title: Systems biological analysis of immunity to dengue

status: Public on Jun 27 2014

city: SÃO PAULO

first: Helder

middle: I.

last: Nakaya

state: SÃO PAULO

address: AVENIDA PROFESSOR LINEU PRESTES, 580, Block 17

country: Brazil

institute: Universidade de São Paulo

summary: Dengue virus (DENV) infects hundreds of millions of people annually, yet there is only a limited knowledge of the host immune response to dengue. Here, we used a systems biological approach to perform a detailed analysis of the innate immune response to DENV infection in the whole blood samples of acutely infected humans in Bangkok, Thailand. Transcriptomic analysis revealed that genes encoding pro-inflammatory mediators and type I IFN related proteins, were associated with high levels of virus during the first few days of infection. Individuals with low or negative viremia at the late stage of fever were enriched with genes associated with pathways involved in cell cycle, proliferation, cell metabolism and translational control. Meta-analysis showed significant enrichment in genes specific for innate cells (monocytes, macrophages and DCs) in the specimens with high VL and enrichment in genes specific for NK cells, CD4+ and CD8+ T cells as well as B cells in specimens with low VL. Furthermore, flow cytometric analysis revealed an expansion in the numbers of CD14+CD16+ monocytes and depletion of CD14dimCD16++ cells and BDCA-1+ myeloid DC in blood. Consistent with this, in a non-human primate model, infection with DENV boosted the numbers of CD14+CD16+ monocytes in the blood and in secondary lymphoid organs. In vitro, freshly isolated blood monocytes infected with DENV up regulated CD16 and mediated robust differentiation of resting B cells to CD27++CD38++ plasmablasts and IgG and IgM secretion. Taken together, these data provide a detailed picture of the innate response to dengue infection in humans, and highlight an unappreciated role for CD14+CD16+ monocytes in promoting the differentiation of plasmablasts and mediating antibody response to DENV.

overall_design: We analyzed whole blood samples from 28 dengue patients (DF n=18, DHF=10) hospitalized at the Siriraj Hospital in Bangkok, Thailand during the season of 2009 The specimens were acquired between days 2 and 9 after onset of symptoms (acute illness), and for 19 patients (DF n=13, DHF=6) also at the convalescence at 4 weeks or later after discharge. Additionally, blood was sampled from 9 healthy, non-infected donors to provide controls for transcriptomic and immunological analysis.

middle: I

first: Marcin

last: Kwissa

first: Bali

last: Pulendran


title: Effects of two strains of Lactobacillus fermentum on germ free rats

status: Public on Jun 25 2014

city: Palmerston North

first: Wayne

last: Young

address: Tennent Drive

country: New Zealand

institute: AgResearch

summary: Transcription profiling of intestinal tissue from germ free rats mono-colonised with one of two strains of Lactobacillus fermentum; AGR1485 or AGR 1487

overall_design: Two colour microarray, reference design. 2 treatments (AGR1485 or AGR1487) and 2 tissues analysed (colon or duodenum): Biological replicates: 6

first: Rachel

last: Anderson


title: RUNX1 positively regulates a cell adhesion and migration program in murine hemogenic endothelium prior to blood emergence

status: Public on Aug 05 2014

city: manchester

first: michael

last: lie-a-ling

address: The University of Manchester | Wilmslow Road

department: Stem Cell Biology

country: United Kingdom

institute: Cancer Research UK Manchester Institute

type: Expression profiling by high throughput sequencing

type: Genome binding/occupancy profiling by high throughput sequencing

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

overall_design: Refer to individual Series


title: High intake of dietary sugar enhances bisphenol A (BPA) disruption and reveals ribosome-mediated pathways of toxicity

status: Public on Jun 04 2014

city: Boston

first: Alan

last: Branco

address: 665 Huntington Ave.

department: Environmental Health

country: USA

institute: Harvard School of Public Health


title: Molecular characterization of 4-NQO induced F344 rat tongue carcinogenesis: alteration of multiple gene expression and hypomethylation of PTGS2 proximal promoter

status: Public on Aug 04 2014

city: Northbrook

first: Michael

last: Falduto

state: IL

address: 1808 Janke, Unit M

institute: GenUs BioSystems, Inc.

summary: The 4-NQO induced rat tongue carcinogenesis model presenting considerable histologic and molecular similarity to oral cancers commonly seen in humans is very useful for investigating oral carcinogenesis.  In order to understand the molecular basis of oral carcinogenesis and identify gene biomarkers and potential chemopreventive targets for future studies, we characterized the molecular changes in oral squamous cell carcinoma (SCC) samples generated from this model system using F344 rats by performing gene expression microarray and methylation analysis of selected genes.  Microarray studies identified 1735 genes to be upregulated by at least 2 fold (p<0.05, n=11) and 1803 genes to be downregulated by at least 50% (p<0.05, n=11) in SCC in comparison to the adjacent normal tissues and 28 KEGG pathways to be altered in SCC (p<0.01).  Among the altered genes, keratins and keratin associated proteins were found to be differentially regulated and the keratin profile appeared to an important biomarker for oral SCC.  PTGS2 and PTGS2 relevant genes, which are potential targets of chemoprevention and therapy, were also found to be upregulated in SCC and confirmed by qRT-PCR.   The upregulation of PTGS2 appeared to correlate with hypomethylation of its proximal promoter.  Methylation analysis of other selected genes showed that the first exon of APC2 was methylated in normal tissues, and the methylation level increased moderately in SCC samples (p<0.01, n=8).   These results demonstrate that 4-NQO induced tongue carcinogenesis in F344 rats is accompanied by alteration of multiple gene expression, hypomethylation of PTGS2 and increased methylation of APC2.

overall_design: Gene expression in untreated normal vs.4-NQO induced tongue tumors in F344 rats (n=11).

first: Xinjian

last: Peng

first: William

middle: D

last: Johnson

first: Wenping

last: Li

first: Karen

middle: E

last: Torres

first: David

middle: L

last: McCormick


title: Time-series DNA occupancy during the yeast respiratory cycle

status: Public on Aug 06 2014

city: Tsuruoka

first: Douglas

middle: Brian

last: Murray

state: Yamagata

address: Nipponkoku 403-1, Daihouji

country: Japan

institute: Institute for Advanced Biosciences

type: Genome variation profiling by genome tiling array

summary: We use metabolically synchronous, continuously-grown yeast cultures to measure DNA occupancy and track the global patterns with respect to the metabolic state of the culture, showing a genome-wide nucleosome focusing in the reductive phase, followed by clearance of the promoter regions

overall_design: 32 timepoints protein-bound (pDNA) vs. genomic (gDNA) over 3 respiratory cycles + 3 MNase-digested naked DNA control samples.

first: Cornelia

last: Amariei

middle: B


title: RUNX1 positively regulates a cell adhesion and migration program in murine hemogenic endothelium prior to blood emergence (RNA-seq)

summary: During ontogeny the transcription factor RUNX1 governs the emergence of definitive hematopoietic cells from specialized endothelial cells, called hemogenic endothelium (HE). The ultimate consequence of this endothelial-to-hematopoietic transition is the concomitant activation of the hematopoietic program and down-regulation of the endothelial program. However, due to the rare and transient nature of the HE, little is known about the initial role of RUNX1 within this population. We therefore developed and implemented a highly sensitive DamID (DNA adenine methyltransferase identification) based methodology, including a novel data analysis pipeline, to map early RUNX1 transcriptional targets in HE cells. This novel transcription factor binding site identification protocol should be widely applicable to other low abundance cell types and factors. Integration of the RUNX1 binding profile with gene expression data revealed an unexpected early role for RUNX1 as a positive regulator of cell adhesion and migration associated genes within the HE. This suggests that RUNX1 orchestrates HE cell positioning and integration prior to the release of hematopoietic cells. Overall, our genome-wide analysis of the RUNX1 binding and transcriptional profile in the HE provides a novel comprehensive resource of target genes that will facilitate the precise dissection of the role of RUNX1 in early blood development.

overall_design: mRNA profiles of mouse ES derived Haemogenonic Endothelium (cKit+ Tie2+ CD41-) were generated by deep sequencing using the SOLiD 5500XL Genetic Analyser (Applied Biosystems). Two biological duplicates of each of the following lines was sequenced: iDam & BryGFP (both wt background) and iDam_runx1-/- (iDamko) & Ainv18_runx1-/- (Ainv18ko). The latter two lines are Runx1 knockouts.

last: Lie-A-Ling

first: Elli

last: Marinopoulou

first: Yaoyong

first: Rahima

last: Patel

first: Monika

last: Stefanska

first: Constanze

last: Bonifer

first: Crispin

last: Miller

first: Valerie

last: Kouskoff

first: Georges

last: Lacaud


title: Human enteroendcrine cell responses to infection with Chlamydia trachomatis

status: Public on Jun 03 2014

city: Stockholm

first: Aldona

last: Dlugosz

address: Karolinska Huddinge

department: Gastroenterology and hepatology

country: Sweden

institute: Karolinska Institutet

summary: The aim of this study was to perform a microarray analysis of the response pattern of EEC from both large and small bowel to infection in vitro, using Chlamydia trachomatis infection as a model.

overall_design: Two human EEC lines: LCC-18, derived from a neuroendocrine colonic tumour, and CNDT-2, derived from a small intestinal carcinoid, were infected with C. trachomatis serovar LGV II strain 434 (ATCC VR-902B). Penicillin G was used to induce persistent infection.  Gene expression levels in infected and persistently infected EEC cells were investigated by microarray analysis

first: Sandra

last: Muschiol

first: Katherina

last: Zakikhany

first: Ghazaleh

last: Assadi

first: Mauro

last: D'Amato

first: Greger

last: Lindberg


title: Time Course of Gene Expression in Rat-1 Fibroblasts Following Alpha-1a Adrenergic Receptor Stimulation with Phenylephrine.

status: Public on Aug 01 2014

city: Loma Linda

first: Daniel

middle: P

last: Morris

state: CA

address: Loma LInda University

department: Center for Perinatal Biology

institute: Loma LInda University

summary: In mammals, increasing evidence supports the generality of cotranscriptional gene regulation and the idea that genetic control often occurs subsequent to RNA polymerase II (Pol II) recruitment. In our recent experiments, we have used Pol II Chromatin Immunoprecipitation (ChIP) to investigate relationships between the mechanistic events that control acute stress response (ASR) gene activation following stimulation of the alpha1a-Adrenergic Receptor expressed in rat-1 fibroblasts.  We validate the temporal accuracy of our Pol II ChIP assay by comparison to major transcriptional events assessable by microarray and PCR analysis of precursor and mature mRNA.  Initial temporal microarray analysis of gene activation following agonist addition identified genes that were upregulated and provided a temporal profile of changes in polyadenylated mRNA levels.  Combined with PCR analysis of pre-mRNA, total RNA, polyadenylated RNA and the Pol II ChIP data, we demonstrate complex multilevel gene regulation including a diverse set of cotranscriptional mechanisms.   Given our data, we propose that analysis of a genes regulation must begin with global assessement of changes in transcriptional behavior to identify events that are actually rate limiting if reductionist mechanistic dissection is to distinguish events that are regulated from the larger set of mechanisms available to most genes.

