title: Genome-wide gene expression profiles in lung tissues of pig breeds differing in resistance to porcine reproductive and respiratory syndrome virus

city: Tai’an

first: Yunliang

state: Shandong

address: No. 61 Daizong Avenue

department: College of Animal Science and Veterinary Medicine

institute: Shandong Agricultural University

summary:
Porcine reproductive and respiratory syndrome caused by porcine reproductive and respiratory syndrome virus (PRRSV) is an infectious disease characterized by severe reproductive deficiency in pregnant sows, respiratory symptoms in piglets, and high mortality. In this study, we employed Affymetrix microarray chip technology to compare the gene expression profiles of lung tissue samples from Dapulian (DPL) pigs (a Chinese indigenous pig breed) and Duroc×Landrace×Yorkshire (DLY) pigs after infection with PRRSV. During infection with PRRSV, the DLY pigs exhibited the range of clinical features that typify the disease, while the DPL pigs exhibited only mild signs of the disease. The percentage of CD8+ T cells in the DPL pigs was significantly higher than that in the DLY pigs at 21 days post-infection (dpi) (p< 0.05). Interleukin (IL) 1 beta (IL-1β) and IL-2 levels showed significant differences between the DPL and DLY pigs at 0 and 7 dpi (p< 0.01). For IL-10, the DLY pigs had significantly higher values than the DPL pigs at 0 and 7 dpi (p< 0.01). Significant differences were apparent between the DPL and DLY pigs in terms of their tumor necrosis factor-alpha (TNF-α) and interferon (IFN)-gamma (IFN-γ) levels at 0 and 7 dpi (p< 0.01). Microarray data revealed 16 differentially expressed genes in the lung tissue samples from the DLY and DPL pigs (q≤5%), of which LOC100516029 and LOC100523005 were up-regulated in the PRRSV-infected DPL pigs, while the other 14 genes were down-regulated in the PRRSV-infected DPL pigs compared with the PRRSV-infected DLY pigs. The expression levels of 10 of the 16 genes, namely CCDC84, C6ORF52, THYMOSIN, PRVE, HSPCB, CYP2J2, AMPD3, TOR1AIP2, PTGES3, and ACOX3, were validated by real-time quantitative RT-PCR. This study provides a platform for further investigation of the molecular mechanisms underlying the differential immune responses to PRRSV infection in different breeds or lines of pig.
We investigated the response of lung tissues from Dapulian (DPL) pigs (a Chinese indigenous pig breed) and Duroc×Landrace×Yorkshire (DLY) pigs infected with porcine reproductive and respiratory syndrome virus (strain JXA1) by using the Affymetrix Porcine Genome Array.

overall_design: Sixteen healthy 30-day-old weaned DPL pigs were selected from the Jiaxiang Dapulian farm, Jining City, China, and 15 healthy 30-day-old weaned DLY pigs were obtained from a commercial farm with high standards of animal health. These pigs were free from PRRSV, porcine circovirus type 2 (PCV2), pseudorabies virus (PRV), and classical swine fever virus (CSFV) as determined by ELISA tests for serum antibodies; the absence of PRRSV was also confirmed by real-time quantitative reverse transcription PCR (qRT-PCR). Pigs were randomly assigned into two groups and reared in separate places: the PRRSV-infected group consisted of 11 DPL and 10 DLY pigs, and the control group consisted of five DPL and five DLY pigs. Infections in the pigs proceeded via inoculation with 2 ml of a viral suspension of PRRSV (at a tissue culture infectious dose of 105) by dripping the solution into the nasal cavity of each pig. The control group was treated with an identical volume of PBS by the same method. Rectal temperatures and clinical examinations on the pigs were recorded daily during the experiment. Anticoagulant-treated blood and untreated blood samples were collected separately at 0, 7, 14, and 21 days post-infection (dpi) from the infected and control groups for assaying CD4+, CD8+, cytokine (interleukin (IL) 1 beta (IL-1β), IL-2, IL-10, interferon (IFN)-gamma (IFN-γ), tumor necrosis factor-alpha (TNF-α), and immunoglobulin G (IgG) protein levels. Lung samples for microarray analysis and real-time qRT-PCR analysis were collected from six infected DLY and DPL pigs (three pigs for each breed) immediately post-slaughter at 28 dpi.   Total RNA was isolated from lung tissue samples and purified using an RNeasy Mini kit according to the manufacturer’s protocol. RNA was prepared using the GeneChip (AFF-900623) one cycle target for the labeling and control reagents, and the labeled RNA was hybridized in an Affymetrix Hybridization Oven 640 for sequencing.

first: J

middle: Y

last: Xing

first: F

first: L

last: Yang

first: Y

last: Zhang

first: N

last: Li

first: C

middle: H

middle: L

last: Wen


title: Expression data from maize stems attacked by European corn borer (ECB, Ostrinia nubilalis) larvae

status: Public on Jun 01 2013

city: Gainesville

first: Alisa

last: Huffaker

state: FL

department: Chemistry Research Unit

country: USA

institute: USDA-ARS CMAVE

summary:
ECB larvae remain damaging pests of conventiational maize production. To better understand the physiological and molecular changes occuring in stem tissue during insect attack we explored the biochemical and transcriptional profiles in these tissues.
We used microarrays to detail the transcriptional changes associated with ECB attack and considered these in the context of biochemical markers of plant defense and total protein levels.

overall_design: Maize internode tissue was selected from untreated control plants and those which 5th instar ECB larvae had bored into for 48 h for RNA extraction and hybridization on Affymetrix microarrays.

first: Eric

last: Schmelz

first: Nicole

last: Dafoe


title: Characterization of cholesterol loading effect on the gene expression of bone marrow derived macrophages of AKR and DBA/2 ApoE-deficient mice

status: Public on Jun 30 2013

city: Cleveland

first: Jeff

last: Hsu

state: OH

address: 9500 Euclid Ave

department: Cellular and Molecular Medicine

institute: Cleveland Clinic Lerner Research Institute

summary: Strain effects on the response to cholesterol loading in bone marrow derived macrophages (BMM) are not well studied.  The atherosclerosis susceptible strain, DBA/2 on the ApoE deficient background and the atherosclerosis resistant AKR strains show differences in cholesterol handling when loaded with AcLDL.  To understand the molecular basis for these differences, BMM from both strains were loaded with acetylated low desnisty lipoprotein (AcLDL) and gene expression quantified.  BMMs from AKR greatly upregulated transcripts involved in the lysosomal trafficking pathway.  This experiment strongly suggest that upregualtion of the lysosomal pathway in response to AcLDL maybe protective against atherosclerosis.  In addition we find that transcripts containing the sterol response element (SRE) motif had strong strain-loading interactions suggesting a strain response to SRE response.

overall_design: 32 BMM cultures from AKR (n=16) and DBA/2 (n=16) mice of both genders (16 males and 16 females) were loaded with AcLDL (n=16) or control media (n=16) resulting in 4 biological replicates for each of the conditions, gender, loading, and strain.

first: Stela

middle: Z

last: Berisha

first: Jeffrey

first: Johnathan

middle: D

last: Smith


title: Changes in Gene Expression within the Ventral Tegmental Area Following Loss-of-Control Alcohol Drinking by Alcohol-Preferring (P) Rats

city: Westfield

first: Mark

middle: William

last: Kimpel

state: IN

address: 15032 Hunter Court

department: Psychiatry

institute: Indiana University

summary: The objective of this study was to determine changes in gene expression in the ventral tegmental area (VTA) following loss-of-control alcohol drinking by alcohol-preferring (P) rats. Adult female P rats (n = 7) were given concurrent access to 10, 20 and 30% EtOH for four 1-hr sessions daily for 10 weeks followed by 2 cycles of 2 weeks of abstinence and 2 weeks of EtOH access. Rats were killed by decapitation 3 hr after the 4th daily EtOH-access session at the end of the second 2-week relapse period. An age-matched water control group of female P rats (n = 8) was also killed. RNA was prepared from micropunch samples of the VTA from individual rats; analyses were conducted with Affymetrix Rat 230.2 chips. Ethanol intakes were 1.5-2.5 g/kg per sessions, resulting in blood levels >200 mg% at the end of the 4th session. There were 211 named genes that were significantly different (FDR = 0.1) between the water and EtOH groups. Bioinformatics analyses indicated alterations in (a) transcription factors that reduced excitation-coupled transcription and promoted exocitotic neuronal damage involving clusters of genes associated with Nfkbia, Fos and Srebf1; (b) genes that reduced cholesterol and fatty acid synthesis, and increased protein degradation; and (c) genes involved in cell-to-cell interactions and regulation of the actin cytoskeleton. Among the named genes, there were 62 genes in common with differences between alcohol-naïve P and non-preferring (NP) rats, with 43 of the genes changing in the opposite direction following excessive binge-like drinking. These genes are involved in a pro-inflammatory response, and enhanced response to glucocorticoids and steroid hormones.  Overall, the results of this study indicated that excessive binge-like alcohol drinking by P rats may be altering the expression of genes that promote neuronal damage.

overall_design: Comparison of Differences in Gene Expression in the Ventral Tegmental Area of Rat Lines Selectively Bred for High or Low Alcohol Consumption

first: William

middle: J

last: McBride

middle: W

first: Jeanette

middle: N

last: McClintick

first: Zheng-Ming

last: Ding

first: Howard

last: Edenberg

first: Richard

last: Bell

first: Zachary

middle: A

last: Rodd


title: Genomic Grade Index (GGI): Feasibility in routine practice and impact on treatment decisions in early breast cancer

status: Public on Jun 03 2013

city: Boston

first: Otto

last: Metzger

state: MA

address: 450 Brookline ave, Yawkey 1238

institute: Dana Farber Cancer Institut

summary: Genomic Grade Index (GGI) is a 97-gene signature that improves histologic grade (HG) classification in invasive breast carcinoma. In this prospective study we sought to evaluate the feasibility of performing GGI in routine clinical practice and its impact on treatment recommendations. Patients with pT1pT2 or operable pT3, N0-3 invasive breast carcinoma were recruited from 8 centers in Belgium. Fresh surgical samples were sent at room temperature in the MapQuant Dx™ PathKit for centralized genomic analysis. Genomic profiles were determined using Affymetrix U133 Plus 2.0 and GGI calculated using the MapQuant Dx™ protocol, which defines tumors as low or high Genomic Grade (GG-1 and GG-3 respectively). 180 pts were recruited and 155 were eligible. The MapQuant test was performed in 142 cases and GGI was obtained in 78% of cases (n=111). Reasons for failures were 15 samples with <30% of invasive tumor cells (11%), 15 with insufficient RNA quality (10%), and 1 failed hybridization (<1%). For tumors with an available representative sample (≥ 30% inv. tumor cells) (n=127), the success rate was 87.5 %. GGI reclassified 69% of the 54 HG2 tumors as GG-1 (54%) or GG-3 (46%). Changes in treatment recommendations occurred mainly in the subset of HG2 tumors reclassified into GG-3, with increased use of chemotherapy in this subset.  The use of GGI is feasible in routine clinical practice and impacts treatment decisions in early-stage breast cancer.

overall_design: Total RNA was extracted from fresh tumor tissues comprising ≥30% invasive tumor cells and hybridized on Affymetrix microarrays if the RIN was  ≥ 7.


