title: Transcriptome profiling of rabbit parthenogenetic blastocysts developed under in vivo conditions

status: Public on Sep 21 2012

city: Valencia

first: M. Desemparats

last: Saenz-de-Juano

state: Valencia

address: Camino de Vera s/n

department: Animal Science

institute: Universidad Politécnica Valencia

summary: Parthenogenetic embryos are one attractive alternative as a source of embryonic stem cells, although many aspects related to the biology of parthenogenetic embryos and parthenogenetically derived cell lines still need to be elucidated.  The present work was conducted to investigate the gene expression profile of rabbit parthenote embryos cultured under in vivo conditions using microarray analysis.

overall_design: Transcriptional microarray study that compares gene expression of 6 day parthenote rabbit embryos to their in vivo counterparts. Biological replicates used: 4 replicates for control embryos, 4 replicates for parthenote embryos

first: C

last: Naturil

first: M

middle: D

first: D

last: Peñaranda

first: J

last: Vicente

first: F

last: Marco-Jiménez


title: Pathogen recognition and activation of the innate immune response in zebrafish

status: Public on Nov 01 2012

city: Leiden

first: Michiel

last: van der Vaart

address: Einsteinweg 55

department: IBL

country: Netherlands

institute: University of Leiden

summary: We use the zebrafish embryo model to study the similarities and differences in the innate immune response against three different bacterial pathogens. Therefore, we injected E. tarda, Salmonella, or M. marinum into the caudal vein of 28 hours post fertilization (hpf) zebrafish embryos and analysed their gene expression profile at 8 hours or 4 days after infection by microarrays. The results show that infections with the gram-negative  bacteria E. tarda and S. typhimurium, which are lethal within 1-2 days, induce a strong early immune response at 8 hours after infection. In contrast, infection with M. marinum leads to a chronic infection that only induces a strong response at 4 days post infection.

overall_design: This microarray study was designed to determine the gene expression profile during infection with Salmonella typhimurium, Mycobacterium marinum, and Edwardsiella tarda. RNA was isolated from single embryos and each treatment group consisted of three embryos: (1) Wildtypes injected with PBS 8 hours post infection (hpi), (2) S. typhimurium-infected wildtypes 8hpi, (3) wildtypes injected with PBS/2%PVP 8hpi , (4) M. marinum-infected wildtypes 8hpi, (5) wildtypes injected with PBS/2%PVP 4 days post infection (dpi), (6) M. marinum-infected wildtypes 4dpi, (7) wildtypes injected with PBS 8hpi (E. tarda control), (8) E. tarda-infected wildtypes 8hpi. Embryos were grown at 28.5–30°C in egg water and manually dechorionated at 24 hours post fertilization (hpf). Subsequently, embryos were infected at 28 hpf by micro-injecting 200 colony forming units (CFU) of S. typhimurium SL1027, E. tarda or Mycobacteria marinum M20 bacteria into the caudal vein, or were mock-injected with buffer as a control.  After injections embryos were transferred into fresh egg water and incubated for 8 h or 4 days at 28°C. After the incubation period, single embryos were snap-frozen in liquid nitrogen and RNA was isolated for microarray analysis. All treatment groups were analyzed using a common reference approach.

middle: J

last: van Soest

first: H

middle: P

last: Spaink

first: A

middle: H

last: Meijer


title: Myostatin inactivation effects on myogenesis in vitro and in vivo

status: Public on Sep 30 2012

city: Torrance

first: Robert

last: Gelfand

state: CA

address: 1124 W. Carson St

department: surgery

country: USA

institute: LABiomed at Harbor UCLA,  and Charles Drew Univ

summary:
ABSTRACT   Stimulating the commitment of implanted dystrophin+ muscle derived stem cells (MDSC) into myogenic, as opposed to lipofibrogenic, lineages is a promising therapeutic strategy for Duchenne muscular dystrophy (DMD). To examine whether counteracting myostatin, a negative regulator of muscle mass and a pro-lipofibrotic factor, would help this process, we compared the in vitro myogenic and fibrogenic capacity of MDSC from wild type (WT), myostatin knockout (Mst KO), and mdx (DMD model) (mdx) young mice under various modulators, the expression of key stem cell and myogenic genes, and the capacity of these MDSC to repair the injured gastrocnemius in aged mdx mice with exacerbated lipofibrosis. Surprisingly, the potent in vitro myotube formation by WT MDSC was refractory to modulators of myostatin expression or activity, and the Mst KO and mdx MDSC failed to form myotubes under any condition, despite all MDSC expressed Oct-4 and various stem cell genes and differentiated into other lineages. The genetic inactivation of myostatin or dystrophin in MDSC was associated with silencing of critical genes for early myogenesis (Actc1, Acta1, and MyoD). WT MDSC implanted into the injured gastrocnemius of old mdx mice significantly improved myofiber repair and reduced fat deposition and, to a lesser extent, fibrosis. In contrast to their in vitro behavior, Mst KO MDSC in vivo also significantly improved myofiber repair, but had no significant effects on lipofibrotic degeneration. In conclusion, while WT MDSC are considerably myogenic in culture and stimulate muscle repair after injury in the aged mdx mouse, myostatin genetic inactivation blocks myotube formation in vitro but the myogenic capacity is recovered in vivo under the influence of the host tissue environment, presumably by reactivation of key genes originally silenced in the Mst KO MDSC.
Key words: dystrophin, mdx mouse, Duchenne, fibrosis, dystrophy

overall_design: One sample each of mouse wild type (WT), myostatin knockout (KO), muscular dystrophy model mdx, and the transgenic OCT4 promoter plus reporter were grown, RNA was isolated, and subjected to the SABiosciences mouse stem cell oligo array.

first: Nestor

last: Gonzalez-Cadavid


title: Gene expression analysis of peripheral blood mononuclear cells prior to and following vaccination of human volunteers with the novel TB vaccine candidate MVA85A

status: Public on Sep 28 2012

city: Oxford

first: Magali

last: Matsumiya

address: Roosevelt Drive

country: United Kingdom

institute: Jenner Institute, University of Oxford

summary: A greater understanding of the relationships between a vaccine, the immune response it induces, and protection from disease would greatly facilitate vaccine development. Modified Vaccinia virus Ankara expressing antigen 85A (MVA85A) is a novel tuberculosis (TB) vaccine designed to enhance responses induced by Bacille Calmette-Guerin (BCG). Antigen-specific interferon-γ (IFN-γ) production is greatly enhanced by MVA85A and peaks one week post-vaccination, however, the variability in response between healthy individuals is extensive. In this study we have sought to characterize the early changes in gene expression following vaccination with MVA85A and understand how these are related to long-term immunogenicity. 24 volunteers were vaccinated with 10^8 pfu MVA85A. 12 volunteers were vaccinated intramuscularly and 12 intradermally. Volunteers were healthy and did not have HIV, HCV, HBV or latent or active tuberculosis. Blood for this study was taken on the day of vaccination, immediately prior to the vaccine being given (day 0), and 2 and 7 days post-vaccination.

overall_design: Volunteers with a prior BCG vaccination were vaccinated with 1x10^8 pfu MVA85A either intradermally (id) or intramuscularly (im). Blood was taken immediately prior to vaccination (day 0) and 2 and 7 days post-vaccination. PBMCs were separated and frozen down. PBMCs were then thawed and RNA was extracted directly for microarray analysis. Some arrays contain control samples: from volunteers, incubated with either media alone or antigen 85, MVA85A or MVA wild type. These samples were used separately.


title: Transcriptional Responses of Schistosoma japonicum Exposed in vivo to Sub-Lethal Dosages of Praziquantel

status: Public on Sep 27 2012

city: Brisbane

first: Geoffrey

last: Gobert

address: 300 Herston Rd

country: Australia

institute: QIMR

summary: We have used a Schistosoma japonicum infected murine model with in vivo sub-lethal dosages of praziquantel against adult parasites. Differential gene expression of parasites was followed between 30 minutes and 24 hours post- drug administration, using a whole transcriptome microarray platform. Differential gene expression was considered separately between parasite gender.

overall_design: Total RNA was isolated from adult (7 week post cercarial challenge) Schistosoma japonicum male and females.  Gene expression was determined through hybridisation on an Agilent custom designed oligo microarray.

middle: N


title: Gene expression changes in initiation and progression of oral squamous cell carcinomas revealed by laser microdissection and oligonucleotide microarray analysis

status: Public on Sep 11 2012

city: Bunkyo-ku

first: Kaoru

last: Mogushi

state: Tokyo

address: 2-1-1 Hongo

department: Intractable Disease Research Center

country: Japan

institute: Juntendo University

summary:
Background. Oral carcinogenesis is a complex process involving multiple genes. However, the genetic changes involved in this process are not demonstrated in the identical oral squamous carcinomas (OSCCs).
Methods. According to the pathological characteristics, parts of normal tissues, oral dysplastic lesions (ODLs), and invasive cancers were procured from the identical OSCCs using laser microdissection (LMD), and large scale gene expression profiling was carried out on 33 samples derived from 11 OSCCs.
Results. We analyzed genes differentially expressed in normal tissues vs. ODLs and ODLs vs. invasive tumors and identified the 15 candidate genes that continuously increasing or decreasing in its expression during oral carcinogenesis. One of these, ISG15 was chosen for further characterization. Real-time quantitative reverse transcriptase-polymerase chain reaction and immunohistochmistry analysis confirmed that ISG15 expression was consistently increasing during oral tumorigenesis. ISG15 high expression was significantly associated with poor prognosis (P=0.027). In addition, patients whose tumor had high ISG15 expression had worse 5-year survival rate than patients whose tumors had a low expression level (P=0.019).
Conclusions. We identified the 15 genes that are continuously increasing or decreasing in its expression during oral carcinogenesis. One of these, ISG15 is likely to be associated with both dysgenesis and tumorigenesis, and may be a potential prognostic marker in these malignancies.

overall_design: Microarray samples of invasive tumor, adjacent dysplastic lesions and noncancerous normal tissues were collected from 11 patients with primary OSCCs. We analyzed genes differentially expressed in (i) normal vs. dysplastic tissues and (ii) dysplastic vs. tumor tissues.

first: Jun

last: Sumino

first: Narikazu

last: Uzawa

first: Norihiko

last: Okada

first: Ken

last: Miyaguchi

first: Ken-Ichiro

last: Takahashi

first: Hiroaki

last: Sato

first: Chieko

last: Michikawa

first: Yoshimi

last: Nakata

first: Hiroshi

last: Tanaka

first: Teruo

last: Amagasa


title: Seasonal Changes in Patterns of Gene Expression in Avian Song Control Brain Regions

status: Public on Oct 01 2012

city: Urbana

first: Kirstin

last: Replogle

state: IL

address: 1206 W Gregory Drive

institute: University of Illinois

summary: Photoperiod and hormonal cues drive dramatic seasonal changes in structure and function of the avian song control system. Little is known, however, about the patterns of gene expression associated with seasonal changes. Here we address this issue by exposing Gambel’s white-crowned sparrows to season-appropriate cues and extracting RNA from the telencephalic song control nuclei HVC and RA across multiple time points that capture different stages of growth and regression. We chose HVC and RA because while both nuclei change in volume across seasons, the cellular mechanisms underlying these changes differ. We thus hypothesized that different genes would be expressed between HVC and RA. We tested this by using the extracted RNA to perform a cDNA microarray hybridization developed by the SoNG initiative. We then validated these results using qRT-PCR. Supporting our hypothesis, only 59 of the 363 genes of interest were found to vary by more than |1.5| fold in expression in both nuclei, while 132 gene expression changes were HVC specific and 172 genes were RA specific. We then assigned many of these genes to functional categories relevant to the different mechanisms underlying seasonal change in HVC and RA, including neurogenesis, apoptosis, cell growth, dendrite arborization and axonal growth, angiogenesis, endocrinology, growth factors, and electrophysiology. This revealed categorical differences in the kinds of genes regulated in HVC and RA. These results show that different molecular programs underlie seasonal changes in HVC and RA, and that gene expression is time specific across different reproductive conditions. Our results provide insights into the complex molecular pathways that underlie adult neural plasticity.