overall_design: This microarray analysis reports on the temporal changes in polyadenylated mRNA levels in proliferating rat-1 fibroblasts following stimulation of the alpha-1a Adrenergic Receptor with filter sterilized 10 uM phenylephrine (PE). Cells were treated and harvested at 70 to 80% confluence. Rat-1 cells under these conditions are still mid-log phase and continue to proliferate for at least another replicative cycle.  Message levels in untreated cells were determined for 3 biological replicates, but all other time points are single replicates as sufficiently detailed dissection made replicates expensive and unnecessary, given that clear trending behavior in the expression profiles demonstrates profile accuracy.

first: Beilei

last: Lei

first: Gregory

last: Michelotti

first: Debra

middle: A

last: Schwinn


title: Loss of Sip1 leads to migration defects and retention of ectodermal markers during lens development

status: Public on Jun 01 2014

city: Newark

first: Melinda

middle: K.

last: Duncan

state: DE

address: 327 Wolf Hall

department: Biological Sciences

institute: University of Delaware

summary:
We report the application of  RNA-sequencing technology for the high-throughput profiling of mammalian lens gene expression at embryonic day 15.5.  The lens has a particularly biased transcriptome, with the top 50 genes encoding approximately 90% of the protein content.  Using RNA-Seq, we have shown that there are over 7,700 genes being expressed in the lens at embryonic day 15.5.  As expected, the crystallins and many structural genes were amoung the most highly expressed; however, numerous genes expressed at lower transcript abundance were also identified.  This study provides a framework for the application of RNA-Seq technology towards characterization of the mammalian lens transcriptome during development.
Using high-throughput RNA-sequencing, gene expression in the mammalian lens was compared between an inbred C56Bl/6<har> strain and a mix background strain at E15.5.  This analysis identifies almost 2,000 genes being differentially expressed between the inbred and mixed background lenses, ranging from 6.5 fold upregulated to 5.2 fold downregulated in the mixed background compared to the inbred strain.  This list does not include unknown/predicted genes or pseudogenes which are known to change between strains.  Further, it appears that approximately 98% of these genes are altered at levels less than 2.5 fold.  This study therefore provides a fold change threshold cutoff (2.5 fold) to use in the analysis of differentially expressed lens genes at E15.5 using RNA-Seq technology as it takes into account genetic variation due to background strain differences.
SIP1 encodes a DNA-binding transcription factor that regulates multiple developmental processes as highlighted by the pleiotropic defects observed in Mowat-Wilson Syndrome, which results from mutations in this gene.  Further, in adults, dysregulated SIP1 expression has been implicated in both cancer and fibrotic diseases where it functionally links TGFb signaling to the loss of epithelial preferred gene expression.  In the ocular lens, an epithelial tissue important for vision, Sip1 is co-expressed with epithelial markers such as E-cadherin, and is required for the complete separation of the lens vesicle from the head ectoderm during early ocular morphogenesis.  However, the function of Sip1 after early lens morphogenesis is still unknown.   Here, we conditionally deleted Sip1 from the developing mouse lens shortly after lens vesicle closure, leading to defects in coordinated fiber cell tip migration, defective suture formation and cataract.  Interestingly, RNA-Sequencing analysis on Sip1 knockout lenses identified 190 differentially expressed genes, all of which are distinct from previously described Sip1 target genes involved in EMT/cancer.  Furthermore, 34% of the upregulated genes in the Sip1 knockout lenses are normally downregulated as the lens transitions from the lens vesicle to early lens, while 49% of the genes downregulated in the Sip1 knockout lenses are normally upregulated during early lens development.  Overall, these data imply that Sip1 plays a major role in reprogramming the lens vesicle away from a surface ectoderm cell fate towards that necessary for the development of a transparent lens and demonstrate that Sip1 regulates distinctly different sets of genes in different cellular contexts.

overall_design:
RNA-Seq of inbred background wild type lenses at E15.5
RNA-Seq comparison of mixed background wild type controls and inbred wild type (C57Bl/6<har>) lenses at E15.5
RNA-Seq comparison of mixed background wild type controls and Sip1 conditional knockout lenses at E15.5

first: Abby

last: Manthey

middle: K


title: DNA methylation variability in a pilot study group with ischemic stroke

status: Public on May 27 2014

city: Melbourne

first: Mark

last: Ziemann

state: VIC

address: 85 Commercial Rd

department: Bioinformatics Working Group

country: Australia

institute: Burnet Institute

type: Methylation profiling by high throughput sequencing

summary: Elevated plasma homocysteine is an independent risk factor for cardiovascular disease and stroke, however the etiology remains poorly understood. Elevated homocysteine is known to inhibit methyltransferases including DNA methyltransferases, but no methylome-wide analysis of elevated homocysteine has been reported. Peripheral blood genomic DNA methylation in 8 Singaporean-Chinese ischemic stroke patients (4 male, 4 female) with varying homocysteine titer and hypertensive status were profiled using methyl-CpG binding domain (MBD) protein-enriched genome sequencing (MBD-seq) on Illumina Genome Analyzer IIx. A methylome wide screen was undertaken for gender, total plasma homocysteine, hypertension and age. The data show considerable variability within the small cohort, including at genes which are related to one carbon metabolism and cardiovascular disease.

overall_design: Peripheral blood genomic DNA methylation in 8 Singaporean-Chinese ischemic stroke patients (4 male, 4 female) was profiled using methyl-CpG binding domain (MBD) protein-enriched genome sequencing (MBD-seq) on Illumina Genome Analyzer IIx. Methylation parrterns were correlated with homocysteine levels, lypertensive status, gender and age.

first: Harikrishnan

last: KN

first: Antony

last: Kaspi

first: Deidre

last: De Silva

first: Kyaw

middle: T

last: Moe

first: Assam

last: El-Osta


title: Gene expression in reprogramming MEF fractions FACS-sorted by Oct4, Klf4 and EpCAM expression

city: Stanford

first: Yury

last: Goltsev

address: 3220 CCRS, Baxter lab,

department: Department of Microbiology and Immunology

institute: Stanford Medical School

summary: After 8 days of OKSM induction via doxycycline, Nanog-Neo secondary MEFs (Wernig et al. Nature Biotechnology 2008) were FACS sorted by KLF4, Oct4, and EpCAM expression. Four major subsets of MEFs have been sorted and analysed for gene expression.

overall_design: 4 cell types

first: Eli

last: Zunder


title: Reprogramming of Endothelium Into Hematopoietic Progenitors by Defined Factors and Vascular Induction

status: Public on Jul 11 2014

city: New York

first: Olivier

last: Elemento

state: NY

address: 1305 York Avenue

institute: WEILL MEDICAL COLLEGE OF CORNELL UNIV

summary: Generation of abundant engraftable hematopoietic cells from autologous tissues promises new therapies for hematologic diseases. Differentiation of pluripotent stem cells into hematopoietic cells results in emergence of cells that have poor engraftment potential.  To circumvent this hurdle, we have devised a vascular niche model to phenocopy the developmental microenvironment of hemogenic cells thereby enabling direct transcriptional reprogramming of human endothelial cells (ECs) into hematopoietic cells. In this approach, transduction of human umbilical vein ECs (HUVECs) or adult human dermal microvascular ECs (hDMECs) with transcription factors (TFs), FOSB, GFI1, RUNX1, and SPI1 (FGRS) and induction with a instructive vascular niche feeder layer in a xenobiotic- and serum-free microenvironment results in generation of long-term engraftable hematopoietic multilineage progenitors (rEC-HMLPs).  The rEC-HMLPs had robust proliferative and multilineage colony forming units (CFU) potential, including granulocytic/monocytic, megakaryocytic, erythroid and lymphoid lineages. When transplanted, hDMEC-derived rEC-HMLPs were capable of long-term multilineage primary and secondary hematopoietic engraftment. A subset of engrafted rEC-HMLPs phenotypically and functionally resembled cord blood cells. By conditionally expressing the FGRS TFs, we further optimized reprogramming of ECs into rEC-HMLPs manifesting features of self-renewing multi-potent progenitor populations (MPPs).  Our approach replicates critical aspects of hematopoietic development and essential role of vascular niche induction in orchestrating hematopoietic specification and may prove useful for engineering autologous engraftable hematopoietic cells for treatment of inherited and acquired blood disorders. .

overall_design: Transcriptome sequencing of rEC-HMLPs, hDMECs, HUVECs and other cell types

first: Vladimir

last: Sandler

first: Raphael

last: Lis

first: Shahin

last: Rafii


title: Transcription analysis of the porcine alveolar macrophage （PAM） response to co-infection of porcine reproductive and respiratory syndrome virus (PRRSV) and M. hyopneumoniae (Mhp)

status: Public on May 30 2014

city: Nanjing

first: li

last: bin

state: Jiangsu

address: Zhong-ling street 50

country: China

institute: Jiangsu Academy of Agricultural Sciences

summary:
Investigation of whole genome gene expression level changes in porcine alveolar macrophage response to co-infection of PRRSV and M. hyopneumoniae
The results in this study will be further described in Bin li et al., 2013. BMC genomics.

overall_design: A 24 chip study using total RNA recovered from four separate group include control, PRRSV, M. hyopneumoniae and PRRSV+M. hyopneumoniae.

first: Bin

last: Li


title: Mapping and manipulating the M. tuberculosis transcriptome using a transcription factor overexpression-derived regulatory network

status: Public on Jul 04 2014

city: RENTON

first: Tige

last: Rustad

state: WASHINGTON

address: 1700 DAYTON AVE NE

institute: Seattle BioMed

summary:
Expression data from transcription factor over expression experiments
(Abstract from paper will be appended after publication)

overall_design: TFOE are matched to the ChIP-seq experiment done simultaneously.

first: Kyle

last: Minch

first: David

last: Sherman


title: LncRNA profile study during Human MSC adipogenic differentiation:  Day0 vs Day3 vs Day6

status: Public on May 22 2014

city: Beijing

first: Runsheng

last: Chen

state: Beijing

address: 15 Datun Road

department: Noncoding RNA

institute: Institute of Biophysics, Chinese Academy of Sciences

summary: LncRNA transcriptional profiling of human mesenchymal stem cells comparing control undifferentiated HMSC  with Day3 and Day6 adipogenic differentiation stages

overall_design: Three-condition experiment, Day0 vs. Day3 vs Day6 cells. Day0: 4 replicates, Day3: 3 replicates and Day6: 3 replicates.

first: Tengfei

last: Xiao

first: Hongling

first: Lihui

last: Liu

first: Yu

last: Sun

first: Huaxia

last: Luo


title: Gene regulation in autophagy and apoptosis juncture

city: Baltimore

first: Hafiz

last: Ahmed

address: 701 East Pratt Street

institute: University of Maryland

summary: Autophagy to apoptosis switching event is an unexplored area. We were interested to explore the gene expression profile at this juncture. Our Microarray data emphasized that among all eNOS and p62 genes were markedly induced. In fuctional level eNOS expression activates mTORC1 followed by inhibition of autophagy. This ultimately allowed accumulation of p62 . Intraccellular accumulation of p62 sequestered unfolded toxic protein aggregates in mitochondria and ER resulting in to impaired redox regulation. Intraccelular ROS generation further sensitized cells for apoptosis and tilted autophagic response to apoptosis.