title: Candidate transcriptomic sources of inbreeding depression in Drosophila melanogaster

status: Public on May 31 2013

city: Vigo

first: Humberto

last: Quesada

state: Galicia

address: Facultad de Biologia. Campus Lagoas-Marcosende

department: Bioquimica, Genetica e Inmunologia

country: Spain

institute: Universidad de Vigo

summary:
The genomic causes of inbreeding depression are poorly known. Several studies have found widespread transcriptomic alterations in inbred organisms, but it remains unclear which of these alterations are causes of the depression and which are mere responses to the ensuing physiological stress.
We made a c-DNA microarray analysis in Drosophila melanogaster attempting to differentiate causes from responses of inbreeding depression. The rationale of the experiment was that, while depression is a general phenomenon producing similar consequences in different inbred lines, its first genetic causes would be different for each inbred line, as they are expected to be caused by the fixation of rare deleterious genes.
Many changes in expression were common to all sets, but fourteen genes, grouped in four expression clusters, showed strong set-specific changes, and were therefore candidates to be sources of the inbreeding depression observed.

overall_design: We took four sets of inbred sublines, each set descending from a different founding pair obtained from a large outbred stock, and compared the expression of the three most depressed sublines and the three least depressed sublines from each set.

first: Carlos

last: García

first: Victoria

last: Avila

first: Armando

last: Caballero


title: Differential accumulation of splice variants and transcripts as a result of PI3K inhibition in T lymphocytes and the potential role of their gene products in T cell silencing

status: Public on May 22 2013

city: Wuerzburg

first: Susanne

last: Kneitz

address: Am Hubland, Biocenter

department: Physiological Chemistry I

country: Germany

institute: University of Wuerzburg

summary: Using measles virus induced T cell suppression as a model, we established that T cell inhibitory protein isoforms can be produced from alternatively spliced pre-mRNAs as a result of virus-mediated ablation of T cell receptor dependent activation of the phosphatidylinositol-3-kinase (PI3K). To asses production of alternative splice variants in response to PI3K abrogation in T cells at a whole cell level, we performed a Human Exon 1.0 ST Array on RNAs isolated from T cells stimulated only or stimulated after PI3K inhibition. We developed a simple algorithm based on a splicing index to detect genes that undergo alternative splicing (AS) or are differentially regulated (RG) on T cell suppression. Applying our algorithm on this model 9% of the genes were assigned as AS, while only 3% were attributed to RG. Though there are overlaps, AS and RG genes differed with regard to functional regulated at the level of AS or RG were found enriched in different functional groups with AS targeting e. g. extra cellular matrix (ECM)-receptor interaction and focal adhesion, while cytokine-receptor interaction, Jak-STAT and p53 pathways were mainly RG. When combined, AS/RG dependent alterations targeted pathways essential for T cell receptor signaling, cytoskeletal dynamics and cell cycle entry strongly supporting the notion that PI3K abrogations interferes with key T cell activation processes at both levels, and that candidates represented within both categories bear the potential to actively contribute to T cell suppression

overall_design: total samples analysed are 8: 4 stimulated and 4 stimulated and inihibited from 4 donors

first: Alice

last: Riedel

first: Boitumelo

last: Mofolo

first: Elita

last: Avota

first: Sibylle

last: Schneider-Schaulies

first: Ayton

last: Meijntjes

first: Nicola

last: Mulder


title: Human gastric mucosa Cells: hTERT-negative para cancerous tissue (Control) vs. hTERT-positive gastric cancer tissue

status: Public on May 21 2013

city: Chongqing

first: Chen

last: Ling

address: Gaotanya Street

department: Department of Gastroenterology

country: China

institute: Xinqiao Hospital

summary: The miRNA expression profiles in one pair of  hTERT-positive gastric cancer tissue and an hTERT-negative para-cancerous tissue. The para-cancerous tissue is at least 5cm away from the cancer tisse. The expression of hTERT of identified by immunohistochemistry before RNA extraction for miRNA assay.

overall_design: One pair of gastric cancer tissue and para-cancerous tissue(Control). Four replicates per array.

first: Yang

last: Shiming


title: Expression of small RNA in Aphis gossypii and its potential role in the resistance interaction with melon

city: University Park

first: Sampurna

last: Sattar

state: PA

address: 138 ASI Building

department: College of Agricultural Sciences

institute: The Pennsylvania State University

type: Non-coding RNA profiling by high throughput sequencing

summary: This study was designed to identify the sRNAs in Aphis gossypii (cotton-melon aphid) during Vat-mediated resistance in teraction with melon

overall_design: Methods: Whole insects were collected from susceptible (Vat-) and resistant (Vat+) plants after 48 hours of feeding. Total RNA was extracted from the aphids and enriched for LMW RNA and small RNA libraries were constructed using standard protocols and deep sequenced using Illumina GAII analyzer.

first: Yan

last: Song

first: James

last: Anstead

first: Ramanjulu

last: Sunkar

first: Gary

last: Thompson


title: FAK and HAS3 inhibition affect the expression of several common genes

city: buffalo

first: Dan

last: Wang

state: NY

address: Elm & Carlton Streets

institute: RPCI

summary:
Purpose: Focal adhesion kinase (FAK), hyaluronan (HA), and hyaluronan synthase-3 (HAS3) have been implicated in cancer growth and progression. FAK inhibition with the small molecule inhibitor Y15 decreases colon cancer cell growth in vitro and in vivo. HAS3 inhibition in colon cancer cells decreases FAK expression and activation, and exogenous HA increases FAK activation. We sought to determine the genes affected by HAS and FAK inhibition and hypothesized that dual inhibition would synergistically inhibit viability.

Methods: We treated SW620 colon cancer cells with Y15 to inhibit FAK. We used two strategies to inhibit HAS: (1) cells were transfected with siRNA (HAS3 inhibited); a scrambled sequence was used as a control (HAS3 scrambled), and (2) cells were treated with the HAS inhibitor 4-methylumbelliferone (4-MU). To determine the effect on viability, MTT assays were performed on transfected cells treated with Y15, and wild type cells treated with Y15 alone, 4-MU alone or Y15+4-MU. Treated and untreated cells were submitted to the gene microarray facility for expression profiling. RT-PCR was done to confirm the results.

Results: HAS and FAK inhibition affected cell viability. Y15 and 4-MU decreased viability in a dose-dependent manner; viability was further inhibited by treatment with Y15+4-MU in combination (p<0.05). HAS-inhibited cells treated with as little as 2 M of Y15 showed significantly decreased viability compared to HAS scrambled cells treated with the same dose (p<0.05), suggesting synergistic inhibition of viability with dual FAK/HAS inhibition. Microarray analysis showed more than 2-fold up- or down-regulation of 121 genes by HAS inhibition, and 696 genes by FAK inhibition (p<0.05). Of 29 genes that were common to both groups, 9 were down-regulated (CBS, DHRS3, EEPD1, ESPN, FAM46C, GRTP1, IL20RA, INHBE, SCNN1A) and 4 were up-regulated (ANXA1, MALL, RGS2, SNAI2). RT-PCR confirmed these findings. Among the genes affected by FAK or HAS3 inhibition were FOX genes (apoptosis, cell cycle regulation), ANXA1 (apoptosis, proliferation), IL8 (cell cycle regulation, adhesion, proliferation), RGS2 (cell cycle regulation), CEACAM6 (adhesion), SNAI2 (transcription regulation), and SFRP5 (apoptosis). Several genes were specific to either FAK or HAS3 inhibition and several were common to both.

overall_design: Gene expression profiles of samples isolated from human colorectal cancer cells (SW620). A comparison of gene expression between untreated cells and cells treated with 4mcM of Y15. A second comparison between cells transfected with siRNA to HAS3 (HAS3-silenced) and cells transfected with a scrambled control sequence (sc). Two replicates each.

first: Melissa

last: Heffler

first: Kelli

middle: B

last: Dunn

first: Song

last: Liu

first: Vita

last: Golubovskaya

first: William

last: Cance


title: Transcriptional and Epigenetic Dynamics During Specification of Human Embryonic Stem Cells

status: Public on May 01 2013

city: Munich

first: Michael

middle: Johannes

last: Ziller

address: Kraepelinstrasse 2-10

department: Translational Psychiatry

institute: Max Planck Institute of Psychiatry

type: Genome binding/occupancy profiling by high throughput sequencing

type: Methylation profiling by high throughput sequencing

type: Expression profiling by high throughput sequencing

summary: Differentiation of human embryonic stem cells (hESCs) provides a unique opportunity to study the epigenetic mechanisms that facilitate cellular transitions in a human context. To that end, we performed comprehensive transcriptional and epigenetic profiling of early populations derived through directed differentiation of hESCs representing each of the three embryonic germ layers. Integration of whole genome bisulfite sequencing, chromatin immunoprecipitation-sequencing and RNA-Sequencing reveals unique events associated with specification towards each lineage. While we observe expected dynamics such as loss of DNA methylation and gain of H3K4me1 at distal putative regulatory elements, we frequently found a germ layer specific switch to H3K27me3 at sites of high DNA methylation in the undifferentiated state. By carefully dissecting these initial events, we may be able to devise more faithful differentiation strategies and gain novel insights in to the robust rewiring of regulatory programs during cellular transitions.

overall_design: 10 Samples in total, 5 in replicate. To better understand the interplay of epigenetic dynamics and transcription factor binding upon in vitro specification of human embryonic stem cells we profiled OCT4, SOX2 and NANOG in hESC and the endoderm master regulatory factor FOXA2 in in vitro derived endoderm cells (dEN). To gain further insights into the relation of DNA methylation and TF binding, we carried out ChIP-bisulfite sequencing for FOXA2 in dEN. Lastly, we were interested in the fate of genes bound by FOXA2 in dEN upon further differentiation and therefore differentiated dEN further towards a hepatocyte like state and performed RNA-Seq.

first: Alex

last: Meissner


title: Segmental Allergen Challenge Regulates Gene Expression In Bronchoalveolar Lavage (BAL) Cells From Atopic and Mild Asthmatic Subjects

city: Madison

first: Stephane

last: Esnault

address: 600 Highland avenue

department: Medicine

institute: University of Wisconsin

summary:
Segmental allergen challenge increases the percentage of eosinophils in bronchoalveolar lavage (BAL) cells. Mepolizumab, an anti-IL-5 therapeutic antibody, decreases the number of eosinophils in bronchoalveolar lavages (BAL).
The use of both procedures allows to define genes that are either expressed by eosinophils or dependent on eosinophil presence in the airways.

overall_design: Cells from Bronchoalveolar lavages (BAL) are obtained by bronchoscopy before (V5) and 48 h after a segmental allergen challenge (V6) in atopic and mild astmatics. This procedure was repeated in the same two subjects 2 months later and 1 month after an injection of mepolizumab (V22 is before challenge and V23 after challenge). Cells were immediately lysed and isolated total RNAs were analyzed using the Human Genome 1.0 ST GeneChip arrays (Affymetrix, Santa Clara, CA).

