title: Regulation of gene expression by putative aspartate racemases, YgeA and AspR, in Salmonella Typhimurium

city: Bangalore

first: Genotypic

last: technology

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

institute: Genotypic Technology

summary: Amino acid racemases are enzymes that catalyze the conversion between L and D- forms of amino acids. While the role of alanine and glutamate raemases in bacteria (specifically Salmonella) are well-studied, relatively less is known about the function of other non-canonical racemases. This study focuses on delineating the role of two such putative aspartate raceases viz. YgeA and AspR in Salmonella Typhimurium. For this purpose, Salmonella strains engineered to lack either one or both of these genes were compared to the wild type strain under planktonic and biofilm-inducing conditions to identify the global changes in gene expression orchestrated by these genes.

sample_organism: Salmonella enterica subsp. enterica serovar Typhimurium

overall_design: Organism : Salmonella Typhimurium , Agilent Custom Salmonella Typhimurium str. 14028S  Gene Expression  8x15k Array (AMADID: 046639) designed  by Genotypic Technology Private Limited.

first: Dipshikha

last: Chakravortty

first: Namrata

last: Iyer


title: Maize death acids, 9-lipoxygenase derived cyclopente(a)nones, display activity as cytotoxic phytoalexins and transcriptional mediators

status: Public on Aug 07 2015

city: La Jolla

first: Alisa

last: Huffaker

state: CA

address: 9500 Gilman Drive #0116

department: Cell & Developmental Biology

country: USA

institute: UC San Diego

summary: Plant damage promotes the interaction of lipoxygenases (LOX) with fatty acids yielding 9-hydroperoxides, 13-hydroperoxides and complex arrays of oxylipins. The action of 13-LOX on linolenic acid enables production of 12-oxo-phytodienoic acid (12-OPDA) and its downstream products, termed jasmonates. As signals, jasmonates have related yet distinct roles in the regulation of plant resistance against insect and pathogen attack. A similar pathway involving 9-LOX activity on linolenic and linoleic acid leads to the 12-OPDA positional isomer, 10-oxo-11-phytodienoic acid (10-OPDA) and 10-oxo-11-phytoenoic acid (10-OPEA), respectively; however, physiological roles for 9-LOX cyclopentenones have remained unclear. In developing maize (Zea mays) leaves, southern leaf blight (Cochliobolus heterostrophus) infection results in dying necrotic tissue and the localized accumulation of 10-OPEA, 10-OPDA and a series of related 14- and 12-carbon metabolites, collectively termed ‘death acids’. 10-OPEA accumulation becomes wound-inducible within fungal-infected tissues and at physiologically relevant concentrations acts as a phytoalexin by suppressing the growth of fungi and herbivores including Aspergillus flavus, Fusarium verticillioides, and Helicoverpa zea. Unlike previously established maize phytoalexins, 10-OPEA and 10-OPDA display significant phytotoxicity. Both 12-OPDA and 10-OPEA promote the transcription of defense genes encoding glutathione S-transferases, cytochrome P450s, and pathogenesis-related proteins. In contrast, 10-OPEA only weakly promotes the accumulation of multiple protease inhibitor transcripts. Consistent with a role in dying tissue, 10-OPEA application promotes cysteine protease activation and cell death which is inhibited by overexpression of the cysteine protease inhibitor maize cystatin-9. Functions for 10-OPEA and associated death acids are consistent with specialized roles in local defense reactions.

overall_design: A total of 6 samples were analyzed, comprised of two treatments: 10-OPEA and DMSO carrier control (5%DMSO/0.1% Tween20 in H20), both in replicates of three.

first: Eric

middle: A

last: Schmelz


title: Exon expression for NCI Sarcoma cell line panel

status: Public on Aug 01 2015

city: Bethesda

middle: C

last: Polley

state: MD

address: 9609 Medical Center Drive, Rm 5W118

department: Biometric Research Branch

institute: National Cancer Institute

summary: Characterization of 68 cell lines derived from human sarcoma and 5 normal counterpart cells,  including drug sensitivity testing, gene expression profiling and microRNA expression profiling have been completed. Data and tools for searching these data will be made publicly available through the NCI Developmental Therapeutics Program. The raw data (.cel files ) are  provided through the GEO website. Sarcoma represents a variety of cancers at arise from cells of mesenchymal origin and have seen limited treatment advances in the last decade. Drug sensitivity data coupled with the transcription and microRNA profiles of a cohort of sarcoma cell lines may help define novel treatment paradigms.

overall_design:
For each cell line, exon expression was measured using Genechip Human Exon 1.0 ST arrays from Affymetrix, interrogating > 1 million exon clusters, to provide comprehensive coverage of the entire genome at the exon and gene expression level.

Please note that there are 2 replicates included in the study:
Arrays 1 (GSM1676295) and 49 (GSM1676338) are replicates of the A-204 cell line
Arrays 9 (GSM1676369) and 50 (GSM1676340) are replicates of the ES-4 cell line

The sample titles represent are the cell line names (e.g. A-204, EW8 etc.).

The drug screening data and details are provided in the 'NCI-Sarcoma-median-log10-IC50.csv' and 'drug_screening_readme.txt', respectively.

first: Anne

last: Monks

first: Beverley

last: Teicher


title: CLL exosomes modulate the transcriptome and behaviour of recipient stromal cells and are selectively enriched in miR-202-3p [mirBase 15]

status: Public on Aug 31 2015

city: Liverpool

first: Mosavar

last: Farahani

address: Daulby Street

department: Molecular and Clinical Cancer Medicine

country: United Kingdom

institute: University of Liverpool

summary: Bi-directional communication with the microenvironment is essential for homing and survival of cancer cells with implications for disease biology and behaviour. In chronic lymphocytic leukemia (CLL) the role of the microenvironment on malignant cell behaviour is well described. However, how CLL cells engage and recruit nurturing cells is poorly characterised. Here we demonstrate that CLL cells secrete exosomes that are nanovesicles originating from the fusion of multivesicular bodies with the plasma membrane, to shuttle proteins, lipids, microRNAs (miR) and mRNAs to recipient cells. We characterise and confirm the size (50 - 100 nm) and identity of the CLL-derived exosomes by Electron microscopy (EM), Atomic force microscopy (AFM), flow cytometry and western blotting using both exosomes-specific and CLL-specific markers. Incubation of CLL-exosomes, derived either from cell culture supernatants or from patient plasma, with human stromal cells shows that they are readily taken up into endosomes, and induce expression of genes such as c-fos and ATM as well as enhance proliferation of recipient HS-5 cells. Furthermore, we show that CLL exosomes encapsulate abundant small RNAs and are enriched in certain miRs and specifically hsa-miR-202-3p. We suggest that such specific packaging of miR-202-3p impacts on the expression of 'suppressor of fused' (Sufu), a Hedgehog (Hh) signalling intermediate, in the parental CLL cells. Thus, our data show that CLL cells secrete exosomes that alter the transcriptome and behaviour of recipient cells. Such communication with microenvironment is likely to have an important role in CLL disease biology.

platform_organism:
Homo sapiens
Human alphaherpesvirus 1
Human alphaherpesvirus 2
Macacine alphaherpesvirus 1
Human betaherpesvirus 5
human gammaherpesvirus 4
Herpesvirus saimiri (strain 11)
JC polyomavirus
Human immunodeficiency virus 1
Human betaherpesvirus 6B
Human gammaherpesvirus 8
Merkel cell polyomavirus
Betapolyomavirus hominis
Betapolyomavirus macacae

overall_design: miR analysis was carried out on 3 exosomal samples and 3 corresponding cellular samples from CLL patients.  Exosomes are a discrete population of small (50-100 nm diameter) EVs of endosomal origin with a lipid membrane bilayer and a cup-shaped morphology. We used common reference design which allows visualization of variations between the samples.  Each sample equals one array and each sample compared with common reference (Pool).  The pool or common reference was a collection of 23 RNA samples isolated from 23 CLL cases. We hypothesised that CLL derived exosomes should contain unique miRs that are reflective of CLL cell content and additionally relevant for disease biology.

first: Carlos

last: Rubbi

first: Lu-Ning

last: Liu

first: Joseph

middle: R

last: Slupsky

first: Nagesh

last: Kalakonda


title: Differentiating i-Mixl1 mESCs cultured in the presence or absence of Doxycycline

status: Public on Sep 01 2015

city: New York

first: Dmitri

last: Papatsenko

state: NY

address: One Gustave L. Levy Place

institute: Mount Sinai School of Medicine

summary: We profiled gene expression changes in differentiating i-Mixl1 ES cells(Willey, Ayuso-Sacido et al., 2006, Blood 107(8): 3122-3130)  cultured in the presence or absence of Doxycycline (DOX, 0.1 ug/ml, 3 replicates per treatment/time point).  Total RNA was isolated from EBs harvested at day 2, 3 and 4 (DOX added 1 day after plating of ES cells).  RNA (1 ug) was subjected to one round of linear amplification (RiboAmp System) to yield 10 ug of RNA.  The RNA was indirectly labeled using amino allyl-dUTP('t Hoen, de Kort et al., 2003, Nucleic Acids Res. 31: e20), then conjugated with Cy3 or Cy5.  The labeled RNAs were used to screen a 15K mouse developmental cDNA microarray(Tanaka, Jaradat et al., 2000, Proc. Natl. Acad. Sci. U.S.A. 97: 9127-9132). Pairwise analysis of hybridization results for EBs cultured with or without DOX was performed for samples harvested on each day.  Spotfire(R) software was used for data management and filtering.  Gene expression ratios were normalized after filtering the data to remove low-intensity and poor quality spots.  Data obtained for replicate samples were in excellent agreement.

overall_design: Six experiments total: three time points (day 2, day 3, day 4); for each time point mRNA was collected in the presence or absence of Doxycycline. Three biological replicas were collected for each of the six experiments

first: Papatsenko

last: Dmitri

first: Baron

last: Margaret


title: Gene expression in FACS sorted virus-specific CD8+ T cells

city: Beerse

first: Susanne

last: Johansson

address: Turnhoutseweg 30

department: Infectious Diseases and Vaccines

country: Belgium

institute: Janssen Pharmaceutica

summary:
Defective HBV-specific CD8+ T cells are believed to contribute to a chronic stage of the disease.
To increase the understanding of the defective HBV-specific CD8+ T cell response, gene expression in HBV-specific CD8+ T cells were compared with that in HCV- and CMV-specific CD8+ T cells.

