title: Gene expression signature overlap between shETV1 and BRD32048 in LNCaP and SK-MEL-28

status: Public on Nov 07 2013

city: Boston

first: Marius

last: Pop

address: 450 Brookline ave

institute: DFCI

summary: Identification of BRD32048 as an inhibitor of ETV1 oncogenic transcription factor. This compound was indentified by small molecule mcroarray (a binding assay). It was able to consistently inhibit an ETV1-dependent MMP1-driven luciferase signal. Its direct binding was validated by Suface plasmon resonance (Biacore assay). It inhibits ETV1-driven invasion in ETV1-dependent cell lines. The goal of this gene expression comparison was to interogate the effects of BRD32048 on the global gene expression and to define the degree to which its siganture overlaps with an ETV1-specific shRNA-induced gene expression signature.

overall_design: The gene expression analysis was performed for two ETV1- dependent cell lines. (a) LNCaP (prostate cancer) uses a DOX-inducible system where two different ETV1sh (sh1117 and sh872) are induced for 4 days. In parallel cells were treated with 20 µM BRD32048 for 16 hours. The control was DMSO treated cells. (b) SK-MEL-28 were infected with two different ETV1sh (sh3 and sh5) and selected in puromycin for 4 days. The sh control used was GFPsh. In parallel cells were treated with 20 µM BRD32048 for 16 hours. The control was DMSO treated cells. Total RNA was isolated and measured with expression arrays. The data was normalized (see data processing) and the gene expression signatures (fold change >1.5 in either direction) were intersected between the experimental conditions for each cell line.

first: Nicolas

last: Stransky

first: Levi

last: Garraway


title: Expression analysis of Yersinia intermedia strain ATCC 29909 at 28 C in minimal medium with glucose under aerobic and anaerobic conditions

status: Public on Aug 21 2013

city: Madison

first: Lavanya

last: Babujee

state: WI

address: 425 Henry Mall

department: Genetics

country: USA

institute: UW-Madison

type: Expression profiling by genome tiling array

summary:
Investigation of whole genome gene expression level changes in Yersinia intermedia strain ATCC 29909 in response to oxygen.
The experiments and results have not been published yet (manuscript has been submitted to journal office and is under revision)

overall_design: A 6 chip (whole-genome-tiled array) study using total RNA recovered from the following: 6 separate cultures of Yersinia intermedia strain ATCC 29909 grown in minimal medium with glucose (3 grown in the presence of oxygen and 3 grown without oxygen). Each whole-genome-tiled arrays contained ~320,000 probes representing 3953 genes that included 3887 protein coding genes (and 18 likely pseudogenes), 12 non-coding RNAs and 36 tRNAs. Data from probes corresponding to intergenic regions (and some pseudogenes, rRNA genes and unannotated genes) of the genome were not considered in the present analysis.

first: Venkatesh

last: Balakrishnan

first: Jeremy

middle: D

last: Glasner

first: Patricia

middle: J

last: Kiley

first: Nicole

middle: T

last: Perna


title: Gene expression profiling in the largemouth bass ovary following sub-chronic dietary exposures to the organochlorine pesticides p,p’ DDE and methoxychlor

status: Public on Aug 10 2013

city: Gainesville

first: Christopher

middle: Joseph

last: Martyniuk

state: FL

address: CEHT Mowry Road

department: Physiological Sciences

institute: UF

summary: Largemouth bass (Micropterus salmoides) (LMB) inhabiting Lake Apopka, Florida are exposed to high levels of organochlorine pesticides (OCPs) that exert effects through multiple modes of action.  The objectives of this study were to assess the impacts of two OCPs (p,p'-Dichlorodiphenyldichloroethylene; p,p’ DDE and methoxychlor; MXC) on the reproductive axis of LMB.  Female LMB were fed coated feed over 84 days of either 125 (p,p’ DDE), 10 (MXC), or 0 (control) ppm (mg/kg).  In addition, due to the fact that p,p’ DDE and MXC are suspected anti-androgens, the potent anti-androgenic pharmaceutical flutamide (FLUT) was also fed to a separate group of LMB at 750 ppm.  After 84 days, LMB significantly incorporated p,p’ DDE and MXC into muscle and ovary tissue. Gonadal histology and plasma sex steroids were not significantly different than controls after being fed contaminants.  Microarray analysis revealed that p,p’ DDE and FLUT regulated more genes in common that either chemical compared to MXC, consistent with data suggesting that p,p’ DDE is a more potent anti-androgen than MXC.  There was a significant positive correlation between 71 commonly regulated genes in all three treatments, suggesting that these transcripts may be responding to a common anti-androgenic mode of action.  Cell processes affected by all three treatments included leukocyte cell adhesion, ossification, platelet function and inhibition, xenobiotic metabolism, fibrinolysis, and thermoregulation.  Most striking was that all three chemicals depressed gene networks related to immune function and inflammation.  This study adds to a growing number of fish transcriptomics studies investigating chemicals with an anti-androgenic MOA.

overall_design: 4 biological replicates per group; control, methoxychlor, p,p DDE, and flutamide

first: Chris

first: Melinda

last: Prucha

first: Nicholas

last: Doperalski

first: Kevin

last: Kroll

first: David

last: Barber

first: Nancy

last: Denslow


title: Effect of maternal exposure to dioxin on the pituitary and hypothalamic expression of genes in PND70 male pups

city: Fukuoka

first: Tomoki

last: Takeda

address: 3-1-1 Maidashi, Higashi-ku

department: Pharmaceutical sciences

country: Japan

institute: Kyushu University

summary: Our previous studies have revealed that treatment of pregnant rats with 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD, 1 μg/kg) at gestational day (GD) 15 reduces the pituitary synthesis of luteinizing hormone (LH) during late fetal and early postnatal period, leading to imprinting of defects in sexual behaviors at adulthood. However, it remains obscure how the attenuation of pituitary LH links to sexual immaturity. To address this issue, we firstly performed a DNA microarray analysis to identify the gene(s) responsible for dioxin-induced sexual immaturity, using the pituitary and hypothalamus of male pups, at the age of postnatal day (PND)70, born from TCDD-treated dams. Among the reduced genes, we focused on gonadotropin-releasing hormone (GnRH) in the hypothalamus, because of its role in sexual behaviors suggested so far. The present study strongly suggests that maternal exposure to TCDD fixes the status of the lowered expression of GnRH in the offspring by reducing steroidogenesis at perinatal stage, and this is the mechanism for the imprinting of defects in sexual behaviors at adulthood.

overall_design:
Total RNA was isolated from the pituitary and hypothalamus of PND70 male pups born from the dams treated with TCDD (1 μg/kg) or vehicle at GD15, using an RNeasy Mini Kit (QIAGEN). To identify the gene(s) the altered expression of which is fixed and linked to defects in sexual behaviors, the profile of gene expression was analyzed using the Illumina RatRef-12 Expression BeadChip.
This series includes two dataset; hypothalamic and pituitary samples (each case; N=3x2). The normalization applied each dataset.

first: Hideyuki

last: Yamada


title: Expression data from 22  human myotubes

status: Public on Aug 08 2013

city: Berlin

first: Anna

middle: Maria

last: Pakula

address: Lindenberger Weg 80

department: Experimental and Clinical Research Center (ECRC),Max-Delbrück-Centrum feur Molekulare Medizin (MDC) Berlin, Institut de Myologie NMR-Spectroscopy Laboratory Université Pierre et Marie Curie, Paris 6

country: Germany

institute: Charite University Berlin

summary:
Expression data from 22  human myotubes (7 healthy controls, 4 Dysferlinopathy (DYSF), 4 Caveolinopathy 3 (CAV3), 4 Facioscapulohumeral muscular dystrophy(FSHD) and 3 Four and a half LIM 1 protein deficiency FHL1).cDNA microarray data showed that cyclin A1 levels are specifically elevated in FSHD vs. other muscular disorders such as CAV3, DYSF, FHL1 and healthy control. Data could be confirmed with RT-PCR and Western blot analysis showing up-regulated levels of cyclin A1 also on the protein level.
Comparison of gene expression among 4 different muscular dystrophies and helathy controls. Looking for genes expression specifically changed (down/upregulated)  in FSHD.
In these data sheet we include expression data obtained for human cells lines derived from human V.lateralis muscle, shown as mean value. From 59 different expressed genes, Cyclin A1 was selected as a highly overexpressed (28 fold) gene in FSHD if compared to DYSF, CAV3, FHL1 and healyhy controls.

first: Joanna

last: Schneider

first: Jürgen

last: Janke

first: Ute

last: Zacharias

first: Herbert

last: Schulz

first: Norbert

last: Hübner

first: Anja

last: Mahler

first: Andreas

last: Spuler

first: Simone

first: Pierre

last: Carlier

first: Michael

last: Boschmann


title: Spatially restricted position-dependent implications of lamin A promoter occupancy on gene activity (ChIPs and MeDips)

status: Public on Jul 14 2013

city: Oslo

first: Philippe

last: Collas

address: PO Box 1112 Blindern

department: Institute of Basic Medical Sciences

country: Norway

institute: University of Oslo

type: Genome binding/occupancy profiling by genome tiling array

type: Methylation profiling by genome tiling array

summary: Interactions between the nuclear lamina (NL) and chromatin are thought to occur through large lamin association domains (LADs) and correlate with gene repression in these domains. We show that binding of lamin A/C (LMNA) to promoters occurs on discrete domains that are associated with distinct transcriptional outputs. Chromatin immunoprecipitation identifies thousands of LMNA-bound promoters, primarily linked to signaling functions. LMNA often occupies narrow domains on promoters, yet LMNA-bound promoters are often contiguous. LMNA-bound genes are overall repressed, but repression correlates with co-enrichment in repressive histone marks rather than LMNA occupancy per se. Genes marked by LMNA and H3K4me3 escape LMNA-associated repression in the absence of repressive histone marks. Positioning of LMNA on promoters relative to the TSS correlates with distinct transcriptional outputs: whereas upstream-distal binding can be transcriptionally permissive, TSS occupancy is associated with promoter inactivity. Perturbation in NL organization causes reorganization of lamin promoter occupancy and uncouples LMNA binding from promoter inactivity. Our results show the existence of many spatially restricted LMNA binding events on promoter regions, with distinct position-dependent transcriptional outputs.

overall_design: ChIPs were done from cultured untreated and LMNA-downregulated adipose stem cell (ASC) chromatin. MeDIPs were done from LMNA-downregulated ASCs. ChIP and MeDIP DNA was hybridized onto the aforementioned HG-18 Nimbegen promoter arrays.

first: P

first: E

last: Lund


title: Exon array analysis of the response to bevacizumab/erlotinib in advanced non-small cell lung cancer

status: Public on Jul 30 2013

city: St. Gallen

first: Florent

last: Baty

address: Rorschacherstrasse 95

department: Lung Center

country: Switzerland

institute: Cantonal Hospital St. Gallen

summary:
In the current study, we used exon arrays and clinical samples from a previous trial (SAKK 19/05) to investigate the expression variations at the exon-level of 3 genes potentially playing a key role in modulating treatment response (EGFR, KRAS, VEGFA).
Exon-level biomarkers for the response to targeted therapy bevacizumab/erlotinib were identified in patients with metastatic non-small cell lung cancer

overall_design: Multicenter, prospective, open-label, single-arm, phase II trial.