first: Yury

last: Bochkov

first: Elizabeth

last: Kelly

first: Nizar

last: Jarjour


title: The Pelvic Radiation and Vorinostat (PRAVO) Study - Histone Deacetylase Inhibitor Activity

status: Public on May 08 2013

city: Lørenskog

first: Ert

last: Kalanxhi

address: Lørenskog

department: Clinical and Molecular Oncology

country: Norway

institute: Akershus University Hospital

summary: The study objective was to propose molecular mechanisms of action of the histone deacetylase inhibitor vorinostat. In the PRAVO phase 1 study, patients that were scheduled to receive pelvic palliative radiation to 30 Gy in 3-Gy fractions for gastrointestinal carcinoma, were enrolled onto four sequential dose levels of vorinostat, starting at 100 mg daily with dose escalation in increments of 100 mg. Endpoints included treatment safety and tolerability, tumor response, and biological activity of vorinostat. For the purpose of identifying biomarkers of vorinostat action, peripheral blood mononuclear cells, representing normal tissue exposed to vorinostat, were used. The samples were collected, one at baseline and two on-treatment samples. The time points for sample collection were chosen based on our previous data from experimental colorectal carcinoma models exposed to vorinostat, demonstrating that the maximum tumor histone acetylation 2-3 hours after drug exposure was restored to baseline after 24 hours. In PRAVO study patients, tumor histone hyperacetylation was observed 3 hours after vorinostat administration.

overall_design: From the 17 patients enrolled onto the PRAVO study, a full set of three samples was obtained from 14 individuals: one baseline sample collected prior to commencement of vorinostat treatment (T0), and two on-treatment samples collected 2 and 24 hours after the patient had received the preceding daily dose of vorinostat (T2 and T24). Individual vorinostat dose levels were 100 mg (D100), 200 mg (D200), 300 mg (D300), or 400 mg (D400).

first: Anne

last: Ree


title: Exogenous Sulfide Reverses the Alteration of Transcriptional Profiling of the des1-1 Mutant (Arabidopsis thaliana)

status: Public on Apr 25 2013

city: Sevilla

first: Cecilia

last: Gotor

address: Avda. Américo Vespucio, 49

institute: Instituto de Bioquímica Vegetal y Fotosíntesis

summary: Arabidopsis thaliana cells contain different O-acetylserine(thiol)lyase (OASTL) enzymes that catalyze the biosynthesis of cysteine. Recently, we have deeply investigated about one of the minor OASTL-like protein located in the cytosol, named DES1, highlighting some important clues about its metabolic function. We have demonstrated that DES1 catalyzes the desulfuration of L-cysteine to sulfide plus ammonia and pyruvate, instead of the biosynthesis of Cys, and thus, is a novel L-cysteine desulfhydrase (EC 4.4.1.1). The functionality of DES1 is being revealed by the phenotype of the T-DNA insertion mutants des1-1 and des1-2. We have performed a comparative transcriptomic analysis on leaves of the des1-1 and Col-0 wild type plants grown for 30 days under long-day conditions. The normalized data from the replicates showed differential expression of 1614 genes in the des1-1 mutant, with 701 genes down-regulated and 913 genes up-regulated by more than twofold, with a False Discovery Rate (FDR) of < 0.05 and an intensity signal restriction of lgSignal >7. This des1-1 transcriptional profile show a strong alteration when compared to a previous comparative transcriptomic analysis performed on leaves of the des1-1 and Col-0 wild type plants grown for 20 days under identical long-day conditions (GSE 19244). We have also performed a comparative transcriptomic analysis on leaves of the des1-1 and Col-0 wild type plants grown for 20 days and treated with sodium sulfide for 10 additional days. The comparison of the transcriptional profile of des1-1+Na2S versus Col-0+Na2S clearly shows that exogenous sulfide reversed the transcriptional level differences between the mutant and the wild type to reach similar transcriptional patterns as the array GSE19244. Our results suggest a role of sulfide as transcriptional regulator in the des1-1 mutant background.

overall_design: Using the Affymetrix ATH1 GeneChips, we performed two comparative transcriptomic analyses on leaves of the des1-1 and Col-0 wild type plants grown on soil under long-day conditions. One was performed on plants grown for 30 days and the other on plants grown for 20 days and treated for 10 additional days with 200 mM Na2S. Three biological replicates were performed for each sample and hybridized to the chips. We made the comparison of des1-1 versus wild-type and des1-1+Na2S versus wild-type+Na2S to classify the differently expressed genes in the mutant plant.

first: Consolación

last: Álvarez

first: Irene

last: García

first: Luis

middle: C

last: Romero


title: Apurinic/apyrimidinic endonuclease/redox factor-1 (Ape1/Ref-1) activates Notch signaling through Jagged1 expression and promotes colon cancer progression

status: Public on Apr 17 2013

city: Gwangju

first: Ho Jin

last: You

address: Seosuk-dong 375

department: Pharmacology

country: South Korea

institute: Chosun University School of Medicine

summary: To investigate the possible role of Ape1/Ref-1 in tumorigenicity of colon cancer and explored the oncogenic mechanism of Ape1/Ref-1 in colon cancer cells.

overall_design: Control and Ref-1 overexpressing SW480cells, control and Ref-1-deficient SW480 cells. Duplicate

first: M

last: Kim

first: H

first: S

middle: P

last: Yoon

last: Lim

last: Cha

first: Y

last: Jeon

middle: G

last: Park

first: I

last: Chang


title: Expression data generated from post-mortem human brain tissue originating from neurologically and neuropathologically control individuals

status: Public on Jun 27 2013

city: London

first: Mina

last: Ryten

address: Queen Square

department: Department of Molecular Neuroscience

country: United Kingdom

institute: UCL Institute of Neurology

summary:
This data set was generated by the UK Brain Expression Consortium and consists of gene expression data generated from post-mortem human brain samples, dissected from 10 brain regions and originating from a large cohort of neurologically and neuropathologically normal individuals.
The UK Brain Expression Consortium has generated gene expression data on a large cohort of neurologically and neuropathologically normal individuals in order to better understand gene expression differences across the human brain.

This SuperSeries is composed of the SubSeries listed below.

overall_design: 1231 samples are analysed in total and these samples originate from 134 Caucasian individuals. From each individual, up to ten brain regions were sampled and analysed. Gene-level and exon-level analyses result in 2462 GEO Samples.

first: Daniah

last: Trabzuni

first: Robert

last: Walker

first: Colin

last: Smith

first: Adaikalavan

last: Ramasamy

first: Sebastian

last: Guelfi

first: Michael

middle: E

last: Weale

first: John

last: Hardy


title: Populus tremula (European aspen) shows no evidence of sexual dimorphism in gene expression, phenotype, secondary defence or herbivory

status: Public on Apr 20 2013

city: Umeå

first: Nathaniel

middle: Robert

last: Street

address: Umeå Plant Science Centre

department: Plant Physiology

country: Sweden

institute: Umeå University

summary: We profiled gene expression and phenotypic traits in Populus tremula to examine evidence of sexual dimorphism and sex biased gene expression.

overall_design: Ten trees of each sex were sampled and profiled using single channel microarrays

middle: R


title: Identification of novel candidate oncogenes in chromosomal region 17p11.2-p12 in human osteosarcoma

status: Public on Apr 15 2013

city: Amsterdam

first: Joeri

last: Both

state: Noord Holland

address: Meibergdreef 9

department: Genome Analysis

country: Netherlands

institute: Amsterdam Medical Center

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

summary: in 25% - 30% of all OS cases the chromosome region 17p11.2-p12 is aberrant. Using SNP array in conjunction with expression microarrays we try to identify genes which can be classified as oncogens or are in someway benificial to the survival of the tumor.

overall_design: To identify minimal significant amplified region(s) that is(are) aberrant in osteosarcoma tumorigenesis, with a special emphasis on but not limitied to chromosome region 17p11.2-p12

first: Thijs

last: Wu

first: Johannes

last: Bras

first: Gerard

last: Schaap

first: Frank

last: Baas

first: Theo

last: Hulsebos


title: Effects of fertility on gene expression and function of the bovine endometrium

status: Public on Apr 23 2013

city: Columbia

first: Thomas

last: Spencer

state: MO

address: 920 East Campus Drive

department: Animal Sciences

institute: University of Missouri

summary: To identify heifers of contrasting fertility, serial rounds of artificial insemination (AI) were conducted in 201 synchronized crossbred beef heifers.  The heifers were then fertility classified based on number of pregnancies detected on day 35 in the four AI opportunities.  The reproductive tracts of a subset of the classified heifers were obtained on day 14 of the estrous cycle.  Microarray analysis revealed differences in the endometrial transcriptome based on fertility classification.

overall_design: Endometrium from 36 fertility-classified heifers (highly fertile, n=14; subfertile, n=12; infertile, n=10) was analyzed for differences in their transcriptome using a bovine microarray.

first: Megan

last: Minten


title: RNA sequencing analysis of abdominal adipose tissue in 7 week old juvenile broiler chickens divergently selected for abdominal fatness or leanness

status: Public on Apr 16 2013

city: Newark

first: Larry

middle: Albert

last: Cogburn

state: DE

address: 531 South College Ave.

department: Animal and Food Sciences

institute: University of Delaware

summary: Chickens divergently selected for either high abdominal fat content (fat genotype) or low abdominal fat content (lean genotype) at Station Recherches Avicoles, Institut National de la Recherche Agronomique Nouzilly, France were used to profile abdominal fat gene expression at 7 weeks of age. The fat line (FL) and lean line (LL) chickens differ in various phenotypic and metabolic measurements, including abdominal fatness, plasma glycemia and triiodothyronine (T3). The FL and LL chickens represent unique models for characterizing biomedical and agricultural traits. Massively parallel RNA sequencing (RNA-Seq) was completed on an Illumina HiSeq 2000 System for transcription analysis of FL and LL abdominal fat. Statistical analysis was completed using CLC Genomics Workbench software. A total of 1,703 genes were differentially expressed in the FL versus LL adipose tissue [FDR<0.05 and fold change (FL/LL) > 1.2]. The differentially expressed genes include metabolic enzymes, acute phase proteins, growth factors, coagulation factors, immune factors, vasoregulators and transcription factors involved in various pathways. Several of the functional genes identified are also positional candidate genes within quantitative trait loci (QTL) in an F2 population created from an intercross of the FL and LL lines. Keywords: Divergently selected chickens, fatness, transcriptional profiling, differentially expressed genes

overall_design: Abdominal fat mRNA profiles of fat line (FL) and lean line (LL) chickens at 7 weeks of age were generated by deep sequencing (on an Illumina HiSeq 2000 system) employing several sequencing schemes to determine depth of coverage from 1, 4, and 8 multiplexed libraries per sequencing lane. Transcriptional analysis was completed by averaging short paired-end sequence reads (101 bp) for each bird across three sequencing depths.

first: C

last: Resnyk

last: Chen

first: H

last: Huang

middle: H

first: E

last: Bihan-Duval

first: M

last: Duclos

first: J

last: Simon

first: L


title: Sputum cell gene expression following allergen challenge

first: Sameer

last: Mathur

state: WI

address: 600 Highland Ave.

institute: University of Wisconsin-Madison

summary:
Sputum cells collected before (visit 2) and after (visit 4) allergen challenge in asthma patients were isolated and RNA purified for analysis on gene expression arrays.
Human subject recruitment part of NIH sponsored protocol as part of the Eosinophil Program Project Grant (PI: Dr. Nizar Jarjour)

overall_design: Sputum cell RNA collected from induced sputum cells before and 48 hours after whole-lung allergen challenge.

