title: Dermal Wound Transcriptomic Responses to Infection with Pseudomonas aeruginosa versus Klebsiella pneumoniae

status: Public on Jan 01 2014

city: Cambridge

first: Tsute

last: Chen

address: 245 First Street

department: Microbiology

institute: The Forsyth Institute

summary: Bacterial infections of wounds are associated with poor healing and worse scarring. We sought to identify transcriptomic patterns associated with impaired healing of wounds infected with Klebsiella pneumoniae (K.p.) or Pseudomonas aeruginosa (P.a.) using a rabbit ear wound model. Wounds created on post-operative day (POD) 0 were infected on POD3, within the inflammatory phase of healing. On POD4 the infected wounds were harvested for microarray/transcriptome analysis. Other wounds with 24-hour infections were treated with topical antibiotic to promote biofilm formation and harvested on POD6 or POD12. On POD4 before antibiotic treatment, both wounds contained elevated transcripts that enriched predominantly into inflammation/infection-response pathways and functions characteristic of infiltrating leukocytes. But there were 5-fold more elevated transcripts in P.a.- than K.p.-infected wounds. Additionally, unique to P.a.-infected wounds, was a minor network of inflammation/infection-response molecules with predicted upstream regulation predominated by type I interferons. Also on POD4, Dnr-transcripts of both wounds were enriched into stress-response pathways such as EIF2 signaling. But there were 8-fold more Dnr-transcripts in P.a.- than K.p.-infected wounds, and many more of them enriched in the function, cell death, suggesting that resident dermal cells of P.a.-infected wounds failed to survive a more destructive P.a. infection. On POD6, following two days of antibiotic treatment, the biofilm-colonized wounds expressed magnitudes fewer inflammation and stress-response transcripts. However, a single regulatory network of P.a.-infected wounds was found to consist of Upr-transcripts enriching immune/infection-response functions predicted to be regulated by type I interferons, which was similar to the network unique to P.a.-infected wounds on POD4. On POD12, genes expressed by K.p.-infected wounds suggesting healing, while for P.a.-infected wounds they suggested stalled healing. The similarities and differences between the wound responses to these infections further define the molecular foundations of healing impaired by infections.

overall_design: Rabbit ear Wounds created on post-operative day (POD) 0 were infected with Klebsiella pneumoniae (K.p.) or Pseudomonas aeruginosa (P.a.) on POD3 and harvested on POD4 for RNA extraction. Other wounds with 24-hour infections were treated with topical antibiotic to promote biofilm formation and harvested on POD6 or POD12.

first: Kai

middle: P

last: Leung

first: Peter

last: D’Arpa

first: Akhil

last: Seth

first: Matthew

last: Geringer

first: Rasha

last: Hammamieh

first: Marti

last: Jett

first: Wei

last: Xu

first: Seok

last: Hong

first: Robert

last: Galiano

first: Thomas

middle: A

last: Mustoe


title: Time-series transcription microarray data of Streptomyces coelicolor M145

status: Public on Dec 31 2013

city: Beijing

first: Keqian

last: Yang

address: NO.1 Beichen West  Road, Chaoyang District

country: China

institute: IMCAS

summary: The present work aimed at providing noval reference genes (RGs) for streptomycetes by global quantitative analysis of gene expression profile. By using the time-series microarray data obtained in different culture medium (SMM in the present work and modified R5 from publication), the stably expressed genes of S. coelicolor were screened. Further statistical, bioinformatic and biological function analysis picked out 13 candidate RGs. According to qRT-PCR assays, 5 genes with high stability were selected and used for  validation in other streptomycetes to assess their prevalence. Additionally, the absolute gene expression level reflcted by RNA-seq was also taken into consideration in the present work to guide the appropriate RGs selection for streptomycetes.

overall_design: Transcriptional profiling of S. coelicolor M145 at different growth phases (exponential, transitional and stationary phase)

first: S

last: Li

first: X

first: W

last: Wang


title: Global transcriptional study of Burkholderia pseudomallei wild type and ∆BPSS1356 mutant strains

city: Minden

first: Hokchai

last: Yam

state: Pulau Pinang

address: Jalan Batu Uban

department: School of Biological Sciences

country: Malaysia

institute: University Sains Malaysia

summary: This study describes the global transcriptional changes upon deletion of a hypothetical gene BPSS1356. The BPSS1356 deletion strain of B. pseudomallei was generated via homologous recombination. Global gene expression profiling of wild type and ∆BPSS1356 mutant strains was performed to elucidate of biological functions of BPSS1356.

overall_design: The wild type and ∆BPSS1356 mutant strains were grown using Luria Bertani medium until exponential phase. Total RNAs were isolated from both strains and subjected to microarray analysis. The experiment was performed with three biological replicates for each strain. The microarray data obtained from both strains were compared.

first: Nazalan

last: Najimudin


title: eQTL analysis of many thousands of expressed genes while simultaneously controlling for hidden factors

status: Public on Jan 07 2014

city: New York

first: Yael

last: Strulovici-Barel

state: NY

address: 1300 York Avenue

department: Department of Genetic Medicine

country: USA

institute: Weill Cornell Medical College

type:
Expression profiling by array
SNP genotyping by SNP array

summary:
Motivation: Identification of eQTL, the genetic loci that contribute to heritable variation in gene expression, can be obstructed by factors that produce variation in expression profiles if these factors are unmeasured or hidden from direct analysis.
Methods: We have developed a method for Hidden Expression Factor analysis (HEFT) that identifies individual and pleiotropic effects of eQTL in the presence of hidden factors. The HEFT model simultaneously accounts for the effects of genotypes while learning hidden factors, where we make use of the complete likelihood of a unified multivariate regression and factor analysis model to derive a ridge estimator for combined factor learning and detection of eQTL. HEFT requires no pre-estimation of hidden factor effects, no iterative model selection, it provides p-values, and is extremely fast, requiring just a few hours to complete an eQTL analysis of thousands of expression variables when analyzing hundreds of thousands of SNPs on a standard 8 core 2.6G desktop.
Results: By analyzing simulated data, we demonstrate that HEFT can correct for an unknown number of hidden factors and outperforms related hidden factor methods for eQTL analysis, where the improved performance is particularly evident in the detection of eQTL with multivariate effects. To demonstrate a real-world application, we applied HEFT to identify eQTL affecting gene expression in human lung tissue for a study that included presumptive hidden factors. The analysis identified a number of eQTL with direct relevance to lung disease that could not be found without a hidden factor analysis, including cis-eQTL for GTF2H1 and MTRR, genes that have been independently associated with lung cancer.

overall_design:
We have developed HEFT, a fast multivariate method that detect eQTLs by analyzing thousands of traits simultaneously in the presence of hidden factors. HEFT employs a combined regression factor analysis approach to analyze the gene expression and genotype data sets, looking for univariate or multivariate eQTLs that regulate gene expression, while simultaneously controlling for both orthogonal or non-orthogonal hidden factors. We show by extensive simulation that HEFT outperforms competing methods, and by applying HEFT to a study that included presumptive hidden factors, we identified a number of eQTL with direct relevance to lung disease that could not be found without a hidden factor analysis.
HEFT analysis results file (includes all results, not just top hits) linked below as supplementary file.

first: Chuan

last: Gao

first: Nicole

last: Tignor

first: Jacqueline

last: Salit

first: Neil

last: Hackett

first: Ronald

middle: G

last: Crystal

first: Jason

last: Mezey


title: Carbon Source Induced Gene Expression

city: Madison

first: Adam

last: Book

state: WI

address: 1550 Linden Drive

department: GLBRC

institute: University of Wisconsin Madison

summary:
Investigation of whole genome gene expression level changes in Streptomyces sp. SirexAA-E (ActE) when grown on different carbon sources.  The results of this study demonstrate that ActE upregulates a small number of genes specific for the utilization of the avaliable carbon source.
Cellulolytic Streptomyces sp. SirexAA-E (ActE), isolated from the pinewood-boring wasp Sirex noctilio, has a genome enriched for biomass utilization. The secreted proteomes obtained from growth on pure polysaccharides catalyzed hydrolysis of cellulose, mannan, and xylan with specific activities comparable to Spezyme CP, a commercial cellulase preparation. During reaction of an ActE secretome with cellulose, reducing sugar release was markedly stimulated in the presence of O2. ActE also expresses and secretes an expanded repertoire of enzymes during growth on natural and pre-treated biomass. These results indicate a new microbial contribution to biomass utilization that is widely distributed in natural environments by insects

overall_design: Streptomyces sp. ActE was grown in minimal medium supplimented with 0.5% carbon source (glucose, sigmacell-20, xylan, chitin, cellobiose, or AFEX).  Cells were grown for 7 days and total RNA was extracted from the cell pellet.  At least 3 biological replicates were performed for each carbon source (glucose, 3; sigmacell, 3; xylan, 5; chitin, 3; cellobiose 3; AFEX 3).  Each biological replicate contained 3 technical replicates. The complete dataset were RMA Background Corrected, quantile normalized, the RMA algorithm was utilized by DNAStar ArrayStar.

first: Taichi

middle: E

last: Takasuka

middle: J

first: Cameron

middle: R

last: Currie

first: Brian

last: Fox


title: CLK:BMAL1 is a pioneer-like transcription factor [MNase-Seq]

status: Public on Jan 06 2014

city: College Station

first: Jerome

middle: S

last: Menet

state: TX

address: 301 Old Main Drive, Building 1530, ILSB

department: Dept of Biology

institute: Texas A&M University

type: Genome binding/occupancy profiling by high throughput sequencing

summary: The mammalian circadian clock relies on the master genes CLOCK (CLK) and BMAL1 and drives rhythmic gene expression to regulate biological functions under circadian control. We recently uncovered a surprising disconnect between the rhythmic binding of CLK:BMAL1 on DNA and the transcription of its target genes, suggesting that they are regulated by as yet uncharacterized mechanisms. Here we show that rhythmic CLK:BMAL1 DNA binding promotes rhythmic chromatin opening. The underlying mechanisms include CLK:BMAL1 binding to nucleosomes and rhythmic chromatin modifications, including the incorporation of the histone variant H2A.Z. This rhythmic chromatin remodeling mediates the rhythmic binding of other transcription factors adjacent to CLK:BMAL1, suggesting that the activity and the tissue-specific expression of these other transcription factors contribute to the genome-wide CLK:BMAL1 heterogeneous transcriptional output. These data therefore indicate that the clock regulation of transcription relies on the rhythmic regulation of chromatin accessibility and suggest that the concept of pioneer function extends to acute gene regulation, well beyond the current confines of developmental/cell specification.

overall_design: Mouse liver nucleosome profile assayed by MNase-Seq over 6 time points of the 24h light:dark cycle (4 wild-type and 4 Bmal1-/- mice per time point). Illumina libraries containing a mononucleosome insert were sequenced using Ilumina HiSeq2000.

first: Stefan

last: Pescatore

first: Michael

last: Rosbash


title: Multiple tissue RNA sequencing of 17 Arabidopsis thaliana MAGIC founder accessions

status: Public on Dec 11 2013

city: Salt Lake City

first: Richard

middle: M

last: Clark

state: Utah

department: Department of Biology

institute: University of Utah

type: Expression profiling by high throughput sequencing

summary: We produced RNA-Seq reads from messenger RNA isolated from seedling, root, and floral bud tissue for 17 MAGIC founder accessions (inbred strains) of Arabidopsis thaliana (see Gan et al. 2011. Nature, 477:419-23 for a description of the MAGIC genetic mapping resource). The resulting RNA-Seq data provide a resource to assess tissue-specific expression across different accessions of A. thaliana. Note that comparable read data for accessions Col-0 and Can-0, which are also founders of the MAGIC lines, has previously been released under GEO series GSE30795 (Gan et al. 2011. Nature, 477:419-23).