first: Sacha

last: Rothschild

first: Martin

last: Früh

first: Daniel

middle: C

last: Betticher

first: Cornelia

last: Dröge

first: Richard

last: Cathomas

last: Rauch

first: Oliver

last: Gautschi

first: Lukas

last: Bubendorf

first: Susanne

last: Crowe

first: Francesco

last: Zappa

first: Miklos

last: Pless

last: Brutsche


title: Four parameters increase the sensitivity and specificity of the exon array analysis and disclose 25 novel aberrantly spliced exons in myotonic dystrophy

status: Public on Sep 05 2013

city: Nagoya

first: Kinji

last: Ohno

address: 65 Tsurumai, Showa-ku

department: Graduate School of Medicine

institute: Nagoya University

summary: Myotonic dystrophy type 1 (DM1) is an RNA gain-of-function disorder in which abnormally expanded CTG repeats of DMPK sequestrate a splicing trans-factor MBNL1 and upregulate another splicing trans-factor CUGBP1. To identify a diverse array of aberrantly spliced genes, we performed the exon array analysis of DM1 muscles. We analyzed 72 exons by RT-PCR and found that 27 were aberrantly spliced, whereas 45 were not. Among these, 25 were novel and especially splicing aberrations of LDB3 exon 4 and TTN exon 45 were unique to DM1. Retrospective analysis revealed that four parameters efficiently detect aberrantly spliced exons: (i) the signal intensity is high; (ii) the ratio of probe sets with reliable signal intensities (that is, detection above background P-value=0.000) is high within a gene; (iii) the splice index (SI) is high; and (iv) SI is deviated from SIs of the other exons that can be estimated by calculating the deviation value (DV). Application of the four parameters gave rise to a sensitivity of 77.8% and a specificity of 95.6% in our data set. We propose that calculation of DV, which is unique to our analysis, is of particular importance in analyzing the exon array data.

overall_design: Affymetrix HuEx1.0 ST exon array analysis of three control muscles and three myotonic dystrophy muscles

first: Yoshihiro

last: Yamashita

first: Tohru

last: Matsuura

first: Jun

last: Shinmi

first: Yoshinobu

last: Amakusa

first: Akio

last: Masuda

first: Mikako

last: Ito

first: Masanobu

last: Kinoshita

last: Ibi

first: Ko

last: Sahashi


title: Identification of Rat foreskin biomarkers of in utero dibutyl phthalate exposure

status: Public on Jul 12 2013

city: Wilmington

first: Jack

last: Pike

address: 1600 Rockland Road

department: Urology Research

institute: AI duPont Hospital for Children

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

overall_design: Refer to individual Series


title: Identification of Rat foreskin biomarkers of in utero dibutyl phthalate exposure [Illumina]

summary: Dibutyl phthalate was administered to pregnant Sprague Dawley rats from gestational days 16-20 at either a 100 mg/kg/day or 500 mg/kg/day dose level.  This timeframe covers the reproductive masculinization window which corresponds to increased androgen signalling.  Dibutyl phthalate has been shown to disrupt testosterone production leading to male reproductive abnormalities.  As such, we selected this exposure window for our study and examined gene expression changes in the male rat foreskin, which expresses the androgen receptor.  We collected tissue samples at both gestational day 20 to identify gene expression changes immediately after exposure, and postnatal day 5 to identify gene expression changes persisting after birth using microarray analysis (Illumina RatRef 12 Bead Chips).  To determine whether gene expression changes were brought on by decreased androgen signalling or additional effects of dibutyl phthalate exposure, we exposed rats to the potent androgen receptor antagonist flutamide (5 mg/kg/day) during the same period of development.  Gene expression changes were compared to determine which were brought on by disruption of androgen signalling and which were the result of other aspects of chemical exposure.

overall_design: Two foreskin samples per litter were pooled for gene expression microarray analysis using the Illumina ratRef-12 v1.0 expression beadchip.

first: Erin

last: McDowell

first: Suzanne

last: McCahan

first: Kamin

last: Johnson


title: The physicochemistry of capped nanosilver predicts it biological activity in brain endothelial (RBEC4) cells

status: Public on May 31 2013

city: Durham

first: William

last: Ward

state: NC

address: 109 TW Alexander Dr

department: NHEERL

institute: United States EPA

summary: This study uses the RBEC4 cell model to examine if nanosilver of different sizes (10nm and 75nm) and cappings (citrate and polyvinylpyrrolidone(PVP)) affect its cellular permeability and genomic response.

overall_design: RBEC4 cells (95% confluent) were screeened for changes in gene expression after 18 hour exposure to 1.0 ppm of PVP or citrate coated nanosilver particles at 10 or 75 nanometer sizes.  Analysis indicated that the cellular transcription profile alter by nanosilver 10nm+PVP was distinct from it 75nm counterpart and both sizes of citrate-coated particles.

first: Bellina

last: Veronesi

first: Brian

last: Chorley

first: Beena

last: Valant


title: A master cistromic circuit governing hepatic fibrogenesis [expression array]

status: Public on Apr 29 2013

city: La Jolla

first: Ruth

last: Yu

state: CA

address: 10010 N Torrey Pines Rd

department: Gene Expression Lab

institute: Salk Institute

summary: Liver fibrosis is a reversible wound-healing response to liver injury and hepatic stellate cells (HSCs) are central cellular players that mediate hepatic fibrogenesis. However, the molecular mechanisms that govern this process remain unclear. Expression profiling was used to explore the potential impact of VDR signaling in TGFβ1 and TGFβ1+1,25(OH)2D3-treated primary rat HSCs. Notably, 1,25(OH)2D3 treatment attenuated the culture-induced activation of HSCs, such that the transcriptome of treated cells closely resembled that of freshly isolated quiescent cells (Figure 2A), and co-treatment of 1,25(OH)2D3  together with TGFβ resulted in considerable repression of a large set of TGFβ induced genes. We also demonstrated that in primary mouse HSCs, calcipotriol potently repressed fibrotic gene expression, suggesting that the anti-TGFβ properties of VDR agonists are likely conserved across mammalian species.

overall_design: Total RNA from primary rat HSCs were isolated and treated 1,25(OH)2D3 (100nM) for 24 hours to determine how Vitamin D ligands can impact the activated stellate cell state.

first: Christopher

last: Liddle

first: Ning

last: Ding

first: Ronald

middle: M

last: Evans


title: The effect of artificial microRNA p-27-5p on breast cancer cells

status: Public on Apr 15 2013

city: Taipei

first: Hsueh-Fen

last: Juan

address: No. 1, Sec. 4, Roosevelt Road

department: institute of molecular and cellular biology

country: Taiwan

institute: National Taiwan university

summary: MicroRNAs are a group of non-coding small RNAs with lengths around 21~23nt and function as inhibitors to repress mRNA translation by targeting their 3' untranslated region. Recent research shows that microRNAs are involved in many biological processes such as cell growth, development and cancer, etc. Here, we introduce a novel artificial microRNA p-27-5p which can inhibit cell proliferation in breast cancer cell lines. This data shows the expression changes in breast cancer cell line T-47D with the effect of artificial miR-p-27-5p.

overall_design: 4 total samples were analyzed. We generated mimic/control paired samples with 2 repeats.

first: Hsuan-Cheng

last: Huang

first: Arthur

last: Shih

first: Ya-Ya

last: Chang

first: Chung-Cheng

last: Hsu

first: Wen-Hsiung

last: Li


title: DNA copy number gain at 1q23.3 is associated with poor survival in metastatic bladder cancer [Affymetrix]

status: Public on Jul 07 2013

first: Markus

last: Riester

state: MA

address: 3 Blackfan Circle

department: Biostatistics & Computational Biology

institute: Dana-Farber Cancer Institute

summary: Metastatic urothelial carcinoma (UC) of the bladder is associated with multiple somatic copy number alterations (SCNAs). We evaluated SCNAs to identify predictors of poor survival in patients with metastatic UC treated with platinum chemotherapy.

overall_design:
We obtained overall survival (OS) and DNA copy number data from UC patients in a Spanish discovery cohort and three validation cohorts.

GISTIC was used to identify altered regions, and associations between copy number gains/losses and OS were determined by a Cox proportional hazard model adjusting for performance status and visceral disease

The output files of the GISTIC 2.0 software are linked as supplementary files on Series record along with readme.txt file describing the contents of each file/column.


title: Effect of myotonic dystrophy on pre-mRNA alternative splicing in skeletal muscle

status: Public on Jun 15 2013

city: Rochester

first: Stephen

last: Welle

state: NY

address: 601 Elmwood Avenue

institute: University of Rochester

summary: Misregulated alternative splicing appears to be a major factor in the pathogenesis of myotonic dystrophy. The present study was done to further explore alternative splicing in this condition by doing exon-level analysis of mRNA from skeletal muscle of 8 subjects with type 1 myotonic dystrophy, 7 subjects with type 2 myotonic dystrophy, 8 disease controls (subjects with facioscapulohumeral muscular dystrophy), and 8 healthy controls . The ratios of signals from the various exons of a gene provided an index of altered exon inclusion/exclusion that was independent of the overall expression of that gene. There were numerous transcripts for which there was evidence of abnormal alternative splicing in subjects with myotonic dystrophy. For many of these transcripts, the abnormal splicing was confirmed by an independent RT-PCR approach.

overall_design: 31 subjects, one sample per subject, four groups: healthy subjects (n = 8), facioscapulohumeral dystrophy (n = 8), type 1 myotonic dystrophy (n = 8), type 2 myotonic dystrophy (n = 7)

first: Charles

middle: A

last: Thornton


title: The ETHYLENE RESPONSE FACTOR 6 Acts as a Central Regulator of Leaf Growth under Water-Limiting Conditions in Arabidopsis thaliana

status: Public on Apr 06 2013

city: Ghent

first: Marieke

last: Dubois

address: Technologiepark 927

department: PSB

country: Belgium

institute: VIB-PSB

summary: Leaf growth is a complex developmental process that is continuously fine-tuned by the environment. Various abiotic stresses, including mild drought stress, have been shown to inhibit leaf growth in Arabidopsis thaliana (Arabidopsis), but the underlying mechanisms remain largely unknown. Here we identify the redundant Arabidopsis transcription factors ETHYLENE RESPONSE FACTOR 5 (ERF5) and ERF6 as master regulators which adapt leaf growth to environmental changes. ERF5 and ERF6 gene expression is induced very rapidly and specifically in actively growing leaves after sudden exposure to osmotic stress that mimics mild drought. Subsequently, enhanced ERF6 expression inhibits cell proliferation and leaf growth by a process involving GA and DELLA signaling. Using an ERF6 inducible overexpression line, we demonstrate that the GA-degrading enzyme GA2-OX6 is transcriptionally induced by ERF6 and that consequently DELLA proteins are stabilized. As a result, ERF6 gain-of-function lines are dwarfed and hypersensitive to osmotic stress, while growth of erf5erf6 loss-of-function mutants is less affected by stress. Next to its role in plant growth under stress, ERF6 also activates the expression of a plethora of osmotic stress-responsive genes, including the well-known stress tolerance genes STZ, MYB51 and WRKY33. Interestingly, the activation of the stress tolerance genes by ERF6 occurs independently from the ERF6-mediated growth inhibition. Together, these data fit into a leaf growth regulatory model in which ERF5 and ERF6 form a missing link between the previously observed stress-induced 1-aminocyclopropane-1-carboxylic acid (ACC) accumulation and DELLA-mediated cell cycle exit and execute a dual role by regulating both stress tolerance and growth-inhibition.