middle: K


title: Targeting IRAK1 as a therapeutic approach for Myelodysplastic Syndrome

city: Cincinnati

first: Garrett

last: Rhyasen

state: OHIO

address: 3333 Burnet Ave

institute: CCHMC

summary: Myelodysplastic Syndromes (MDS) result from expansion of defective hematopoietic stem/progenitor clones. There is an urgent need to develop targeted therapies capable of eliminating the defective MDS clones. We identified that IRAK1, an immune modulating kinase, is overexpressed and hyperactivated in MDS. MDS-propagating clones treated with a small-molecule IRAK1 inhibitor (IRAK1/4-Inh) exhibited impaired expansion and increased apoptosis, which coincided with TRAF6/NF-κB inhibition. Suppression of IRAK1, either by RNAi or with IRAK1/4-Inh, is selectively detrimental to MDS clones as normal CD34+ cells are preserved. Based on conclusions derived from an integrative gene expression analysis, we combined IRAK1 and BCL2 inhibitors and found that co-treatment collaboratively and selectively eliminated MDS clones. In summary, these findings implicate IRAK1 as a drugable target in MDS.

overall_design: MDSL cells were transduced with lentivirus encoding shRNA targeting human IRAK1 and a negative control (pLKO) for 2.5 days. GFP positive cells were sorted for RNA extraction, labeling, and hybridization. A total of four samples were included, and two groups are assigned. Two replicates are for each group. Comparison comprises mRNA expression profile of TRAF6 knockdown (shT6) v.s. control vector (pLKO). Additionally, MDSL cells were treated with either DMSO or IRAK inhibitor for 24hrs. Cells were subjected to RNA extraction, labeling, and hybridization. A total of four samples were included, and two groups are assigned.

first: Lyndsey

last: Bolanos

first: Jing

last: Fang

first: Andres

last: Jerez

first: Mark

last: Wunderlich

first: Carmela

last: Rigolino

first: Lesley

last: Matthews

first: Marc

last: Ferrer

first: Noel

last: Southall

first: Rajarshi

last: Guha

first: Johnathan

last: Keller

first: Craig

last: Thomas

first: Levi

last: Beverly

first: Agostino

last: Cortelezzi

first: Esther

last: Olivia

first: Maria

last: Cuzzola

first: Jaroslaw

last: Maciejewski

first: James

last: Mulloy

first: Daniel

middle: T

last: Starczynowski


title: MicroRNA-dependent regulation of transcription in lung cancer

city: Seville

first: Sonia

last: Molina-Pinelo

address: Avda. MAnuel Siurot s/n

institute: IBIS

summary: The objective is to establish robust transcriptional regulation differences between squamous cell carcinoma (SCC) and adenocarcinoma (ADC) by studying miRNA and concurrent transcriptional profiles. This series represents the miRNA profiles only (not mRNA). The related mRNA data is in Series GSE42998.

overall_design: The present study was performed in 44 tumour samples following surgical resection for clinical early stage NSCLC (20 lung adenocarcinoma and 24 squamous cell lung cancer). Mature human miRNA expression was detected and quantified using the TaqMan® Low Density Arrays (TLDA). The Human MicroRNA Card Set v2.0 array is a two card set containing a total of 384 TaqMan® MicroRNA Assays per card to enable accurate quantification of 667 human microRNAs, all catalogued in the miRBase database.Expression of target miRNAs was normalized in relation to the expression of RNU48.  Cycle threshold (Ct) values were calculated using the SDS software v.2.3 using automatic baseline settings and a threshold of 0.2. Relative quantification of miRNA expression was calculated by the 2−ΔCt method (Applied Biosystems user bulletin no. 2 (P/N 4303859)).

first: Gabriel

last: Gutiérrez

first: M

middle: D

last: Pastor

first: Marta

last: Hergueta

first: Gema

last: Moreno-Bueno

first: Rocío

last: García-Carbonero

first: Ana

last: Nogal

last: Suárez

last: Salinas

first: Francisco

last: Pozo-Rodríguez

first: Fernando

last: Lopez-Rios

last: Agulló-Ortuño

first: José

last: Palacios

first: Amancio

last: Carnero

first: Luis

last: Paz-Ares


title: Expression data from bovine liver

status: Public on Apr 09 2013

city: São Paulo

first: Carla

last: Piccinato

state: SP

address: Rua Albert Einstein, 627- 2SS Bloco A

department: Instituto de Ensino e Pesquisa Albert Einstein

country: Brazil

institute: Hospital Albert Einstein

summary: Female sex steroid hormones, estradiol-17β (E2) and progesterone (P4) regulate reproductive function and gene expression in a broad range of tissues. Given the central role of the liver in regulating homeostasis including steroid hormone metabolism, we sought to understand how E2-17β and P4 interact to affect global gene expression in liver. Eight ovariectomized cows were randomly assigned to 4 treatment groups applied in a replicated Latin Square design: 1) No hormone supplementation, 2) E2-17β treatment (ear implant), 3) P4 treatment (intravaginal inserts), and 4) E2-17β combined with P4. After 14 d of treatment, liver biopsies were collected, allowing 28 d intervals between periods. Changes in gene expression in the liver biopsies were monitored using Affymetrix bovine-specific arrays. Treatment with E2-17β altered expression of 479 genes, P4 472 genes, and combined treatment significantly altered expression of 468 genes. In total, 578 genes exhibited altered expression including a remarkable number (346 genes) that responded similarly to E2-17β, P4, or combined treatment. Additional evidence for similar gene expression effects of E2-17ß and/or P4 were: principal component analysis placed almost every treatment array at a substantial distance from control arrays; Venn diagrams indicated overall treatment effects for most regulated genes; clustering analysis indicated the two major clusters had all treatments upregulating (cluster 1; 172 genes) or downregulating (cluster 2: 173 genes) expression. Thus, unexpectedly, common biological pathways are regulated by E2-17β and/or P4 in liver. Future studies are needed to elucidate mechanism(s) responsible for overlapping actions of E2-17β and P4 on the liver transcriptome. KEYWORDS: estradiol, progesterone, global gene expression, liver, cows.

overall_design: randomized Latin square design with 4 treatment groups

first: Milo

last: Wiltbank


title: Gene expression in synthetic nasal medium

status: Public on Apr 10 2013

city: Tuebingen

first: Bernhard

last: Krismer

address: Elfriede-Aulhorn-Str. 6

department: IMIT

institute: University of Tuebingen

summary:
Staphylococcus aureus prefers the human anterior nares as its habitat, but nothing is known about the nutritional situation in this ecological niche. Analysis of nasal secretions showed a complex mixture of nutrients at low concentration. Based on these findings a synthetic nasal medium (SNM) was composed, mimicking nasal secretions.
We used microarrays in order to investigate pathways and expression patterns important in a synthetic medium mimicking nasal secretions compared to standard laboratory complex medium

overall_design: Staphylococcus aureus USA300 was inoculated in complex medium (BM) or synthetic nasal medium (SNM) to an OD578nm of 0.005 and grown under aerobic conditions until OD578nm of 0.02. RNA was stabilized and extracted at this early growth phase and hybridization was made on Affymetrix microarrays. The aim was to identify genes which are important during growth under the limited conditions present during colonization of human nares

first: Andreas

last: Peschel


title: The Neuron-specific chromatin regulatory subunit BAF53b is necessary for synaptic plasticity and memory.

status: Public on Mar 24 2013

city: Vancouver

first: Annie

middle: Vogel

last: Ciernia

state: British Columbia

address: 2215 Wesbrook Mall room 4550, Centre for Brain Health

country: Canada

institute: University of British Columbia

summary: We performed an RNA Sequencing experiment on dorsal hippocampal tissue from four groups of animals: Baf53b+/- homecage (Baf53b+/- HC); Baf53b+/- behavior (Baf53b+/- Beh); wildtype homecage (WT HC); and wildtype behavior (WT Beh).  Homecage animals were sacrificed directly from the animal's cage. Behavior animals were sacrificed thirty minutes following Object Location Memory training.  The objective of this study was to examine activity regulated gene expression following a learning event (HC vs Beh) in wildtype and Baf53b+/- mutant mice.

overall_design: Examination of gene expression following a learning event in wildtype and Baf53b+/- mutant mice in dorsal hippocampus.

last: Vogel-Ciernia

first: Marcelo

last: Wood

first: Christophe

last: Magnan

first: Pierre

last: Baldi


title: Genotype modulates gene expression profiles in the uterus in response to preconceptual folate supplementation.

status: Public on Mar 31 2013

city: Baton Rouge

first: Claudia

last: Kappen

state: LA

address: 6400 Perkins Road

department: Developmental Biology

institute: Pennington Biomedical Research Center

summary: Periconceptual supplementation of women with folate is considered a great success for public health. Higher folate status, either by supplementation, or via the mandatory fortification of grain products in the United States, has lead to significant reduction in the incidence of neural tube defects. Besides birth defects, folate deficiency has been linked to a variety of morbidities, most notably to increased risk for cancer. However, recent evidence suggests that excess folate may be detrimental - for birth defect incidence or in the progression of cancer. How folate mediates beneficial or detrimental effects is not well understood. It is also unknown what molecular responses are elicited in women taking folate supplements, and thus experience a bolus of folate on top of the status achieved by fortification.  To characterize this response, we performed gene expression profiling experiments on uterus tissue of pregnant mice after a preconceptional regimen of supplementation with folinic acid. We suggest that folinic acid supplementation affects expression of genes that contribute to protein synthesis and localization, genes that play a role for mitochondrial biology and oxidative phosphorylation, and genes encoding nucleotide-binding proteins, including protein kinases and GTP-binding intracellular signaling factors. The extent of such a response is strongly modulated by the genetic background. Finally, we suggest that folinic acid supplementation in this paradigm may affect histone methylation status, a potential avenue to mechanisms of gene regulation.

overall_design: Gene expression profiles were generated from uterus tissue. Female mice were either C57BL/6 wildtype, or homozygous for a Folr4 mutation, and received injections of either saline of folininc acid, respectively.

first: J

middle: M

last: Salbaum


title: Transcriptional profiling of abdominal adipose tissue in juvenile broiler chickens divergently selected for high or low body weight

status: Public on Apr 06 2013

first: Larry

last: Cogburn

summary: Chickens divergently selected for either high growth (HG genotype) or low growth (LG genotype) by F.H. Ricard at SRA-INRA, Nouzilly France were used for time-course transcriptional profiling of abdominal fat during juvenile development (1 to 11 weeks of age) to identify differentially expressed genes. The HG and LG chickens are different in various phenotypic and metabolic measurements, including growth rate, abdominal fat, plasma glycemia, insulinemia, T4, T3, triglyceride and NEFA. Thus, the HG and LG chickens are valuable as a model for biomedical and agricultural traits. The Del-Mar 14K Chicken Integrated Systems microarrays were used for a transcriptional scan in abdominal adipose during juvenile development using a balanced block hybridization design. Log2-transformed fluorescence intensities were analyzed with the linear mixed model (MIXED) procedure in SAS (SAS Institute Inc., Cary, NC, USA). A total of 3,957 differentially expressed functional genes were identified (FDR<0.05) as having a significant effect of age (2,918), genotype (312), or an age by genotype interaction (727). The differentially expressed genes include adipokines, metabolic enzymes, acute phase proteins, growth factors, coagulation factors, immune factors and transcription factors involved in various pathways.   Keywords: abdominal fat, divergently selected chickens, growth, transcriptional profiling, differentially expressed genes, lipogenesis

overall_design: A balanced block design was used for microarray hybridizations, where half of the birds of each genotype and age were labeled with Alexa Flour 647 (red) and the other half with Alexa Flour 555 (green). Four biological replicates were used for each genotype (HG or LG) at six different ages (1, 3, 5, 7, 9 and 11 wk).

