title: The Sinorhizobium meliloti SyrM regulon: effects on global gene expression are mediated by syrA and nodD3 (SyrM)

status: Public on Mar 31 2015

city: Stanford

first: Melanie

last: Barnett

address: 371 Jane Stanford Way

department: Biology

institute: Stanford University

summary: We characterized transcriptomes of a strain overexpressing syrM.  Our work shows that the syrM transcriptome shares similar gene expression changes to the syrA and nodD3 transcriptomes and that nodD3 and syrA may be the only targets directly activated by SyrM.  We propose that most of the gene expression changes observed when nodD3 is overexpressed are due to NodD3 activation of syrM expression, which in turn stimulates SyrM activation of syrA expression.  The subsequent increase in SyrA abundance alters activity of the ChvI-ExoS-ExoR circuit, resulting in broad changes in gene expression.

platform_organism:
Sinorhizobium meliloti
Medicago truncatula

overall_design: Gene expression profiling of a Sinorhizobium meliloti nodD1, nodD2, nodD3 mutant overexpressing syrM was performed using custom Affymetrix GeneChips

first: Sharon

last: Long


title: Alteration of mRNA and microRNA expression profiles in rat muscular type vasculature in early postnatal development [mRNA]

status: Public on Apr 30 2015

city: Mannheim

first: Harsh

last: Dweep

state: baden wurttemberg

address: Theodor-Kutzer-Ufer 1-3

department: Medical Research Center, Medical Faculty of Mannheim of the University of Heidelberg

country: Germany

institute: University of Heidelberg

summary: This study tested the hypothesis that mRNA expression profiles change in the muscular type rat saphenous artery during early postnatal development. To explore this, we performed mRNA microarray analysis on muscular type saphenous arteries of young (10-12 days) and adult (2-3 months) rats.

overall_design: For one sample four saphenous arteries from 2 young animals (n = 4 samples per group) or two saphenous arteries from one adult animal (n = 4 samples per group) were used to profile mRNA (n = 8; GeneChip® Rat Gene 1.0) expression changes during the muscular type rat saphenous artery during early postnatal development. In this study, 10-12 days old (“young”) and 2 - 3 months old (“adult”) male Wistar rats.

first: Dina

last: Gaynullina

first: Torsten

last: Gloe

first: Olga

middle: S

last: Tarasova

first: Carsten

last: Sticht

first: Norbert

last: Gretz

first: Rudolf

last: Schubert


title: Immune Gene Expression Profile of Conventional and Regulatory T cells

city: Gainesville

first: Christopher

middle: A.

last: Fuhrman

state: FL

address: 1275 Center Drive, BMSB J513

department: Pathology, Immunology and Laboratory Medicine

country: USA

institute: University of Florida

summary: Understanding human regulatory T cells (Tregs) heterogeneity may identify markers of disease pathogenesis and facilitate the development of optimized cellular therapeutics. To better elucidate human Treg subsets, we conducted direct transcriptional profiling of CD4+FOXP3+Helios+ thymic-derived Treg (tTreg) and CD4+FOXP3+Helios- peripherally-induced Treg (pTreg), followed by comparison to CD4+FOXP3-Helios- T conventional (Tconv) cells. This analysis revealed that the coinhibitory receptor T-cell immunoglobulin and immunoreceptor tyrosine-based inhibitory motif domain (TIGIT) was highly expressed on tTreg.

overall_design: In this study CD4 T cells were stained for the Treg-associated transcription factors FOXP3 and Helios, and subsequently FACS sorted to yield three populations: tTreg (CD4+FOXP3+Helios+), pTreg (CD4+FOXP3+Helios–) and the reference population Tconv (CD4+FOXP3–Helios–).  A direct transcriptional profile was obtained from the recovered RNA from the populations defined as tTreg, pTreg, and Tconv.

middle: A

first: Howard

middle: R

last: Seay

first: Priya

last: Saikumar Lakshmi

first: Robert

middle: L

last: Whitener


title: Mapping and Analysis of Caenorhabditis elegans Transcription Factor Binding Specificities

status: Public on Apr 23 2015

city: Toronto

first: Kamesh

last: Narasimhan

state: Ontario

address: 160 college Street

country: Canada

institute: Donnelly Centre for Cellular and Biomolecular Research

summary: The nematode Caenorhabditis elegans is a powerful model for studying gene regulation,  as it has a compact genome and a wealth of genomic tools. However, identification of   regulatory elements has been hampered by the fact that DNA binding motifs are known   for only 71 (9%) of the estimated 763 high-confidence sequence-specific transcription   factors (TFs). To address this problem, we performed protein binding microarray (PBM)   experiments on representatives of canonical TF families in the C. elegans TF repertoire,  obtaining motifs for 129 distinct TFs. Moreover, we can infer motifs for 97 additional   TFs that have DNA binding domains that are very similar to those already characterized,   resulting in a total coverage of binding specificities for almost 40% of the C. elegans TF  repertoire. These data highlight the diversification of binding motifs for the nuclear   hormone receptor (NHR) and C2H2 zinc finger families, and reveal unexpected diversity   of motifs for others, including the T-box and DM families. Enrichment of motifs in the   promoters of functionally related genes is consistent with known biology in many cases,   and also identifies putative new regulatory roles for poorly characterized TFs. The motifs   are available at http:// http://cisbp.ccbr.utoronto.ca.

overall_design: Protein binding microarray (PBM) experiments were performed for a set of 129 diverse C. elegans transcription factors. Briefly, the PBMs involved binding GST-tagged DNA-binding proteins to two double-stranded 44K Agilent microarrays, each containing a different DeBruijn sequence design, in order to determine their sequence preferences. Details of the PBM protocol are described in Berger et al., Nature Biotechnology 2006.

first: Samuel

last: Lambert

first: Ally

middle: W

last: Yang

first: Jeremy

last: Riddell

first: Sanie

last: Mnaimneh

first: Hong

last: Zheng

first: Mihai

last: Albu

first: Hamed

last: Najafabadi

first: John

last: Reece-Hoyes

first: Juan

last: Fuxman Bass

first: Albertha

middle: J

last: Walhout

first: Matthew

middle: T

last: Weirauch

first: Timothy

last: Hughes


title: The Sinorhizobium meliloti SyrM regulon: effects on global gene expression are mediated by syrA and nodD3 (SyrA)

first: Melanie

last: Barnett

state: CA

summary: We characterized transcriptomes of a strain overexpressing syrA.  Our work shows that the syrA transcriptome shares similar gene expression changes to the syrM and nodD3 transcriptomes and that nodD3 and syrA may be the only targets directly activated by SyrM.  We propose that most of the gene expression changes observed when nodD3 is overexpressed are due to NodD3 activation of syrM expression, which in turn stimulates SyrM activation of syrA expression.  The subsequent increase in SyrA abundance alters activity of the ChvI-ExoS-ExoR circuit, resulting in broad changes in gene expression.

overall_design: Gene expression profiling of Sinorhizobium meliloti overexpressing syrA was performed using custom Affymetrix GeneChips

first: Sharon

last: Long


title: Microarray analysis of cortical cells of maize primary root grown under aereobic conditions with or without ethylene treatment

status: Public on Apr 01 2015

city: Nagoya

first: Hirokazu

last: Takahashi

state: Aichi

address: Furo-cho, Chikusa

department: Graduate School of Bioagricultural Sciences

country: Japan

institute: Nagoya University

summary:
Aerenchyma is continuous gas space between shoot and roots that contributes to the internal aeration in plants. In response to excess water stress and the plant hormone ethylene, maize (Zea mays) forms aerenchyma in root cortical cells by programmed cell death (PCD).
The aim of this study was to understand the molecular mechanism of ethylene-induced aerenchyma formation by identifying genes that are up- or down-regulated by ethylene treatment in the maize root cortical cells isolated by laser microdissection.

overall_design: Gene expression analysis in cortical cells of maize primary root

first: Takaki

last: Yamauchi

first: Imene

last: Rajhi

first: Naoko

middle: K

last: Nishizawa

first: Mikio

last: Nakazono


title: Germline unbalanced translocations arise from diverse mutational mechanisms including chromothripsis

status: Public on Apr 22 2015

city: Atlanta

first: M. Katharine

last: Rudd

address: 1518 Clifton Rd, CNR 5043

department: Human Genetics

institute: Emory University School of Medicine

type: Genome variation profiling by genome tiling array

summary: Unbalanced translocations are a relatively common type of copy number variation and are a major contributor to neurodevelopmental disorders. We analyzed the breakpoints of 57 unique unbalanced translocations to investigate the mechanisms of how they form. 51 are simple unbalanced translocations between two different chromosome ends, and six rearrangements have more than three breakpoints involving two to five chromosomes. Sequencing 37 breakpoint junctions revealed that simple translocations have between zero and four basepairs (bp) of microhomology (n=26), short inserted sequences (n=8), or paralogous repeats (n=3) at the junctions, indicating that translocations do not arise primarily from non-allelic homologous recombination, but instead form most often via non-homologous end joining or microhomology-mediated break-induced replication. Three simple translocations fuse genes that are predicted to produce in-frame transcripts of SIRPG-WWOX, SMOC2-PROX1, and PIEZO2-MTA1, which may lead to gain of function. Three complex translocations have inversions, insertions, and multiple breakpoint junctions between only two chromosomes. Whole- genome sequencing and fluorescence in situ hybridization analysis of two de novo translocations revealed at least 18 and 33 breakpoints involving five different chromosomes. Breakpoint sequencing of one inherited translocation involving four chromosomes uncovered multiple breakpoints with inversions and insertions. All of these breakpoint junctions had zero to four bp of microhomology consistent with germline chromothripsis, and both de novo events occurred on paternal alleles. Breakpoint sequencing of our large collection of chromosome rearrangements offers a comprehensive analysis of the molecular mechanisms behind germline translocation formation.

overall_design: High resolution array CGH; two-color experiment, clinical patient vs. normal control gDNA; sex mis-matched

first: Brooke

last: Weckselblatt

first: Karen

middle: E

last: Hermetz

first: M


title: Copy number variation of human intestinal stem cells with different passage in culture (five pedifrees, passage 5 and 25)

status: Public on May 29 2015

city: Houston

first: Frank

last: McKeon

state: TX

address: 3455 Cullen Blvd

department: Biology and Biochemistry

institute: University of Houston

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

summary: Stem cells of the gastrointestinal tract, pancreas, liver, and other columnar epithelia collectively resist cloning in their elemental states. Here we demonstrate the cloning and propagation of highly clonogenic, “ground state” stem cells of the human intestinal and colon. To assess the genomic stability of our intestinal stem cells, we serially passaged five independent intestinal stem cell pedigrees derived from the ileum of one late fetal demise case and tested them after 50 (passage 5; P5) and 250 days (P25) of continuous proliferation. DNA from cells at these passages cells was analyzed by SNP array based copy number variation analysis (CNV).  Although at P25,  there are aneuploidy in some of pedigrees, there are very few CNV at P5 in all pedigrees.

overall_design: SNP array based copy number variation study was performed for 5 pedigrees from human fetal intestinal stem cells (passage 5 and 25) to assess genomic stability at chromosomal level.

first: Xia

last: Wang

first: Yusuke

last: Yamamoto

first: Ting

last: Zhang

first: Wa

last: Xian


title: The Sinorhizobium meliloti SyrM regulon: effects on global gene expression are mediated by syrA and nodD3 (ChvI-SyrA)

summary: We characterized transcriptomes of strains containing a K214T mutation in chvI, with and without overexpression of syrA.  Our work shows that overexpression of syrA suppresses many of the transcription changes observed in the chvI K214T mutant.