overall_design: Tetramer specific CD8+ T cells from chronic HBV or HCV-infected patients and one healthy individual were sorted by flow cytometry. Cells not specific for the particular tetramer were included as controls. Cells were frozen until use. RNA was extracted and then amplified and converted to cDNA before hybridization to Affymetrix microarrays.

first: Bianca

last: Martin

first: Bertram

last: Bengsch

first: Robert

last: Thimme

first: Ilse

last: Van den Wyngaert

first: Marianne

last: Tuefferd

first: Gregory

last: Fanning

first: Jeroen

last: Aerssens


title: microRNA expression in C3H10T1/2 cells treated with BMP7 vs vehicle

status: Public on Jul 22 2015

city: Boston

first: Yu-Hua

last: Tseng

state: MA

address: 1 Joslin Place

institute: Joslin Diabetes Center Harvard Medical School

summary: Multipotent C3H10T1/2 cells can be induced to differentiate into mature brown adipocytes by 3-days BMP7 pretreatment followed by standard adipogenic induction.

platform_organism:
Homo sapiens
Mus musculus
Rattus norvegicus

overall_design: In this study, we used microRNA array to identify the microRNAs that were regulated by 3-days BMP7 treatment in C3H10T1/2 cells. One BMP7-treated sample and one vehicle-treated sample were used in this study to obtain the fold expression of microRNAs between BMP7 vs vehicle.

first: Tseng

last: Yu-Hua

first: Zhang

last: Hongbin


title: Differentially methylated genes in human IL-7Ra high and low EM CD8+ T cells

status: Public on Aug 06 2015

city: LA

first: Sungyong

last: You

address: Beverly Blvd 8400

department: Surgery

institute: Cedars-Sinai Medical Center

summary: Genome wide DNA methylation profiling of IL-7Ra high and low EM CD8+ T cells. The Illumina Infinium 27k Human DNA methylation Beadchip v1.2 was used to obtain DNA methylation profiles across approximately 27,578 CpGs. Samples included 2 IL-7Ra high EM CD8+ T cells and 2 IL-7Ra high EM CD8+ T cells.

overall_design: Bisulphite converted DNA from the 4 samples were hybridised to the Illumina Infinium 27k Human Methylation Beadchip v1.2

first: Insoo

last: Kang

first: Daehee

last: Hwang


title: microRNA expression  profiling of human sarcoma cell lines (~68)  in the Molecular Pharmacology Branch, DTP, DCTD NCI collection of human cell lines

first: Eric

last: Polley

summary: Characterization of ~68 cell lines derived from human sarcoma and 5 normal counterpart cells,  including drug sensitivity testing, gene expression profiling and microRNA expression profiling have been completed. Data and tools for searching these data will be made  publicly available through the NCI Developmental Therapeutics Program. The raw data (RCC files) are  provided through the GEO website. Sarcoma represents a variety of cancers at arise from cells of mesenchymal origin and have seen limited treatment advances in the last decade. Drug sensitivity data coupled with the transcription and microRNA profiles of a cohort of sarcoma cell lines may help define novel treatment paradigms.

overall_design:
For each cell line, microRNA expression was measured on nCounter miRNA Expression Arrays (Nanostring Technologies), providing multiplexed, digital detection and counting of 800 human microRNA's.

Please note that there are 2 replicates included in the study:
A-204-rep1 and A-204-rep2, ES-4-rep1 and ES-4-rep2 resulting total 77 samples.

first: Anne

last: Monks

first: Beverley

last: Teicher


title: Genomic landscape of the developing kidney upon conditional and time-dependent knockout of Wt1

status: Public on Jul 27 2015

city: Cincinnati

first: Rebekah

last: Karns

state: OH

address: 3333 Burnet Ave

department: Gastroenterology, Hepatology, & Nutrition

institute: Cincinnati Children's Hospital Medical Center

summary:
We are characterizing global expression in the whole kidney at developmental stage E18.5, where we have used three Cre strains that result in knock out Wt1 in different cell types during renal development.
Here the purpose is to identify the developmental stage at which the loss of Wt1 impacts kidney development, specifically in the context of a degree of disruption capable of ending in pediatric kidney cancers.

overall_design: Total RNA was isolated from whole kidneys of E18.5 mouse embryos following a variety of conditional knockouts of Wt1, plus appropriate control animals.

first: Rachel

last: Berry

first: Peter

last: Hohenstein

first: Bruce

last: Aronow


title: Single-cell analysis reveals a stem cell program in human metastatic breast cancer cells (Human patients - mammary cells)

status: Public on Jul 20 2015

city: San Francisco

first: Devon

last: Lawson

state: California

address: 513 Parnassus Ave Hsw 1301

department: Anatomy

institute: UCSF

summary: Despite major advances in understanding the molecular and genetic basis of cancer, metastasis remains the cause of >90% of cancer-related mortality1. Understanding metastasis initiation and progression is critical to develop new therapeutic strategies to treat and prevent metastatic disease. Prevailing theories hypothesize that metastases are seeded by rare tumor cells with unique properties, which may function like stem cells in their ability to initiate and propagate metastatic tumors.2 3-5 However, the identity of metastasis-initiating cells in human breast cancer remains elusive, and whether metastases are hierarchically organized is unknown.2 Here we show at the single-cell level that early stage metastatic cells possess a distinct stem-like gene expression signature. To identify and isolate metastatic cells from patient-derived xenograft (PDX) models of human breast cancer, we developed a highly sensitive FACS-based assay, which allowed us to enumerate metastatic cells in mouse peripheral tissues. We compared gene signatures in metastatic cells from tissues with low vs. high metastatic burden. Metastatic cells from low-burden tissues were distinct due to their increased expression of stem cell, EMT, pro-survival, and dormancy-associated genes. In contrast, metastatic cells from high-burden tissues were similar to primary tumor cells, which were more heterogeneous and expressed higher levels of luminal differentiation genes. Transplantation of stem-like metastatic cells from low-burden tissues showed that they have significant tumor-initiating capacity, and differentiate to produce luminal-like cancer cells. Progression to high metastatic burden was associated with increased proliferation and cMYC expression, which could be attenuated by treatment with cyclin dependent kinase (CDK) inhibitors. These findings support a hierarchical model for metastasis, where metastases are initiated by stem-like cells that proliferate and differentiate to produce advanced metastatic disease.

overall_design: 271 samples

first: Nirav

last: Bhakta

first: Kai

last: Kessenbrock

first: Karin

last: Prummel

first: Ying

last: Yu

first: Ken

last: Takai

first: Alicia

last: Zhou

first: Henok

last: Eyob

first: Sanjeev

last: Balakrishnan

first: Chih-Yang

last: Wang

first: Paul

last: Yaswen

first: Andrei

last: Goga

first: Zena

last: Werb


title: siRNA screen for modifiers of Smad4 nuclear translocation

status: Public on Jul 15 2015

first: Alessia

last: Deglincerti

address: 1230 York Ave

institute: The Rockefeller University

summary:
The TGFb signaling pathway is a critical regulator of developmental processes and disease. We developed a system to measure TGFb signaling dynamics by monitoring the localization of Smad4.
We performed an unbiased genome-wide RNAi screen to identify genes involved in ligand-dependent Smad4 nuclear translocation

overall_design: C2C12 GFP-Smad4 reporter cells were transfected with pools of 3 siRNAs targeting individual genes; after 48 hours, cells were stimulated with 2ng/ml TGFb1 for 1 or 6 hours, then fixed and analyzed for Smad4 localization. Two independent experiments were performed, screening 17,582 genes. On each plate, two control wells (siRNA targeting TGFbR1 and XpoI) were included

first: Tomomi

last: Haremaki

first: Aryeh

last: Warmflash

first: Benoit

last: Sorre

first: Ali

middle: H

last: Brivanlou


title: Single-cell analysis reveals a stem cell program in human metastatic breast cancer cells

first: Devon

last: Lawson

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

overall_design: Refer to individual Series. For normalization: For PDX cancer cells, (GSE70552) Ct values were normalized by subtracting the average primary tumor expression from the same individual animal on a per-gene basis. In normal mammary cell experiments, (GSE70554) Ct values were normalized by subtracting the average value of the basal/stem cell population on a per-gene basis. For more detailed information, refer to the Methods section of Lawson DA et al., (2015).


title: Single-cell analysis reveals a stem cell program in human metastatic breast cancer cells (PDX mice - cancer cells)

overall_design: 1022 sampels

first: Nirav

last: Bhakta

first: Kai

last: Kessenbrock


title: miRNA profile of THP-1 macrophage infected with different MTB strains

status: Public on Jul 01 2015

city: Hong Kong

first: Margaret

last: Ip

address: Main clinic building, Prince of Whales Hospital, City one, Shatin

department: Department of Microbiology

country: China

institute: The Chinese University of Hong Kong

summary: We examined the microRNA profiles of THP-1 macrophages upon the MTB infection of (1) Beijing/W and non-Beijing/W clinical strains, and (2) susceptible and multidrug-resistant (MDR-) MTB strains.

overall_design: THP-1 cells were induced differentiation into a macrophage phenotype. Then cells were infected with three MDR (INHR, RIFR) Beijing/W, three sensitive (INHS, RIFS) Beijing/W, three MDR(INHR, RIFR) non-Beijing/W, and three sensitive (INHS, RIFS) non-Beijing/W strains. Total RNA were extracted and transfered into cDNA for miRNA profile analysis. Non-infected cells were used as control.

first: Lin

last: Zheng


title: miRNA profile of macrophage from different TB patients

summary: the microRNA profiles of the host macrophages were studied by microarray in a small cohort with active MTB disease, latent infection (LTBI), and from healthy controls.

overall_design: From each individual in the three cohorts: the healthy (n=3), the latent (n=4), and the active TB patients (n=3), whole blood specimens were collected for monocytes isolation. Monocytes were induced into macrophage in vitro and total RNA were extracted for miRNA profiles analysis.


title: RNA expression analysis after RNA polymerase II transcriptional blocking with α-amanitin

status: Public on Jun 30 2015

city: São Paulo

first: Eduardo

middle: Moraes

last: Reis

state: SP

address: Av. Prof. Lineu Prestes, 748

department: Biochemistry

country: Brazil

institute: University of São Paulo

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

summary: Transcriptional profiling of HeLa cells treated with α-amanitin for 9 h. Relative abundance to untreated control cells was used to evaluate the biogenesis of lncRNAs by RNA polymerase II.

overall_design: Two-condition experiment, alpha-amanitin-treated vs. untretated HeLa cells. Biological replicates: 4 with dye-swap

first: Ana

last: Ayupe

middle: M


title: NF-κB activation impairs somatic cell reprogramming in ageing [IKBA-SR]

city: Oviedo

first: Jose

last: Freije

state: Asturias

address: C/ Fernando Bongera s/n

department: Bioquimica y Biologia Molecular

country: Spain

institute: Universidad de Oviedo

summary:
Transcriptional profiling of human Néstor-Guillermo Progeria Syndrome (NGPS) fibroblasts control, treated with sodium salicylate or transduced with Ikappa B alpha super-repressor.

