title: MicroRNAs of the RPE are essential for RPE differentiation and photoreceptor maturation (mRNA)

status: Public on Jun 16 2015

city: Tel Aviv

first: Metsada

last: Pasmanik-Chor

address: Ramat Aviv

department: Biology

country: Israel

institute: Tel Aviv University

summary: Dysfunction of the retinal pigmented epithelium (RPE) results in degeneration of photoreceptors and vision loss and is correlated with common blinding disorders in humans. Although many protein-coding genes are known to be expressed in RPEs and important for their development and maintenance, virtually nothing is known about the in vivo roles of non-protein coding transcripts in RPEs. The expression patterns of microRNAs (miRNAs) have been analyzed in a variety of ocular tissues, and few were implicated to play role in RPE based on studies in cell lines. Herein, through RPE specific conditional mutagenesis of Dicer1 or DGCR8, the importance of miRNA for RPE differentiation was uncovered. Interestingly, miRNAs were found to be dispensable for maintaining the RPE fate and survival, and yet they are essential for acquisition of important RPE properties such as the expression of genes involved in the visual cycle pathway, pigmentation and cell adhesion. Importantly miRNAs of the RPE were found to be required for maturation of the adjacent photoreceptors, specifically for the morphogenesis of the outer segments. The profiles of miRNA and mRNA altered in the Dicer1 deficient RPE point to a key role of miR-204 in regulation of RPE differentiation program in vivo and uncovers the importance of additional novel RPE miRNAs. The study exposes the combined regulatory activity of miRNAs of the RPE, which is required for RPE differentiation and for the development of the adjacent neuroretina.

overall_design: Effect of Dicer 1 deficiency on RPE miRNA and mRNA.

first: Reut

last: Ohana

first: Benjamin

last: Weiman-Kelman

first: Shaul

last: Raviv

first: Ernst

last: Tamm

first: Ariel

last: Rinon

first: Dvir

last: Netanely

first: Ron

last: Shamir

first: Arie

last: S Salomon

first: Ruth

last: Ashery-Padan


title: Chronic psoriatic skin inflammation leads to increased monocyte adhesion and aggregation

status: Public on Jun 27 2015

city: Cleveland

first: Jackelyn

middle: B

last: Golden

state: Ohio

address: 2109 Adelbert Rd

department: Dermatology

country: USA

institute: Case Western Reserve University

summary: Psoriasis patients exhibit an increased risk of death by cardiovascular disease (CVD) and have elevated levels of circulating intermediate (CD14++CD16+) monocytes. This elevation could represent evidence of monocyte dysfunction in psoriasis patients at risk of CVD, as increases in circulating CD14++CD16+ monocytes are predictive of myocardial infarction and death. An elevation in the CD14++CD16+ cell population has been previously reported in patients with psoriatic disease, which has been confirmed in the cohort of our human psoriasis patients.  CD16 expression was induced in CD14++CD16neg classical monocytes following plastic adhesion, which also elicited enhanced β2 but not β1 integrin surface expression, suggesting increased adhesive capacity. Indeed, we found that psoriasis patients have increased monocyte aggregation among circulating PBMCs which is recapitulated in the KC-Tie2 murine model of psoriasis. Visualization of human monocyte aggregates using imaging cytometry revealed that classical CD14++CD16neg monocytes are the predominant cell type participating in these aggregate pairs. Many of these pairs also included CD16+ monocytes, which could account for apparent elevations of intermediate monocytes. Additionally, intermediate monocytes and monocyte aggregates were the predominant cell type to adhere to TNF-α and IL-17A-stimulated dermal endothelium. Ingenuity Pathway Analysis (IPA) demonstrated that monocyte aggregates have a distinct transcriptional profile from singlet monocytes and monocytes following plastic adhesion, suggesting that circulating monocyte responses to aggregation are not fully accounted for by homotypic adhesion, and that further factors influence their functionality.

overall_design: qRT-PCR Gene Expression Profiling - 30 Samples Analyzed, 10 biological replicates, 10 Control Samples, 20 Test Samples

first: Sarah

middle: G

last: Groft

first: Michael

middle: V

last: Squeri

first: Sara

middle: M

last: Debanne

first: Nicole

middle: L

last: Ward

first: Thomas

middle: S

last: McCormick

first: Kevin

middle: D

last: Cooper


title: Gene expression profiles of PD fibroblasts treated by SNCA expression-control RNAi.

status: Public on Jun 08 2015

city: Kodaira

first: Hirohiko

last: Hohjoh

state: Tokyo

address: 4-1-1 Ogawahigashi

country: Japan

institute: National Institute of Neuroscience, NCNP

summary: We investigated gene expression profiles of Parkinson disease (PD) patient's fibroblasts that were treated by SNCA expression-control RNAi to see adverse effects of the RNAi treatment. The data suggested no significant adverse effects caused by the treatment.

overall_design: Total RNA samples prepared from PD fibroblasts that were treated by SNCA expression-control RNAi and by non-silencing RNAi as a control.

first: Masashi

last: Fukuoka


title: ß-amylase1 mutant Arabidopsis plants show improved drought tolerance due to reduced starch breakdown in guard cells

status: Public on Jun 30 2015

city: Erlangen

first: Christian

last: Prasch

address: Staudtstrasse 5

department: Biochemistry division

country: Germany

institute: FAU Universität Erlangen-Nürnberg

summary: In plants, drought stress is a major growth limiting factor causing cell water loss through open stomata. In this study, guard cell-specific transcripts from drought-stressed Arabidopsis plants were analyzed and a down-regulation of β-amylase 1 (BAM1) was found. In previous studies, BAM1 was shown to be involved in stomatal starch degradation under ambient conditions. Impaired starch breakdown of bam1 mutant plants was accompanied by decreased stomatal opening. Here, we show that drought tolerance of bam1 mutant plants is improved as compared to wild type controls. Microarray-analysis of stomata-specific transcripts from bam1 mutant plants revealed a significant down-regulation of genes encoding aquaporins, auxin- and ethylene-responsive factors and cell-wall modifying enzymes. This expression pattern suggests that reduced water-uptake and limited cell wall extension are associated with the closed state of stomata of bam1 mutant plants. Together these data suggest that regulation of stomata-specific starch turnover is important for adapting stomata opening to environmental needs and its breeding manipulation may result in drought tolerant crop plants.

overall_design: Stress induced gene expression in Arabidopsis leaves and Stomata was measured after exposure to single drought stress. Drought stress conditions were analysed for both, Col-0 plants and a T-DNA insertion line for β-amylase 1. Six week old plants were treated with drought stress (5 days) according to Prasch and Sonnewald, 2013. Two to three biological replicates have been hybridized for each treatment.

first: Uwe

last: Sonnewald


title: Conditioning lesion rat DRG time course

status: Public on Jul 06 2015

city: Piscataway

first: Ronald

middle: P.

last: Hart

state: NJ

address: 604 Allison Rd Rm B430

department: Cell Biology & Neuroscience

institute: Rutgers University

summary: To identify potential regeneration-associated genes, rat dorsal root ganglia (DRG) were lesioned and then sampled at 4, 8, 12, 24, 48, 148, or 296 hrs

overall_design:
A total of 23 samples were examined in 8 time points with 2-3 replicates each.  For each array, lesioned and uninjured DRG samples were run in a two-color experiment.
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submitters of this record cannot locate the raw data

middle: P

first: Jason

last: Carmel


title: Regulation of Rat Hepatic Translation by mTOR

status: Public on Jun 01 2015

city: Providence

first: Joan

last: Boylan

state: RI

address: 593 Eddy Street

department: Pediatrics

institute: Rhode Island Hospital

summary: Our strategy was to manipulate mTOR signaling in vivo, then characterize the transcriptome and translating mRNA in liver tissue.  In adult rats, we used the non-proliferative growth model of refeeding after a period of fasting, and the proliferative model of liver regeneration following partial hepatectomy.  We also studied livers from pre-term fetal rats (embryonic day 19-20) in which fetal hepatocytes are asynchronously proliferating.  All three models employed rapamycin to inhibit mTOR signaling.

overall_design: For the non-proliferative growth model, adult rats were fasted 48hr followed by an IP injection of DMSO (n=3) or rapamycin (250ug/100g body wt) (n=3). Sixty minutes later rats were refed ad libitum for 3hr before sacrifice.  For the proliferative model, one hour preceding a 2/3 partial hepatectomy (PHep) rats were injected IP with DMSO (n=3) or rapamycin (250ug/100g body wt.) (n=3).  Twenty-four hours following PHep, animals were sacrificed.  Fetal rats were injected with  DMSO (n=4) or 50ug of rapamycin (n=4) on day E19 of gestation.  Twenty four hours later (E20), the fetal rats were delivered and livers were removed.  All livers were flash frozen in liquid nitrogen. RNA was extracted from polysomes that were generated using sucrose density fraction, as well as total liver. RNA was hybridized to Affymetrix Genechip Rat Gene 1.0 ST  Arrays.

first: Philip

middle: A

last: Gruppuso


title: Isolation of subtype-specific N-Ras responsive genes in basal-like breast cancer cells

status: Public on Jun 06 2015

city: HOUSTON

first: Eric

middle: C.

last: Chang

state: TX

address: ONE BAYLOR PLZ

department: BREAST CENTER

institute: BAYLOR COLLEGE OF MEDICINE

summary: To identify the the N-Ras-controlled genes in basal-like cells, we used shRNA to repress N-RAS in basal-like SUM102PT, SUM149PT and claudin-low SUM159PT cells. We seek the genes regulated only in basal-like, but not in claudin-low cells, to isolate the genes controlled by N-Ras in a breast cancer subtype-specific fashion. We also overexpressed oncogenic form N-Ras(G12D) in these cells in order to compare the genes regulated by wild-type and oncogenic N-Ras. The shRNA silencing and overexpression were conducted by lentiviral infection in the cells, with non-silencing shRNA-infected cells as the controls. The infected cells were then selected in antibiotics for about 5 days before total RNAs were harvested for microarray analysis.

overall_design: N-Ras was silenced by shRNA or oncogenic N-Ras (G12D) was overexpressed in basal-like SUM102PT, SUM149PT and claudin-low SUM159PT cells.

middle: C

first: Charles

last: Perou


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

overall_design: Refer to individual Series


title: Agilent-custom CGH microarray analysis of hematological malignancies

city: Pittsburgh

first: Svetlana

last: Yatsenko

state: PA

address: 300 Halket St

institute: University of Pittsburgh

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


title: NKX2-5 mutations causative for congenital heart disease retain functionality and are directed to hundreds of targets

status: Public on Jul 07 2015

city: Westmead

first: Ashley

last: Waardenberg

state: NSW

address: 214 Hawkesbury Road

country: Australia

institute: Children's Medical Research Institute

type: Genome binding/occupancy profiling by genome tiling array

summary:
NKX2-5 is a homeodomain transcription factor that plays a central role in the cardiac gene regulatory network, and is commonly mutated in human congenital heart disease. Here, we take a functional genomics approach to congenital heart disease mechanism. We used DamID to establish a robust set of target genes for both wild type NKX2-5 and a mutation lacking the homeodomain (NKX2-5delHD), the latter to model loss-of-function in gene regulatory network. NKX2-5delHD bound hundreds of targets including NKX2-5 wild type targets and a unique set of “off-targets”, and retained partial functionality. We showed that NKX2-5delHD could heterodimerize with NKX2-5 wild type and cofactors, including ubiquitous ETS family members ELK1 and ELK4, through a tyrosine-rich homophilic interaction domain (YRD). NKX2-5delHD off-targets, but not those of an NKX2-5 YRD mutant, were enriched in ETS motifs and were occupied by ELK1/ELK4 proteins, as determined by DamID. Our study reveals unexpected activities for NKX2-5 mutations on chromatin, guided by interactions with their normal cardiac and general cofactors, and suggest potential for a novel type of gain-of-function in congenital heart disease.