sample_organism:
Taeniopygia guttata
Zonotrichia leucophrys gambelii

overall_design: Experimental groups: long-term Short Day (SD); Long Day (LD) with Testosterone (T) for 3, 7, and 21 days (3LD+T, 7LD+T, 21LD+T respectively); SD and removal of T at 1 and 2 days (1SD-T, 2SD-T); two tissues (HVC, RA) collected separately from each individual animal; one experimental sample and one universal SoNG reference sample per array; dye balanced within groups. Six biological replicates per group, five biological replicates in 3LD+T.HVC group.

first: Christopher

middle: K

last: Thompson

first: John

last: Meitzen

first: Karin

middle: L

last: Lent

first: Anne

middle: M

last: Wissman

first: Federico

last: Farin

first: Theo

last: Bammler

first: Richard

last: Beyer

first: David

middle: F

last: Clayton

last: Perkel

first: Eliot

middle: A

last: Brenowitz


title: Comparison of Renca tumor cells growing intrakidney or subcutaneously

status: Public on Sep 08 2012

city: Melbourne

first: Michael

middle: Henry

last: Kershaw

state: Victoria

address: 14 St. Andrews Place

department: Research

institute: Peter MacCallum Cancer Centre

summary:
Tumors can occur in many sites in the body, but how tissues at different anatomical sites affect tumor microenvironments and their subsequent response to therapy is not known. Here we show that different tissues can cause the same tumor to develop fundamentally different microenvironments resulting in dramatic changes in responses to immunotherapy. Whereas established subcutaneous tumors could be eradicated in the majority of mice using a combination of three agonist antibodies, tumors in visceral organs responded much less. Orthotopic kidney tumors had a microenvironment with a higher frequency of alternatively-activated macrophages and their associated molecules. Neutralizing the CCL2 chemokine or IL-13 cytokine, important in macrophage biology led to a greatly improved therapeutic effect. Importantly, a significantly reduced therapeutic response of subcutaneous tumors was observed when visceral tumors were simultaneously present in the same mice.
In this study we sought to compare gene expression of mouse renal cell carcinoma cells growing in the kidney to cells growing subcutaneously. Renca is a renal cell carcinoma cell line (Murphy and Hrushesky, 1973). To produce subcutaneous tumors, mice received 2 x 10^5 Renca. Orthotopic tumors were established by first surgically isolating the organ and then injecting 2 x 10^5 Renca cells intrakidney (IK) into the outer cortex of the kidney in 20 ul of PBS. Tumors were removed from mice 12 days after implantation, when approximately 20-30 mm2. Tumors were snap frozen on liquid nitrogen prior to processing for total RNA followed by analysis on Mouse Gene 1.0 chips.

overall_design: Kidney Renca tumors were excised from 3 BALB/c mice and subcutaneous Renca tumors were excised from another 3 BALB/c mice. cDNA was prepared and hybridized to Mouse Gene 1.0 ST chips.

first: Jennifer

last: Westwood

first: Christel

last: Devaud


title: Transcriptomic changes induced in yeast cells by the lack of potassium in the medium

status: Public on Oct 13 2012

city: Cerdanyola

first: Antonio

last: Casamayor

state: Barcelona

address: Edifici IBB, Campus UAB

country: Spain

institute: Universitat Autonoma de Barcelona

summary: Potassium is the major intracellular cation in S. cerevisiae, which can be concentrated up to 200-300 mM even from relatively low potassium (< 1 mM) environments. This is achieved by mean of a high affinity K+-transport system encoded by the genes TRK1 and TRK2. Recently, our group became interested in the effects of sudden shortage of extracellular potassium. Transcriptomic analysis indicates that lack of potassium drastically alters sulfur metabolism (mainly Met and Cys metabolism), triggers an oxidative stress response and activates the mitochondrial retrograde pathway. We also observe a dramatic halt in the expression of genes required for ribosome biogenesis and translation, as well as decrease in expression of diverse genes (cyclins, protein kinases) required for progression through the cell cycle. Only subsets of these changes were observed in a strain deleted for the TRK1 and TRK2 genes growing in the presence of sufficient potassium (50 mM). Research involving molecular genetics and metabolomic approaches aiming to clarify the primary targets for potassium requirements is currently ongoing.

overall_design:
The effect of a sudden shortage of extracellular potassium was studied using a wt yeast strain. Samples of cell cultures grown in either, in the presence or in the absence of potassium, were taken after 10, 20, 40, 60 and 120 min of potassium shortage.

We compared the expression profile of:
1) WT w/o K vs WT w/ KCl at 10 min:
2) WT w/o K vs WT w/ KCl at 20 min.
3) WT w/o K vs WT w/ KCl at 40 min.
4) WT w/o K vs WT w/ KCl at 60 min.
5) WT w/o K vs WT w/ KCl at 120 min.

Two independent experiments were performed, except for the timepoint of 10 min. For each experiment a dye-swap was carried out.

Chips analyzed:
2 for 10 min
4 for 20 min
4 for 40 min
4 for 60 min
4 for 120 min
Total number of chips: 18

first: Lina

last: Barreto

last: Canadell

first: Daniel

last: Valverde

first: Joaquin

last: Arino


status: Public on Sep 10 2012

city: Boston

first: Nikhil

middle: C

last: Munshi

state: MA

address: 450 Brookline Avenue

department: Hematologic Oncology

institute: Dana-Farber Cancer Institute

summary:
Gene Expression profiling of 170 newly diagnosed Multiple Myeloma patients
Gene Expression profiling of Multiple Myeloma

overall_design: Cells from Healthy donors and Multiple myeloma patients were profiled using  Affymetrix Exon-1.0 ST microarrays

first: Stephane

last: Minvielle

first: Parantu

last: Shah


title: Studies on the Mechanism of Telavancin Decreased Susceptibility in a Laboratory-Derived Mutant

status: Public on Sep 07 2012

city: Normal

first: Arunachalam Muthaiyan

email: amuthai@gmail.com, bjwilkin@ilstu.edu

address: Julian Hall

department: Biological Sciences

institute: Illinois State University

summary: Telavancin is a novel semi-synthetic lipoglycopeptide derivative of vancomycin with a dual mode of action. This study sought to understand knowledge of mechanisms of decreased susceptibility in laboratory-derived mutant. There were multiple significant changes in the transcriptome of TlvDSMED1952 indicating an altered overall physiology of the strain, likely decreased virulence, and changes in cell wall and membrane properties, probably due to multiple genetic changes in the strain.

overall_design: MHB cultures (biological replicates: N=3) were then grown to exponential phase (OD600=0.4). Dye-swapping was performed between samples.

first: Yang

last: Song


title: Differential gene expression profile of y79 retinoblastoma cells in response to Anti - HMGA2 siRNA treatment

status: Public on Aug 01 2012

city: Bangalore

first: Genotypic

last: technology

state: Karnataka

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

country: India

institute: Genotypic Technology

summary: The differential gene expression study was conducted in the  Anti - HMGA2 siRNA treated Retinoblastoma cell (Y79). The transient transfection in Y79 cells were performed using Anti-HMGA2 siRNA . The concentration and the time of incubation  for the transfection was optimised to increase the silencing efficiency and reduce the off -target effects. After 48 hours of transfection the cells were collected and the whole genome cDNA microarray  was performed to interpret the differential gene expression regulated by HMGA2 in Y79 cells. The results of the microarray data has been validated.

overall_design: One-color experiment,Organism: Human , Custom Whole Genome Human 8x60k designed by Genotypic Technology Pvt. Ltd.  (Agilent-027114), Labeling kit: Agilent Quick-Amp labeling Kit (p/n5190-0442)

first: Nalini

last: Venkatesan

first: S

last: Krishnakumar

first: Vikas

last: Khetan

first: Ashwin

last: Reddy


title: DGCR8 HITS-CLIP reveals novel functions for the Microprocessor (CLIP-seq)

status: Public on Jul 15 2012

city: Copenhagen

first: Mireya

last: Plass

address: Robert-Rössle Str. 10

country: Germany

institute: MDC-Berlin

type: Non-coding RNA profiling by high throughput sequencing

summary: The Drosha-DGCR8 complex (Microprocessor) is required for microRNA (miRNA) biogenesis. DGCR8 contains two double-stranded RNA binding motifs that recognize the RNA substrate, whereas Drosha functions as the endonuclease. We have used high-throughput sequencing of RNAs isolated by crosslinking immunoprecipitation (HITS-CLIP) to identify endogenous RNA targets of DGCR8 in mammalian cells. Unexpectedly, miRNAs were not the most abundant targets. DGCR8-bound RNAs comprised several hundred mRNAs as well as snoRNAs and long non-coding RNAs. We found that DGCR8 together with Drosha controls the abundance of several mRNAs, as well as long non-coding RNAs, such as MALAT-1. By contrast, the DGCR8-mediated cleavage of snoRNAs is independent of Drosha, suggesting the involvement of DGCR8 in cellular complexes with other endonucleases. Interestingly, binding of DGCR8 to cassette exons, acts as a novel mechanism to regulate the relative abundance of alternatively spliced isoforms.  Collectively, these data provide new insights in the complex role of DGCR8 in controlling the fate of several classes of RNAs.

overall_design: Comparison of RNAs associated to both endogenous (D8) and overexpressed (T7) DGCR8 in HEK293T cells

first: Sara

last: Macias

first: Agata

last: Stajuda

first: Gracjan

last: Michlewski

first: Eduardo

last: Eyras

first: Javier

last: Caceres


title: CNV and LOH analysis of patient sample PN11-0204

status: Public on Aug 28 2012

city: Nijmegen

first: Rolph

last: Pfundt

address: Geert Grooteplein Zuid 6

department: Genetics

institute: RUNMC

summary: We saw a patient who presented with respiratory distress from birth due to interstitial lung disease. Before the age of three months a diagnosis of nephrotic syndrome was made. Lung biopsy revealed pulmonary interstitial glycogenosis. Despite extensive investigations, no known genetic or infectious cause was found for the congenital nephrotic syndrome. The patient died at the age of 8 months due to respiratory failure. A 20 Mb homozygous region was identified on chromosome 17 in the patient’s DNA, revealing a novel homozygous missense variant in ITGA3 gene.