overall_design: Samples were obtained from three independent experiments and from multiple plates within the experiment. Whole seedlings were harvested rapidly in an excess of RNAlater® solution (Ambion), and after overnight storage at 4°C, dissected under a binocular microscope on a cooling plate with precision microscissors. Dissected leaves were transferred to a new tube, frozen in liquid nitrogen, and ground with a Retsch machine and 3-mm metal balls. RNA was extracted with TriZol (Invitrogen) and further purified with the RNeasy Mini Kit (Qiagen). DNA digestion was done on columns with RNase-free DNase I (Roche). For the identification of genome-wide expression changes, samples of the strong ERF6-overexpressing line (ERF6IOE-S) and the control line (GFP:IOE) were harvested 4 h after transfer to DEX. Two µg of pure RNA samples were hybridized to AGRONOMICS1 Arabidopsis Tiling Arrays (Rehrauer et al., 2010) at the VIB Microarray Facility (Leuven, Belgium).

first: Aleksandra

last: Skirycz

first: Hannes

last: Claeys

first: Katrien

last: Maleux

first: Stijn

last: Dhondt

first: Stefanie

last: De Bodt

first: Robin

middle: V

last: Bossche

first: Liesbeth

last: De Milde

first: Takeshi

last: Yoshizumi

first: Minami

last: Matsui

first: Dirk

last: Inze


title: hsa-miR-92a knock down in Flp-in T-REx 293-PTH-AGO1 cells

status: Public on Apr 26 2013

city: Edinburgh

first: Grzegorz

last: Kudla

address: Crewe Road

department: MRC HGU

country: United Kingdom

institute: University of Edinburgh

summary:
transcriptome profiling of miR-92a inhibitor treated and control cells with the aim of measuring miR-92a influence on its mRNA targets
Abstract: MicroRNAs (miRNAs) play key roles in gene regulation, but reliable bioinformatic or experimental identification of their targets remains difficult. To provide an unbiased view of human miRNA targets we developed a technique for ligation and sequencing of miRNA-target RNA duplexes associated with human Ago1. Here we report datasets of more than 18,000 high-confidence miRNA-mRNA interactions. The binding of most miRNAs includes the 5' seed region, but around 60% of seed interactions are noncanonical, containing bulged or mismatched nucleotides. Moreover, seed interactions are generally accompanied by specific, non-seed basepairing. 18% of miRNA-mRNA interactions involve the miRNA 3' end, with little evidence for 5' contacts, and some of these were functionally validated. Analyses of miRNA:mRNA basepairing showed that miRNA species systematically differ in their target RNA interactions, and strongly overrepresented motifs were found in the interaction sites of several miRNAs. We speculate that these affect the response of RISC to miRNA-target binding.

overall_design: In total 10 samples were analyzed, 5 repeats for each experimental condition.

last: Helwak

first: David

last: Tollervey


title: Genome-wide comparison of the transcriptomes of highly enriched normal and chronic myeloid leukemia stem and progenitor cell populations

status: Public on May 08 2013

city: Baltimore

first: Jessica

last: Gucwa

state: MD

address: 1650 Orleans Street

institute: JHMI

summary:
The resistance of CML leukemic stem cells (LSC) to tyrosine kinase inhibitor therapies targeting BCR-ABL leads to persistence of disease in most cases.  We have identified novel putative therapeutic targets that are differentially expressed in CML LSCs compared to normal hematopoietic stem cells (HSC) by transciptional profiling of stem and progenitor cell populations from CML patients and normal donors.
These data are used to obtain 97 genes that are differentially expressed in CML vs. normal stem and progenitor cells and 236 transcripts that show evidence of alternative exon usage in CML vs. normal stem cells.

overall_design: Bone marrow stem and progenitor cell fractions from 5 patients with newly diagnosed and untreated chronic phase CML and 5 healthy donors were analyzed.  Contrasts between CML vs. normal stem and progenitors overall and CML vs. normal stem cells were performed using Partek Genomic Suite software.  Genes with |log2(fold-change) > 1| and false discovery rate (FDR) of 0.05 were identified as significantly differentially expressed.  To identify genes with evidence of alternative exon useage, contrasts between CML and normal stem cell populations were performed, and genes with an alternative splicing FDR of 0.01 were considered to be alternatively spliced.


title: Genome wide screening for alternative splicing events in pancreatic cancer

status: Public on Aug 01 2013

city: Ulm

first: Karlheinz

last: Holzmann

address: Helmholtzstreet 8/1

department: Medical Faculty

institute: Ulm University

summary: We used Affymetrix GeneChip® Human Exon 1.0 ST Arrays to identify alternative splicing events in 15 samples of PDAC compared to 6 non-tumor samples. Several commercial and open source software approaches for the analysis of differential splicing were tested and a subset of overlapping results was validated using RT-PCR and sequencing.  Splicing variants could be validated in several genes closely related to cancer. Pathway analysis of genes predicted to be alternatively spliced revealed an enrichment of genes in categories closely related to cell-cell interactions and kinase activity.

overall_design: 15 samples of pancreatic ductal adenocarcinoma and 6 non tumor pancreatic samples were analyzed for alternative splicing events

first: Andreas

last: Gerhardinger

first: Uwe

last: Knippschild

first: Marko

last: Kornmann


title: Transcriptome changes in spliceostatin A treated cells

status: Public on Mar 28 2013

city: Toyama

first: Daisuke

last: Kaida

state: Toyama

address: 2630 Sugitani

department: Frontier Research Core for Life Sciences

institute: University of Toyama

summary: Pre-mRNA in eukaryotes is subjected to post-transcriptional modifications, such as capping, polyadenylation and splicing. It is well known that transcription and post-transcriptional modifications are coupled and that this coupling stimulates post-transcriptional modifications, however, the effects of post-transcriptional modifications on transcription are not fully understood. Here, we report that inhibition of U2 snRNP by a splicing inhibitor, spliceostatin A (SSA), and antisense morpholino oligonucleotide to U2 snRNA caused 3’ end down regulation in a gene-specific manner. We also show that U2 snRNP inhibition resulted in the dephosphorylation of second serine residues (Ser2) within heptad repeats of the C-terminal domain (CTD) of Pol II, which is important for transcription elongation, and this dephosphorylation was correlated with splicing inactivation. Interestingly, removal of SSA from the culture media caused restoration of the Ser2 phosphorylation and expression of the 3’ end, suggesting that transcription elongation resumed. These findings suggest that a novel checkpoint mechanism prevents pre-mRNA accumulation and the production of aberrant proteins translated from pre-mRNA upon splicing deficiencies through the dephosphorylation of CTD Ser2.

overall_design: Treated HeLa cells with methanol or spliceosotain A for 3 hours followed by labelling of nascent transcripts with EU for 1 hour. The EU labelled nascent RNA was purified and analyzed on human exon 1.0ST array. Three biological replicates were used for each treatment.

first: Ichiro

last: Takasaki

first: Yumi

last: Kawamura


title: Transcript map of Shewanella oneidensis MR-1

status: Public on Mar 18 2013

city: Berkeley

first: Wenjun

last: Shao

address: 2151 Berkeley Way

department: Molecular and Cell Biology

institute: University of California

summary:
High-resolution tiling analysis of the MR-1  transcriptome under diverse growth conditions
The conditions include aerobic growth in Luria-Bertani broth (LB), aerobic growth in defined lactate minimal medium, anaerobic growth in defined lactate minimal medium with 20mM dimethyl sulfoxide as the electron acceptor, anaerobic growth in defined lactate minimal medium with 10mM iron (III) citrate as the electron acceptor, 10 minutes post heat shock at 42oC
see GSE39468 for tiling data on lactate minimal media

overall_design: Four slides hybridized to mRNA and one “genomic control” array hybridized to genomic DNA

first: Adam

last: Deutschbauer

first: Morgan

middle: N

last: Price

middle: P

last: Arkin


title: Chip-chip from THP1 cells with Pol II, Pol II Ser5-P, H3K9Ac  and from primary monocytes with H3K4Me3

status: Public on Feb 15 2013

city: Duarte

first: Nancy

last: Chen

address: 1500 Duarte Road

department: Diabetes

institute: City of Hope

summary: THP1 cells  were ChIPed with indicated antibodies.

overall_design: Comparison  of selected chromatin marks in THP1 cells and monocytes

first: Rama

last: Natarajan

first: Feng

last: Miao

first: Zhuo


title: Neuron-released α-synuclein is an endogenous ligand of TLR2 for paracrine activation of microglia

status: Public on Feb 28 2013

city: LA

first: Sungyong

last: You

address: Beverly Blvd 8400

department: Surgery

institute: Cedars-Sinai Medical Center

summary: Abnormal accumulation of aggregated proteins and sustained microglial activation are important contributors of neurodegenerative process in neurological diseases. Recent studies have shown that aggregation-prone proteins, such as a-synuclein, the protein implicated in Parkinson’s disease (PD), are released from neuronal cells and thus present in the extracellular fluid, pointing to the possible paracrine effects of these proteins on microglial immune responses. However, the mechanism underlying the disease-associated microglial activation and the role of neuronal proteins in this process remain unknown. Here, we show that extracellular a-synuclein released from neuronal cells is an endogenous ligand of toll-like receptor 2 (TLR2) and activates microglia, which in turn induces neurodegeneration. Interaction between neuron-released a-synuclein and TLR2 and subsequent activation of the TLR2 signaling were demonstrated comprehensively by using computational modeling of signaling network and by the experimental validation in TLR2-deficient microglia both in vitro and in vivo. In contrast to the neuron-released a-synuclein, recombinant a-synuclein proteins, including monomer, oligomer, fibril, or nitrated forms, were not able to interact or activate TLR2, suggesting that neuronal cells have a mechanism of enriching specific forms of a-synuclein capable of activating TLR2 during the process of releasing this protein. Taken together, the results suggest that both neuron-released extracellular a-synuclein and TLR2 might be novel therapeutic targets for modifying neuroinflammation in PD and related neurodegenerative diseases.

overall_design: We collected culture media from differentiated SH-SY5Y cells overexpressing either human a-synuclein (alpha-SCM) or beta-galactosidase (LZCM) and treat these media to primary rat microglia at the concentration of a-synuclein of 1.1M. Transcriptome analyses with microglial cells treated with either aSCM or LZCM at two different time points, 6 h and 24 h.