overall_design: Cells were treated with Tunicamycin as an inducer of both autophagy and apoptosis. At early stage of Tunicamycin treatment 24h , prostate cancer cell PC3 showed activation of autophagic process where apoptosis was not evident. Sustained ER stress with Tunicamycin induced late apoptoisis at 72h of treatment. Hence we isolated total RNA from Untreated cells, cells with Tunicamycin treatment after 24h and 72h. Further the RNA were used to perform whole genome microarray to analyze the gene expression profile at autophagy and apoptosis juncture. The selected genes were also validated by qPCR and western bot. Morover RNAi study were implemented to evaluate the signaling crosstalk at the juncture of autophagy and apoptosis.

first: Prasun

last: Guha


title: Methylation Changes in Arabidopsis Mature Green Seed Parts

status: Public on May 17 2014

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

summary: Seeds are comprised of three major 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 part undergoes distinct developmental programs during seed development. What methylation changes occur 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 two major parts of Arabidopsis mature green stage seeds, the seed coat and embryo, using Illumina sequencing.

overall_design: Illumina sequencing of bisulfite-converted genomic DNA from two parts of Arabidopsis mature green seeds: seed coat (SC) and embryo (EMB).

first: Robert

first: Min

first: Jer

middle: Y

last: Lin

first: Brandon

middle: H

last: Le


title: The MisR regulon in Neisseria gonorrhoeae strain FA19

status: Public on May 16 2014

city: Atlanta

first: Gregory

last: Doho

state: GA

address: 1365B Clifton Rd NE

institute: Emory University

summary: Whole transcriptome analysis of N. gonorrhoeae FA19 and isogenic NGEG_00293 (misR) mutant using RNA-Seq (note that NGO0177 is the misR ORF designation in mapping strain FA1090)

overall_design: Examination of total transcriptomes in N. gonorrhoeae FA19 WT and an FA19 misR::kan isogenic mutant to determine the regulatory impact of the MisR response regulator on cells grown under laboratory conditions.  Illumina HiSeq-2000 next generation sequencing was used to sequence the transcriptomes of each strain.  Reads were mapped against the N. gonorrhoeae FA1090 genome (NCBI accession number NC_002946) because at the time this experiment was run the FA19 genome was incomplete.

first: Justin

last: Kandler

first: William

middle: M

last: Shafer


title: Transcriptome analysis of mesothelioma induced by intraperitoneal injections of asbestos in rats

city: Nagoya

first: Shinya

last: Toyokuni

state: Aichi

address: 65 Tsuruma-Cho, Showa-Ku

department: Pathology

institute: Nagoya University

summary: Human malignant mesothelioma (MM) is an aggressive tumor strongly associated with asbestos exposure. SM patients generally have poorer prognosis compared to EM patients. To identify potential genes accounting for the differential prognosis between these two subtypes, we compared the microarray gene expression profiles of rat SM and EM tissues induced by intraperitoneal injections of 3 types of asbestos (chrysotile,crocidolite and amosite).

overall_design: Carcinogenesis protocol was performed using specific pathogen-free male and female F1 hybrid rats between Fischer344 and Brown-Norway strains. A total of 28 microarrays (Whole Rat Genome Microarray) were used for screening purpose: The 2 arrays were used for knife-scraped peritoneal mesothelial cells, 2 arrays for cultured peritoneal mesothelial cells and 24 arrays for MM samples.

first: Li

last: Jiang

first: Yoriko

last: Yamashita

last: Akatsuka


title: A new Rrf2 repressor family member, SaiR, controls transcription of spxA2 encoding a regulator of the oxidative stress response in Bacillus anthracis.

status: Public on May 21 2014

city: Rockville

first: Bryan

last: Frank

state: MD

address: 9704 Medical Center Drive

department: Dept of Infectious Diseases

institute: The J. Craig Venter Institute

summary: Spx, a member of the ArsC (arsenate reductase) protein family, is highly conserved in Gram-positive bacteria, where it interacts with RNA polymerase to activate transcription in response to toxic oxidants.  In Bacillus anthracis, resistance to oxidative stress requires the activity of two paralogous forms of Spx, SpxA1 and SpxA2.   Suppressor mutations were identified in spxA1 mutant cells that conferred resistance to hydrogen peroxide.  The mutations, which reside in saiR within the operon that also contains the spxA2 gene, caused derepression of spxA2 transcription. The product of saiR is a member of the Rrf2 family of transcriptional repressors.  Derepression of spxA2 in a saiR mutant required SpxA2, indicating an autoregulatory mechanism of spxA2 transcriptional activation.  Reconstruction of SaiR-dependent control of spxA2 was accomplished in Bacillus subtilis, where deletion analysis uncovered two cis-elements within the spxA2 regulatory region that are required for repression.  Both sites bear sequences of dyad symmetry, mutations in which abolished SaiR binding and SaiR-dependent repression of transcription from the spxA2 promoter in vitro.  Previous studies have provided evidence that spxA2 is one of the most highly induced genes in a macrophage infected with B. anthracis.  The work reported herein uncovered a key regulator, SaiR, which controls spxA2 transcriptional activation.

overall_design: Direct comparison of experimental samples to control samples in a two-color hybridization. Two experimental samples were compared against two control samples in triplicate for each.

first: Marcus

last: Jones

first: Peter

last: Zuber

first: Michiko

last: Nakano


title: Transgenerational actions of environmental compounds on reproductive disease and identification of epigenetic biomarkers of ancestral exposures.

city: Pullman

first: Michael

last: Skinner

state: WA

address: Abelson 507

department: SBS

institute: WSU

type: Methylation profiling by genome tiling array

summary:
Environmental factors during fetal development can induce a permanent epigenetic change in the germ line (sperm) that then transmits epigenetic transgenerational inheritance of adult-onset disease in the absence of any subsequent exposure. The epigenetic transgenerational actions of various environmental compounds and relevant mixtures were investigated with the use of a pesticide mixture (permethrin and insect repellant DEET), a plastic mixture (bisphenol A and phthalates), dioxin (TCDD) and a hydrocarbon mixture (jet fuel, JP8). After transient exposure of F0 gestating female rats during the period of embryonic gonadal sex determination, the subsequent F1-F3 generations were obtained in the absence of any environmental exposure. The effects on the F1, F2 and F3 generations pubertal onset and gonadal function were assessed. The plastics, dioxin and jet fuel were found to promote early-onset female puberty transgenerationally (F3 generation). Spermatogenic cell apoptosis was affected transgenerationally. Ovarian primordial follicle pool size was significantly decreased with all treatments transgenerationally. Differential DNA methylation of the F3 generation sperm promoter epigenome was examined. Differential DNA methylation regions (DMR) were identified in the sperm of all exposure lineage males and found to be consistent within a specific exposure lineage, but different between the exposures. Several genomic features of the DMR, such as low density CpG content, were identified. Exposure-specific epigenetic biomarkers were identified that may allow for the assessment of ancestral environmental exposures associated with adult onset disease.
Environmental factors during fetal development can induce a permanent epigenetic change in the germ line (sperm) that then transmits epigenetic transgenerational inheritance of adult-onset disease in the absence of any subsequent exposure. The epigenetic transgenerational actions of various environmental compounds and relevant mixtures were investigated with the use of a pesticide mixture (permethrin and insect repellant DEET), a plastic mixture (bisphenol A and phthalates), dioxin (TCDD) and a hydrocarbon mixture (jet fuel, JP8). After transient exposure of F0 gestating female rats during the period of embryonic gonadal sex determination, the subsequent F1-F3 generations were obtained in the absence of any environmental exposure. The effects on the F1, F2 and F3 generations pubertal onset and gonadal function were assessed. The plastics, dioxin and jet fuel were found to promote early-onset female puberty transgenerationally (F3 generation). Spermatogenic cell apoptosis was affected transgenerationally. Ovarian primordial follicle pool size was significantly decreased with all treatments transgenerationally. Differential DNA methylation of the F3 generation sperm promoter epigenome was examined. Differential DNA methylation regions (DMR) were identified in the sperm of all exposure lineage males and found to be consistent within a specific exposure lineage, but different between the exposures. Several genomic features of the DMR, such as low density CpG content, were identified. Exposure-specific epigenetic biomarkers were identified that may allow for the assessment of ancestral environmental exposures associated with adult onset disease.

overall_design: Methylated sperm DNA was isolated from rats ancestrally exposed to plastics (Bip), vinclozolin (Vip), pesticides (Pip), dioxin (Hip), jet fuel (Jip) or control vehicle (Cip).  Three independent samples from each treatment group were obtained.  Differential DNA methylation between treatment groups was determined using Nimblegen microarrays.  For each treatment, treated samples were paired with control samples and hybridized together on arrays (Bip1/Cip1, Bip2/Cip2, Bip3/Cip3, Vip1/Cip1, etc.), resulting in three arrays per treatment group.

first: M

last: Manikkam

first: Carlos

last: Gurerrero-Bosagna

first: R

last: Tracey

first: Md

last: Haque


title: Toxoplasma gondii merozoite gene expression

status: Public on May 02 2014

city: St Louis

middle: Sean

last: Behnke

state: MO

address: 660 S. Euclid Ave

department: Molecular Microbiology

institute: Washington University School of Medicine

summary:
Background:
Considerable work has been carried out to understand the biology of the intermediate stages, the tachyzoite and bradyzoite, of Toxoplasma gondii in large part due to the accessible culturing methods for these stages.  However, culturing methods for stages beyond the bradyzoite, including the merozoite and sexual stages, have not been developed hindering the ability to study a large portion of the parasite’s life cycle.  We begin to unravel the molecular aspects of the merozoite stage focusing on gene expression.

Results:
To initiate this, we harvested merozoite parasites and hybridized mRNA to the Affymetrix Toxoplasma GeneChip.  We analyzed the merozoite data in context of the life cycle by combining it with a previously published study that generated array data for the oocyst, tachyzoite, and bradyzoite stages (Fritz HM et al. PLoS One, 2012).  Principal component analysis highlights the unique profile of the merozoite samples, placing them approximately half-way on a continuum between the tachyzoite/bradyzoite and oocyst samples.  Prior studies have shown that antibodies to surface antigen p30 (SAG1) and many dense granule proteins do not label merozoites, and our microarray data confirms that these genes are not expressed at this stage.  Also, the expression for many rhoptry and microneme proteins is drastically reduced while the expression for many surface antigens is increased at the merozoite stage.  Gene Ontology and KEGG analysis reveals that genes involved in transcription/translation and many metabolic pathways are upregulated at the merozoite stage, highlighting unique growth requirements of this stage.  We also show that an upstream promoter region of a merozoite specific gene is sufficient to control stage specific expression at the merozoite stage.