Somatic cell reprogramming involves rejuvenation of adult cells and relies on the ability to erase age-associated molecular marks. Accordingly, reprogramming efficiency declines with ageing, and age-associated features such as genetic instability, cell senescence or telomere shortening negatively affect this process. However, the regulatory mechanisms that constitute age-associated barriers for cell reprogramming remain largely unknown. Here, by using cells from patients with premature ageing, we demonstrate that NF-κB activation is a critical barrier for the generation of induced pluripotent stem cells (iPSCs) in ageing. We show that NF-κB repression occurs during cell reprogramming towards a pluripotent state. Conversely, ageing-associated NF-κB hyperactivation impairs generation of iPSCs by eliciting reprogramming repressors DOT1L and YY1, reinforcing cell senescence signals and down-regulating pluripotency genes. We also show that genetic and pharmacological NF-κB inhibitory strategies significantly increase the reprogramming efficiency of fibroblasts from Néstor-Guillermo Progeria Syndrome (NGPS) and Hutchinson-Gilford Progeria Syndrome (HGPS) patients, as well as from normal aged donors. Finally, we demonstrate that DOT1L inhibition in vivo ameliorates the accelerated ageing phenotype and extends lifespan in a progeroid animal model. Collectively, our results provide evidence for a novel role of NF-κB in the control of cell fate transitions and reinforce the interest of studying age-associated molecular impairments to implement cell reprogramming methodologies, and to identify new targets of rejuvenation strategies.

overall_design: Human NGPS fibroblasts were treated with sodium salicylate, transduced with Ikappa B alpha super-repressor or left untreated. RNA was extracted and transcriptional profiling was obtained with GeneChip Human Gene 2.0 ST Arrays.

first: Fernando

middle: G

last: Osorio

first: Clara

last: Soria-Valles

first: Carlos

last: Lopez-Otin


title: Analysis to evaluate the presence of 5’ cap in intragenic lncRNAs

summary: RNA aliquots were digested with 5’-phosphate-dependent exonuclease (5'-exo) following pre-treatment with tobacco acid pyrophosphatase (TAP) to release the 5’ cap and render the RNA susceptible to 5’ exonuclease digestion (TAP+/5'-exo+). Two color array hybridizations were performed and  TAP+/5'-exo+ samples were compared with TAP-/5'-exo+ control samples.

overall_design: Two-condition experiment, TAP+/5'-exo+  vs. TAP-/5'-exo+  treated total RNA samples. Biological replicates: 4 with dye swap


title: RNA half-life analysis after transcriptional blocking with actinomycin D

summary: Transcriptional profiling of HeLa cells treated with actinomycin D for increasing amounts of time. Relative abundance to  control cells was used to estimate the half-life of lncRNAs.

overall_design: Two-condition experiment, actinomycin D-treated vs. untreatted HeLa cells. Biological replicates: 2. Technical replicates: 2.


title: Differentially regulated circulating microRNAs in post-menopausal women suffering from osteoporotic femoral-neck  fractures

status: Public on Jun 26 2015

city: Vienna

first: Matthias

last: Hackl

state: Austria

address: Leberstrasse 20

country: Austria

institute: TAmiRNA GmbH

summary: Osteoporosis is the consequence of altered bone metabolism resulting in the systemic reduction of bone strength and increased risk of fragility fractures. MicroRNAs (miRNAs) regulate gene expression on a post-transcriptional level are known to take part in the control of bone formation and bone resorption. Recently, targeted secretion of miRNAs from cells originating from various tissues has been described, which allows for their minimal-invasive detection in serum/plasma and use as biomarkers for presence and progression of pathological conditions. One pilot study has reported circulating miRNAs in serum and tissue of fracture patients. However, further studies are required to explore whether a dysbalance in bone homeostasis of fracture patients can reliably be reflected by specific circulating miRNAs, and whether these miRNAs might serve as drugable targets.  Here, we report results from a comprehensive multiplex study of 175 miRNAs in serum samples obtained from 7 patients with osteoporotic fractures at the femoral neck, and 7 age-matched controls. Following elaborate quality control statistical analysis of this exploratory dataset identified 9 microRNAs with altered serum levels in response to fracture (adjusted p-value < 0.1). Of these, hsa-miR-10a/b gave excellent discrimination of both groups (AUC = 1.0), and clustering of samples based on the top10 miRNAs confirmed the high discriminatory power of circulating microRNAs for osteoporotic fractures. In the next step 3 miRNAs with unknown roles in osteogenic differentiation and 4 miRNA from a previous study were tested for their effects on osteogenic differentiation. Of these, 3 miRNAs showed robust effects on osteogenic differentiation.  Overall, these data provide important insights into changes in serum miRNA in post-traumatic patients. Future studies will show, whether this knowledge can be used to improve current diagnostic methodologies to predict fracture risk and design novel treatment strategies for osteoporosis patients.

overall_design: Two groups with n=7 per group; one groups represents cases with osteoporotic fractures, the control group is age-matched without fractures

first: Sylvia

last: Weilner

first: Verena

last: Keider

first: Michael

last: Wagner

first: Susanna

last: Skalicky

first: Peter

last: Dovjak

last: Pietschmann

first: Regina

last: Grillari

first: Johannes

first: Benjamin

last: Salzer

first: Christian

last: Gabriel

first: Florian

last: Hildner


title: RNA expression analysis after MCF-7 cell treatment with demethylating agent 5-Aza-2’-deoxycitidine (5-Aza)

first: Eduardo

last: Reis

summary: Transcriptional profiling of MCF-7 cells treated with 5-Aza for 96 h. Relative abundance to untreated control cells was used to estimate the effect of DNA demethylation on the expression of the RNAs.

overall_design: Two-condition experiment, 5-Aza-treated vs. untretated MCF-7 cells. Biological replicates: 2. Technical replicates: 2.


title: RNA expression analysis after  Mia PaCa 2 cell treatment with demethylating agent 5-Aza-2’-deoxycitidine (5-Aza)

summary: Transcriptional profiling of Mia PaCa 2 cells treated with 5-Aza for 96 h. Relative abundance to untreated control cells was used to estimate the effect of DNA demethylation on the expression of the RNAs.

overall_design: Two-condition experiment, 5-Aza-treated vs. untretated Mia PaCa 2 cells. Biological replicates: 2. Technical replicates: 2.

first: Ana

last: Ayupe


title: Influence of dietary sucrose and copper content in a rat model of non-alcoholic fatty-liver disease

city: Anchorage

first: Jason

middle: Lee

last: Burkhead

state: AK

address: 3211 Providence Dr

department: Biological Sciences

institute: University of Alaska Anchorage

summary: Nutrigenomics analysis was used to investigate the molecular responses to dietary Cu deficiency independently and in combination with 30% (w/w) sucrose in a mature rat model of NAFLD. Low Cu significantly decreased hepatic and serum Cu, and induced NAFLD-like histopathology, mild steatosis, up-regulated transcripts in inflammation and hepatic stellate cell activation, and significantly increased oxidative stress. Rats fed low Cu together with 30% sucrose also developed insulin resistance, increased ATP citrate lyase and FASN expression, and greater oxidative stress. High sucrose with adequate Cu also promoted inflammation and fibrosis, but not steatosis. This study indicates that low dietary Cu and sucrose consumption are singular and synergistic dietary factors in promotion of NAFLD and NASH that act independently of obesity or severe steatosis, likely by promoting oxidative stress and activation of inflammation and fibrosis.

overall_design: Mature (6 months old) male Wistar Rats that had been allowed ad libitum access to Mazuri rodent pellets were used in the study. Twenty-four rats were divided into four groups and fed for 12 weeks with diets based on the Purified AIN76A formulation, modified for target sucrose and Cu content (Custom Animal Diets, Bangor, NJ). Sucrose and copper content in diets were as follows: ‘A’ CuD/30%- Cu deficient (<0.3 mg Cu/kg)/30% sucrose, ‘B’ CuA/30%- Cu adequate (125 mg/kg)/30% sucrose, ‘C’ CuD/10%- <0.3 mg/kg Cu/10% sucrose, and ‘D’ CuA (125 mg/kg Cu)/10% sucrose (control). Starch and dextrin were used to equalize carbohydrates.


title: Molecular characterization of Notch1 positive progenitor cells in the developing retina

city: Miami

first: Dmitry

last: Ivanov

state: FL

address: 1638 NW 10th Avenue

department: Ophthalmology

institute: University of Miami Miller School of Medicine

summary: The oscillatory expression of Notch signaling in neural progenitors suggests that both repressors and activators of neural fate specification are expressed in the same progenitors. Since Notch1 regulates photoreceptor differentiation and contributes (together with Notch3) to ganglion cell fate specification, we hypothesized that genes encoding photoreceptor and ganglion cell fate activators would be highly expressed in Notch1 receptor-bearing (Notch1+) progenitors, directing these cells to differentiate into photoreceptors or into ganglion cells when Notch1 activity is diminished.

overall_design: To identify these genes, we used microarray analysis to study expression profiles of whole retinas and isolated from them Notch1+ cells at embryonic day 14 (E14) and postnatal day 0 (P0). To isolate Notch1+ cells, we utilized immunomagnetic cell separation. RNA from Notch1+ cells and whole retinas at E14 and P0 was extracted and used for microarray analysis. We processed individual samples that each contained 200,000-500,000 Notch1+ cells. A total of three independent biological replicates in the early stage (E14) of retinal development and four independent biological replicates in the late stage (P0) of retinal development were obtained for comparative profiling of Notch1+ cells and whole retinas.


title: Reverse phase protein arrays (RPPAs): effects of MPS1 inhibition on signaling pathways in GBM cells

status: Public on Jun 25 2015

first: Uma

middle: T

last: Shankavaram

address: 9000 Rockville Pike

department: NCI

institute: NIH

summary: To determine the biological effects of MPS1 inhibition (both by siRNA and Drug (NMSP715)) on signaling pathways in GBM cells (U251 &U87), we profiled the modulation of phosphorylated and non-phosphorylated proteins using RPPA

overall_design: Relative protein levels for each sample were determined by interpolation of each dilution curves from the standard curve antibody slide. All the data points were normalized for protein loading and transformed to a linear value. Linear values were transformed to Log2 value and then median‐centered for hierarchical cluster analysis.

