RNAs (circRNAs) in pancreatic ductal adenocarcinoma(PDAC) and to provide more reliable biomarkers and new potential diagnostic and therapeutic targets for PDAC. The circRNA expression levels were measured in 20 paracancerous tissues and 20 PDAC tissues using Arraystar Human CircRNA Array Analysis. We identified significantly different expression of circRNAs between the two groups and showed distinguishable circRNAs expression patterns in the samples. The levels and patterns of circRNA expression were significantly different between paracancerous tissue and PDAC tissue. This study evaluated circRNAs expression profiles and their ability to serve as reliable biomarkers and new potential diagnostic and therapeutic targets for PDAC.

overall_design: Twenty fresh-frozen PDAC samples and twenty paracancerous tissues were collected, and total RNA was extracted. Subsequently, RNA was labeled and hybridized. Agilent Feature Extraction software (version 11.0.1.1) was used to analyze acquired array images. Quantile normalization and subsequent data processing were performed using the R software package.

first: Huaizhi

last: Wang

first: Shixiang