Conclusion:
The merozoite represents the first developmental stage within the gut of the definitive host.  Determining the correct conditions that coax the parasite into the merozoite stage in vitro may allow the parasite to complete sexual development. The data presented here describe the global gene expression profile of merozoite stage and the creation of transgenic parasite strains that will be useful in unlocking how the parasite senses and responds to the felid gut environment to initiate coccidian development.

overall_design: The ToxoGeneChip microarray was used to measure both tachyzoite and merozoite mRNA expression in the type II TgNmBr1 strain.

middle: S

first: P

last: Zhang

first: J

last: Dubey

first: L

last: Sibley


title: Effect of EtOH on neural stem cells derived from human embryonic stem cells

status: Public on Apr 19 2014

first: Yong

last: Kim

address: 10833 Le Conte Ave, 73-022 CHS

institute: UCLA

summary: We have performed gene expression microarray analysis to profile transcriptomic signatures affected by EtOH during neural differentiation of human embryonic stem cells

overall_design: H1 human embryonic stem cells were differentiated into neural rosettes and neural progenitor cells in the presence or absence of 20mM EtOH treatment. Undifferentiated passage 40 H1 cells were used as a parental control. Total RNA was isolated from biological duplicates and subjected to gene expression profiling analysis using Affymetrix Human Genome U133 plus 2.0 Array


title: High-Resolution and Allele-Specific Genome-wide Replication Profiles in Human Primary Basophilic Erythroblasts

status: Public on May 01 2014

city: Bronx

first: Eric

last: Bouhassira

address: 1300 Morris PArk Ave

department: Cell Biology

institute: Albert Einstein College Of Medicine

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

overall_design: Refer to individual Series

first: Rituparna

last: Mukhopadhyay

first: Julien

last: Lajugie

first: Nicolas

last: Fourel

first: Ari

last: Selzer

last: Schizas

first: Jessica

last: Mar

first: Chii

last: Lin

first: Melvenia

last: Martin

last: Ryan

first: Mirit

last: Aladjem


title: The molecular changes that have occurred in breast cancer cells through the introduction of the MZF-1 fragment

status: Public on May 15 2014

city: Taichung

first: Jer-Yuh

last: Liu

address: Hsueh-Shih Road

department: Graduate Institute of Cancer Biology

country: Taiwan

institute: China Medical University

summary:
We used microarray gene expression analyses to search for epithelial-mesenchymal transition (EMT)-related genes that exhibited the greatest differences in expression in the MZF-1 fragment vector-transfected cells relative to the empty vector-transfected cells.
Of the 22,203 genes analyzed in both cell lines, 1209 genes had a two-fold increase and 1557 genes had a two-fold decrease in Hs578T-M(S3) cells (P<0.05), and 1272 genes increased and 1494 genes decreased by a similar amount in MDA-MB-231-M(V4) cells. Combined, 821 of the same genes from both cell lines were up-regulated, and 931 of the same genes from both cell lines were down-regulated. The biological functions of these affected genes were diverse and included 11 EMT-related genes (ITGA5, SERPINE1 GNGI1, SEAP1, TIMP1, FN1, TMEFF1, SNAI2, VIM, CALD1 and MSN) which were down-regulated, and 5 MET-related genes (CDH1, TSPAN13, OCLN, KRT19 and DSP) which were up-regulated.

overall_design: To understand functions of MZF-1/Elk-1 heterodimers, we transfected the binding site-derived peptide to the cells to interrupt heterodimer formation, their DNA binding activity, PKCα expression, cell migration and tumorigenicity were decreased, and the mesenchymal-epithelial transition (MET) was present.

first: JerYuh


title: Nascent strand with BrdU or lambda exonuclease

summary: Nascent strand were purified with either the  BrdU or the  lambda exonuclease methods from culture human basophilic erythroblasts and sequenced/

overall_design:
Two methods were compared to isolated the Nascent strand, lambda exonuclease digestion or immunoprecipitation after pulse labelling with BrdU
The following files were generated by combining round 1 and 2 sample files;
FNY01_2_2_Ery_NS_BrdU_macs_summits.bed
FNY01_2_2_Ery_NS_BrdU_macs_peaks.bed
FNY01_2_2_Ery_NS_lexo_macs_peaks.bed
FNY01_2_2_Ery_NS_lexo_macs_summits.bed

first: Michael


title: Gene expression profile of human osteosarcoma and modified MSCs

status: Public on Apr 03 2014

city: Taipei

first: Jir-You

last: Wang

address: Department of Orthopaedic & Traumatology, Taipei Veterans General Hospital, 201, Sec 2, Shih-Pai Road, Taipei 112, Taiwan

department: Department of Orthopaedics & Traumatology

institute: Taipei Veterans General Hospital

summary: Analysis of gene changes in different genes modulation in MSCs and compared to primary human osteosarcoma cells

overall_design: Total RNA isolated from human parental MSCs and from MSCs siRB, OeMyc, SiRb-OeMyc and primary human osteosarcoma cells

first: Wei-Ming

last: Chen

first: Shih-Chieh

last: Hung


title: Allele specific timing of replication

summary: We have characterized allele-specific regulation of replication in human cultured primary basophilic erythroblasts using TimEX-seq. We show that in most of the genome the timing of replication of the two chromosome homologs is robustly and tightly regulated since the two alleles replicate almost at the same time. We also show that small genetic differences such as SNPs and indels do not affect replication timing. We identify two major causes of replication asynchrony: the presence of large structural variants and parental imprinting.  Both are associated with the formation of asynchronously replicated domains that can reach several megabases in size. We also report that replication timing domains have a previously undetected fine structure.

overall_design:
Compare DNA content in cells in S and G1 phase of cell cycle using TimEX-seq
The goal of these experiments was to measure the timing of replication in human basophilic erythroblasts in an allele-specific manner by comparing DNA content in cells in S and G1 phase of cell cycle using TimEX-seq. Cells in S phase were obtained by sorting propidium iodide stained exponentially growing basophilic erythroblasts produce after 14 days of culture of circulating  peripheral blood stem and progenitor cells. The cells in G1, which are used to normalize the results from the cells in S phase for mapability, were  circulating mononuclear cells (WBCs) which are in the G1 cell for the cell cycle at 99.5%. The processed files represent S/G1 ratio values which are surrogate values for the timing of replication.  Allele-specific TimEX-seq profiles and hi-resolution non-allele specific profiles are provided at different smoothing levels.

The following processed files are derived from the multiple files as indicated below;
>FNY01_3_2_Ery_MAT_S.bed is generated from
FNY01_3_2_Ery_round *_S_Phase.bed
>FNY01_3_2_Ery_PAT_S.bed is generated from
FNY01_3_2_Ery_round *_S_Phase.bed
>FNY01_3_2_Ery_MAT_G1.bed is generated from
FNY01_3_2_WBC_round *_G1_600.bed
FNY01_3_2_WBC_round *_G1_300.bed
>FNY01_3_2_WBC_PAT_G1.bed is generated from
FNY01_3_2_WBC_round *_G1_600.bed
FNY01_3_2_WBC_round *_G1_300.bed
>FNY01_3_2_Ery_S_G1 ratio_MAT_100kb_smooth.bedGraph is from
FNY01_3_2_Ery_MAT_S.bed
FNY01_3_2_Ery_MAT_G1.bed
>FNY01_3_2_Ery_S_G1 ratio_PAT_100kb_smooth.bedGraph is from
FNY01_3_2_Ery_PAT_S.bed
FNY01_3_2_Ery_PAT_G1.bed
>FNY01_3_2_Ery_S_G1 ratio_unsmooth.bedGraph,
FNY01_3_2_Ery_S_G1 ratio_20Kb_smooth.bedGraph,
and FNY01_3_2_Ery_S_G1 ratio_100Kb_smooth.bedGraph are from
FNY01_3_2_Ery_round *_S_Phase.bed
FNY01_3_2_WBC_round *_G1_600.bed
FNY01_3_2_WBC_round *_G1_300.bed
>FNY01_3_2&3_3_Ery* files are generated from 14 .bed files linked to the corresponding sample records.
Please note that *3_3* files follow the same pattern as *3_2*


title: Transcriptomic analysis of breast cancer

status: Public on Apr 15 2014

city: Jeddah

first: Manikandan

last: Jayapal

address: King Fahd Medical Research Center | King Abdulaziz University | PO BOX 80216, Jeddah 21589. KSA.

country: Saudi Arabia

institute: King Abdulaziz University

summary: Transcriptomic analysis of fresh breast cancer tissue versus normal tissues. The Study comprising 45 Saudi-Arabian subjects was designed to take advantage of transcriptomics to prospectively explore the roles of lifestyle and genetic susceptibility in the occurrence of breast cancer.

overall_design: Total RNA isolated from 45 surgically resected breast cancer tissues and 8 healthy breast tissues (3 from Affymetrix) and purified, labeled, and hybridized to Affymetrix Human Gene 1.0 ST Array.

first: J

last: Manikandan

first: S

last: Karim

first: A

last: Dallol

last: Buhmeida

first: H

middle: R

last: Schulten

last: Merdad

first: M

last: Alqahtani


title: Induced expression of the C19MC miRNAs in HTR-8/SVneo cells

status: Public on Apr 08 2014

city: Pittsburgh

first: Jean-Francois

last: Mouillet

state: PA

address: 204 Craft Ave

department: MWRI - OBGYN and Reproductive Sciences

institute: University of Pittsburgh

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


title: Induced expression of the C19MC miRNAs in HTR-8/SVneo cells (microRNA)

summary: Analyze miRNA expression levels in HTR-8/SVeo cells stably transfected with a BAC plasmid containing the entire C19MC miRNA cluster

overall_design: HTR-8/SVeo cells were transfected with a modified BAC plasmid containing the entire C19MC miRNA cluster and carrying a zeocin selection cassette. Several independent clones and a mixed population of transfected cells were analyzed and compared to non-transfected HTR-8/SVeo cells and primary human trophoblasts that express the C19MC miRNAs endogenously

first: Lan

last: Xie

first: Tianjiao

last: Chu

first: Yoel

last: Sadovsky


title: Methylation Changes in Soybean Cotyledon Stage Seed Parts

first: Bob

last: Goldberg

summary: Seeds are comprised of three major 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 part undergoes distinct developmental programs during seed development. What methylation changes occur 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 cotyledon stage seeds, the seed coat, embryonic cotyledons, and embryonic axis, using Illumina sequencing.

overall_design: Illumina sequencing of bisulfite-converted genomic DNA from three parts of soybean cotyledon stage seeds: seed coat (COT-SC), embryonic cotyledons (COT-COT), and embryonic axis (COT-AX).