overall_design: Genomic DNA was obtained from peripheral blood samples of the patient with interstitial lung fibrosis and nephrotic syndrome. Copy number variation (CNV) screening by means of microarray analyses was carried out on the Affymetrix GeneChip 250k (NspI) SNP array platform (Affymetrix, Inc., Santa Clara, CA, USA), which contains 25-mer oligonucleotides representing a total of 262,264 SNPs. Hybridizations were performed according to the manufacturer’s protocols. Copy numbers and “long contiguous stretches of homozygosity” (LCSH/LOH) were determined using the 2.0 version of the CNAG (Copy Number Analyzer for Affymetrix GeneChip mapping) software package (Nannya Y, Sanada M, et al (2005) "A robust algorithm for copy number detection using high-density oligonucleotide single nucleotide polymorphism genotyping arrays." Cancer Res; 65: 6071–6079.). The average resolution of this array platform, described by McMullan et al is 150–200 kb (Mc McMullan DJ, Bonin M et al. (2009), “Molecular karyotyping of patients with unexplained mental retardation by SNP arrays: a multicenter study” Hum Mutat. Jul;30(7):1082-92).

first: Kirsten

middle: Y

last: Renkema


title: Gene expression changes in  embryonic PECAM-1+ cells from Gata2 +9.5 enhancer targeted mice

status: Public on Jul 17 2012

city: Madison

first: Kirby

middle: Dean

last: Johnson

state: WI

address: 1300 University Avenue

department: Pharmacology

institute: University of Wisconsin-Madison

summary:
We have generated a nonconditionall deletion of an E-box - GATA motif composite element from a putative enhancer 9.5 kb downstream of the Gata2 1S promoter. The mutation results in  lethality at E13.5 to E14.5 with embryos exhibiting dectects in definitive hematopoiesis and vasculature integrity.  Hematopoietic stem and progenitor cells are nearly absent from these mice and Gata2 expression is severely reduced in Pecam-1+ endothelial cells from E12.5-12.5 embryos but is expressed at normal levels in the embryonic brain.
We have employed gene expression profiling in Pecam-1+ cells from wild type and Gata 2+9.5 mutant littermates to identify genes involved in maintaining vascular integrity.

overall_design: The Gata2+9.5 mutation was backcrossed into the C57Bl/6J background.   Anti-CD31 antibody bound to magnetic beads was used to enrich for PECAM-1+ cells from four Gata2+9.5 E12.5 embryos and four wild type littermates from two litters. A single RNA sample from each embryo was used for array hybridization.

first: Emery

last: Bresnick


title: Expression data of RNA isolated from C57/BL6 mouse aortic endothelial cells (MAECs)

status: Public on Jul 11 2012

city: Los Angeles

first: Ayca

last: Erbilgin

address: 675 Charles E Young Dr South

department: Medicine/Cardiology

institute: University of California, Los Angeles

summary:
Our goal is to study the contribution of endothelial, smooth muscle, and macrophage gene expression to early atherosclerosis using vessels from healthy, pre-lesioned, and lesioned mice. To accomplish this, we developed a method to isolate endothelial cells directly from the aorta and quantitate transcripts in RNA isolated from these cells.
We performed expression array analysis on RNA isolated directly from the vascular cells of individual control, pre-lesioned, and atherosclerotic mouse aortas. Array expression analysis was not performed on smooth muscle cells or macrophages.

overall_design:
RNA from MAEC of pre-lesioned hyperlipidemic and normal-lipidemic mice was isolated, amplified, and arrayed.
Mouse aortas were also treated in either media (DMEM) or media containing either LPS, oxLDL, or oxPAPC for 4 hours prior to RNA isolation and amplification.
Only samples with a RIN of 7.0 or greater were used for analysis.

first: Aldons

last: Lusis


title: Unique expression, processing regulation, and regulatory network of peach (Prunus persica) miRNAs

status: Public on Jul 03 2012

city: Kearneysville

first: HONG

last: ZHU

state: WV

address: 2217 Wiltshire Rd.

institute: USDA-AFRS

summary: We performed small RNA deep sequencing and identified 47 peach-specific and 47 known miRNAs or families with distinct expression patterns. Together, the identified miRNAs targeted 80 genes, many of which have not been reported previously. Like the model plant systems, peach has two of the three conserved trans-acting siRNA biogenesis pathways with similar mechanistic features and target specificity. Unique to peach, three of the miRNAs collectively target 49 MYBs, 19 of which are known to regulate phenylpropanoid metabolism, a key pathway associated with stone hardening and fruit color development, highlighting a critical role of miRNAs in regulation of peach fruit development and ripening. We also found that the majority of the miRNAs were differentially regulated in different tissues, in part due to differential processing of miRNA precursors. Up to 16% of the peach-specific miRNAs were differentially processed from their precursors in a tissue specific fashion, which has been rarely observed in plant cells. The miRNA precursor processing activity appeared not to be coupled with its transcriptional activity but rather acted independently in peach. Collectively, the data characterizes the unique expression pattern and processing regulation of peach miRNAs and demonstrates the presence of a complex, multi-level miRNA regulatory network capable of targeting a wide variety of biological functions, including phenylpropanoid pathways which play a multifaceted spatial-temporal role in peach fruit development.

overall_design: Identification of peach miRNAs and their targets from four different tissues

first: Hong

last: Zhu

first: Zongrang

last: Liu

first: Rui

last: Xia


title: Embedding siRNA sequences targeting Apolipoprotein B100 in shRNA and miRNA scaffolds results in differential processing and in vivo efficacy

status: Public on Jul 10 2012

city: Amsterdam

first: Piotr

last: Maczuga

state: Nord Holland

address: Meibergdreef 61

institute: UniQure

type: Expression profiling by high throughput sequencing

summary:
Purpose: Identical predicted small interfering RNA (siRNA) sequences targeting Apolipoprotein B100 (siApoB) were embedded in shRNA (shApoB) or miRNA (miApoB) scaffolds and a direct compariso  of the possible aspecific off-target effects in vivo was performed. Next generation sequencing (NGS) of small RNAs originating from shApoB- or miApoB-transfected cells revealed substantial differences in processing, resulting in different siApoB length, 5’ and 3’ cleavage sites and abundance of the guide or passenger strands.
Methods [1]: Total liver RNA sequencing libraries for the Illumina sequencing platform were generated using high-quality total RNA as input and the Illumina TrueSeq RNA v2 Sample preparation kit according to the manufacturer’s protocol. Each read file (sample), in the FASTQ format, was individually aligned against the mouse reference genome (15 May 2012 NCBI build 38.1) using CLC Bio-Genomic Workbench and the expression abundance for each gene (RPKM) was calculated according to Montazavi et al.
Result [1]s: Based on our previous observations that shApoB and miApoB are differentially processed and that miApoB has a different passenger, we checked for possible aspecific off-target effects in vivo. NGS liver transcriptome analysis was performed 8 weeks p.i. for animals injected with 1x1011 gc AAV encoding shScr, shApoB, miScr and miApoB. We investigated whether shApoB and miApoB processing differences translate into differences in gene expression in injected animals. A total number of 266 genes were significantly changing (p <0,05) in miApoB-injected mice compared to miScr. Additionally 106 genes were found to be significantly up or down-regulated in the shApoB mice compared to shScr. Off-target predictions using Smith-Waterman algorithm for the most abundant guide and passenger strand variants were performed to investigate if any of the observed changes results from aspecific interactions. None of the changing genes had predicted targets for the guide or passenger strands of shApoB or miApoB.
Conclusions [1]: An important observation is that none of the changes in gene expression in AAV-miApoB and AAV-shApoB can be explained by possible aspecific down-regulation of non-target transcripts.
Methods [2]: For NGS analysis cells were transfected with 4 µg shApoB- or miApoB-expression plasmids using Lipofectamine 2000 reagent and total RNA was isolated from cells 48 hr post-transfection using Trizol (Invitrogen, Carlsbad, CA) according to the manufacturer’s protocol. Total RNA sequencing libraries for the Illumina sequencing platform were generated using high-quality total RNA as input and the Illumina TrueSeq RNA v2 Sample preparation kit according to the manufacturer’s protocol. The NGS small RNA raw data set was analyzed using the CLC_bio genomic workbench (CLC Bio, Aarhus, Denmark). The obtained reads were adaptor-trimmed, which decreased the average read size from ~36bp to ~25bp. The custom adapter sequenced used for trimming all the bases extending 5’ was: GTGACTGGAGTTCC-TTGGCACCCGAGAATTCCA. All reads containing ambiguity N symbols, reads shorter than 15 nt, longer than 55 nt in length and reads represented less than 10 times were discarded. Next, both data sets from shApoB and miApoB samples were grouped based on the match to the reference sequence and the obtained unique small RNAs were aligned to the sequence of pre-miApoB: GATCCTGGAGGCTTGC-TGAAGGCTGTATGCTGATGGACAGGTCAATCAATCTTGTTTTGGCCACTGACTGACAAGATTGAGACCTGTCCATCAGGACACAAGGCCTGTTACTAGCACTCACATGGAACAAATGGCCCAGATCTGGCCGCAG or shApoB: GATCCCCGATTGATTGACCTGTCCATTTCAAGAGAATGGACAGGTCAATCAATC-TTTTTCAGCTT sequence, respectively. To relatively represent the expression counts for the small RNAs obtained in the experiment, reads per million (rpm) or percentage of reads based on the total number of reads matching the reference shApoB or miApoB sequence were calculated
Results [2]: The small RNAs were aligned against their reference sequence resulting in 541.939 reads matching shApoB and 1.525.211 reads matching miApoB (Fig S1 and S2). Analysis of the length distribution of the reads indicated that siApoB guide strand originating from shApoB ranged between 19 and 23 nt, with the most abundant one being 21 nt-long. Surprisingly, siApoB guide from miApoB scaffold ranged from 23 to 25 nt with the 24 nt-long strand being the predominant variant. This finding was rather unexpected considering that the predicted guide strand of siApoB was 21 nt long for both shApoB and miApoB scaffolds. Analysis of the processed 5’ ends of the siApoB guide strand indicated that most of the reads matched position +1 relative to the predicted cleavage site for shApoB, while all the reads matched position 0 for miApoB. The 3’ ends of the siApoB guide strand had a more heterogeneous pattern and ranged from -1 to +3 for shApoB and +1 to +4 for miApoB.   Next, we looked at the sequence distribution and percentage of reads for both the guide and passenger siApoB strands originating from the shApoB and miApoB scaffolds. A substantial difference between the two is that the guide from shApoB is in the 3’ arm and hence Dicer or other endonuclease  defines the cleavage position while the guide is present in the 5’ arm of miApoB, where Drosha defines the cleavage. Thus, defining the length and exact cleavage position for the guide and passenger strands is very important since even single nucleotide differences may result in significant changes in the predicted targets of the siRNAs. Moreover, the passenger siRNA* strand, if not degraded efficiently, may bind to unanticipated targets and cause off-target effects. As expected, 44.4% of the reads originating from shApoB matched the siApoB guide strand but processing was shifted at position +1 (Fig. 2d, upper panel). Surprisingly only 12.1% of the reads matched perfectly the predicted siApoB guide strand of 21 nt and starting at position 0. The reads matching the passenger siApoB* strand were represented in much lower percentage with the predominant one being only 5.3%.   Analysis of the guide strand from the siApoB reads originating from the miApoB scaffold indicated that they all started at the predicted cleavage site. Surprisingly, the predominant, 22.3% of reads were 24 nt-long. Furthermore 5.1% reads were 23 nt- and 1.9% were 25 nt-long. A substantial number of 62% of the reads was found matching the passenger siApoB* strand and ranged between 20 and 22 nt in length. In conclusion, both shApoB and miApoB scaffolds did not yield the predicted siApoB guide or siApoB* passenger sequences after processing from the cellular RNAi machinery. The guide from miApoB was cleaved much more precisely by Drosha at its 5’ end compared to shApoB that gave more heterogeneous pools of sequences following processing.
Conclusions[2]: An unexpected discovery in the current study was that siRNA processing by the cellular RNAi machinery did not follow the generally accepted and described cleavage sites for both molecules shApoB and miApoB siApoB guide strand originating from the shApoB scaffold was more heterogeneous in cleavage sites and length compared to the product originating from the miApoB scaffold. Most likely, differential cleavage mechanism defined the heterogeneity in the guide and passenger strands. Additionally, shRNAs with 19 bp stem or less are not necessarily recognized by Dicer and maybe be processed differently. The heterogeneity seen with the shApoB can also be explained by the potential for 2 or 3 uridines to be added following termination of pol III transcription. The main pool of guide sequences originating from miApoB was 24 nt-long although we used the scaffold of cellular pri-mir-155 that produces a 23 nt mature miRNA. However, a 24 nt-long siApoB sequence did not compromise efficacy because when placed in the miApoB scaffold, the ApoB target sequence was extended at the 3’ end with 4 nt until the loop.   Another important observation is that the siApoB*