first: Christopher

middle: W

last: Resnyk

first: Wilfrid

last: Carre

first: Xiaofei

last: Wang

first: Jean

last: Simon

first: Sam

last: Aggrey

first: Tom

last: Porter


title: Expression profile of HeLa THOC1-depleted  stable cell lines (HeTH-4)

status: Public on Jan 31 2013

city: SEVILLA

first: María

last: Domínguez

state: SEVILLA

address: C/AMÉRICO VESPUCIO S/N

department: BIOLOGÍA MOLECULAR

institute: CABIMER

summary:
THO/TREX is an eukaryotic conserved complex with a role at the interface between transcription and mRNP biogenesis/export that in yeast has been shown to play an important role in preventing transcription-associated genome instability. However, whereas a role of mammalian THO/TREX in mRNA processing and export seems clear, a role on either transcription or genome stability is still being argued. In this work we show, by microarray analysis of gene expression, that THO depletion in human cell lines has a global effect on transcription, with a significant impact on genes involved in transcription and DNA metabolism.
We performed a microarray analysis of gene expression on  THOC1-depleted cells in order to know if there was a change in the genome-wide expression profile. Our data data suggest that the absence of THOC1 has a global effect on transcription process

overall_design: Three repeats HeTH-4 and three repeats of HeTH-4 +DOX (THOC1-depleted cells)

middle: S

last: Domínguez-Sánchez

first: Rosa

last: Luna Varo

first: Andrés

middle: A

last: López


title: Expression data from 6-month Helicobacter felis-infected WT and Gli1-/- mouse stomachs

status: Public on Jan 24 2013

city: Ann Arbor

first: Mohamad

last: El-Zaatari

address: 1150 W Medical Ctr Dr

institute: University of Michigan

summary: Gli1 is necessary for the progression from chronic gastric inflammation to metaplasia in the stomach. We therefore compared the expression patterns between 6-month H. felis infected WT and Gli1-/- stomachs.

overall_design: Pooled tissue from the gastric fundi of 3 mice per group. Groups are WT, WT + H. felis (6 months), Gli1-/-, and Gli1-/- +H. felis (6 months). All the infected and control mice were obtained from the same experiment.

first: Merchant

last: Juanita

first: El-Zaatari

last: Mohamad


title: Inferring Epitopes of a Polymorphic Antigen Amidst Broadly Cross-Reactive Antibodies Using Protein Microarrays: a Study of OspC Proteins of Borrelia burgdorferi

status: Public on Apr 12 2013

city: Irvine

first: Elisabeth

last: Baum

state: CA

address: Med Surge II

institute: University of California Irvine

summary: Epitope mapping studies aim to identify the binding sites of antibody-antigen interactions to enhance the development of vaccines, diagnostics and immunotherapeutic compounds.  However, mapping is a laborious process employing time- and resource-consuming ‘wet bench’ techniques or epitope prediction software that are still in their infancy. For polymorphic antigens, another challenge is characterizing cross-reactivity between epitopes, teasing out distinctions between broadly cross-reactive responses, limited cross-reactions among variants and the truly type-specific responses.  A refined understanding of cross-reactive antibody binding could guide the selection of the most informative subsets of variants for diagnostics and multivalent subunit vaccines. We explored the antibody binding reactivity of sera from human patients and Peromyscus leucopus rodents infected with Borrelia burgdorferi to the polymorphic outer surface protein C (OspC), an attractive candidate antigen for vaccine and improved diagnostics for Lyme disease. We constructed a protein microarray displaying 23 natural variants of OspC and quantified the degree of cross-reactive antibody binding between all pairs of variants, using Pearson correlation calculated on the reactivity values using three independent transforms of the raw data: (1) logarithmic, (2) rank, and (3) binary indicators. We observed that the global amino acid sequence identity between OspC pairs was a poor predictor of cross-reactive antibody binding. Then we asked if specific regions of the protein would better explain the observed cross-reactive binding and performed in silico screening of the linear sequence and 3-dimensional structure of OspC. This analysis pointed to the C-terminal helix of the structure as a major determinant of type-specific cross-reactive antibody binding. We developed bioinformatics methods to systematically analyze the relationship between local sequence/structure variation and cross-reactive antibody binding patterns among variants of a polymorphic antigen, and this method can be applied to other polymorphic antigens for which immune response data is available for multiple variants.

sample_organism:
Homo sapiens
Peromyscus leucopus

overall_design: Antibody profiling was performed on sera from Borrelia burgdorferi infected and non-infected humans and Peromyscus leucopus rodents against 23 variants of the surface protein OspC . For infected human serum samples, the OspC type of the infecting B. burgdorferi strain is unknown; for experimentally-infected P. leucopus serum samples, it is known. Of human serum samples, 55 were from infected individuals and 25 from naive controls. Of P. leucopus serum samples, 23 were from infected individuals and 7 were from naive controls.

first: Arlo

middle: Z

last: Randall

first: Michael

last: Zeller

first: Alan

last: Barbour


title: RNA deep sequencing reveals novel candidate genes and polymorphisms in boar testis and liver tissues with divergent androstenone levels.

status: Public on Feb 09 2013

city: Bonn

first: Sudeeep

last: Sahadevan

state: NRW

address: Endenicher Allee 15

department: Institute of Animal Science

institute: University of Bonn

summary: Boar taint described as an offensive odor that is released while cooking pork. Androstenone, a steroid mainly synthesized in testis and metabolized in liver is one of the major causes of boar taint. The aim of the present study was to investigate transcriptome differences in boar testis and liver tissues with divergent androstenone levels using RNA deep sequencing (RNA-Seq). For this purpose, mRNA expression from testis and liver  tissue samples from 10 boars, 5 samples  each for high and low androstenone levels were quantified and analyzed. The results shows that in testis samples 46 genes were differentially regulated whereas 25 genes showed differential expression in the liver.  Digital gene expression analysis identified genes in keratin family, desmoplakin and Interferon-induced protein family for as candidate genes for low androstenone testis sample and genes in flavin monooxygenease family, cytochrome P450 family and hydroxysteroid dehydrogenase family as candidate genes for low androstenone liver sample. Additionally, the results revealed that mutations in  genes IRG6, DSP, IFIT2 were specific for low androstenone testis tissues and mutations in genes FMO5, HIST1H4K and TSKU were specific for low androstenone  liver samples.

overall_design: Testis and liver mRNA profile of high and low androstenone level were generated by RNA deep sequencing, in five animal for each group, Ilumina HiSeq 2000

first: Asep

last: Gunawan

first: Sudeep

first: Christiane

last: Neuhoff

first: Cristiane

last: Große-Brinkhaus

first: Ahmed

last: Gad

first: Luc

last: Frieden

first: Dawit

last: Tesfaye

first: Ernst

last: Tholen

first: Christian

last: Looft

first: Karl

last: Schellander

first: Mehmet

middle: U

last: Cinar


title: Ler regulation in EPEC

city: Birmingham

first: Chrystala

last: Constantinidou

department: School of Biosciences

institute: University of Birmingham

summary: Transcriptional profiling of wt and ler- EPEC and O157 E. coli strains at mid log and early stationary growth phases

sample_organism:
Escherichia coli O157:H7 str. EDL933
Escherichia coli O127:H6 str. E2348/69

overall_design: wt vs. Ler- at OD 0.3 and 0.9. Biological replicates: 4 independently grown. Four replicates per array.

first: C


title: Laser Capture Microdissection-Reduced Representation Bisulfite Sequencing (LCM-RRBS) maps changes in DNA methylation associated with gonadectomy-induced adrenocortical neoplasia in the mouse

status: Public on Mar 21 2013

city: St. Louis

first: Maximiliaan

last: Schillebeeckx

address: 4444 Forest Parkway

department: Genetics

institute: Washington University in St. Louis

summary: DNA methylation is a mechanism for long-term transcriptional regulation and is required for normal cellular differentiation. Failure to properly establish or maintain DNA methylation patterns leads to cell dysfunction and diseases such as cancer. Identifying DNA methylation signatures in complex tissues can be challenging due to inaccurate cell enrichment methods and low DNA yields. We have developed a technique called Laser Capture Microdissection-Reduced Representation Bisulfite Sequencing (LCM-RRBS) for the multiplexed interrogation of the DNA methylation status of CpG Islands and promoters. LCM-RRBS accurately and reproducibly profiles genome-wide methylation of DNA extracted from microdissected fresh frozen or formalin-fixed paraffin-embedded tissue samples. To demonstrate the utility of LCM-RRBS, we characterized changes in DNA methylation associated with gonadectomy-induced adrenocortical neoplasia in the mouse. Compared to adjacent normal tissue, the adrenocortical tumors showed reproducible gains and losses of DNA methylation at genes involved in cell differentiation and organ development. LCM-RRBS is a rapid, cost-effective, and sensitive technique for analyzing DNA methylation in heterogeneous tissues and will facilitate the investigation of DNA methylation in cancer and organ development.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: Laser capture microdissection-reduced representation bisulfite sequencing and reduced representation bisulfite sequencing on human blood leukocyte, human endometrial tumor, mouse liver tissue, and mouse normal and neoplastic adrenal tissue

first: Robi

last: Mitra


title: Kruppel-like factor 5 is Required for Villus Formation and Terminal Differentiation of the Intestinal Epithelium

first: Yan

last: Xu

state: OH

institute: Cincinnati Children's Hospital Medical Center

summary:
To identify putative KLF5 target genes that may mediate villus morphogenesis and epithelial maturation, we performed microarray analysis on intestinal samples isolated on E14.5, prior to the initiation of villus formation.
Total RNA was isolated from dissected intestine segments located ~1.5 cm anterior to the cecum from E14.5 Klf5D/D and Klf5wt/wtShhEGFP/Cre+ embryos (n=3 samples/genotype, each sample a pool of two intestines). Gene expression profiles were compared using Affymetrix Mouse Gene 1.0 ST Array.
Genes involved in the regulation of "epithelial cell differentiation/maturation”, “cell adhesion”, and “lipid synthesis, metabolism, and localization”. Consistent with the lack of terminally differentiated cell types in the intestines of E18.5 Klf5D/D fetuses.

first: Sheila

last: Bell

first: Liqian

last: Zhang

first: Valerie

last: Besnard

first: Susan

last: Wert

first: Noah

last: Shroyer

first: Jeffrey

last: Whitsett


title: Pharmacogenomic profiling of Akt in helper T cell activation

status: Public on Mar 16 2013

city: Pittsburgh

first: Jing

last: Cheng

address: 3550 Terrace street

institute: University of Pittsburgh

summary: 1) identify, at the genome-wide level, the genes that are differentially expressed in activated Th cells, with or without Akt inhibition and 2) conduct bioinformatics analyses to identify the pathways and possible mechanisms involved.