first: Seung-Jae

last: Lee

first: Daehee

last: Hwang


title: Fgd5 indentifies hematopoietic stem cells in the murine bone marrow is is not required for definitive hematopoiesis

status: Public on Apr 22 2014

city: Boston

first: Isabel

last: Beerman

address: 200 Longwood Ave, WAB 156

institute: Boston Childrens Hospital

type:
Third-party reanalysis
Expression profiling by array

summary: Analysis of purified murine hematopoietic samples

overall_design:
122 Affymetrix MOE430 2.0 arrays generated from purified steady-state murine hematopoietic cell types were re-normalized together using gcRMA in R. Their GSE Series numbers are as follows:
GSE34723, GSE11982, GSE7302, GSE8407,GSE9717, GSE10627, GSE10246, GSE12581, GSE6506, GSE11110, GSE12001, GSE9810, GSE4142, GSE7764, GSE9810, GSE6875, GSE6681

first: Derrick

last: Rossi

first: Pankaj

last: Mandal

first: Roi

last: Gazit


title: Structural polymorphism in the promoter of pfmrp2 confers tolerance to mefloquine and chloroquine in Plasmodium falciparum [expression]

status: Public on Feb 07 2013

city: Singapore

first: Sachel

last: Mok

address: 60 Nanyang Drive

country: Singapore

institute: Nanyang Technological University

summary: Drug resistance in Plasmodium falciparum remains a challenge for the malaria eradication programs around the world. With the emergence of artemisinin resistance, the efficacy of the partner drugs in the artemisinin combination therapies (ACT) that include quinoline based drugs is becoming critical. So far only few resistance markers have been identified and verified from which only two ABC transmembrane transporters namely PfMDR1 and PfCRT have been experimentally verified. Another P. falciparum ABC transporter, the multidrug resistance-associated protein (PfMRP2) represents an additional possible factor of drug resistance in P. falciparum. In this study, we identify a parasite clone that is derived from the 3D7 P. falciparum strain and which shows increased resistance to chloroquine and mefloquine through the trophozoite and schizont stages. We demonstrate that the resistance phenotype is caused by a 4.1 kb deletion in the 5’ upstream region of the pfmrp2 gene that leads to an alteration in the pfmrp2 transcription that result in increased levels of PfMRP2 protein. These results also suggest the importance of putative promoter elements in regulation of gene expression during the P. falciparum intra-erythrocytic developmental cycle and the potential of such genetic polymorphisms to underlie drug resistance phenotypes. Presented here are the data from microarray-based genome-wide transcriptomic and genomic studies of the drug-sensitive and drug-resistant 3D7 clones 11C/wt and 6A/mut.

overall_design: 2 P. falciparum lab clones derived from 3D7 strain were harvested during the intra-erythrocytic cycle at 8hr intervals over 48 hours to obtain a total of 6 time point samples per clone. RNA from a total of 12 samples were extracted. Synthesis of target DNA was carried out as  described in Bozdech, Z., S. Mok & A. P. Gupta, (2013) DNA microarray-based genome-wide analyses of Plasmodium parasites. Methods in molecular biology 923: 189-211 and used in replicate microarray hybridizations against a common RNA reference pool of 3D7 strain.

first: Zbynek

last: Bozdech


title: Cardiac phase-targeted dynamic load on left ventricle differentially regulates phase-sensitive gene expressions and pathway activation

city: Fukuoka

first: tomomi

last: ide

state: Fukuoka

address: 3-1-1 Maidashi, Higashi-ku

department: GRADUATE SCHOOL OF MEDICAL SCIENCES

institute: KYUSHU UNIVERSITY

summary: Each heart was assigned to one of the following three conditions: phasic systolic overload (SO), phasic diastolic overload (DO), and no loading throughout the cardiac cycle (control; CN). We created SO by isovolumic contraction (peak systolic LVP > 170 mmHg) at a constant diastolic volume with end-diastolic pressure (EDP) equals 0 mmHg. For DO, we increased LVV in diastole so that EDP reached 40 mmHg, and unloaded quickly in systole to minimize LVP generation. At the end of 3 hours, the myocardium from each heart was collected for subsequent analyses.

overall_design: rat heart subjected to phasic systolic overload and diastolic overload

first: Ken

last: Onitsuka

first: Tomomi

last: Ide

first: Shinobu

last: Arai

first: Yuko

last: Hata

first: Yoshinori

last: Murayama

first: Kazuya

last: Hosokawa

first: Takafumi

last: Sakamoto

first: Tomoyuki

last: Tobushi

first: Kazuo

first: Takeo

last: Fujino

first: Kenji

last: Sunagawa


title: Dynamics of epigenetic regulation of gene expression during Plasmodium falciparum life cycle

status: Public on Mar 02 2013

first: Archana

last: Gupta

department: School Of Biological Sciences

type: Genome binding/occupancy profiling by array

summary: In order to study the role of chromatin remodeling in transcriptional regulation associated with the progression of the P. falciparum intraerythrocytic development cycle (IDC), we mapped the temporal pattern of chromosomal association with histone H3 and H4 modifications using chromatin-immunoprecipitation coupled to microarray (ChIP-on-chip).

overall_design: Genome-wide distribution of 13 histone modifications for 6 h time points of the 48 h P. falciparum IDC was done using ChIP-on-chip and compared to corresponding transcriptional profiles across the genome

first: A

first: W

middle: H

last: Chin

first: L

last: Zhu

first: Z


title: Structural polymorphism in the promoter of pfmrp2 confers tolerance to mefloquine and chloroquine in Plasmodium falciparum.

first: Sachel

type:
Expression profiling by array
Genome variation profiling by array

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

overall_design: Refer to individual Series

first: Zbynek


title: Estrus Synchronization and Ovarian Hyper Stimulation Treatments Have Negligible Effects on Cumulus Oocyte Complexes Gene Expression: Induction of Ovulation Causes Major Expression Changes

status: Public on Feb 01 2013

city: Columbia

first: Cansu

last: Agca

state: MO

address: 1600 E. Rollins St

department: Veterinary Pathobiology

institute: University of Missouri

summary: The effects of exogenous hormones used for estrus synchronization, and ovarian hyper stimulation on cumulus oocyte complexes (COCs) gene expression in sexually mature rats were determined using microarrays. Gene expression in COCs collected from GnRH (Gtrt), GnRH+eCG (G+Etrt), and GnRH+eCG+hCG (G+E+Htrt) treatments were compared to COCs from naturally cycling (NC) rats. There was no significant difference in gene expression among NC, Gtrt and G+Etrt. Over 2600 genes were significantly different between NC and G+E+Htrt (P<0.05). Genes encoding proteins that are involved in prostaglandin synthesis (Ptgs2, Pla2g4a, Runx1); cholesterol biosynthesis (Hmgcr, Sc4mol, Dhcr24); receptors that allow cholesterol uptake (Ldlr, Scarb1); regulate progesterone synthesis (Star); inactivate estrogen (Sult1e1); and downstream effectors of LH signal (Pgr, Cebpb, Creb3l1, Areg, Ereg, Adamts1) were upregulated in G+E+Htrt. Genes encoding proteins that are involved in DNA replication (Ccne2, Orc5l, Rad50, Mcm6); reproductive developmental process and granulosa cell expansion (Gdf9, Bmp15, Amh, Amhr2, Bmpr1b, Tgfb2, Foxl2, Pde3a, Esr2, Fshr, Ybx2, Ccnd2, Ccnb1ip1, Zp3); maternal effect genes that are important for embryo development (Zar1, Npm2, Nlrp5, Dnmt1, H1foo, Zfp57); amino acid degradation and ketogenesis (Hmgcs2 , Cpt1b) were downregulated in G+E+Htrt. These results on rat model show that hormones used for estrus synchronization (Gtrt) and ovarian hyper stimulation (G+Etrt) had minimal effects on gene expression. However, induction of ovulation (G+E+Htrt) caused major changes in gene expression of rat COCs. This study provides comprehensive information about regulated genes during late follicle development and ovulation induction.

overall_design: Four experimental groups were used and there were 6 animals in each group. Total of 24 arrays were used. Only raw data used in publication.

first: Akin

last: Yakan

first: Yuksel


title: IL-27 Inhibits HIV-1 Infection in Human Macrophages by Down-regulating Host Factor SPTBN1 during Monocyte to Macrophage Differentiation

status: Public on Jan 18 2013

city: Frederick

first: Richard

last: Lempicki

address: PO Box B

department: Clinical Services Program

institute: Leidos Biomedical Research, Inc.

summary:
The susceptibility of macrophages to HIV-1 infection is modulated during monocyte differentiation. IL-27 is an anti-HIV cytokine that also modulates monocyte activation. Here, we present new evidence that IL-27 promotes monocyte differentiation into macrophages that are non-permissive for HIV-1 infection.
While IL-27 treatment does not affect expression of macrophage differentiation markers or macrophage biological functions, it confers HIV resistance by down-regulating spectrin beta non-erythrocyte 1 (SPTBN1), a required host factor for HIV-1 infection. IL-27 down-regulates SPTBN1 through a TAK-1-mediated MAPK signaling pathway. Knockdown of SPTBN1 strongly inhibits HIV-1 infection of macrophages; conversely, overexpression of SPTBN1 markedly increases HIV susceptibility of IL-27 treated macrophages. Moreover, we demonstrate that SPTBN1 associates with HIV-1 gag proteins. Collectively, our results underscore the ability of   IL-27 to protect macrophages from HIV-1 infection by down-regulating SPTBN1, thus indicating that SPTBN1 is an important host target to reduce HIV-1 replication in one major element of the viral reservoir.

overall_design: 2 samples with different treatments were analyzed. Genes with absolute fold change >= 5 were selected.

first: Lue

last: Dai

first: Kristy

middle: B

last: Lidie

first: Qian

last: Chen

first: Joseph

middle: W

last: Adelsberger

first: Xin

last: Zheng

first: DaWei

last: Huang

first: Jun

last: Yang

first: H

last: Lane

first: Tomozumi

last: Imamichi


title: MiRNA/gene profiling unveils early molecular changes and NRF2 activation in a rat model recapitulating human HCC

city: Candiolo

first: Davide

last: Cora'

state: TO

department: Dept. of Oncology

country: Italy

institute: Piemonte Orientale University and IRCCS Candiolo Cancer Institute

summary: Studies on gene and/or microRNA (miRNA) dysregulation in the early stages of hepatocarcinogenesis are hampered by the difficulty of diagnosing early lesions in humans. Experimental models recapitulating human hepatocellular carcinoma (HCC) are then entailed to perform this analysis. We performed miRNA and gene expression profiling to characterize the molecular events involved in the multistep process of hepatocarcinogenesis in the Resistant-Hepatocyte rat model. A high percentage of dysregulated miRNAs/genes in HCC were similarly altered in early preneoplastic lesions positive for the stem/progenitor cell marker cytokeratin-19, indicating that several HCC-associated alterations occur from the very beginning of the carcinogenic process. Our analysis also identified miRNA/gene-target networks aberrantly activated at the initial stage of hepatocarcinogenesis. Activation of the NRF2 pathway and up-regulation of the miR-200 family were among the most prominent changes. The relevance of these alterations in the development of HCC was confirmed by the observation that NRF2 silencing impaired while miR-200a overexpression promoted HCC cell proliferation in vitro. Moreover, T3-induced in vivo inhibition of the NRF2 pathway accompanied the regression of cytokeratin-19 positive nodules, suggesting that activation of this transcription factor contributes to the onset and progression of preneoplastic lesions towards malignancy. The finding that 78% of genes and 57% of dysregulated miRNAs in rat HCC have been previously associated to human HCC as well underlines the translational value of our results. Conclusions: this study indicates that most of the molecular changes found in HCC occur in the very early stages of hepatocarcinogenesis. Among these, the NRF2 pathway plays a relevant role and may represent a new therapeutic target.

overall_design: 20 nodules (10 weeks after initiation with DENA), 4 adenomas (10 months), 5 eHCCs (10 months) and 9 aHCCs (14 months) were dissected. 10 controls also included.