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: Liver mRNA profiles of C57BL/6 9 weeks after intravenous AAV injection of 1x1011 gc per animal (~4x1012 gc/kg) of AAV-shRNA, AAV-miRNA or PBS via the tail vein. Next Generation Sequencing on Illumina platform

first: Jacek

last: Lubelski

first: Richard

last: van Logtenstein

first: Florie

last: Borel

first: Bas

last: Blits

first: Erwin

last: Fakkert

first: Adalberto

last: Costessi

first: Derek

last: Butler

first: Sander

last: van Deventer

first: Harald

last: Petry

first: Annemart

last: Koornneef

first: Pavlina

last: Konstantinova


title: Ovarian cancer cell lines [Baseline profiling]

status: Public on Jul 01 2012

city: Tampa

first: Steven

last: Eschrich

state: FL

address: 12902 Magnolia Drive

department: Biostatistics & Bioinformatics

institute: Moffitt Cancer Center

summary: Analysis of a panel of 41 human ovarian cancer cell lines for the study of ovarian cancer biology, drug response and drug sensitivity.

overall_design: Ovarian cancer cell lines were either obtained from the American Type Culture Collection (ATCC, Manassas, VA) (CAOV3, OV90, OVCAR3, SKOV3, TOV112D), the European Collection of Cell Cultures, Salisbury, England (A2780CP, A2780S); Kyoto University, Kyoto, Japan (CHI, CHIcisR, M41, M41CSR, Tyknu, and TyknuCisR), or were kind gifts from Dr. Patricia Kruk, Department of Pathology, College of Medicine, University of South Florida, Tampa, FL; and Susan Murphy, PhD, Dept of OBGYN/Division of GYN Oncology, Duke University, Durham, NC (A2008, C13, CAOV2, FUOV1, HeyA8, IGR-OV1, IMCC3, IMCC5, MCAS, OV2008, OVCA420, OVCA429, OVCA432, OVCA433, OVCAR4, OVCAR5, OVCAR8, Dov13, BG1, Ovary1847, OVCAR10, OVCAR2, SK-OV-4). Cell lines were maintained in RPMI-1640 (Invitrogen; Carlsbad, California) supplemented with 10% fetal bovine serum (Fisher Scientific; Pittsburg, PN), 1% sodium pyruvate, 1% penicillin/streptomycin (Cellgro; Manassas, VA), and 1% nonessential amino acids (HyClone; Hudson, New Hampshire). Mycoplasma testing was performed every six months following manufacturer’s protocol (Lonza, Rockland ME).

first: Johnathan

last: Lancaster

first: Douglas

last: Marchion


title: Profiling of transcription start site expression in Drosophila and the human K562 cell line using RAMPAGE

status: Public on Aug 29 2012

city: Woodbury

first: Philippe

last: Batut

state: NY

address: 500 Sunnyside Blvd.

institute: CSHL

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

sample_organism:
Drosophila melanogaster
Homo sapiens

platform_organism:
Drosophila melanogaster
Homo sapiens

overall_design: Refer to individual Series


title: Expression data from superior cervical ganglion cultured cells and whole tissue

status: Public on Jul 07 2012

city: Athens

first: William

last: Kisaalita

state: GA

address: Dritmier Engineering Center

institute: University of Georgia

summary: A transcriptomic expression comparison was done among superior cervical ganglion (SCG) cells cultured on 2D substrates, 3D porous polystyrene scaffolds, and in freshly dissected tissue (in vivo surrogate), with the goal of assessing the feasibility of establishing the meaning of 3D and associated physiological relevance at the molecular level

overall_design: SCG cells were cultured on 2D surfaces and in 3D scaffolds. Chemical cues are controlled by coating. Only spacial properties of the culture systems were compared. Cells from freshly dissected tissue were used as in vivo surrogates for positive control of 3D cells.

first: Yinzhi

last: Lai


title: Expression data from L3 stage Caernorhabditis elegans after arsenic exposure

status: Public on Jun 29 2012

city: Laurel

first: Jada

last: Lewis

state: MD

address: 8301 Muirkirk Road

institute: FDA

summary: We used microarrays to explore the global affect on gene expression in C. elegans after exposure to arsenic

overall_design: L3 stage N2 worms were incubated for 6 hrs in sodium arsenite containing media of concentrations .003 and .03. Three independent extractions of RNA were performed from no exposure, .003 exposure, and .03 exposure worms.

first: Surasri

last: Sahu

first: Isha

last: Patel

first: Hediye

last: Cinar


title: Gene expression profile of Wharton-jelly mesenchymal stem cells at 12th in vitro expansion cycle compared to Wharton-jelly mesenchymal stem cells at 4th in vitro expansion cycle

status: Public on Jun 28 2012

city: Chieti

first: Valentina

last: Gatta

state: Abruzzo

address: Via Colle dell'Ara

department: Aging Research Center (CESI)

country: Italy

institute: G. d’Annunzio University Foundation Chieti

summary: Mesenchymal stem cells (MSCs) are generally considered the main tool box for cell-based therapies and compared to embryonic stem cells (ESCs), MSCs exhibit many advantages. It has been shown that UC matrix (the Wharton’s Jelly surrounding umbilical vessels) contains a great number of mesenchymal cells. The abundant amount of Wharton’s Jelly (WJ) makes it an attractive source of MSCs for cell-based therapies. recently have been highlighted the changes in protein expression profiling during in vitro expansion of WJ-MSC, probably related to the gradual reduction of their staminal plasticity and to the biological cellular mechanism occurring in the cellular aging. The aim of the present work was to analyze the transcriptomic profile useful to the definition of WJ-MSC characteristics and therefore identify possible different new marker candidates. In these contest, changes in gene expression profiles occurring during WJ-MSC in vitro growth wile by analyzed in order to find possible modulation related to their long expansion and fast growth abilities. We analyzed the changes in total RNA expression at the 12th in vitro expansion cycle compared to the 4th in vitro expansion cycle.

overall_design: In this study we performed gene expression profiles of a total of 6 experiment. Three different cell pools at 12th and 4th in vitro expansion cycles were used (UC2, UCA and UCB). On the total of 6 experiments 3 were biological replicates, 2 technical replicates and 1 dye-swap replicate.

first: Marco

last: D'Aurora

first: Sara

last: Franchi

last: Marchisio

first: Laura

last: Pierdomenico

first: Paola

last: Lanuti

first: Sebastiano

last: Miscia

first: Liborio

last: Stuppia

first: Giandomenico

last: Palka


title: Expression data from GW9662 treated FVB wild-type mouse mammary tumors

status: Public on Jun 26 2012

city: Washington

first: Robert

middle: I

last: Glazer

state: DC

address: 3970 Reservoir Rd, NW

department: Oncology

institute: Georgetown University

summary: Microarrays were used to analyse global gene expression changes in tumors from wild-type mice treated with GW9662

overall_design: RNA was isolated (RNeasy Mini Kit, Qiagen) from progestin/DMBA induced mammary tumors from  wild-type mice treated with GW9662

first: Hongyan

last: Yuan


title: Real-time quantitative PCR analysis of rat embryonic stem cells (ESCs)

city: Manhattan

first: Mark

last: Weiss

state: KS

address: Coles Hall, Room 115

department: Anatomy and Physiology

institute: Kansas State University

summary: Validation study of a focused microarray for evaluation of undifferentiated rat ESCs.Using a focused microarray, undifferentiated embryonic stem cells (ESCs) can be distinguished from differentiated ESCs and other cells derived from the early embryo since they have a unique gene expression pattern associated with pluripotency and lack of markers of differentiation.  To date, however, such an array has not been developed for the rat species and differences in genomes of rat and human or rat and mouse preclude the use of ESC focused human or mouse microarrays for the rat.  Here, we developed a focused microarray for screening rat ESCs and provide validation data that this array can distinguish undifferentiated rat ESCs from rat trophoblast stem cells (TS), rat extraembryonic endoderm cells (XEN), mouse embryonic fibroblast feeder cells (MEFs) and rat ESCs that have been differentiated in vitro.  We used this tool to compare rat ESCs which have been expanded in a conventional rat ESC medium containing two inhibitors, e.g., GSK3 and MEK inhibitors, and leukemia inhibitory factor (LIF), and found expression of Cdx2, a gene associated with trophoblast determination.  The rat ESC focused microarray described in this report has utility for rapid screening rat ESCs.  This will enable optimization of culture conditions in the future.

sample_organism:
Mus musculus
Rattus norvegicus

overall_design: A microarray was designed to compare the expression of 84 rat genes by various rat stem cell types and rat embryonic stem cell derived embryoid bodies. Relative fold changes in gene expression described by the microarray distinguish rat embryonic stem cells from other rat cell types, including rat embryonic stem cell derived embryoid bodies and mouse embryonic fibroblasts.

first: He

last: Hong

first: James


title: Expression data from Porcine pregnant

city: Beijing

first: ligang

last: wang

address: 2 Yuanmingyuan West Road

country: China

institute: institute of animal sciense

summary: Gene differential expression in different pregnant periods and different tissues are detected.

overall_design: Sow ovary and myometrium were selected for RNA extraction and hybridization on Affymetrix microarrays. 9 pigs were divided into three time-points groups: non-pregnant (NP, n=3), early pregnant (EP, n=3), and late pregnant (LP, n=3). The differentially expressed genes in each group were identified.

first: Ligang

last: Wang

first: Lixian


title: Gene expression profile of cancer cells and macrophages growing as a co-culture

status: Public on May 31 2012

city: Warsaw

first: Magdalena

last: Król

address: Nowoursynowska 159

department: Physiological Sciences

country: Poland

institute: Warsaw University of Life Sciences

summary:
Molecular mechanisms of the cancer cells-macrophages interactions growing in vitro conditions as a co-culture. The five canine mammary cancer cell lines were cultured with monocytes sorted from the canine blood for 72hrs. Then, the cancer cells and macrophages were sorted and the gene expression analysis was conducted. The control for each co-cultured cell line was the same cell line growing as a single culture, whereas the control for the macrophages growing in a co-culture conditions were macrophages growing as a single culture.
Solid tumors are comprised of various cells, like cancer cells, resident stromal cells, migratory hemopoietic cells and so on. These cells regulate tumor growth and metastasis. Macrophages are probably the most important element of the interactions within the tumor microenvironment. However, the molecular mechanism how the tumor environment can educate tumor-associated macrophages (TAMs) toward a tumor-promoting phenotype still remains unknown. Moreover, there are no information how the presence of macrophages change the cancer cells phenotype. Exploring the underlying molecular mechanisms of these phenomena was the aim of this study.  Solid tumors are comprised of various cells, like cancer cells, resident stromal cells, migratory hemopoietic cells and so on. These cells regulate tumor growth and metastasis. Macrophages are probably the most important element of the interactions within the tumor microenvironment. However, the molecular mechanism how the tumor environment can educate tumor-associated macrophages (TAMs) toward a tumor-promoting phenotype still remains unknown. Moreover, there are no information how the presence of macrophages change the cancer cells phenotype. Exploring the underlying molecular mechanisms of these phenomena was the aim of this study.