first: Uday

middle: B

last: Maachani

first: Kevin

last: Camphausen


title: RNA expression analysis after DU-145 cell treatment  with demethylating agent 5-Aza-2’-deoxycitidine (5-Aza)

summary: Transcriptional profiling of DU-145 cells treated with 5-Aza for 72 h. Relative abundance to untreated control cells was used to estimate the effect of DNA demethylation on the expression of the RNAs.

overall_design: Two-condition experiment, 5-Aza-treated vs. untreated DU-145 cells. Biological replicates: 2. Technical replicates: 2.


title: Characterization of the Bradyrhizobium japonicum NtrC regulon by DNA Microarray analysis.

city: Arlington

first: Woo-Suk

last: Chang

state: TX

address: 501 S. Nedderman Dr. , Life Science Building 216

department: Biology

institute: University of Texas at Arlington

summary: The Bradyrhizobium japonicum NtrC regulatory protein influences gene expression in response to changes in intracellular nitrogen status. Under conditions of low nitrogen, phosphorylation of NtrC results in up-regulation of a number of genes involved in nitrogen metabolism and nitrogen acquisition. To better define the exact nature of NtrC’s influence on gene expression, a ntrC mutation was created in B. japonicum and transcriptional profiling was performed by DNA microarray analysis of both the mutant and wild type strains.

overall_design: Bradyrhizobium japonicum USDA 110 and a ntrC mutant in the USDA 110 background were cultured in minimal medium supplemented with either 10mM glutamate (low nitrogen) or  10mM ammonium and 10mM glutamate (high nitrogen) as nitrogen sources. Four comparisons were performed: wild type high nitrogen vs. mutant high nitrogen, wild type low nitrogen vs. wild type high nitrogen, wild type low nitrogen vs. mutant low nitrogen, and mutant low nitrogen vs. mutant high nitrogen.  For each of the four comparisons, three biological replicates were prepared for each strain and dye swap replications were performed for each hybridization producing a total of six arrays per comparison and 24 arrays in total.

first: William

middle: L

last: Franck

first: Jing

last: Qiu

first: Gary

last: Stacey


title: Differential Expression of miRNAs: Implication in Colon Cancer Racial Health Disparity

city: Stony Brook

first: Yuanhao

last: Zhang

address: AMS Department,Stony Brook University

department: Applied Mathematics and Statistics

institute: Stony Brook University

summary: We have demonstrated that the miR-182 level, in addition to being significantly increased in colon cancer compared to adjacent normal colon tissue, is also significantly increased in African American(AA) compared to Caucasian American (CA) colon cancer. Since miR-182 has been previously associated with decreased survival in colon cancer patients and with increased liver metastases, this observation supports the concept that biological differences between AA and CA colon cancers may contribute to AA disparities in colon cancer survival.

overall_design: We aimed to identify miRNAs that were associated with effects of both tumor and race by generating Agilent miRNA expression profiles on paired colon cancer and adjacent normal colon collected from AA and CA colon cancer subjects. For the 30 paired Stony Brook University (SBU) colon cancer and adjacent normal colon samples, attempts were made to control for other covariates such as age, colon cancer location, stage, BMI and smoking in the selection of the CA samples .  However no attempt was made to control for the other covariates in the 30 paired Washington University (WU) colon cancer and adjacent normal colon samples.

first: Ellen

last: Li

first: Jennie

last: Williams


title: NCI Sarcoma Cell Line Panel

first: Eric

last: Polley

address: 9609 Medical Center Drive, Rm 5W118

institute: National Cancer Institute

overall_design: Refer to individual Series


title: Subcellular distribution of RNAs in HeLa cells

summary: HeLa cells were fractioned in nucleus and cytoplasm to investigate the subcellular distribution of lncRNAs.

overall_design: Two-condition experiment, nuclear fraction vs. cytoplasmatic fraction from HeLa cells. Biological replicates: 2 with dye-swap


title: Context Influences on TALE-DNA Binding Revealed by Quantitative Profiling

status: Public on Jun 11 2015

first: Julia

last: Rogers

state: Massachusetts

address: 45 Shattuck Street

department: BCMP

institute: Harvard Medical School

summary: Transcription Activator Like Effector (TALE) proteins have been described as recognizing DNA using a simple DNA-binding code, which has allowed for their use in many techniques requiring precise targeting of genomic loci. The TALE DNA binding domain is composed of an array of short repeats that differ in two key DNA-contacting positions, the repeat variable diresidues (RVD); the identities of the amino acids at these positions determine which base the repeat binds. While this simple code has been used successfully to design TALEs to target specific sequences, off-target binding has also been observed, indicating the need for a more rigorous understanding of the factors that determine TALE specificity. In this study, we assayed the DNA binding specificities of 21 TALE proteins of different lengths and RVD compositions using custom-designed Protein Binding Microarrays (PBMs). Position weight matrices derived from these data were used to develop a model to predict the specificity of any TALE protein. This modeling shows the large influence of protein length, RVD position, and neighboring RVD identity on binding specificity, indicating that the simple cipher-like code does not fully capture the complexity of TALE-DNA binding.

overall_design: A set of 21 TALE proteins, with numbers of TALE repeats ranging from 8.5 to 18.5, was chosen to cover all 16 possible RVD pairs. Three types of custom PBMs were designed to test the effects of substitutions in the binding sites on binding.

first: Luis

last: Barrera

first: J

middle: K

last: Joung

first: Martha

last: Bulyk


title: Somatic cell fusions reveal extensive heterogeneity in basal-like breast cancer [methylation27]

status: Public on Jun 10 2015

first: Kornelia

last: Polyak

address: 450 Brookline Ave

department: Medical Oncology

institute: Dana-Farber Cancer Institute

summary: Basal-like and luminal breast tumors have distinct clinical behavior and molecular profiles, yet the underlying mechanisms are poorly defined. To interrogate processes that determine these distinct phenotypes and their inheritance pattern, we generated somatic cell fusions and performed integrated genetic and epigenetic (DNA methylation and chromatin) profiling. We found that the basal-like trait is generally dominant and it is largely defined by epigenetic repression of luminal transcription factors. Definition of super-enhancers highlighted a core program common in luminal cells but high degree of heterogeneity in basal-like breast cancers that correlates with clinical outcome. We also found that protein extracts of basal-like cells is sufficient to induce luminal-to-basal phenotypic switch implying a trigger of basal-like autoregulatory circuits. We determined that KDM6A might be required for luminal-basal fusions, and identified EN1, TBX18, and TCF4 as candidate transcriptional regulators of luminal-to-basal switch. Our findings highlight the remarkable epigenetic plasticity of breast cancer cells.

overall_design: Bisulphite converted DNA from the 9 samples were hybridised to the Illumina Infinium 27k Human Methylation Beadchip.

first: Reo

last: Maruyama

first: Mary

middle: J

last: Fackler


title: Effect of PML/RARa on the transcriptome of maturing myeloid populations in vivo

status: Public on Jun 24 2015

first: Scott

last: Kogan

address: 513 Parnassus, S-561, Box 0451

department: Laboratory Medicine

summary: Transcriptional profiling of murine cells at the GMP, Early promyelocyte (Early Pros) and Late promyelocyte (Late Pros) stages, isolated from Wt or MRP8-PML/RARa transgenics after 2 rounds of sorting.

overall_design: Two-conditions experiment: Wt vs PML/RARa. 3 populations: GMP, Early Pros, Late Pros. 3-4 biological replicates/population (20 samples total)

first: Coline

last: Gaillard


title: Exposure of Salmonella enterica serovar Typhimurium to three humectants used in the food industry: NaCl, KCl and glycerol

status: Public on Jun 15 2015

city: Dublin 4

first: Sarah

last: Finn

address: University College Dublin

country: Ireland

institute: Centre for Food Safety

summary: Salmonella Typhimurium was exposed to NaCl, KCl and glycerol (equilibrated to the same water activity) for 1, 6 and 24 h after which the expression profiles were examined using microarray. An non-exposed early stationary phase culture grown in LB medium was used as the control.

sample_organism: Salmonella enterica subsp. enterica serovar Typhimurium str. ST4/74

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

overall_design: Carried out using 3 biological replicates for each sample; each sample hybridised in a two-channel hybridization against Salmonella genomic DNA as the comparator/reference

first: Lisa

first: Kristian

last: Händler

first: Peter

last: McClure

first: Alejandro

last: Amézquita

first: Jay

last: C.D. Hinton

first: Séamus

last: Fanning


title: Differential isoform expression and selective muscle involvement in muscular dystrophies

status: Public on Jun 17 2015

city: Helsinki

last: Hackman

address: Haartmaninkatu 8

department: Dpt. of Medical Genetics

country: Finland

institute: Folkhälsan research Center/University of Helsinki

summary: To test the hypothesis that different muscles may express variable amounts of different isoforms of muscle genes, we applied a custom-designed exon microarray containing probes for 57 muscle-specific genes to assay the transcriptional profiles in sets of human adult, lower limb skeletal muscles.

overall_design: Muscle biopsies from 15 individuals were selected for analysis dissected from 21 anatomically different muscles collected from eight men and seven women, ranging from 61 to 91 years The muscle tissue samples collected included samples from 11 different thigh muscles––vastus medialis, vastus lateralis, vastus intermedialis, sartorius, gracilis, semimembranosus, semitendinosus, biceps femoris, adductor magnus, adductor longus, and rectus femoris––and 10 lower leg muscles––flexor digitorum longus, extensor digitorum longus, tibialis posterior, tibialis anterior, peroneus longus/brevis, extensor hallucis longus, gastrocnemius lateralis, gastrocnemius medialis, flexor hallucis longus, and soleus. Approximately five to seven muscle pieces were collected from each individual muscle sampled. The muscle sample pieces obtained for histological analysis measured roughly 10 mm x 5 mm, and the pieces for RNA isolation 5 mm x 5 mm. The samples were obtained directly from the proximal vital parts of the amputated limbs and processed immediately following their removal to avoid tissue degradation.To test the hypothesis that different muscles may express variable amounts of different isoforms of muscle genes, we applied a custom-designed Agilent exon microarray containing probes for 57 muscle-specific genes to assay the transcriptional profiles in sets of human adult, lower limb skeletal muscles

first: Sanna

last: Huovinen


title: Autoantigen microarrays reveal autoantibodies associated with proliferative nephritis and active disease in pediatric systemic lupus erythematosus

city: Stanford

first: Jamie

last: Haddon

address: CCSR Rm 2250, 269 Campus Drive West

department: Immunology & Rheumatology

institute: Stanford University

summary:
Introduction:   Pediatric systemic lupus erythematosus (pSLE) patients often initially present with more active and severe disease than adults, including a higher frequency of lupus nephritis. Specific autoantibodies, including anti-C1q, anti-DNA and anti-alpha-actinin, have been associated with kidney involvement in SLE, and DNA antibodies are capable of initiating early stage lupus nephritis in severe combined immunodeficiency (SCID) mice. Over 100 different autoantibodies have been described in SLE patients, highlighting the need for comprehensive autoantibody profiling. Knowledge of the antibodies associated with pSLE and proliferative nephritis will increase the understanding of SLE pathogenesis, and may aid in monitoring patients for renal flare.