The supplementary bed file contains all binding regions detected for the N/C-terminal fusions reported in the manuscript, in addition to probe locations, ready to upload directly into UCSC browser (mm9).

overall_design: DamID-chip TF binding analysis. N and C-terminal Dam fusions to ELK1, ELK4 and SRF vs. Input (dam-only) in HL-1 atrial cardiomyocytes. N-terminal Dam fusions to NKX2-5, NKX2-5YRD^(Y-A) and NKX2-5ΔHD (homeodomain deletion) vs. Input (dam-only) in HL-1 atrial cardiomyocyte.

first: Romaric

last: Bouveret

middle: J

last: Schonrock

first: Mirana

last: Ramialison

first: Tram

last: Doan

first: Danielle

last: de Jong

first: Antoine

last: Bondue

first: Gurpreet

last: Kaur

first: Stefanie

last: Mohamed

first: Hananeh

last: Fonoudi

first: Chiann-mun

last: Chen

first: Merridee

last: Wouters

first: Shoumo

last: Bhattacharya

first: Nicolas

last: Plachta

first: Sally

last: Dunwoodie

first: Gavin

last: Chapman

first: Cedric

last: Blanpain

first: Richard

last: Harvey


title: Identification of a microRNA signature for the diagnosis of fibromyalgia

city: Kanagawa

first: Satoko

last: Takizawa

state: Kamakura

institute: Toray Industries, Inc.

summary: To identify changes in miRNA expression profiles (miRNome) of fibromyalgia patients for the development of a quantitative diagnostic method of FM. 20% of the miRNAs analyzed (233/1212) showed down-regulation of at least 2-fold in patients. Hsa-miR223-3p, hsa-miR451a, hsa-miR338-3p, hsa-miR143-3p, hsa-miR145-5p and hsa-miR-21-5p were at least 4-fold inhibited.

overall_design: miRNA content of PBMCs (Peripheral Blood Mononuclear Cells) from either 11 fibromyalgia patients or 10 healthy controls isolated with Ficoll-Paque Premium (GE Healthcare) was examined by microarray analysis. Inhibition of hsa-miR223-3p, hsa-miR451a, hsa-miR338-3p, hsa-miR143-3p, hsa-miR145-5p was further confirmed by qRT-PCR analysis.

first: Elisa

last: Oltra


title: Agilent-custom CGH microarray analysis of hematological malignancies [copy number]

first: Svetlana

last: Yatsenko

summary: copy number analysis

overall_design: Copy number analysis in 15 samples and 2 transformed cell lines( Kasumi-1 and Kasumi-3) from patients with hematological malignancies


title: Effect of Traumatic Brain Injury, Erythropoietin and Anakinra on Hepatic Metabolizing Enzymes and Transporters in an Experimental Rodent Model

city: Seattle

first: James

middle: William

last: MacDonald

state: WA

address: 4225 Roosevelt Way NE

department: Environmental and Occupational Health Sciences

institute: University of Washington

summary: In contrast to the considerable in vitro and in vivo data demonstrating a decrease in cytochrome P450 (CYP) activity in inflammation and infection, clinically, traumatic brain injury (TBI) results in an increase in CYP and UDP glucuronosyltransferases (UGT) activity. The objective of this study was to determine the effects of TBI alone and along with treatment with either erythropoietin (EPO) or anakinra on gene expression of hepatic inflammatory proteins and drug metabolizing enzymes and transporters in a cortical contusion impact (CCI) injury animal model. Microarray-based transcriptional profiling was used to determine the effect on gene expression at 24 h, 72 h and 7 days post-CCI.

overall_design: Fifty male Sprague Dawley rats (Harlan, Indianapolis, IN) approximately three months of age (335 ± 28 g) were used in this study. Animals were randomly assigned to one of four groups: (a) Intact sham, (b) CCI-injured + EPO 2,500 IU/kg (Procrit, Amgen, Thousand Oaks,CA) (c) CCI-injured + anakinra 100 mg/kg (Kineret, Amgen, Thousand Oaks, CA) and (d) CCI-injured + vehicle (saline). Five intact sham animals and five animals in each treatment group at specified time points post-CCI (24 h, 72 h and 7 days) were overdosed with a mixture of CO2 (80%) and O2 (20%). The rats were then decapitated; a cardiac blood sample collected, brains and livers were rapidly extracted. The median lobe of the liver was extracted and placed on ice. Six tissue punches were collected and placed into microcentrifuge tubes, snap frozen and then stored at -80º C.

first: Gail

last: Anderson

first: Todd

last: Peterson

first: Cole

last: Vander Haar

first: Fred

last: Farin

first: Theo

middle: K

last: Bammler

middle: W

first: Eric

last: Kantor

first: Michael

middle: R

last: Hoane


title: Differential miRNA expression of inherently high- and low-active inbred mice

city: College Station

first: Michelle

last: Dawes

address: 213K Heldenfelds

department: Health and Kinesiology

institute: Texas A&M University

summary: To further our understanding of the biological mechanisms regulating voluntary physical activity levels, we measured differential miRNA expression in two strains of mice that have been repeatedly shown to have inherently high and low voluntary physical activity levels measured by wheel running. RNA from skeletal muscle (soleus and extensor digitorum longus (EDL)) and nucleus accumbens in the brain tissues were evaluated by microarray. There were no other variables besides inherent strain differences.  Thirteen miRNAs from nucleus accumbens, 22 from soleus, and nine miRNAs from EDL were determined to be differentially expressed by microarray analysis. RT-qPCR validated mir-342b-3p and 466d-3p to be differentially expressed in the NA, and miR-466b-3p in the soleus.

overall_design: Eight week 12 (6♂, 6♀) C57L/J and 12 (6♂, 6♀) C3H/HeJ mice were individually housed for 1 week with locked running wheel. At 9 weeks, animals were sacrificed and Soleus, Nucleus Accumbens, and EDL tissues were harvested and frozen. RNA from these tissues was extracted with Quiagen miRNeasy kit, column DNase purification, quality measured on bioanalyzer. Four samples from each tissue (male mice only) were used to differential miRNA analysis on microarray. No biological replicates used. Spike-in controls used in labeling and hybridization.

first: Kelli

last: Kochan


title: Agilent-custom CGH microarray analysis of hematological malignancies [copy number and loss of heterozygosity]

summary: Copy number analysis and loss of homozygosity mapping

overall_design: Ten samples from patients with hematological malignancies


title: Genome Wide Nucleosome Mapping for HSV-1 shows Nucleosomes are deposited at preferred positions during acute infection

city: Philadelphia

first: Nigel

last: Fraser

address: 3101 Walnut St

department: Dept. of Microbiology

institute: Upenn

type: Genome binding/occupancy profiling by array

summary: HSV is a large double stranded DNA virus, capable of causing a variety of diseases from the common cold sore to devastating encephalitis.  Although DNA within the HSV virion does not contain any histone protein, within 1 h of infecting a cell and entering its nucleus the viral genome acquires some histone protein (nucleosomes).  During acute infection, partial micrococcal nuclease (MNase) digestion does not give the classic ladder band pattern, seen on digestion of cell DNA or latent viral DNA.  However, complete digestion does give a mono-nucleosome band, strongly suggesting that there are some nucleosomes present on the viral genome during the acute infection, but that they are not evenly positioned like cell DNA, with a 200bp repeat pattern.  Where then are the nucleosomes positioned?  Here we perform HSV-1 genome wide nucleosome mapping, at a time when viral replication is strong (6hr PI), using a microarray consisting of 50mer oligonucleotides, covering the whole viral genome (152kb).  Arrays were probed with MNase-protected fragments of DNA from infected cells.  Cells were not treated with crosslinking agents, thus we are only mapping tightly bound nucleosomes.  The data show that nucleosome deposition is not random.  The distribution of signal on the arrays suggest that nucleosomes are located at preferred positions on the genome, and that there are some positions that are not occupied (NFR or NDR), or occupied at a low frequency in the population of genomes.  Occupancy of only a fraction of the possible sites may explain the lack of a typical MNase partial digestion band ladder pattern for HSV DNA during acute infection.  On average, DNA encoding Immediate Early, Early and Late genes appear to have a similar density of nucleosomes.  This distribution of nucleosomes is discussed in relation to genome DNA sequence and gene expression.

sample_organism:
Homo sapiens
Human alphaherpesvirus 1

overall_design: In total 18 samples; 12 control files (5 different conditions) with the corresponding 8 RIP samples

first: Jaewook

last: Oh

first: Iryna

middle: F

last: Sanders

middle: Z

last: Chen

first: Hongzhe

last: Li

first: John

last: Tobias

first: R

middle: B

last: Isett

first: Sindura

last: Penubarthi

first: Hao

last: Sun

first: Don

last: Baldwin


title: Lipocalin 2 (LCN2), the TNF-like receptor TWEAKR and its ligand TWEAK act downstream of NFAT1 to regulate breast cancer cell invasion

status: Public on May 31 2015

city: Paris

first: Pierre

last: de la Grange

address: 29, rue du Faubourg Saint-Jacques

department: Paris Biotech Santé

country: France

institute: GenoSplice technology

summary:
NFAT1 is a transcription factor that elicits breast carcinoma cells to become invasive, contributing thus to formation of metastases. The molecular mechanisms by which NFAT1 operates in this respect are still poorly known. Here, we report that NFAT1 increases Lipocalin 2 (LCN2) mRNA and protein expression by binding to specific sites in the LCN2 gene promoter region. We show that the LCN2 protein is required downstream of NFAT1 to increase breast cancer cell invasion.
We demonstrate that the NFAT1/LCN2 axis is sufficient to regulate expression of the TNF-like receptor TWEAKR at the RNA level and of its ligand, TWEAK, at the protein level. We show, however, that TWEAKR mediates an anti-invasive effect in breast cancer cells whereas, depending on LCN2 expression, TWEAK has either anti- and pro-invasive capacities. Thus, we identify LCN2 and TWEAKR/TWEAK as critical downstream effectors of NFAT1 to regulate breast cancer cell motility and invasive capacity.

overall_design: A six chip study using total RNA recovered from three separate siRNA control transiently transfected cultures of MDA-MB-231 breast cancer cells and three separate siRNA LCN2 transiently transfected cultures of MDA-MB-231 breast cancer cells .