first: Robert

first: Min

first: Jer

last: Lin

first: Jungim

last: Hur

first: Brandon

last: Le


title: Haemophilus parasuis F9 transcriptome in biofilm and planktonic cultures using RNA sequencing

status: Public on Apr 02 2014

city: Barcelona

first: BERNARDO

last: BELLO ORTI

state: Barcelona

address: Bellaterra

department: Bacteriology

country: Spain

institute: CReSA

summary:
Purpose: Study transcriptome differences between biofilm, planktonic and stationary cultures.
Methods: Total mRNA from in vitro cultures was extracted and sequenced using Ion Torrent PGM sequencer.
Results: Characteristic transcriptomic profile was observed for biofilm, planktonic and stationary cultures. Biofilm and planktonic were similar biological states.
Conclusions: Results suggest that H. parasuis F9 has more active metabolism during biofilm or planktonic growth when compared to stationary culture. Some identified membrane-related genes could play an important role in biofilm life.

overall_design: RNA profiles of 36 hours biofilm or planktonic cultures were generated and compared with stationary culture profile.

first: B

last: Bello-Orti

first: V

last: Aragon


title: Induced expression of the C19MC miRNAs in HTR-8/SVneo cells (mRNA)

summary: Analyze gene expression profiles in HTR-8/SVeo cells stably transfected with a BAC plasmid containing the entire C19MC miRNA cluster

first: Tinjiao


title: LncRNA/mRNA expression profiling for THP-1 macrophages and THP-1 macrophage-derived foam cells

status: Public on May 20 2014

city: Guangzhou

first: Yan-Wei

last: Hu

address: No.1838,Dadaobei Road

institute: Nanfang Hospital

summary:
By identifying differentially expressed LncRNAs/mRNAs in THP-1 macrophages and THP-1 macrophage-derived foam cells, we select some differentially expressed LncRNAs and explore their roles in atherosclerosis process.
We already find that some LncRNA can effect cholesterol metabolism and level of inflammation factor, which may influence atherosclerosis process.

overall_design: In the study presented here, 6 human samples were used to acquire expression profiles, which provide futher insight into the pathologies of atherosclerosis

first: YanWei


title: Role of DksA in nitrosative stress

status: Public on Mar 31 2014

city: Irvine

first: Michael

last: McClelland

address: 132 Med Surge I

department: Microbiology & Molecular Genetics

institute: University of California, Irvine

type: Expression profiling by genome tiling array

summary: Transcriptional profiles of wt and dksA minus Salmonella enterica sv Typhimurium 14028S in E salts minimal medium in response to 5 mM DETANONOate for 30 min

sample_organism: Salmonella enterica subsp. enterica serovar Typhimurium str. 14028S

overall_design: Total RNA was harvested from three biological replicates of wt and dksA mutant cultures exposed or unexposed to 5mM DETANONOate for 30min in E salts minimal medium.

first: Calvin

last: Henard

first: Andres

last: Vasquez-Torres

first: Steffen

last: Porwollik


title: Expression data from Mus musculus white adipose tissue

status: Public on Mar 15 2014

city: Stockholm

first: Takahiro

last: Seki

address: Nobels vag16

institute: Karolinska Institutet

summary: We used microarrays to detail the gene expression profile during WAT -beige transition by treatment of beta adrenergic receptor agonist .

overall_design: Stromal vascular fractions (SVF) from mice (n = 3/group) that received vehicle or beta3 adrenergic receptor agonist, CL, treatment were served for RNA extraction and hybridization on Affymetrix microarrays. We are trying to find out angiogenic factors genes dynamics during white adipose tissues (WAT) - beige transition.

first: Yihai

last: Cao


title: Novel linkages between DCE-MRI and genomic profiling in locally advanced and inflammatory breast cancer

city: Durham

first: Mark

last: Dewhirst

state: NC

address: Research Dr.

department: Radiation Oncology

institute: Duke University

summary:
Gene expression signatures have the capacity to identify clinically significant features of breast cancer and can predict which individual patients are likely to be resistant to neoadjuvant therapy, thus providing the opportunity to guide treatment decisions.
Data used in publication: Clin Cancer Res. 2006;12:819–826. 89. Dressman et.al., Gene Expression Profiles of Multiple Breast Cancer Phenotypes and Response to Neoadjuvant Chemotherapy
Combining DCE-MRI imaging and genomics have identified putative genomic biomarkers that are associated with risk for pCR following neoadjuvant chemotherapy.  Furthermore, IBC gene expression profiles were associated with long term overall survival.  The genomic profiles identified in this pilot study are preliminary but novel, and thus of great interest to validate as biomarkers in independent datasets.

overall_design: 37 breast tissue samples were collected under ultrasound guidance from patients with stage IIB/III breast cancer before four cycles of neoadjuvant liposomal doxorubicinpaclitaxel chemotherapy combined with local whole breast hyperthermia. Gene expression analysis was done using Affymetrix U133 Plus 2.0 GeneChip arrays.

first: Sharareh

last: Siamakpour-Reihani

first: Kouros

last: Owzar

first: Chen

last: Jiang

first: Peter

last: Scarbrough

first: Oana

middle: I

last: Craciunescu

first: Janet

last: Horton

first: Holly

last: Dressman

first: Kimberly

last: Blackwell

middle: W


title: RNA expression analysis of lineage-negative marrow progenitors after Cebpa knockdown.

status: Public on Mar 11 2014

city: Baltimore

first: Ou

last: Ma

address: 1650 Orleans St. RM270

department: Oncology

institute: Postdoctoral Fellow

summary: Analysis of global RNA expression of Cebpa knockdown lineage-negative marrow cells reveals known and potentially novel C/EBPa targets.

overall_design: Total RNA from lineage-negative marrow progenitors transduced with vector or Cebpa shRNA and cultured under myeloid differentiation condition for 2 days were compared.

first: Alan

last: Friedman


title: Vascular Endothelial Growth Factor Receptor 3 (VEGFR3) controls hippocampal neural stem cell conversion into progenitor cells

status: Public on Mar 06 2014

city: New Haven

first: Taehyuk

last: Kang

state: CT

address: 300 George

department: Neurology

institute: Yale University

summary: Neural stem cells (NSCs) continuously produce new neurons within the adult mammalian hippocampus. However, this process declines with age and this decline correlates with defects in cognitive function and mood. Molecular mechanisms that activate quiescent NSCs to generate progenitor cells in vivo remain poorly understood. Here we show that adult hippocampal NSCs express VEGFR3, a key regulator of vascular and neural development, and are activated by the VEGFR3 ligand VEGF-C to enter the cell cycle and convert into progenitor cells. Conditional deletion of Vegfr3 in NSCs leads to a decline in hippocampal neurogenesis. Functionally, this is associated with increased anxiety behavior and compromised NSC activation in response to VEGF-C and physical activity. These findings establish VEGFR3 expression as a hallmark of adult mouse NSCs and demonstrate a specific requirement for VEGF-C/VEGFR signaling in NSC activation. Enhancing VEGFR3 signaling by VEGF-C may improve neurogenesis and mood during aging.

overall_design: Vegfr3 YFP and Vegfr3 YFP-negative cells were FACS-sorted from two separated groups of Vegfr3::YFP mice (16 mice/ each group; 12-30.10^5 Vegfr3YFP cells/group). Vegfr3 YFP  and Vegfr3 YFP-negative cells were suspended in CCM were seeded in 24-well plates with or without VEGF-C (50ng/ml). After an 18h-culture period, the cells were collected in eppendorf tubes, washed in PBS, and the total RNAs were extracted by Qiagen RNA Micro kit (QIAGEN, Valencia, CA). For each culture condition, the pellets from the two groups of  Vegfr3 YFP or Vegfr3 YFP-negative cells were pooled. The RNA integrity number (RIN) of each RNA sample was checked by 2100 Bioanalyzer of Agilent Technologies (Santa Clara, CA). The mRNA library construction were performed by SMARTer Ultra Low RNA Kit for Illumina Sequencing pherchased from Clontech Laboratory (Mountain View, CA) using manufacturer's protocol. And then, the validated libraries were applied to the 75 bp, paired end sequencing process of HiSeq 2500 (Illumina) to generate raw sequencing FASTQ data files. All sequencing procedures from RNA extraction to FASTQ generation were carried out by YCGA (Yale Center for Genome Analysis, West Haven, CT). The quality control check of FASTQ files was carried out by FastQC:ReadQC (version 0.52) analysis in Galaxy web-based platform and the sequences passed on ‘per base sequence quality’ were mapped on the UCSC mm10 mouse genome (Dec. 2011 Mus musculus assembly (Genome Reference Consortium Mouse Build 38)) using Tophat-2.0.9 including Bowtie-2-2.1.0 and Samtools-0.1.18. As the option of library type in Tophat, ‘fr-unstranded’ for Illumina TruSeq protocol was set as the default and the option of ‘no-novel-juncs’ was chosen to quantify the reference annotation only. Cuffdiff, a separate program of Cufflinks-2.1.1, analyzed the differentially regulated transcriptional level among the reference transcriptoms of our samples and the results were visualized and further manipulated by CummeRbund-2.12.

first: Tae

first: Jean-Leon

last: Thomas


title: Genome-wide activity of unliganded Estrogen Receptor alpha in breast cancer cells [RNA-Seq]

status: Public on Mar 03 2014

city: Orbassano

first: Giulio

last: Ferrero

state: TO

address: Regione Gonzole, 10

department: Dept. Clinical and Biological Sciences

country: Italy

institute: University of Turin

summary: ERα is essential for the anti-proliferative response of breast cancer cells not only to estrogen antagonists, but also to estrogen withdrawal by means of aromatase inhibitors. We explored here one of the simplest explanation for this, consisting in the possibility that ERα may have a wide genomic function in absence of ligands. The genomic binding of ERα in the complete absence of estrogen was then studied using hormone-dependent MCF7 cells, by chromatin immunoprecipitation sequencing. From these data, 4.2K highly significant binding events were identified, which were further confirmed by comparing binding events in cells expressing ERα to cells silenced for ERα. Apo-ERα binding sites were distributed close to genes with functions associated to cell growth and epithelial maintenance and show significant overlap with binding of other transcription factors important for luminal epithelial breast cancer. Interestingly, we found that upon ERα silencing cognate gene transcription in absence of estrogen is downregulated and this is accompanied by increased H27Kme3 at ERα binding sites. RNA-Seq experiments showed that unliganded ERα controls basal transcription widely, including both coding and noncoding transcripts. Genes affected by ERα silencing can be easily functionally related to mammary epithelium differentiation and maintenance, especially when considering downregulated genes. Additional functions related to inflammatory and immune response was observed. Our data unravel unexpected actions of ERα in breast cancer cells and provide a novel framework to understand success and failure of hormone therapy in breast cancer.

overall_design: Examination of unligandend estrogen receptor alpha (aERα) DNA interactions in control and aERα siRNA treated MCF7 cells.

first: Livia

last: Caizzi

first: Santina

last: Cutrupi

first: Francesca

last: Cordero

first: Cecilia

last: Ballarè

first: Valentina

last: Miano

first: Stefania

last: Reineri

first: Laura

last: Ricci

first: Olivier

last: Friard

first: Alessandro

last: Testori

first: Davide

last: Corà

first: Michele

last: Caselle

first: Luciano

last: Di Croce

last: De Bortoli


title: Transcriptome study in rhesus monkey

city: Beijing

first: Jia-Yu

last: Chen

address: No.5 Yiheyuan Road Haidian District

department: Institute of Molecular Medicine

institute: Peking University

summary: RNA-Seq technology was widely used to study gene expression, splicing structure and RNA editing. To facilitate transcriptome study in rhesus macaque, and provide an evolutionary context to understand human biology, we performed 90bp × 2, paired-end, strand-specific, polyA-postive RNA-Seq in 10 tissues of the same macaque animals. The data were deposited under accession number GSE42857 and GSE34426.