Methods:  We used autoantigen microarrays composed of 140 recombinant or purified antigens to compare the serum autoantibody profiles of new-onset pSLE patients (n=45) to healthy controls (n=17). We also compared pSLE patients with biopsy-confirmed class III or IV proliferative nephritis (n=23) and without significant renal involvement (n=18). We performed ELISA with selected autoantigens to validate the microarray findings. We created a multiple logistic regression model, based on the ELISA and clinical information, to predict whether a patient had proliferative nephritis, and used a validation cohort (n=23) and longitudinal samples (88 patient visits) to test its accuracy.

Results:  Fifty autoantibodies were at significantly higher levels in the sera of pSLE patients compared to healthy controls, including anti-B-cell activating factor (BAFF). High levels of anti-BAFF were associated with active disease. Thirteen serum autoantibodies were present at significantly higher levels in pSLE patients with proliferative nephritis than those without, and we confirmed five autoantigens (dsDNA, C1q, collagens IV & X and aggrecan) by ELISA. Our model, based on ELISA measurements and clinical variables, correctly identified patients with proliferative nephritis with 91% accuracy.

Conclusions:  Autoantigen microarrays are an ideal platform for identifying autoantibodies associated with both pSLE and specific clinical manifestations of pSLE. Using multiple regression analysis to integrate autoantibody and clinical data permits accurate prediction of clinical manifestations with complex etiologies in pSLE.

platform_organism:
Escherichia coli
Gallus gallus
Homo sapiens
Bos taurus
Oryctolagus cuniculus
Mus musculus

overall_design: We analyzed new-onset pSLE patients (n=45) and healthy controls (n=17)

first: David

first: Imelda

last: Balboni

first: Paul

last: Utz


title: miRNAs expression profiling from mouse heart after Ang II (angiotensin II) (1500ng/kg/min) infusion for 3 days and 7 days

status: Public on Jun 05 2015

city: Beijing

first: xia

last: wang

address: No.10 Xitoutiao, You An Men

institute: Captial medical university

summary: Angiotensin II stimulates fibroblast proliferation and substantially alters gene expression patterns leading to cardiac remodeling, but the mechanisms for such differences are unknown. MicroRNAs are a novel mechanism for gene expression regulation. Herein we tested the miRNAs patterns in mouse heart using microarray assay, and investigated their role in angiotensin II-induced cardiac remodeling.

overall_design: In this study, nine samples (three groups) from mouse were used to acquire the miRNA expression profiling and the function of the abudant miRNAs in the heart were analyzed by bioinformatic methods.

first: Hui-Hua

last: Li

first: Xia

last: Wang


title: Seasonal gene expression kinetics between diapause phases in Drosophila virilis group speciesand overwintering differences between diapausing and non-diapausing females

status: Public on Jun 03 2015

city: Tampere

first: Tiina

middle: Susanna

last: Salminen

address: Biokatu 6, Finn-Medi 1

department: BioMediTech

institute: University of Tampere

summary: Most northern insect species experience a period of developmental arrest, diapause, which enables them to survive over the winter and postpone reproduction until favorable conditions. We studied the timing of reproductive diapause and its long-term effects on the cold tolerance of Drosophila montana, D. littoralis and D. ezoana females in seasonally varying environmental conditions. At the same time we traced expression levels of 219 genes in D. montana using a custom-made microarray. We show that the seasonal switch to reproductive diapause occurs over a short time period, and that overwintering in reproductive diapause has long-lasting effects on cold tolerance. Some genes, such as Hsc70, Jon25bi and period, were upregulated throughout the diapause, while others, including regucalcin, couch potato and Thor, were upregulated only at its specific phases. Some of the expression patterns induced during the sensitive stage, when the females either enter diapause or not, remained induced regardless of the later conditions. qPCR analyses confirmed the findings of the microarray analysis in D. montana and revealed similar gene expression changes in D. littoralis and D. ezoana. The present study helps to achieve a better understanding of the genetic regulation of diapause and of the plasticity of seasonal responses in general.

platform_organism:
Drosophila virilis
Drosophila montana

overall_design: Custom made DNA microarray for Drosophila montana and D. virilis. Current experiment includes 8 samples (7 to 250 days old diapausing or non-diapausing D. montana females) with two or three biological replicates

middle: S

first: Laura

last: Vesala

first: Asta

last: Laiho

first: Mikko

last: Merisalo

first: Anneli

last: Hoikkala

first: Maaria

last: Kankare


title: Transcriptomic comparison of chlorhexidine tolerant and sensitive Salmonella Typhimurium

status: Public on Jun 06 2015

address: Belfield

department: School of Public Health, Physiotherapy & Sports Science

institute: University College Dublin

summary: Transcriptional profiles of a chlorhexidine tolerant Salmonella Typhimurium were compared to its, chlorhexidine sensitive, isogenic progenitor isolate. RNA was extracted from mid-log phase cells from both isolates, without chlorhexidine exposure and following exposure to 1 µg/ ml of chlorhexidine for 30 minutes. Transcriptional profiles of the tolerant isolate were compared to the sensitive isolate, with and without chlorhexidine exposure.

first: Orla

last: Condell

first: Karen

last: Power

first: Kristian

last: Händler

first: Sarah

last: Finn

first: Áine

last: Sheridan

first: Kjell

last: Sergeant

first: Jenny

last: Renaut

first: Catherine

last: Burgess

last: Hinton

first: Jarlath

middle: E

last: Nally


title: Gene expression profiling of Phalaenopsis orchids

status: Public on Jun 02 2015

city: Taipei

first: Ming Che

last: Shih

address: No.128, Sec. 2, Academia Rd., Nangang Dist

department: Agricultural Biotechnology Research Center

country: Taiwan

institute: Academia Sinica, Taiwan

summary: cDNA sequences were collected from Orchidstra database (http://orchidstra.abrc.sinica.edu.tw/). 43662 genes were presented and 67038 probes were designed on this chip.

overall_design: Expression profiling was analyzed using a customized oligonucleotide array probed with RNA extracted from various tissues from Phalaenopsis orchids including leaf, root, floral organs and flower stages after pollination.

first: Ming-Che


title: Comparative transcriptional profiling analysis of developing melon (Cucumis melo L.) fruit from climacteric and non-climacteric varieties

status: Public on Jun 01 2015

city: Perth

first: Montse

last: Saladie-Foraste

state: Western Australia

address: 35 Stirling Highway; Crawley

department: School of Chemistry and Biochemistry

country: Australia

institute: University of Western Australia

summary:
Investigation gene expression level changes in four different melon fruits at four different developmental satges
Transcriptomic analysis of developing melon fruits from two climacteric (cvs. Védrantais and Dulce) and two non-climacteric (cv. Piel de sapo and accession PI 161375) at 15, 25, 35 Days After Pollination (DAP) and Harvest stage

overall_design: The microarray contained 75,000 probes based on a previously validated microarray [Mascarell-Creus et al. 2009] but arranged in a modified 4-plex design, covering 17,443 melon unigenes derived from expressed sequence tags. These unigenes represent 10,649 genes in the melon genome (38% of the total predicted genes). A total of 48 samples were submitted. Only 47 were hybridize and a total of 41 were used to normalize the data.

first: Montserrat

last: Saladié

first: Joaquin

last: Cañizares

first: Michael

last: Phillips

first: Manuel

last: Rodriguez-Concepcion

first: Christian

last: Larrigaudière

first: Yves

last: Gibon

first: Mark

last: Stitt

first: John

last: Lunn

first: Jordi

last: Garcia-Mas


title: Gene expression during dark-induced leaf abscission in Populus x tremula

status: Public on May 28 2015

city: Umeå

first: Urs

last: Fischer

state: Schweden

address: Swedish Agricultural University

department: Forest Genetics and Plant Physiology

country: Sweden

institute: Umeå Plant Science Centre

summary:
Identification of abscission regulated genes
Genes involved in auxin transport and response are down-regulated in axils of shaded leaves.

overall_design: For dark-induction experiments, fully expanded leaves with a petiolar angle of 75 ° to 90 ° from 1.5 m to 2 m tall trees were selected. Leaf blades were covered with aluminum bags for 9 days under standard greenhouse conditions. Control samples were bagged in transparent plastic bags of the same weight.

first: Xu

last: Jin


title: Microarray gene expression analysis: Batch effect removal improves the cross-platform consistency

city: Odense C

first: Martin

middle: Jakob

last: Larsen

address: Sdr. Boulevard 29

department: Dept. of Clinical Genetics

country: Denmark

institute: Odense University Hospital

summary: Microarray is a powerful technique that has been used extensively for genome-wide gene expression analysis. Several different microarray technologies are available, but lack of standardization makes it challenging to compare and integrate data from different platforms. Furthermore, batch related biases within datasets are common, but are often not tackled prior to the data analysis, potentially affecting the end results. In the current study, a set of 234 breast cancer samples were analyzed on two different microarray platforms. The aim was to compare and evaluate the reproducibility and accuracy of gene expression measurements obtained from our in-house 29K array platform with data from Agilent SurePrint G3 microarray platform. The 29K dataset contained known batch-effects associated with the fabrication procedure. We here demonstrate how the use of ComBat batch adjustments method can unmask true biological signals by successfully overcoming systematic technical variations caused by differences between fabrication batches and microarray platforms. Paired correlation analysis revealed a high level of consistency between data obtained from the 29K gene expression platform and Agilent SurePrint G3 platform, which could be further improved by ComBat batch adjustment. Particularly high-variance genes were found to be highly reproducibly expressed across platforms. Furthermore, high concordance rates were observed both for prediction of estrogen receptor status and intrinsic molecular breast cancer subtype classification, two clinical important parameters. In conclusion, the current study emphasizes the importance of utilizing proper batch adjustment methods to reduce systematically technical bias when comparing and integrating data from different fabrication batches and microarray platforms.