first: Benoît

last: Gaudineau

first: Marjorie

last: Fougère

first: Frédéric

last: Guaddachi

last: Lemoine

first: Sébastien

last: Jauliac


title: Temporal gene expression of the cyanobacterium Arthrospira in response to gamma rays

city: Mol

first: Rob

last: Van Houdt

address: Boeretang 200

department: Interdisciplinary Biosciences

country: Belgium

institute: SCK-CEN

summary: The edible cyanobacterium Arthrospira is highly resistant to ionising radiation. How theses cells can escape, protect or repair the radiation damage is not known, and requires additional molecular investigation. Therefore, in this study, Arthrospira cells were shortly exposed to different doses of 60Co gamma rays and the dynamic response of Arthrospira cells to irradiation was investigated by monitoring its gene expression and cell physiology, after irradiation. The dynamic transcriptome and associated physiological traits showed clearly two events: (1) an intense global emergency response with general reprogramming of carbon and energy metabolism and (2) a recovery period. Genes expressed during early response indicated a reduction of photosynthesis and reduced tricarboxilic acid (TCA) and Calvin Benson Cycles, while a likely activation of pentose phosphate pathway. Activation of biosynthesis of additional carbon storage molecules, compatible solutes, vitamins and sugars transport occurred after irradiation. In addition the cells enhance the restoration of the redox homeostasis. The repair mechanism of Arthrospira cells involve mainly proteases for cellular cleaning and removal of damaged proteins, single strand DNA repair and restriction modification system. During recovery, Arthrospira relies on the powerful antioxidant Glutathione molecule, for ROS detoxification. The exposed cells expressed during recovery period also again highly the arh genes, coding for a group of novel proteins which were detected in our previous irradiation studies, which confirms our hypothesis that they are a key element in the radiation resistance and merit further detailed investigation.     This study provides new insights into phasic response and the cellular pathways involved the radiation resistance of microbial cells, in particularly for photosynthetic organisms as the cyanobacterium Arthrospira.

overall_design: The irradiation was performed using BRIGITTE facility at the Belgian Reactor N°2 (BR2). The irradiation was done inside a closed canister under water, surrounded by 60Co gamma rays sources (Energy of 1.33 Mev and 1.17 Mev). Different doses of gamma rays were given, i.e. 800 Gy, 1600 Gy and 3200 Gy, at a constant dose rate of 20000 Gy h-1. The time required for irradiation was dose-dependent, i.e. 2.4 minutes for 800 Gy, 4.8 minutes for 1600 Gy and 9.6 minutes for 3200 Gy. During irradiation, the cultures were in the dark, and the temperature inside the irradiation canister was automatically monitored and ranged between 26-27°C. In parallel, three other cultures were maintained at the same conditions but outside the irradiation facility, as non-irradiated controls.

first: Hanene

last: Badri

first: Pieter

last: Monsieurs

first: Ilse

last: Coninx

first: Robin

last: Nauts

first: Ruddy

last: Wattiez

first: Natalie

last: Leys


title: Olfactory mucosa gene expression treated with systemic dexamethasone in mice

city: Beijing

first: Jun

last: Tian

address: No.2 Anzhen Road, Chaoyang District

department: Department of Otolaryngology Head & Neck Surgery

country: China

institute: Beijing Anzhen Hospital, Capital Medical University

summary: To gain a global view of the effect of systematic glucocorticoid treatment on gene expression in the olfactory mucosa (OM), we profiled these changes in a murine model of olfaction in order to identify underlying molecular mechanisms.

overall_design: In the study presented here, 27 wild-type, 6- to 8-week-old, male C57BL/6 mice were randomly divided into three groups, and were respectively injected with dexamethasone daily for 2 weeks (WK2) (intraperitoneally, 1mg/kg), with saline only for 2 weeks as control group (Ctrl) and with dexamethasone for one day as short term group (D1) (n=9/group). Three olfactory epithelium samples with optimal expression of olfactory marker protein (OMP) from each treatment group were selected to analyze global gene expression.

first: Yongxiang

last: Wei


title: Arabidopsis Forever Young Flower (FYF): 35S::FYF+GR

city: Taichung

first: chen

middle: wei

last: han

address: No.250 Kuo-Kuang Rd

department: Institute of Biotechnology, NCHU

country: Taiwan

institute: National Chung Hsing University Institute of Biotechnology CHY LAB

summary: Transcriptional profiling of  35S::FYF+GR transgenic plant's floral buds(DEX treat) compared to  35S::FYF+GR transgenic plant's floral buds(mock treat). DEX : Dexamethasone

overall_design: Two-condition experiment: 35S::FYF+GR(DEX treat) vs 35S::FYF+GR(mock treat)  floral buds, Biological replicates : 1 DEX treatment 1  mock treatment

first: Chang

middle: H

last: Yang

first: Ming

last: Chen

first: Wein


title: Exome sequencing identifies somatic mutations of DDX3X in natural killer/T-cell lymphoma

status: Public on May 29 2015

city: Shanghai

first: Zhaohui

last: Gu

state: Shanghai

address: 197 Rui Jin Road II

department: School of Medicine

institute: Shanghai Jiao Tong University

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

summary:
With the whole genome SNP array information obtained from tumor and matched normal control, we could evaluate the acquired copy number alterations (CNAs) and uniparental disomies (UPDs) .
Here we identified somatic mutations by whole-exome sequencing in 25 NKTCL patients and extended validation through targeted sequencing in an additional 80 cases.

overall_design: To detect acquired CNVs and UPDs in NKT patients, we genotyped both tumor and matched normal samples.

first: Zhu

first: Saijuan


title: Enhancing Mammary Differentiation by Overcoming Lineage Specific Epigenetic Modification and Signature Gene Expression of Fibroblast Derived iPSCs

status: Public on May 28 2015

city: Bethesda

first: WeiPing

state: MD

address: Bldg 8, Room 1A11, NIDDK/NIH

department: GCL

institute: NIDDK/NIH

summary: Recent studies showed that Induced pluripotent stem cells (iPSCs) could hold memory of their origin and exhibit skewed differentiation potential. This finding reveals a severe limit for the application of iPSCs in cell-based therapy in case certain cell types are not available for reprograming from patients. Here we show that under a typical condition for mammary differentiation, iPSCs derived from mouse mammary epithelium cells (ME-iPSCs) exhibit mammary signature gene expression and chromatin epigenetic modification, leading to smooth progress for mammary gland formation. In contrast, iPSCs reprogramed from tail fibroblasts (TF-iPSCs) displayed fibroblast specific signature that is not compatible for mammary differentiation both in vitro and in vivo. Strikingly, when co-culturing with ME-iPSCs or under pregnant condition, the fibroblast specific signature of TF-iPSCs was erased and the cells gained enhanced ability for mammary differentiation. These findings provide new insights into the precise control of differentiation conditions for future personalized cell-based therapy.

overall_design: Microarray analysis of three cell types with three biological replications.

first: Yuying

last: Li

first: Andy

last: Zhang

first: Weiping

first: Rui-Hong

last: Wang

first: Xiao-Ling

last: Xu

first: Chu-Xia

last: Deng


title: Expression analysis of Clostridium difficile wild type and fur (ferric uptake regulator) mutant in high iron.

status: Public on May 27 2015

city: Iowa City

first: Craig

middle: D.

last: Ellermeier

state: IA

address: 51 Newton Rd 3-630 BSB

department: Microbiology

institute: University of Iowa

summary:
Investigation of whole genome gene expression level changes in a Clostridium difficile fur (ferric uptake regulator) mutant, compared to the wild type strain 630 erm.
The fur mutant analyzed in this study is further described in Ho and Ellermeier (2015) J. Bacteriology

overall_design: A microarray study using total RNA recovered from three separate wild type cultures of Clostridium difficile 630 erm strain and three separate cultures of a fur mutant strain (ltrA::ermR) were grown in Tryptone-Yeast Extract medium containing 0.25 mM ferric chloride .  Each chip measures the expression level of 3,786 of the 3,787 open reading frames of the C. difficile 630 genome with 18 probes (60 oligomers each) for each gene.

first: Theresa

last: Ho


title: SETDB1 Represses Endogenous and Exogenous Retroviruses in B Lymphocytes [array]

city: Saint Louis

first: Patrick

last: Collins

state: MO

address: 1217 Oakleaf dr

department: Pathology and Immunology

institute: Washington University

summary: Genome stability relies on epigenetic mechanisms that enforce repression of endogenous retroviruses (ERVs). Current evidence suggests that distinct chromatin-based mechanisms repress ERVs in cells of embryonic origin (histone methylation-dominant) versus more differentiated cells (DNA methylation-dominant). However, the latter aspect of this model has not been tested. Remarkably, and in contrast to the prevailing model, we find that repressive histone methylation catalyzed by the enzyme SETDB1 is critical for suppression of specific ERV families and exogenous retroviruses in committed B-lineage cells from adult mice. The profile of ERV activation in SETDB1-deficient B cells is distinct from that observed in corresponding embryonic tissues, despite the loss of repressive chromatin modifications at all ERVs. We provide evidence that, upon loss of SETDB1, ERVs are activated in a lineage-specific manner depending on the set of transcription factors available to target proviral regulatory elements. These findings have important implications for genome stability in somatic cells, as well as the interface between epigenetic repression and viral latency.

overall_design: Expression profiling in Setdb1 C/C and Setdb1 D/D pro-B cells either directly from the bone marrow or bcl2-transgenic pro-B cells cultured in IL-7 for four days

middle: L

first: Katherine

last: Kyle

first: Takeshi

last: Egawa

first: Yoichi

last: Shinkai

first: Eugene

middle: M

last: Oltz


title: Expression data from Rhesus macaques (Macaca fuscata) brain

status: Public on May 25 2015

city: Wako

first: Eiji

last: Matsunaga

address: Hirosawa 2-1

institute: RIKEN Brain Science Institute

summary:
Japanese macaques learn to use rakes to acquire food, and this learning is associated with rapid electrophysiological and morphological changes in the brain.
To examine the molecular mechanisms of these plastic changes, we performed comprehensive gene expression analysis with a cDNA microarray and identified many candidate genes.

overall_design: We compared gene expressions between experimental  (Rhesus_E) and control (Rhesus_C) animals from Surrounding areas of the lateral sulcus. We also compared gene expressions between experimental  (IPS_E) and control (IPS_C) animals from Surrounding areas of the Intraparietal sulcus.

first: Sanae

last: Nambu

first: Atsushi

last: Iriki


title: The fission yeast MTREC complex targets CUTs and unspliced mRNAs to the nuclear exosome [RIP-ChIP]

status: Public on May 22 2015

city: Canberra

first: Tamas

last: Fischer

state: ACT

address: Building 131, Garran Rd

department: The John Curtin School of Medical Research

institute: The Australian National University

summary: Cryptic unstable transcripts (CUTs) are rapidly degraded by the nuclear exosome, however, the way they are recognized and targeted to the exosome is not fully understood. The recently identified Schizosaccharomyces pombe MTREC complex has been shown to promote degradation of meiotic mRNAs and regulatory ncRNAs. Here, we report that the MTREC complex is also the major nuclear exosome targeting complex for CUTs and unspliced mRNAs. MTREC complex specifically binds to CUTs, meiotic mRNAs and unspliced mRNA transcripts and targets these RNAs for degradation by the nuclear exosome, while the TRAMP complex has only a minor role in this process. The MTREC complex physically interacts with the nuclear exosome and with various RNA-binding and -processing complexes, coupling RNA processing to the RNA degradation machinery. Our study reveals the central role of the evolutionarily conserved MTREC complex in RNA quality control, and in the recognition and elimination of aberrant, cryptic transcripts.

overall_design: All experiments were performed twice in biological replicates.