overall_design: Examination of RNA expression across tissues (seedling, root, floral bud) for 17 Arabidopsis thaliana accessions (Bur-0, Ct-1, Edi-0, Hi-0, Kn-0, Ler-0, Mt-0, No-0, Oy-0, Po-0, Rsch-4, Sf-2, Tsu-0, Wil-2, Ws-0, Wu-0, Zu-0).

first: Joshua

last: Steffen

first: Robert

middle: T

last: Greenhalgh

first: Edward

last: Osborne

first: Andre

middle: H

last: Kurlovs

first: Li

last: Lei

first: Christopher

last: Toomajian


title: Transcriptome analysis of alternative splicing events regulated by SRSF10 reveals position-dependent splicing modulation.

status: Public on Jan 22 2014

city: Tianjin

first: Xuexia

last: Zhou

address: 154 Anshan Road

department: Tianjin Neurological Institute

institute: Tianjin Medical University General Hospital

summary: Splicing factor SRSF10 is known to function as a sequence-specific splicing activator. Here, we used RNA-seq coupled with bioinformatics analysis to identify the extensive splicing network regulated by SRSF10 in chicken cells. We found that SRSF10 promoted both exon inclusion and exclusion. Functionally, many of SRSF10-verified alternative exons are linked to pathways of stress and apoptosis. Importantly, reconstituted SRSF10 in knockout cells recovered wild-type splicing patterns and considerably rescued the stress-related defects. Together, our results provide mechanistic insight into SRSF10-regulated alternative splicing events in vivo and demonstrate that SRSF10 plays a crucial role in cell survival under stress conditions.

overall_design: RNA-seq for wide type (WT) and SRSF10-deficient (KO) chicken DT40 cells

first: Wenwu

last: Wu

first: Ying

last: Feng


title: expression data from 14 tissues of maize

status: Public on Jan 23 2014

city: beijing

first: qiuxue

last: zhang

address: 12 Zhong Guan Cun South Street, Haidian District

institute: biotechnology research institute  ,Chinese Academy of Agricultural Sciences

summary:
The genes specifically express in some tissue may usually play an important role in the development of the tissue. At vegetative growth stage, some genes may up-regulated to promote the nutrition absorbtion and transportation. However during the reproductive stage, some genes may up-regulated to regulate the flowering and seed development.
We used microarrays to identify significantly differentially expressed genes between seed and non-seed tissues.

overall_design: Different tissues of maize were selected at vegetative growth stage and reproductive stage for RNA extraction and hybridization on Affymetrix microarrays. We sought to identify significantly differentially expressed genes between seed and non-seed tissues. To that end, Big trumpet period maize inbred line B73 was use to collect nutritive tissues include root, stem, stem tip and leaf; 10, 15, 20 and 25 DAP (days after pollination) embryo and endosperm; ear and silk before pollination. Each sample has three replications.

first: Rumei

last: Chen

first: Chunyi

last: Zhang

first: Lei

last: Wang

first: Liang

last: Yin

first: Suzhen

last: Li

first: Xiaoqing

last: Liu

first: Qiuxue


title: Gene expression analysis of Pseudomonas putida KT2440 Wild Type and its exopolysaccharide mutants under water stress

status: Public on Dec 23 2013

city: Kgs Lyngby

first: Gamze

last: Gulez

address: Miljoevej 113

department: Environmental Engineering

country: Denmark

institute: Technical University of Denmark

type: Expression profiling by genome tiling array

summary: Alginate, a major exopolysaccharide (EPS) produced by P. putida, is known to create hydrated environments and alleviate the effect of water limitation. In addition to alginate, P. putida is capable of producing cellulose (bcs), putida exopolysaccharide a (pea), and putida exopolysaccharide b (peb). However, unlike alginate, not much is known about their roles under water limitation. Hence, in this study we examined the role of different EPS under water stress. To create environmentally realistic water stress conditions as observed in soil, we used Pressurized Porous Surface Model (PPSM). Our main hypothesis was that under water stress, absence of alginate would be compensated by the other EPS. To test our hypothesis, we investigated colony morphologies and whole genome transcriptomes of P. putida KT2440 WT and its mutants deficient in either alginate or all known EPS

overall_design: A custom-made Nimblegen (WI, USA) whole genome one-color oligonucleotide expression array (12x135K with 45-60 mer probes) of P. putida KT2440 was used to investigate effect of water stress on the  differential expression of the whole genome. In this study  Pseudomonas putida KT2440 wild type (WT) and two of its mutants deficient either in alginate (Alg-), or all known EPS (EPS-) production were used  and grown under dry (water stress) and wet (without water stress) conditions.  (Deleted genes in Alg-: PP1277-PP128; in EPS-: PP1277-1288 (alg) + PP2634-2638 (bcs) + PP3132-3142 (pea) + PP1795-1788 (peb)) (Nilsson et al., 2011).39. Nilsson, M., Chiang, W.C., Fazli, M., Gjermansen, M., Givskov, M., and Tolker-Nielsen, T. (2011) Influence of putative exopolysaccharide genes on Pseudomonas putida KT2440 biofilm stability. Environ Microbiol. 13 (5):1 357-1369

first: Barth

middle: F

last: Smets

first: Arnaud

last: Dechesne

last: Workman

first: Ali

last: Altintas

first: Tim

last: Tolker-Nielsen

first: Mustafa

last: Fazli


title: Global mapping of estrogen receptor and histone modifications in breast tumor samples uncovers distinct patterns for aromatase inhibitor resistance

status: Public on Dec 05 2013

city: Amsterdam

first: Wilbert

last: Zwart

address: Plesmanlaan 121

country: Netherlands

institute: NKI

summary: ChIP-seq on primary breast cancer tumor samples for Era, H3K4me3, H3K27me3. Patients had a poor or good outcome after aromatase inhibitor treatment. Differential binding patterns between good and poor outcome patients were identified for each marker, predicting response to treatment

overall_design: comparing ER, H3K4me3 and H3K27me3 patterns between two breast cancer patient populations

first: Arno

last: Velds


title: Gene expression in human hepatocellular carcinoma

status: Public on Feb 15 2014

city: Daejeon

first: Bu-Yeo

last: Kim

address: 1672 Yuseongdae-ro, Yuseong-gu

department: Herbal Medicine Research Division

country: South Korea

institute: Korea Institute of Oriental Medicine

summary: Transcription profiling of hepatocellular carcinoma using two color microarray.

overall_design: Experimental samples: Hepatocellular carcinoma, Common reference: Normal liver tissue. One replicate per array.

first: Kee-Ho

last: Lee


title: Gene expression profiling under exposure to high altitude hypoxic environment

status: Public on Dec 18 2013

city: New Delhi

last: Sarkar

address: Lucknow Road, Timarpur.

country: India

institute: DIPAS

summary: Understanding molecular mechanism associated with high altitude exposure during acclimatization/adaptation/maladaptation. Data reveals specific components of the complex molecular circuitry underlying high altitude pulmonary edema.

overall_design: Individualized outcome prediction were constructed through expression profiling of 39400 genes in sea level sojourners who were acclimatized to high altitude and grouped as controls (n=14), high altitude natives (n=14) and individuals who developed high altitude pulmonary edema within 48-72 hours after air induction to high altitude (n=17).

first: Soma


title: Epigenome analysis of human brain gliomas (part 2)

status: Public on Dec 12 2013

first: Tao

last: Jiang

address: Tiantan Xili No.6, Dongcheng District

department: Neurosurgery

institute: Beijing Tiantan Hospital, Capital Medical University

summary: Genome wide DNA methylation profiling of 33 human glioblastoma samples. The Illumina Infinium 27k Human DNA methylation Beadchip v1.2 was used to obtain DNA methylation profiles across approximately 27,000 CpGs in glioma samples.

overall_design: Bisulphite converted DNA from the 33 glioblastoma samples were hybridised to the Illumina Infinium 27k Human Methylation Beadchip v1.2

first: Zheng


title: Epigenome analysis of human brain gliomas

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

overall_design: Refer to individual Series


title: Zebrafish embryos: Control MO vs. Lin28A MO vs. Lin28B MO injected

status: Public on Nov 19 2013

city: Kasugai

first: Yasuo

last: Ouchi

state: Aichi

address: 1200 Matsumoto-cho

department: Department of Biomedical Sciences

country: Japan

institute: Chubu University

summary: miRNA profiling of zebrafish embryos comparing control MO with Lin28A MO or Lin28B MO injected embryos at 5hpf

overall_design: One-condition experiment

first: Takashi

last: Iwamoto


title: Adrenocortical Carcinoma Gene Expression Profiling [Affymetrix]

status: Public on Nov 21 2013

city: Tempe

first: Kimberly

middle: J.

last: Bussey

state: AZ

address: 1001 S. McAllister Ave.

institute: Arizona State University

summary:
Background: Adrenocortical carcinoma (ACC) is associated with poor survival rates.  The objective of the study was to analyze ACC gene expression profiling data prognostic biomarkers and novel therapeutic targets.
Methods: 44 ACC and 4 normal adrenal glands were profiled on Affymetrix U133 Plus 2 expression microarrays and pathway and transcriptional enrichment analysis performed.  Protein levels were determined by western blot.  Drug efficacy was assessed against ACC cell lines.  Previously published expression datasets were analyzed as validation data sets.
Results: Pathway enrichment analysis identified marked dysregulation of cyclin-dependent kinases and mitosis.   Over-expression of PTTG1, which encodes securin, a negative regulator of p53, was identified as a marker of poor survival.  Median survival for patients with tumors expressing high PTTG1 levels (log2 ratio of PTTG1 to average beta-actin <-3.04 ) was 1.8 years compared to 9.0 years if tumors expressed lower levels of PTTG1 (P<0.0001).  These findings were confirmed by our analysis of previously published datasets.  Treatment of ACC cell lines with vorinostat decreased securin levels and inhibited cell growth (IC50s of 1.69 uM and 0.891 uM, for SW-13 and H295R, respectively).
Conclusion: Over-expression of PTTG1 is correlated with poor survival in ACC.  PTTG1/securin is a prognostic biomarker and warrants investigation as a therapeutic target.

overall_design: RNA from forty-four adrenocortical carcinomas and four normal adrenal glands was extracted, labeled, and hybridized to Affymetrix U133 Plus 2 arrays.  The resulting data was normalized by gcRMA with quantile normalization and background subtraction after using the ExpressionFileCreator in GenePattern.  Data was then floored at 5.5 using PreprocessDataset, and filtered to remove 1) probes with more than 35 floored values and/or 2) probes where all values from one batch were floored while values from the other batch were not.  Further batch effects were minimized using ComBat with the parametric option.   Data was then floored at 2.  Differentially expressed genes were determined using a T-test with multiple comparison correction as implemented by Comparative Marker Selection in Gene Pattern.  Genes with the corrected p-value < 0.005 and the FDR < 0.075 were selected for further study.  For comparing high to low grade or primary to recurrence, the FDR cut-off was increased to < 0.13.  Survival analysis was conducted using Prism 6 (GraphPad) to generate Kaplan-Meier curves that were compared by log-rank.