overall_design: First identify the differentially expressed genes  at 2,6 and 12h time points after TCR stimulation compared with 0h time point in the absence of Akti1/2 and presence of Akti1/2 , then identify differentially expressed gene sets that were dependent on Akt among the three different time point groups . There are duplicate samples for each time point.

first: Lawrence

middle: P

last: Kane


title: microRNA expression in human brain development

city: Albuquerque

first: shannon

last: bruse

state: New Mexico

address: 2425 ridgecrest drive SE

institute: lovelace respiratory research institute

summary: Profile the expression of micoRNAs in the human brain at prenatal, early childhood, and adult timepoints

overall_design: 37 prenatal cerebral tissue samples, 11 postnatal cerebral tissue samples, 2 adult total brain samples (FirstChoice Human Brain Reference RNA cat# AM6050 and FirstChoice Human Brain Total RNA cat# AM7962*. *The current FirstChoice Human Brain Total RNA (2013), is from a 78 year old white female, while the FirstChoice Total RNA used in this deposited data set was from an 81 year old white male, which is no longer available through Ambion/Life Technologies.)

first: Shannon

last: Bruse

first: Michael

last: Moreau

first: Linda

last: Brzustowicz


title: Gene expression analysis of human microRNA-150 expression in PL21 and HL60 cells

status: Public on Jan 15 2013

city: Seattle

first: Vivian

middle: G.

last: Oehler

state: WA

address: 1100 Fairview Ave. North, D4-100

department: Clinical Research Division

institute: Fred Hutchinson Cancer Research Center

summary: Analysis of gene expression changes associated with lentiviral vector mediated expression of  pre-microRNA-150 expression in the AML cell lines PL21 and HL60 cells. To identify genes, direct putative miRNA-150 targets, biological and molecular functions and pathways that distinguish cells that express miR-150 from those that do not.

overall_design: Total RNA isolated from HL60 or PL21 cells transduced with pre-microRNA-150 or empty vector control and assayed by gene expresssion analysis 20 days post transduction. Two replicates were performed for each condition (miR-150 and control) in each of two cell lines (HL60 and PL21).

first: V

middle: G

last: Morris


title: Comparison study between Uremic patient with Healthy control

city: Stockholm

first: Elham

last: Dadfar

institute: Karolinska Institutet

summary: Patients with chronic kidney disease (CKD) have significantly increased morbidity and mortality resulting from infections and cardiovascular diseases. Since monocytes play an essential role in host immunity, this study was directed to explore the gene expression profile and to identify differences in activated pathways in monocytes relevant to the pathophysiology of atherosclerosis and increased susceptibility to infections. Monocytes from CKD patients (stages 4 and 5, eGFR <20 ml/min x 1.73 m2) and healthy donors were collected from peripheral blood. Microarray gene expression profile was done and data were interpreted by Genespring software and Panther tools website. Western blot was done to validate the pathway members. The results demonstrated that 487 and 258 genes were differentially up- and down regulated respectively in the patient group. Pathways involved in the inflammatory response were highly expressed and the Wnt/β- catenin signaling pathway was the most significant pathway expressed in the patient group (P=0.02). Since this pathway has been attributed to a variety of inflammatory manifestations, the current finding may contribute to dysfunctional monocytes in CKD patients. To develop strategies to interfere with this pathway may improve host immunity and prevent cardiovascular complications in CKD patients.

overall_design: Six gene expression Affymetrix chip were used. Three for each group

first: Heevy

last: Al-Chaqmaqchi

first: Ali

last: Moshfegh

first: Josefin

last: Paulsson

first: Moustapha

last: Hassan

first: Stefan

last: Jacobson

first: Joachim

last: Lundahl


title: Gene expression profile in spleens of mice 24 hours after total body irradiation.

status: Public on Jan 08 2013

city: Salt Lake City

first: Thai

last: Cao

state: UT

address: 30 North 1900 East, SOM5C402

institute: University of Utah

summary: A major challenge in bone allogeneic marrow (BM) transplantation is overcoming engraftment resistance to avoid the clinical problem of graft rejection.  Identifying genes and pathways that regulate BM engraftment may reveal molecular targets for overcoming these engraftment barriers.  Previously, we developed a mouse model of BM transplantation that utilizes recipient conditioning with non-myeloablative total body irradiation followed by transplantation of allogeneic BM cells.  We defined TBI doses that lead to graft rejection, that are permissive for engraftment, and mouse strain variation with regards to the permissive TBI dose.  We now report gene expression analysis, using the Agilent Mouse 8x60K v3 expression arrays, in spleen of mice conditioned with TBI doses for evaluation in correlation to the expected engraftment phenotype.  The spleens of mice given TBI demonstrated extensive differential gene expression, compared with un-irradiated controls, at both multiple testing-corrected P < .05 and fold change greater than or equal to  2 levels. Functional analysis revealed significant enrichment for up-regulation of canonical pathways involved in inflammation, even when treated with TBI doses not permissive for engraftment.  Consistent with this the most significantly associated upstream regulators included lipopolysaccharide, tumor necrosis factor, and a toll-like receptor.  Unique to engrafting mice, however, were enrichment for a down-regulated canonical pathway related to B-cell development.  Results from this analysis have identified canonical pathways and upstream regulators of BM engraftment in mice and may lead to new approaches to overcome the problem of graft rejection complicating clinical BM transplantation.

overall_design: Each individual sample was pooled from 3 mice and performed in triplicate for each experimental group (TBI 300 cGy, 400 cGy, or 500 cGy) and for each strain mice (BALB.K or B10.BR)  for statistical analysis.  Additional arrays were perfromed for TBI 800 cGy (BALB.K) and TBI 900 cGy (B10.BR) for anlaysis of gene expressive after myeloablative condition.


title: Mouse Diversity Array SNP Genotyping of B10.BALBChr16 and BALB.B10Chr16 Reciprocal Consomic Strain Mice

status: Public on Jan 10 2013

summary: To identify novel mechanisms regulating allogeneic hematopoietic cell engraftment, we previously used a forward genetic approach and described identification, in mice, of the Bmgr5 bone marrow (BM) engraftment quantitative trait locus (QTL).  This QTL confers dominant and large allele effects for engraftment susceptibility.  It was localized to chromosome 16 by classical quantitative genetic techniques in a segregating backcross bred from susceptible BALB.K and resistant B10.BR mice.  We now report verification of the Bmgr5 QTL using reciprocal chromosome 16 consomic strains.  The BM engraftment phenotype in these consomic mice shows that Bmgr5 susceptibility alleles are not only sufficient but also indispensable for conferring permissiveness for allogeneic BM engraftment.  Using panels of congenic mice, we resolved the Bmgr5 QTL into two separate subloci, termed Bmgr5a and Bmgr5b, each conferring permissiveness for the engraftment phenotype and both fine mapped to an interval amenable to positional cloning.  Candidate Bmgr5 genes were then prioritized using whole exome DNA sequencing and microarray gene expression profiling.  Further studies are needed to elucidate the genetic interaction between Bmgr5a and Bmgr5b and identify causative genes and underlying gene variants.  This may lead to new approaches for overcoming the problem of graft rejection in clinical hematopoietic cell transplantation.

overall_design: B10.BALBChr16 and BALB.B10Chr16 consomic strain mice were constructed in our laboratory for validation of bone marrow engraftment and graft-vs-host diseaes QTLs.  The parental strains for consomic line construction were B10.BR (B10.BR-H2k H2-T18a/SgSnJJrep) and BALB.K (C.C3-H2k/LilMcdJ).  The JAX Mouse Diveristy 620K SNP Array was used to verify adequate removal of residual background heterozygosity.  Liver DNA was delivered to JAX Mouse Diversity Genotyping Array Service (Jackson Laboratory) for the SNP Array genotyping.


title: Niche-dependent expression profiles of intratumoral heterogenous ovarian clear cell carcinoma cells

status: Public on Jan 07 2013

city: Haifa

first: Maty

last: Tzukerman

address: Efron, 1

country: Israel

institute: Technion

summary: Exploring the expression profile of ovarian clear cell carcinoma cancer cell subpopulations- derived tumors grown within a murine and a human cellular tissues.

overall_design: RNA samples were obtained from laser micro-dissected from two cancer cell subpopulations (CCSPs C12 and C13)- derived tumors that developed within a murine (intratumoral) and a human (intra-teratoma) and from  in vitro grown cells;  a total of 9 RNA samples of CCSP's C12 and 9 RNA samples of CCSP's C13 .

first: Sagi

last: Abelson

first: Yeela

last: Shamai

first: Liron

last: Berger

first: Karl

last: Skorecki


title: Predicted signaling pathways involved in the pathogenesis of meningiomas and EGFL6 as a potential novel serum biomarker for benign meningiomas

status: Public on Jan 01 2013

city: Shanghai

first: Xuanchun

last: Wang

address: 12 Wulumuqi Road (Middle)

institute: Huashan Hospital

summary: Purpose: In this study, we try to investigate the possible signaling pathways involved in the tumorigenesis of fibroblastic and anaplastic meningiomas. We also attempt to investigate EGFL6 gene expression in brain arachnoidal tissues and various tumors and to measure EGFL6 levels in serum samples from healthy people and patients with various tumors by using ELISA.  Experimental Design: Differential gene expression profiles between meningiomas and brain arachnoidal tissues were established by using Affymetrix GeneChip Human U133 Plus 2.0 Array. KEGG pathway analysis was performed to identify potential gene pathways that may be involved in the pathogenesis of meningiomas. Quantitative real-time PCR (qRT-PCR) was performed to validate the differentially expressed genes in the KEGG pathways. EGFL6 mRNA levels were also determined in brain arachnoidal tissues, meningiomas, and other tumors by qRT-PCR. EGFL6 levels were measured in serum samples from healthy people and patients with various tumors by using ELISA.   Results: Fibroblastic meningioma exhibited upregulated PI3K/Akt and TGFβ signaling pathways, and accelerated G1/S progression cell cycle. KEGG analysis also demonstrated that focal adhesion and ECM-receptor interaction pathways were activated in anaplastic meningioma. Benign meningiomas had significantly higher levels of EGFL6 mRNA than brain arachnoidal tissues and atypical and anaplastic meningiomas (P<0.001). EGFL6 gene was also highly expressed in ovarian cancer, but expressed lowly in all other investigated tumors. EGFL6 was hardly detectable in serum samples of healthy people. The mean serum EGFL6 concentration was 675, 118, and 126 pg/ml in patients with benign, atypical, and anaplastic meningiomas respectively. Patients with ovarian cancers also had high serum EGFL6 levels (mean concentration: 617 pg/ml). Patients with all other investigated tumors, however, had low levels of serum EGFL6 with mean concentration less than 240 pg/ml.   Conclusion: We proposed that deregulation of cell cycle and PI3K/Akt pathways might play important roles in the tumorigenesis of fibroblastic meningioma. It was also suggested that the activated integrin-mediated signaling pathways were involved in the pathogenesis of anaplastic meningioma. We presented evidence that EGFL6 might serve as a novel serum biomarker for benign meningioma and ovarian cancer. It was also suggested that EGFL6 could help discriminate benignancy or malignancy of meningiomas before surgery or at early time points.