overall_design: Gene expression profiling of a Sinorhizobium meliloti chvI K214 mutant overexpressing syrA was performed using custom Affymetrix GeneChips


title: Invasion and metastasis related long non-coding RNA expression profiles in hepatocellular carcinoma

status: Public on Mar 26 2015

city: Fuzhou

first: Xiaolong

last: Liu

state: Fujian

address: 312，Xihong Road

department: Mengchao Hepatobiliary Hospital

country: China

institute: Fujian Medical University

summary: Aberrant expression of LncRNAs might be responsible for the HCC invasion and metastasis. we employed the LncRNAs microarray technology to study the LncRNAs expression profiles at genome-wide in hepatocellular carcinoma (HCC)tissue samples with early recurrence (less than 1 year, with invasion and metastasis out of liver) and late recurrence (longer than 2 years, without invasion and metastasis out of liver), which had different recurrent/metastatic potentials, by using normal liver tissue as control to screen the dysregulated LncRNAs which are potentially involved in the recurrence, invasion and metastasis process of HCC

overall_design: two condition experiment, invasion and metastasis VS. non-invasion and metastasis HCC tissues and normal control tissues.

first: Yunhzne

last: Gao

first: Geng

last: Chen

first: Yongyi

last: Zeng

first: Jinhua

first: Minjie

last: Li

first: Jingfeng


title: Exploration of PRC2 sigal at gene promoters

status: Public on May 01 2015

first: Rod

last: Bremner

state: ON

address: 600 University Ave

department: Lunenfeld-Tanenbaum Research Institute

institute: Mount Sinai Hospital

type: Genome binding/occupancy profiling by genome tiling array

summary: Performed H3K27me3 ChIP-chip analysis to defien genomic regions with this mark, which indicates the presence of the PRC2 complex

overall_design: Untreated SW-13 adrenocortical carcinoma cells were lysed and ChIP analysis was performed to pull down H3K27me3 labelled chromatin. Purified DNA of that chromatin was hybridized to Agilent ChIP arrays. This experiment was repeated 3 times.

first: Mohamed

last: Abou El Hassan

first: Katherine

last: Huang


title: No Viral Association Found in a Set of Differentiated Vulvar Intraepithelial Neoplasia Cases by Human Papillomavirus and Pan-Viral Microarray Testing

status: Public on Mar 25 2015

city: San Francisco

first: Charles

last: Chiu

address: 185 Berry Street, Box 0134

department: Laboratory Medicine

institute: University of California, San Francisco

summary: The Virochip microarray (version 5.0, Viro5AGRS-60k platform, GPL19902) was used to screen FFPE sections from dVIN tissue to broadly screen for all known viruses.

overall_design: We used the Virochip microarray to screen for all known viruses in 10 dVIN samples, normal vulvar skin biopsy and a  HPV-positive metastatic cervical cancer tissue sample

middle: Y

first: Ozlen

last: Saglam


title: Gene expression changes in Porphyromonas gingivalis W83 after inoculation in rat oral cavity

status: Public on Apr 07 2015

city: Shenyang

first: Jian

last: Zhao

state: Liaoning Province

address: Nanjing North St. 117

department: Department of Periodontology

institute: School of Stomatology, China Medical University

summary: The aim of this study is to investigate the alterations in gene expression in Porphyromonas gingivalis W83 after inoculation in rat oral cavity. P.gingivalis W83 inoculation in rat oral cavity caused inflammatory responses in gingival tissues and destroyed host alveolar bone. Microarray analysis revealed that 42 genes were upregulated, and 22 genes were downregulated in the detected 1786 genes in the inoculated P.gingivalis W83. Products of these upregulated and downregulated genes are mainly related to transposon functions, cell transmembrane transportation, protein and nucleic acid metabolism, energy metabolism, cell division and bacterial pathogenicity.P.gingivalis W83 has a pathogenic effect on host oral cavity. Meanwhile, inflammatory oral environment alters P.gingivalis W83 gene expression profile. These changes in gene expression may limit the proliferation and weaken the pathogenicity of P.gingivalis W83, and favor themselves to adapt local environment for survival.

overall_design: 3 samples were picked up from wild strain P.gingivalis W83 and inoculated P.gingivalis W83, respectively. The total RNA was extracted and labeled with Klenow, and then hybridism with P.gingivalis W83 chip. The commercial GeneChip P.gingivalis W83 Genome Array used here was provided by CapitalBio Corporation (http://www.capitalbio.com/en/index.asp, Beijing, China), a service provider authorized by Roche NimbleGen (Wisconsin, USA). Five replicates of the genome were included per chip. An average of 19 different 60-base oligonucleotides (60-mer probes) represented each gene in the genome. Array hybridization, washing, scanning and data analysis were performed at the CapitalBio Corporation, Beijing, China and carried out according to the NimbleGen’s Expression user’s guide. The arrays were scanned using MS200 scanner (NimbleGen), and NimbleScan software (NimbleGen) was used to extract fluorescent intensity raw data from the scanned images. The expression data of probes were normalized using quantile normalization and expression data of genes were generated using the Robust Multichip Average (RMA) algorithm. In a comparison analysis, two class unpaired method in the Significant Analysis of Microarray software (SAM, version 3.02) was performed to identify significantly differentially expressed genes between TEST and CONTROL groups. Genes were determined to be significantly differentially expressed with a selection threshold of false discovery rate, FDR<5% and fold change＞2.0 in the SAM output result.

first: Qian


title: The Sinorhizobium meliloti SyrM regulon: effects on global gene expression are mediated by syrA and nodD3

first: Melanie

last: Barnett

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

overall_design: Refer to individual Series


title: Identification of miRNAs associated with chemotherapiutic response in lung adenocarcinomas

status: Public on Mar 22 2015

city: Chuo-ku

first: Motonobu

last: Saito

state: Tokyo

address: 5-1-1 Tsukiji

institute: National Cancer Center

summary: Expression profiling of chemo-responders and non-responders reveals miRNAs expression differences, we therefore demonstrated that miRNAs could be a therapeutic biomarker of chemotherapy to lung adenocarcinoma (LADC). we have employed miRNAs microarray expression profile as a discovery platform to identify miRNAs differentially expressed between responders and non-responders to platinum-based doublet chemotherapy. In total 40 cases of our study cohort, including 16 responders and 24 non-responders, we found that a 3-miRNAs signature (miR-1290, miR-196b, and miR-135a*) could predict the responder with the highest accuracy in study cohort (82.5%). This finding further validated in an independent additional cohort.

overall_design: MiRNA microarray expression was measured in 40 LADC cases, including 16 responders and 24 non-responders to platinum-based doublet chemotherapy.

first: Kouya

last: Shiraishi

first: Takashi

last: Kohno

first: Kenji

last: Matsumoto

first: Arisa

last: Igarashi

first: Keisuke

last: Oboki


title: Loss of HSulf-1 promotes altered lipid metabolism in ovarian cancer

status: Public on Mar 20 2015

city: Rochester

first: Asha

last: Nair

address: 200 1ST ST SW

institute: Mayo Clinic

summary: Loss of HSulf-1 potentially contributes to the metabolic alterations associated with the progression of ovarian pathogenesis, specifically impacting the lipogenic phenotype of ovarian cancer cells that can be therapeutically targeted

overall_design: This study was carried out using human samples in triplicates, and were grown in three different cultures - Sh1, Sh2 and NTC

first: Viji

last: Shridhar

first: Debarshi

last: Roy


title: Regulation of the pstSCAB operon in Corynebacterium glutamicum by the regulator of acetate metabolism RamB

status: Public on Mar 19 2015

city: Bielefeld

first: Hironori

last: Taniguchi

institute: Bielefeld University

summary: <Background>  The pstSCAB operon of Corynebacterium glutamicum, which encodes an ABC transport system for uptake of phosphate (Pi), is induced during the P i starvation response. The two-component regulatory system PhoRS is involved in this response, but partial Pi starvation induction of pstSCAB in a ∆phoRS mutant indicated the involvement of additional regulator(s). Regulation of pstSCAB also involves the global transcriptional regulator GlxR.  <Results>  DNA affinity chromatography identified the regulator of acetate metabolism RamB as a protein binding to pstS promoter DNA in vitro. Gel mobility shift assays and mutational analysis of the pstS promoter region revealed that RamB binds to two sites localized at positions -74 to -88 and -9 to +2 with respect to the transcriptional start site of pstSCAB. Reporter gene studies supported the in vivo relevance of both binding sites for activation of pstSCAB by RamB. DNA microarray analysis revealed that expression of many Pi starvation inducible genes reached higher levels during the Pi starvation response on minimal medium with glucose as sole carbon source than in Pi starved acetate-grown C. glutamicum cells.  <Conclusions>  In C. glutamicum, RamB is involved in expression control of pstSCAB operon. Thus, transcriptional regulation of pstSCAB is complex involving activation by the phosphate-responsive two-component regulatory system PhoSR and the regulators of carbon metabolism GlxR and RamB.

overall_design: Gene expression of C. glutamicum ATCC13032 after 90 min of phosphate starvation was compared in CGXII medium with different carbon sourse (4% glucose or 2% acetate) at the exponential growth phase. Biological duplicates were analyzed with dye-swaps.

first: Ulrike

last: Sorger-Herrmann

first: Volker

middle: F

last: Wendisch


title: Real-time quantitative miRNA PCR analysis of human plasma samples; circulating miRNAs miR-34a and miR-150 associated with colorectal cancer progression

city: Dublin

first: Sinead

last: Aherne

address: Glasvevin

country: Ireland

institute: Dublin City University

summary: Background: Screening for the early detection of colorectal cancer is important to improve patient survival. The aim of this study was to investigate the potential of circulating cell-free miRNAs as biomarkers of CRC, and their efficiency at delineating patients with polyps and benign adenomas from normal and cancer patient groups.   Methods: The expression of 667 miRNAs was assessed in a discovery set of 48 plasma samples comprising normal, polyp, adenoma, and early and advanced cancer samples. Three miRNAs (miR-34a, miR-150, and miR-923) were further examined in a validation cohort of 97 subjects divided into the same five groups, and in an independent public dataset of 40 CRC samples and paired normal tissues.  Results: High levels of circulating miR-34a and low miR-150 levels distinguished groups of patients with polyps from those with advanced cancer (AUC=0.904), and low circulating miR-150 levels separated patients with adenomas from those with advanced cancer (AUC=0.875). In addition, the altered expression of miR-34a and miR-150 in an independent public dataset of forty CRC samples and paired normal tissues was confirmed.  Conclusion: We identified two circulating miRNAs capable of distinguishing patient groups with different diseases of the colon from each other, and patients with advanced cancer from benign disease groups.

overall_design: qPCR miRNA expression profiling. Plasma samples from 48 donors comprising 8 normal, 8 polyp, 16 adenoma samples, 8 early stage cancer samples (stage I/II), and 8 advanced cancer samples (stage III/IV) were used. RNA was extracted from equal volumes of plasma from each donor.