first: Yang

last: Zhou

first: Jianguo

last: Zhu

first: Géza

last: Schermann

first: Corina

last: Ohle

first: Katja

last: Bendrin

first: Rie

last: Sugioka-Sugiyama

first: Tomoyasu

last: Sugiyama

first: Tamás


title: Whole-genome expression profiling of C. elegans larvae and adults

status: Public on May 21 2015

city: Ann Arbor

first: X.Z Shawn

last: Xu

state: Michigan

address: 210 Washtenaw Ave, Room 6115A

institute: Life Sciences Institute, University of Michigan

summary: Temperature, as a universal enviromental factor, has prolonged effect on physiological and pathological functions of different species. In order to expolore the temperol effect of temperature on C.elegans longevity, we used microarray to check the whole-genome expression profiling of L4 larvae and Day3-old adults of C.elegans maintaining at different temperature

overall_design: Adult worms are collected after maintained at 25 degree and 15 degree for 3days from later L4 stage, while Larva worms are collected after growing at 25 degree and 15 degree from embryo to late L4 stege. Then total RNA are extracted with TRI reagent(Life Technologies) from~120 adults or ~300 larvae. The concentrations and quality of total RNA are checked with Thermo Nanodrop 2000c(Thermo Scientific,WilminGton,DE) and Agilent 2100 BioAnalyzer (Agilent Technologies, Palo Alto, CA). Total RNA samples were hybrydized with Affymetrix C. elegans Gene 1.1 ST Array Strip. Preparation of cDNA, hybridization, quality controls and scanning of arrays were performed according to the manufacturer's protocol (Affymetrix, Santa Clara, CA) at the microarray core facility of University of Michigan .

first: X

first: Bi

last: Zhang


title: Expression analysis of Listeria monocytogenes LO28 delta-lhrC1-5 mutant and LO28 wt

status: Public on May 19 2015

city: Odense

first: Birgitte

middle: Haar

last: Kallipolitis

address: Campusvej 55

department: Biochemistry and Molecular Biology

country: Denmark

institute: University of Southern Denmark

summary:
Investigation of whole genome gene expression level changes in Listeria monocytogenes LO28 delta-lhrC1-5 mutant, compared to the wild type strain. The lhrC1-5 genes encode the regulatory sRNAs LhrC1-5. The microarray studied the gene expression of unstressed cells and cells exposed to cefuroxime for 30 min.
The lhrC1-5 mutant employed in this study is further described in Sievers et al. (2014) A multicopy sRNA of Listeria monocytogenes regulates expression of the virulence adhesin LapB. Nucleic Acids Res. 42:9383-98.

overall_design: A twelve chip study using RNA extracted from 6 different cultures of L. monocytogenes LO28 delta-lhrC1-5 (three unstressed and three stressed cultures) and 6 different cultures of L. monocytognes LO28 wild-type (three unstressed cultures and three stressed cultures).

first: Susanne

last: Sievers


title: Multiplexed Component Analysis to identify genes contributing to the inflammatory responses during acute SIV infection

city: Baltimore

first: Lucio

last: Gama

state: MD - EUA

address: 733 N Broadway St - BRB 831

department: Molecular and Comparative Pathobiology

institute: Johns Hopkins School of Medicine

summary:
Expression profiling by NanoString nCounter gene expression system

Inflammatory response genes play an important role during acute HIV and SIV infection. Using an SIV macaque model for AIDS and CNS disease, we measured mRNA expression of 92 genes before and at multiple time points during acute SIV infection in three tissues: Peripheral blood mononuclear cells, mesenteric lymph nodes (MLN) and peripheral blood mononuclear cells (PBMC). Studying the overall changes of mRNA expressions over time or analyzing the correlation between the gene measurements and SIV RNA in plasma can result in limited interpretations. This is due to several reasons including but not limited to: 1) lack of prior information on how cells react to changes in gene expressions; and 2) biological responses typically involve many genes working together. To approach this problem, we combine multiple preprocessing methods with two multivariate analysis methods, namely principal component analysis and partial least square regression, to create a multiplexed set of 12 “judges”. Each of the judges simultaneously observes all the variables and emphasizes a unique type of gene expression response that could be significant, for example, depending on whether the cell responds to the absolute or relative size of gene expression changes. By incorporating multiple potential biological models of response, it is possible to identify genes that are consistently ranked as high “contributing” genes in different scenarios, i.e., genes that have a higher weight when we classify the data based on different classification schemes. We then use statistical analysis to verify that the consistently high-ranking genes are also statistically significant. We also investigate whether genes are tissue-specific, identify clusters of genes that co-vary together and study their correlation with regard to other gene clusters. The multiplex component analysis method introduced in this paper is a powerful tool to analyze complex gene datasets, identify significant genes, and generate testable hypotheses.

overall_design:
In this study we inoculated 20 pig-tailed macaques with two SIV strains (SIV/17E-Fr and the swarm SIV/DeltaB670), and mock-inoculated 4 animals for control. Infected animals were sacrificed at 4 time points, as following: 6 animals sacrificed at 4 days, 6 at 7 days, 6 at 14 days and 2 at 21 days post-infection. Animals were perfused before necropsy to decrease blood contamination in the tissues. Organs were then culled, and RNA was extraction for NanosString analysis using a set of 92 probes specifically generated for macaque genes. Data were then analyzed by multiple preprocessing methods with two multivariate analysis methods.

The following files contains raw data for the listed samples, respectively;
GAMA Nanostring RAW MLN.xlsx - all MLN samples
GAMA Nanostring RAW PBMC.xlsx - all PBMC samples
GAMA Nanostring RAW Spleen 1.xls - PT01-04SP, PT71-74SP, PT141-144SP
GAMA Nanostring RAW Spleen 2.xls - PT41-44SP, PT75-76SP, PT145-146SP, PT211-212SP
GAMA Nanostring RAW Spleen 3.xls - PT45-46SP

Please note that, in the associated publication, we describe a multiplexed component analysis to identify genes that highly contribute to inflammation during SIV acute infection. This analysis was done by compiling results generated by different types of data transformations and data normalizations (more than 12 for each tissue) and the relevant algorithms/mathematical processes will be discussed in detail. Therefore, only raw data is presented in this record (i.e. each sample data table contains raw data).

first: Iraj

last: Hosseine

first: Feilim

last: MacGabhann


title: Genetic ablation of CD38 protects against Western diet-induced exercise intolerance and metabolic inflexibility

status: Public on May 20 2015

city: Cincinnati

first: Jing

last: Chen

state: OH

address: 3333 Burnet Ave

institute: CCHMC

summary: CD38, a multi-functional membrane receptor and enzyme, consumes NAD+ to generate products such as cyclic-ADP-ribose. CD38 knockout mice show elevated tissue and blood NAD+ level. Chronic feeding of high-fat, high-sucrose diet to wild type mice leads to exercise intolerance and reduced metabolic flexibility. Loss of CD38 by genetic mutation protects mice from diet-induced metabolic deficit. These animal model results suggest that elevation of tissue NAD+ through genetic ablation of CD38 can profoundly alter energy homeostasis in animals that are maintained on a calorically-excessive Western diet.

overall_design: Mouse gastrocnemius muscle samples were used in a factor design, where genotype could be WT or KO, and exercise could be sedentary or treadmill. 4 biological replicates were included in each group.

first: Shian-Huey

last: Chiang

first: W

last: Harrington

first: Guizhen

last: Luo

first: Naphtali

middle: O

last: Milliken

first: John

last: Ulrich

first: Deepak

last: Rajpal

first: Ying

last: Qian

first: Tiffany

last: Carpenter

first: Rusty

last: Murray

first: Robert

middle: S

last: Geske

first: Stephen

middle: A

last: Stimpson

first: Henning

last: Kramer

first: Curt

middle: D

last: Haffner

first: J

last: Becherer

first: Frank

last: Preugschat

first: Andrew

middle: N

last: Billin


title: Transcriptomic analysis of glycolaldehyde-treated wild type cells and a synthetic strain

city: Toulouse

first: Ceren

last: Alkim

address: 135 avenue de Rangueil

institute: LISBP-INSA

summary: A synthetic pathway for (D)-xylose assimilation was stoichiometrically evaluated regarding its potential to produce selected value-added compounds and implemented in Escherichia coli strains. The pathway proceeds via the isomerization of (D)-xylose to (D)-xylulose, the phosphorylation of (D)-xylulose to obtain (D)-xylulose-1-phosphate (Xyl1P), and the aldolase cleavage of the latter to yield glycolaldehyde and DHAP. Both compounds can be further processed via the annotated natural metabolic network. Stoichiometric analyses showed that the synthetic pathway provides an efficient access to the value-added two-carbon (C2) compounds ethylene glycol and glycolic acid, which are either inaccessible via the annotated metabolic network of E. coli or produced at 20 % lower theoretical yield, respectively. The simultaneous expression of xylulose-1 kinase and Xyl1P aldolase activities, which were provided by human ketohexokinase-C and human aldolase-B, respectively, was necessary and sufficient to restore growth of a (D)-xylulose-5-kinase (ΔxylB) mutant on xylose. In this strain, ethylene glycol was the major metabolic end-product and produced at a molar yield of 0.47. Further metabolic engineering provided strains that assimilated the entire C2 fraction back into the central metabolism, or that produced 4.3 g/l glycolic acid at a molar yield of 0.9 in shake flasks.

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

overall_design: The wild-type (WT) culture and synthetic strain (PEN205) were used for the microarray analysis. PEN205 is a ΔxylB deleted strain that express the synthetic pathway. WT and PEN205 were grown to the logarithmic phase of growth in M9 minimal medium supplemented with xylose. PEN205 culture RNA was extracted when their OD was around 1. WT culture were split into two equal aliquots at the OD of ~1 and further cultivated in the presence or absence of 10 mM glycolaldehyde. After 30 min of incubation, cells were used for RNA extraction as well.

first: Yvan

last: Cam

first: Debora

last: Trichez

first: Vincent

last: Trebosc

first: Amélie

last: Vax

first: François

last: Bartolo

first: Philippe

last: Besse

first: Jean

last: François

first: Thomas

last: Walther


title: Effect of Catecholamines on the Dental Pathogen Aggregatibacter actinomycetemcomitans

status: Public on May 12 2015

city: Louisville

first: Whitney

middle: Ann

last: Weigel

state: Kentucky

address: 501 S Preston St

department: OIID

institute: University of Louisville

summary: The two-component system qseBC is a putative prokaryotic adrenergic receptor. In Aggregatibacter actinomycetemcomitans (Aa), it was shown that the qseBC responds significantly to the presence of both catecholamines and ferrous iron. In addition, growth is significantly increased in the presence of both. Therefore, we performed a custom Aa microarray in order to determine the effects of catecholamines and catecholamines and iron (CAT-Fe) on Aa.

overall_design: Aggregatibacter actinomycetemcomitans was grown in triplicate in a chemically defined media (CDM) supplemented with either 100uM of ferrous chloride or 50uM of norepinephrine or both. At mid-log, RNA was harvested using the Qiagen Lipid Tissue Minikit.

first: Xiahong

last: Li

first: Don

last: Demuth


title: Whole cell response to nitrogen deprivation in the diatom Phaeodactylum tricornutum

city: Trondheim

first: Per

last: Winge

address: Høgskoleringen 5e

department: Department of Biology

country: Norway

institute: Norwegian University of Science and Technology

summary: We combined transcriptional and metabolite analyses to monitor the effect of N deficiency at different molecular levels in order to get better insight on the acclimation strategies P. tricornutum employs under nitrogen limitation. Physiological data like neutral lipid measurement, cell growth and other cell chemistry measurements further complemented our molecular data. We showed that P. tricornutum is able to remobilize nitrogen through catabolism of various internal nitrogen-containing resources such as amino acids and proteins. N starvation was also accompanied by reduction in pigment pools as well as photosynthetic capacity. The global expression data showed that majority of metabolic changes were related to carbon and lipid metabolism. Decreased levels of carbon skeletons due to suppression of the Calvin cycle was compensated by breakdown of chrysolaminaran leading to up-regulation of OPPP, glycolysis, pyruvate metabolism and TCA cycle. These pathways provide precursors for fatty acid biosynthesis. In addition, remodeling of membrane lipids and up-regulation of the de novo TAG biosynthetic pathway was further supported by physiological measurements of neutral lipids, indicating TAG accumulation under N limitation. Our study gives a detailed image of adaptation of P. tricornutum to N starvation, and can be used for future metabolic manipulations to increase TAG production.