first: Ye

last: Gong


title: Transcriptoma comparison of mantle cell lymphoma of c-myc-3'RR/Cdk4R24C mice and c-myc-3'RR/p53+/- mice

city: Valbonne - Sophia-Antipolis

first: Kevin

last: Lebrigand

address: 660 route des lucioles

country: France

institute: IPMC/CNRS

summary: Mantle cell lymphoma (MCL) is a B cell malignancy characterized by a monoclonal proliferation of lymphocytes with co-expression of CD5, CD43 but not CD23. We have developed two murine models of MCL-like lymphoma.  Breeding Cdk4R24C mice (a knock-in strain that express a Cdk4 protein resistant to inhibition by p16INK4a and other INK4 family members) with c-myc-3’RR transgenic mice (prone to develop aggressive Burkitt lymphoma-like lymphoma) leads in c-myc/Cdk4R24C mice to development of clonal blastoid MCL-like lymphoma. Breeding p53+/- mice with c-myc-3’RR transgenic mice lead to the development of several mature B cell lymphomas including MCL. In this study we compare MCL transcriptomas of c-myc-3'RR/Cdk4R24C mice and c-myc-3'RR/p53+/- mice.

overall_design: B splenocytes from 2 c-myc/Cdk4R24C lymphoma mice and 2  c-myc-3'RR/p53+/- mice were investigated

first: Yves

last: Denizot

first: P

last: Barbry

first: K


title: Epigenome analysis of Rett syndrome monozygotic twins samples

status: Public on Dec 27 2012

city: Chuoshi

first: Kunio

last: Miyake

state: Yamanashi

address: 1110 Shimokato

country: Japan

institute: Yamanashi University

type: Methylation profiling by genome tiling array

summary:
Genome wide DNA methylation profiling of  Rett syndrome monozygotic twins.
The Illumina Infinium 450k Human DNA methylation Beadchip v1.2 was used to obtain DNA methylation profiles in primary skin fibroblast cells from Rett syndrome monozygotic twins.

overall_design: Bisulphite converted DNA from the 2 samples were hybridised to the Illumina Infinium 450k Human Methylation Beadchip

first: Takeo

last: Kubota


title: Pancreatic cancer FG cells: Core 3 synthase stable expression vs vector control

status: Public on Nov 21 2012

city: Omaha

first: prakash

last: Radhakrishnan

state: NE

address: 985950 Nebraska Medical Center

department: Eppley Cancer Center

institute: University of Nebraska Medical Center

summary: Purpose: Core 3 derived glycans, a major type of O-glycan expressed by normal epithelial cells of the gastrointestinal tract, are downregulated during malignancy, because of loss of expression of functional β3-N-acetylglucosaminyltransferase-6 (core 3 synthase). We investigated the expression of core 3 synthase in normal pancreas and pancreatic cancer and evaluated the biological effects of re-expressing core 3 synthase in pancreatic cancer cells that had lost expression. Experimental Design: We determined that pancreatic tumors and tumor cell lines have lost expression of core 3 synthase. We therefore re-expressed in human pancreatic cancer cells (Capan-2 and FG) to investigate the contribution of core 3 glycans to malignant progression. Results: Pancreatic cancer cells expressing core 3 synthase showed reduced in vitro cell proliferation, migration and invasion compared with vector control cells. Expression of core 3 O-glycans induced altered expression of β1 integrin, decreased activation of focal adhesion kinase, led to the down regulation of expression of several genes including REG1α and FGFR3, and altered lamellipodia formation. The addition of a GlcNAc residue by core 3 synthase leads to the extension of the tumor associated Tn structure on MUC1. Orthotopic injection of FG cells expressing core 3 synthase into the pancreas of nude mice produced significantly smaller tumors and decreased metastasis to the surrounding tissues compared to vector control FG cells. Conclusions: These findings indicate that expression of core 3 derived O-glycans in pancreatic cancer cells suppresses tumor growth and metastasis through modulation of glycosylation of mucins and other cell surface and extracellular matrix proteins.

overall_design: Two-condition experiment, Core 3 synthase stable expression (C3)  vs. vector control (PLVX) cells. Biological replicates: 3 Core 3 synthase stable expression, 3 vector control, independently grown and harvested. One replicate per array.

first: Prakash

first: Paul

last: Grandgenet

first: Ashley

last: Mohr

first: Stephanie

last: Bunt

first: Fang

last: Yu

first: Michael

last: Hollingsworth


title: Effect of furfural on the Clostridium beijerinckii NCIMB 8052 transcriptome

status: Public on Dec 06 2012

city: Wooster

first: Yan

last: Zhang

address: 1680 Madison Avenue

institute: The Ohio State University

summary: Furfural is the prevalent microbial inhibitor generated during pretreatment and hydrolysis of lignocellulosic biomass to monomeric sugars, but the molecular response of Clostridium beijerinckii NCIMB 8052 to this compound is unknown. To discern the effect of furfural on C. beijerinckii and to  gain insights into the molecular mechanisms of action and detoxification, we studied the physiological changes of furfural-stressed cultures during acetone-butanol-ethanol (ABE) fermentation, and profiled differentially expressed genes by genome-wide transcriptional analysis. C. beijerinckii exposed to furfural stress during the acidogenic growth phase produced 13% more ABE than the unstressed control. The growth and ABE by C. beijerinckii ceased following exposure to furfural stress during the solventogenic growth phase. By comparing gene expression of furfural-stressed cultures to that of the unstressed control, at both the acidogenic and solventogenic phases, we ascertained that furfural induces expression of several genes including those that code for heat shock proteins, redox enzymes and cofactor associated proteins, and ATP-binding cassette transporters, and represses genes belonging to the phosphotransferase system, two-component system, chemotaxis and cell motility. Based on these results, we discuss the underpinning for furfural-mediated change in ABE fermentation by the solventogenic Clostridium species.

overall_design: C. beijerinckii 8052 pre-culture was incubated anaerobically to attain acidogenic or solventogenic growth phase. The culture was then subdivided into two bottles. One bottle was challenged with furfural and the other bottle was left unchallenged. After 3 h growth, C. beijerinckii 8052 samples were collected, during which the original concentration of furfural in the growth medium was reduced to more than half. Total RNA was isolated, purified, converted to enriched mRNA, and dye-coupled (Alexa Fluor 555) complementary cRNA. This was followed by hybridization and microarray data analysis.

first: Thaddeus

middle: C

last: Ezeji


title: Comparative Genome-Wide Transcriptional Analysis of Bilateral Internal Mammary Arteries

status: Public on Oct 31 2012

city: Boston

first: Lan

last: Hu

address: 450 Brookline Ave

institute: Dan-Farber Cancer Institute

summary: In Coronary Artery Bypass Grafting (CABG), the combined use of Left or Right Internal Mammary Artery (LIMA or RIMA) -collectively known as Bilateral IMAs (BIMAs)- provides a survival advantage over the LIMA alone. Several studies analyzed the gene expression in LIMAs and other conduits, however they either used a candidate gene approach or analyzed a small number of samples. Additionally, RIMA has never been analyzed compared to LIMA. Here we report a genome-wide transcriptional analysis of BIMA to investigate the expression profile of these conduits in patients undergoing CABG. Marginal differences were reported between LIMA and RIMA (p <0.05) using a linear model for microarray data. Ingenuity Pathway Assist (IPA) analysis found no consistent set of over-represented pathways and no trends in patterns of gene expression. As expected, in comparing the BIMAs to the aorta, we found differences in pathways and processes associated with atherosclerosis, inflammation, and cell signaling. Although evidence in favor of the use of BIMA in CABG has been available for over a decade, their routine use in clinical practice remains very low accounting for only 4% of CABG procedures in the US. Despite differences in embryologic development, our genome-wide transcriptional analysis, show marginal differences between LIMA and RIMA. Taken together, clinical and genomic analyses provide evidences that could impact the independent or combined use of the BIMAs as a conduit in CABG.

overall_design: We selected 32 patients from whom we had frozen archival tissue from aorta, LIMA, and RIMA in the Cardiovascular Blood and Tissue Bank at the Valley Columbia Heart Center . The mammary and aortic tissues were harvested at time of CABG. The surgeon dissected the two most distal aspects of LIMA and RIMA segments and obtained a ≥1cm sample for the tissue bank. The tissue sample was placed in a cryomold and processed as a “frozen section” specimen using standard OCT gel. Total RNA was extracted using Qiagen RNeasy Mini Kit, RNA integrity was assessed using the Agilent 2100 BioAnalyzer and RNA quantities and purity were determined using a NanoDrop Spectrophotometer. RNA samples were amplified using the NuGen Ovation RNA Amplification System V2 The resulting cDNA was labeled and hybridized to the Affymetrix U133A 2.0 GeneChip. 73 arrays at the end.

first: Juan

middle: B

last: Grau

first: John

last: Quackenbush

first: Giovanni

last: Ferrari

first: Christopher

last: Johnson

first: Andrew

last: Mak

first: Richard

last: Shaw

first: Kathleen

last: Sayles

last: Strobeck


title: Small Marine Neurotoxin Elicits Common Antibody Response in Zebrafish and Sea Lions

status: Public on Jan 03 2013

first: James

middle: William

last: MacDonald

address: 4225 Roosevelt Way NE

department: Environmental and Occupational Health Sciences

institute: University of Washington

summary: The neurotoxic amino acid, domoic acid, is naturally produced by marine phytoplankton and presents a significant health threat to marine mammal and human populations.  Currently, diagnostic tools to assess exposure are not available, yet concerns regarding health impacts associated with low-level repetitive exposure are growing.  Here we applied a laboratory zebrafish model to assess exposure to asymptomatic doses of domoic acid in a nine-month low-level repetitive exposure study.  Blood analyses, whole brain gene expression, and functional lymphocyte proliferation assays analyzed at 11 time points revealed a quantifiable antibody response that was temporally correlated with upregulated immune response genes and significantly increased spontaneous lymphocyte proliferation.  The antibody response was further validated in field exposed California sea lions and provides the first biomarker for chronic exposure assessment.

overall_design: Time series domoic acid exposure of zebrafish.

last: Beyer

first: Theodor

last: Bammler

first: Kathi

last: Lefebvre

first: Elizabeth

middle: R

last: Frame

first: Emma

last: Hiolski

first: David

middle: J

last: Marcinek


title: Expression analysis of a full Lsr locus knockout in Haemophilus influenzae strain CZ4126/02

status: Public on Oct 19 2012

city: Philadelphia

first: Benjamin

last: Janto

state: PA

department: Microbiology & Immunology

institute: Drexel University College of Medicine

summary: Investigation of whole genome gene expression differences in a full (nine-gene) Lsr locus knockout strain compared to the wild-type strain (CZ4126/02). This Lsr mutant is unable to import the autoinducer-2 (AI-2) quorum sensing molecule nor mediate any potential LsrR-based transcriptional regulation.

overall_design: WT and Lsr-KO strains were grown in two different media to two or three different time-points. RNA was extracted from these sampling conditions in two separate cultures (biological replicates). Each of these RNA samples was run on two different H. influenzae supragenome arrays (technical replicates). 3-13 probes represent each subcluster (gene) and two replicate probe sets are included on each custom NTHi supragenome chip. Thus, under each sampling condition, 8 separate values are obtained per strain and used for WT:Lsr-KO comparisons.