first: Pia

last: Sulas


title: Intrinsic glioma subtypes in EORTC 26951 (part 1)

city: Rotterdam

first: Pim

last: French

address: Dr Molewaterplein 50

department: Neurology

country: Netherlands

institute: Erasmus MC

summary: Background: Intrinsic glioma subtypes (IGS) are molecularly similar tumors that can be identified based on unsupervised gene-expression analysis. Here, we have evaluated the clinical relevance of these subtypes within EORTC26951, a randomized phase III clinical trial investigating adjuvant procarbazine, CCNU (lomustine) and vincristine (PCV) chemotherapy in anaplastic oligodendroglial tumors. Our study is the first to include gene-expression profiles of formalin-fixed and paraffin-embedded (FFPE) clinical trial samples. Methods: Gene-expression profiling was performed in 140 samples: 47 fresh frozen and 93 FFPE, on HU133_Plus_2.0 and HuEx_1.0_st arrays (Affymetrix), respectively.  Results: All previously identified six intrinsic glioma subtypes are present in EORTC26951. This confirms that different molecular subtypes are present within a well-defined histological subtype. Intrinsic subtypes are highly prognostic for overall- (OS) and progression-free survival (PFS). They are prognostic for PFS independent of clinical (age, performance, tumor location), molecular (1p19qLOH, IDH1 mutation, MGMT methylation) and histological parameters. Combining known molecular (1p19LOH, IDH1) prognostic parameters with intrinsic subtypes improves outcome prediction (Proportion of Explained Variation 30% v 23%). Specific genetic changes (IDH1, 1p19qLOH and EGFR amplification) segregate into different subtypes. We identified one subtype, IGS-9 (characterized by a high percentage of 1p19qLOH and IDH1 mutations), that especially benefits from PCV chemotherapy. Median OS in this subtype was 5.5 years after radiotherapy (RT) alone v 12.8 years after RT/PCV; P=0.0349; HR 2.18, 95% CI [1.06, 4.50]. Conclusion: Intrinsic subtypes are highly prognostic in EORTC26951 and improve outcome prediction when combined with other prognostic factors. Tumors assigned to IGS-9 benefit from adjuvant PCV

overall_design: A total of 140 samples were included in this study, profiles of 95 were FFPE derived samples run on exon arrays. 12 samples (part 2) can also be found in GSE16011 (PMID 19920198 and 16357140), and 6 from Oncomine (part 3).

first: Lale

last: Erdem

first: Lonneke

last: Gravendeel

first: Johan

last: de Rooi

first: Paul

last: Eilers

first: Ahmed

last: Idbaih

first: Wim

middle: G

last: Spliet

first: Wilfred

middle: F

last: den Dunnen

first: Johannes

middle: L

last: Teepen

first: Pieter

last: Wesseling

first: Peter

last: Sillevis Smitt

last: Kros

first: Thierry

last: Gorlia

first: Martin

last: van den Bent


title: Gene expression profiling in endothelial precursor cells of patients protected from microvascular complications

city: Gainesville

first: Ashay

middle: Dilip

last: Bhatwadekar

address: 1600 SW Archer Road

department: Pharmacology and Therapeutics

institute: University of Florida

summary: In this study, we examined the impact of modulating the TGF-β/PAI-1 axis in CD34+ cells function from diabetic patients and controls.  Using gene array studies, we found that diabetics, protected from microvascular complications despite suboptimal glycemic control, had reduced level of TGF- β1 and PAI-1 transcripts in their CD34+ cells compared to age, sex, duration and degree of glycemic control -matched diabetics with microvascular complications. Treatment with neutralizing antibody to TGF- β1 in murine hematopoietic stem cells (HSC) enhanced in vivo repopulation potential of these cells in bone marrow transplantation; reduced the time required for cell division of single cells, increased survival of the progenitor cells and reduced TGF-β1 expression. TGF- β1 phosphorodiamidate morpholino oligomers (PMO) treatment reduced PAI-1 mRNA expression in diabetic (p<0.01) and non-diabetic (p=0.05) CD34+ cells. Inhibition of PAI-1 promoted CD34+ cell proliferation and migration in vitro.Targetting TGFβ-1/PAI-1 system offers a promising therapeutic strategy for restoring vascular reparative function in diabetic CD34+ cells and hematopoietic stem cells, enhancing key functions needed for cell therapy.

overall_design: Peripheral blood from either age matched controls (n=5), diabetics with long standing poorly controlled diabetes and no microvascular complications (n=4), and diabetics with long-standing poorly controlled diabetes with severe microvascular complications (n=5) was obtained and CD34+ cells were isolated.  RNA was extracted followed by AffyNugen amplification, and the cDNA was probed to Human RSTA Affymetrix 2.0 chip

first: Sugata

last: Hazra

first: Valerie

last: Stepps

middle: D

first: Michael

middle: E

last: Boulton

last: Higgins

first: Elena

last: Nikonova

first: Carl

last: Pepine

first: Catherine

last: Thut

first: Eva

last: Finney

first: Ewa

last: Sitnicka

first: Patrick

last: Iversen

first: Francis

last: Ruscetti

first: David

last: Stone

first: Stephen

last: Bartelmez

first: Maria

last: Grant


title: Genome-wide analysis of hypothalamic gene expression in prenatally undernourished male rat offspring under high fat diet

status: Public on Jan 17 2013

city: Villeneuve d'Ascq

first: christophe

last: breton

address: Cité Scientifique

country: France

institute: University of Lille 1

summary: Based on the developmental origin of health of disease hypothesis, we previously showed that prenatal 70% maternal food restriction (FR30) predisposes the offspring to development of pathologies in adulthood. In the present study, we focused on the hypothalamus gene expression profile of standard and high fat (HF)-fed FR30 adult offspring.

overall_design: Total RNA obtained from isolated hypothalami of control standard and high fat-fed adult offspring compared to prenatally undernourished (FR30) counterparts.

first: D

last: Vieau

first: C

last: Breton

last: Laborie

first: M

last: Lukaszewski


title: ChIP-chip from Candida albicans cells with GFP-LYS142, GFP-LYS143, GFP-LYS14, and GFP-LYS144

status: Public on Dec 01 2013

city: San Francisco

first: Jose

middle: Christian

last: Perez

department: Microbiology and Immunology

institute: University of California, San Francisco

summary: LYS142, LYS143, LYS14 and LYS144 compose a family of recently duplicated transcription regulators in C. albicans. They have differentiated from one another by acquiring a largely separate set of target genes. Chromatin immunoprecipitation (ChIP) of GFP-LYS142, GFP-LYS143, GFP-LYS14 and GFP-LYS144 followed by array hybridization (Agilent) uncovered a network of target genes controlled by these regulators in the yeast C. albicans.

overall_design: Comparison of IP/input in tagged strains to untagged cells immunoprecipitated with the same antibody.

first: J

first: Alexander

last: Johnson


title: Redox regulation of auxin and strigolactone signaling in the control of Arabidopsis thaliana root growth

status: Public on Jan 10 2013

city: Murcia

first: Pedro

last: Diaz-Vivancos

address: Campus Universitario de Espinardo, 25

department: Plant Breeding

country: Spain

institute: CEBAS-CSIC

summary: Reduced glutathione (GSH) is required for cell cycle initiation and auxin-regulated root meristem development. Transcriptome profiling of the roots and shoots of the root meristemless 1 (rml1) mutant, which has about 3% of the wild type GSH, revealed a divergent auxin and strigolactone response linked to the arrest of the cell cycle.

overall_design: Plants of the rml1 mutant and Columbia-0 ecotype were harvested and separated into roots and shoots, then RNA extraction and Affymetrix Agronomics Tiling Array were performed.

first: Daniel

last: Schnaubelt

first: Yingping

last: Dong

first: Guillaume

last: Queval

first: Belen

last: Marquez-Garcia

first: Gareth

last: Howell

first: Matthew

last: Hannah

first: Christine

last: Foyer


title: Environmentally Induced Transgenerational Epigenetic Reprogramming of Primordial Germ Cells and Subsequent Germline [Affymetrix]

city: Pullman

first: Michael

middle: K

last: Skinner

state: WA

address: Abelson 507

department: SBS

institute: WSU

summary:
A number of environmental factors (e.g. toxicants) have been shown to promote the epigenetic transgenerational inheritance of disease and phenotypic variation. Transgenerational inheritance requires the germline transmission of altered epigenetic information between generations in the absence of direct environmental exposures. The primary periods for epigenetic programming of the germline is associated with primordial germ cell development and during fetal gonadal sex determination. The current study examined the actions of an agricultural fungicide vinclozolin on gestating female (F0 generation) progeny in regards to the primordial germ cell (PGC) epigenetic reprogramming of the F3 generation (i.e. great-grandchildren). The F3 generation primordial germ cell transcriptome and epigenome (DNA methylation) was altered transgenerationally. Interestingly, the differential DNA methylation regions (DMR) and altered transcriptomes were distinct between the onset of gonadal sex determination at embryonic day 13 (E13) and after cord formation in the testis at embryonic day 16 (E16). A larger number of DMR and transcriptional alterations were observed in the E13 PGC than E16 germ cells. Observations demonstrate an altered transgenerational epigenetic reprogramming and function of the primordial germ cells and subsequent male germline is a component of vinclozolin induced epigenetic transgenerational inheritance of disease. Insights into the molecular control of germline transmitted epigenetic inheritance are provided.
The combined observations demonstrate ancestral exposure of a gestating female during fetal gonadal sex determination can promote transgenerational alterations in the primordial germ cell and subsequent male germline epigenetic and transcriptional programming. This altered germline programming leads to the epigenetic transgenerational inheritance of disease and phenotypic variation. Observations support the role of the primordial germ cell programming in the molecular mechanism involved and provides insights into the molecular mechanisms that control the epigenetic transgenerational inheritance phenomena. Results suggest a cascade of epigenetic and transcriptional events during germ cell development is needed to obtain the mature germline epigenome that is then transmitted transgenerationally.

overall_design: RNA samples from  PGC of 2 F3-control lineage groups were compared to PGC of 2 F3-vinclozolin lineage groups for two embryonic age E13 and E16

first: Carlos

last: Guerrero-Bosagna

last: Haque

first: Eric

last: Nilsson

first: John

last: McCarrey


title: RNF20 and USP44 regulate embryonic stem cell differentiation by modulating H2B monoubiquitylation

status: Public on Jan 03 2013

city: Rehovot

first: Gilad

last: Fuchs

address: Rehovot

country: Israel

institute: Weizmann Institute of Science

summary: Embryonic stem cells (ESCs) maintain high genomic plasticity, essential for their capacity to enter diverse differentiation pathways. Post-transcriptional modifications of chromatin histones play a pivotal role in maintaining this plasticity. We now report that one such modification, monoubiquitylation of histone H2B on lysine 120 (H2BK120ub1), catalyzed by the E3 ligase RNF20, increases during ESC differentiation and is required for efficient execution of this process. This increase is particularly important for the transcriptional induction of long genes during ESC differentiation. Furthermore, we identify USP44 as a deubiquitinase whose downregulation by differentiation signals contributes to the increase in H2BK120ub1. Our findings suggest that optimal ESC differentiation requires dynamic changes in H2B ubiquitylation patterns, which must occur in a timely and well-coordinated manner.

overall_design: RNF20 depleted or control NTera2 cells stimulated with RA for 72 hours

first: Efrat

last: Shema

first: Rita

last: Vesterman

first: Mahmood

last: Haj-Yahya

first: Ashraf

last: Brik

first: Eytan

last: Domany

first: Moshe

last: Oren


title: Differential gene expression from microarray analysis distinguishes woven and lamellar bone formation in the rat ulna following mechanical loading

status: Public on Jan 01 2013

city: St. Louis

first: Jennifer

last: McKenzie

address: 660 S. Euclid, Box 8233

department: Orthopedic Surgery

institute: Washington University in St. Louis

summary: The objective of our study was to use a microarray to distinguish the molecular responses between woven and lamellar bone formation induced through mechanical loading.    The micorarray identified numerous genes and pathways that were differentially regulated for woven, but not lamellar bone formation.