overall_design: This submission represents RNA-Seq: cerebellum, lung, kidney, heart and spleen component of study.

first: Chuan-Yun

last: Li


title: Identification of genes associated with TGF-beta/Smad3-mediated renal inflammation and fibrosis by RNA sequencing

status: Public on Mar 26 2014

city: Hongkong

first: Qin

last: ZHOU

address: Room 601, Inflammation Lab. Li Ka Shing Institute of Medical Building, Shatin, NT

department: The Chinese University of Hong Kong

institute: Li Ka Shing Institute of Health Sciences

summary: In this study, we employed high-throughput RNA sequencing (RNA-Seq) to identify the Smad3-dependent lncRNAs related to renal inflammation and fibrosis in Smad3 knockout (KO) mouse models of unilateral ureteral obstructive nephropathy (UUO) and immunologically-induced anti-glomerular basement membrane glomerulonephritis (anti-GBM GN).

overall_design: 12 kidney tissue samples of Smad3 KO/WT mice from normal control, UUO at day 5 or anti-GBM GN at day 10 models (n=2 in each group) for whole transcriptome RNA-sequencing.

last: Zhou

first: Huiyao

last: Lan


title: A natural expression variant reveals a novel mechanism of insect resistance in boreal forest trees.

status: Public on May 06 2014

city: Quebec

first: Isabelle

last: Giguere

state: Quebec

address: 1030, avenue de la Medecine

country: Canada

institute: Universite Laval

summary:
We report the discovery of a beta-glucosidase gene (Pgβglu-1) whose expression underpins natural resistance to a major forest pest, the spruce budworm (SBW) in white spruce (Picea glauca (Voss.) Moench). We performed a microarray experiment to compare resistant (R) and non-resistant (N-R) trees.
Pgβglu-1 transcripts levels uniquely were up to 1000 times higher in phenotypically resistant trees and correlated with accumulation of acetophenones compounds that reduce SBW development. These resistance traits were heritable, temporally correlated with the emergence of the most damaging larval stages and were highly variable in the natural population across a large geographic area. The recombinant gene product specifically catalyzed the release of biologically active acetophenones from their glucoside precursors. SBW outbreaks have become more frequent and intense; therefore, the phenotypic diversity resulting from variation in Pgβglu-1 expression may be a key for the adaptability of spruce populations.

platform_organism:
Picea glauca
Picea sitchensis

overall_design: Transcriptome profiling was carried out with needles from 7 resistant and 7 non-resistant trees (harvested on June 17th, 2010), and 3 samples per tree (n=42) with a custom microarray developed for spruce species and comprising oligonucleotide probes for 23,853 unique P. glauca gene sequences (Raherison et al., 2012).

first: Nathalie

last: Delvas

first: John

last: MacKay

first: Eric

last: Beauce


title: Layer 4 Visual Cortex Star Pyramid Monocular Deprivation Microarray Study

status: Public on Apr 12 2014

city: Boston

first: Benjamin

last: Okaty

state: MA

address: 77 Avenue Louis Pasteur

institute: Harvard Medical School

summary: Microarray expression profiling of manually sorted m-citirin-labeled layer 4 visual cortex star pyramid neurons from deprived and non-deprived hemispheres.

overall_design: Monocular deprivation by TTX-injection (at P12-13 and again at P13-14), followed by manual sorting of m-Citrin-labeled Layer 4 Visual Cortex Star Pyramid neurons in deprived and non-deprived hemispheres. RNA was extracted using PicoPure RNA Isolation Kit, reverse transcribed, and amplified using a standard T7 IVT protocol (Affymetrix Small Sample Target Labeling Assay Version II).

first: Celine

middle: C

last: Stenimetz

first: Ken

last: Sugino

first: Yasuyuki

last: Shima

first: Michael

last: Rutlin

first: Vedatkumar

last: Tavarty

first: Mary

last: Lambo

first: Chris

last: Hempel

first: Suzanne

last: Paradis

first: Sacha

last: Nelson

first: Gina

middle: G

last: Turrigiano


title: Gene expression profiling of formalin fixed paraffin embedded tumor tissue identifies gastric cancer patients who are at high risk after curative surgery plus adjuvant chemoradiotherapy

status: Public on Mar 01 2014

city: Seoul

first: Insuk

last: Sohn

address: 50, Irwon-Dong, Gangnam-Gu

country: South Korea

institute: samsung cancer research Institute

summary:
Gastric cancer is the second most common cause of cancer-related death worldwide.  Up to 80% of patients who undergo curative surgical resection develop locoregional or distant recurrence.  A recent large-scaled meta-analysis on 3,838 patients from 17 trials has demonstrated survival benefit from adjuvant chemotherapy when compared to surgery alone. Furthermore, INT-0116 study has demonstrated a survival benefit from postoperative chemoradiation therapy with 5-fluorouracil and leucovorin in gastric cancer patients. Despite these advances, 5-year disease-free survival rates remain poor for patients diagnosed with stage III or IV gastric cancer (stage IIIA, 57.6%, stage IIIB, 39.6%; and stage IV 26.3%) underscoring the need for development of new targeted agents. On the other hand those diagnosed with stage Ib/II gastric cancer have moderate 5 year recurrence rate (76.2%) and suggest the presence of significant molecular heterogeneity with varying prognosis.
We hypothesized that gene expression of profiling of formalin fixed paraffin embedded tumor (FFPET) samples using whole genome cDNA-mediated Annealing, Selection, Extension, and Ligation (WG-DASL) assay could be used to develop robust prognostic profiles for gastric cancer treated with chemoradiotherapy that are independent of clinicopathological features. We have identified and validated a gene expression signature that predicts recurrence after curative resection. We also performed pathway analyses to delineate aberrant pathways in aggressive gastric cancer which suggest targeted treatment strategies.

overall_design: RNA was extracted from 2-4 sections of 4-μm thick, FFPET sections. Non-tumor elements were removed by manual microdissection before transfer to the extraction tube guided by hematoxylin and eosin stained slides. The samples with RNA concentrations of <40 ng/μL, A260/A280 ratios <1.5 or A260/230 ratios <1.0 were considered as inadequate samples and were excluded from the analysis.

first: Soonmyung

last: Paik


title: Expression data of Participants of Ornish intervention and Control group

status: Public on Feb 24 2014

city: Windber

first: Darrell

last: Ellsworth

address: 620 Seventh St.

institute: Windber Research Institute

summary: Intensive lifestyle modification is believed to mediate cardiovascular disease (CVD) risk through traditional pathways that affect endothelial function and progression of atherosclerosis; however, the extent, persistence, and clinical significance of molecular change during lifestyle modification are not well known. Our study reveals that gene expression signatures are significantly modulated by rigorous lifestyle behaviors and track with CVD risk profiles over time.

overall_design: We examined the impact of a rigorous CVD risk reduction program on peripheral blood gene expression profiles in 63 participants and 63 matched controls to characterize molecular response to lifestyle modification and identify regulatory pathways important to cardiovascular health.

middle: L

first: Daniel

last: Croft Jr

first: Jamie

last: Weyandt

first: Lori

last: Sturtz

first: Heather

last: Blackburn

first: Kimberly

last: Mamula

first: Marina

middle: N

last: Vernalis


title: Genome-wide gene expression analysis of human whole-blood samples during acute dengue disease and early convalescence

status: Public on Apr 01 2014

city: Singapore

first: Ahmad Nazri

last: Mohamed Naim

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

department: Infectious disease

country: Singapore

institute: Genome institute of Singapore

summary: Dengue patient whole blood samples were analyzed during onset of disease, at defervescence and at early convalescence. Availability of samples at very early time points of disease allows to study the onset of the innate immune response. The main objective of the study is to understand early events during acute dengue disease, and how these events can eventually lead to the obsereved pathology including vascular leakage, thrombocytopenia and lyphocytopenia.

overall_design: Patients with suspected dengue disease gave a blood sample within 72h after onset of fever (DK1). The sample was used to confirm dengue infection by RT-PCR and RNA was stored for microarray. The patients returned for a second sample between 4 and 7 days after onset of fever (DK2) and 15-25 days after onset of fever (DK3). These longitdinal samples were all analyzed by microarray for inter-sample comparison and accross sample comparison. In total eleven patients were analyzed at the three time points indicated.

first: Ahmad

last: Naim

first: Thomas

last: Tolfvenstam

first: Katja

last: Fink

first: Martin

last: Hibberd


title: Vascular histone deacetylation by pharmacological HDAC inhibition [TSA, MBD-seq]

status: Public on Feb 23 2014

city: Melbourne

first: Assam

last: El-Osta

address: 75 Commercial Road

institute: Baker Heart and Diabetes Institute

summary: HDAC inhibitors are thought to regulate gene expression by post-translational modification of histone as well as non-histone proteins. Often studied at single loci, increased histone acetylation is the paradigmatic mechanism of action, however, little is known of the extent of genome-wide changes of the mammalian genome when stimulated by the hydroxamic acids, TSA and SAHA. In primary human vascular endothelial cells we map the chromatin modifications, histone H3 acetylation of lysine 9 and 14 (H3K9/14ac) using chromatin immunoprecipitation (ChIP) coupled with massive parallel sequencing (ChIP-seq). Since acetylation mediated gene expression is often associated with modification of other lysine residues we also examined H3K4me3 and H3K9me3 as well as changes in CpG methylation (CpG-seq). Genome-wide mRNA sequencing indicates the differential expression of about 30% of genes, with almost equal numbers being up- and down- regulated. We observe deacetylation conferred by TSA and SAHA that are associated with decreased gene expression. Histone deacetylation is associated with the loss of p300/CBP binding at gene promoters. This study provides an important framework for HDAC inhibitor function in vascular biology and a comprehensive description of genome-wide deacetylation.

overall_design: HAEC MethylMiner profiles of TSA treated and control samples were generated by deep sequencing, in triplicate, using Illumina GAIIx.

first: Haloom

last: Rafehi

first: Aneta

last: Balcerczyk

first: Sebastian

last: Lunke

first: Antony

last: Kaspi

first: Mark

last: Ziemann

first: Harikrishnan

last: Kn

first: Jun

last: Okabe

first: Ishant

last: Khurana

first: Jenny

last: Ooi

first: Abdul

last: Khan

first: Xiao-Jun

last: Du

first: Lisa

last: Chang

first: Izhak

last: Haviv

first: Samuel

last: Keating

first: Tom

last: Karagiannis


title: Vascular histone deacetylation by pharmacological HDAC inhibition [SAHA, RNA-seq]

overall_design: HAEC mRNA profiles of SAHA treated and control samples were generated by deep sequencing, in triplicate, using Illumina GAIIx.


title: Stress, heritability, tissue type and human methylome variation.

city: Gainesville

first: Connie

last: Mulligan

state: Florida

address: 2033 Mowry Road

department: Department of Anthropology

institute: University of Florida

summary: Genomewide methylation profiles from three tissues (cord blood, placenta, venous blood) derived from 24 mother-child dyads. Data was assayed with the Illumina HumanMethylation 450K Beacdchip and processed with Illumina's GenomeStudio V2011.1 Methylation Module v1.9.0

overall_design:
Bisulfite converted DNA from three tissues derived from 24 dyads, totalling 72 samples, were hybridized to the Illumina HumanMethylation450 BeadChips following the manufacturer's specifications.