first: Stephen

last: Madden

first: David

last: Hughes

first: Barbara

last: Pardini

first: Alessio

last: Naccarati

first: Miroslav

last: Levy

first: Pavel

last: Vodicka

first: Paul

last: Neary

last: Dowling

first: Martin

last: Clynes


title: Expression profiling of E. coli expressing the heterologous sigma70 factor (rpoD) of Lactobacillus plantarum

status: Public on Mar 18 2015

city: Newark

first: Stefan

middle: Marcus

last: Gaida

state: DE

address: 15 Innovation Way

department: Chemical Engineering

institute: University of Delaware

summary: Time course experiment to analyze transcriptional changes to the E. coli transcriptome due to overexpressing the heterologous sigma70 factor (RpoD) of Lactobacillus plantarum. A plasmid control strain (pControl) and the sigma70 overexpression strain (pLPLσ) were cultivated in parallel and after induction of RpoD expression samples for transcriptional profiling were taken in exponential, transition and stationary phase.

platform_organism: Escherichia coli str. K-12 substr. MG1655

overall_design: Samples of the control strain (pControl) and the sigma70 factor overexpression (pLPLσ) of L. plantarum were taken over a time course experiment in exponential (t=4.5 hours after induction), transition (t=6 hours) and stationary (t=9 hours) growth phase.  Two slides per time point were hybridized on a dye swap configuration for each of the two biological replicates.

middle: M

first: Nicholas

last: Sandoval

first: Sergios

last: Nicolaou

first: Yili

last: Chen

first: Keerthi

middle: P

last: Venkataramanan

first: Eleftherios

last: Papoutsakis


title: The importance of vesicular trafficking pathways in genome stability of diploid Saccharomyces cerevisiae cells

status: Public on Mar 16 2015

city: Warszawa

first: Adrianna

last: Skoneczna

address: Pawinskiego 5A

department: Laboratory of Mutagenesis and DNA Repair

country: Poland

institute: Institute of Biochemistry and Biophysics

summary: The ability to survive stress conditions is important for every living cell. Some stresses can affect not only current cell well-being, but may have far-reaching consequences. Uncurbed oxidative stress can cause DNA damage and the decrease in cell survival and/or increase in mutation rate. Some substances generating oxidative damage in the cell act mainly on DNA. Radiomimetic zeocin is a chemoenzyme that causes oxidative damage in DNA, inducing predominantly single or double strand breaks. Such lesions can subsequently lead to chromosomal rearrangements in genomic DNA, especially in diploid cells in which each sequence has its duplicate in the homologous chromosome.  In a global screen for mutants oversensitive to zeocin, we selected 136 genes whose deletion causes the decrease in survival of diploid Saccharomyces cerevisiae cells exposed to this compound. The screen revealed numerous genes connected with stress response, including response to DNA damage stimulus; DNA repair genes, especially connected with homologous recombination and telomere maintenance; genes involved in cell cycle progression, chiefly in control of cell divisions checkpoints, both meiotic and mitotic; and genes involved in remodeling of chromatin. Notably, our screen also demonstrated the involvement of vesicular trafficking system in cell protection against DNA damage. Presented data imply vesicular system in various pathways of cell protection from zeocin-dependent damage, including the role in detoxification and probably more direct role in genome maintenance processes. We show, that cells with vesicular trafficking dysfunction are unable to repair zeocin induced damage, accumulate Rad52 foci and frequently possess an atypical DNA content. Therefore, we postulate that functional vesicular trafficking is crucial for sustaining integral genome.   We believe that numerous new genes implicated in genome maintenance after genotoxic oxidative stress, together with newly discovered vesicular trafficking link to genome integrity, will help revealing novel molecular processes involved in the genome stability of diploid cells.

overall_design: Screen for diploid Saccharomyces cerevisiae deletion strains sensitive to zeocin (the compound generating double strand breaks in DNA). The pool of strains from Yeast knock-out (YKO) collection (Open Biosystems) containing homozygous diploid strains bearing double deletion of non-essential genes and heterozygous diploid strains bearing single deletion of essential genes were exposed to treatment with either 5 or 15 µg/ml zeocin for 1 hour. The change in relative abundance of individual deletion strains in a pool, as a measure of their increased zeocin sensitivity was assessed by comparison to mock treated strain pool using barcode microarrays with two-color hybridization. Four biological replicates of mock-treated vs zeocin treated strains were performed, two of them using the pool of original YKO diploid strains, the other two with the derivative pool, in which all strains bore additional single can1Δ mutation so they were heterozygous at CAN1 locus (Alabrudzinska et al., 2011 PLoS ONE, 6, e21124). Each biological replicate had two technical replicates with dye swapping. A total of 16 individual hybridizations were made. With each hybridization both barcodes: UP-Tag and DOWN-Tag, were analyzed and for technical reasons microarray images for UP-Tag and DOWN-Tag probe sets had to be scanned and quantified independently so there are 32 raw data files associated with this experiment.

first: Kamil

last: Krol

first: Izabela

last: Brozda

first: Marek

last: Skoneczny

first: Maria

last: Bretner


title: Study the transcriptional level changes of induced pluripotent stem (iPS) cells from X-linked Dyskeratosis Congenita (DC) Patients

status: Public on Mar 13 2015

city: Philadelphia

first: BAIWEI

last: GU

state: PA

address: 3615 Civic center BLVD

institute: The Children's Hospital of Philadelphia

summary: Dyskeratosis congenita is a bone marrow failure syndrome characterized by the presence of short telomeres at presentation. The X-linked form is caused by mutations in the gene DKC1, encoding the protein dyskerin. Dyskerin is required for in the assembly and stability of telomerase and is also involved in ribosomal RNA (rRNA) processing where it converts specific uridines to pseudouridine. DC is thought to result from failure to maintain tissues, like blood, that are renewed by stem cell activity, suggesting induced pluripotent stem (iPS) cells from X-linked DC patients may provide information about the mechanisms involved.  Here we show that in iPS cells with DKC1 mutations Q31E, A353V and ΔL37 telomere maintenance is compromised with short telomere lengths and decreased telomerase activity. The degree to which telomere lengths are affected by expression of telomerase during reprograming, or with ectopic expression of wild type dyskerin varies, with recurrent mutation A353V showing the most severe effect on telomere maintenance. A353V cells but not Q31E or ΔL37 cells, are refractory to correction by incorporation of a single copy of a wild type DKC1 cDNA into the AAVS1 safe harbor locus. None of the mutant cells show decreased pseudouridine levels in rRNA or defective rRNA processing. Finally transcriptome analysis of the iPS cells shows that WNT signaling is significantly decreased in all mutant cells, raising the possibility that defective WNT signaling may contribute to disease pathogenesis.

overall_design: 6 human iPS samples were investigated, including 1 WT sample (BMC) from health control, 2 duplicated samples Del371 and Del372 derived from DC patient with Del37mutation, 2 duplicated samples A353V1 and A353V2 derived from DC patient with A353V mutation, 1 sample Q31E derived from DC patient with Q31E mutation.

first: Bai-wei

last: Gu

first: Marisa

last: Apicella

first: Jason

last: Mills

first: Jian-Meng

last: Fan

first: Deborah

last: French

first: Gregory

last: Podsakoff

first: Monica

last: Bessler

first: Philip

last: Mason


title: Epigenetic adaptation to uncontrolled heterochromatin spreading

city: New York

first: Songtao

last: Jia

state: NY

address: 1114, Fairchild center

institute: Columbia University

summary: Heterochromatin, a highly compact chromatin state characterized by histone H3 lysine 9 methylation (H3K9me) and HP1 protein binding, epigenetically silences the underlying DNA and influences the expression of neighboring genes. Therefore the sites of heterochromatin assembly and its subsequent spreading are generally precisely determined. Here we show that in fission yeast, the combined absence of anti-silencing factors Mst2 and Epe1 results in uncontrolled heterochromatin spreading and severe growth defects. Interestingly, these cells quickly recover by accumulating H3K9me at the clr4+ locus, which encodes the H3K9 methyltransferase essential for heterochromatin assembly, thereby leading to reduced expression of Clr4 to restrain heterochromatin spreading. Preventing H3K9me at the clr4+ locus resulted in the accumulation of H3K9me at the rik1+ locus, which encodes another component of the Clr4 complex essential for H3K9me. Our results demonstrate that promiscuous heterochromatin assembly enables fast adaptation in response to changes in chromatin landscape and illustrate a negative feedback mechanism by which cells counteract toxic heterochromatin accumulation.

overall_design: six samples, WT, mst2∆, epe1∆,mst2∆ epe1∆, mst2∆ epe1∆ swi6∆, mst2∆ epe1∆ meu6∆

first: Jiyong

last: Wang


title: Human Plasma: Health vs. High risk vs. Stable Angina vs. AMI

status: Public on Mar 11 2015

city: Beijing

first: Xiangdong

last: Li

address: No. 167 Beilishi Rd

department: Cardiology

institute: Fuwai Hospital, National Center for Cardiovascular Diseases

summary: miRNAs expression profiles were screened by microarray between the Health, Highrisk, Stable Angia, and AMI patients.

overall_design: Biological replicates: 8 replicates in each group.

first: Dongfeng


title: Analysis of the Activity and Regulon of the Two-component Regulatory System Composed by Cjj1484 and Cjj1483 of Campylobacter jejuni

status: Public on Mar 17 2015

city: Albany

first: Craig

last: Parker

address: 800 Buchanan St

department: PSM

institute: USDA ARS

summary: Campylobacter jejuni is a leading cause of bacterial diarrheal disease and a frequent commensal of the intestinal tract of poultry and other animals. For optimal growth and colonization of hosts, C. jejuni employs two-component regulatory systems (TCSs) to monitor environmental conditions and promote proper expression of specific genes. We analyzed the potential of C. jejuni Cjj81176_1484 (Cjj1484) and Cjj81176_1483 (Cjj1483) to encode proteins of a cognate TCS that influences expression of genes possibly important for C. jejuni growth and colonization. Transcriptome analysis revealed that the regulons of the Cjj1484 histidine kinase and the Cjj1483 response regulator contain many common genes, suggesting that these proteins likely form a cognate TCS. We found that this TCS generally functions to repress expression of specific proteins with roles in metabolism, iron/heme acquisition, and respiration. Furthermore, the TCS repressed expression of Cjj81176_0438 and Cjj81176_0439, which had previously been found to encode a gluconate dehydrogenase complex required for commensal colonization of the chick intestinal tract. However, the TCS and other specific genes whose expression is repressed by the TCS were not required for colonization of chicks. We observed that the Cjj1483 response regulator binds target promoters both in unphosphorylated and phosphorylated forms and influences expression of some specific genes independently of the Cjj1484 histidine kinase. This work further expands the signaling mechanisms of C. jejuni and provides additional insights regarding the complex and multifactorial regulation of many genes involved in basic metabolism, respiration, and nutrient acquisition that the bacterium requires for optimal growth in different environments.

overall_design: Three-condition experiment, WT C. jejuni 81-176 SmR  (DRH212) and isogenic ΔCjj1484 (PML360) and ΔCjj1483 (PML335). Biological replicates: 3 81-176 SmR, 3 ΔCjj1484 (PML360),  and 3 ΔCjj1483 (PML335)independently grown to log phase and harvested. Two technical replicates/biological replicate. One replicate per array.   A type 2 gene expression experimental design was used, with fluorescently labeled genomic DNA as a reference channel in each experiment as described by Lucchini, S., et al. 2005.  Infect Immun 73:88-102.