overall_design: Rat forelimb loading was completed in a single bout to induce the formation of woven bone (WBF loading) or lamellar bone (LBF loading).  A set of normal (non-loaded) rats were used as controls.  Microarrays were performed at three timepoints after loading: 1 hr, 1 day and 3 days.

first: Elise

middle: C

last: Bixby

middle: J

last: Silva


title: Genome-wide identification of RNA polymerase, RpoD, and RpoS binding sites in Klebsiella pneumoniae MGH 78578

status: Public on Dec 31 2012

city: La Jolla

first: Bernhard

last: Palsson

address: 417 Powell-Focht Bioengineering Hall, 9500 Gilman Dr.

institute: University of California, San Diego

summary:
Genome-wide identification of RNA polymerase (RNAP) binding sites were performed in Klebsiella pneumoniae MGH 78578 (KP). Anti-RNAP is used to capture the RNAP in KP.
ChIP-chip was performed on tiling array specifically made for KP.

sample_organism: Klebsiella pneumoniae subsp. pneumoniae MGH 78578

overall_design: Comparison ChIP by anti-RNAP antibody vs ChIP by normal mouse IgG (control, mock IP)

first: Joo-Hyun

last: Seo

first: Jay

middle: S

last: Hong

first: Donghyuk

last: Kim

first: Tzu-Wen

last: Huang

first: Pep

last: Charusanti

first: Shih-Feng

last: Tsai

middle: O


title: Transcriptional profile of rve8 in circadian time course

status: Public on Dec 20 2012

city: Durham

first: Polly

middle: Yingshan

last: Hsu

address: Duke University

department: Biology

institute: Duke University

summary: Analysis of Arabidopsis Columbia and rve8-1, a longer period mutant, in circadian time course (ZT72-116). Results provide insight into where RVE8 functions in the clock system and the targets regulated by RVE8.

overall_design: Arabidopsis Col and rve8-1 seedlings (~50 plants/ per sample) were grown in 12 hours light/ 12 hours dark for 7 days before releasing to the constant light. After 72 hours in the constant light, samples were harvested every 4 hours for 2 days. RNA was extracted, labeled and hybridized onto Agronomics1 tiling arrays.

middle: Y

first: Stacey

last: Harmer


title: Genome-wide analysis of renal gene expression during hyperoxaluria development

first: Sunil

last: Joshi

state: Florida

address: 1600 S W Archer Road

department: Pathology, Immunology and Laboratory Medicine

summary:
Previous studies have proposed that production of reactive oxygen species (ROS) is an important contributor to renal injury and inflammation following exposure to oxalate or calcium-oxalate crystals.  The present study was conducted to determine, utilizing global transcriptome analyses, if the NADPH oxidase system is activated in kidneys of rats fed a diet leading to hyperoxaluria and crystal deposition.
HLP was used to induce hyperoxaluria. Hyperoxaluria will lead to crystallization and up regulation of various NADPH oxidase subunits followed by increased expression of different specific genes. It is our hypothesis that crystallization induces inflammation of the kidneys via the activation of renin-angiotensin system (RAS) and production of reactive oxygen species (ROS) through NADPH oxidase complex.  Apocynin was used to block hyperoxaluria and production of reactive oxygen species (ROS) with the inhibition of NADPH oxidase system as Apocynin inhibits membrane translocation of p47 subunit of NADPH oxidase.

overall_design: The present study was designed based on NADPH oxidase system and rats were divided into 4 groups (n= 6/group). Group 1 was fed regular rat chow diet, Group 2 received regular rat chow diet supplemented with 5% (Hydroxy-L-Proline) HLP, Group 3 received rat chow diet with 4 mmol Apocynin to drink, and Group 4 received regular rat chow diet with 5% HLP and 4 mmol Apocynin. After 28 days each rat was euthanized, their kidneys freshly explanted and dissected to obtain both cortex and medulla tissues. So the 4 groups were divided into cortex and medulla forming 8 groups. RNA was isolated from all the 8 specimens

first: Saeed

middle: R

last: Khan

first: Ammon

last: Peck


title: Gene expression profiling in primary AML cells treated with decitabine and cytarabine

status: Public on Dec 18 2012

city: StLouis

first: Nobish

last: Varghese

address: 4444 Forest Park Ave.

institute: Washington University in St.Louis

summary: Acute myeloid leukemia (AML), and other myeloid malignancies, are frequently treated with hypomethylating agents like decitabine. Alterations in the epigenome, induced by decitabine, are likely to result in gene expression changes. The effects of decitabine have not been systemically studied using primary AML samples.

overall_design: We cultured 18 different primary AML samples for 7 days, the last 3 days of which included 100 nM decitabine (DAC) or 100 nm cytarabine (AraC). We hypothesized that decitabine treatment would result in detectable and consistent gene expression changes. For comparison, we also analyzed mRNA from cells treated with DMSO control (mock) and mRNA from uncultured cells taken at the time of diagnosis.

first: Jeffery

middle: M

last: Klco

first: Timothy

last: Ley


title: A mutation in a splicing factor that causes retinitis pigmentosa (RP) has a transcriptome-wide effect on mRNA splicing

status: Public on Dec 25 2012

city: Galway

first: Paul

middle: Kibet

last: Korir

state: Co Galway

address: University Road

department: School of Mathematics, Statistics and Applied Mathematics

country: Ireland

institute: National University of Ireland, Galway

summary:
Background: Substantial progress has been made in the identification of sequence elements that control mRNA splicing and the genetic variants in these elements that alter mRNA splicing (referred to as splicing quantitative trait loci -- sQTLs). Genetic variants that affect mRNA splicing in trans are harder to identify because their effects can be more subtle and diffuse, and the variants are not co-located with their targets. We carried out a transcriptome-wide analysis of the effects of a mutation in a ubiquitous splicing factor that causes retinitis pigmentosa (RP) on mRNA splicing, using exon microarrays.

Results: Exon microarray data was generated from whole blood samples obtained from four individuals with a mutation in the splicing factor PRPF8 and four sibling controls. Although the mutation has no known phenotype in blood, there was evidence of widespread differences in splicing between cases and controls (affecting between 10\% and 25\% of exons). Most probesets with significantly different inclusion (defined as the expression intensity of the exon divided by the expression of the corresponding transcript) between cases and controls had higher inclusion in cases and corresponded to exons that were shorter than average, AT-rich, located towards the 5' end of the gene and flanked by long introns. Introns flanking affected probesets were particularly depleted for the shortest category of introns, associated with splicing via intron definition.

Conclusions: Our results show that a mutation in a splicing factor, with a phenotype that is restricted to retinal tissue, acts as a trans-sQTL cluster in whole blood samples. Characteristics of the affected exons suggest that they are spliced co-transcriptionally and via exon definition.

overall_design: Eight samples consisting of four sibling pairs were analysed. One individual in each pair harboured an RP-causing mutation on the PRPF8 gene (cases). Unaffected siblings were used as controls.

first: Lisa

last: Roberts

first: Raj

last: Ramesar

first: Cathal

last: Seoighe


title: Genome-wide gene expression analysis for Klebsiella pneumoniae MGH 78578

first: Bernhard

last: Palsson

summary: Genome-wide gene expression analysis was performed with the cells in exponential and stationary growth phases. Through these two growth status, 89.6% of currently annotated genes were expressed.

platform_organism: Klebsiella pneumoniae subsp. pneumoniae MGH 78578

overall_design: High-density oligonucleotide tiling arrays consisting of 379,528 50-mer probes spaced 30 bp apart across the whole Klebsiella pneumoniae MGH 78578 genome was used (Roche NimbleGen).

first: Joo-Hyun

last: Seo

first: Jay

last: Hong


title: Rapid changes of gene expression in rat adipose tissue when food was removed

status: Public on Dec 01 2012

city: Umeå

first: Stefan

last: Nilsson

address: Building 6M 3tr

country: Sweden

institute: Umeå University

summary: When food was removed for 6 hours, 43 genes, including Angptl4, changed their expression more than two-fold.

overall_design: Food was removed from young rats at 07:30. Six hours later, samples of epididymal adipose tissue was taken for analysis.

first: Olessia

last: Kroupa

first: Thomas

last: Olivecrona

first: Gunilla


title: Genome-wide differences in expression and alternative splicing in human dendritic cells upon E.coli challenge

status: Public on Nov 28 2012

city: Lisbon

first: Raquel

middle: Ferreira

last: Rodrigues

address: Av. Prof. Egas Moniz, Edifício Egas Moniz - Sala P3-A-16

country: Portugal

institute: Molecular Medicine Institute

summary: The immune system relies on the plasticity of its components to produce appropriate responses to frequent environmental challenges. Dendritic cells (DCs) are critical initiators of innate immunity and orchestrate the later and more specific adaptive immunity. The generation of diversity in transcriptional programs is central for effective immune responses. Alternative splicing is widely considered a key generator of transcriptional and proteomic complexity, but its role has been rarely addressed systematically in immune cells. Here we used splicing-sensitive arrays to assess genome-wide gene- and exon-level expression profiles in human DCs in response to a bacterial challenge. We find widespread alternative splicing events and splicing factor transcriptional signatures induced by an E. coli challenge to human DCs. Alternative splicing acts in concert with transcriptional modulation, but these two mechanisms of gene regulation affect primarily distinct functional gene groups. Alternative splicing is likely to have an important role in DC immunobiology because it affects genes known to be involved in DC development, endocytosis, antigen presentation and cell cycle arrest

overall_design: 6 samples were analysed. 3 were used as controls (non-stimulated replicates) and 3 were stimulated with E.coli for 3 distinct periods: (T1) 4 hours, to cover early changes that occur after the bacterial challenge; (T2) 8 hours, to assess intermediate changes; and (T3) 18 hours, to measure the late response stage. Microarray data pre-processing and summarization was performed using AltAnalyze application, which includes several rigorous statistical methods for data filtering, summarization and determination of differential splicing. Briefly, low quality probesets were removed according to detection above background (DABG) p-value and absolute expression values. Next, probesets were summarized with RMA algorithm and using the AltAnalyze annotations, derived from Ensembl [29] and UCSC databases [30]. Gene expression levels were determined using only probesets targeting constitutive exons. Determination of overall gene level variation was assessed using linear models and empirical Bayes methods s implemented in ‘limma’ package. The B-statistics gives the log odds of differential expression and it requires an ‘a priori’ value for the estimated proportion of differentially expressed genes. To determine this value, we visually inspected the volcano plot, which compares biological significance (represented by fold-changes) with statistical significance (B-values), finding the value which enabled genes to be distinguished from the majority (logFC≤~1.585). Additionally, we verified the P-values corresponding to moderated F-statistics. Using the Benjamini and Hochberg method, all genes selected as differentially expressed had adjusted P-values <0.05. . Detection of alternative splicing variations were determined using splicing-index and FIRMA approaches, calculating MiDAS and normalized intensity p-values (p-value <0.05).