overall_design: This study was performed on a series of 243 frozen primary breast tumors obtained from the bio-banks of the Dept. of Pathology, Odense University Hospital and the Danish Breast Cancer Cooperative Group (DBCG). The tumor samples comprise a subset of a larger series of 253 tumor samples previously reported. Breast tumor tissues from 120 patients with germline mutations in BRCA1 (n = 33) or BRCA2 (n = 22) or familial non-BRCA1/2 cases with no detectable germline mutation in BRCA1 or BRCA2 (n = 65) were included in the study.

first: Mads

last: Thomassen

first: Qihua

last: Tan

first: Kristina

middle: P

last: Sørensen

first: Torben

last: Kruse


title: Two human HCC cells (MHCC97H and MHCC97L): PML-siRNA transfected vs. control

status: Public on Apr 04 2015

city: Shanghai

first: Xin

last: Zhang

state: -- Please select an option --

address: No.180 Fenglin Road, Zhongshan Hospital

institute: Liver Cancer Institution

summary: We found PML was responsible for ATO resistance in HCC cells, PML knockdown cells show better sensitivity to ATO treatment. To further explore the mechanism of PML-induced ATO resistance, we performed a microarray assay to compare the differential gene expression profiles of PML-siRNA-treated (PML knockdown) and negative control siRNA-treated cells.

overall_design: Two-condition experiment, PML-siRNA vs. control cells. Biological replicates: two cell lines and each cell line has 1 control, 1 transfected, independently grown and harvested. One replicate per array. Comparisons were made between PML siRNA group and control group for each cell line


title: Transcriptom analysis of FLT1 regulated genes in metastasis associated macrophages

status: Public on May 14 2015

city: Edinburgh

first: Bin-Zhi

last: Qian

address: 47 Little France Crescent

department: MRC Centre for Reproductive Health

institute: University of Edinburgh

summary: Gene expression changes in metastasis associated macrophage (MAM) with control and FLT1 inhibitory antibody (MF1) were compared using FACS sorted cells from mice bearing pulmonary metastasis of breast tumor cells treated with Ctrl and MF1 antibody

overall_design: A six chip study using total RNA recovered from metastasis associated macrophages from three separate mice treated with FLT1 inhibitory antibody (MF1) and three separate mice treated with control antibody.  Each chip measures the expression level of 42586 genes.

first: Jeffrey

middle: W

last: Pollard


title: Genetic stabilization in Saccharomyces intra- and interspecific hybrids obtained by different hybridization methodologies

status: Public on Mar 30 2015

city: Paterna (Valencia)

first: Laura

last: Pérez Través

address: Avda Catedrático Agustín Escardino

institute: IATA

summary:
In this work, we evaluated the genetic stabilization process, of the intra- (Saccharomyces cerevisiae) and interspecific (S. cerevisiae x Saccharomyces kudriavzevii) hybrids obtained by different non-GMO techniques, under fermentative conditions. Large-scale transitions in genome size, detected by measuring total DNA content, and genome reorganizations in both nuclear and mitochondrial DNA, evidenced by changes in molecular markers, were observed during the experiments. Interspecific hybrids seem to need fewer generations to reach genetic stability than intraspecific hybrids. The largest number of molecular patterns among the derived stable colonies was observed for intraspecific hybrids, particularly for those obtained by rare-mating in which the total amount of initial DNA was larger. Finally, a representative intraspecific stable hybrid underwent a normal industrial process to obtain active dry yeast production as an important point at which inducing changes in genome composition was possible. No changes in hybrid genetic composition after this procedure were confirmed by comparative genome hybridization. According to our results, fermentation steps 2 and 5 –comprising between 30 and 50 generations- suffice to obtain genetically stable interspecific and intraspecific hybrids, respectively.
This work aimed to develop and validate a fast genetic stabilization method for newly generated Saccharomyces hybrids under selective enological conditions. A comparison of the whole stabilization process in intra- and interspecific hybrids showing different ploidy levels, as a result of using different hybridization methodologies, was also made.

overall_design: A stable hybrid strain was compared with itself before and after ADY (active dry yeast) production in order to evaluate the genetic stability of this strain.

last: Pérez-Través

middle: A

last: Lopes

first: Eladio

last: Barrio

first: Amparo

last: Querol


title: Gene expression analysis in sensitive and tolerant Citrus rootstocks under chlorotic conditions

city: Verona

first: Alberto

last: Ferrarini

state: Veneto

address: Strada le Grazie, 15

department: Scientific and Technological Department

country: Italy

institute: University of Verona

summary: Iron chlorosis is one of the major abiotic stresses affecting fruit trees and other crops in calcareous soils. The most evident symptoms are connected to a reduction in growth and yield and in the interveinal chlorosis of leaves.   A custom CombiMatrix 90K microarray was used to identify candidate genes involved in the citrus response to iron deficiency stress, comparing Tarocco Scirè orange [Citrus sinensis (L.) Osbeck] grafted on two different rootstocks, Swingle citrumelo (C. paradisi × Poncirus trifoliata), high sensitive, and Carrizo citrange (C. sinensis × P. trifoliata), tolerant. RNA was extracted from roots of plants grown in two different soils, one volcanic (0% of active lime) used as control, and the other calcareous (10% of active lime).

sample_organism:
Citrus sinensis x Citrus trifoliata
Citrus x paradisi x Citrus trifoliata

overall_design: Root tips of two citrus rootstocks, Carrizo Citrange and Swingle Citrumelo, respectively tolerant and sensitive to iron deficiency, each grown in two different soil (volcanic, considered as a control with 0% of active lime, and chlorotic, with 10% of active lime) were analyzed. Three biological replicates were taken for each sample, resulting in a total of twelve observations.

first: Concetta

last: Licciardello

first: Biagio

last: Torrisi

first: Paola

last: Tononi

first: Maria

last: Allegra

first: Fabiola

last: Sciacca

first: Vera

last: Muccilli

first: Massimo

last: Delledonne

first: Francesco

last: Intrigliolo

first: Giuseppe

middle: R

last: Recupero


title: A small RNA controlled AND-gate regulates extrachromosomal DNA transfer in Salmonella

status: Public on Mar 24 2015

city: Würzburg

first: Kai

last: Papenfort

state: Würzburg

address: Josef-Schneider Str.2/BAU D15

department: RNA Biology

country: Germany

institute: IMIB Würzburg

summary: Horizontal gene transfer via plasmid conjugation is a major driving force in microbial evolution. Transfer of conjugative plasmids is a complex process that needs to be synchronized with the physiological state of the bacterial host. While several host transcription factors are known to control the plasmid-borne transfer control genes, RNA-based regulatory circuits for host-plasmid communication remain unknown. Here, we describe a post-transcriptional mechanism whereby the Hfq-dependent small RNA, RprA, inhibits transfer of pSLT, the virulence plasmid of Salmonella enterica. RprA employs two different seed pairing domains to recognize and activate the mRNAs of both the sigma-factor S and RicI, a cytoplasmic membrane protein. The latter is a hitherto unknown conjugation inhibitor whose transcription requires S. Together, RprA and S constitute a feed-forward loop with AND-gate logic which tightly controls RicI synthesis for selective suppression of plasmid conjugation under membrane stress. This study reports the first sRNA-controlled feed-forward loop based on double target activation and an unexpected function for a core-genome encoded small RNA in controlling extrachromosomal DNA transfer.

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

overall_design: To determine the targets of the small regulatory RNAs RprA/RprA-proc. in S. Typhimurium, we looked at the effect of a short pulse of RprA/RprA-proc. over-expression on the Salmonella transcriptome. To achieve over-expression, the rprA/rprA proc. genes were cloned in the pBAD plasmid and induced with 0.2% L-arabinose for 10 min. We then extracted the total RNA for transcriptional profiling. A strain carrying the pBAD plasmid w/o insert was used as negative control (also induced by L-arabinose). 3 biological replicates were performed. This sRNA target identification strategy has been described in Papenfort et al; Molecular Microbiology (2006) 62(6), 1674–1688.

first: Elena

last: Espinosa

first: Josep

last: Casadesús

first: Jörg

last: Vogel


title: miR-K12-6-5p expression changes of human transcripts

status: Public on Feb 11 2015

city: Bethesda

first: Joseph

last: Ziegelbauer

state: MD

address: 10 Center Dr. 6N110

institute: NIH / National Cancer Institute

summary:
Transcriptional profiling of BJAB cells expressing miR-K12-6-5p.
To identify host RNA targets of KSHV miRNAs, we took advantage of the observation that RNAs targeted by miRNAs often display small reductions in their steady-state levels, perhaps as a result of their impaired translation. Accordingly, we examined cellular transcript accumulation by array-based expression profiling under four sets of conditions in which KSHV miRNAs were expressed.

overall_design: Cells transfected with negative control miRNA compared to miR-K12-6-5p.

first: Don

last: Ganem


title: What makes the blood cell-based miRNome disease specific? -  miRNA analysis of leukocyte subsets in lung cancer patients and  controls

status: Public on Dec 31 2014

city: Saarbrücken

first: Christina

last: Backes

address: Campus, Building E 2.1

department: Chair for Clinical Bioinformatics

institute: Saarland University

summary: Background: There is ample evidence of blood-born miRNA signatures for various  human diseases. To dissect the origin of disease-specific miRNA expression in  human blood cells, we separately analyzed the miRNome of eosinophilic and  neutrophilic granulocytes, monocytes, B-cells, T-cells, and natural killer cells, each in  lung cancer patients and healthy individuals.  Results: We found specific miRNA expression patterns for each immune cell type and  also depending on the cell origin, line of defense, and function. The overall  expression pattern of each leukocyte subtype showed great similarities between lung  cancer patients and healthy controls. However, for each cell subtype we identified  miRNAs that were deregulated in lung cancer patients including hsa-miR-21, a well-  known oncomiR associated with poor lung cancer prognosis that was up-regulated in  all subtype comparisons of lung cancer versus controls. While the miRNome of cells  of the adaptive immune system allowed only a weak separation between patients and  controls, cells of the innate immune system allowed perfect or nearly perfect  classification.  Conclusions: Leukocytes of lung cancer patients show a cancer-specific miRNA  expression profile. Our data also show that cancer specific miRNA expression pattern  of whole blood samples are not determined by a single cell type. The data indicate  that additional blood components, like erythrocytes, platelets, or exosomes might  contribute to the disease specificity of a miRNA signature.