first: P

last: Luethy

first: S

last: Huynh

first: C

first: D

last: Hendrixson


title: HDA6 mediated euchromatic silencing acts independently of DNA methylation

city: Beaucouzé

first: Etienne

last: Bucher

address: 42 rue Georges Morel

country: France

institute: IRHS

summary: Transcriptome of epic1 (hda6-8) a weak allele of HDA6 that does not affect DNA methylation

overall_design: 2 samples:silex, epic1, with 1 replicate each

first: Emilija

last: Hristova

first: Kateryna

last: Fal

first: David

last: Windels


title: Whole brain RNA from congenic littermates does not support a general effect of Nxf1 CAST alleles on alternative pre-mRNA processing

status: Public on Mar 10 2015

city: La Jolla

first: Gene

last: Yeo

address: 2880 Torrey Pines Scenic Dr. Room 3805/Yeo Lab

institute: UCSD

summary: Microarray hybridization was used to compare RNA from mouse brains with opposite genotypes at the Mvb1 (Nxf1) modifier locus for known alternative processing events.

overall_design:
6 samples of total brain RNA, from 3 littermate pairs, were hybridized to splicing-sensitive microarrays
*Addendum
Depending on the analysis software used, these CEL files may not load correctly using default parameters. This is due to the custom chip type of MJAY not being used during the array scanning step. There are three workarounds known for this problem so far.
1) If using APT, use multiple --chip-type parameters. Specifically, --chip-type mjay --chip-type MJAY --chip-type MoEx-1_0-st-v1.1sq
2) Edit the CEL file by converting to text using the APT command apt-cel-convert, then replacing the MoEx-1_0-st-v1.1sq in the DatHeader line with MJAY (all caps).
3) Edit the .pgf, .clf, and antigenomics.bmp files to use the MoEx-1_0-st-v1.1sq array instead of MJAY for the chip_type and lib_set_name options. (works on AltAnalyze software)

first: Bruce

last: Hamilton


title: Effective population size, extended linkage disequilibrium and signatures of selection in the rare dog breed Lundehund

status: Public on Mar 09 2015

city: Hannover

first: Ottmar

last: Distl

address: Buenteweg 17 p

department: Institute for Animal Breeding and Genetics

institute: University of Veterinary Medicine Hannover

summary: The Lundehund is an old dog breed with remarkable anatomical features including polydactyly in all four limbs and extraordinary flexibility of the spine. We genotyped 28 Lundehund using the canine Illumina high density beadchip to estimate the effective population size (Ne) and inbreeding coefficients as well as to identify potential regions of positive selection. The decay of linkage disequilibrium was slow with r2=0.95 in 50 kb distance. The last 7-200 generations ago, Ne was at 10-13. An increase of Ne was noted in the very recent generations with a peak value of 19 for Ne at generation 4. The FROH estimated for 50-, 65- and 358-SNP windows were 0.87, 087 and 0.81, respectively. The most likely estimates for FROH after removing identical-by-state segments due to linkage disequilibria were at 0.80-0.81. The extreme loss of heterozygosity has been accumulated through continued inbreeding over 200 generations within a probably closed population with a small effective population size. The mean inbreeding coefficient based on pedigree data for the last 11 generations (FPed=0.10) was strongly biased downwards due to the unknown coancestry of the founders in this pedigree data. The long-range haplotype test identified regions with genes involved in processes of immunity, olfaction, woundhealing and neuronal development as potential targets of selection. The genes QSOX2, BMPR1B and PRRX2 as well as MYOM1 are candidates for selection on the Lundehund characteristics small body size, increased number of digits per paw and extraordinary mobility, respectively.

overall_design: The objectives of the present study were to genotype 28 Lundehund using the canine Illumina high density beadchip (Illumina, San Diego, CA, USA) to estimate the effective population size (Ne) from data on linkage disequilibria (LD). We identified runs of homozygosity (ROH) as regions with a local loss of genetic variation. Inbreeding coefficients were calculated on the basis of pedigree data (FPed) and genotype information (FROH, FIS) to compare the results of these different methods for this population. We applied the long-range haplotype test to search for potential selective sweeps.

first: Sophia

last: Pfahler


title: Bovine granulosa cells of dominant follicles; comparison of growing vs plateau

status: Public on Mar 06 2015

city: Quebec

first: Annie

last: Girard

state: Quebec

address: 2440, boul. Hochelaga

department: Sciences animales

institute: Université Laval

summary: Granulosa cells originating from two different phases of antral follicle growth (growing and plateau) were compared in follicles with a diameter of 9mm or more. Growing follicle is the reference.

overall_design: Two conditions experiment (Growing and Plateau); Four biological replicates for each group; Two technical replicates per samples (dye-swap).

first: Isabelle

last: Dufort

first: Gabriel

last: Douville

first: Marc-André

last: Sirard


title: Bovine granulosa cells of dominant follicles; comparison of plateau vs atretic

summary: Granulosa cells originating from two different phases of antral follicle growth (plateau and atretic) were compared in follicles with a diameter of 9mm or more. The plateau follicle is the reference.

overall_design: Two conditions experiment (Plateau and Atretic); Four biological replicates for each group; Two technical replicates per samples (dye-swap).


title: A nucleosome turnover map reveals that the stability of histone H4 Lys20 methylation depend on histone recycling in transcribed chromatin [ChIP]

city: Stockholm

first: Karl

last: Ekwall

address: Alfred Nobels Alle 7

country: Sweden

institute: Karolinska Inst

summary: Nucleosome composition actively contribute to the chromatin structure and accessibility. To preserve chromatin state during replication, transcription and DNA repair, cells have evolved mechanisms to evict or recycle histones, generating a landscape of differentially aged nucleosomes. To map the stability of nucleosomes, we have adapted the recombination induced tag exchange (RITE) method to Schizosaccharomyces pombe histone H3. The RITE method allows us to study replication-independent protein turnover both through the occurrence of, in our case, new histone H3 and the disappearance or preservation of old histone H3. We contrast the RITE system to nucleosome turnover measured by chromatin incorporation of an epitope-tagged H3 under an inducible promoter. We confirm previous findings that stable nucleosomes are found at heterochromatin, but also at coding regions of actively transcribed genes. Genome-wide comparisons with several chromatin marks showed that high turnover nucleosomes correlate with H2A.Z, acetylated H4 and H3K4me2. The histones with high turnover are primarily found at the nucleosomes on the 5´and/or 3´ edges of the transcribed unit. In addition, in this study we have determined genome-wide maps of all three methylation marks at H4K20. All methylation of H4K20 appeared in low turnover nucleosomes and particularly in euchromatic regions. H4K20me1 marks stable nucleosomes at loci proximal to nucleosome depleted regions (NDR) and H4K20me2/3 were found further inside of transcribed units, especially at coding regions of long genes expressed at low levels. Further, this transcription-dependent accumulation of histone methylations was dependent on the histone chaperone complex FACT (Facilitates Chromatin Transcription), as predicited from its role in recycling nucleosomes during transcription.

overall_design: In total 28 samples: 26  ChIP DNA files, 2 Input files. Two related datasets using 1) H4K20 methylation (antibodies against each me1, me2 and me3, compared between WT and set9-delta cells) and 2) nucleosome turnover, with 2 systems, i) RITE and ii) pInv. Each of these are compared 2h (after induction) to 0h. Input files not used for comparisons, and therefore only provided as CEL files for reference.

first: J

last: Svensson

first: Pauline

last: Audergon

first: Victoria

last: Menendez-Benito

first: Manu

last: Shukla

first: Indranil

last: Sinha

first: Ulrika

last: Norman-Axelsson

first: Elisabet

last: Jemt

first: Jason

middle: C

last: Tanny

first: Robin

last: Allshire


title: Bovine granulosa cells of dominant follicles; comparison of growing vs atretic

summary: Granulosa cells originating from two different phases of antral follicle growth (growing and atresia) were compared in follicles with a diameter of 9mm or more. Growing follicle is the reference.

overall_design: Two conditions experiment (Growing and Atresia); Four biological replicates for each group; Two technical replicates per samples (dye-swap).


title: Transcriptomic Evaluation of Pyrococcus furiosus strains engineered to produce 3HP

status: Public on Mar 07 2015

city: Raleigh

first: Aaron

last: Hawkins

state: NC

address: 840 Main Campus Dr

institute: North Carolina State University

summary:
A hybrid array setup containing WT Pyrococcus furiosus genes plus heterologous genes for engineered pathway producing 3HP from maltose and CO2 was used to study the impact of heterlogous pathway on native metabolic systems
Four different experiments were run:
1) Pfu WT vs Pfu COM1;
2) Pfu COM1 vs MW56 (strain containing 3 heterologous genes from Metallosphaera sedula for production of 3HP);
3) Pfu COM1 vs MW76 at 72C before and after 3HP production;
4) MW76 at 72C before and after 3HP production at high agitation

sample_organism:
Pyrococcus furiosus
Pyrococcus furiosus DSM 3638
Pyrococcus furiosus COM1

overall_design:
Two or four condition arrays; 2 biological replicates, independently grown and harvested, RNA combined before RT
Please note that
[1] The *normdata.xlsx files contain the normalized data from each array/channel (prior to analyzing data from all slides in loop with JMP Genomics 5 (SAS, NC), using a mixed effects ANOVA model)
[2] The data column headers indicate strain_treatement_dye-assignment-slide (or replicate) # (e.g. COM1_72C_cy3_4)
[3] The *xlsx contains merged data from 2-6 arrays resulted from a mixed effects ANOVA model analyses
[4] The processed data files associated with each sample are indicated in the corresponding sample description field.

first: Hong

last: Lian

first: Benjamin

last: Zeldes

first: Andrew

last: Loder

first: Gina

last: Lipscomb

first: Gerrit

last: Schut

first: Matthew

last: Keller

first: Michael

last: Adams

first: Robert

last: Kelly


title: Sex related differences in murine transcriptional response to TCDD toxicity

status: Public on Mar 01 2015

city: Toronto

first: Stephenie

last: Prokopec

address: 661 University Avenue, Suite 510

institute: Ontario Institute for Cancer Research

summary: 2,3,7,8-Tetrachlorodibenzo-p-dioxin (TCDD) is an environmental contaminant that produces myriad toxicities in most mammals. In rodents alone, there is a huge divergence in the toxicological response across species, as well as among different strains within a species. But there are also significant differences between males and females animals of a single strain. These differences are inconsistent across model systems: the severity of toxicity is greater in female rats than males, while male mice and guinea pigs are more sensitive than females. Because the specific events that underlie this difference remain unclear, we characterized the hepatic transcriptional response of adult male and female C57BL/6 mice to 500μg/kg TCDD at multiple time-points. The transcriptional profile diverged significantly between the sexes. Female mice demonstrated a large number of altered transcripts as early as 6h following treatment, suggesting a large primary response. Conversely, male animals showed the greatest TCDD-mediated response 144h following exposure, potentially implicating significant secondary responses. Nr1i3 was statistically significantly induced at all time-points in the sensitive male animals. This mRNA encodes the constitutive androstane receptor (CAR), a transcription factor involved in the regulation of xenobiotic metabolism, lipid metabolism, cell cycle and apoptosis. Surprisingly though, changes at the protein level (aside from the positive control, CYP1A1) were modest, with only FMO3 showing clear induction, and no genes with sex-differences. Thus, while male and female mice show transcriptional differences in their response to TCDD, their association with TCDD-induced toxicities remains unclear.

overall_design:
Adult male and female C57BL/6 mice were treated by gavage with either 500 ug/kg TCDD in corn oil or corn oil vehicle alone. Animals were euthanized at either 6, 24, 72 or 144 hours after treatment and tissues were harvested. RNA was isolated from hepatic tissue and the transcriptome for each animal assayed on an individual microarray.