first: Ana

last: Grosso

first: Luis

last: Moita


title: Genome-wide gene expression and identification of RNA polymerase, RpoD, and RpoS binding sites in Klebsiella pneumoniae MGH 78578

country: USA

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

overall_design: Refer to individual Series


title: Expression Profiles of miRNAs in brown fat of mice at room temperature and cold exposure (8C)

status: Public on Nov 01 2012

city: Zurich

first: Markus

last: Stoffel

state: ZH

address: Schafmattstr. 22

department: Molecular Health Science

institute: ETH Zurich

summary: microRNAs levels were measured in brown adipose tissue of male C57Bl6N mice that were kept at RT or during cold exposure (8°C) for 24 hrs. Several miRNAs including myomirs were identified to be regulated in response to cold.

overall_design: Brown adipose tissue from 2 groups of 8 weeks old male C57Bl6N mice at room temperature (n=3) or after cold exposure n=3) at 8°C for 24 hrs were excised and RNA was extracted using Trizol and the manufactureres recommended procedure. miRNA expression levels were determined using Agilent microRNA expression analysis platform.

first: Ferdinand

last: von Meyenn


title: Identification of re-capping substrates for the cytoplasmic capping enzyme complex

city: Columbus

first: Brian

middle: Alexander

last: Kennedy

state: Ohio

address: 278 Chittenden AVE

institute: The Ohio State University

summary: The analysis of capped RNAs by massively parallel sequencing has identified a large number of previously unknown transcripts, some of which are small RNAs and others are 5’ truncated forms of  RefSeq genes. The latter may be generated by endonuclease cleavage or by stalling of Xrn1 at defined sites. With the exception of promoter-proximal transcripts the caps on all of these are added post-transcriptionally by a cytoplasmic capping enzyme complex that includes capping enzyme and a kinase that converts 5’-monophosphate ends to a diphosphate capping substrate. We previously described a modified form of capping enzyme with dominant negative activity against cytoplasmic capping (DN-cCE). A tet-inducible form of this was used to identify substrates for cytoplasmic capping by treating cytoplasmic RNA from control and induced cells with and without Xrn1. Surviving RNA was analyzed on Affymetrix Human Exon 1.0 arrays and scored for changes in probe intensity as a function of its position on each RefSeq gene to derive a factor (alpha) that could be compared between sets. Notably, transcriptome-wide changes were not evident unless RNA was treated with Xrn1. This analysis identified 2,666 uncapped mRNAs in uninduced cells, 672 mRNAs that appeared in the uncapped pool in cells expressing DN-cCE, and 835 mRNAs that were in both populations. Changes in cap status of 10 re-capping targets and 5 controls were assessed by 3 independent measures; susceptibility to Xrn1, recovery with a biotin-tagged DNA primer after ligating a complementary RNA oligonucleotide to uncapped 5’ ends, and binding or exclusion from a high affinity cap-binding matrix comprised of immobilized eIF4E and the corresponding binding domain of eIF4G.

overall_design: 3 biological replicates of 4 different samples comparing XRN1 treatment/non-treatment and Dox induction/non-induction of K294A

first: Chandrama

last: Mukherjee

first: Deepak

last: Patil

middle: A

first: Baskar

last: Bakthavachalu

first: Juan

last: Gutierrez

first: Ralph

last: Bundschuh

first: Daniel

last: Schoenberg


title: Exon arrays from HeLa cells transfected with GFP-ZRANB2 vector

status: Public on Dec 15 2012

city: Sydney

last: Morris

state: NSW

address: Anderson Stuart Building, room N452, University of Sydney

department: Physiology

country: Australia

institute: University of Sydney

summary: Human ZRANB2 mRNA is alternatively spliced to give two variants with different 3’ ends. Both isoforms are present in the nucleus of human cells. ZRANB2 binds to mRNA, as well as the essential splicing factors U170K and U2AF35, and the novel splicing component SFRS17A (formerly known as XE7). It has been shown to alter splicing patterns of Tra2β1 minigene primary transcripts in a dose-dependent manner. It is still unclear what role ZRANB2 plays in the regulation of alternative splicing. To determine the endogenous transcripts that are targeted by ZRANB2 at the genome wide level, we decided to perform exon microarray studies and analyzed the suitability of this method to examine splicing differences in human cells overexpressing a splicing factor.

overall_design: GFP-ZRANB2 construct containing isoform 2 (short form, SF) of ZRANB2 was used. This construct includes exon 1 through to alternative exon 10. Isoform 2 was chosen since it has been shown previously to affect alternative splicing of a Tra2β1 minigene. HeLa cells were transfected with GFP-ZRANB2, control vector GFP or were left untransfected. RNA was extracted using a Qiagen RNA extraction kit. Experiments were run in 5 replicates.

first: Francine

middle: Z

last: Marques

first: Helena

last: Mangs

first: Marietta

last: Markus

first: Oleg

last: Raitskin

first: Ruth

last: Sperling

first: Yee

middle: H

last: Yang


title: Analysis of transcriptome changes in HeLa cells after knock-down of variant U1.8 snRNA

status: Public on Oct 01 2012

city: Oxford

first: Martin

last: Dienstbier

address: South Parks Road

department: Sir William Dunn School of Pathology

institute: University of Oxford

summary: U1 small nuclear (sn)RNA, required for splicing of pre-mRNA, is encoded by genes on chromosome 1p36. Imperfect copies of these ‘true’ (t)U1 snRNA genes, located on chromosome 1q12-21, were thought to be pseudogenes. However, many of these ‘variant’ (v)U1 snRNA genes produce fully-processed transcripts that are packaged into potentially functional particles. Using antisense oligonucleotides, we have achieved functional knockdown of a specific vU1 snRNA in HeLa cells and identified over 400 transcriptome changes following interrogation of the Affymetrix Human Exon ST 1.0 array.

overall_design: Total RNA from 4 biological repeats of vU1.8 snRNA and control knock-down were analysed using Affymetrix Human Exon ST 1.0 Array.

first: Dawn

last: O'Reilly

first: Shona

last: Murphy


title: Design of a Tobacco Exon Array with application to investigate the differential cadmium accumulation property in two tobacco varieties

status: Public on Nov 16 2012

city: Neuchatel

first: Sam

last: Ansari

state: Neuchatel

address: Quai Jeanrenaud 5

department: Research & Development

institute: Philip Morris Products SA

summary:
For decades the tobacco plant has served as a model organism in plant biology to answer fundamental biological questions in the areas of plant development, physiology, and genetics. Due to the lack of sufficient coverage of genomic sequences, however, none of the expressed sequence tag (EST)-based chips developed to date cover gene expression from the whole genome. The availability of Tobacco Genome Initiative (TGI) sequences provides a useful resource to build a whole genome exon array, even if the assembled sequences are highly fragmented. Here, the design of a Tobacco Exon Array is reported and an application to improve the understanding of genes regulated by cadmium (Cd) in tobacco is described.
From the analysis and annotation of the 1,271,256 Nicotiana tabacum fasta and quality files from methyl filtered genomic survey sequences (GSS) obtained from the TGI and ~56,000 ESTs available in public databases, an exon array with 272,342 probesets was designed (four probes per exon) and tested on two selected tobacco varieties.
Two tobacco varieties out of 45 accumulating low and high cadmium in leaf were identified based on the GGE biplot analysis, which is analysis of the genotype main effect (G) plus analysis of the genotype by environment interaction (GE) of eight field trials (four fields over two years) showing reproducibility across the trials. The selected varieties were grown under greenhouse conditions in two different soils and subjected to exon array analyses using root and leaf tissue to understand the genetic make-up of the Cd accumulation. An Affymetrix Exon Array was developed to cover a large (~90%) proportion of the tobacco gene space. The Tobacco Exon Array will be available for research use through the Affymetrix array catalogue. As a proof of the exon array usability, we have demonstrated that the Tobacco Exon Array is a valuable tool for studying Cd accumulation in tobacco leaves. Data from field and greenhouse experiments supported by gene expression studies strongly suggested that the difference in leaf Cd accumulation between the two specific tobacco cultivars is dependent solely on genetic factors and genetic variability rather than on the environment.

overall_design: 22 samples were used with 3 different experimental factors: [1] 2 different tissues (leaves and roots/lateral), [2] 2 different mutations (V5 and V21), and [3] 2 different stimuli (Soil 1 and Soil 2). 2-3 biological replicates were used. One sample did not pass QC and is not included in this submission.

first: Florian

last: Martin

first: Lucien

last: Bovet

first: Audrey

last: Cordier

first: Mario

last: Stanke

first: Irfan

last: Gunduz

first: Manuel

last: Peitsch

first: Nikolai

middle: V

last: Ivanov


title: Environmentally Induced Epigenetic Transgenerational Inheritance of Altered Sertoli Cell Transcriptome and Epigenome:  Molecular Etiology of Male Infertility [Affymetrix]

status: Public on Sep 27 2012

first: Michael

last: Skinner

summary: Environmental toxicants have been shown to induce the epigenetic transgenerational inheritance of adult onset disease, including testis disease and male infertility.  The exposure of a gestating female during the period of gonadal sex determination has been shown to promote sperm epimutations, differential DNA methylation regions (DMR), that transmit transgenerational disease to subsequent generations.  The current study was designed to determine the impact of an altered sperm epigenome on the subsequent development of an adult somatic cell (Sertoli cell) that influences the onset of a specific disease (male infertility).  A gestating female rat (F0 generation) was exposed to the agriculture fungicide vinclozolin during gonadal sex determination and then the subsequent F3 generation progeny used for the isolation of Sertoli cells and assessment of testis disease.  As previously observed, a spermatogenic cell apoptosis was observed. The Sertoli cells that provide the physical and nutritional support for the spermatogenic cells were isolated and alterations in gene expression examined.  Over 400 genes were differentially expressed in the F3 generation control versus vinclozolin lineage Sertoli cells.  A number of specific signaling pathways and cellular processes were identified to be transgenerationally altered.  One of the key metabolic processes affected was pyruvate/lactate production that is directly linked to spermatogenic cell viability.  The Sertoli cell epigenome was also altered with over 100 promoter differential DNA methylation regions (DMR) modified in the vinclozolin F3 generation Sertoli cell.  The genomic features and overlap with the sperm DMR were investigated.  Observations demonstrate that the transgenerational sperm epigenetic alterations subsequently alters the development of a specific somatic cell (Sertoli cell) epigenome and transcriptome that then has a role in the adult onset disease (male infertility).  The environmentally induced epigenetic transgenerational inheritance of testis disease appears to be a component of the molecular etiology of male infertility.