overall_design: Axenic cultures of Phaeodactylum tricornutum were grown in f/2 medium and kept in exponential growth at 15ºC under continuous white fluorescent light (60 µmol photons m-2 s-1) inside the shaking incubator for three weeks. Three or four replicates and parallels of the start culture were transferred to media supplemented with complete f/2 nutrients (replete) or f/2 without nitrate (deplete). Cells were incubated in batch cultures with a start cell density of 5×10^4 ml-1 in 75 cm2 sterile culture flasks and volume of 220 ml. Cell counting and variable in vivo Chl a fluorescence (Fv/Fm) was measured daily. For the other experiments, samples were harvested 48 h and 72 h after the beginning of the treatment.

first: Leila

last: Alipanah

first: Jens

last: Rohloff

first: Tore

last: Brembu

first: Atle

last: Bones

first: Torfinn

last: Sparstad


title: The fission yeast MTREC complex targets CUTs and unspliced mRNAs to the nuclear exosome [expression array]

first: Tamas

last: Fischer

summary:
Cryptic unstable transcripts (CUTs) are rapidly degraded by the nuclear exosome, however, the way they are recognized and targeted to the exosome is not fully understood. The recently identified Schizosaccharomyces pombe MTREC complex has been shown to promote degradation of meiotic mRNAs and regulatory ncRNAs. Here, we report that the MTREC complex is also the major nuclear exosome targeting complex for CUTs and unspliced mRNAs. MTREC complex specifically binds to CUTs, meiotic mRNAs and unspliced mRNA transcripts and targets these RNAs for degradation by the nuclear exosome, while the TRAMP complex has only a minor role in this process. The MTREC complex physically interacts with the nuclear exosome and with various RNA-binding and -processing complexes, coupling RNA processing to the RNA degradation machinery. Our study reveals the central role of the evolutionarily conserved MTREC complex in RNA quality control, and in the recognition and elimination of aberrant, cryptic transcripts.
Genome-wide expression analysis of MTREC, Nuclear Exosome, TRAMP, Nrd complex members

overall_design: All experiments were performed twice in biological replicates, except that rmn1Δ and mmi1Δ mei4-P572 were perfomed once.

first: Yang

last: Zhou

first: Jianguo

last: Zhu

first: Géza

last: Schermann

first: Corina

last: Ohle

first: Katja

last: Bendrin

first: Rie

last: Sugioka-Sugiyama

first: Tomoyasu

last: Sugiyama

first: Tamás


title: Extensive re-wiring of epithelial-stromal co-expression networks in breast cancer - ER-positive breast cancer validation dataset

city: Montreal

first: Morag

last: Park

state: Quebec

address: 1160 Ave. des Pins O.

department: Goodman Cancer Research Centre

country: Canada

institute: McGill University

summary:
Background: Epithelial-stromal crosstalk plays a critical role in invasive breast cancer (IBC) pathogenesis; however, little is known on a systems level about how epithelial-stromal interactions evolve during carcinogenesis.

Results: We develop a framework for building genome-wide epithelial-stromal co-expression networks composed of pairwise co-expression relationships between mRNA levels of genes expressed in the epithelium and stroma across a population of patients. We apply this method to laser capture micro-dissection expression profiling datasets in the setting of breast carcinogenesis. Our analysis shows that epithelial-stromal co-expression networks undergo extensive re-wiring during carcinogenesis, with the emergence of distinct network hubs in normal breast, ER-positive IBC, and ER-negative IBC, and the emergence of distinct patterns of functional network enrichment. In contrast to normal breast, the strongest epithelial-stromal co-expression relationships in IBC mostly represent self-loops, in which the same gene is co-expressed in epithelial and stromal regions. We validate this observation using an independent laser capture micro-dissection dataset and confirm that self-loop interactions are significantly increased in cancer by performing computational image analysis of epithelial and stromal protein expression using images from the Human Protein Atlas.

Conclusions: Epithelial-stromal co-expression network analysis represents a new approach for systems-level analyses of spatially-localized transcriptomic data. The analysis provides new biological insights into the re-wiring of epithelial-stromal co-expression networks and the emergence of epithelial-stromal co-expression self-loops in breast cancer. The approach may facilitate the development of new diagnostics and therapeutics targeting epithelial-stromal interactions in cancer.

overall_design: 36 flash-frozen human primary breast cancer samples were subjected to laser capture microdissection to separately isolate matched tumor epithelial and tumor-associated stromal components. RNA was isolated, subjected to 2 rounds of amplification, and hybridized on Agilent 4x44K microarrays along with a common reference (single round-amplified commercially obtained Universal Human Reference RNA) in a dyeswap design. For two samples of tumor-associated stroma, a second technical replicate was performed. Samples were labelled as ER-positive based on ESR1 gene expression levels in the tumor epithelium, using univariate Gaussian mixture model-based clustering via the mclust package in R.

first: Hallett

middle: T

last: Hallett

first: Greg

last: Finak

first: Francois

last: Pepin

first: Svetlana

last: Sadekova

first: Nicholas

last: Bertos


title: Influence of Erythropoietin on Microvesicles Derived from Mesenchymal Ste cells(MSC) protecting renal function of Chronic Kidney Disease

status: Public on May 09 2015

city: Nanjing

first: Yan

last: Wang

address: 300 Guangzhou Road

institute: the First Affiliated Hospital of Nanjing Medical University

summary: miRNA profiles of the MSC-MVs and EPO-MVs were analyzed with a quantitative PCR (qPCR)-based array of the whole mice genome. Further analysis revealed differences in the miRNAs of 212 EPO-MVs (fold change ≥ 1.5 compared to the MSC-MVs), which constituted approximately 22.64% of all of the evaluated mouse miRNAs. Of all of the differences, 70.28% of the changes in the EPO-MV group involved upregulation

overall_design: To study the differential miRNA expression in MV and EPO-MV which might contributed to the better treatment in chronic kidney disease, we performed miRNA expression profiling of the culture supernatant of MSC with or without EPO incubation using the miRCURY LNA Array (v.18.0) (Exiqon, Vedbaek, Denmark).

first: Weihong

last: Zhao


title: Gene expression profiling in IBD rat treat with MSC transplantation

status: Public on May 08 2015

city: Guangzhou

first: Yanfen

last: Xing

address: No.1. Panfu Rd

institute: Guangzhou First People’s Hospital

summary: Investigation of whole genome gene expression level changes in Inflammatory bowel disease rats after MSC transplantation, compared to IBD control rats, and to explore the mechanism of MSC transplantation.

overall_design: A four chip study using total RNA recovered from two separate IBD rats after MSC transplantation and two separate IBD control rats. Each chip measures the expression level of 26,419 genes from normal rat and IBD rat treated with MSC transplantation.

first: Yaming

last: Wei

first: Yanwen

last: Cao


title: Mouse primary T-ALL microRNA microarray

city: Lausanne

first: Fabian

last: Junker

state: VD

address: EPFL SV ISREC - UPRAD, SV2533, Station 19

department: ISREC

country: Switzerland

institute: Ecole polytechnique fédérale de Lausanne

summary: Primary mouse cells (CD4-CD8- (DN) and CD4+CD8+ (DP) thymus and T-ALL (early-stage - ES and late-stage - LS) and mouse T-ALL cell line M295 were assessed for microRNA expression

overall_design: For DN, DP, ES_T-ALL and LS_T-ALL cells, n=3 biological replicates were used. M295 is one 1 replicate

first: Antoine

last: Chabloz

first: Ute

last: Koch

first: Freddy

last: Radtke


title: microRNA expression in CUTLL1 cells

summary: T-ALL cell line CUTLL1 was assessed for microRNA expression. Cells were treated with DMSO (ctr) or DAPT (10uM) to inhibit Notch1 cleavage for 3d and then harvested.

overall_design: 3 biological replicates were used per group (DMSO, n=3; DAPT, n=3).


title: C9ORF72 GGGGCC expanded repeats produce splicing dysregulation which correlates with disease severity in amyotrophic lateral sclerosis [HuEx-1_0-st]

city: Sheffield

first: Paul

middle: Roy

last: Heath

state: S. Yorks

address: SITraN, 385a Glossop Road

department: Academic Neurology Unit

country: United Kingdom

institute: University of Sheffield

summary:
Objective: An intronic GGGGCC-repeat expansion of C9ORF72 is the most common genetic variant of amyotrophic lateral sclerosis (ALS) and frontotemporal dementia. The mechanism of neurodegeneration is unknown, but a direct effect on RNA processing mediated by RNA foci transcribed from the repeat sequence has been proposed.
Results: Gene level analysis revealed a number of differentially expressed networks and both cell types exhibited dysregulation of a network functionally enriched for genes encoding ‘RNA splicing’ proteins.  There was a significant overlap of these genes with an independently generated list of GGGGCC-repeat protein binding partners.  At the exon level, in lymphoblastoid cells derived from C9ORF72-ALS patients splicing consistency was lower than in lines derived from non-C9ORF72 ALS patients or controls; furthermore splicing consistency was lower in samples derived from patients with faster disease progression.  Frequency of sense RNA foci showed a trend towards being higher in lymphoblastoid cells derived from patients with shorter survival, but there was no detectable correlation between disease severity and DNA expansion length.
Significance: Up-regulation of genes encoding predicted binding partners of the C9ORF72 expansion is consistent with an attempted compensation for sequestration of these proteins.  A number of studies have analysed changes in the transcriptome caused by C9ORF72 expansion, but to date findings have been inconsistent.  As a potential explanation we suggest that dynamic sequestration of RNA processing proteins by RNA foci might lead to a loss of splicing consistency; indeed in our samples measurement of splicing consistency correlates with disease severity.

overall_design: Gene expression profiling utilised total RNA extracted from lymphoblastoid cell lines derived from human ALS patients (n=56),  and controls (n=15).    Thirty-one of the ALS patients had a mutation of C9ORF72.

first: Johnathan

last: Cooper-Knock

first: Joanna

middle: J

last: Bury

middle: R

first: Matthew

last: Wyles

first: Adrian

last: Higginbottom

first: Catherine

last: Gelsthorpe

first: J

last: Highley

first: Guillaume

last: Hautbergue

first: Magnus

last: Rattray

first: Janine

last: Kirby

first: Pamela

last: Shaw


title: Dicer1 imparts essential survival cues in Notch driven T-ALL via miR-21 mediated tumor suppressor Pdcd4 repression