Cord blood samples C1 and C20 in GSE54399 have been shown to have maternal blood contamination in an analysis reported in Morin et al., 2017, Clinical Epigenetics. Sample C1 likely has maternal blood contamination due to improper sample collection and Sample C20 is likely to be a mis-labeled maternal venous blood sample. These samples (GSM1314363 and GSM1314382) have been removed from this series.

first: David

last: Hughes

first: Nicole

last: Rodney


title: Whole Blood Gene Expression Profiling Predicts Therapeutic Response in Polyarticular Juvenile Idiopathic Arthritis at 4 Months

status: Public on Feb 26 2014

city: Oklahoma City

first: Bart

last: Frank

state: OK

institute: OMRF

summary: To determine whether gene expression profiles from peripheral whole blood could be used to determine therapeutic outcome in a cohort of children with newly diagnosed polyarticular JIA.

overall_design: 19 samples were obtained from healthy childhood controls and 93 samples from patients with juvenile idiopathic arthritis. For patient samples, they were collected prior to treatment (month 0) or 4 months after treatment.

first: Kaiyu

last: Jiang

first: Ashley

middle: D

last: Sawle

middle: B

first: Yanmin

last: Chen

first: Carol

last: Wallace

first: James

last: Jarvis


title: Vascular histone deacetylation by pharmacological HDAC inhibition [TSA, ChIP-seq]

first: Assam

last: El-Osta

overall_design: HAEC ChIP-seq profiles for 3 histone marks of TSA treated and control samples were generated by deep sequencing, in triplicate, using Illumina GAIIx.

first: Haloom

last: Rafehi

first: Aneta

last: Balcerczyk

first: Sebastian

last: Lunke

first: Antony

last: Kaspi

first: Mark

last: Ziemann

first: Harikirshnan

last: Kn

first: Jun

last: Okabe

first: Ishant

last: Khurana


title: Vascular histone deacetylation by pharmacological HDAC inhibition [TSA, mouse, ChIP-seq]

overall_design: Mouse ChIP-seq profiles for histone acetylation treated and control samples were generated by deep sequencing, using Illumina GAIIx.

first: Harikrishnan

first: Jenny

last: Ooi

first: Abdul

last: Khan

first: Xiao-Jun

last: Du

first: Lisa

last: Chang

first: Izhak

last: Haviv

first: Samuel

last: Keating

first: Tom

last: Karagiannis


title: Vascular histone deacetylation by pharmacological HDAC inhibition [SAHA, ChIP-seq]

first: Assam

overall_design: HAEC ChIP-seq profiles for 3 histone marks of SAHA treated and control samples were generated by deep sequencing, in triplicate, using Illumina GAIIx.


title: RNA-seq transcriptomes of term not in labour and term in labour human myometrial tissue

status: Public on Feb 17 2014

city: Coventry

first: Andrew

last: Blanks

address: Clifford Bridge Road

department: Warwick Medical School

institute: University of Warwick

summary:
Purpose: To chart the human myometrial transcriptomes before and after the onset of labour.
Methods: Tophat splice junction mapping of paired-end reads, HTSeq to generate counts, cufflinks to track transcripts, DESeq, edgeR and baySeq to detect differentially expressed genes and principal component analysis for clustering analyses.
Results: We mapped on average 14 million paired-end reads per sample (counting each end individually) to the human genome (build hg19) and covered the expressed transcriptome about 13 times with a TopHat-HTSeq workflow. We performed a comparative analysis with an analogous microarray study (Mittal et al., 2010) and found some overlap between the RNA-seq and the microarray data.
Conclusions: Our study is the first RNA-seq study of the human myometrium before and after the onset of labour. We show that while microarray and RNA-seq studies may complement each other, RNA-seq has a much greater resolution.

overall_design: At term with and at term without labour human myometrial mRNA profiles were generated by deep sequencing, using Illumina GAIIx (five biological replicates each).

first: Yi-Wah

last: Chan

first: Hugo

last: van den Berg

first: Jonathan

last: Moore

first: Siobhan

last: Quenby


title: Comparing the samples with and without RNA amplification

status: Public on Feb 20 2014

first: Oleg

last: Suslov

state: FL

address: 1149 S. Newell Drive

department: Neuroscience

summary: Diverse cell types have unique transcriptional signatures that are best interrogated at single-cell resolution. Here we describe a novel RNA amplification approach that allows for high fidelity gene profiling of individual cells. This technique significantly diminishes the problem of 3’bias and therefore enables detection of all regions of transcripts, including the recognition of mRNA with short or completely absent polyA tails, identification of noncoding RNAs, and discovery of the full array of splice isoforms from any given gene product. We assess this technique using statistical and bioinformatics analysis of microarray data in order to establish the limitations of the method. To demonstrate the applicability of the method, we conducted single cell profiling of individual cells, acutely isolated from the mouse subventricular zone (SVZ) – a well-characterized, discrete yet highly heterogeneous neural structure involved in persistent neurogenesis. Importantly, this method revealed multiple splice variants of key germinal zone gene products, as well as an unexpected coexpression, within individual cells, of several mRNAs that are considered markers of distinct and separate SVZ cell types. These findings were independently confirmed using RNA-FISH, contributing to the utility of this new technology that offers genomic and transcriptomic analysis of small numbers of, in this case, extremely dynamic and clinically relevant cells.

overall_design: Gene expression ratios between two samples the LN229 glioma cell line (LN) and a collection of human neural stem/progenitor cells (Prog) were compared before and after RNA amplification. Samples without amplification (control sample) - 5 replicates, 20 ng amplification samples - 5 replicates,1ng amplification samples - 5 replicates, 20 pg amplification samples - 6 replicates


title: Vascular histone deacetylation by pharmacological HDAC inhibition

last: El-Osta

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

HDAC inhibitors are thought to regulate gene expression by post-translational modification of histone as well as non-histone proteins. Often studied at single loci, increased histone acetylation is the paradigmatic mechanism of action, however, little is known of the extent of genome-wide changes of the mammalian genome when stimulated by the hydroxamic acids, TSA and SAHA. In primary human vascular endothelial cells we map the chromatin modifications, histone H3 acetylation of lysine 9 and 14 (H3K9/14ac) using chromatin immunoprecipitation (ChIP) coupled with massive parallel sequencing (ChIP-seq). Since acetylation mediated gene expression is often associated with modification of other lysine residues we also examined H3K4me3 and H3K9me3 as well as changes in CpG methylation (CpG-seq). Genome-wide mRNA sequencing indicates the differential expression of about 30% of genes, with almost equal numbers being up- and down- regulated. We observe deacetylation conferred by TSA and SAHA that are associated with decreased gene expression. Histone deacetylation is associated with the loss of p300/CBP binding at gene promoters. This study provides an important framework for HDAC inhibitor function in vascular biology and a comprehensive description of genome-wide deacetylation.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: Refer to individual Series

first: Haloom

last: Rafehi

first: Aneta

last: Balcerczyk

first: Sebastian

last: Lunke

first: Antony

last: Kaspi

first: Mark

last: Ziemann

first: Harikirshnan

first: Jun

first: Sam


title: Spectrum, clinical correlates and clinical implications of BRAF-inhibitor resistance mechanisms in melanoma

status: Public on Feb 19 2014

city: Westmead

first: Gulietta

last: Pupo

state: NSW

address: Darcy Road

institute: University of Sydney

summary: Multiple BRAF inhibitor resistance mechanisms have been described, however their relative frequency, clinical correlates, and effect on subsequent therapy have not been assessed in patients with metastatic melanoma. Excised progressing BRAFV600 mutant melanoma metastases (Prog) from patients treated with dabrafenib (n=22) or vemurafenib (n=8) were analyzed for known resistance mechanisms.  Oncogenic signaling in Prog and matched pre-treatment tumors was examined using gene expression analysis. Resistance mechanisms were correlated with clinicopathologic features and outcome. A resistance mechanism was identified in 21/38 (55%) Prog samples from 30 patients; BRAF splice variants (n=12, 32%), N-RAS mutations (n=3, 8%), BRAF amplification (n=3, 8%), MEK1/2 mutations (n=3, 8%) and an AKT1 mutation (n=1, 3%). Four Progs tumours displayed multiple resistance mechanisms, and four patients with multiple Progs demonstrated inter-tumoral heterogeneity of resistance mechanisms. Six (21%) of 29 Progs showed loss of MAPK activity by gene expression analysis. These MAPK-inhibited Progs had unknown resistance mechanisms, and these patients had a shorter progression-free survival than patients with MAPK re-activated Progs. There were no responses to subsequent targeted therapy, even when the identified mechanism of resistance was predicted to be responsive. Heterogeneity of resistance mechanisms was common between patients, within patients and within individual tumors. The MAPK pathway remained inhibited in a subset of resistant tumors with unknown mechanisms of resistance, and the outcomes of patients with these tumors are poor. The use of sequential targeted therapies based on the molecular characteristics of a single progressing biopsy is unlikely to provide improved clinical outcomes.

overall_design: Total RNA was obtained from fresh-frozen melanoma tumour samples from patients before commencing treatment with dabrafenib or vemurafenib and at time of tumour progression.

first: Helen

last: Rizos


title: De novo transcriptome analysis profiles gene expression underlying seasonal polyphenism in butterfly wing patterns

status: Public on Feb 15 2014

city: Irvine

first: Ali

last: Mortazavi

state: California

address: 2300 Biological Sciences III

department: Developmental & Cell Biology

institute: University of California Irvine

summary: In the eastern United States the buckeye butterfly, Junonia coenia, shows a seasonal wing color polyphenism where adults emerging in the spring are pale brown, while those emerging in the autumn are dark red. This variation can be artificially induced in laboratory colonies, thus making J. coenia a useful model system to examine the developmental basis of phenotypic plasticity. We used RNA-seq to generate the first set of assembled transcripts for this species while simultaneously quantifying relative gene expression associated with development of alternative seasonal color morphs. The assembled consolidated wing transcriptome was 77.55 Mb. 16,251 contigs of over 1000bp in length were assembled, of which 3,145 were differentially expressed between stages and/or color morphs. Depending on the developmental stage, between 547 and 1420 transcripts were significantly differentially expressed between brown and red wing morphs. These extensive differences in gene expression stand in stark contrast to the much smaller numbers found in previous studies on genetic wing pattern variation, and suggest that environmentally induced phenotypic shifts may arise from very broad systemic processes. Overall gene ontology (GO) analyses revealed that genes associated with structural constituents of ribosomes and oxygen transport were significantly upregulated in the pale brown morph, while genes associated with peptidase activity were very significantly upregulated in the dark red morph. Focused analyses of candidate endocrine and pigmentation pathways revealed a number of notable genes upregulated in the red morph, including several ecdysone-related genes and cinnabar, an ommochrome pigment gene implicated in color pattern variation in other butterflies. Surprisingly, we found numerous melanin-related transcripts, including tan and yellow-family genes, strongly upregulated in the red morph, leading us to speculate that red pigmentation in autumn J. coenia may include red or brown melanins in addition to ommochromes. While we identified several endocrine and pigmentation genes as obvious candidates for color morph differentiation, we speculate that the majority of gene expression differences we observed were due to thermal stress response. The buckeye transcriptome provides a basis for further developmental studies of phenotypic plasticity.