first: Elizabeth

last: Stephan

first: Shripad

last: Sinari

first: Kathryn

last: Coan

first: Clive

last: Grant

first: Richard

last: Komorowski

first: David

last: Mount

first: Michael

last: Demeure


title: Adrenocortical Carcinoma Gene Expression Profiling


title: Alterations in the gene expression profile in patients treated with cyclophosphamide

status: Public on Nov 15 2013

city: Stockholm

first: Ali

last: Moshfegh

department: Oncology & Pathology

country: Sweden

institute: Karolinska Institutet

summary:
Investigation of whole genome gene expression level changes in patients treated with cyclophosphamide
We have studied the gene expression profile for 11 patients with different types of hematological malignancies but all of them have been treated with CP i.v.

overall_design: Eleven patients were enrolled in this study. All of them were treated by i.v. infusion of CP 60 mg/kg/day once for 2 days followed by TBI. Blood samples were collected from each patient before the start of CP infusion, 6 h after CP first dose, before CP second dose (24 h after first dose) and 6 h after it.

first: Ibrahim

last: El-Serafi

first: Manuchehr

last: Abedi-Valugerdi

first: Zuzana

last: Potácová

first: Parvaneh

last: Afsharian

first: Moustapha

last: Hassan


title: Adrenocortical Carcinoma Gene Expression Profiling [Agilent]

summary: Adrenocortical carcinoma (ACC) is an aggressive endocrine tumor with a poor 5 year survival rate of 10-20%.  We used expression profiling to assess the transcriptional changes associated with ACC as compared to normal adrenal glands with the goal of identifying new targets for treatment.  Fourteen ACC tumors were profiled on both Affymetrix U133 Plus 2 or Agilent 22K Human Genome arrays; an additional six tumors were profiled on one or the other array.  The data demonstrate a marked dysregulation of the cell cycle control, focused on sister chromatid adhesion and cytokinesis in the G2/M transistion.  Genes associated with this pattern, and identified because of coordinate expression with CDC2, were capable of clustering ACC into two clusters that almost completely recapitulated histological grade.  Exploration of the data sets by both Gene Set Enrichment Analysis and GeneGo Interactome analysis identified additional dysregulation of the IGF2-IGF1R axis, aside from IGF2 over-expression, as an early event present in low grade tumors.  Additionally, p53 and MDM2 were consistently identified as drivers in leading edge analyses of the tumors, implicating the p53 pathway in ACC pathogenesis.  Finally, over-expression of PTTG1, which encodes securin, and is involved in sister chromatid adhesion as well as negative regulation of p53, was associated with poor prognosis in our samples.  Taken together, these data point toward a tumor type driven in part by dysregulated IGF2 signaling in the context of a lack of a functional p53 response, with potential vulnerabilities in the G2/M transition that may make viable therapeutic targets.

overall_design: RNA from fifteen adrenocortical carcinomas and a pool of  four normal adrenal glands was extracted, labeled, and hybridized to Agilent Human 1A Oligo Microarray (v2) chips.  The resulting data was first background subtracted.  Each array then had the median intenisty subtracted from each channel, and finally both M and A values were quantile normalized across arrays.  All calculations were done in R using the Bioconductor packages of marray and limma.

last: Barrett

first: Kathleen

last: Delgiorno


title: C/EBPα poises B cells for rapid reprogramming into iPS cells [array]

status: Public on Nov 17 2013

city: Houston

first: Bruno

last: Di Stefano

address: 1 Baylor Plaza

department: Molecular and Cellular Biology

institute: Baylor College of Medicine

summary: Somatic cell reprogramming into pluripotent stem cells induced by Oct4, Sox2, Klf4 and Myc (OSKM) occurs at low frequencies and with a considerable delay involving a stochastic phase. In contrast, transdifferentiation of B cells into macrophages induced by C/EBPα is fully efficient and initiated almost immediately. We now discovered that a pulse of C/EBPα in B cell precursors followed by OSKM expression dramatically enhances reprogramming to pluripotency, overcoming the stochastic phase. The cells simultaneously activate mesenchymal-epithelial transition and pluripotency genes to high levels within 2 days, correlating with promoter demethylation and accessibility to Oct4 binding. The conditioning effect of C/EBPα is shared with C/EBPβ but not with transcription factors that induce erythroid, neuronal and muscle fates, which are innocuous or inhibitory. Surprisingly, OSKM induce the transient upregulation of macrophage genes in B cells, including Cebpa and Cebpb, as well as trophectoderm genes. Since both C/EBPs are functionally expressed in trophoblasts their unique pluripotency-conditioning capacity might reflect an early embryonic function. Our findings have removed a major hurdle in elucidating mechanisms that establish pluripotency.

overall_design: Change in gene expression during reprogramming of B-cells into iPS cells, comparing the time 0h (B-cells) to cells induced with OKSM, pre-treated or not with estradiol to induce C/EBPa, at different time points.

first: Thomas

last: Graf


title: Expression data from mesenchymal stromal cells isolated from the umbilical cord tissue (UCX®) and cultivated in ATMP-compatible media

status: Public on Dec 16 2013

city: Braunschweig

first: Robert

last: Geffers

address: Inhoffenstr. 7

department: Dep. Molecular Bacteriology

country: Germany

institute: HCI - Helmholtz Centre for Infection Research

summary:
Standardization of MSC manufacturing is urgently needed to facilitate comparison of clinical trial results. Here, we compare gene expression of MSC generated by the adaptation of a proprietary method for isolation and cultivation of a specific umbilical cord tissue-derived population of Mesenchymal Stromal Cells (MSCs)
The adaptation focused on different stages of production, from cell isolation steps to cell culturing and preservation. The origin and quality of reagents were considered and steps for avoiding microbiological and endotoxin contamination of the final cell product were implemented. Cell isolation efficiency, MSC surface markers and genetic profiles originating from the use of different medium supplements were compared. The ATMP-compliant UCX® product was also cryopreserved avoiding the use of DMSO, an added benefit in the use of these cells as an ATMP. Cells were analysed for expansion capacity and longevity. The final cell product was further characterised by flow cytometry, differentiation potential, and tested for contaminants at various passages. Gene expression profiles, genetic stability and immune properties were analysed.

overall_design: human umbilical cord tissue-derived MSCs (UCX®) were isolated using clinical grade enzymes  and cultivated in flask or bags using α-MEM basal medium with 1 g/L glucose and 2 mM glutamine supplemented with either FBS,human serum or human platelet lysate.

first: José

last: Martins

first: Jorge

last: Santos

first: Joana

last: Almeida

first: Mariana

last: Filipe

last: Teixeira

first: Sílvia

first: Ana

last: Água-Doce

first: Alexandre

last: Varela

first: Mari

last: Gilljam

first: Birgitta

last: Stellan

first: Susanne

last: Pohl

first: Kurt

last: Dittmar

first: Werner

last: Lindenmaier

first: Evren

last: Alici

first: Luís

last: Graça

first: Pedro

last: Cruz

first: Helder

first: RitaN

last: Bárcia


title: C/EBPα poises B cells for rapid reprogramming into iPS cells

first: Bruno

last: Di Stefano

summary: C/EBPα induces transdifferentiation of B cells into macrophages at high efficiencies and enhances reprogramming into induced pluripotent stem cells (iPSCs) when co-expressed with Oct4, Sox2, Klf4 and Myc (OSKM). However, how C/EBPα accomplishes these effects is unclear. We now found that transient C/EBPα expression followed by OSKM activation induces a 100 fold increase in iPSC reprogramming efficiency, involving 95% of the cells. During this conversion pluripotency and epithelial-mesenchymal transition genes become dramatically up-regulated and 60% of the cells express Oct4 within 2 days. C/EBPα acts as a pathbreaker since it transiently makes the chromatin of pluripotency genes more accessible to DNase I. It also induces the expression of the dioxygenase Tet2 and promotes its translocation to the nucleus where it binds to regulatory regions of pluripotency genes that become demethylated following OSKM induction. In line with these findings, overexpression of Tet2 enhances OSKM‐induced B cell reprogramming. Since the enzyme is also required for efficient C/EBPα-induced immune cell conversion, our data suggest that Tet2 provides a mechanistic link between iPSC reprogramming and B cell transdifferentiation. The rapid iPS reprogramming approach described should help to fully elucidate the process and has potential clinical applications.


title: RNA-seq in neurons derived from iPSCs in controls and patients with schizophrenia and 22q11 del

status: Public on Nov 01 2013

city: Bronx

first: Herb

last: Lachman

address: 1300 Morris Park Ave., F103

department: Psychiatry

institute: Albert Einstein College of Medicine

summary: Individuals with 22q11.2 Deletion Syndrome (22q11.2 DS) are a specific high-risk group for developing schizophrenia (SZ), schizoaffective disorder (SAD) and autism spectrum disorders (ASD). Several genes in the deleted region have been implicated in the development of SZ, e.g., PRODH and DGCR8. However, the mechanistic connection between these genes and the neuropsychiatric phenotype remains unclear. To elucidate the molecular consequences of 22q11.2 deletion in early neural development, we carried out RNA-seq analysis to investigate gene expression in differentiating human neurons derived from induced pluripotent stem cells (iPSCs) of 22q11.2 DS SZ and SAD patients. Eight cases (ten iPSC-neuron samples in total including duplicate clones) and seven controls (nine in total including duplicate clones) were subject to RNA sequencing. Using a systems level analysis, differentially expressed genes/gene-modules and pathway of interests were identified. We observed ~2-fold reduction in expression of almost all genes in the 22q11.2 region in SZ (37 genes reached p-value < 0.05, 36 of which reached a false discovery rate < 0.05). Outside of the deleted region, 745 genes showed significant differences in expression between SZ and control neurons (p<0.05). Function enrichment and network analysis of the differentially expressed genes uncovered converging evidence on abnormal expression in key functional pathways, such as apoptosis, cell cycle and survival, and MAPK signaling in the SZ and SAD samples.

first: Deyou

last: Zheng

first: Mingyan

last: Lin


title: LncRNAs expression profiles in the livers of 20-month-old male HBx transgenic mice and C57BL/6 wild-type mice

status: Public on Nov 04 2013

city: shanghai

first: jinfeng

last: huang

address: No.800 xiangyin road

institute: second military medical university

summary: The hepatitis B virus X protein (HBx) has been implicated as an oncogene in both epigenetic modifications and genetic regulation during hepatocarcinogenesis, but the underlying mechanisms are not entirely clear. Long non-coding RNAs (lncRNAs), which regulate gene expression with little or no protein-coding capacity, are involved in diverse biological processes and in carcinogenesis. We asked whether HBx could promote hepatocellular carcinoma (HCC) by regulating the expression of lncRNAs.In this study, we investigated the alteration in expression of lncRNAs induced by HBx using microarrays, and our results indicate that HBx transgenic mice have a specific profile of liver lncRNAs compared with wild-type mice.

overall_design: For these experiments, six each of 20-month-old male HBx-transgenic mice and wild-type C57BL/6 mice were sacrificed and the livers were removed. Every three livers were pooled as one sample; therefore, each group was represented by two samples. The total RNA was extracted from the four samples and used for microarray experiments. Mouse LncRNA Array (4 x 44K, ArrayStar, Rockville, MD) were used to monitor the expression level of approximately 14000 lncRNAs identified from the NCBI RefSeq, UCSC, RNAdb2.0, NRED, Fantom3.0 and UCRs. LncRNAs differentially expressed were identified by comparing expression levels in HBx-transgenic mice and wild-type mice.