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

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: Refer to individual Series


title: miRNA profilng in IL-2 induced CD4+T cells

status: Public on May 07 2015

city: rasht

first: Najmeh

last: Ranji

state: Guilan

address: iran. rasht. rasht branch , islamic azad university

department: Genetics

country: Iran

institute: islamic azad university

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

summary: To evaluate role of miRNAs in proliferation and death of T cell, we performed miRNA profiling in activated CD4+T cells after IL-2 induction and depletion. Proliferation rate of IL-2 induced cells was measured by MTT assay. Then quantitative RT-PCR arrays on 739 miRNAs revealed up- and down-regulation of 170 miRNAs in IL-2 induced CD4+T cells relative to IL-2 depleted ones.

overall_design: For miRNA profiling, total RNA from activated CD4+T cells in the presence and the absence of IL-2 (0.75 n/ml) after 3 days was extracted. RNA isolation was carried out using miRCURYTM RNA isolation kit. cDNA synthesis and Q-RT-PCR were performed with miRCURY LNATM universal RT microRNA PCR kit. Both kits were purchased from Exiqon (Vedbaek, Denmark). According to manufacturer’s instructions, to synthesize cDNA, total RNA was added to enzyme mix, reaction buffer, and RNA spike-in (control RNA). Then, the mixture was incubated 60 min at 42 °C and 5 min at 95 °C. To perform Q-RT-PCR array, cDNA was added to SYBR green master mix and was dispensed into the 384-well plates (by a specific LNATM primer pair/ well); then the reaction was performed using a real-time PCR cycler (Roche LC480, USA) according to this program: 95°C for 10 min, 45 cycles at 95˚C for 10 sec, 60˚C for 1 min. For miRNA profiling, two 384-well plates (human panel I & II) were used and each reaction was performed twice. Each panel contained 6 reference primer sets as well as one control primer set (that targeted a synthetic spike-in RNA) and an inter-plate calibrator in triplicate. To analyze Q-RT-PCR data, GenEx software and ΔΔCT method were used. By Normfinder, SNORD49A (snoRNA U49) gene was identified as optimal reference gene for normalization. Fold change of each miRNA was calculated by the equation 2−ΔΔCT and logarithmically transformed (base 2). P-values were adjusted for multiple comparisons using Dunn-Benferroni correction.

first: Majid

last: Sadeghizadeh

first: Morteza

last: Karimipoor

first: Mohammad

last: Shokrgozar

first: Roohollah

last: Sistani

first: Seyed

last: Paylakhi


title: Genome wide map of Stat3 binding sites in C6 rat glioma cells [NimbleGen]

city: Uppsala

first: Marcin

last: Kruczyk

address: Husargatan 3

country: Sweden

institute: Uppsala University

summary: We report a map of Stat3 binding sites in C6 rat glioma cells. The data was obtained using whole genome technology using NimbleGen microarrays.

overall_design: Examination of  Stat3 binding sites in C6 rat glioma cell line

first: Jan

last: Komorowski

first: Bozena

last: Kaminska


title: Transcriptional Profile of Mycobacterium tuberculosis Replicating in Human Type II Alveolar Epithelial A549 cell line

status: Public on Mar 31 2015

city: New York

first: Suman

last: Laal

state: NY

address: 423 Esat 23rd Street, 18N

department: Pathology

institute: VA/NYU

summary: Infection with Mycobacterium tuberculosis (M. tb) is initiated when an aerosol droplet carrying a few bacilli is inhaled into an alveolus. Alveolar epithelial cells (AEC) (type II and type I) are among the first cells encountered by the infecting bacteria and greatly outnumber macrophages in the alveolus. M. tb replicates dramatically (>20,000 fold) in a “non-migrating” compartment in the lung prior to the development of the cell-mediated immune response in aerosol-infected mice (Wolf AJ, 2008).  M. tb DNA has been found in type II AEC in autopsied lung tissue of latently infected individuals (Hernandez-Pando R et. al, 2000; Barrios-Payan J et. al 2012), and M. tb-infected AEC in broncho-alveolar lavage (BAL) and in sputum samples from TB patients indicates the infection of these cells in active as well as latent human TB (Eum SY et. al, 2010).  M. tb has been shown to infect and replicate in the human type II AEC line, A549, and passaging of M. tb through A549 increases M. tb invasiveness (Bermudez LE et.al, 2002).  In this work, we have used DNA microarray analysis to investigate the transcriptome of M. tb replicating in type II AEC (A549) compared to M. tb grown logarithmically in Middlebrook 7H9 broth media in order to identify M. tb adaptations to this intracellular environment as well as M. tb mechanisms/factors contributing to M. tb replication and increased invasiveness in primary infection.

overall_design: The global gene expression of M. tb H37Rv replicating in A549 cells at 72 hr was compared to that of M. tb grown to log phase in Middlebrook 7H9 media.

first: Krishna

middle: K

last: Singh

first: Michelle

middle: B

last: Ryndak


title: Chromatin remodeling and histone mRNA accumulation in bovine germinal vesicle oocytes

status: Public on May 05 2015

city: Quebec

first: Remi

last: Labrecque

state: QC

address: 2440, boulevard Hochelaga

department: Animal Science

institute: Laval University

summary: The objective of the study was to compare the transcriptome of the bovine oocyte according to the chromatin configuration of the germinal vesicule

overall_design: Bovine oocyte (4 biological replicates) were collected and grouped according to the different chromatin configuration of the germinal vesicule described by Lodde et al. 2007. Four GV stages corresponding to the state of chromatin condensation were used (GV0; GV1; GV2 and GV3). Multiples microarray comparison were performed. First a reference design (GV0 as a reference) were used for a total of three comparisons (GV0 vs GV1; GV0 vs GV2 and GV0 vs GV3), then another comparison was performed between the last two groups (GV2 vs GV3). Each comparison was performed using a dye-swap set-up.

first: Rémi

first: Cecilia

last: Dieci

first: Valentina

last: Lodde

first: Irene

last: Tessaro

first: Alberto

last: Luciano

first: Marc-André

last: Sirard


title: DNA methylation profiles in alcohol-associated hepatocellular carcinoma

city: Verona

last: Ferrarini

state: Veneto

address: Strada le Grazie, 15

department: Scientific and Technological Department

country: Italy

institute: University of Verona

summary: Alcohol is a major risk factor for hepatocellular carcinoma (HCC) although the mechanisms underlying the alcohol-related liver carcinogenesis are still poorly understood. Alcohol is known to increase hepatocarcinogenesis possibly by inducing aberrant DNA methylation through the reduced provision of methyl groups within the hepatic one-carbon metabolism. Whether the epigenetically-regulated pathways in alcohol-associated HCC can be reversible or modifiable by nutritional factors is unknown.   The aim of the present study was to investigate the genome wide promoter DNA methylation profiles along with array-based, gene expression profiles in non-viral, alcohol-associated HCC. From eight HCC patients the methylation status and transcriptional levels of all annotated genes were compared by analyzing HCC tissue and the cancer-free surrounding liver tissue, following curative surgery.   After merging both the DNA methylation and gene expression data, we identified 159 hypermethylated-repressed, 30 hypomethylated-induced, 49 hypermethylated-induced and 56 hypomethylated-repressed genes. A number of potentially novel candidate tumor-suppressor genes (FAM107A, IGFALS, MT1G, MT1H, RNF180) demonstrated promoter hypermethylation and transcriptional repression in alcohol-associated HCC. Notably, promoter DNA methylation appeared as the regulatory mechanism for the transcriptional repression of genes controlling the retinol metabolic pathway (ADH1A, ADH1B, ADH6, CYP3A43, CYP4A22, RDH16) and SHMT1, a key gene within one-carbon metabolism.   A genome-wide DNA methylation approach linked up with array-based gene expression profiles allowed identifying a number of novel, epigenetically-regulated candidate tumor-suppressor genes in alcohol-associated hepatocarcinogenesis. Retinol metabolism genes and SHMT1 are also epigenetically-regulated through promoter DNA methylation in alcohol-associated hepatocarcinogenesis.

overall_design: 16 samples (8 control samples from non-neoplastic liver tissue, 8 test samples from hepatocellular carcinoma) from 8 patients affected from hepatocellular carcinoma were analyzed.

first: Silvia

last: Udali

first: Patrizia

last: Guarini


title: Galectin-9 suppresses growth of hepatocellular carcinoma in vivo

status: Public on Mar 01 2015

city: Kamakura

first: Satoshi

last: Kondo

state: Kanagawa

address: Tebiro 6-10-1

department: New Projects Development Division

institute: Toray Industries,Inc.

summary: Galectin-9 suppresses growth of Li-7 cells, a cell line of human hepatocellular carcinoma, in xenograft model analysis.

overall_design: Micro RNA expression in xenografts of Li-7 cells, a cell line of hepatocellular carcinoma, with or without administration of galectin-9 were assessed.

first: Koji

last: Fujita

first: Tsutomu

last: Masaki


title: miRNA expression profile in MDA-MB-231 cells on LPA stimulation

city: Lyon

first: Olivier

last: Peyruchaud

state: Rhone Alpes

address: UFR de medicine Lyon Est (Domaine Laennec), 7-11 Rue Guillaume Paradin

institute: INSERM U1033

summary:
LPA is a natural bioactive lipid with growth factor-like functions due to activation of series of six G protein-coupled receptors (LPA1-6).
In this study we determine the LPA induced early-miRNA expression profile in human breast cancer cell lines MDA-MB-231

overall_design: MDA-MB-231 cells were serum starved for 24h and then stimulated with LPA (1µM) for 45min. The controls were the serum starved unstimulated cells. Three replicates were included in this study.

first: Debashish

last: Sahay


title: Zebrafish liver: Tg(fabp10a:pt-beta-catenin) versus non-transgenic control siblings

status: Public on Apr 30 2015

city: San Francisco

first: Kimberley

middle: Jane

last: Evason

state: CA

address: 513 Parnassus Ave, Room M545

institute: University of California, San Francisco

summary: To investigate mechanisms by which activated β-catenin signaling promotes liver tumor formation and to identify potential therapeutics for these cancers, we generated transgenic zebrafish expressing hepatocyte-specific activated β-catenin (Tg(fabp10a:pt-β-cat) zebrafish.  As adults, these animals show increased liver size, decreased survival, and histologic abnormalities similar to human HCC.  To further characterize our model, we used microarray analysis to compare gene expression in Tg(fabp10a:pt-β-cat) zebrafish livers to that of non-transgenic control sibling livers.

overall_design: This experiment includes 2 biological replicates.  Each replicate represents one Tg(fabp10a:pt-beta-catenin) zebrafish compared to non-transgenic control sibling.