overall_design: We obtained EDTA and PAXgene blood from 7 healthy subjects and 7 lung cancer patients and isolated the  CD3, CD19, CD15, CD14, and CD56 positive cell fractions from the EDTA blood samples to compare the miRNomes of the cell subsets of healthy individuals versus lung cancer patients.

first: P

last: Leidinger

first: C


title: Myelomatous plasma cells display an aberrant gene expression pattern similar to that observed in normal memory B cells

city: Seville

first: Alicia

last: Báez

address: Avenue Manuel Siurot

institute: IBIS

summary: In the current study we have evaluated the hypothesis that myelomatous plasma cells (mPCs) might simultaneously gain the gene expression pattern acquired by a normal plasma cell (PC) along its maduration process but without losing the expression pattern displayed by memory B cells (MBCs) which confer these cells their long-term viability. Thus, mPCs would aberrantly share both activation and anti-apoptotic gene expression patterns from PCs and MBCs counterparts, respectively. This information may be an important contribution to the field of multiple myeloma (MM) research.

overall_design: 6 samples of normal PCs, 6 samples of mPCs and 5 samples of MBCs paired by two and hybrydized against a pool of 6 samples of naive B cells (NBCs)


title: 5-hydroxymethylcytosine marks promoters in colon that resist hypermethylation in cancer [ExpressionArray]

status: Public on Feb 03 2015

city: Cambridge

first: Chandra

last: Chilamakuri

address: Robinson Way

institute: Cancer Research UK Cambridge Institute

summary: The discovery of cytosine hydroxymethylation (5-hmC) as a mechanism that potentially controls DNA methylation changes typical of neoplasia prompted us to investigate its behavior in colon cancer. 5-hmC is globally reduced in proliferating cells such as colon tumors and the gut crypt progenitors, from which tumors can arise. Here, we show that colorectal tumors and cancer cells express Ten-Eleven Translocation (TET) transcripts at levels similar to normal tissues. Genome-wide analyses show that promoters marked by 5-hmC in normal tissue, and those identified as TET2 targets in colorectal cancer cells, are resistant to methylation gain in cancer. In vitro studies of TET2 in cancer cells confirm that these promoters are resistant to methylation gain independently of sustained TET2 expression. We also find that a considerable number of the methylation gain-resistant promoters marked by 5-hmC in normal colon overlap with those that are marked with poised bivalent histone modifications in embryonic stem cells. Together our results indicate that promoters that acquire 5-hmC upon normal colon differentiation are innately resistant to neoplastic hypermethylation by mechanisms that do not require high levels of 5-hmC in tumors. Our study highlights the potential of cytosine modifications as biomarkers of cancerous cell proliferation.

overall_design: messenger RNA levels were measured in total RNA extracted from primary colon tissues. Normal away are at least 20cm from tumors.

first: Santiago

last: Uribe-Lewis

first: Rory

last: Stark

first: Thomas

last: Carroll

first: Mark

last: Dunning

first: Silvia

last: Halim

first: Sarah

last: Vowler


title: Expression data from cochlea isolated from N-myc mutant and wild-type mice at E15

status: Public on Sep 16 2014

city: Valladolid

last: Schimmang

address: Sanz y Fores 3

institute: CSIC

summary:
The aim of this study consists in detecting genes regulated by N-myc in the murine cochlea
In this data set we present 2688 genes differentially regulated by Nmyc in the murine cochlea. These data serve as a platform for verifying their differential regulation by N-myc via RNA in situ hybridisation or other techniques.

overall_design: 4 Total samples were analyzed. A pairwise comparison between two wild-type and 2 N-myc mutants samples was conducted. Genes with a FDR up to 14% are presented. Briefly, the robust microarray analysis (RMA) algorithm was used for background correction, intra- and inter-microarray normalization, and expression signal calculation. Once the absolute expression signal for each gene (i.e., the signal value for each probe set) was calculated in each microarray, a method [called significance analysis of microarray (SAM)] was applied to calculate significant differential expression and find the gene probe sets that characterized the highly metastatic samples. The method uses permutations to provide robust statistical inference of the most significant genes and provides P valuesadjusted to multiple testing using false discovery rate (FDR).

first: Diego

last: López


title: 5-hydroxymethylcytosine marks promoters in colon that resist hypermethylation in cancer [Methylation27 Array]

overall_design: DNA methylation levels were measured in genomic DNA extracted from primary colon tissues.

last: Lewis


title: Global Microarray Analysis of Bacillus sp. N16-5 Salt Stress Adaptation

status: Public on Jan 03 2015

first: Liang

last: Yin

address: N0.1 Beichen Road

institute: institute of microbiology, chinese acadmy of science

summary: The alkaliphilic halotolerant bacterium Bacillus sp. N16-5 often faces salt stress in its natural habitats. One-color microarrays was used to investigate transcriptome expression profiles of Bacillus sp. N16-5 adaptation reactions to prolonged grown at different salinities (0%, 2%, 8% and 15% NaCl) and the initial reaction to suddenly alter salinity from 0% to 8% NaCl.

overall_design: Salt induced gene expression was measured when culture was grown on different salinities (0%, 2%, 8% and 15% NaCl) to mid-logarithmic phase. And salt induced gene expression was also measured at 0 min, 10 min, 30 min, 60min, 120min after a sudden change salinity from 0% to 8% NaCl.

first: Yanfen

last: Xue

first: Yanhe

last: Ma


title: Molecular homology and difference between spontaneous canine mammary cancer and human breast cancer.

status: Public on Sep 07 2014

city: New York

first: Deli

last: Liu

state: New York

address: 1300 York Ave

institute: Weill Cornell Medicine

type: Genome variation profiling by genome tiling array

summary: Spontaneously occurring canine mammary cancer represents an excellent model of human breast cancer, but is greatly understudied. To better use this valuable resource, we performed whole-genome sequencing, whole-exome sequencing, RNA-seq, and/or high-density arrays on twelve canine mammary cancer cases, including seven simple carcinomas and four complex carcinomas. Canine simple carcinomas, which histologically match human breast carcinomas, harbor extensive genomic aberrations, many of which faithfully recapitulate key features of human breast cancer. Canine complex carcinomas, which are characterized by proliferation of both luminal and myoepithelial cells and are rare in human breast cancer, seem to lack genomic abnormalities. Instead, these tumors have about 35 chromatin-modification genes downregulated and are abnormally enriched with active histone modification H4-acetylation, whereas aberrantly depleted with repressive histone modification H3K9me3. Our findings indicate the likelihood that canine simple carcinomas arise from genomic aberrations, whereas complex carcinomas originate from epigenomic alterations, reinforcing their unique value. Canine complex carcinomas offer an ideal system to study myoepithelial cells, the second major cell lineage of the mammary gland. Canine simple carcinomas, which faithfully represent human breast carcinomas at the molecular level, provide indispensable models for basic and translational breast cancer research.

overall_design: Comparison of CNAs from canine mammary simple carcinomas and complex carcinomas

first: Shaying

last: Zhao


title: Gene expression of flower buds between rdr6-15 and wild-type under drought stress condition

status: Public on Sep 02 2014

city: Yokohama

first: Akihiro

last: Matsui

state: Kanagawa

address: 1-7-22 Suehiro-cho, Tsurumi-ku

department: Center for Sustainable Resource Science

country: Japan

institute: RIKEN

summary: To understand ta-siRNA-mediated regulation network in response to abiotic stress during flower development, gene expression profiles of flowering buds between rdr6-15 and wild-type under moderate drought stress and control condition were measured using microarray. 512 genes were bilaterally regulated by drought stress signal and RDR6-mediated signal.

overall_design: rdr6-15 and wild-type plants (Arabidopsis thaliana ecotype Columbia) were grown on 30g of vermiculite soil of plastic pot for 2 weeks. Then, water depletion (drought stress treatment) was applied for 1 week. Water content of the soil was decreased to less than 20%. 10 flower buds were collected for each experiment. The experiment was repeated 3-times.

first: Kayoko

last: Mizunashi

first: Maho

last: Tanaka

first: Motoaki

last: Seki


title: miRNA expression in RA and OA human fibroblast-like synoviocytes

status: Public on Sep 01 2015

city: strasbourg

first: philippe

last: georgel

address: 1 Place de l'Hopital

country: France

institute: strasbourg university

summary:
Homo sapiens
microRNAs (miRNAs) are invovolved in the regulation of multiple cellular processes and have been linked to many conditions in humans, including rheumatic diseases such as rheumatoid arthritis (RA). Here, we used high throughput expression analysis to assess the overall miRNA expression level in FLS isolated from RA patients in comparison with miRNA expressed in FLS from osteoarthritic (OA) patients.

overall_design: FLS isolated from synovial biopsies from 4 RA and 4 OA patients were cultivated for 4 passages. Cells were lysed and RNA purified (Trizol). Then miRNA expression was performed using the Qiagen  Human miRNome miScript miRNA PCR Array (V16.0, 384-well) profiling the expression of the 1066 most abundantly expressed and best characterized miRNA sequences in the human miRNA genome (miRNome) as annotated in miRBase Release 16 (www.mirbase.org).

first: Philippe

last: Georgel

first: Ghada

last: Alaseh


title: Overall functional diversity of microbial communities in three full-scale activated sludge bioreactors

city: Beijing

first: Yu

last: Xia

state: Beijing

address: Tsinghua University, Haidian District

department: Environmental school

institute: Tsinghua Univeristy

summary: Understanding microbial community diversity is thought to be crucial for improving process functioning and stabilities of wastewater treatment systems. However, current studies largely focus on taxonomic groups based on 16S rRNA, which are not necessarily linked to functioning, or a few selected functional genes. Here we launched a study to profile the overall functional genes of microbial communities in three full-scale wastewater treatment systems. Triplicate activated sludge samples from each system were analyzed using a high-throughput metagenomics tool named GeoChip 4.2, resulting in the detection of 38,507 to 40,647 functional genes. A high similarity of 75.5% to 79.7% shared genes was noted among the nine samples. Moreover, correlation analyses showed that the abundances of a wide array of functional genes were associated with system performances. For example, the abundances of overall nitrogen cycling genes had a strong correlation to total nitrogen (TN) removal rates (r = 0.7647, P < 0.01). The abundances of overall carbon cycling genes were moderately correlated with COD removal rates (r = 0.6515, P < 0.01). Lastly, we found that influent chemical oxygen demand (COD inf) and total phosphorus concentrations (TP inf), and dissolved oxygen (DO) concentrations were key environmental factors shaping the overall functional genes. Together, the results revealed vast functional gene diversity and some links between the functional gene compositions and microbe-mediated processes.

platform_organism: Bacteria Archaea Eukaryota Viruses

overall_design: Three full-scale wastewater treatment systems located in the same city were investigated. Triplicate samples were collected in each site.