Please note that 7 samples (out of total 65 samples) were identified as outliers and therefore the data were processed without the outliers as well. The normalized data without outliers were provided in the 'normalized_data_without_outliers.txt' file.

middle: D

first: John

last: Watson

first: Jamie

last: Lee

first: Raimo

last: Pohjanvirta

first: Paul

last: Boutros


title: Role of Fft3 in nuclear organization [DamID-chip, ChIP-chip]

status: Public on Mar 02 2015

city: Hamburg

first: Babett

last: Steglich

address: Martinistrasse 52

institute: Universitätsklinikum Hamburg-Eppendorf

type: Methylation profiling by genome tiling array

summary: In eukaryotic cells, local chromatin structure and chromatin organization in the nucleus both influence transcriptional regulation. At the local level, the Fun30 chromatin remodeler Fft3 is essential for maintaining proper chromatin structure at centromeres and subtelomeres in fission yeast. Using genome-wide mapping and live cell imaging, we show that this role is linked to controlling nuclear organization of its targets. In fft3Δ cells, subtelomeres lose their association with the LEM domain protein Man1 at the nuclear periphery and move to the interior of the nucleus. Furthermore, genes in these domains are upregulated and active chromatin marks increase. Fft3 is also enriched at retrotransposon-derived long terminal repeat (LTR) elements at the borders of subtelomeres and at tRNA genes. In cells lacking Fft3, these sites lose their peripheral positioning and show reduced nucleosome occupancy. We propose that Fft3 has a global role in mediating association between specific chromatin domains and components of the nuclear envelope by maintaining chromatin structure required for anchoring DNA insulators to nuclear pores.

overall_design:
For DamID samples, we recorded methylation levels for Dam fusion proteins and compared them to Dam-only control samples.
For ChIP samples, we compared immuno-precipitated DNA to mock or input controls.

first: Annelie

last: Strålfors

first: Olga

last: Khorosjutina

first: Jenna

last: Persson

first: Agata

last: Smialowska

first: Jean

last: Javerzat

first: Karl

last: Ekwall


title: Murine liver tissue, Mdr2-/+ control vs Mdr2-KO

city: Jerusalem

first: Dr. Daniel

last: Goldenberg

address: Ein-Karem

department: Gene Therapy Institute

country: Israel

institute: Hadassah Medical Center

summary: Chronic liver inflammation precedes the majority of hepatocellular carcinomas (HCC). Here, we explore the connection between chronic inflammation and DNA methylation in the liver at the late precancerous stages of HCC development in Mdr2/Abcb4-knockout (Mdr2-KO) mice, a model of inflammation-mediated HCC.  Using methylated DNA immunoprecipitation (MeDIP) followed by hybridization with Agilent CpG Islands (CGIs) microarrays we found specific CGIs in 76 genes which were hypermethylated in the Mdr2-KO liver compared to age-matched controls. Methylation of thirty among these genes was highly specific to the studied HCC model. We revealed that in most tested cases, the observed hypermethylation resulted from an age-dependent decrease of methylation of the specific CGIs in control livers with no decrease in mutant mice. Chronic inflammation did not change global levels of DNA methylation in Mdr2-KO liver, but caused a 2-fold decrease of the global 5-hydroxymethylcytosine level in mutants compared to controls. This decrease could result from a less efficient age-dependent demethylation of specific CpG sites in the liver of Mdr2-KO mutants, as described above. Expression of some tested hypermethylated genes was increased in Mdr2-KO livers compared to controls (28%), others were either similarly expressed (44%), or not expressed in the liver (28%). Liver cell fractionation revealed, that the relative hypermethylation of specific CGIs in Mdr2-KO compared to control livers affected either hepatocyte, or non-hepatocyte, or both fractions. There was only episodic correlation between changes of gene methylation and expression in cell fractions. Conclusion: Chronic liver inflammation causes hypermethylation of specific CGIs, which may affect both hepatocytes and non-hepatocyte liver cells. These changes may serve as markers of an increased regenerative activity and of a precancerous microenvironment in the chronically inflamed liver.

overall_design: Two-condition experiment, Mdr2-KO vs Mdr2-/+ liver tissue from 12m-old male FVB strain mice. Biological replicates: 3 control replicates, 3 knockout replicates.

first: Daniel

first: Evgeniy

last: Stoyanov

first: Guy

last: Ludwig


title: CGH array profiles of melanoma cell lines

city: Doha

first: Francesco

middle: Maria

last: Marincola

address: Al Nasr Tower, AL Corniche Street, PO Box 26999

country: Qatar

institute: Sidra Medical and Research Center

summary: Dysfunction in type I interferon (IFN) signaling occurs in patients with stage II or more advanced cancer. After screening the effects of a panel of 12 melanoma cell lines on PBMCs of healthy volunteers of IFNalpha signal pathway, two groups of melanoma cell lines could be identified one with stronger suppression (low pSTAT-1 group) than the other (high pSTAT-1 group). Comparative genomic hybridization (CGH) identified consistent amplification of 12q22-24 as a genomic marker for the immune suppressive melanoma cell lines. This region corresponded to higher transcription of the NOS1 gene located in that region in the low pSTAT1 group and NOS1 expression was identified as causal factor in melanoma induced immune suppression.

overall_design: Twelve melanoma cell lines were analyzed. Genomic DNA of the cell line sample was labeled with Cy5 and reference normal PBMC DNA was labeled with Cy3.


title: Modification of miRNA profile in Caco-2 cells by dietary lipids

city: Madrid

first: Lidia

middle: Ángeles

last: Daimiel-Ruiz

state: Madrid

address: Ctra. Cantoblanco, Km 8

department: Nutritional Genomics of Cardiovascular Disease and Obesity

country: Spain

institute: Institute IMDEA Food

summary: The aim of this study was to detect miRNAs modified by biactive dietary lipids in a cellular model of enterocytes. The selected model was Caco-2 cells

overall_design:
Differentiated Caco-2 cells were incubated with micelles containing the lipids for 24 and 48 hours. The expression leveles of the miRNAs were compared with cells treated with empty micelles. Four control and choelsterol samples, three DHA samples and two CLA samples were analyzed
variables: Control (Empty micelles), Cholesterol 250 µM 48h, DHA 200 µM 24h, CLA 200µM 24h
Biological replicates
Control: Samples 137, 159, 160, 210
Cholesterol: Samples 150, 151, 152, 219
DHA: Samples 141, 142, 143
CLA: Samples 144, 146

first: Alberto

last: Dávalos


title: Maize plants (Zea may) : WT (Alice) vs. Yellow stripe mutants (ys1 or ys3) (qPCR)

city: Tokyo

first: Tomoko

last: Nozoye

address: 1-1-1 yayoi bunkyo-ku

institute: The University of Tokyo

summary: qPCR gene expression profiling of Yellow stripe 1 (ys1) and ys3 mutants. ys1 and ys3 are recessive mutants of maize (Zea mays L.) that result in symptoms typical of Fe deficiency, i.e., interveinal chlorosis of the leaves. The objective of the present work was to identify the genes involved in the ys1 and ys3 phenotypes, so as to extend our understanding of Fe homeostasis in maize.

overall_design: Root or shoot of WT vs. ys1 or ys3 mutants under Fe sufficient or Fe deficient conditions respectively.


title: Tumorigenic carryover effects of early life exposure to dichloroacetic acid in male B6C3F1 mice

status: Public on Feb 26 2015

city: RTP

first: Susan

last: Hester

address: 109 TW Alexander Dr

institute: US EPA

summary:
Here we investigated the longterm carryover effects of dichloroacetic acid (DCA), a common by-product of drinking water chlorination, on hepatic tumorigenesis in mice.
Our findings demonstrate that postnatal exposure to a common drinking water contaminant results in longterm carryover effects on tumorigenesis, potentially via epigenetic events altering cellular respiration and metabolism.

overall_design:
The gene expression study followed a stop-promotion design in which 7d male B6C3F1 mice received the following treatments:
deionized water alone (dH2O, control); 0.06% phenobarbital (PB), a rodent liver mitogen and tumor promoter; or DCA (3.5g/L) for 10 weeks followed by dH2O for 90 weeks.

first: Charles

last: Wood

first: Brian

last: Chorley

first: Gleta

last: Carswell

first: Hongzu

last: Ren

first: Beena

last: Vallanat

first: Anna

last: Fisher

first: Bill

last: Ward

first: Anthony

last: DeAngelo


title: Rat DNA methylation in the Nucleus Accumbens in Incubation of Cocaine Craving

status: Public on Feb 27 2015

city: Montreal

first: Moshe

last: Szyf

address: McIntyre Medical Building, 3655 Promenade Sir William Osler, Room 1309

department: Pharmacology

institute: McGill University

summary: DNA methylation profiling of nucleus Accumbens of rats that self administered cocaine and were subjected to 1 or 30 withdrawal days with or without extinction tests.

overall_design: The groups consist of 1. Saline rats (Sal.) 2. Rats that self-administered cocaine for 10 days and that were subjected to a withdrawal period of 1 day (1W) 3. Rats that self-administered cocaine for 10 days and that were subjected to a withdrawal period of 1 day and to an extinction test for assessment of cue-induced cocaine-seeking behavior (1C) 4. Rats that self-administered cocaine for 10 days and that were subjected to a withdrawal period of 30 days (30W) 5. Rats that self-administered cocaine for 10 days and that were subjected to a withdrawal period of 30 days and to an extinction test for assessment of cue-induced cocaine-seeking behavior (30C)

first: Gal

last: Yadid


title: Rat gene expression in the Nucleus Accumbens in Incubation of Cocaine Craving

summary: Gene expression profiling of nucleus Accumbens of rats that self administered cocaine and were subjected to 1 or 30 withdrawal days with or without extinction tests.


title: Role of DNA Methylation in the Nucleus Accumbens in Incubation of Cocaine Craving

type:
Expression profiling by array
Methylation profiling by array

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

overall_design: Refer to individual Series


title: Rat DNA methylation in the Nucleus Accumbens in Incubation of Cocaine Craving and treatments with DNA methylation modifying drugs

summary: DNA methylation profiling  of nucleus Accumbens of rats that self administered cocaine, were subjected to 30 withdrawal days, were treated with aCSF, RG108 or SAM and were subjected to extinction tests.

overall_design: The groups consist of: 1. Rats that self-administered cocaine for 10 days and that were subjected to a withdrawal period of 30 days, were injected in the nucleus accumbens with aCSF and were subjected to an extinction test for assessment of cue-induced cocaine-seeking behavior (aCSF) 2. Rats that self-administered cocaine for 10 days and that were subjected to a withdrawal period of 30 days, were injected in the nucleus accumbens with RG108 and were subjected to an extinction test for assessment of cue-induced cocaine-seeking behavior (RG108) 3. Rats that self-administered cocaine for 10 days and that were subjected to a withdrawal period of 30 days, were injected in the nucleus accumbens with SAM and were subjected to an extinction test for assessment of cue-induced cocaine-seeking behavior (SAM)


title: Using the Porcine SNP60k array to discover copy number variations in high and low fertility boars

status: Public on Feb 21 2015

city: Guelph

first: Tamas

last: Revay

address: 50 Stone Rd E

department: Biomedical Sci

institute: University of Guelph

summary: The raw data from the Porcine SNP60k array was used to discover copy number variations in high and low fertile breeding boars. Analysis was done in SNP and Variation Suite ver. 7.7.8. (SVS, GoldenHelix Inc.) Results were published in Revay et al., BMC Genomics 2015

overall_design: Arrays were performed on 13 Landrace, 3 Duroc and 20 Yorkshire boars of high and low fertility by the service provider DNA Landmarks.