first: Macrina

last: Francisco

first: Vladislava

last: Juric

first: Sanjeev

last: Balakrishnan

first: Maria

last: Lopez Pazmino

first: John

last: Gordan

first: Sanjay

last: Kakar

first: Jan

last: Spitsbergen

first: Andrei

last: Goga

first: Didier

middle: Y

last: Stainier


title: Regulation of microRNA during cardiomyocyte maturation in sheep

city: Adelaide

first: Janna

last: Morrison

state: SA

address: City East Campus, P5-50

department: School of Pharmacy and Medical Sciences

institute: University of South Australia

summary: Background: There is a limited capacity to repair damage in the mammalian heart after birth, which is primarily due to the inability of cardiomyocytes to proliferate after birth. This is in contrast to zebrafish and salamander, in which cardiomyocytes retain the ability to proliferate throughout life and can regenerate their heart after significant damage. Recent studies in zebrafish and rodents implicate microRNAs (miRNAs) in the regulation of genes responsible for cardiac cell cycle progression and regeneration, in particular, miR-133a, the miR-15 family, miR-199a and miR-590. However, the significance of these miRNAs and miRNA in general in the regulation of cardiomyocyte proliferation in large mammals, including humans, where the timing of heart development relative to birth is very different than in rodents, is unclear. To determine the involvement of miRNAs in the down-regulation of cardiomyocyte proliferation occurring before birth in large mammals, we investigated miRNA and target gene expression in sheep hearts before and after birth. The experimental approach included targeted transcriptional profiling of miRNA and target mRNA previously identified in rodent studies as well as genome-wide miRNA profiling using microarrays. Results: The cardiac expression of miR-133a increased and its target gene IGF1R decreased with increasing age, reaching their respective maximum and minimum abundance when the majority of ovine cardiomyocytes were quiescent. The expression of the miR-15 family members was variable with age, however, four of their target genes decreased with age. These latter profiles are inconsistent with the direct involvement of this family of miRNA in cardiomyocyte quiescence in late gestation sheep. The expression patterns of ‘pro-proliferative’ miR-199a and miR-590 were also inconsistent with their involvement in cardiomyocyte quiescence. Consequently, miRNA microarray analysis was undertaken, which identified six discrete clusters of miRNA with characteristic developmental profiles. The functions of predicted target genes for the miRNA in four of the six clusters were enriched for aspects of cell division and regulation of cell proliferation suggesting a potential role of these miRNA in regulating cardiomyocyte proliferation.  Conclusion: The results of this study show that the expression of miR-133a and one of its target genes is consistent with it being involved in the suppression of cardiomyocyte proliferation, which occurs across the last third of gestation in sheep. The expression patterns of the miR-15 family, miR-199a and miR-590 were inconsistent with direct involvement in the regulation cardiomyocyte proliferation in sheep, despite studies in rodents demonstrating that their manipulation can influence the degree of cardiomyocyte proliferation. miRNA microarray analysis suggests a coordinated and potentially more complex role of multiple miRNA in the regulation of cardiomyocyte quiescence and highlights significant differences between species that may reflect their substantial differences in the timing of this developmental process.

overall_design: RNA, (2 µg) from three heart samples from each of the 91 d (fetus), 141 d (fetus), 5 d (postnatal) and 173 d (postnatal) groups, was used for analysis according to standard procedures. The experimental design included three biological replicates from each of the four normal developmental ages in sheep and thus a total of 12 samples was analyzed.

middle: L

first: Song

last: Zhang

first: Ross

last: Tellam

first: Doug

last: Brooks

first: Caroline

last: McMillen

first: Enzo

last: Porrello

last: Botting


title: Comparison of gene expression profile of muscle samples from growth promoters-treated and control calves.

status: Public on May 04 2015

city: legnaro

first: sara

last: pegolo

address: viale dell'università 16

institute: university of padua

summary: A bovine oligo microarray platform (GPL7053) was used to evidence differences in gene expression profiles from thirty (30) muscle samples from growth promoters-treated cows and ten (10) from control animals.

overall_design: In this study, we analyzed forty (40) bovine biceps brachii samples, thirty (30) from growth promoters treated cows and ten (10) from control animals. Gene expression profiling was performed using the Agilent-015354 Bos taurus Oligo Microarray platform (GPL7053) based on single-colour detection (Cyanine-3 only). Microarrays were scanned with Agilent scanner G2565BA (barcode on the left, DNA on the back surface, scanned through the glass) at a resolution of 5 microns; all slides were scanned twice at two different sensitivity settings (XDRHi 100% and XDRLo 10%); the scanner software created a unique ID for each pair of XDR scans and saved it to both scan image files. Feature Extraction (FE) 9.5 used XDR ID to link the pairs of scans together automatically when extracting data. The signal left after all the FE processing steps have been completed is ProcessedSignal that contains the Multiplicatively Detrended, Background-Subtracted Signal.

first: Sara

last: Pegolo

first: Luca

last: Bargelloni


title: A chromatin code for alternative splicing involving a putative association between CTCF and HP1α proteins

city: Stockholm

first: Eneritz

last: Agirre

address: Solnavägen 9

department: MBB

institute: Karolinska Institutet

summary: Alternative splicing is primarily controlled by the activity of splicing factors and by the elongation of the RNA polymerase II (RNAPII). Recent experiments have suggested a new complex network of splicing regulation involving chromatin, transcription and multiple protein factors. In particular, the CCCTC-binding factor (CTCF), the Argonaute protein AGO1, and members of heterochromatin protein 1 (HP1) family have been implicated in the regulation of splicing associated to chromatin and the elongation of RNAPII. These results raise the question of whether these proteins may associate at the chromatin level to modulate alternative splicing.

overall_design: RNA extraction from MCF-7 and MCF-10A cell lines. Splicing changes between these two cell lines were measured using a splice junction array (Affymetrix HJAY).

first: Nicolás

last: Bellora

first: Mariano

last: Alló

first: Amadís

last: Pagès

first: Paola

last: Bertucci

first: Alberto

last: Kornblihtt

first: Eduardo

last: Eyras


title: Transcriptional analyses of mandarins seriously infected by “Candidatus Liberibacter asiaticus”

status: Public on Apr 10 2015

first: Meirong

last: Xu

address: Wushan rode 483, Tianhe

institute: South China Agricultural University

summary:
HLB is suggested to be caused by the phloem-limited fastidious prokaryotic α-proteobacterium “Candidatus Liberibacter spp.” Previous studies focused on the proteome and transcriptome analyses of citrus 5 to 35-week-after “Ca. L. spp.” inoculation.
In this study, gene expression profiles was analyzed using mandarin of Citrus reticulate Blanco cv. jiaogan leaves after 2-year infection with “Ca. L. asiaticus”.

overall_design: The Affymetrix GeneChip® citrus genome were applied to study the molecular pathways mediated by “Ca. L. asiaticus” inoculated 3-year-old jiaogan seedlings. Each of them was graft-inoculated with one sweet orange scions with or without “Ca. L. asiaticus” in Dectember, 2009. RNA samples from three mandarin trees infected with 'Candidatus Liberibacter asiaticus' and three uninfected trees were used for affymatrix genochip

first: Zheng

last: Zheng

first: Xiaoling

last: Deng


title: The transient inactivation of the master cell cycle phosphatase Cdc14 causes genomic instability in diploid cells of Saccharomyces cerevisiae.

city: Durham

first: Thomas

last: Petes

state: NC

address: 213 Research Drive

department: Molecular Genetics and Microbiology

institute: Duke University School of Medicine

summary: Genomic instability is a common feature found in cancer cells. Accordingly, many tumor suppressor genes identified in familiar cancer syndromes are involved in the maintenance of the stability of the genome during every cell division, and are commonly referred to as caretakers. Inactivating mutations and epigenetic silencing of caretakers are thought to be the most important mechanism that explains cancer-related genome instability. However, little is known of whether transient inactivation of caretaker proteins could trigger genome instability and, if so, what types of instability would occur. In this work, we show that a brief and reversible inactivation, during just one cell cycle, of the key phosphatase Cdc14 in the model organism Saccharomyces cerevisiae is enough to result in diploid cells with multiple gross chromosomal rearrangements and changes in ploidy. Interestingly, we observed that such transient inactivation yields a characteristic fingerprint whereby trisomies are often found in small-sized chromosomes and gross chromosome rearrangements, often associated with concomitant loss of heterozygosity (LOH), are mainly detected on the rDNA-bearing chromosome XII. Taking into account the key role of Cdc14 in preventing anaphase bridges, resetting replication origins and controlling spindle dynamics in a well-defined window within anaphase, we speculate that its transient inactivation causes cells to go through a single mitotic catastrophe with irreversible consequences for the genome stability of the progeny.

overall_design:
The details of these experiments are in press in Genetics (Oliver Quevedo, Cristina Ramos-Pérez, Thomas D. Petes, and Félix Machín) but will be described briefly below.
The diploid S. cerevisiae strain FM1468 is homozygous for a temperature-sensitive allele of CDC14 which encodes a phosphatase that is important in regulating the cell cycle. The strain was constructed by mating cdc14-1 derivatives of two sequence-diverged haploids, one isogenic with W303-1A (JSC12) and one isogenic with YJM789. The resulting diploid is heterozygous for about 55,000 SNPs (St. Charles, J. and Petes, T. (2013) PLoS Genetics 9: e1003434; PMID 23593029). In addition, the strain is homozygous for the ade2-1 ochre mutation and heterozygous for an insertion of SUP4-o, a gene encoded a tRNA ochre suppressor. The SUP4-o gene is located near the right telomere of chromosome IV and is inserted on the YJM789-derived homolog. The FM1468 strain forms pink colonies because a single copy of SUP4-o partially suppresses the red colony phenotype associated with the ade2 mutation. In the wild-type genetic background, a mitotic crossover between SUP4-o and the centromere of IV produces a red/white sectored colony with the red sector containing no copies of SUP4-o and the white sector containing two copies of SUP4-o (St. Charles and Petes, 2013).
To map the position of the crossover and to examine recombination events resulting in loss of heterozygosity (LOH) throughout the genome, we used SNP-specific microarrays (St. Charles et al., 2012; Genetics 190: 1267-1284; PMID 22267500). These arrays contained about 50,000 oligonucleotides, allowing us to monitor LOH at about 13,000 positions in the genome. Each of these single-nucleotide polymorphism (SNP) was represented by four 25-base nucleotides, two for the Watson and Crick strands of the YJM789-derived SNP and two for the Watson and Crick strands of the W303-1A-derived SNP. The sequences and locations of each of these oligonucleotides has been published (St. Charles et al., 2012). As described below, by measuring the level of hybridization to these oligonucleotides, we identified the location of LOH events throughout the genome in FM1468. It should also be noted that the microarrays detect changes in chromosome number in addition to detecting LOH events.
A total of 13 sectored colonies were examined. Each colony was given a number and letter indicate the sectors. For example, 1A and 1B are different sectors of one FM1468 colony. The key to the color of these colonies is: 1A (white), 1B (pink); 2A (pink), 2B (red); 3A (white), 3B (pink); 4A (white), 4B (pink); 5A (white), 5B (red); 6A (white), 6B (pink); 7A (white), 7B (pink); 8A (pink), 8B (red); 9A (white), 9B (pink); 10A (white), 10B (pink), 10C (red); 11A (white), 11B (pink), 11C (red); 12A (white), 12B (red); 13A (white), 13B (red). Note that colonies 10 and 11 were tri-colored colonies, and microarrays were done on all three sectors. In summary, microarry analysis was done on 28 sectors derived from 13 colonies.

first: Oliver

last: Quevedo

first: Cristina

last: Ramos-Pérez

first: Félix

last: Machín


title: Integrated molecular portrait of triple negative breast tumors from Mexican women using archived clinical samples

first: Magali

last: Olivier

address: 150 cours Albert Thomas

institute: IARC

type:
Expression profiling by array
Third-party reanalysis

summary: Triple negative breast tumours from archived formalin fixed paraffin embeded samples of the National Cancer Institute of Mexico were analyzed for differential gene expressión.