overall_design: Dye-swap experiment, each cell line growing in the co-culture conditions was compared to the same cell line growing as a single culture, macrophages growing in the co-culture conditions were compared to the macrophages growing as the single culture.

first: Karol

last: Pawłowski

first: Małgorzata

last: Gajewska

first: Alicja

last: Majewska

first: Tomasz

last: Motyl


title: Tissue-specific ChIP-seq of C. elegans Rb/E2F

city: New Haven

first: Valerie

last: Reinke

state: CT

address: 333 Cedar St

institute: Yale University School of Medicine

type: Genome binding/occupancy profiling by high throughput sequencing

summary: The Rb/E2F tumor suppressor regulates gene expression to control the onset and timing of differentiation in many different cell types during development.  This critical function makes Rb/E2F a frequent target for inactivation in tumors of diverse tissue origin.  However, the mechanisms by which Rb/E2F governs tissue-specific gene regulation in vivo are poorly understood.  We have determined the genome-wide binding profiles for components of the C. elegans Rb/E2F transcriptional regulatory pathway in the germ line, the intestine, and broadly in somatic tissues.  Rb/E2F exhibits highly tissue-specific regulation, with unique sets of target genes that are activated or repressed depending on whether cells are in a progenitor (germ line) or terminally differentiated (somatic) state.  In particular, LIN-35 binding is impaired in the germ line relative to the soma.  Moreover, in the intestine, LIN-35 binds independently of EFL-1/DPL-1 at broad intergenic sites at which the heterochromatin protein HPL-2 also binds.  Finally, recently defined âHOTâ sites, which are non-specifically bound by many unrelated factors, appear to be restricted primarily to somatic tissues, suggesting that germ line chromatin is in a state that globally restricts promiscuous association of regulatory factors.  In sum, these tissue-specific binding profiles led to significant mechanistic insights into tissue-specific properties of Rb/E2F function in C. elegans that are likely relevant to other organisms.

overall_design: Staged C. elegans worms carrying different transgenes expressing GFP-transcription factors under different promoters were treated to ChIP-seq in biological replicate.  A total of eleven different transgenic lines were analyzed.  Three transcription factors (LIN-35, EFL-1 and DPL-1) were each tagged with GFP and expressed under the pie-1 promoter (germline), the ges-1 promoter (intestine), or their endogenous promoter (somatic expression), for a total of nine lines.  In addition, LIN-35:GFP was expressed under the mex-5 promoter (germline), and HPL-2 was expressed under the ges-1 promoter, for an additional two lines.  All strains with germline expression were analyzed as young adults, while the intestine or somatic expressed lines were analyzed as L1s.  For each replicate of each transgenic line at the appropriate stage, anti-GFP was used to immunoprecipitate the tagged transcription factor, and the factor-enriched chromatin was subjected to Illumina sequencing.  As a control, for every ChIP sample, the input (without immunoprecipitation) was also sequenced.

first: Michelle

last: Kudron

first: Wei

last: Niu

first: Zhi

last: Lu

first: Guilin

last: Gerstein

first: Michael

last: Snyder


title: Genome-wide gene expression analysis of 16HBE14 human bronchial epithelial cells in response to Neisseria

status: Public on Jun 01 2012

city: Singapore

first: Ahmad Nazri

last: Mohamed Naim

address: 60 Biopolis Street, Genome, #02-01

department: Infectious disease

country: Singapore

institute: Genome institute of Singapore

summary:
We looked at host gene expression signatures common and specfic to occasionally pathogenic N. meningitidis and commensal N. lactamica.
We hypothesise that similar host cell responses during early interactions with N. meningitidis and N. lactamica could inform common mechanisms of colonisation of commensals while differential host cell responses could be capable of altering the outcome of the colonisation process.

overall_design: Total RNA obtained from 16HBE14 cells infected with the different strains of Neisseria from 0 to 7 hours are compared to mock-infected controls at the respective timepoints. 192 samples are analysed. There are 4 to 8 biological replicates per condition.

first: Hazel

middle: E

last: Wong

first: Ming-Shi

last: Li

first: J

middle: S

last: Kroll

first: Martin

last: Hibberd

first: Paul

middle: R

last: Langford


title: Molecular characterisation of circulating tumor cells in human metastatic colorectal cancer

status: Public on Jun 30 2012

city: Santiago de Compostela

first: Miguel

last: Abal

state: A Coruña

address: Trav Choupana s/n

department: Medical Oncology

institute: University Clinical Hospital

summary: Metastatic colorectal cancer (mCRC) relies on the detachment of aggressive malignant cells from the primary tumor into the bloodstream, these Circulating Tumor Cells (CTC) being the principal source of the further metastasis. Here, we approached the massive molecular profiling of the CTC population isolated from mCRC patients. Clinically, the presence of CTC is associated with poor prognosis and there exists a clear necessity for more specific and efficient chemotherapies in the treatment of mCRC. Immunoisolation of CTC from these patients combined with a whole transcriptome amplification and hybridization onto gene expression arrays, lead us to specifically describe for the first time a CTC population with adhesive and migratory characteristics, in addition to a modulated expression of genes related to cell death and survival. Furthermore, bioinformatic analysis provided with an armamentarium of highly specific and sensitive valuable markers that should impact on the management and follow-up of mCRC patients. Finally, molecular profiling of CTC resulted in the identification of new therapeutic targets, like TGF-β1 impairing, specifically targeting the CTC population which should improve the efficacy in the eradication and prevention of CRC metastasis. In conclusion, molecular profiling of CTC represents an innovative and promising approach in the clinical management of mCRC patients.

overall_design: Circulating Tumor Cells (CTC) were immunoisolated from six metastatic colorectal patients (mCRC). Moreover, blood from three healthy donors were obtained, immunoisolating non-specific cellularity background. RNA was extracted and globally amplified with a Whole Transcriptome Amplification system. Samples were hybridized onto agilent arrays and CTC specific genes were obtained. Gene networks were built with IPA software and a gene ontology analysis was performed. Eleven candidate genes were validated by real time PCR. Finally, TGFB1 was evaluated as a potential drugable target against CTC population.

first: Jorge

last: Barbazán

first: Lorena

last: Alonso-Alconada

first: Laura

last: Muinelo-Romay

first: María

last: Vieito

first: Alicia

last: Abalo

first: Marta

last: Alonso-Nocelo

first: Sonia

last: Candamio

first: Elena

last: Gallardo

first: Beatriz

last: Fernández

first: Ihab

last: Abdulkader

last: Casares

first: Antonio

last: Gómez-Tato

first: Rafael

last: López-López


title: Integrative Gene Expression Profiling Reveals G6PD-Mediated Resistance to RNA-Directed Nucleoside Analogues in B-Cell Neoplasms

city: Chicago

first: Samuel

last: McBrayer

address: 303 E Superior

institute: Northwestern University

summary: 8-amino-adenosine (8-NH2-Ado) inhibits RNA synthesis and specifically inhibits synthesis of mRNAs with short half-lives.  We hypothesize that the mRNAs affected code for proteins important in apoptosis and glucose metabolism.  Gene Expression Arrays will help us understand which gene families may be affected by this drug and give us a better understanding of mechanism of action of this drug

overall_design:
1.  MM.1S cells treated with 8-amino-adenosine for 0, 5 hrs and 17 hrs.
(myeloma cells sensitive to the drug)
2.  U266 cells treated with 8-amino-adenosine for 0, 5 hrs and 17 hrs.
(myeloma cells resistant to the drug).
3.  Jeko cells treated with 8-amino-adenosine for 0, 5 hrs and 17 hrs.
(Mantle cell lymphoma cells sensitive to drug)
4.  Granta cells treated with 8-amino-adenosine for 0, 5 hrs and 17 hrs.
(Mantle cell lymphoma cells resistant to drug).

first: Michael

last: Yarrington

first: Jun

last: Qian

first: Gang

last: Feng

first: Mala

last: Shanmugam

first: Varsha

last: Gandhi

first: Nancy

last: Krett

first: Steven

middle: T

last: Rosen


title: Promoter activity profiling throughout the Drosophila life cycle reveals role of transposons in regulatory innovation

status: Public on Aug 30 2012

first: Philippe

last: Batut

summary: Since their discovery, transposable elements have been proposed to play a central role in the evolution of their host genomes through their ability to regulate gene expression, in particular by providing transcription start sites (TSSs) for host genes. To investigate their contribution to developmental gene expression, we developed RAMPAGE, a high-throughput 5'-complete cDNA sequencing approach to accurately discover TSSs, characterize their transcripts, and quantify their expression. This strategy, which directly delineates the expression profiles of individual promoters and was designed to offer optimal sample multiplexing capabilities, represents an advantageous alternative to standard RNA-Seq for a wide range of transcriptome profiling applications. We used RAMPAGE in a genome-wide study of promoter activity throughout 36 stages of the life cycle of Drosophila melanogaster, and describe here a comprehensive dataset that represents the first developmental timecourse of promoter usage. We found that over 40% of developmentally expressed genes have at least 2 promoters, and that alternative promoters generally implement distinct regulatory programs. Transposons harbor TSSs driving the expression of hundreds of annotated genes, and they often impart their own expression specificity upon the genes they regulate. Detailed analysis of particular transposons identified sequence elements encoding these regulatory properties. Our results show that transposable elements contribute significantly to the generation of standing variation and to the evolution of gene regulatory networks, by distributing stereotyped regulatory modules throughout the genome.

overall_design:
This dataset represents a whole-genome, single-base resolution profiling of transcription start site (TSS) expression throughout 36 stages of the life cycle of Drosophila melanogaster. These profiles were established using RAMPAGE, a high-throughput, high-accuracy 5'-complete cDNA sequencing method implemented on the Illumina platform. Embryos, larvae, pupae and adult flies were collected at specific stages of development, and RAMPAGE profiles were established for pools of whole organisms. The data was analyzed using custom scripts and algorithms that are all available upon request.