overall_design: RNA samples from  Sertoli cell of 3 F3-control lineage groups are compared to Sertoli cell of 3 F3-vinclozolin lineage groups

first: Carlos

last: Guerrero-Bosagna

first: Marina

middle: I

last: Savenkova

last: Haque

first: Eric

middle: E

last: Nilsson


title: Chd1 chromatin remodelers maintain nucleosome organization and repress cryptic transcription

status: Public on Sep 15 2012

city: Canberra

first: Tamas

last: Fischer

state: ACT

address: Building 131, Garran Rd

department: The John Curtin School of Medical Research

institute: The Australian National University

summary:
Proper chromatin organization is essential for defining transcription units and maintaining genomic integrity in eukaryotes. Mutations affecting the chromatin structure can lead to increased cryptic transcription and genomic instability. In this study we found that deletion of the Schizosaccharomyces pombe Chd1-type chromatin remodelers, hrp1 and hrp3, causes strong, genome-wide accumulation of antisense transcripts, while the amount of coding mRNA transcripts is mostly unaffected. Nucleosome mapping revealed a specific role for Chd1-remodelers in the positioning of nucleosomes in gene coding regions. While the arrangement of nucleosomes in promoter regions was similar to WT, nucleosome organization within coding regions was remarkably irregular in hrp1∆hrp3∆ strain. We extended our analysis to other mutations associated with enhanced cryptic transcription activity, such as set2∆, alp13∆, and FACT complex subunit pob3∆. While nucleosomes were severely depleted in the pob3∆ strain, nucleosome positioning was less affected. In sharp contrast, nucleosome organization in the alp13∆ and set2∆ strains was indistinguishable from WT. These data indicate multiple mechanisms in the repression of cryptic promoter activity in eukaryotic cells.
Genome-wide profiling of H3K9/K14 acetylation
Genome-wide expression analysis of either Alp13-, Set2-, Hrp3 or Hrp1 and Hrp3-deficient cells
Genome-wide expression analysis of either Hrp1, Hrp3, or Hrp1 and Hrp3-deficient cells
Nucleosome mapping experiments

overall_design:
ChIP for the detection of the genome-wide acetylation profile of H3K9/K14 was performed for a wildtype strain and the deletion strains of Set2, Alp13 and the double knock-out of Hrp1 and Hrp3. Each experiment was performed twice in biological replicates
All experiments were performed twice in biological replicates, except for the expression array of set2Δ. The replicates of hrp3Δ and hrp1Δhrp3Δ were performed with a slightly different array design
All experiments were performed twice in biological replicates. The replicates of hrp3Δ and hrp1Δhrp3Δ were performed with a slightly different array design
MNase treated sample were comparatively hybridized with genomic DNA of corresponding strain, WT, hrp1d hrp3d, pob3d in biological duplicates, set2d, alp13d, mit1d, hrp1d, hrp3d analysis was performed once

first: Bianca

middle: P

last: Hennig

first: Katja

last: Bendrin

first: Yang

last: Zhou


title: Expression data from non-demented controls (NDCs) and Alzheimer's disease (AD) patients

status: Public on Sep 06 2012

city: Jerusalem

first: Amit

last: Berson

address: The Edmond J. Safra Campus, Givat Ram

department: Biological Chemistry

institute: The Hebrew University of Jerusalem

summary:
AD is the leading cause of dementia in the elderly. However, disease etiology is still practically unknown. To gain insight into the molecular mechanisms underlying this disease we used the Affymetrix exon arrays to profile the alternative splicing landscape of human entorhinal cortex samples from AD patients and controls. We found a few hundred events of alternative spicing that characterize the AD entorhinal cortex and may have profound effect on the pathogenesis of this disease.
Expression was analyzed using Affymetrix Human Exon 1 S.T arrays

overall_design: samples from 3 female NDCs and 3 female AD patients were included in this study

first: Hermona

last: Soreq


title: Gene expression comparison of liver tissue from C57BL/6J and KK/HIJ mice

status: Public on Oct 18 2012

city: San Antonio

first: Magalie

last: Leduc

state: TX

institute: Texas Biomedical Research Institute

summary: A QTL intercross was performed bewteen C57BL/6J and KK/HIL for albuminurea, asthma and cardiovascular related phenotypes. Several QTL were identified for most phenotypes. We performed microarray analysis from liver samples to identify genes differentially expressed between the parental strains. The results helped us narrow down the QTL and identify the candidate genes based on differential expression between the parental strains.

overall_design: At 8 weeks of age, the large lobe of the liver from 3 male and 3 females C57BL/6J and KK/HIJ (12 mice total) was collected. The mice were separated individuallly for 3 days and fasted for 4 hours prior to the tissue collection. The mice were sacrificed by cervically dislocation and perfused with PBS prior to the liver collection.

first: Annerose

last: Berndt

first: Holly

last: Savage

first: Tim

last: Stearns

first: Beverly

last: Paigen


title: Lamin b receptor regulates nuclear architecture and gene expression in olfactory neurons

status: Public on Aug 30 2012

city: San Francisco

first: Eleanor

middle: Josephine

last: Clowney

state: CA

department: Anatomy

institute: UCSF

summary:
Gene positioning and regulation of nuclear architecture are thought to influence gene   expression. Here, we show that in mouse olfactory neurons, silent olfactory receptor   (OR) genes from different chromosomes converge in a small number of heterochromatic   foci. These foci are OR-exclusive and form in a cell-type-specific and differentiation-   dependent manner. The aggregation of OR genes is developmentally synchronous with   the downregulation of Lamin b Receptor (LBR) and can be reversed by ectopic   expression of LBR in mature olfactory neurons. LBR-induced reorganization of nuclear   architecture and redistribution of OR loci results in misregulation of OR transcription and   disruption of the targeting specificity of the olfactory neurons. Our observations are   consistent with a model of spatial regulation of OR expression and provide evidence for   the instructive role of nuclear architecture and compartmentalization in gene regulation   and differentiation.
A complex probe was made by array capture to label mouse olfactory receptor genes by DNA FISH; this microarray data verifies the composition of that probe.

overall_design: Probe was made by array capture and elution from a custom olfactory receptor genomic region tiling array. Probe was verified on a chr1-4 tiling array.

first: E

middle: J


title: High contaminant loads in Lake Apopka mesocosms affect the ovarian transcriptome in largemouth bass [April]

status: Public on Aug 31 2012

city: Gainesville

first: Christopher

middle: Joseph

last: Martyniuk

state: FL

address: CEHT Mowry Road

department: Physiological Sciences

institute: UF

summary: Lake Apopka (Fl, USA) experienced heavy uses of organochlorine pesticides (OCPs) in the 1950s-1970 during an intense agricultural period.  As a result, the region remains heavily contaminated and was declared a Superfund site by the US Environmental Protection Agency.  Aquatic organisms inhabit the freshwater systems in and around Lake Apopka, however the impacts of sub chronic exposure to OCPs in this natural environment are not known.  The objectives of this study were to determine the effects of the contamination on the reproductive axis of largemouth bass (LMB) (Micropterus salmoides).  In October (2007), healthy LMB were stocked into natural mesocosms and remained in mesocosms before being sampled in January 2008 (at early oogenesis). Additional LMB were placed into mesocosms for 2 months in February (2008) and sampled in April (2008) (oocyte maturation).  LMB placed in these mesocosms for four months had a 2-20X higher contaminant load for OCPs (e.g. DDE, dieldrin, methoxychlor) than LMB collected from reference sites. Gonadosomatic index for LMB collected in April from the mesocosms were not different that LMB from reference sites.  Vitellogenin levels in LMB collected from the mesocosms in January and April were not significantly different than fish collected from Welaka in late vitellogenin or early maturation respectively. Steroids were depressed in mesocosm fish. Microarray analysis revealed that the expression profiles of genes in the LMB ovary were unique compared to LMB collected form reference sites.  Transcripts that showed altered abundance in LMB from the mesocosms were insulin-like growth factor I and steroidogenic acute regulatory protein.  Interestingly, differentially expressed transcripts showed a significant and positive correlation for LMB sampled in January and April despite the 3 month period in between samplings.  Sub-network enrichment analysis for cellular processes showed that retinoic acid metabolism and germ-cell development were decreased in mesocosm-exposed fish but processes such as vitellogenesis, amino acid catabolism, granulosa cell function, vitamin D metabolism, and hormone biosynthesis were increased in mesocosm-exposed fish.  These data suggest that (1) LMB from the mesocosms are exhibiting unique gene profiles that may impair normal reproduction and that (2) microarray analysis in the field can provide site specific information by discriminating LMB from reference and polluted sites.

overall_design: 8 microarrays on LMB collected from the wild in April. These include St John River (n=4) and animals placed in Apopka mesocosms (n=4).

first: Melinda

middle: S

last: Prucha

first: Nick

last: Doperelski

first: Kevin

last: Kroll

first: David

last: Barber

first: Nancy

middle: D

last: Denslow


title: High contaminant loads in Lake Apopka mesocosms affect the ovarian transcriptome in largemouth bass


title: Amiloride modulates alternative splicing in leukemic cells and re-sensitizes Bcr-AblT315I mutant cells to imatinib

status: Public on Sep 17 2012

city: kaohsiung

first: wen-hsin

last: chang

address: 100,Shih-Chuan 1st Road,Kaohsiung

institute: Kaohsiung Medical University

summary: We have discovered that amiloride can produce a genome-wide effect on alternative splicing of various RNA transcripts, most importantly including those of the apoptotic factors, in K562 leukemic cells.

overall_design: Target was prepared from 4 biological replicates of 0.5 mM amiloride-treatment for 24hr and 3 control untreatment from K562 cells and hybridized to the Affymetrix Human Exon 1.0 ST Array. The values of the hybridized probesets were normalized and analyzed for gene expression using Partek software.

first: Wen-Hsin

last: Chang

first: Ta-Chih

last: Liu

first: Wen-Kuang

last: Yang

first: Chien-Chih

last: Lee

first: Yi-Hsiung

last: Lin

first: Tsai-Yun

last: Chen

first: Jan-Gowth


title: In utero allergen exposure reprograms primary developmental patterns of lung gene expression and influences respiratory phenotype in rat models of asthma susceptibility.

status: Public on Oct 11 2012

city: Boston

first: Alvin

middle: T.

last: Kho

state: MA

address: 320 Longwood Avenue

department: Informatics Program

institute: Boston Children's Hospital

summary: Transcriptome of whole lung of rat from 3 genetic strains, 3 postnatal time points and 2 exposures (saline versus ovalbumin) in (mainly) 4 replicate measurements per condition.

overall_design: Total RNA obtained from whole lung of rat from 3 genetic strains, 3 postnatal time points and 2 exposures (saline versus ovalbumin) in (mainly) 4 replicate measurements per condition.

middle: T

first: Andre

last: Ponton

first: Feige

last: Kaplan


title: High contaminant loads in Lake Apopka mesocosms affect the ovarian transcriptome in largemouth bass [January]

first: Christopher

overall_design: 12 microarrays on LMB collected from the wild in January. These include St John River (n=4), DeLeon Springs (n = 4), and animals placed in Apopka mesocosms (n=4).


title: Exon arrays from HeLa cells transfected with RBM4-specific siRNA

status: Public on Jul 15 2012

last: Morris

summary: RBM4 is a RNA-binding protein (RBP) able to modulate splicing by promoting exon inclusion and shares an import pathway with other splicing factors in the nucleus. In earlier studies we found that RBM4 interacts and colocalizes with WT1, which has been implicated in 10–15% of Wilms’ tumours and more recently in leukemya, is considered to be a tumour suppressor. RBM4, a RBP whose splicing effect is inhibited by the +KTS isoform of the tumour-suppressor/activator WT1, exhibits altered expression in different tumours, and may be essential for proliferation. Moreover, RBM4 binds to a number of RNAs of genes involved in acute myeloid leukaemia and cell cycle control. These results suggest that RBM4 may be involved in alternative splicing, tumorigenesis and particularly leukaemogenesis. To determine the endogenous transcripts that are targeted by RBM4 at the genome-wide level, we decided to perform exon microarray studies.

overall_design: RBM4-specific siRNA has been used for knockdown of RBM4 in HeLa cells. RNA was extracted using a Qiagen RNA extraction kit from untransfected, mock and siRNA-transfected HeLa cells and quality of RNA for microarray analysis was checked using a Bioanalyzer 2100 (Agilent Technologies). Experiments were run in triplicates.

first: M

last: Markus

first: Francine

last: Marques

first: Yee

first: Brian