first: Anh

last: Quach

first: Laurence

last: Maignel

last: Sullivan

first: Allan

last: King


title: NanoString assays of miRNA in MCF7 and MCF10A cells and in extracellular vesicles (EVs) derived from these cells.

city: Columbus

first: Lianbo

last: Yu

state: OH

address: 1800 Cannon Drive

department: Center for Biostatistics

institute: The Ohio State University

summary: The goal of this study is to identify unique miRNA profiles of EVs from MCF7 and MCF10A cells that distinguish their cellular origin.

overall_design: 654 human mature miRNAs were analyzed in NanoString assays to identify miRNA with high abundance in MCF7 EVs and the greatest fold change for MCF7 EVs relative to MCF10A EVs.

first: Nicole

last: Guzman

first: Kitty

last: Agarwal

first: Dilip

last: Asthagiri

first: Motoyasu

last: Saji

first: Matthew

last: Ringel

first: Michael

last: Paulaitis


title: Global transcriptional analysis of Campylobacter jejuni NCTC 11168 in response to epinephrine and norepinephrine.

status: Public on Feb 10 2015

city: Beijing

first: Fuzhou

last: Xu

address: No. 9, Shuguanghuayuan Middle Rd.

department: Institute of Animal Science and Veterinary Medicine

institute: Beijing Academy of Agriculture and Forestry Sciences

summary: During colonization in the host gastrointestinal tract, the enteric bacteria Campylobacter jejuni is exposed to a variety of signaling molecules including the catecholamine hormones epinephrine (Epi) and norepinephrine (NE). NE has been determined to stimulate the growth of C. jejuni as well as increase its pathogenicity. To investigate the mechanisms of NE or Epi on the biology of C. jejuni, the global gene expression profiles of C. jejuni NCTC 11168 cultured in iron-restricted medium were analyzed in response to NE or Epi. Totally, 183 and 156 genes were differentially expressed by NE and Epi respectively, with 102 differentially expressed genes common between the two treatments. These genes are involved in diverse cellular functions including iron uptake systems, motility, virulence, oxidative stress response, nitrosative stress tolerance, enzyme metabolism, DNA repair and metabolism and ribosomal protein biosynthesis. Adherence to and invasion of Caco-2 cells by C. jejuni were enhanced upon exposure to NE or Epi. These results indicated that NE and Epi have similar effects on the gene expression of C. jejuni and that the effects on gene expression may contribute to elucidate the mechanisms on interaction between host and C. jejuni.

sample_organism: Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819

overall_design: Transcriptional profiles were analyzed using microarray to compared the epinephrine (Epi) or norepinephrine (NE) treated and untreated Campylobacter jejuni NCTC 11168. NE or Epi treated and untreated cultures of C. jejuni NCTC 11168 were collected at the mid-log phase (～36 h cultures). Three (for NE or Epi treated culture) or four (for untreated control culture) independent biological replicates were performed. Total RNA was extracted using RiboPure™-Bacteria Kit (Ambion, Life Technologies) according to the manufacturer’s instructions. The quality and quantity of total RNA were determined by an Agilent Bioanalyzer 2100. Total RNA was amplified and labeled by Low Input Quick Amp Labeling Kit, One-Color, following the manufacturer’s instructions. Labeled cRNA were purified by RNeasy mini kit (QIAGEN, GmBH, Germany). Each Slide was hybridized with 600ng Cy3-labeled cRNA using Gene Expression Hybridization Kit (Agilent technologies, Santa Clara, CA, US) in Hybridization Oven, according to the manufacturer’s instructions. After 17 hours hybridization, slides were washed in staining dishes with Gene Expression Wash Buffer Kit (Agilent technologies, Santa Clara, CA, US), followed the manufacturer’s instructions. Slides were scanned by Agilent Microarray Scanner with default settings, Dye channel: Green, Scan resolution=5μm, PMT 100%, 10%, 16bit. Data were extracted with Feature Extraction software 10.7. Raw data were normalized by Quantile algorithm, Gene Spring Software 11.0. The genes with fold change ≥ 1.5 and P < 0.05 were selected as differentially expressed.

first: Fangfang

last: Guo

first: Cun

last: Wu

first: Guolin

last: Cui

first: Ximin

last: Zeng

first: Bing

last: Yang

first: Hongzhuan

last: Zhou

first: Xia

last: Su

first: Jun

last: Lin


title: Mutations in the SIX1/2 pathway and the DROSHA/DGCR8 miRNA microprocessor complex underlie high-risk blastemal type Wilms tumors

status: Public on Feb 18 2015

city: Wuerzburg

first: Susanne

middle: Elma

last: Kneitz

address: Biozentrum, Am Hubland

department: Physiologigcal Chemistry

institute: University of Wuerzburg

summary: Blastemal histology in chemotherapy-treated pediatric Wilms tumors (nephroblastoma) is associated with adverse prognosis. To uncover the underlying tumor biology and find novel therapeutic leads for this subgroup of patients, we analyzed 58 blastemal-type Wilms tumors by exome and transcriptome sequencing and validated our findings in a large independent replication cohort. Recurrent mutations identified either somatically or in the germline included a hotspot mutation (Q177R) in the homeodomain of SIX1 and SIX2 in tumors with high proliferative potential, mutations in microprocessor genes like DROSHA, DGCR8, DICER1 and DIS3L2, and alterations in IGF2, MYCN, and TP53, the latter being strongly associated with dismal outcome. DROSHA and DGCR8 mutations had a strong effect on miRNA expression patterns in tumors, which was functionally validated in cell lines transfected with mutant DROSHA.

overall_design: total samples analyzed are 16, each done as technical replicate

first: Romina

last: Vardapour

last: Ludwig

first: Manfred

last: Gessler


title: Streptococcus mutans UA159 vs. fabM mutant strain (UR117), pH7 vs. pH5/5.5

status: Public on Feb 15 2015

city: Rochester

first: Roberta

last: Faustoferri

address: 601 Elmwood Ave. Box 611

department: Center for Oral Biology

institute: University of Rochester Medical Center

summary: Transcriptional analysis of glucose shock vs. steady-state growth in the parent strain and an acid sensitive mutant strain of S. mutans

overall_design: RNA was extracted from 4 replicate samples of S. mutans UA159 and UR117 (fabM mutant strain) grown in continuous culture to a steady-state pH value of 7.  The cultures were exposed to a glucose shock (200mM) and samples were collected upon achieving culture pH value of 5.5.  pH control was re-established and cultures were allowed to grow to a steady-state pH value of 5 (for UA159) and 5.5 (for fabM mutant).  RNA was labeled with Cy3.  For each replicate, labeled RNA was hybridized to slides along with Cy5-labeled reference RNA, extracted from S. mutans UA159 cultures grown to mid-log.

first: Jonathon

last: Baker

first: Jacqueline

last: Abranches

first: Jose

middle: A

last: Lemos

first: Robert

middle: G

last: Quivey


title: miRNA profiling of MCF7 autocrine hGH

status: Public on Dec 31 2014

city: Houston

first: Xiang H.-F.

last: Zhang

state: Texas

address: One Baylor Plaza

department: Beast Center

institute: Baylor College of Medicine

summary: MicroRNAs are widely expressed in the normal pubertal mammary gland and orchestrate mammary gland development by regulating cell proliferation, differentiation, apoptosis, and metabolism. Although human Growth hormone(hGH) plays fundamental roles in normal mammary gland development and elevated autocrine hGH levels have been documented to contribute to breast cancer, whether hGH should influence the expression pattern and the functional roles of miRNAs in this context remain unknown.This study explores the effects of autocrine hGH on microRNA expression in MCF7 cell.

overall_design: MCF7 cells with stably integrated hGH and Mut hGH were cultured for a total of 24 h in serum-free medium before processing for RNA preparation. Total miRNA was isolated, labeled and hybridized to the miRNA microarray as described by the manufacturer (Invitrogen). The hybridized slides were then analyzed on a GenePix scanner.

first: Pengxu

last: Qian

first: Weijie

first: Peter

last: Lobie

first: Tao

last: Zhu


title: Tobacco-induced microRNAs profile alterations in human spermatozoa: a preliminary study for further knowledge of toxical spermatogenesis impairment

status: Public on Jan 01 2015

city: MARSEILLE CEDEX 09

first: Aurelie

last: Bergon

address: parc scientifique de Luminy, case 928

institute: TAGC INSERM U1090

summary:
Tobacco smoking generates deleterious effects on human semen quality but mechanisms by which cigarettes smoking can impact spermatogenesis are poorly understood. Recent works have shown that spermatozoa RNAs can be used to understand mechanisms involved in tobacco induced spermatogenesis impairment. We performed a prospective study of 8 smoker and 8 non-smoker patients in an university hospital. All patients were selected according to an occupational exposure standardized questionnaire and the sperm parameters. We performed gene expression and miRNA microarrays using RNA extracts from spermatozoa of 8 smokers and 8 non-smokers. Quantification of selected miRNA was performed using quantitative RT-PCR.
We show that 16 genes were differentially expressed between smokers and non-smokers, of which 5 were upregulated and 11 were down regulated in smokers. 23 microRNAs were differentially expressed, of which 16 were upregulated and 7 were down regulated in smokers. Quantitative RT-PCR confirmed the down regulation in smokers for 3 microRNAs. Moreover in smokers, one of the upregulated genes is a putative target for one down regulated microRNA.

This is a preliminary and innovating study on spermatozoa RNA extracts in the field of infertility. This preliminary study shows that large scale approaches are non invasive diagnostic tools that may help elucidate the mechanisms that mediate the response to tobacco smoke exposure on human spermatogenesis. This could be used to design biomarkers of human spermatogenetic damage, and help elucidate the fine regulatory mechanisms that mediate responses to environmental agent exposure during human spermatogenesis.

overall_design: miRNAs were extracted from spermatozoa of 8 patients including: 4 non-smokers and 4 smokers

first: Catherine

last: Metzler-Guillemain

first: Cyrille

last: Lepoivre

first: Geneviève

last: Victorero

first: Aurélie

first: Jeanne

last: Perrin

first: Irène

last: Sari-Minodier

first: Nicolas

last: Boulanger

first: Pascal

last: Rihet

last: Nguyen


title: DNA Methylation Changes and Childhood Asthma in the Inner City [gene expression]

status: Public on Feb 02 2015

city: Aurora

first: David

last: Schwartz

state: CO

address: Anschutz Medical Campus

department: Medicine

institute: University of Colorado, Anschutz Medical Campus

summary: Background:  Epigenetic marks, like asthma, are heritable. They are influenced by the environment, direct the maturation of T cellslymphocytes, and have been shown to enhance the development of allergic airways disease in mice.  Thus, we hypothesized that epigenetic marks are associated with allergic asthma in inner-city children.  Methods:  We compared methylation patterns and gene expression in inner-city children with persistent atopic asthma versus healthy controls, using DNA and RNA from peripheral blood mononuclear cells (PBMCs) from inner city children aged 6-12 years with persistent atopic asthma children and healthy controls.     Results were externally validated with the GABRIELA study population.    Results:  Comparing asthmatics (N=97) to controls (N=97), we identified 81 regions that were differentially methylated.  Several immune genes were hypomethylated in asthmatics, including IL-13, RUNX3, and a number of specific genes relevant to natural killer cells (KIR2DL4, KIR2DL3, KIR3DL1, and KLRD1) and T cells lymphocytes (TIGIT).   14 differentially methylated regions (DMRs) were associated with the serum IgE concentration of IgE, including RUNX3.  These results were internally and externally validated with a global methylation assessment using a different methodology in our inner-city cohort and an independent European cohort (GABRIELA).  Hypo- and hypermethylated genes tended to be associated with increased and decreased gene expression, respectively (P<0.6x10-11 for asthma and ; P<0.01 for IgE).  To further explore the relationship between methylation and gene expression, we created a matrix of genomic changes in methylation versus transcriptional changes (methyl eQTL) for asthma, and identified cis- and trans-regulated genes whose expression was related to asthma asthma-associated methylation marks.