Supplementary files:
Dmel_Combined_+.bw: bigWig coverage by cDNA 5' ends (+ strand).
Dmel_Combined_-.bw: bigWig coverage by cDNA 5' ends (- strand).
Dmel_All_RAMPAGE_peaks.bed: BED file describing all RAMPAGE peaks.
Dmel_GeneTSS_RAMPAGE_peaks.bed: BED file describing all peaks attributed to annotated genes.
GeneTSS_expression_RAMPAGE_RPM.txt: Expression matrix for all genic peaks (RPM: reads per million).
Transposon_expression_RAMPAGE_RPM.txt: Expression matrix for all RepeatMasker-annotated transposon classes (RPM: reads per million).
Genome build: dm3

first: Alexander

last: Dobin

first: Charles

last: Plessy

first: Piero

last: Carninci

first: Thomas

last: Gingeras


title: Methylation profiling defines a widespread field defect in histologically normal prostate tissue associated with prostate cancer

city: Madison

first: Bing

last: Yang

address: 1111 Highland Ave

department: Urology

institute: UW-Madison

type: Methylation profiling by genome tiling array

summary:
We evaluated the presence of genome-wide epigenetic differences at 385,000 loci using Encode HG18 DNA methylation arrays in 5 non-tumor-associated (NTA) and 4 histologically undistinguished tumor-associated (TA) prostate tissues.
We identified 615 probes to be differentially methylated (p<0.05) in TA prostate, with 537 (87%) hypomethylated and 78 (13%) hypermethylated.

overall_design: comparison of methylation in NTA to TA prostate tissue

first: David

last: Jarrard


title: Melanoma-derived exosomes educate bone marrow progenitor cells toward a pro-metastatic phenotype through upregulation of the MET oncoprotein.

status: Public on May 27 2012

city: Madrid

first: Gema

last: Moreno-Bueno

state: Madrid

address: Arturo Duperier

department: Biochemistry

institute: IIB

summary:
Tumor-derived exosomes are emerging as mediators of tumorigenesis with a tissue-specific address and message. We explored the function of melanoma-derived exosomes in formation of primary tumors and metastatic progression in both murine models and patients. Whereas exosomes from highly metastatic melanoma cells increased the metastatic behavior of primary tumor cells by educating bone marrow (BM) progenitor cells via the MET receptor, exosomes from low metastatic melanoma cells did not alter the incidence of metastases. Melanoma-derived exosomes induced vascular leakiness at pre-metastatic sites, and reprogrammed BM progenitor cells towards a pro-vasculogenic phenotype (c-Kit+Tie2+MET+). Reducing MET expression in tumor-derived exosomes diminished the pro-metastatic behavior of BM cells. Importantly, MET expression was upregulated in circulating BM progenitor cells (CD45-CD117low and CD45-CD117lowTIE2+) isolated from stage III and stage IV melanoma patients. Rab1a, Rab5b, Rab7, and Rab27a were highly expressed in melanoma and Rab27a RNA interference decreased exosome production and/or soluble angiogenic factors in melanoma cells, thereby preventing mobilization of BM progenitor cells, tumor growth and metastasis. Finally, we identified a melanoma signature in exosomes isolated from metastatic melanoma patients, comprised of TYRP2, VLA-4, Hsp70, an Hsp90 isoform and MET oncoprotein, which together with Rab proteins, appear to represent exosome-specific proteins with prognostic potential, and may provide new therapeutic targets.
Identification of molecular finger associated to exosome effects in metastatic organs

overall_design: Microarray  analysis of genes differentially expressed in the lungs 24 and 48 hours after B16-F10 exosome tail vein injection compared to control.

first: Héctor

last: Peinado

first: Maša

last: Alečković

first: Simon

last: Lavotshkin

first: Irina

last: Matei

first: Bruno

last: Costa-Silva

first: Marta

last: Hergueta-Redondo

first: Caitlin

last: Williams

first: Guillermo

last: Garcia-Santos

first: Ayuko

last: Nitadori-Hoshino

last: Hoffman

first: Benjamin

last: Garcia

first: Margaret

last: Callahan

first: Jianda

last: Yuan

first: Vilma

last: Martins

first: Rosandra

last: Kaplan

first: Mary

last: Brady

first: Jedd

middle: D

last: Wolchok

first: Paul

middle: B

last: Chapman

first: Yibin

last: Kang

first: Jacqueline

last: Bromberg

last: Lyden


title: KC001: Genome wide expression profiling of the mesodiencephalic region led to the identification of novel factors involved in early and late dopaminergic development.

status: Public on Jul 09 2012

city: Utrecht

first: Marian

last: Groot Koerkamp

state: Utrecht

address: Heidelberglaan 25

institute: Princess Maxima Center for Pediatric Oncology

summary: Meso-diencephalic dopaminergic (mdDA) neurons are critical for motor control and cognitive functioning and their loss or dysfunction is associated with disorders such as Parkinson’s disease (PD), schizophrenia and addiction. However, relatively little is known about the molecular mechanisms underlying mdDA neuron development and maintenance. Here, we determined the spatiotemporal map of genes involved in the development of mdDA neurons to gain further insights into their molecular programming. Genome-wide gene expression profiles of the developing ventral mesencephalon (VM) were compared at different developmental stages leading to the identification of novel regulatory roles of neuronal signaling through nicotinic acthylcholine receptors (Chrna6 and Chrnb3 subunits) and the identification of novel transcription factors (OC1 and 2)) involved in the generation of mdDA neuronal  field. We show here that Pitx3 in cooperation with Nurr1 are the critical components in the activation of the Chrna6 and b3 subunits in mdDA neurons. Furthermore, we provide evidence of two divergent  regulatory pathways resulting in the expression of Chrna6 and Chrnb3 respectively.

overall_design: Embryonic ventral midbrain (VM) tissue was used to generate RNA samples for microarray analysis. Each sample consists of pooled RNA from three embryonic VMs, and is hybridized twice (in both dye orientations) against a common reference RNA (KC001-ref) consisting of pooled RNA from adult VMs. Each embryonic stages E10.5, E11.5, E12.5 and E13.5 is analysed from three independant samples.

first: Koushik

last: Chakrabarty

first: Lars

middle: V

last: Oerthel

first: Anita

last: Hellemons

middle: G

last: Koerkamp

first: Frank

last: Holstege

first: Jeroen

last: Pasterkamp

first: Marten

middle: P

last: Smidt


title: A Genome-wide DNA Methylation Study in Colorectal Carcinoma

status: Public on May 23 2012

first: Muhammad

middle: Ghulam

last: Kibriya

address: 900 E 57th Street

department: Health Studies

institute: The University of Chicago

summary: Genome wide DNA methylation profiling of tumor and surrounding healthy colonic mucosa from patients with colorectal carcinoma. The Illumina Infinium 27k Human DNA methylation Beadchip v1.2 was used to obtain DNA methylation profiles across 27,578 CpG loci covering 14,475 genes.

overall_design: Samples included a total of 48 paired normal and tumor samples from 24 patients.  The paired samples were put on the same chip.

last: Raza

first: Farzana

last: Jasmine

first: Shantanu

last: Roy

first: Rachelle

last: Paul-Brutus

first: Ronald

last: Rahaman

first: Charlotte

last: Dodsworth

last: Rakibuz-Zaman

first: Mohammed

last: Kamal

first: Habibul

last: Ahsan


title: Genome-wide analysis of SPARC(secreted protein acidic and rich in cysteine)-responsive gene expression in HTR-8/SVneo cells

status: Public on Apr 28 2012

city: Shanghai

first: Yahong

last: Jiang

address: 2140 Xietu Road

institute: Shanghai Institute of Planned Parenthood Research

summary: SPARC is  a matricellular glycoprotein that plays critical roles in the pathologies associated with obesity and diabetes, as well as tumorigenesis. The objective of this study was to investigate the role of SPARC in the process of trophoblast invasion which shares many similarities with tumor cells invasion. Our results reveals that hormones, cell adhesion molecules, ECM molecules, growth factors and cytokines all are mediated by SPARC in EVT invasion.

overall_design: HTR-8/SVneo cells were transfected with SPARC siRNA or a 25-nucleotide universal negative control siRNA using Lipofectamine 2000 according to the manufacturer’s protocol. Seventy-two hours after transfection, cells were harvested and RNA was isolated using standard procedures.

first: Zhaogui

last: Sun


title: Identifying radiation exposure biomarkers from mouse blood transcriptome

city: Logan

first: Daniel

last: Hyduke

state: UT

address: 4105 Old Main Hill ENGR 402S

department: Biological Engineering

institute: Utah State University

summary: Here, we present a whole-genome survey of the murine transcriptomic response to physiologically-relevant radiation doses, 2 and 8 Gy.

overall_design: There are 18 distinct biological samples here.  Mice were exposed to ionizing radiation (Cesium-138 source) and whole blood was collected by cardiac puncture 6 hours post treatment.  Doses were 0 (7 samples), 2 (5 samples), and 8 (6 samples) gy.

first: Evagelia

last: Laiakis

first: Heng

middle: H

last: Li

first: Albert

middle: J

last: Fornace Jr


title: Methylation in Taiwanese HCC tumor and adjacent tissues

status: Public on May 16 2012

city: NY

first: Regina

last: Santella

address: 630 West 168th St

department: Environmental Health Sciences

institute: Columbia University

summary: We analyzed tumor and adjacent non-tumor tissues from 62 Taiwanese HCC cases using Illumina HumanMethylation 27 chips. After Bonferroni adjustment, a total of 2,324 CpG sites significantly differed in methylation level, with 684 CpG sites significantly hypermethylated and 1,640 hypomethylated in tumor compared to non-tumor tissues. Array data were validated with pyrosequencing in a subset of 5 of these genes; correlation coefficients ranged from 0.92 to 0.97.

overall_design: 62 tumor and 62 adjacent non tumor tissues

middle: M

first: Shuang

last: Wang


title: Differential expression of genes after over expression of hsa-miR-128 in human embryonic kidney cells (HEK293T cells)

status: Public on May 10 2012

city: Delhi

first: Neeru

last: Saini

address: Mall Road

department: FGU

institute: IGIB

summary: The experiment was deigned to identify the genes which get altered after the over expression of hsa-miR-128 in HEK293T cells. The HEK293T cells plated in 6-well plate were transfected with 4 micrograms of cloned miR-128 (p128) in three biological replicates.

overall_design: Biological triplicates of 2 samples were used viz. control HEK293T cells (c), HEK293T cells transfected with 4 micrograms of the cloned hsa-miR-128(t).


title: Chromatin architectures at fission yeast transcriptional promoters and replication origins

status: Public on Apr 24 2012

city: Buffalo

first: Michael

last: Buck

address: 701 Ellicott St

institute: SUNY at Buffalo

summary: We have used micrococcal nuclease (MNase) digestion followed by deep sequencing in order to obtain a higher-resolution map than previously available of nucleosome positions in the fission yeast, Schizosaccharomyces pombe. Our data confirm an unusually short average nucleosome repeat length, ~152 bp, in fission yeast and that transcriptional start sites (TSSs) are associated with nucleosome-depleted regions (NDRs), ordered nucleosome arrays downstream and less regularly spaced upstream nucleosomes. In addition, we found enrichments for associated function in four of eight groups of genes clustered according to chromatin configurations near TSSs. At replication origins, our data revealed asymmetric localization of Pre-Replication Complex (pre-RC) proteins within large NDRs—a feature that is conserved in fission and budding yeast and is therefore likely to be conserved in other eukaryotic organisms.

overall_design: Examination of nucleosome positioning in Schizosaccharomyces pombe

first: Joel

middle: A

last: Huberman

first: Piotr

last: Mieczkowski

first: Robert

last: Givens


title: Expression data from H2K mouse myogenic precursor cells

status: Public on Apr 20 2012

first: Jim

last: Holaska

state: IL

address: 5841 S. Maryland Ave, MC 6088

department: Medicine, Section of Cardiology

institute: University of Chicago

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

summary: Mutations in the inner nuclear membrane protein emerin cause muscular dystrophy. Current evidence suggests that the muscle wasting is related to defects in muscle progenitor cell differentiation and regeneration. We obtained miRNA and mRNA expression data from wildtype and emerin-null cells and looked at gene expression differences between them.