first: Luisa

middle: N

last: Hiller

first: Jennifer

last: Kress-Bennett

first: Rory

last: Eutsey

first: Margaret

middle: E

last: Dahlgren

first: Joshua

last: Earl

first: Evan

last: Powell

first: Azad

last: Ahmed

first: Ramaz

last: Geguchadze

first: Mike

last: Passineau

last: Post

first: Fen

first: Garth

last: Ehrlich


title: The role for TNF-alpha in murine type 1 and 2 diabetes

status: Public on Nov 22 2012

first: Manoj

last: Bhasin

state: MA

address: 330 Brookline Avenue  RN 380E

institute: Beth Israel Deaconess Medical Center

summary: To search for new therapeutic targets for type 1 & 2 diabetes, we have applied genome wide transcriptional profiling and systems biology oriented bioinformatics analysis to examine the impact of the Power mix(PM) and Alpha-1 Anti-Trypsin( AAT) regimens upon pancreatic lymph node (PLN) and fat, a crucial tissue for insulin dependent glucose disposal, in new onset diabetic NOD mice.

overall_design: Transcriptional profiles of fat and PLNs in normal (non diabetic) NOD mice (NOR), new onset diabetic (DIA), new onset diabetic NOD mice treated with AAT or PM were perfromed in this study

middle: K

first: Terry

last: Strom

first: Maria

last: Koulmanda

first: Towia

last: Libermann


title: Genome-wide analysis of gene expression in lymph nodes and vaccination site in mice vaccinated with adenovirus and MVA mixed formulations

status: Public on Dec 01 2012

city: Oxford

first: Arturo

last: Reyes-Sandoval

state: Oxfordshire

address: ORCRB, Roosevelt Dr.

department: The Jenner Institute

institute: University of Oxford

summary: Gene expression analysis in lymph nodes and site of injection (intradermal) after vaccination with adenovirus (Ad), modified vaccinia Ankara (MVA) or a mixed formulation of Ad+MVA. The hypothesis tested in the present study was that co-administration of two viral vectors induce a differential gene expression in the site of vaccination (dermis) and the draining lymph nodes that ultimately influences the protective ability of a vaccine against pre-erythrocytic malaria.

overall_design: Total RNA was isolated from the vaccination site (dermis) and lymph nodes after vaccination with adenovirus, MVA or Ad+MVA mixed co-administration after 6h and 24h (ear biopsies) and 9h, 24h and 72h for lymph nodes. Differential gene expression was assessed between vaccinated and non-immunized mice. Four ear biopsy samples did not pass quality control, and are not included in this submission.

first: Anita

last: Milicic


title: Combining laser microdissection and RNA-seq to chart the transcriptional landscape of fungal development

status: Public on Oct 01 2012

city: Bochum

first: Minou

last: Nowrousian

address: Universitaetsstr. 150

department: Molecular and Cellular Botany

institute: Ruhr-University Bochum

summary: RNA-seq analysis of developmental stages from the filamenous ascomycete Sordaria macrospora. Using laser capture microdissection, we separated protoperithecia (young fruiting bodies) from the surrounding hyphae. RNA isolation and amplification from 150 protoperithecia yields enough material for RNA-seq analysis. The resulting data were compared to RNA-seq data from whole mycelial exctracts (total vegetative and total sexual mycelium) to characterize the genome-wide spatial distribution of gene expression during sexual development. We analyzed total vegetative mycelium, total sexual mycelium, and protoperithecia from the wild type as well as protoperithecia from the sterile mutant pro1. Additionally, we used the RNA-seq information to improve the predicted S. macrospora gene models, and annotated UTRs for more than 50 % of the genes.

overall_design: 8 samples were sequenced (2 independent biological replicates for the four conditions "wt sex: SM2, SM7", "wt veg: SM1, SM6", "wt proto: SM4, SM5", "pro1 proto: SM8, SM9", each on one Illumina/Solexa lane (GAII or HiSeq, single reads of 36 or 100 bases))

first: Ines

last: Teichert

first: Gabriele

last: Wolff

first: Ulrich

last: Kück


title: Expression data from wheat following Hessian fly larval attack.

city: Lincoln

first: Chitvan

last: Khajuria

address: 103 Entomology Hall

institute: University of Nebraska-Lincoln

summary:
The Hessian fly (HF, Mayetiola destructor) is a biotrophic insect that interacts with wheat on a typical gene-for-gene basis. Identification of the genes which are differentially expressed during wheat-HF interactions may provide critical information to better understand the plant resistance mechanisms. Microarray analyses of transcripts, including those encoding various lipases, lipid transfer proteins, enzymes involved in oxylipin synthesis, and enzymes involved in wax and cutin synthesis, revealed that the abundance of many of these transcripts increased rapidly in resistant plants after HF attack, but did not change in susceptible plants.
We conducted the genome-wide transcriptional analysis of gene expression to identify the genes from wheat plants which were differentially express during compatible and incompatible wheat-Hessian fly interactions at 6, 12, and 24 hrs.

overall_design: Two wheat lines “Molly” and “Newton” were used in the experiment. Molly contains R gene H13 and have incompatible interaction with Hessian fly larvae whereas Newton is susceptible and has compatible interaction with Hessian fly larvae. Total RNA was extracted from larval feeding site which is 1.5-2 cm of the second leaf sheath and hybridized on Affymetrix microarrays. Tissues were collected at three time points (6, 12, and 24 hr) after the Hessian fly egg hatching. The data obtained from each treatment were compared with the uninfested control within each wheat line under identical conditions.

first: Xuming

last: Liu

first: Haiyan

last: Wang

first: Mingshun

last: Chen


title: Sorafenib inhibits epithelial-mesenchymal transition through an epigenetic-based mechanism in human lung epithelial cells

status: Public on Oct 11 2012

city: Shenzhen

first: Desheng

last: Gong

address: No.7 PengFei road

institute: Agricultural Genomes Institute at Shenzhen

summary: The epithelial to mesenchymal transition (EMT) has been well recognized for many decades as an essential early step in the progression of primary tumors towards metastases. Widespread epigenetic reprogramming of DNA and histone modifications tightly regulates gene expression and cellular activity during carcinogenesis, and epigenetic therapy has been developed to design efficient strategies for cancer treatment. As the first oral agent approved for the clinical treatment of cancer, sorafenib has significant inhibitory effects on tumor growth and EMT. However, a detailed understanding of the underlying epigenetic mechanism remains elusive. In this manuscript, we performed a ChIP-Seq assay to evaluate the activity of sorafenib on the genome-wide profiling of histone modifications. We demonstrate that sorafenib largely reverses the changes in histone modifications that occur during EMT in A549 alveolar epithelial cells. Sorafenib also significantly reduces the coordinated epigenetic switching of critical EMT-associated genes in accordance with their expression levels. Furthermore, we show that sorafenib potentiates histone acetylation by regulating the expression levels of histone-modifying enzymes. Collectively, these findings provide the first evidence that sorafenib inhibits the EMT process through an epigenetic mechanism, which holds enormous promise for identifying novel epigenetic candidate diagnostic markers and drug targets for the treatment of human malignancies.

overall_design: To further explore the underlying epigenetic mechanisms of EMT regulation by sorafenib, we chose conventional markers of active euchromatin such as H3K9ac and H3K4me3, and contrasted their architecture with the repressive structures associated with H3K27me3 and H3K9me3. The profiling of these four selected histone modifications was performed using ChIP-seq on control, TGF-β1-treated and sorafenib-treated cells. We further performed pair-wise comparisons among the three treatment conditions to assess the changes in the histone modifications within specific genomic regions during EMT.

first: Juyong

last: Zhang

first: Yue-Lei

first: Guanyu

last: Ji

first: Yi

first: Zhaowei

last: Gao

first: Xiaoyan

last: Ding

first: Fei


title: Temporal expression data from zebrafish pineal gland

city: Tel Aviv

first: Shahar

last: Alon

address: Tel Aviv University

department: Department of Neurobiology, The George S. Wise Faculty of Life Sciences

institute: Tel Aviv University

summary: Microarray data allowed detection of genes that have circadian expression pattern in the zebrafish pineal gland

overall_design: Adult (0.5-1.5 years old) transgenic zebrafish, Tg(aanat2:EGFP)Y8, which express enhanced green fluorescent protein (EGFP) in the pineal gland under the control of the aanat2 regulatory regions, were used. Fish were raised under 12-hr light:12-hr dark (LD) cycles, in a temperature controlled room, and transferred to constant darkness (DD) for tissue collection. Fish were anesthetized in 1.5 mM Tricane (Sigma), sacrificed by decapitation, and pineal glands were removed under a fluorescent dissecting microscope. Starting from circadian time (CT) 14, pineal glands were collected at 4-hr intervals for 48 hours (12 time points identified as CT 14, 18, 22, 2, 6, 10, 14b, 18b, 22b, 2b, 6b and 10b). Pools of 12 pineal glands were prepared at each time-point and total RNA was extracted using the RNeasy Lipid Tissue Mini Kit (QIAGEN), according to the manufacturer's instructions.

first: Yoav

last: Gothilf


title: Role of ILK in cardiac regeneration

status: Public on Dec 25 2012

city: Toronto

first: Sara

last: Arab

state: ONT

address: 610 University Avenue

department: Cardiology

institute: Toronto General Hospital

summary: Two different mouse models of cardiac-specific ILK expression (ILKS343D and ILKR211A) were used to investigate the role of ILK in cardiac regeneration

overall_design: 4 groups with 3 mice (biological replicates) in each group with the total of 12 heart samples were used in this microarray experiment

first: John

last: Coles

first: Alexandra

last: Traister


title: Transcriptomic profile of yeast cells lacking the high affinity K+-transport system

status: Public on Oct 13 2012

city: Cerdanyola

first: Antonio

last: Casamayor

state: Barcelona

address: Edifici IBB, Campus UAB

institute: Universitat Autonoma de Barcelona

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

overall_design:
We compare the expression profile of two yeast strains: WT and trk1 trk2 double mutant, growing in a Translucent K-free medium containing 50 mM KCl until OD600 = 0.6.
Two independent experiments were performed, and for each experiment a dye-swap was carried out.
Total number of chips analyzed: 4.

first: Lina

last: Barreto

first: David

last: Canadell

first: Daniel

last: Valverde

first: Joaquin

last: Ariño


title: Gene expression data of two different strains of laying hens from a small group housing system

status: Public on Sep 12 2012

city: Hannover

first: Ottmar

last: Distl

address: Buenteweg 17p

department: Institute for Animal Breeding and Genetics

institute: University of Veterinary Medicine Hannover

summary: Comparative analysis of gene expression profiles in newly developed housing systems is important to understand gene functions in chicken for adaptation and possible gene-environment interactions among layer lines. Therefore, the objective of this study was to characterize the molecular processes that are different among the two layer lines Lohmann Selected Leghorn (LSL) and Lohmann Brown (LB) using whole genome RNA expression profiles. Despite their approximately identical egg production performance these layer lines differ markedly in other phenotypic traits. The two layer lines were kept under the production environment of the newly developed small group housing system Eurovent German with two different group sizes and three tiers.

overall_design: We used a chicken RNA microarray to identify differentially expressed genes among the two layer lines LSL and LB.

first: Christin

last: Habig