first: Jin-feng

last: Huang

first: Ying-jun

last: Guo

first: Chen-xi

last: Zhao

first: Yue

last: Wang

first: Guan-nan

last: Tang

first: Shu-han

last: Sun


title: Gene expression analysis of Salmonella enterica serovar Typhimurium strain SL1344 swap

status: Public on Nov 09 2013

city: Dublin

first: Shane

last: Dillon

address: Trinity College

department: Department of Microbiology

country: Ireland

institute: Moyne Institute of Preventive Medicine

summary: We performed transcriptome abundance analysis of Salmonella Typhimurium strain SL1344 swap which has been genetically engineered to express the hns open-reading frame from the stpA promoter and the stpA open reading frame from the hns promoter. This strain is designated SL1344(swap). Transcript abundance was compared with that of wild-type SL1344. This comparison was performed to determine the effect of chromosome location of the expression of two related global regulators and how alterations to their expression patterns would impact on their regulons.

platform_organism: Salmonella enterica subsp. enterica serovar Typhimurium str. SL1344

overall_design:
Three independent RNA samples were harvested from wild-type SL1344 and SL1344(swap) grown to exponential phase (OD600nm = 0.3) and hybridized to a microarray containing multiple probes for each of the SL1344 open reading frames.
Please note that the original raw data file for the 'SL1344_wildtype_BR2' sample is unavailable, however, the 'wildtype SL1344 BR2.gpr' contains the raw data missing only the header information.

first: Stephen

last: Fitzgerald

middle: C

first: Karsten

last: Hokamp

first: Charles

last: Dorman


title: RNA-seq (Illumina and PacBio) of hESC

status: Public on Oct 30 2013

city: Stanford

first: Kin Fai

last: Au

address: James H. Clark Center, 1st Floor East, 318 Campus Drive,

department: Statistics

institute: Stanford

summary: We used PacBio data to identify more reliable transcripts from hESC, based on which we can estimate gene/transcript abundance better from Illumina data.

overall_design: PacBio long reads and Illumina short reads were generated from the same hESC cell line H1. PacBio reads were error-corrected by Illumina reads to identify transcripts. rSeq is used to estimate gene/transcript abundance of the identified transcriptome.

first: Kin-Fai

first: Jason

last: Underwood

first: Vittorio

last: Sebastiano

first: Lawrence

last: Lee

first: Brian

last: Williams

first: Honoratus

last: Van Bakel

first: Eric

last: Schadt

first: Wing

last: Wong


title: Transcriptome profiling of Bemisia tabaci reveals stage-specific gene expression signatures for thiamethoxam resistance

city: Beijing

first: Nina

last: Yang

state: Beijing

address: 12 Zhongguancun Nandajie, Haidian District

institute: Chinese Academy of Agricultural Sciences

summary: To investigated the stage-specific gene expression response to thiamethoxam in the Bemisia tabaci, we have designed the Agilent eArray platform to identify stage-regulated gene expression towards thiamethoxam exposure.

overall_design: All the B biotype Bemisia tabaci were maintained on cabbage. Thiamethoxam susceptible (TH-S) was cultured without exposure to any chemical insecticides, Thiamethoxam resistance (TH-R) strain exhibited >70-fold resistance to thiamethoxam in comparision to the TH-S strain. Eggs were incubated in 24hours collected as one sample. The fourth nymphs were collected as another sample. The one-day-old unmated adult females were collected as the third samples. Both of the samples were collected from the TH-R, TH-S strains, respectively

first: Wen

last: Xie

first: Xin

first: Youjun

last: Zhang


title: Expression data from WT and Eed KO neonatal mouse LT-HSC

status: Public on Sep 24 2013

city: Boston

first: Huafeng

state: MA

address: 450 Brookline Ave

institute: Dana-Farber Cancer Institute

summary:
Recent studies point to a pivotal role of polycomb repressive complex 2 (PRC2) in stem cell function and cancer. Loss of function approaches targeting individual PRC2 subunits have however generated findings that are difficult to reconcile.
Here, we prevent assembly of both Ezh1- and Ezh2-containing PRC2 complexes by conditional deletion of Eed, a core subunit, and assess glodbal gene expression changs in LT-HSCs.

overall_design: LT-HSC (long-term hematopoietic stem cells) were sorted from bone marrow of  9-day old wild type (Lin-Sca1+Kit+CD48-CD150+) or Eed KO animals (Lin-Sca1+CD48-CD150+). Each sample was double or triple sorted to ensure high purify.

first: Stuart

last: Orkin


title: Gene expression in organized and disorganized human breast epithelial cells

status: Public on Oct 01 2013

city: Berkeley

first: Sabine

last: Becker-Weimann

state: CA

address: 1 Cyclotron Rd

department: Life Sciences

institute: Lawrence Berkeley National Laboratory

summary: We have reported more than a dozen microenvironmental factors whose signaling must be integrated in order to effect an organized, functional tissue morphology. In order to identify underlying commonalities in gene transcription associated with the phenotype, we compared the gene expression of organized and disorganized epithelial cells of the HMT-3522 breast cancer progression series: the non-malignant S1 cells that form polarized spheres (‘acini’), the malignant T4-2 cells that form large tumor-like clusters, and the ‘phenotypically reverted’ T4-2 cells that polarize as a result of correction of the microenvironmental signaling.

overall_design: 24 samples were analyzed: 5 samples were non-malignant S1 cells that formed organized spherical structures ('acini'), 5 samples were the isogenic malignant counterpart of S1 cells, namely the T4-2 cells, which grow into disorganized large cell clusters; and 14 samples of T4-2 cells that had been treated with different reverting agents, these reverting agents cause the T4-2 cells to 'revert' in phenotype so that they resemble the structures formed by S1 cells.

first: Mina

last: Bissell

first: Yasuhito

last: Onodera

first: Aylin

last: Rizki


title: C/EBPα poises B cells for rapid reprogramming into iPS cells [RNA-Seq]

first: Bruno

last: Di Stefano

overall_design: Change in gene expression, comparing primary B-cells treated with estradiol for 18h to induce C/EBPa to untreated cells.

first: Thomas

last: Graf


title: Gene expression data from lateral ventricle choroid plexuses of developing and adult rats

status: Public on Sep 17 2013

city: Lyon

first: Ingrid

last: Kratzer

address: Rue Guillaume Paradin

country: France

institute: INSERM

summary: Choroid plexuses (CP) develop early during development. They form a barrier between the blood and the cerebrospinal fluid, and fulfill important protective and nutritive functions. We used Affymetrix microarrays to assess whether CP of the lateral ventricles (LVCP) have similar functions in developing and adult brain. We identified distinct families of protective and transport genes and found that most of these genes were already well expressed during development.

overall_design: 2 batches of CP from embryonic day E19, postnatal day 2 and adult rats were processed for RNA extraction and hybridization on Affymetrix microarrays.

first: Nathalie

last: Strazielle

first: Jean

last: Ghersi-Egea


title: Next Generation Metatranscriptome Sequencing of an Anaerobic Hexadecane-Degrading Microbial Consortia

status: Public on Oct 29 2013

city: La Jolla

first: Mallory

last: Embree

address: PFBH/EBU3a, 9500 Gilman Drive Rm. 414

department: Bioengineering

institute: University of California, San Diego

summary: Purpose: Identification of transcriptionally active genes in the unculturable community constituent, Smithella, during hexadecane degradation; Differential gene expression analysis of hexadecane-relevant genes acoss three different conditions; Extension of metatranscriptomic datasets to other community constituents to identify interspecies relationships.

overall_design: mRNA profiles were generated for this community across three different conditions (hexadecane-, butyric acid-, caprylic acid-degrading conditions) using a modified version of Nextera and sequenced using Illumina's Miseq platform.

first: Karsten

last: Zengler


title: Nicotinic acetylcholine receptors and EGF induce c-Kit ligand/Stem Cell Factor (SCF) in a β-arrestin-1 and E2F1 dependent manner in NSCLC

status: Public on Nov 10 2013

city: Tampa

first: Jonathan

last: Nguyen

state: FL

department: Tumor Biology

institute: Moffitt Cancer Centre & Research Institute

summary: Lung cancer remains the leading cause of cancer-related deaths worldwide. β-arrestin-1 (ARRB1), a scaffolding protein involved in the termination or desensitization of signals arising from activated G-protein-coupled receptors (GPCRs) has been shown to play a role in invasion and proliferation of many cancers, including nicotine-induced proliferation of human non–small cell lung cancers (NSCLCs). In this study, we analyzed nicotine induced and β-arrestin-1 dependent genes from the microarray data. Our analysis show that SCF (Stem cell factor) strongly differentiated smokers from non-smokers implying an important role of this gene in NSCLCs. SCF, a major cytokine is the ligand for the c-Kit proto-oncogene. Here we elucidate the molecular mechanisms by which nicotine as well as EGF induces the expression of SCF in lung adenocarcinoma cell lines A549 and H1650. ChIP assays and transient transfection experiments showed that transcription factor E2F1 can positively regulate SCF expression at the transcriptional level; depletion of E2F1 or β-arrestin-1 prevented the nicotine-mediated induction of SCF. Given that the binding of SCF to c-Kit leads to activation of multiple downstream signaling pathways including Src, PI3K, MEK and EGFR pathways, our data suggest that the SCF plays a central role in lung carcinogenesis, and may be a potential therapeutic target for combating NSCLC. Studies presented here also provide evidence that SCF along with nicotine promotes self-renewal and proliferation of lung cancer stem cells (CSCs). Our findings reveal an important role and prognostic significance of SCF that can serve as a novel prognostic and predictive biomarker for NSCLC.

overall_design: Transfection of A549 cell line with control siRNA, Beta arrestin siRNA and then stimulation of nicotine

first: Deepak

last: Perumal

first: Smitha

last: Pillai

first: Domenico

last: Coppola

first: Srikumar

last: Chellappan


title: Divergent Compensatory Responses to High Fat Diet Between C57BL6/J and C57BLKs/J Inbred Mouse Strains

status: Public on Sep 21 2013

city: Indianapolis

first: Emily

middle: K

last: Sims

state: IN

address: 705 Riley Hospital Drive, Room 5960

institute: Indiana University School of MEdicine

summary: To assess whether changes in islet gene expression contribute to differences in phenotypes in response to high fat diet or tretament with pioglitazone, Agilent Whole Mouse Genome Oligo Microarrays were performed on RNA isolated from islets of 4 mice per each treatment group for discovery analysis of gene expression.

overall_design: Male 8 week-old BL6 and BLKS mice were fed normal chow (18% kcal from fat), HFD (42% kcal from fat), or HFD supplemented with the PPAR-γ agonist pioglitazone (PIO) (140 mg PIO/kg diet) for 16 weeks.

first: Carmella

last: Evans Molina

first: Raghu

last: Mirmira


title: miRNA expression data from normal and Malignant hematopoietic cells

status: Public on Oct 31 2013

city: Baltimore

first: Amol

middle: Carl

last: Shetty

state: Maryland

address: 670 W. Baltimore Street, Floor 3

department: Institute for Genome Sciences

institute: University of Maryland Baltimore

summary:
This data was used to identify miRNA signatures that can be used to calssify specific leukemia types including AML, precursor B ALL, precursor T ALL, and normal hematopoietic progenitor and mature populations
This data was used to identify miRNA signatures that can be used to calssify specific leukemia types including AML, precursor B ALL, precursor T ALL, and normal hematopoietic progenitor and mature populations

overall_design: AML cell lines and patient samples, B ALL cell lines and Patient samplest, T ALL cell lines and patient samples, norma B cells, normal granulocytes, normal monocytes, normal T cells and normal CD34+ cells were used for RNA extraction and hybridization on Affymetrix microarrays. All the AML, B ALL, T ALL cell lines were cultured in vitro under appropriate culture conditons and harvested in their log phase growth for RNA extraction. AML, B ALL, and T ALL patient samples were collected...(I assume these are the PBMCs from eitehr peripheral blood or bone marrow from patients, please confirm). Normal B cells, granulocytes, monocytes, and T cells were purified from human peripheral blood of normal healthy donors.