platform_organism:
Mus musculus
synthetic construct

overall_design: Case vs. control with a technical replicate of each

first: James

first: Adam

last: Koch


title: Relationship between Genome-Wide DNA Methylation and Gene Expression in Uterine Leiomyoma

status: Public on Apr 30 2012

first: Antonia

last: Navarro

address: 303 E. Superior st

department: OB/GYN

type:
Expression profiling by array
Methylation profiling by array

summary:
Uterine leiomyomas, or fibroids, represent the most common benign tumor of the female reproductive tract. Fibroids become symptomatic in 30% of all women and up to 70% of African American women of reproductive age. Epigenetic dysregulation of individual genes has been demonstrated in leiomyoma cells; however, the in vivo genome-wide distribution of such epigenetic abnormalities, however, remains unknown.
Principal Findings: We characterized and compared genome-wide DNA methylation and mRNA expression profiles in uterine leiomyoma and matched adjacent normal myometrial tissues from 18 African-American women. We found 55 genes with differential promoter methylation and concominant differences in mRNA expression in uterine leiomyoma versus normal myometrium. Eighty percent of the identified genes showed an inverse relationship DNA methylation status and mRNA expression in uterine leiomyoma tissues, and the majority of genes (62%) displayed hypermethylation associated with gene silencing. We selected two genes, the known tumor suppressors KLF11 and DLEC1, and verified promoter hypermethylation and mRNA repression using bisulfite sequencing and real-time PCR. Incubation of primary leiomyoma smooth muscle cells with a DNA methyltransferase inhibitor restored KLF11 and DLEC1 mRNA levels.

overall_design: paired LM and MM tissue samples


title: Gene expression of wild-type and Ppar-beta null primary keratinocytes, with and without infection with an activated Hras retrovirus, with and without the Ppar-beta specific ligand GW0742

status: Public on Apr 12 2012

city: University Park

first: Combiz

last: Khozoie

state: PA

address: 312 Life Sciences Building

institute: The Pennsylvania State University

summary: Differential gene expression profiles were observed in response to Hras in either wild-type or Ppar-beta null primary keratinocytes and differentail gene edxpression profiles by GW0742 were only found in wild-type keratinocytes.

overall_design: Primary keratinocytes from wild-type and Ppar-beta null mice were either mock infected or infected with an Hras encoding retrovirus and treated with or without 1 uM GW0742 for 24 hours.

first: Bokai

last: Zhu


title: Expression data from CCL185 carcinoma cell line transiently infected with EBV

status: Public on Apr 11 2012

city: Shreveport

first: Rona

middle: S.

last: Scott

state: LA

address: 1501 Kings Highway

department: Microbiology and Immunology

institute: Louisiana State University Health Sciences Center-Shreveport

summary:
Epstein-Barr virus(EBV) is associated with malignancies from lymphoid and epithelial origin. In many cases, an incomplete EBV association is noted and confoundswhate role the virus plays in oncogenesis. A number of viral proteins have been shown to interact with epigenetic factors to regulate both viral and host gene expression. Thus, we hypothesize that EBV may inadvertantly induce epigenetic alterations to the host genome that are maintained upon loss of the virus. If proven, these results would broaden EBV's role in tumorigenesis and provide a mechanism for how a tumor virus can act in a "hit-and-run" fashion.
We examined EBV-induced epigenetic alterations in a setting of viral redundancy and loss.

overall_design: With mounting evidence that EBV can induce epigenetic alterations, we developed a transient infection model where a clonal derivative (designated cl3) from the CCL185/A549 cell line was infected with a recombinant EBV carrying neomycin resistance cassette in place of the BDLF3 open reading frame. Infected cells were passaged ten times, and then selection pressure was removed for an additional ten passages to allow for viral loss. Three transiently-infected EBV-negative clones were identified by single cell cloning (designated 10-9, 10-10, and 10-14).  Uninfected parental clone and cells transfected with pcDNA3 plasmid were passaged alongside the transiently-infected clones.  Each sample was analyzed in duplicate.

first: Krista

last: Queen


title: Rapid evolution in fungal reproductive genes as revealed by evolutionary analyses of expressed sequence tags in Neurospora

status: Public on Apr 05 2012

city: Uppsala

first: Nicklas

last: Samils

address: Almas allé 5

department: Forest Mycology and Plant Pathology

country: Sweden

institute: Swedish University of Agricultural Sciences

summary: Neurospora intermedia is a heterothallic filamentous ascomycete. In this study we use microarray technology to study the difference in gene expression between vegetative growth and early reproductive development.

overall_design: Neurospora intermedia FGSC#8882 mat-A and FGSC#8782 mat-a. Solid synthetic crossing medium (SCM)  was used as a nutrient regime before sampling and processing. Two different conditions were sampled: vegetative mycelial tissue and young reproductive mycelial tissue.

first: Kristiina

last: Nygren

first: Andreas

last: Wallberg

first: Jason

last: Stajich

first: Jeffrey

last: Townsend

first: Magnus

last: Karlsson

first: Hanna

last: Johannesson


title: Genome-wide analysis of the grapevine stilbene synthase multigenic family: genomic organization and expression profiles upon biotic and abiotic stresses

status: Public on May 21 2012

city: Legnaro

first: Alessandro

last: Vannozzi

state: PD

address: via dell'Università 16

department: DAFNAE

institute: University of Padova

summary: In this study a complete characterization of the STS multigenic family in grapevine has been performed, commencing with the identification, annotation and phylogenetic analysis of all members and integration of this information with a comprehensive set of gene expression analyses including healthy tissues at differential developmental stages and in leaves exposed to both biotic (downy mildew infection) and abiotic (wounding and UV-C exposure) stresses. At least thirty-three full length sequences encoding VvSTS genes were identified, which, based on predicted amino acid sequences, cluster in 3 principal subgroups designated A, B and C. The majority of VvSTS genes cluster in subgroups B and C and are located on chr16 whereas the few gene family members in subgroup A are found on chr10. Microarray and mRNA-seq expression analyses revealed different patterns of transcript accumulation between the different groups of VvSTS family members and between VvSTSs and VvCHSs. Indeed, under certain conditions the transcriptional response of VvSTS and VvCHS genes appears to be diametrically opposed suggesting that flow of carbon between these two competing metabolic pathways is tightly regulated at the transcriptional level.

overall_design: Examination of transcriptome profile in Vitis vinifera cv Pinot noir leaf discs pools trated upon biotic and abiotic stresses. 7 samples examined: Control (=wounded 0h), wounded 24h, wounded 48h, UV-C treated 24h, UV-C treated 48h, Plasmopara viticola infected 24h, Plasmopara viticola infected 48h.

first: Ian

last: Dry

first: Marianna

last: Fasoli

first: Sara

last: Zenoni

first: Margherita

last: Lucchin


title: Mouse high grade astrocytoma cells (GL261) treated with neural stem/precursor cell (NPC) conditioned medium or non-conditioned medium (control)

status: Public on May 01 2012

city: Lund

first: Ulrike

last: Nuber

address: Klinikgatan 26

institute: Lund University

summary: Primary astrocytomas of high histopathological grade (HG-astrocytomas) are largely restricted to older patients and are almost invariably fatal despite multimodal therapy. Here, we show that the young brain has an endogenous defense mechanisms against HG-astrocytomas. Neural precursor cells (NPCs) migrate to HG-astrocytomas, reduce glioma expansion and prolong survival by releasing a group of fatty-acid ethanolamides that have agonistic activity on the vanilloid receptor (transient receptor potential vanilloid subfamily member-1; TRPV1). TRPV1 expression is much higher in HG-astrocytomas than in the tumor-free brain and TRPV1 stimulation triggers tumor cell-death via the activating transcription factor-3 (ATF3) controlled branch of the ER-stress pathway. The anti-tumourigenic response of NPCs is lost with aging. NPC-mediated tumor suppression can be mimicked in the old brain by systemic administration of the synthetic vanilloid Arvanil, indicating that TRPV1 agonists hold potential as new HG-astrocytoma therapeutics.

overall_design:
The goal of this microarray study was understand how neural stem / precursor cell (NPC) induced high grade astrocytoma cell-death is controlled by changes in gene expression. We investigated the gene-expression pattern in mouse high grade astrocytoma GL261 cells after incubation with NPC non-conditioned medium (controls) or NPC-conditioned medium by microarrays and found that endoplasmic reticulum stress genes like the activating transcription factor-3 (ATF3) were robustly up-regulated in NPC-conditioned medium treated mouse high grade astrocytoma cells, compared to controls.
Comparison of two experimental groups (conditioned medium treated versus non-conditioned medium treated) in three dye swap experiments (6 arrays used in total).


title: Urinary bladder in constant darkness: time course

city: Kyoto

first: Hiromitsu

last: Negoro

state: Kyoto

address: 54 Shogoin-Kawara-cho, Sakyo-ku

institute: Kyoto University, Graduate School of Medicine

summary: Analysis of urinary bladder in wild-type C57BL/6 females sacrificed every 4 hours at six time points under constant darkness after acclimation for 2 weeks under 12-hour light and 12-hour dark conditions. Results provide insight into circadian gene expression patterns in normal urinary bladder.

overall_design: Analysis of urinary bladder in wild-type C57BL/6 females sacrificed every 4 hours at six time points (n=2 for each time (CT 0, 4, 8, 12 and 20)) under constant darkness after acclimation for 2 weeks under 12-hour light and 12-hour dark conditions.

first: Akihiro

last: Kanematsu

first: Tomonori

last: Oura

first: Shigeyuki

last: Matsui

first: Masao

last: Doi

first: Hitoshi

last: Okamura

first: Yasuhiko

last: Tabata

first: Osamu

last: Ogawa


title: Expression data from mouse tissues

status: Public on Apr 02 2012

city: Milano

first: Simone

middle: Paolo

last: Minardi

state: Italy

address: Via Adamello

department: Microarray and NGS Unit

institute: Cogentech

summary:
The role of p53 in assuring longevity through prevention of cancer is well established, but how it specifically regulates aging is still controversial. Our assumption is that distinct p53-pathways regulate tumor suppression and aging and that p66Shc is one of the master regulators of the p53 aging function. p66Shc longevity determinant protein acts as a downstream target of p53 and it is indispensable for the ability of activated p53 to induce elevation of intracellular oxidants and apoptosis.
We used microarray  to gain insight into the mechanism of the physiological activation of p53-p66Shc pathway

overall_design: Total RNA was extracted from  freshly isolated thymus, liver, heart and lung of two months old mice (pool of four mice for each genotype)

first: Enrica

last: Migliaccio


title: Neonatal diethylstilbestrol exposure alters the metabolic profile of uterine epithelial cells.

status: Public on May 15 2012

city: Saint Louis

first: Yan

last: Yin

state: MO

address: 660 S. Euclid Ave. CB8123

department: Medicine

institute: Washington University in St. Louis

summary: Developmental exposure to diethylstilbestrol (DES) causes reproductive tract malformations, affects fertility and increases the risk of clear cell carcinoma of the vagina and cervix in humans. Previous studies on a well-established mouse DES model demonstrated that it recapitulates many features of the human syndrome, yet the underlying molecular mechanism is far from clear. Using the neonatal DES mouse model, the present study uses global transcript profiling to systematically explore early gene expression changes in individual epithelial and mesenchymal compartments of the neonatal uterus.  Over 900 genes show differential expression upon DES treatment in either one or both tissue layers. Interestingly, multiple components of the Peroxisome Proliferator-Activated Receptor gamma (PPAR gamma)-mediated adipogenic/lipid metabolic pathway, including PPARgamma itself, are targets of DES in the neonatal uterus. TEM and Oil Red O staining further demonstrate a dramatic increase in lipid deposition in the uterine epithelial cells upon DES exposure. Neonatal DES exposure also perturbs glucose homeostasis in the uterine epithelium. Some of these neonatal DES-induced metabolic changes appear to last into adulthood, suggesting a permanent effect of DES on energy metabolism in uterine epithelial cells. This study extends the list of biological processes that can be regulated by estrogen or DES, and provides a novel perspective for endocrine disruptor induced reproductive abnormalities.