overall_design: Transcriptomic analysis of the 12 tumor samples was done with the FFPE-designed WG-DASL HT assay (Illumina) according to manufacturer’s instructions. This assay measures 29,285 annotated transcripts derived from the RefSeq database corresponding to 20,727 unique genes. Briefly, 200ng of total RNA were reverse-transcribed into biotinylated cDNA, which was then primer-extended with the Assay Specific Oligos. The cDNA was then amplified with universal primers and hybridized to Illumina Human WG DASL HT Expression BeadChip arrays. The Illumina Genome Studio V2010.2 was used to obtain the signal values (AVG-Signal), with no normalization and no background subtraction.The performance of hybridizations was evaluated by assessing the presence of outliers and the noise-to-signal ratios by calculating the ratio of centiles P95/P05 prior to normalisation for each sample. We defined outliers as samples with P95/P05 ratio <9.5. All samples were found to show a correct noise-to-signal ratio (P95/P05>9.6).  For differential gene expression analysis, the public dataset GSE32124, which includes 33 fresh frozen tissue samples, generated on the Illumina HumanHT-12 v4.0 beadChip, and which contains 99.98% of the 29,285 probes of the Human WG DASL HT BeadChip was used as normal breast tissue control.

first: Felipe

middle: V

last: Paniagua


title: Expression data from U87MG subclones

status: Public on Feb 12 2015

city: La Jolla

first: Clark

middle: C.

last: Chen

address: 3855 Health Science Drive #0987

institute: University of California San Diego

summary:
U87MG is a glioblastoma cell line that shows substantial heterogeneity despite long-term passaging.
We used microarrays to identify variations in gene expression that are associated with phenotypic differences among subclones derived from U87MG.

overall_design: U87MG was plated dilutely such that individual colonies arising from single cells could be readily isolated and propagated as subclones.

first: David

last: Kozono

middle: C


title: Comparison of gene expression of WT and PerM mutant M. tuberculosis H37Rv grown in high and reduced magnesium

status: Public on Jan 05 2015

first: Sabine

last: Ehrt

state: New York

address: 413 East 69th Street

department: Microbiology & Immunology

institute: Weill Cornell Medical College

summary: M. tuberculosis membrane protein PerM is required for persistence in chronic mouse infection. In vitro, the perM mutant requires increased magnesium for replication and survival, with elongation and lysis in low-magnesium media. To gain insight into the function of PerM, we compared the transcriptomes of wt and perM mutant Mtb grown in high (2000 μM) and reduced (250 μM) Mg2+ in three independent experiments. Transcriptome analysis of the perM mutant grown in reduced magnesium revealed upregulation of cell division and cell wall biosynthesis genes.

overall_design: Bacteria were grown for 5 days in Sauton’s media containing 250 or 2000 μM MgCl2 and 0.05% Tween 80. Three independent experiments were performed.

first: Nichole

last: Goodsmith


title: Real-time quantitative PCR analysis of human leukemic B-cells [CC treatment]

status: Public on Mar 07 2015

city: Lodz

first: Ida

last: Franiak-Pietryga

address: Pabianicka 62

country: Poland

institute: Copernicus Memorial Hospital in Lodz

summary:
Fresh blood samples were collected from 8 CLL (chronic lymphocytic leukemia) previously untreated patients before and after 2 weeks of the first cycle of CC (cladribine, cyclophosphamide) treatment. Peripheral blood mononuclear cells (PBMNCs) were separated from EDTA blood by layering on the Histopaque 1077 and centrifuging on a density gradient. Mean B-cell CD19+ purity was ≥95% as measured by flow cytometry (FC).
Microarray analysis was performed using 0.5 microgram of RNA transcribed to cDNA. Prepared cDNA samples were subjected to RT-PCR in duplicate in the TaqMan 7900HT Sequence Detection System (Applied Biosystems).

overall_design: qPCR gene expression profiling. Intensity of gene expression in CLL cells collected from particular patient before treatment was compared with the gene expression signals in CLL cells from the same patient after 2 weeks of treatment.

first: Aleksandra

last: Salagacka


title: Transcriptome analyses of the Corynebacterium glutamicum strains adapted to supraoptimal growth temperatures

status: Public on Jan 06 2015

city: Kyoto

first: Shinichi

last: Oide

address: 9-2 Kizugawadai, Kizugawa

institute: Research institute of Innovative Technology for the Earth (RITE)

summary: C. glutamicum strains adapted to higher growth temperatures were obtained through an adaptive laboratory evolution experiment. To elucidate molecular basis for thermotolerance acquired by the evolved strains, we examined transcriptional responses of the evolved and parental strains to thermal stress using microarray technology.

overall_design: Each strain was grown at the optimal growth temperature (33 ℃). When OD610 reached around 7, the growth temperature increased to 41 ℃, and transcriptional changes of the evolved and parental strains were examined with microarray technology.

first: Wataru

last: Gunji

first: Hideaki

last: Yukawa

first: Masayuki

last: Inui


title: Development of cucumber (Cucumis sativus L.) genotyping array

status: Public on May 01 2015

city: Rishon Le-Zion

first: Ron

last: Ophir

address: Hamacabim St.

department: Fruit Tree Sciences

country: Israel

institute: Agricultural Research Organization - the Volcani Center

summary: Genotyping arrays are tools for high throughput genotyping, which is required in genome-wide association studies (GWAS). Since the first cucumber genome draft was reported, genetic maps were constructed mainly based on simple-sequence repeats (SSRs) or on combinations of SSRs and other sequence-related amplified polymorphism (SRAP). In this study we developed the first cucumber genotyping array which consisted of 32,864 single nucleotide polymorphisms (SNPs). These markers cover the cucumber genome every 2.1Kb and have parents/F1 hybridizations as a training set. The training set was validated with Fludigm technology and had 98% concordance. The application of the genotyping array was illustrated by constructed a genetic map of 600 cM in length based on recombinant inbred lines (RIL) population of a 9930XGy14 cross of which compromise of 11564 SNPs. The markers collinearity between the genetic map and genome references of the two parents estimated as R2=0.97. Moreover, this comparison supports a translocation in the beginning of chromosome 5 that occurred in the lineage of 9930 and Gy14 as well as local variation in the recombination rate. We also used the array to investigate the local allele frequencies along the cucumber genome and found specific region with segregation distortions. We believe that the genotyping array together with the training set would be a powerful tool in applications such as quantitative-trait loci (QTL) analysis and GWAS.

overall_design: The samples included 6 replicates of 9930, 5 replicates of GY14 and 5 replicates of the F1 progeny of these two strains. In addition, 134 recombinant inbred lines (F7 and F8) from the same cross.

first: Mor

last: Rubinstein

first: Yiqun

last: Weng


title: Transcriptomic analysis of APC knockdown in proliferating primary myoblasts

status: Public on Jan 01 2015

first: Fabien

last: Le Grand

address: 8 avenue Rockefeller

department: Melis

institute: Institut Neuromyogene

summary:
APC is a key regulator of canonical Wnt signalling since it participates to beta-catenin targeting to proteasomal degradation when the pathway is inactive. Moreover, independently of Wnt signaling, APC regulates several cellular functions such as mycrotubule dynamics, chromosome segregation, cell adhesion. Although APC has been widely studied for its implication in initation and progression of several cancers, its role in satellite cells (skeletal muscle stem cells) has never been investigated.
Here we used microarrays and to clarify APC functions and we identified several pathways and cellular processes to be affected following APC silencing.

overall_design: We cultured satellite cells-derived primary myoblasts in proliferating conditions and we transfected them either by a siRNA targeting APC or by a control siRNA. 48 hours after transfection, cells were processed for RNA extraction.

first: Alice

last: Parisi


title: Selective elimination of mitochondria mutations in the germline by genome editing

status: Public on Apr 23 2015

city: Madison

first: Karen

middle: Dyer

last: Montgomery

state: WI

address: 504 S Rosa Rd, Ste 101

department: Cytogenetics

country: USA

institute: WiCell

type: Genome variation profiling by genome tiling array

summary: Currently there is no treatment for mitochondrial disease, a group of devastating inherited disorders caused by mutations in mitochondrial DNA (mtDNA). Here we report a strategy to prevent the germline transmission of mitochondrial diseases. This technique is based on the specific elimination of mutated mtDNA through the use of mitochondria targeted nucleases. Our approaches represent a potential therapeutic avenue for preventing the transgenerational transmission of human mitochondrial diseases caused by mutations in mtDNA.

overall_design: A total of 4 samples were analyzed. Test samples were compared to sex-matched reference samples.

first: Alejandro

last: Ocampo

first: Benjamin

middle: S

last: Nisler


title: Murine FAE and VE in BALB/cA mice

status: Public on Apr 18 2015

first: Gaku

last: Nakato

address: 701W 168th street HHMC

institute: Columbia University Medical Center

summary: M cells in the follicle-associated epithelium (FAE) of Peyer’s patches (PPs) serve as a main portal for external antigens. Limitation in the number of M cells has hampered identification of their specific molecules until recently. Efforts by us as well as others has gradually unraveled the molecular mechanisms for the development and differentiation of M cells. However, molecular mechanisms of antigen transcytosis and M cell differentiation were not fully elucidated. Recent studies reported that small non-coding RNAs including microRNA (miRNA) regulate gene expression that controls various biological processes such as cellular differentiation and functions. In fact, intestinal epithelial miRNAs play a critical role in goblet cell differentiation and maturation. However, the expression and function of miRNAs in FAE including M cell that function as the sentinels in the mucosal immune system are largely unknown. To address this notion, we performed microarray analysis to characterize expression profiles of miRNA in intestinal villous epithelium (VE) and FAE of PP. We also generated mice with intestinal epithelial cell-specific deletion of Dicer1 (DicerΔIEC), in which intestinal phenotypes including M-cell differentiation and epithelial morphology were examined. The microarray analysis identified that 72 miRNAs were up-regulated whereas 11 miRNAs were down-regulated, in FAE compared to VE. DicerΔIEC mice displayed a prominent decrease in mature M cells, suggesting an essential role of miRNAs in maturation of the cell type. Furthermore, electron micrographs clearly showed that depletion of miRNA caused the loss of endosomal structures in M cells. In addition, antigen uptake in M cells was impaired in DicerΔIEC mice compared to control floxed Dicer mice. These results raised the possibility that miRNAs play a significant role in the regulation of M cells maturation, and consequently secure mucosal immune homeostasis.

overall_design: Follicle associated epithelium  or villous epithelium was isolated from Peyer's patch(PP). PP was soaked Hank's balanced salt solution (HBSS;GIBCO) containing 30mM EDTA. After incubation at 4℃ for 20 min, FAE or VE was isolated by manipulation with fine needle under stereomicroscopic monitoring.  The isolated epithelial cell sheets were kept in ice-cold HBSS until RNA extraction(n=2).

first: G

first: K

last: Hase

first: H

last: Ohno


title: Real-time quantitative PCR analysis of cucumber mitogen activated protein kinase cascade genes in various tissues

city: Hang zhou

first: Jie

last: Wang

state: Zhe jiang province

address: Yu hangtang road 388 of West Lake District

department: Horticulture

institute: Zhejiang university

summary: We used Bio-Rad laboratories, lnc. PCR assay panel to analyze expression levels of MAPK genes in various tissues or organs. Cucumber plants of the ‘Jinyan No.4’ cultivar were reared in growth chambers at 28 ± 1 °C with a photoperiod of 16 h light/8 h dark and light intensity of 400 μmol m−2 s−1. The roots, leaves, stems, female flower buds (approximately 3 d before anthesis), male flower buds (approximately 1.0 cm in length), and fruits (10 d after pollination) were collected from flowering plants for tissue expression analysis.

overall_design: The experiment was designed to gain insight into the temporal and spatial transcription patterns of 58 MAPK cascade genes in cucumber.

first: Changtian

last: Pan

first: Lu

last: Gang