first: Curt

middle: I

last: Civin


title: Analysis of the Cerebral Cortex and Hippocampus Transcriptome Reveals Unique Molecular Changes in the Ts1Cje Mouse Model of Down Syndrome

status: Public on Sep 05 2013

city: Medford

first: Heather

last: Wick

address: 161 College Ave

department: Department of Computer Science

institute: Tufts University

summary:
Down syndrome is characterized by a complex phenotype that includes developmental disabilities and congenital anomalies. The molecular origin of these abnormalities is poorly understood. The objective of this study is to analyze whole transcriptome changes in the cortex and hippocampus of the Ts1Cje mouse model of Down syndrome to identify signaling pathways and cellular processes that are consistently perturbed in both brain regions. These pathways will offer a new opportunity for therapeutic interventions to improve cognition in Down syndrome.
We refined the translocation breakpoints of MMU12 and MMU16 described previously and established the brain transcriptional map for both monosomic (MMU12) and trisomic (MMU16) regions in Ts1Cje mice. We showed that the hippocampus have more differentially regulated genes, however, the directions of regulation of these genes were generally similar in both brain regions. The secondary genome-wide effect implicated genes known to play major roles in cellular functions that are affected in Down syndrome. Functional analyses highlighted the importance of NFAT signaling, oxidative stress, neuroinflammation, hormone metabolism and olfactory perception via G-protein signaling. This study offers novel targets for therapeutic intervention in Down syndrome.

overall_design: We analyzed the cerebral cortex and hippocampus whole transcriptome from 8-10 weeks old Ts1Cje (n=6) and wild-type (n=5) using Affymetrix mouse gene 1.0 ST array. Data were normalized and analyzed to identify and accurately map genes that are significantly differentially expressed. Functional analyses were performed using GSEA and DAVID to better characterize cellular processes and pathways that are consistently affected in both brain regions.

first: Faycal

last: Guedj

first: Jeroen

last: Pennings

first: Donna

last: Slonim

first: Diana

middle: W

last: Bianchi


title: Colonic gene expression data of acute and chronic dextran sodium sulphate (DSS) colitis mice

status: Public on Sep 03 2013

city: Leuven

first: Ingrid

last: Arijs

address: Herestraat 49

department: Clinical and Experimental Medicine

country: Belgium

institute: KULeuven

summary:
The lack of suitable animal models reflecting chronically relapsing inflammation and tissue remodeling have hindered fibrosis research in inflammatory bowel diseases (IBD). This study investigated changes in connective tissue in a chronic murine model using different cycles of dextran sodium sulphate (DSS) to mimic the relapsing nature of the disease.
We used whole gene expression arrays to study differences in colonic gene expression levels between acute and more chronic DSS colitis,

overall_design: Acute and chronic relapsing colonic inflammation was induced in C57BL6 female mice using several cycles of exposure to DSS in drinking water, followed by recovery phases. Total RNA, extracted from snap frozen colon from five mice per condition was used to analyze mRNA expression via Affymetrix Mouse Gene 1.0 ST arrays.

first: Christine

last: Breynaert

first: Tom

last: Dresselaers

first: Clémentine

last: Perrier

last: Cremer

first: Leentje

last: Van Lommel

first: Kristel

last: Van Steen

first: Marc

last: Ferrante

first: Frans

last: Schuit

first: Séverine

last: Vermeire

first: Paul

last: Rutgeerts

first: Uwe

last: Himmelreich

first: Jan

last: Ceuppens

first: Karel

last: Geboes

first: Gert

last: Van Assche


title: Genomic profiling of type-1 adult diabetic and aged normoglycemic mice liver

status: Public on Sep 06 2013

city: Campinas

first: Flávia

middle: Gerelli

last: Ghiraldini

state: São Paulo

address: Av Bertrand Russel sno.

department: Structural and Functional Biology

country: Brazil

institute: Unicamp

summary: Here we characterized and compared differential gene expression from diabetic and normoglycemic NOD mice and from aged and young-adults Balb/c mice.

overall_design: Total RNA from NOD diabetic (3 weeks with glicemia over 500mg/dl) and normoglycemic NOD mice from the same age was used. To compare the effects of aging in genomic expression, total RNA from young-adult Balb/c (9 weeks old) and middle-aged Balb/c (47 weeks old) were used.

first: André

last: Bortolini

first: Dirk

last: Kleinjan

first: Nick

last: Gilbert

first: Maria

middle: L

last: Mello


title: Gene expression data from compstatin treated E.coli-Induced primate sepsis model

status: Public on Aug 31 2013

city: Oklahoma City

first: florea

last: lupu

address: 825 NE 13th Street

institute: Oklahoma Medical Research Foundation

summary:
Severe sepsis leads to massive activation of coagulation and complement cascades that could contribute to multiple organ failure (MOF) and death. To investigate the role of the complement and its crosstalk with the hemostatic system in the pathophysiology and therapeutics of sepsis, we have used a potent inhibitor (compstatin) administered early or late post E. coli challenge in a baboon model of sepsis-induced MOF.
Microarray was used to study the affect of complement pathway on global gene expression pattern in sepsis, aims on exploring and discovering the new target genes as potential drugs for the early treatment and prevention of sepsis.

overall_design: Lung and liver tissues were obtained from three normal healthy animals (as Ctl), three animals challenged with sublethal dose of E. coli as SLEC, three animals treated with Compstatin at different sepsis stages after E.coli challenge as SLEC-CST0 and SLEC-CST5. All the animals challenged with E. coli were sacrified at 24 hours post challenge. Total RNAs were isolated from these tissues, hybridized with Affymetrix Human Genome  GeneChip U133A 2.0.

first: Hua

last: Zhu

first: Florea

last: Lupu


title: Genome-wide expression profiling of Hic-5 knockdown in PshTert-AR human myofibroblasts

status: Public on Aug 26 2013

city: Adelaide

first: damien

last: leach

address: woodville road

country: Australia

institute: the university of adelaide

summary:
Identifying the effect of the co-regulator Hic-5 (TGFB1I1) on global androgen receptor transcriptional activity in PShTert-AR prostate fibroblast cells with view to further elucidating the broader biological role of Hic-5  on fibroblast spceific androgen signaling.
Knockdown of Hic5 for 48 hours in PShTert-AR cells significantly altered the androgen regulation of approximately 1347 genes. The effect of Hic-5 knockdown was to suppress androgen regulation of approximately 85% of those transcripts, by either reducing androgen mediated repression or activition of gene expression.

overall_design: PShTert-AR cells were transfected with 10nM non-specific control siRNA (NS) or with commercially avaliable Hic-5 specific siRNA (siHic5) for 24hrs. Cells were kept in 5% hormone stripped FBS RPMI for a further 24 hours and subsequently treated with either ethanol vehicle control or 10nM DHT for 16hr.  Total RNA was extracted. Nine independent vehicle and 9 DHT siNS and siHic5 samples were pooled into three groups of vechicle and DHT treated siNS and siHic5 samples and hybrydised to Affymetrix Human Gene 1.0 ST array chips.

first: Damien

middle: A

last: Leach

first: Grant

last: Buchanan


title: Next Generation Sequencing of different ovine muscle's Transcriptomes

status: Public on Dec 01 2013

city: Tai'an

first: Dong

last: fei

state: Shandong

address: No.61 Daizong street

institute: Shandong Agricultural University

summary: We report the application of single-molecule-based sequencing technology for high-throughput profiling of different ovine muscle's transcriptomes. 9.27 gigabases of sequence from two different breeds of sheep.

overall_design: Examination of 2 different muscle's transcriptomes in 2 breed types.

first: Chunlan

last: Zhang

first: Jianmin

last: Wang


title: Surface proteoglycans expressions in oral squamous cell carcinoma

status: Public on Nov 01 2013

city: Parma

first: Silvia

last: Rossi

state: Parma

address: Viale Usberti, 11/A

department: Genetics, Microbiology, Anthropology ed Evolution

country: Italy

institute: COMT - Centre for Molecular and Translational Oncology, University of Parma

summary:
In the effort to identify novel, relevant prognostic factors for the clinical monitoring of patients affected by squamous cell carcinomas of the oral cavity (SCCOC) we have pursued a molecular screening at the gene and protein level on 166 surgical specimens derived from patients with an accessible clinical history and >2 years follow-up. The screening was focalized on cell surface proteoglycans (PGs) based upon the assumption that altered expression of individual or groups of PGs may predict disease course and therapeutic response, and thereby allow for a clusterization of patients in discrete subsets. The 11 PGs contemplated in the screening and including syndecan-1-4 (SDC1-SDC4), glypican-1-6 (GPC1-GPC6) and NG2,  were found to be transcribed at variable levels and with a decreasing frequencies SDC1>SDC4>SDC2>SDC3>GPC4>GPC3>GPC1 >GPC5>CSPG4>GPC6>GPC2. SCCOC cells de novo transcribed GPC2, GPC5 and NG2 and regulated all SDCs, GPC1, -3, -4 and -6, suggesting that an altered surface profile of PG is a characterizing trait of these tumor cells
In situ distributional analysis of these PGs on a total of  149 cases revealed many fewer lesions actually translated the molecules which were detected with a frequency range of 14% (SDC2) to 92% (SDC1). Noteworthy was, however, that SDC2 was present in the intra-lesional stroma and in association with neovessels in all the cases, suggesting that this specific PG was a key element of stromal fibroblasts and angiogenic structures. Poor translational efficacy of several of the PGs was accompanied by an apparent retention of the molecules within the cytoplasm of SCCOC cells. This finding suggest that modulated expression of cell surface PGs may be a representative secondary event in SCCOC and that these carcinoma cells do not mount up an effective intracellular machinery for proper shuttling and membrane incorporation of the PGs.

overall_design: A total of 166 surgical specimens of primary SCCOC were collected after informed consent from individuals who underwent surgical removal of the tumor lesions and RNA from 119 surgical specimens were extracted; a pool of RNAs extracted from 5 normal epithelia tissues  was adopted as a sample calibrator (HEALTHY sample). cDNA from each samples and from pool of normal epithelial were loaded on TLDA and amplified. HEALTHY sample were amplified 20 times in two replicates (in each TLDA card); each patient sample were amplified 1 time in two replicates and 7 samples of them were loaded two times in a separate TLDA card (for a total of 4 replicates).

first: Nicoletta

last: Bertani

first: Mariolina

last: Gulli

first: Robert

last: Perris


title: Genome-wide characterization of allelic chromatin in human fibroblast and lymphoblastoid cell lines by high-density allele-specific analyses

status: Public on Oct 18 2013

city: Montreal

first: Tomi

last: Pastinen

state: QC

address: 740 Dr Penfield

department: Human & Medical Genetics

country: Canada

institute: McGill University

type: Genome binding/occupancy profiling by genome tiling array

summary: Cis-regulatory variants are predicted to mediate the majority of the common genetic risk associated to complex disease, yet the specific causal variants have thus far been poorly characterized. Allele-specific (AS) assessment of chromatin modifications has the potential to elucidate specific cis-regulatory mechanisms. However, development of chromatin landscapes at allelic resolution has been challenging since sites of variable signal strength require substantial read depth not commonly applied in next-generation sequencing based approaches. In this study, we addressed this by directly assessing AS chromatin states through parallel analyses of input DNA and chromatin immunoprecipitates (ChIP) on high-density Illumina genotyping arrays. Allele-specificity for the histone modifications H3K4me1, H3K4me3, H3K27ac, H3K27me3 and H3K36me3 was assessed using ChIP samples generated from 14 lymphoblast and 6 fibroblast cell lines.