overall_design: We separated UE from the UM from vehicle (oil)- or DES-treated postnatal day 5 (P5) mice, and prepared biological triplicates of RNA from pooled specimens (n≥3). Those samples were analyzed on two MouseWG-6 BeadChips, which detects 45,200 transcripts including more than 26,000 annotated genes in the NCBI RefSeq database. Difference of at least twofold in signal intensity of each given probe set with a P-value less than 0.05 was considered statistically significant.

first: Liang

last: Ma


title: Genetic and epigenetic determinants of neurogenesis and myogenesis

status: Public on Mar 26 2012

city: Seattle

first: Stephen

last: Tapscott

state: WASHINGTON

address: 1100 Fairview N. Ave

department: Human Biology

institute: Fred Hutch Cancer Research Center

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

overall_design: Refer to individual Series

first: Abraham

last: Fong

first: Zizhen

last: Yao

first: Jun

middle: W

last: Zhong

first: Yi

last: Cao

first: Walter

middle: L

last: Ruzzo

first: Robert

middle: C

last: Gentleman


title: Genome-wide gene expression to dibenzofuran in Sphingomonas wittichii RW1

status: Public on Apr 18 2012

city: Lausanne

first: Edith

last: Coronado

state: Vaud

address: UNIL-Sorge

department: Microbiologie Fondamental

country: Switzerland

institute: UNIL

summary: Sphingomonas wittichii RW1 is a bacterium isolated for its ability to degrade the toxic polyaromatic hydrocarbon dibenzofuran (dbf) and its polychlorinated derivatives. Its genome consists of a chromosome and two plasmids, encoding for more than 5300 genes. We studied genome-wide expression of strain RW1 to dbf in three different experimental setups, including both batch cultures and chemostats, comparing in all cases to the transcriptome of cells grown on phenylalanine as carbon source. A short exposure to DBF in chemostat or in batch, provoked the up-regulation of the ECF sigma 24, catalases, peroxiredoxins, chaperones, an aquaporin, several OmpA domain-containing proteins and the down-regulation of genes involved in TCA cycle, oxidative phosphorylation, amino acid metabolism and ribosomal proteins. When growing strain RW1 on DBF, genes known to be involved in DBF degradation were induced 2 to 4 fold. Additionally, two cluster of genes, putatively participating in the gentisate and meta-cleavage branches of the DBF degradation pathway, were induced from 12 to 19 fold.

overall_design: Three experiments are summarized here. 1. Compares the response of exponentially growing S.wittichii RW1 cells on phenylalanine (Phe), washed and resuspended in Phe for 30 min, with that of cells resuspended in DBF medium for 30 min (Phe1_shock, DBF1_schock, etc.). 2. Compares response of RW1 cells grown in batch medium with Phe or DBF as sole carbon and energy source, and harvested in exponential phase (Phe1_long, DBF1_long, etc. triplicates). 3. Comparison of transcriptome of RW1 cells grown continuously in chemostat on phenylalanine as carbon-limited substrate, with cells that have experienced instant exposure to phenylalanine plus DBF. This is done by pulsing DBF to maximum solubility and a simultaneous change in feed medium to Phe+ DBF. Samples before transition (Phe ctrl1-chem, etc. quadruplates), after 30 min (DBF 30m1-chem, etc), 1 h, 2 h and 6 h (DBF6h1-chem, etc.).

first: Jan

middle: R

last: van der Meer


title: Characterisation of mRNA and microRNA in human mast cell exosomes and their transfer to other mast cells and blood CD34 progenitor cells

status: Public on Apr 16 2012

city: Gothenburg

first: Karin

last: Ekström

address: Medicinaregatan 1G

institute: Krefting Research Centre

summary:
Background: Exosomes are nanovesicles of endocytic origin believed to be involved in communication between cells. Recently, it has been shown that mast cell exosomes contain RNA named "exosomal shuttle RNA". The aim of this study was to evaluate whether exosomal shuttle RNA could play a role in the communication between human mast cells and between human mast cells and human CD34 positive progenitor cells. Results: Exosomes from the human mast cell line HMC-1 contain RNA. The exosomes contain no or very little ribosomal RNA compared to their donor cells. The mRNA and microRNA content in exosomes and their donor cells was examined using microarray analyses. We found 116 microRNA in the exosomes and 134 microRNA in the cells, from which some were expressed at different level. DNA microarray experiments revealed the presence of approximately 1800 mRNAs in the exosomes, which represent 15% of the donor cell mRNA content. Transfer experiments revealed that exosomes and their RNA can transfer to other HMC-1 cells and to CD34 positive progenitors.  Conclusions: To conclude, HMC-1 exosomes contain mRNA and microRNA that can be transferred to other mast cells and to CD34 progenitors. This shuttle of exosomal RNA may represent a powerful mode of communication between cells where cells send genetic information to other cells over a distance via exosomes.

[miRNA profiling] Identification of microRNA was performed by Exiqon (www.exiqon.com). Briefly, the quality of the total RNA was verified by an Agilent 2100 Bioanalyzer. Total RNA from the exosome and the HMC-1 cell samples were labelled with Hy3 and Hy5 fluorescent stain, respectively, using the miRCURY Hy3/Hy5 power labelling kit. The Hy3-labelled exosome samples and a Hy5-labeled mast cells were mixed pair-wise and hybridized to the miRCURY? LNA array (v9.2). The hybridization was performed according to the miRCURY? LNA array manual using a Tecan HS4800 hybridization station (Tecan Systems, Inc. San Jose, CA). The miRCURY? LNA array microarray slides were scanned by a ScanArray 4000 XL scanner (Packard Biochip Technologies, Billerica, MA ,USA) and the image analysis was carried out using the ImaGene 6.1.0 software (BioDiscovery, Inc, El Segundo, CA USA). The quantified signals were normalized using the global Lowess (LOcally WEighted Scatterplot Smoothing) regression algorithm. MicroRNA with signals equal to or below the background signal in 2 or more of the 4 replicate measurements were identified as absent in that slide. The limit for a miRNA to be listed as detectable was set to signal intensities higher than 3 x background (3 x median Hy3 or Hy5 for the total slide). In addition, where signals were detected for <3 of the slides, they were considered unreliable and excluded from sets of detected miRNAs. The experiment was performed in triplicate samples. The signal was calculated as the mean value of the log2MeanRatio Hy3/Hy5 for the triplicates ± SD.

platform_organism:
Homo sapiens
Mus musculus
Rattus norvegicus
Human alphaherpesvirus 1
Human betaherpesvirus 5
human gammaherpesvirus 4
JC polyomavirus
Human immunodeficiency virus 1
Human gammaherpesvirus 8
Betapolyomavirus hominis
Betapolyomavirus macacae

overall_design:
[mRNA profiling] Exosomes were prepared from the supernatant of HMC-1 cells by differential centrifugations and filtration. RNA was isolated from the exosomes and their parental cells using Trizol . The microarray experiments were performed by SweGene (www.swegene.org/) according to Affymetrix microarray DNA chip analysis (n=4). p0739_E1, p0739_ E2, p0739_E3 and p0739_E4 for the exosomes samples and p0739_C1, p0739_C2, p0739_C3, and p0739_C4 for the HMC-1 cells.

[miRNA profiling] Exosomes were prepared from the supernatant of HMC-1 cells by differential centrifugations and filtration. RNA was isolated from the exosomes and their parental cells using Trizol followed by RNeasy clean-up. The microarray experiments were performed by Exiqon.

first: Hadi

last: Valadi

last: Lötvall


title: Bifunctional Activity of members of the Arabidopsis NF-YA Transcription Factor Family

status: Public on Apr 25 2012

city: Irapuato

first: Enrique

middle: Ibarra

last: Laclette

state: Guanajuato

address: Km 9.6 Libramiento Norte Carretera Irapuato-León, A.P. 629

country: Mexico

institute: Laboratorio Nacional de Genomíca (LANGEBIO), Centro de Investigación y Estudios Avanzados del IPN (CINVESTAV)

summary: Five members of the Arabidopsis thaliana NF-YA gene family are strongly induced by several stress conditions via transcriptional and miR169-related posttranscriptional mechanisms. These transcription factors participate in gene regulation via two different mechanisms, one depending on binding to the CCAAT-box in the promoter of regulated genes and the other, independent of the CCAAT-box, in which NF-YA prevents the interaction of the NF-YB/YC heterodimer with transcription factors.

overall_design: Three biological  and two technical (in swap) replicates for each genotype were obtained for each treatment (DMSO (mock) and estradiol  24h after induction). Mock samples were pooled and used as a reference.

first: Marco

last: Leyva-González

last: Ibarra-Laclette

first: Alfredo

last: Cruz-Ramírez

first: Luis

last: Herrera-Estrella


title: Identification of target genes of tumor suppressor microRNAs in human cancer

status: Public on Feb 09 2012

city: Chiba

first: Naohiko

last: Seki

state: Chiba

address: 1-8-1 Inohana,Chuo-ku

department: School of Medicine

institute: Chiba University

summary: To identify target genes of tumor suppressive microRNAs in human cancer, several cell lines (bladder cancer, prostate cancer, renal cell carcinoma, and head and neck squamous cell carcinoma) were subjected to Agilent whole genome microarrays. miR-517a, miR-218, miR-145, miR-1 and miR-874 function as tumor suppressors.

overall_design: Human cancer cell lines (BOY, T24, A498, PC3, DU145, FaDu, SAS, HSC3, IMC3) were transfected with miRNAs (miR-517a, miR-218, miR-145, miR-1, miR-874). The miRNA-transfected human cancer cell lines were compared to control cell lines.


title: Expression data from peripheral blood lymphocytes of major depression, subsyndromal symptomatic depression, and healthy controls

status: Public on Mar 21 2012

city: Shanghai

first: Zezhi

last: Li

address: 600 South Wan Ping Road Shanghai 200030, China

department: Division of Mood Disorders

institute: Shanghai Mental Health Center, Shanghai Jiao Tong University School of Medicine, Shanghai, China

summary:
Several studies have suggested that SSD is a transitory phenomena in the depression spectrum and is thus considered a subtype of depression. However, the pathophysioloy of depression remain largely obscure and studies on SSD are limited. The present study compared the expression profile and made the classification with the leukocytes by using whole-genome cRNA microarrays among drug-free first-episode subjects with SSD, MDD, and healthy controls.
We used microarrays to detail the global programme of gene expression to develop blood-based gene expression profiles models for classification of subsyndromal symptomatic depression and major depressive disorder

overall_design: The present study compared the expression profile and made the classification with the leukocytes by using whole-genome cRNA microarrays among drug-free first-episode subjects with SSD, MDD, and matched controls (8 subjects in each group). Support vector machines (SVMs) were utilized for training and testing on candidate signature expression profiles from signature selection step.

first: Zhenghui

last: Yi