overall_design: peripheral blood mononuclear cells (PBMCs) from 97 atopic asthmatic and 97 nonatopic nonasthmatic children

first: Ivana

middle: V

last: Yang

first: Brent

middle: S

last: Pedersen

first: Andrew

last: Liu


title: MiRNA profiling of meningioma of different grades and histological subtypes

city: Homburg

first: Nicole

last: Ludwig

address: Kirrberger Strasse

department: Human Genetics

institute: Saarland University

summary: Although meningiomas are one of the most frequent primary intracranial tumors, there are only a few studies dealing with gene regulation processes in meningiomas. MiRNAs are key regulators of gene expression and regulation and miRNA profiles offer themselves as biomarkers for cancer development and progression. To investigate the role of miRNAs during meningioma growth and progression, we compared expression of 1205 miRNAs in 55 meningioma samples of different tumor grades and histological subtypes. We were able to classify histological subtypes in WHO grade I meningiomas with up to 97% accuracy (meningothelial versus fibroblastic) and different WHO grades with up to 93% accuracy (WHO I versus WHO III). We found significant downregulation of miRNAs on chromosome 1p36 and within two large miRNA clusters on 14q32 in high grade meningiomas, two regions that are yet associated with meningioma progression. We also identified several miRNAs associated with epithelial to mesenchymal transition differentially expressed in meningothelial meningioma compared to fibroblastic meningioma. Combined, our data show that meningiomas of different WHO grades and histological subtypes show a specific miRNA expression profile. Some individual miRNAs can also serve as potential biomarkers for meningioma progression.

overall_design: Tumor miRNA profile of 55 meningioma tumor samples, including 11 samples of each meningotheliall, fibroblastic and transitional meningioma (WHO grade I), atypical meningioma (WHO grade II) and anaplastic meningioma (WHO grade III).


title: Circulating miRNA in serum of Wilms tumor patients

summary:
Abstract:
Background: MiRNA signatures in human sera have been reported for various tumor diseases. Here we generated miRNA profiles analyzing 1205 mature miRNA transcripts of serum samples of Wilms tumor patients, taken prior and after chemotherapy according to SIOP protocol 2001. Using a feature subset selection filter approach we identified a minimal number of miRNAs with a maximum contribution for the classification between treated and untreated patients and between patients and controls.
Results: Analyzing 1205 mature miRNAs, we separated controls and Wilms tumor patients prior chemotherapy with an accuracy of 0.81. We obtained a similar accuracy (0.82) for the separation between controls and sera of Wilms tumor patients after preoperative chemotherapy. We identified 23 miRNAs that were differentially expressed in both comparisons. Subset selection improved the overall classification accuracy between controls and Wilms tumor patients prior and after chemotherapy to 0.94 and 0.91, respectively. Subset selection also allowed separating between Wilms tumor patients prior and after chemotherapy with an accuracy of 0.98.
Conclusion: Our analysis identified serum based miRNA signatures that allowed separating between controls, untreated Wilms tumor patients, and Wilms tumor patients after chemotherapy with high accuracy for each of these comparisons.

overall_design: Serum miRNA profile of 16 Wilms tumor patients before and after preoperative chemotherapy, 19 sera of children without malignant disease

first: Jana

last: Schmitt


title: Effects of PCB 153 on genome-wide gene expression in the liver of Atlantic Cod (Gadus murhua)

city: Bergen

first: Fekadu

last: Yadetie

address: Thormøhlensgt. 53A/B

department: Biology

country: Norway

institute: University of Bergen

summary: Genome-wide gene expression assay was used to map the genes affected in the liver of Atlantic cod treated with the persistent environmental pollutant polychlorinated biphenyl 153 (PCB 153) (0.5, 2 and 8 mg/kg body weight).

overall_design: Analyzed samples from each of control, 0.5, 2 and 8 mg/BW PCB 153 treated group (n = 3 for 2mg/kg group, and n = 4 for each of the other groups). Liver total RNA from each fish was reverse transcribed and Cy3-labled and hybridized.

first: Odd

last: Karlsen

first: Marta

last: Eide

first: Christer

last: Hogstrand

first: Anders

last: Goksøyr


title: A Genome-wide Gene Expression Analysis and Database in Transgenic Mice during Development of Amyloid or Tau Pathology

status: Public on Dec 24 2014

city: London

first: Dervis

last: Salih

address: Gower St

department: Dementia Research Institute

country: United Kingdom

institute: University College London

summary: The purpose of this project was to compare whole genome expression in 5 transgenic mice with human genes for dementia that result in either plaques or tangle pathology to the expression in wild-type control mice and to each other at different stages of disease progression.

overall_design: Total RNA was obtained from hippocampus, cortex and cerebellum in four lines of ‘amyloid’ transgenic mice (mutant human APP and APP/PSEN1  genes) and ‘TAU’ transgenic mice (mutant human MAPT gene) as well as wild-type control mice at 8,16, 32 and 72 weeks

first: M

last: Matarin

first: D

last: Yasvoina

last: Cummings

last: Guelfi

first: W

last: Nahaboo

first: T

last: Moens

first: Paublete

middle: R

last: Moreno

first: S

last: Ali

last: Perona

first: R

last: Desai

first: K

middle: J

last: Smith

first: J

last: Latcham

last: Fulleylove

last: Richardson

last: Hardy

first: F

last: Edwards


title: Expression data from Senescence Process of citrus

status: Public on Dec 03 2014

city: Wuhan

first: Ding

last: Yuduan

address: No.1,Shizishan Street · Hongshan District · Wuhan · Hubei Province · 430070 · P.R.China

institute: Huazhong Agricultural University

summary: The postharvest senescence processes of citrus fruits were analyzed transcriptomic. The present study was aimed to: further uncover the rind-flesh communication of hesperidium; characterize the differential storage behaviors of different citrus varieties; reveal the important changes during storing process; and demonstrate the specific non-climacteric characteristics of citrus fruits.

sample_organism:
Citrus sinensis
Citrus maxima
Citrus unshiu
Citrus reticulata

overall_design: We chose four major table fruit varieties of citrus: satsuma mandarin (Citrus unshiu Marc) (M), ponkan (Citrus reticulata Blanco) (K), newhall navel orange (Citrus sinensis L. Osbeck) (O) and shatian pummelo (Citrus grandis Osbeck) (P). They were sampled every 10 days during 50 DAH (days after harvest), almost covering the commercial storage period of loose-skin citrus.

first: Yuduan

last: Ding

first: Jiwei

last: Chang

first: Yunjiang

last: Cheng


title: miRNA expression profiling of NB4 control cells versus NB4 cells treated with SAHA (Vorinostat)

status: Public on Dec 22 2014

city: Naples

first: carmela

last: dell'aversana

address: Pietro Castellino 111

country: Italy

institute: IGB - Institute of Genetics and Biophysics - CNR

summary: For a long time, the BARD1 (BRCA1-associated RING domain 1) protein has been considered as a BRCA1 (BReast Cancer susceptibility gene 1, early onset) interactor, and tumor suppressor mutated in breast and ovarian cancers. Despite its functions in a stable heterodimer with BRCA1, there is increasing evidence for BRCA1-independent functions of BARD1. Here, we investigated BARD1 expression and function in human acute myeloid leukemias and their modulation by epigenetic mechanisms and microRNA. We show that the HDACi (histone deacetylase inhibitor) Vorinostat reduces BARD1 mRNA levels by increasing miR-19a and miR-19b expression levels. Moreover, we identify specific BARD1 isoforms that might act as tumor diagnostic and prognostic markers.

overall_design: Two-condition experiment: untreated NB4 cells (control) vs. NB4 cells treated with 5µM SAHA (Vorinostat) for 6h. Biological replicates: 3 control, 3 treated, independently grown and harvested at 6 hours. One replicate per array.

first: Christoph

last: Eicken

first: Carmela

last: Dell'Aversana


title: The human miRNA repertoire of different blood compounds

status: Public on Jun 16 2014

city: Saarbrücken

first: Christina

last: Backes

address: Campus, Building E 2.1

department: Chair for Clinical Bioinformatics

summary:
Background: MiRNAs from body fluids gain more and more attraction as biomarker candidates. Besides serum, patterns from whole blood are increasingly considered as markers for human pathologies. Usually, the contribution of different cell types to the respective signature remains however unknown. In this study we provide insights into the human miRNome of different compounds of the blood including CD3, CD14, CD15, CD19, CD56 positive cells as well as exosomes.
Methods: We measured the miRNA repertoire for each cell type and whole blood for two individuals at three time points over the course of one year in order to provide evidence that the cell type miRNomes can be reproducibly detected.
Results: For measurements repeated after 24 hours we found on average correlation of 0.97, even after one year profiles still correlated with 0.96, demonstrating the enormous stability of the cell type specific miRNomes. Highest correlation was found for CD15 positive cells, exceeding Pearson correlation of 0.99. For exosomes a significantly higher variability of miRNA expression was detected. In order to estimate the complexity and variability of the cell type specific miRNomes, we generated profiles for all considered cell types in a total of seven unaffected individuals. While CD15 positive cells showed the most complex miRNome consisting of 328 miRNAs, we detected significantly less miRNAs (186, p = 1.5*10-5) in CD19 positive cells. Moreover, our analysis showed functional enrichment in many relevant categories such as onco-miRNAs and tumor miRNA suppressors. Interestingly, exosomes were enriched just for onco-miRNAs but not for miRNA tumor suppressors.
Conclusion: In sum, our results provide evidence that blood cell type specific miRNomes are very consistent between individuals and over time.

overall_design: We obtained EDTA and PAXgene blood from 7 healthy subjects and  isolated the  CD3, CD19, CD15, CD14, and CD56 positive cell fractions from the EDTA blood samples (timepoint t0). In addition, we repeated the experiment one year later (t1) and one year and a day later (t2) for two samples.

first: Petra

last: Leidinger


title: Physiological and cell morphology adaptation of Bacillus subtilis at near-zero specific growth rates: a transcriptome analysis.

status: Public on Nov 19 2014

city: Groningen

first: Wout

last: Overkamp

address: Nijenborgh 7

country: Netherlands

institute: Rijksuniversiteit Groningen, Department of Molecular Genetics

summary: B. subtilis was cultured in a retentostat at extremely low growth rates and the adaptation of B. subtilis to these near-zero growth conditions was studied by analysis of the transcriptome and genome. During retentostat culturing the specific growth rate decreased to a minimum of 0.00006 h-1, corresponding to a doubling time of 470 days. Transcriptome analysis shows that while cells under near-zero growth conditions exhibit many characteristics of stationary phase cells, they are also fundamentally different. Stress resistance mechanisms were only mildly induced in response to the progressively decreasing growth-rate and while glucose was still supplied, cells were ready for utilization of alternative carbon sources. Genome resequencing, of samples taken 40 days after inoculation to reach zero-growth conditions, indicated that only minor changes in the genome occurred and that these most likely did not play a role in the transcriptional responses.

platform_organism: Bacillus subtilis subsp. subtilis str. 168

overall_design:
Total of 8 samples; 4 timepoints with each 2 biological replicates. First timepoint is used as reference. Total number of hybridizations is 24.