overall_design: Allele-specificity of chromatin was assessed in 14 lymphoblast and 6 fibroblast cell lines by assaying PolII & histone ChIP samples (H3K4me1, H3K4me3, H3K27ac, H3K27me3, H3K36me3)  in parallel with gDNA and cDNA on high-density Illumina genotyping arrays.

first: Nicholas

last: Light

first: Veronique

last: Adoue

first: Bing

last: Ge

first: Shu-Huang

last: Chen

first: Tony

last: Kwan


title: Expression analysis of human CRABP1 gene and R131A CRABP1 mutant in HT1080 cells

status: Public on Sep 01 2013

city: Moscow

first: Andrei

last: Komelkov

address: Kashirskoye shosse, 24

department: Institute of Carcinogenesis

country: Russia

institute: N.N.Blokhin Russian Cancer research Center

summary:
Investigation of whole genome gene expression level changes in HT1080 fibrosarcoma cell line after transfection CRABP1 gene and R131A CRABP1 mutant (arginine-alanine substitution in a protein active site, protein lacks the ability to interact with retinoic acid),
compared to HT1080 line transfected with empty pLXSN vector.

overall_design: A twelve samples on one chip study using total RNA recovered from four separate cultures of HT1080 human fibrosarcoma cell line transfected with empty pLXSN vector, four HT1080 cell line cultures  transfected with CRABP1 gene and four HT1080 cell line cultures  transfected with R131A CRABP1 mutant. Each sample on a chip measures the expression level of 44,049 genes from human genome with three-fold technical redundancy.

first: Yaroslav

last: Kainov


title: Leukocyte-adjusted epigenome-wide association studies of blood from solid tumor patients

status: Public on Aug 29 2013

city: Cincinnati

first: Scott

last: Langevin

state: OH

address: 160 Panzeca Way, ML0056

department: Department of Environmental Health

institute: University of Cincinnati College of Medicine

summary: Epigenome-wide association study (EWAS) of blood samples from a case-control study of bladder cancer. The Illumina Infinium 27k Human DNA methylation Beadchip v1.2 was used to obtain DNA methylation profiles across approximately 27,000 CpGs in peripheral blood. Samples included peripheral blood samples from 223 incident cases of bladder cancer and 205 control subjects.

overall_design: Bisulphite converted DNA from the 428 samples were hybridized to the Illumina Infinium 27k Human Methylation Beadchip v1.2

first: S

first: K

last: Kelsey


title: Methylation Changes in Soybean Mid-Maturation Seed Parts

city: Los Angeles

first: Bob

last: Goldberg

address: 610 Charles E Young Drive East

department: Molecular, Cell and Developmental Biology

institute: University of California, Los Angeles

type: Methylation profiling by high throughput sequencing

summary: Seeds are comprised of three majors parts of distinct parental origin: the seed coat, embryo, and endosperm.  The maternally-derived seed coat is important for nurturing and protecting the seeds during development.  By contrast, the embryo and the endosperm are derived from a double fertilization event, where one sperm fertilizes the egg to form the diploid zygote and the other sperm fertilizes the central cell to form the triploid endosperm.  Each seed parts undergo distinct developmental programs during seed development.  What methylation changes occurring in the different seed parts, if any, remains unknown. To uncover the possible role of DNA methylation in different parts of the seed, we characterized the methylome of three major parts of an early maturation stage seed: seed coat, embryonic cotyledons, and embryonic axis using Illumina sequencing.

overall_design: Illumina sequencing of bisulfite-converted genomic DNA from three parts of an mid-maturation (B1) stage seed: seed coat (B1-SC), embryonic cotyledons (B1-COT), and embryonic axis (B1-AX).

middle: B

first: Min

first: Jer-Young

last: Lin

first: Brandon

last: Le


title: Three human glioma stem cell lines sorted for CD133 and one human neural precursor line sorted for CD133 to identify tumor-specific miRNA dysregulation.

status: Public on Aug 02 2013

city: Charlottesville

first: Roger

last: Abounader

state: Virginia

department: Microbiology

institute: University of Virginia

summary:
Several novel potential oncogenic and tumor suppressor miRNAs were identified by using the appropriate controls for stem cells.
Expression profiles for human miRNAs in six samples were generated.

overall_design: The Agilent platform GPL7731 was used to analyze six RNA samples: CD133- human NPC, CD133+ human NPC, CD133- B4 glioma, CD133+ B4 Glioma, CD133+  NCH441 glioma, CD133+ NCH644 glioma

first: Desiree

last: Floyd


title: A Serine Sensor for Multicellularity in a Bacterium

status: Public on Oct 22 2013

city: Seattle

first: Arvind

last: Subramaniam

state: WA

address: 1100 Fairview Ave N

department: Basic Sciences Division

institute: Fred Hutchinson Cancer Center

type: Non-coding RNA profiling by high throughput sequencing

summary: We report the discovery of a simple environmental sensing mechanism for biofilm formation in the bacterium Bacillus subtilis that operates without the involvement of a dedicated RNA or protein. Certain serine codons, the four TCN codons, in the gene for the biofilm repressor SinR caused a lowering of SinR levels under biofilm-inducing conditions. Synonymous substitutions of these TCN codons with AGC or AGT impaired biofilm formation and gene expression. Conversely, switching AGC or AGT to TCN codons upregulated biofilm formation. Genome-wide ribosome profiling showed that ribosome density was higher at UCN codons than at AGC or AGU during biofilm formation. Serine starvation recapitulated the effect of biofilm-inducing conditions on ribosome occupancy and SinR production. As serine is one of the first amino acids to be exhausted at the end of exponential phase growth, reduced translation speed at serine codons may be exploited by other microbes in adapting to stationary phase.

sample_organism: Bacillus subtilis subsp. subtilis NCIB 3610 = ATCC 6051 = DSM 10

overall_design: 4 samples for ribosome profiling and 2 samples for total mRNA profiling

first: Aaron

last: DeLoughery

first: Niels

last: Bradshaw

first: Yun

first: Erin

last: O'Shea

first: Richard

last: Losick

first: Yunrong

last: Chai


title: Differential gene expression profile of newly diagnosed versus relapse acute promyelocytic leukemia

city: Bangalore

first: Genotypic

last: technology

state: Karnataka

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

institute: Genotypic Technology

summary: The aim of this study was to gain insight into the potential mechanism of resistance to arsenic trioxide and to identify genes that are modulated in the malignant promyelocytes at the time of relapse in APL patients. We analyzed the gene expression profile by the whole genome microarray of primary promyelocytes obtained from 8 newly diagnosed and 8 at relapse patients.

overall_design:
Agilent one-color experiment,Organism: Human ,Agilent Whole Genome Human 4x44k (AMADID: 014850)  , Labeling kit: Agilent Quick-Amp labeling Kit (p/n5190-0442)
newly diagnosed versus relapse acute promyelocytic leukemia

first: Vikram

last: Mathews

first: Ezhilarasi

last: Chendamarai


title: EDL933 cultured in bovine small intestine content (BSIC) vs M9 minimal media

status: Public on Aug 01 2013

city: Saint-Genes-Champanelle

first: Yolande

last: BERTIN

address: Centre INRA de Clermont-Ferrand-Theix

institute: Institut National de Recherche Agronomique

summary:
Enterohemorrhagic Escherichia coli (EHEC) are transmitted from cattle to human by means of contaminated food products resulting from fecal contamination.
Transcriptome analysis was performed to gain further insight into the metabolic pathways required for persistence and growth of EHEC in the bovine intestine.
Understanding the physiology of EHEC in the gut of ruminants is critical to identifying the potential nutritional basis to limiting EHEC shedding.
A global transcriptome analysis was performed to gain further insight into the metabolic pathways required for persistence and growth of EHEC in the bovine intestine.
DNA microarrays were performed using RNA from EHEC O157:H7 EDL933 incubated in bovine small intestine content (BSIC) compared with cells incubated in M9-minimal media.

overall_design:
Four biological replicates collected for bacterial cultures on separate days for each media and labelled following a dye-switch design :
For each media two replicates labeled in Cy3 and two replicates in Cy5.

last: Bertin

first: Anne

last: de la Foye

first: Christiane

last: Deval


title: Gene expression analysis of metastatic and non-metastatic osteosarcoma cell lines

status: Public on Jul 19 2013

city: Woolloongabba

first: Liliana

middle: Beatriz

last: Endo-Munoz

state: Queensland

address: TRI, 37 Kent St

department: Diamantina Institute

institute: University of Queensland

summary: Analysis of two metastatic OS cell lines, KHOS and KRIB, and two non-metastatic OS cell lines, HOS and U2OS. Results show differences in gene expression between cell lines with different ability to metastasise in vivo.

overall_design: Each of the four cell lines were analyzed in tripicate. Total RNA was extracted from each triplicate cell line culture with Trizol. cRNA was amplified using the Ambion Illumina Total Prep RNA Amplification Kit. Concentration was determined in NanoDrop and qulity checked in the Agilent Bioanalyzer, before hybridizing to Illumina HT-12 BeadChip Array.

first: Nicholas

last: Saunders


title: The glycolytic and gluconeogenic transcriptome of Pseudomonas putida KT2440

status: Public on Jul 23 2013

city: Cantoblanco

first: Juan

middle: Carlos

last: Oliveros

state: Madrid

address: Darwin 3

country: Spain

institute: CNB, CSIC

summary: Pseudomonas putida KT2440 is a metabolically versatile soil bacterium useful both as a model biodegradative organism and as a host of catalytic activities of biotechnological interest. In this report, we present the high-resolution transcriptome of P. putida grown in different carbon sources as revealed by deep sequencing of the corresponding RNA pools. Examination of the data from growth on glycolytic (glucose, fructose) and gluconeogenic (succinate or glycerol) substrates revealed that > 20% of the P. putida genome is differentially expressed depending on the ensuing metabolic regime. Changes affected not only metabolic genes but also a suite of global regulators, e.g. the rpoS sigma subunit of RNAP, various cold-shock proteins and the three HU histone-like proteins. Specifically, the genes encoding HU subunit variants hupA, hupB and hupN drastically altered their expression levels (and thus their ability to form heterodimeric combinations) under the different growth conditions. Furthermore, we found that the two small RNAs crcZ and crcY, known to inhibit the Crc protein that mediates catabolite repression in P. putida, were both down-regulated by glucose.

overall_design: cDNA libraries from Pseudomonas supplemented with different carbon sources (glucose, glycerol, fructose, succinate) were sequenced using HiSeq 2000 to yield 91 paired-end reads. Gene expression values were compared.