overall_design: mRNA profiling of hind wings from 4 developmental stages of two color morphs (Rosa and Linea) of the buckeye butterfly (J. coenia), generated by deep sequencing, in triplicate, using Illumina GAII or HiSeq 2000.

first: Emily

middle: V

last: Daniels

first: Rabi

last: Murad

first: Robert

last: Reed


title: Vascular histone deacetylation by pharmacological HDAC inhibition [TSA, RNA-seq]

first: Assam

overall_design: HAEC mRNA profiles of TSA treated and control samples were generated by deep sequencing, in triplicate, using Illumina GAIIx.

first: Harikrishnan

last: Kn

last: Okabe

first: Ishant

last: Khurana

first: Jenny

last: Ooi

first: Abdul

last: Khan

first: Xiao-Jun

last: Du

first: Lisa

last: Chang

first: Izhak

last: Haviv

first: Samuel

last: Keating

first: Tom

last: Karagiannis


title: Effect of cortisol on S. Typhimurium parental strain and an isogenic scsA mutant

status: Public on Feb 28 2014

city: Norwich

first: Arthur

last: Thompson

address: Colney Lane

institute: Institute of Food Research

summary: S. Typhimurium 112910a parental strain and an isogenic ΔscsA strain were grown to stationary phase in SPI2 inducing minimal medium (MM5.8 - Erikkson et al., 2006 Inf & Imm., 74:1243) with or without supplementation with 1µM cortisol

platform_organism: Salmonella enterica subsp. enterica serovar Typhimurium str. DT104

platform_organism: Salmonella enterica subsp. enterica serovar Typhimurium str. LT2

platform_organism: Salmonella enterica subsp. enterica serovar Enteritidis

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

platform_organism: Salmonella enterica subsp. enterica serovar Gallinarum str. 287/91

overall_design: 4 samples (stat phase wt, stat phase wt + 1µM cortisol, stat phase ΔscsA, stat phase ΔscsA + 1µM cortisol) and 3 biological replicates for each sample.

first: Elin

last: Verbrugghe


title: TGF-β/Smad3 Stimulates Stem Cell/Developmental Gene Expression and Vascular Smooth Muscle Cell De-Differentiation

status: Public on Feb 04 2014

city: Madison

first: Xudong

middle: daniel

last: Shi

state: WI

address: 1111 Highland Ave

department: Surgery

institute: University of Wisconsin

summary:
In order to determine a mechanism through which TGF-b/Smad3 promote these effects, Affymetrix gene expression arrays were performed on primary rat SMCs infected with Smad3 and stimulated with TGF-b or infected with GFP alone.
More than 200 genes were differentially expressed (>2.0 fold change, p<0.05) in TGF-b/Smad3 stimulated SMCs. We then performed GO term enrichment analysis using the DAVID bioinformatics database and found that TGF-b/Smad3 activated the expression of multiple genes related to either development or cell differentiation, several of which have been shown to be associated with multipotent stem or progenitor cells.

overall_design: Vascular smooth muscle cells from 3 rats were infected with adenovirus expressing Smad3 and treated with TGF-B for 24 h (TGF-B/Smad3 group).  Adenovirus expressing GFP (GFP group) was control.  TGF-B/Smad3 treated or control cells were used for RNA extraction and hybridization on Affymetrix microarrays (n=3).

first: Daniel

last: DiRenzo

first: Lian-Wang

last: Guo

first: Sarah

last: Franco

first: Bowen

last: Wang

first: Stephen

last: Seedial

first: K

last: Kent


title: Exploring genome-wide DNA methylation profiles altered in hepatocellular carcinoma using Infinium HumanMethylation 450 BeadChips

status: Public on Jan 30 2014

city: New York

first: Jing

last: Shen

address: 650 W. 168th St. Black Building Rm.1608

institute: Columbia University

summary: We examine genome-wide DNA methylation profiles in 66 pairs of HCC tumor and adjacent non-tumor tissues. After Bonferroni adjustment, a total of 130,512 CpG sites significantly differed in methylation level in tumor compared to non-tumor tissues, with 28,017 CpG sites hypermethylated and 102,495 hypomethylated in tumor tissues. Most (60.1%) significantly hypermethylated CpG sites are located in CpG islands. These results demonstrate the significance of aberrant DNA methylation in HCC tumorigenesis.

overall_design: Bisulfite modification of 1µg DNA was conducted using an EZ DNA Methylation Kit (Zymo Research, Irvine, CA) according to the manufacturer’s procedure. The Infinium Methylation 450K assay was performed according to Illumina’s standard protocol. Six HCC tumor/adjacent non-tumor tissue pairs were processed on the same chip to avoid chip-to-chip variation.

first: Regina

last: Santella


title: RNA-seq: technical variability and sampling

status: Public on Jan 15 2014

first: Lauren

last: McIntyre

address: 2033 Mowry Rd

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

sample_organism:
Drosophila melanogaster
Drosophila simulans


title: RNA-seq: technical variability and sampling (male)

summary:
Background: RNA-seq is revolutionizing the way we study transcriptomes. mRNA can be surveyed without prior knowledge of gene transcripts. Alternative splicing of transcript isoforms and the identification of previously unknown exons are being reported. Initial reports of differences in exon usage, and splicing between samples as well as quantitative differences among samples are beginning to surface. Biological variation has been reported to be larger than technical variation. In addition, technical variation has been reported to be in line with expectations due to random sampling. However, strategies for dealing with technical variation will differ depending on the magnitude. The size of technical variance, and the role of sampling are examined in this manuscript.
Results:  Independent Solexa/Illumina experiments containing technical replicates are analyzed. When coverage is low, large disagreements between technical replicates are apparent. Exon detection between technical replicates is highly variable when the coverage is less than 5 reads per nucleotide and estimates of gene expression are more likely to disagree when coverage is low. Although large disagreements in the estimates of expression are observed at all levels of coverage.
Conclusions:  Technical variability is too high to ignore. Technical variability results in inconsistent detection of exons at low levels of coverage. Further, the estimate of the relative abundance of a transcript can substantially disagree, even when coverage levels are high. This may be due to the low sampling fraction and if so, it will persist as an issue needing to be addressed in experimental design even as the next wave of technology produces larger numbers of reads. We provide practical recommendations for dealing with the technical variability, without dramatic cost increases.

overall_design: Three independent samples of D. simulans male heads were collected with each sample representing a unique pool of biological material. Each sample was prepared according to manufacturer's instructions and then the same library was run on two lanes of a Solexa/Illumina flow cell, resulting in two technical replicates for each biological replicate, runs were 36 base-pair paired end.

first: Kenneth

middle: K

last: Lopiano

first: Alison

last: Morse

first: Victor

last: Amin

first: Ann

last: Oberg

first: Linda

middle: J

last: Young

first: Sergey

last: Nuzhdin


title: Microbial community functional structures in wastewater treatment plants as characterized by GeoChip

first: Xiaohui

address: 15 beisanhuan east road, chaoyang district, beijing, 100029

institute: Beijing University of Chemical Technology

summary: To understand microbial community functional structures of activated sludge in wastewater treatment plants (WWTPs) and the effects of environmental factors on their structure, 12 activated sludge samples were collected from four WWTPs in Beijing. GeoChip 4.2 was used to determine the microbial functional genes involved in a variety of biogeochemical processes. The results showed that, for each gene category, such as egl, amyA, nir, ppx, dsrA sox and benAB, there were a number of microorganisms shared by all 12 samples, suggestive of the presence of a core microbial community in the activated sludge of four WWTPs. Variance partitioning analyses (VPA) showed that a total of 53% of microbial community variation can be explained by wastewater characteristics (25%) and operational parameters (23%), respectively. This study provided an overall picture of microbial community functional structures of activated sludge in WWTPs and discerned the linkages between microbial communities and environmental variables in WWTPs.

platform_organism: Bacteria Archaea Eukaryota Viruses

overall_design: Four full-scale wastewater treatment systems located in Beijing were investigated. Triplicate samples were collected in each site.


title: RNA-seq: technical variability and sampling (female)

overall_design: Three independent samples of D. melanogaster female heads were collected with each sample representing a unique pool of biological material. Each sample was prepared according to manufacturer's instructions and then the same library was run on two lanes of a Solexa/Illumina flow cell, resulting in two technical replicates for each biological replicate, runs were 36 base-pair paired end.


title: Characterization of Heart Valve Leaflets from Adult and Juvenile Rapacz Familial Hypercholesterolemic Swine

status: Public on Jan 11 2014

first: Ana

middle: Maria

last: Porras

address: 1550 Engineering Drive #2153

department: Biomedical Engineering

institute: UW-madison

summary: Rapacz Familial Hypercholesterolemic (RFH) swine have been used extensively in the vascular biology field as a robust model of complex atherosclerotic lesions. However, the heart valves from RFH swine have not been evaluated and it is unknown whether these animals develop calcific aortic valve disease without dietary intervention. Histological assessment of heart valve leaflets isolated from juvenile and adult swine revealed RFH swine develop the early hallmarks of the disease at two years of age. The goal of this microarray study was to gain some insight into the cellular and molecular mechanisms that lead to the observed hallmarks and initiation of the disease.

overall_design: RNA samples from three juvenile wild type, and three juvenile and four adult RFH swine aortic valve leaflets were isolated, processed, and hybridized to Affymetrix GeneChip Porcine Genome microarrays according to the manufacturer's instructions. The mean expression values of each probeset in the adult RFH samples were compared to those in the juvenile RFH samples. Likewise, the mean expression values of each probeset in the juvenile RFH samples were compared to those in the juvenile wild type samples.

first: Kristyn

last: Masters


title: Genome-wide activity of unliganded Estrogen Receptor-α in breast cancer cells

status: Public on Mar 02 2014

city: Orbassano

first: Giulio

last: Ferrero

address: Regione Gonzole, 10

institute: University of Turin


title: Gene expression changes of Streptomyces coelicolor M145 under external and internal disturbances

status: Public on Dec 31 2013

city: Beijing

first: Keqian

last: Yang

address: NO.1 Beichen West  Road, Chaoyang District

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 variation of S. coelicolor M145, ΔscbR2 mutation with jadomycin addition at 30 h.

first: J

last: Ji

first: W