The 4 timepoints are defined as follows: From 2 replicate retentostat cultures, 4 timepoints are taken during the course of 42 days. Replicate samples from the two cultures were taken on similar days. For retentostat 1 (i.e. rep1): 0, 7, 18 and 42 days. For retentostat 2 (i.e. repl2): 0, 6, 20 and 40 days.

Timepoint 1, 2 and 3 were compared to reference timepoint 0, using all hybridization data available. All time points were compared with each other using a 'factorial design' or 'fully crossed design' hybridisation scheme, including dye swaps for each time point.
For example, to compare timepoint 1 versus the reference, not only the direct comparisons of 0vs1 and 1vs0 were used, but data from all hybridizations containing timepoint 1 was taken with various weightfactors depending on slide quality. The comparison resulted in a single value shown in the matrix table. The same accounts for timepoint 2 and 3.

The 'README.txt' contains processing/normalization strategy, list of raw data files used for each (merged) data column etc.

first: Oscar

last: Kuipers


title: Gene expression profiling of brains from bovine spongiform encephalopathy (BSE)-infected cynomolgus macaques

status: Public on Jun 10 2014

city: Goettingen

first: Gabriela

last: Salinas

state: Lower-Saxony

address: Kreuzbergring 57

department: Department of Pathology

institute: Universitaetsmedizin Goettingen

summary: We performed gene expression profiling of total RNA from brain samples derived from BSE-infected versus non-infected cynomolgus macaques (Macaca fascicularis).

overall_design: Total RNA from brain samples derived from 7 BSE-infected (6 intracerebrally, 1 orally infected) versus 5 non-infected controls were compared using GeneChip Rhesus macaque Genome Array.

first: Dirk

last: Motzkus

first: Maura

last: Barbisin

first: Silvia

last: Vanni

first: Ann

last: Schmädicke

last: Salinas-Riester

first: Lennart

last: Opitz

first: Giuseppe

last: Legname


title: Effects of the insulin degrading enzyme silencing on the transcriptome of HepG2 cells

status: Public on Sep 06 2014

city: Nuthetal

first: Olga

last: Pivovarova

address: Arthur-Scheunert-Allee 114-116

department: Clinical Nutrition

institute: German Institute of Human Nutrition

summary: Insulin degrading enzyme (IDE) is a major enzyme responsible for insulin degradation in the liver. The modulation of insulin degrading enzyme activity is hypothesized to be a link between T2DM and liver cancer. Results provide insight into role of IDE in proliferation and other cell functions.

overall_design: HepG2 cells were transfected with 96nM siRNA for IDE or AllStars Negative Control siRNA (Qiagen) using Lipofectamine 2000 (Invitrogen). 16 h after transfection, cells were treated with 10 nM insulin (Sigma Aldrich) or vehicle for 24 h in serum starvation condition. Total RNA was extracted. For each of the 4 conditions, 3 biological replicates were included.

first: Iryna

last: Ilkavets

first: Carsten

last: Sticht

first: Sergei

last: Zhuk

first: Steven

last: Dooley

first: Andreas

last: Pfeiffer

first: Natalia

last: Rudovich


title: microRNA expression profiling during Adipocytic differentiation of human MSCs (hMSC-TERT)

status: Public on Sep 09 2014

city: Riyadh

first: Nehad

last: Alajez

address: 1st floor College of Medicne

department: Anatomy

country: Saudi Arabia

institute: King Saud University College of Medicine

summary: We have employed whole microRNA microarray to identify changes in microRNA expression in human bone marrow MSCs (hMSC-TERT) during adipocytic differentiation in culture on day 7 and day 13

overall_design:
Human MSC line (hMSC-TERT) were subjectd to adipocytic differentiation for 7 days or 13 days, subsequently, RNA was extracted. The samples were labeled using the miRCURY LNA™ microRNA Hi-Power Labeling Kit, Hy3™/Hy5™ and hybridized on the miRCURY LNA™ microRNA Array (6'th GEN). Array product number 208400; Array version 6'th GEN, Array batch number 34014, miRBase version 17.

The 'Legends_rawdata.pdf' contains the column headers (of raw data files) and their detailed description.

first: Li

last: Chen

first: Moustapha

last: Kassem


title: Genome-wide analysis of perinatal effect of NF-kabbaB inhibition by pyrrolidine dithiocarbamate (PDTC) on the kidneys of Fawn-Hooded Hypertensive (FHH) rats at ages 2 days, 2 weeks and adult

status: Public on Jun 15 2014

city: Utrecht

first: Sebastiaan

last: Wesseling

address: Heidelberglaan 100

department: Nephrology & Hypertension

institute: UMC Utrecht

summary: Microarray was performed on kidneys of Fawn-Hooded Hypertensive (FHH) rats in order to elucidate the so-called "beneficial" effect of perinatal treatment with PDTC.

overall_design: In total, 59 samples were used. At least 4 rats per treatment groups. 2d, 2w and adult rats with or without PDTC treatment. Total 12 groups.


title: Expression data from pig oviduct in response to X or Y chromosome bearing spermatozoa

status: Public on May 20 2014

city: Sheffield

first: Carmen

last: Alminana

address: Tree Root Walk

department: Academic Unit of Reproductive and Developmental Medicine, Human Metabolism Department

institute: University of Sheffield

summary: The objective of the present study is to investigate if females have the ability to recognise X or Y chromosome bearing spermatozoa and present a different response to different spermatozoa.

overall_design: In order to investigate if females have the ability to recognise X or Y chromosome bearing spermatozoa and present a different response to different spermatozoa. Samples of semen were sorted for chromosomal sex by ﬂow cytometric-sorting. Using laparoscopic insemination one oviduct was inseminated with X spermatozoa and the contralateral oviduct was inseminated with Y spermatozoa.This allowed us to obtain samples from the oviduct in contact with X sperm and Y sperm in the the contrlateral oviduct from the same sow. Oviduct pig samples were collected for RNA isolation and hybridization on Affymetrix microarrays. Four biological replicates were performed (n= 4 sows) and a total of 8 arrays were used for microarrays study (4 arrays for oviduct samples in contact with X spermatozoa and 4 arrays for oviduct samples in contact with Y spermatozoa.

first: Ignacio

last: Caballero

first: Paul

last: Heath

first: Afsaneh

last: Maleki-Dizaji

first: Inmaculada

last: Parrilla

first: Cristina

last: Cuello

first: Maria

last: Gil

first: Jose

middle: L

last: Vazquez

first: Juan

first: Jordi

last: Roca

first: Emilio

last: Martinez

first: William

last: Holt

first: Alireza

last: Fazeli


title: Transcriptome characterization of immune suppression from battlefield-like stress

status: Public on Oct 27 2014

city: Fort Detrick

first: seid

last: muhie

state: MD

address: 568 Doughten Dr

department: Systems Biology Enterprise

institute: USACEHR

summary: Transcriptome alterations of leukocytes from soldiers who underwent eight-weeks of Army Ranger training (RASP, Ranger Assessment and Selection Program) were analyzed to evaluate impacts of battlefield-like stress on the immune response.  About 1,400 transcripts were differentially expressed between pre- and post-RASP leukocytes.  Upon functional analysis, immune response was the most enriched biological process, and most of the transcripts associated with the immune response were down-regulated.  Microbial pattern recognition, chemotaxis, antigen presentation, and T-cell activation were among the most down-regulated immune processes.  Post-RASP leukocytes exposed ex vivo to Staphylococcal enterotoxin B (SEB) showed a markedly impaired immune response to this superantigen compared to pre-RASP leukocytes, consistent with suppression of the immune response revealed by transcriptome analyses.

overall_design: A total of 20 subjects were included in the pre- and post-RASP study. The microarray was done using two chanel custom arrays consisting of about 9000 probes.

first: Seid

last: Muhie

first: Rasha

last: Hammamieh

first: Christiano

last: Cummings

first: David

last: Yang

first: Marti

last: Jett


title: Expression data from one year old leaves of Populus simonii by chilling stress (4°C, 10h).

status: Public on May 16 2014

city: Beijing

first: Jin

middle: Hui

last: Chen

state: Beijing

address: No. 35, Qinghua East Road

department: College of Biological Sciences and Biotechnology, Beijing Forestry University

institute: Beijing Forestry University

summary:
We take the one year old plant for chilling stress (4°C, 10h) and controls.Use the Affymetrix poplar gene chip to decrypt the gene functions and mechanisms in Populus simonii leaves.
We used microarrays to detail the global programme of gene expression during chilling stress (4°C, 10h).

overall_design: Populus simonii leaves were taken from chilling stress (4°C, 10h) and controls for RNA extraction and hybridization on Affymetrix microarrays.BH11269-2_Zdqe 13 and BH11269-2_Zdqe 14 from chilling stress (4°C, 10h) treatments, CK1 and CK2 controls.

first: Deqiang

last: Zhang

first: Yuepeng

last: Song

first: Qingqing


title: Gene expression profile of replicative senescence in normal human diploid fibroblasts.

status: Public on Apr 10 2014

city: Kamakura

first: Satoshi

last: Kondo

state: Kanagawa

address: Tebiro 6-10-1

department: New Projects Development Division

institute: Toray Industries,Inc.

summary: Transcriptional profiling of normal human diploid fibroblasts(TIG-3) comparing late passage with early passage.

overall_design: Total RNA was isolated using TRIzol reagent and were analyzed using the human 3D-Gene DNA chip (Toray) that contains 25000 genes. The genome wide transcriptional response of senescent cells(more than 70 population doublings)(Replicative) were compared to that of proliferating cells(less than 40 population doublings)(Young).

first: Yoshinori

last: Imai

first: Eiji

last: Hara


title: Analysis of altered microRNA expression profiles in proximal renal tubular cells in response to calcium oxalate monohydrate crystal adhesion

status: Public on Apr 22 2014

first: BH

last: Wang

address: jiefang road 1095

institute: Tongji hospital

summary: The present study aims to assess the potential changes in microRNAs of proximal renal tubular cells in response to the adhesion of calcium oxalate monohydrate (COM) crystals.

overall_design: microRNA microarray was applied to evaluate the expression of HK-2 cells exposed to COM crystals for 0 and 24 hours.

first: Bohan

first: Xiao

last: Yu


title: Unique microRNA profiles in EGFR-mutated lung adenocarcinomas

status: Public on Mar 10 2014

city: Oslo

first: Maria

middle: Moksnes

last: Bjaanæs

address: Ullernchausseen 70

department: Department of genetics

institute: Oslo Universitetssykehus

summary: We have examined the microRNA expression in 154 lung adenocarcinoma samples and 20 paired normal lung tissue samples and investigated the microRNA expression to clinical variables, EGFR- and KRAS- mutational status and time to progression.

overall_design: 174 samples are analyzed. 154 from lung adenocarcinoma tumor tissue and 20 from paired normal lung tissue samples. No replicates or control samples included.

first: Aslaug

last: Helland