first: Juhyun

last: Kim

first: Pablo

last: Nikel

first: Víctor

last: de Lorenzo

first: Rafael

last: Silva-Rocha


title: Nogo-B protects mice against lipopolysaccharide-induced acute lung injury

status: Public on Jul 12 2013

city: Nanjing

first: wujian

last: xu

state: Jiangshu

address: 305 Esat Zhongshan Road

department: The department of respiratory disease

country: China

institute: Jinling Hospital

summary: Purpose: Acute lung injury (ALI) is a severe clinical disorder characterized by diffused capillary-alveolar barrier damage and noncardiogenic lung edema induced by excessive inflammation reactions. Nogo-B, a member of the reticulon 4 protein family, plays a critical role in modulating macrophages and neutrophils’ function in inflammation. Its role in ALI remains unclear.   Methods: Pulmonary expression of Nogo-B was investigated in a LPS-induced ALI mice model. The effects and the underline mechanisms of Nogo-B expression on the severity of lung injury was assessed using histological examination, Bronchoalveolar lavage fluid (BALF) protein and inflammatory cells and cytokines measurement, and microarray analysis.   Results: Nogo-B was normally highly expressed in the lungs of naïve C57BL/6 mice. Intra-tracheal instillation of LPS significantly repressed the Nogo-B expression in lung tissues and BALF cells of ALI mice. In addition, over-expression of pulmonary Nogo-B using an adenovirus vector which expresses a Nogo-B-RFP-3-flag fusion protein (Ad-Nogo-B) significantly prolonged the survival time of mice challenged with lethal dose of LPS. Histological results and BALF protein measurement convinced that Ad-Nogo-B treated mice had less severity of lung injury and alveolar protein exudation, as compared with control adenovirus treated mice (Ad-RFP). They also had higher MCP-1 secretion and alveolar macrophages infiltration, but lower neutrophils infiltration. Finally, using microarray analysis, we identified a protective gene, PTX3, was highly elevated in Ad-Nogo-B treated mice.   Conclusions: Nogo-B played a protective role in LPS-induced ALI, which might exert its role through modulation of inflammatory response and PTX3 secretion.

overall_design: A total of 12 samples from mice treated with or without LPS in the presence of Ad-Nogo-B or Ad-RFP transfection (n=3 for each group)

first: qiang

last: li


title: Expression data from mammary tumors from a Diversity Outcross x PyMT mouse cross

status: Public on Jul 06 2013

city: Bethesda

first: Kent

last: Hunter

state: MD

address: 37/4048 37 Convent Drive

department: Center for Cancer Research

country: USA

institute: National Cancer Institute

summary: Mouse genetic crosses were established between the PyMT model of metastatic breast cancer and the G5 generation of the Diversity Outcross (DO). Tumors were harvested from the animals for gene expression analysis to identify genes associated with progression to distant metastatic disease.

overall_design: Gene expression of 133 samples from the Diversity Outcross were assayed on Affymetrix chips.


title: Expression data from mammary tumors from MOLF/Ei x PyMT mouse crosses and Diversity Outcross x PyMT mouse crosses

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

overall_design: Refer to individual Series


title: poplar bent study-TRANSCRIPTOMIC ANALYSIS OF POPLAR STEM ACCOMMODATION TO REPEATED BENDING Species: Populus tremula x Populus aba

city: evry

first: stephanie

last: huguet

address: 2 rue gaston cremieux

institute: inra

summary:
affy_pop_2011_08 - poplar bent study - genes regulated by PtaZFP2 in absence of mechanical stress - genes regulated by PtaZFP2 after one bending.Species: Populus tremula x Populus alba-- The laboratory previously established a poplar transgenic line overexpressing PtaZFP2 under the control of an estradiol-inducible promoter. - the experiment, conducted on 3-month-old hydroponically-grown poplars, consists in the comparison of WT poplars treated with estradiol and the PtaZFP2-overexpressing line treated with estradiol. We also compared unbent and bent PtaZFP2-overexpressing poplars. The applied strain is quantitatively controlled (Coutand & Moulia, 2000, JExpBot; coutand et al., 2009, Plant Physiology) -
27 arrays - poplar; gene knock in (transgenic)

overall_design: 27 samples are wt; for this experiment only the bending comparaison are studied.

first: Stephanie

last: Huguet

first: Alberto

last: Macho

first: Mélanie

last: Decourteix

first: Nathalie

last: Leblanc-fournier

first: Sandrine

last: Balzergue

first: Marie-Laure

last: Martin-Magniette


title: Effect of maternal methionine supplementation on the transcriptome of bovine preimplantation embryos

status: Public on Jun 21 2013

city: Madison

first: Francisco

last: Peñagaricano

state: Wisconsin

address: 1675 Observatory Drive

department: Animal and Dairy Sciences

institute: University of Wisconsin-Madison

summary: Maternal nutrition exclusively during the periconceptional period can induce remarkable effects on both oocyte maturation and early embryo development, which in turn can have lifelong consequences. The objective of this study was to evaluate the effect of maternal methionine supplementation on the transcriptome of bovine preimplantation embryos. Holstein cows were randomly assigned to one of two treatments differing in level of dietary methionine (1.89 Met vs. 2.43 Met % of metabolizable protein) from calving until embryo flushing. High quality preimplantation embryos from individual cows were pooled and then analyzed by RNA sequencing.

overall_design: A total of eight Holstein dairy cows were used in this study. Preimplantation embryos recovered from each cow were pooled in order to generate two replicates per cow assayed. Each pool consisted of 2-4 expanded blastocysts with excellent quality. Overall, a total of 16 embryo pools underwent RNA extraction, amplification, and subsequent sequencing.

first: Milo

last: Wiltbank

first: Hasan

last: Khatib


title: Dose-dependent dual roles of PDGF-BB–PDGFR-β in vascular remodeling and opposing effects of anti-PDGF drug-induced metastasis

status: Public on Jul 22 2013

city: Stockholm

first: Ola

last: Larsson

department: Department of oncology-pathology

institute: Karolinska Institutet

summary: Anti-PDGF agents are routinely used as a key component in front-line therapy for the treatment of various cancers. However, molecular mechanisms underlying their impact on vascular remodeling in relation to the dose issue remain poorly understood. Here we show that in high PDGF-BB-producing tumors, anti-PDGF drugs significantly inhibited tumor growth and metastasis by preventing pericyte (PC) loss and vascular permeability. Surprisingly, the same anti-PDGF-BB drugs promoted tumor cell dissemination and metastasis in PDGF-BB-low-producing or negative tumors by ablating PCs from tumor vessels. At the molecular level, we show that the PDGFR-β signaling pathway in PCs mediated the opposing effects and persistent exposure of PCs to PDGF-BB led to marked downregulation of PDGFR-β. Inactivation of the PDGFR-β signaling system led to decreased levels of integrin α1β1, resulted in impaired adhesion of PCs to collagen I, IV and laminin, two principal extracellular matrix components in blood vessels for interaction with these integrins. Our data suggest that tumor PDGF-BB levels may serve as an important biomarker for selection of tumor-bearing hosts for beneficial therapy and unsupervised practice of this group of drugs could potentially promote tumor invasion and metastasis.

overall_design: Pericytes were isolated and treated with PDGF-BB or control for 5 days.


title: DNA methylome and transcriptome analysis of normal and HBx transgenic mouse liver

status: Public on Jun 19 2013

city: Seoul

first: Sun-Min

last: LEE

address: Shinchon-dong Seodeamun-gu

department: Biochemistry

institute: Yonsei University

summary: A genome-wide integrated methylome and transcriptome analysis of the early stage of hepatocellular carcinoma development that induced by HBx. The HBV x (HBx) protein, which plays a critical role in the development of HCC, was shown to interact with several epigenetic factors, such as DNMT3A and HDAC1. Most HBx transgenic (TG) mice spontaneously develop HCC at about 1 year of age, providing genetic validation of the oncogenic potential of HBx even in the absence of viral integration and chronic inflammation. Therefore, it would be intriguing to study the regulatory role of HBx in the epigenome and its impact on HCC development. We performed a genome-wide analysis to examine the differences in DNA methylation patterns and RNA transcriptions between cancer and normal liver cells.

overall_design: High-throughput sequencing analysis of MIRA (methylated CpG island recovery assay) and mRNA at 3 mouth old age mouse liver

last: Lee

first: Jae-Bum

last: Bae


title: Global Gene Expression of hematopoietic stem cells expressing endogenous NrasG12D/G12D, NrasG12D/+, Nras+/+

status: Public on May 29 2013

city: Guangzhou

first: jinyong

last: wang

state: Guangdong

address: 190 Kaiyuan road

institute: Guangzhou Institutes of Biomedicine and Health, Chinese Accademy of Sciences

summary: Oncogenic NRAS mutations are frequently identified in human myeloid leukemias. In mice, expression of endogenous oncogenic Nras (NrasG12D/+) in hematopoietic cells leads to expansion of myeloid progenitors, increased long-term reconstitution of bone marrow cells, and a chronic myeloproliferative neoplasm (MPN). However, acute expression of NrasG12D/+ in a pure C57BL/6 background does not induce hyperactivated GM-CSF signaling or increased proliferation in myeloid progenitors. It is thus unclear how NrasG12D/+ signaling promotes leukemogenesis. Here we show that hematopoietic stem cells (HSCs) expressing NrasG12D/+ serve as MPN initiating cells. They undergo moderate hyperproliferation with increased self-renewal. The aberrant NrasG12D/+ HSC function is associated with hyperactivation of ERK1/2 in HSCs. Conversely, downregulation of MEK/ERK by pharmacological and genetic approaches attenuates the cycling of NrasG12D/+ HSCs and prevents the expansion of NrasG12D/+ HSCs and myeloid progenitors. Our data delineate critical mechanisms of oncogenic Nras signaling in HSC function and leukemogenesis.

overall_design: three NrasG12D/G12D HSCs samples, three NrasG12D/+ HSCs samples, two Nras+/+ HSCs control samples.

first: Jinyong

last: Wang

first: Jing

last: Zhang


title: Genome-wide variation of cytosine modifications between European and African populations and the implications for complex traits

status: Public on Jul 01 2013

city: Chicago

first: Wei

state: Illinois

address: 840 S. Wood Street

department: Pediatrics & Institute of Human Genetics

institute: University of Illinois

type: Methylation profiling by genome tiling array

summary: Elucidating cytosine modification difference between human populations can enhance our understanding of ethnic specificity in complex traits such as disease predisposition and drug response. In this study, cytosine modification levels in 133 HapMap lymphoblastoid cell lines (LCLs) derived from individuals of European or African ancestry were profiled using the Illumina HumanMethylation450 BeadChip. Approximately 13% of the analyzed CpG sites showed differential modification between the two populations at false discovery rate (FDR) of 1%. CpG sites with greater modification levels in European descents were enriched in the proximal regulatory regions, while those greater in African descents were biased toward gene bodies. More than half of the detected population-specific cytosine modifications could be explained by genetic variation. A substantial proportion of local modification quantitative trait loci (mQTL) exhibited population-specific effects, suggesting that genetic epistasis and/or genotype × environment interaction could be common. Distinct inter-individual correlations were observed between gene expression and cytosine modifications in both proximal promoters and gene bodies, demonstrating a regulatory role of inter-individual variation in cytosine modification. Furthermore, a number of SNPs (single nucleotide polymorphisms) previously identified for complex traits with known racial disparities could be annotated as mQTLs for population-specific CpGs. Our findings revealed abundant population-specific cytosine modifications and the underlying genetic basis, as well as the relatively independent contribution of genetic and epigenetic variations to population differences in gene expression.

overall_design: 60 unrelated CEU and 73 unrelated YRI samples from the HapMap Project were profiled for cytosine modification levels.

first: Eileen

last: Dolan

first: Lucy

last: Godley


title: Genome-wide gene expression profiling of high-grade osteosarcoma cell lines

status: Public on Jun 06 2013

city: Oslo

first: Marieke

middle: Lydia

last: Kuijjer

address: Gaustadalléen 21

country: Norway

institute: Centre for Molecular Medicine Norway

summary: We performed genome-wide gene expression data of high-grade osteosarcoma cell lines, as well as on mesenchymal stem cells, and osteoblasts, and performed global test analysis in order to determine the most significantly affected KEGG pathways.

overall_design: Genome-wide gene expression analysis was performed on 19 high-grade osteosarcoma cell lines. Significantly differentially expressed genes were determined between osteosarcoma cells and two different sets of control samples - osteoblasts [n=3, GEO accession number GSE33382] and mesenchymal stem cells [n=12, GEO accession number GSE28974]. Global test was applied to the different analyses, in order to determine the most affected signaling pathways in osteosarcoma cells.

first: Elisabeth

last: Peterse

first: Brendy

middle: E

last: van den Akker

first: Inge

last: Briaire-deBruijn

first: Massimo

last: Serra

first: Leonardo

last: Meza-Zepeda

last: Myklebost

first: Bass

last: Hassan

first: Pancras

last: Hogendoorn

first: Anne-Marie

last: Cleton-Jansen


title: Expression signature as a biomarker for prenatal diagnosis of trisomy 21

city: Ljubljana

first: Ales

last: Maver

address: Slajmerjeva 3

country: Slovenia

institute: Clinical institute of medical genetics Ljubljana Slovenia

summary: To date, a universal biomarker panel with a potential to predict high-risk pregnancies or adverse pregnancy outcome does not exist. Transcriptomic approach, a measure of gene expression levels across the genome, is a powerful tool to capture differentially expressed genes (DEG) in various conditions, including human trisomy of chromosome 21 (Ts21). DEG can be used to design a biomarker set as a diagnostic-predictive tool for various conditions of heterogeneous aetiology in a prenatal setting. In the search of novel biomarker set to predict high-risk pregnancies, we performed global expression profiling to find DEG in Ts21 used as a model. Subsequently we performed targeted validation and diagnostic performance evaluation on a larger group of case and control samples.  Initially, transcriptomic profiles of 10 cultivated amniocyte samples with Ts21 and 9 with normal euploid constitution were determined using Agilent 4x44K expression microarrays. DEG were discovered using linear regression modelling implemented in limma package. Datasets from Ts21 transcriptomic studies available at GEO repository were incorporated to select our preliminary top DEG. Subsequently, selected top DEG were validated using RT-PCR quantification on independent sample of 16 cases with Ts21 and 32 controls, as well as new datasets from previously performed expression studies in Ts21. The classification was performed using support vector machine classification kernel and evaluated using leave-one-out cross validation approach.

overall_design: Transcriptomic profiles of 10 cultivated amniocyte samples with Ts21 and 9 with normal euploid constitution were determined using Agilent 4x44K expression microarrays.

first: Marija

last: Volk

first: Luca

last: Lovrecic

first: Peter

last: Juvan

first: Borut

last: Peterlin


title: A transcriptome-wide RNAi screen in the Drosophila ovary reveals factors of the germline piRNA pathway

status: Public on May 10 2013

city: Cold Spring Harbor

first: Benjamin

last: Czech

state: NY

address: 1 Bungtown Rd

institute: Cold Spring Harbor Laboratory


title: Directed shotgun proteomics guided by RNA-Seq identifies a complete expressed prokaryotic proteome

status: Public on Apr 23 2013

city: Zurich

first: Ulrich

last: Omasits

address: Wolfgang Pauli-Str. 16

department: IMSB Institute of Molecular Systems Biology

country: Switzerland

institute: ETH Zurich

summary: Prokaryotes are, due to their moderate complexity, particularly amenable to the comprehensive identification of the protein repertoire expressed under different conditions. We applied a generic strategy to identify a complete expressed prokaryotic proteome, which is based on the analysis of RNA and proteins extracted from matched samples. Saturated transcriptome profiling by RNA-seq provided an endpoint estimate of the protein-coding genes expressed under two conditions which mimic the interaction of Bartonella henselae with its mammalian host. Directed shotgun proteomics experiments were carried out on four subcellular fractions. By specifically targeting proteins which are short, basic, low abundant and membrane localized, we could eliminate their initial under-representation compared to the estimated endpoint. A total of 1,250 proteins were identified with an estimated false discovery rate below 1%. This represents 85% of all distinct annotated proteins and around 90% of the expressed protein-coding genes. Genes, whose transcripts were detected, but not their corresponding protein products, were found highly enriched in several genomic islands. Additionally, genes that lacked an ortholog and a functional annotation were not detected at the protein level, and possibly include over-predicted genes in genome annotations. Furthermore, a dramatic membrane proteome re-organization was observed including differential regulation of autotransporters, adhesins and hemin binding proteins. Particularly noteworthy was the complete membrane proteome coverage which included expression of all members of the VirB/D4 type IV secretion system, a key virulence factor.

overall_design: Transcriptome and proteome analysis of B.henselae in two conditions and duplicates: uninduced and induced for host invasion.

first: Maxime

last: Quebatte

first: Daniel

middle: J

last: Stekhoven

first: Claudia

last: Fortes

first: Bernd

last: Roschitzki

first: Mark

middle: D

last: Robinson

first: Christoph

last: Dehio

first: Christian

last: Ahrens


title: A transcriptome-wide RNAi screen in the Drosophila ovary reveals factors of the germline piRNA pathway [RNA-Seq]

summary: The Drosophila piRNA pathway provides an RNA-based immune system that defends the germline genome against selfish genetic elements. Two inter-related branches of the piRNA system exist: somatic cells that support oogenesis only employ Piwi, whereas germ cells utilize a more elaborated pathway centered on the three gonad-specific Argonaute proteins Piwi, Aubergine, and Argonaute3. While several key factors of each branch have been identified, our current knowledge is insufficient to explain the complex workings of the piRNA machinery. Here, we report a reverse genetic screen spanning the ovarian transcriptome in an attempt to uncover the full repertoire of genes required for piRNA-mediated transposon silencing in the female germline. Our screen reveals new key factors of piRNA-mediated transposon silencing, including the novel piRNA biogenesis factors, CG2183 (GASZ) and Deadlock. Last, our data uncovers a previously unanticipated set of factors preferentially required for repression of different transposons types.

overall_design: Examination of total RNA levels from nos-GAL4 or tj-GAL4 driven UAS-dsRNA knockdowns of control genes and piRNA pathway components in ovaries of Drosophila melanogaster by deep sequencing (using Illumina HiSeq2000).

first: Jonathan

last: Preall

first: Jon

last: McGinn

first: Gregory

last: Hannon


title: Effects of MDMA and Venlafaxine treatment in Dark Agouti rats

status: Public on Jun 01 2013

city: Budapest

first: Viola

last: Tamasi

address: Nagyvarad sqr 4

department: Genetic, Cell- and Immunobiology

country: Hungary

institute: Semmelweis University

summary: The aim of this study was to examine the hippocampus, frontal cortex and dorsal raphe of Dark Agouti rats with gene expression arrays (Illumina RatRef bead arrays) looking for possible mechanisms and new candidates contributing to the effects of a single dose of MDMA (15 mg/kg) 3 weeks earlier or venlafaxine (40 mg/kg) administration for 3 weeks continously. We also examined the possible interaction between the single dose MDMA treatment and the continous venlafaxine treatment described above.

overall_design: With the present study we tried to evaluate the effects of a single, neurotoxic dose of 3,4-methylenedioxymethamphetamine (MDMA) and/or 3 weeks long venlafaxine (VLX) treatment in the dorsal raphe, frontal cortical or hippocampal neurons in Dark Agouti rats. For the analysis of MDMA long-term effects rats were treated once with 15 mg/kg MDMA i.p. in a volume of 1 ml/kg 3 weeks prior to sacrificing the animals. In the case of VLX, the animals were administered 40 mg/kg of the drug for 3 weeks via Alzet 2001 minipumps inserted under the skin of the rats. In the third group rats received the mentioned treatment protocols simultaneously. Vehicle and sham-operated controls were used for comparison. For microarray analysis all groups consisted of 8 animals. Every two randomly selected samples from the same brain regions were pooled resulting in 4 pooled samples per region and treatment. From the total 48 pooled samples 2 were excluded because of quality control reasons. For RNA extraction Trizol reagent was used and microarray analysis was done by Service XS (Netherlands) according to Illumina protocols (San Diego, CA, USA). Results were validated with Fluidigm GEx (San Francisco, CA, USA) arrays using TaqMan Gene Expression (Carlsbad, CA, USA) assays. In this study no replicates were used.

last: Petschner

first: Csaba

last: Adori

first: Romeo

last: Ando

first: Eszter

last: Kirilly

first: Laszlo

last: Tothfalusi

first: Gyorgy

last: Bagdy


title: Transcriptional Profiling in Non-Human Primates Infected With Lassa Virus to Understand the Immune Response to Lassa Infection

status: Public on Jun 18 2013

city: Boston

first: Judy

last: Yen

state: MA

address: 620 Albany St., Rm 401H

department: NEIDL/Microbiology

institute: Boston University School of Medicine

summary: Lassa fever virus (LASV) is a significant human pathogen that is endemic to several countries in West Africa.  Infection with Lassa leads to the development of hemorrhagic fever in a significant number of public health cases and it is considered a potential bioweapon. Little is known about the complex immune mechanisms governing response to LASV infection, or the genetic determinants of susceptibility and resistance to infection. In the study presented here, we have used a whole-genome, microarray-based approach to determine the temporal host response to infection in the peripheral blood mononuclear cells of non-human primates (NHP) infected with LASV. Sequential sampling over the entire disease course showed that there are specific transcription signatures of the immune response to LASV infection, including the rapid up- regulation of interferon-responsive genes and toll-like receptor signaling pathways. However, this increase in early innate responses was coupled with a lack of pro- inflammatory cytokine response in LASV infected NHPs. There was a distinct lack of cytokines such as IL1b and IL23a, while immune suppressive cytokines such as IL27 and IL6 were upregulated. Comparison of cytokine gene expression with the amount of detectable protein in Lassa infected NHPs suggests that gene expression precedes the protein detection and thus is possibly a better tool for early diagnostics of the disease. Our results provide a comprehensive picture of the immune response to hemorrhagic LASV infection and provide a foundation for biomarker identification to allow clinical diagnosis of Lassa infection through analysis of the host response.

sample_organism:
Macaca fascicularis
Homo sapiens

overall_design: RNA was isolated from a total of 46 PBMC samples from 15 cynomologus macaques infected with Lassa Virus.  Samples were obtained at sequential timepoints post-infection, and included a pre-infection specimen from each animal.  A subset of 30 samples (11 animals) were then processed and hybridized onto the Agilent 2-color arrays.

first: Shikha

last: Malhotra

middle: Y

first: Sara

last: Garamszegi

first: John

last: Trefry

first: Joshua

last: Johnson

first: Anna

middle: N

last: Honko

first: Lisa

last: Hensley

middle: H

last: Connor


title: A transcriptome-wide RNAi screen in the Drosophila ovary reveals factors of the germline piRNA pathway [smallRNA-Seq]

first: Benjamin

last: Czech

overall_design: Examination of small RNA levels from nos-GAL4 or tj-GAL4 driven UAS-dsRNA knockdowns of control genes and piRNA pathway components in ovaries of Drosophila melanogaster by deep sequencing (using Illumina HiSeq2000).

last: Preall

last: McGinn