first: Xianghua

last: Wen


title: Autophagy mediates the mitotic senescence transition

status: Public on Jul 31 2014

first: Chandra

last: Chilamakuri

summary: ER:RAS-G12V expressing IMR90 cells were given 100nM 4-OHT and assessed for transcriptional profiling at various time points.

overall_design: IMR90 cells expressing a 4-hydroxytamoxifen (4-OHT) inducible estrogen receptor (ER)-coupled RAS-G12V (ER:RAS-G12V) were given 100nM 4-OHT for these eight time points (0, 2, 8, 24hrs, 2, 4, 6 and 8days) then analysed for transcriptional profiling using the illumina expression array platform (human-6 v2 Expression BeadChips). There were three biological replicates (batch A, B and D) for each of the time points.

first: Masako

last: Narita

first: Suraj

last: Menon


title: Expression data from neuroblastoma of TH-MYCN/KI Alk mice

status: Public on Jun 24 2014

city: paris

first: Alex

last: Cazes

state: Please select...

address: 26 rue d'Ulm

institute: Institut Curie

summary: Neuroblastoma is an embryonal neoplasm that remains of dramatic prognosis in its aggressive forms. Activating mutations of the ALK tyrosine kinase receptor have been identified in sporadic and familial cases of this cancer. We generated knock-in mice carrying the two most frequent Alk mutations observed in neuroblastoma patients. We used microarrays to detail the global programme of gene expression underlying the impact of ALK mutations on neuroblastoma formation in a MYCN amplified background.

overall_design: We selected several murine neuroblastoma tumors for RNA extraction and hybridization on Affymetrix microarrays. We generated three groups of tumors:  10 MYCN amplified tumors, 11 MYCN amplified/ALK F1174L tumors and 10 MYCN amplified/ALK R1275Q tumors.

first: Isabelle

last: Janoueix-Lerosey


title: Preclinical analysis of acquired resistance after prolonged efficacious metronomic oral topotecan chemotherapy plus pazopanib therapy in advanced ovarian carcinoma

status: Public on Feb 04 2014

city: Montreal

first: Maria

middle: Luz

last: Jaramillo

state: Quebec

address: 6100 Royalmount Ave

country: Canada

institute: National Research Council of Canada

summary: An alternative or follow-up adjunct to conventional maximum tolerated dose (MTD) chemotherapy now in advanced phase III clinical trial assessment is metronomic chemotherapy?the close regular administration of low doses of drug with no prolonged breaks. A number of preclinical studies have shown metronomic chemotherapy can cause long term survival of mice with advanced cancer, including metastatic disease, in the absence of overt toxicity, especially when combined with targeted antiangiogenic drugs. However, similar to MTD chemotherapy acquired resistance eventually develops, the basis of which is unknown. Using a preclinical model of advanced human ovarian (SKOV-3-13) cancer in SCID mice, we show that acquired resistance can develop after terminating prolonged (over 3 months) successful therapy utilizing daily oral metronomic topotecan plus pazopanib, an oral antiangiogenic tyrosine kinase inhibitor (TKI). Two resistant sublines were isolated from a single mouse, one from a solid tumor (called KH092-7SD, referred to as 7SD) and another from ascites tumor cells (called KH092-7AS, referred to as 7AS). Using these sublines we show acquired resistance to the combination treatment is due to tumor cell alterations that confer relative refractoriness to topotecan. The resistant phenotype is heritable, associated with reduced cellular uptake of topotecan and could not be reversed by switching to MTD topotecan or to another topoisomerase-1 inhibitor, CPT-11, given either in a metronomic or MTD manner nor switching to another antiangiogenic drug, e.g. the anti-VEGFR-2 antibody, DC101, or another TKI, sunitinib. Thus, in this case cross resistance seems to exist between MTD and metronomic topotecan, the basis of which is unknown. However, gene expression profiling revealed several potential genes that are stably upregulated in the resistant lines, that previously have been implicated in resistance to various chemotherapy drugs, and which, therefore, may contribute to the drug resistant phenotype.

overall_design: Two-condition experiment, ovarian cell line (SKOV-3-13) sensitive to daily oral metronomic topotecan plus pazopaniband treatemnt compared to two in- vivo selected resistant sublines from a solid tumor (called KH092-7SD) and another from ascites tumor cells (called KH092-7AS). Biological replicates: 4 independently grown and harvested cell line passages. Two technical replicate per condition (including dye swap).

first: William

last: Cruz-Muñoz


title: Characterization of A. baumannii Mitomycin C (MMC)  response

status: Public on Nov 14 2013

city: A CORUÑA

first: JESUS

last: ARANDA

address: AS XUBIAS

institute: CHUAC

summary: Transcriptional profiling of A. baumannii ATCC 17978 comparing treated-MMC cultures with non-MMC treated cultures

overall_design: Two-condition experiment A. baumannii 17978 MMC+ vs A. baumannii 17978 MMC-. Biological replicates:3, Technical replicates:2

first: Margarita

last: Poza

first: Jesús

last: Aranda

first: Germán

last: Bou


title: Streptococcus mutans UA159 with or without 8.4% oxygen vs. nox mutant strain. pH5

status: Public on Apr 01 2014

city: Rochester

first: Roberta

middle: C

last: Faustoferri

state: NY

address: 601 Elmwood Ave. Box 611

department: Center for Oral Biology

country: USA

institute: University of Rochester Medical Center

summary: Transcriptional analysis of the effects of oxygen concentraion in S. mutans

overall_design: RNA was extracted from 3 or 4 replicate samples of S. mutans UA159, UA159 grown in 8.4 % oxygen concentration and MU1020 (∆nox) grown in continuous culture to steady-state pH values of 5.  RNA was labeled with Cy3.  For each replicate, labeled RNA was hybridized to slides along with Cy5-labeled reference RNA, extracted from S. mutans UA159 cultures grown to mid-log.

first: Jonathon

last: Baker

first: Adam

middle: M

last: Derr

first: Robert

last: Quivey


title: complex i-Analysis of complex I mutants

status: Public on Sep 10 2014

city: evry

first: Soubigou-Taconnat

last: Ludivine

address: 2 rue gaston crémieux

department: URGV

institute: INRA

summary: rs12-03_complex-i - complex i - Can we identify differences between mutants affecte din different subunits of complex I - direct comparison between col-0 (wild type) and 4 mutants, each mutants having different levels of residual complex I. Three biological replicates were processed

overall_design:
12 dye-swap - gene knock out
The levels of residual complex I for the 4 mutants are as follows: mwfe (5%), 18K (traces), ca2 (10%), and 51K (0%).

first: Sandrine

last: Balzergue

first: Ludivine

last: Taconnat

first: Etienne

last: Meyer

first: Marie-Laure

last: Martin-Magniette


title: HIV gp120 modulates the vaginal transcriptome

status: Public on Mar 01 2014

city: Mumbai

first: Atmaram

last: Bandivdekar

state: Maharashtra

address: Jehangir Merwanji Street

department: Division of Biochemistry

country: India

institute: National Institute for Research in Reproductive Health, Indian Council of Medical Research

summary: During sexual transmission of HIV-1 from male to female partners, the vagina is the initial site of contact with HIV infected semen. The mechanism of HIV traversing the CD4 negative multi-layered stratified squamous epithelial barrier of the vagina to infect sub-epithelial susceptible immune cells, is hitherto unknown. HIV gp120 binds to several host proteins on vaginal epithelial cells. To gain an insight into the physiologic changes that may occur in vaginal epithelial cells in response to interactions with HIV gp120, and obtain an understanding of the molecular mechanisms by which HIV breaches the vaginal epithelium, a global snap shot of gene expression profiles in the vaginal epithelial cell line Vk2/E6E7, treated with HIV gp120 was determined. The vaginal epithelial cell line Vk2/E6E7 was treated with HIV gp120 (83nM) for 24 hr, and Agilent one colour, microarrays were performed.

overall_design: Agilent one-color experiment,Organism: Human ,Agilent-Custom Whole Genome Human 8x60k designed by Genotypic Technology Pvt. Ltd. (AMADID: 027114), Labeling kit: Agilent Quick-Amp labeling Kit (p/n5190-0442)

middle: H

first: Deepak

middle: N

last: Modi

first: Sashaina

last: Fanibunda


title: Identification of the phosphotransacetylase (pta) and acetate kinase (ackA) regulons in Streptococcus mutans UA159

status: Public on May 11 2013

city: Busan

first: Jeong Nam

last: Kim

address: Biology Building 402, Busandaehang-ro, 63beon-gil 2, Geumjeong-gu

department: Microbiology

country: South Korea

institute: Pusan National University

summary: Transcriptional comparisons between wild-type Streptococcus mutans UA159 and two mutant strains (∆ackA and ∆ackA pta).

overall_design: On growth condition in defined FMC medium, WT vs. either ∆ackA or ∆ackA pta mutants. Biological replicates: 10 control, 5 each mutant, independently grown and harvested. One replicate per array.

last: Burne


title: Gene expression signatures for MMP19 full length cDNA transfection in A549 cells.

status: Public on Jan 11 2013

city: Pittsburgh

first: Guoying

last: Yu

state: PA

address: 3500 Terrace St., W1200

department: Departmnet of Medicine

institute: University of Pittsburgh

summary: To further understand the role of MMP19 in IPF, particularly in genotype and phenotype changes, we have employed whole genome microarray expression profiling as a discovery platform to identify the target genes of MMP19 in epithelial cells. Gene expression analysis showed that 8358 genes were differentially expressed at p-value 0.05 level and 748 genes were significantly changed with MMP19 expression, which covers matrix protien and cell proliferation, motality and phenotype changes (EMT). Among them, PTGS2 was revealed as one of the most significantly up-regulated genes. And PTGS2 up-regulation in IPF lungs was verified by immunohistochemical (IHC), qRT-PCR and Western-blot as well.

overall_design: A549 is a typical epithelial cell line from ATCC which are widely used in the lung cell biology studies in vitro. To define the role of MMP19 in epithelial cells, we employed Agilent whole genome gene expression microarray profiling to identify genotype alteration with overexpression of MMP19 to find the target genes of MMP19, further to explore the function of MMP19 in the unique microenironment of IPF


title: Comparison of genomic H3K9ac status in CD4 T cells with diverse progress of chronic hepatitis B

status: Public on Aug 28 2012

city: Xi'an

first: ke

last: wang

state: Shaanxi

address: Yanta west road 276#

department: First Affiliated Hospital of Medical College

country: China

institute: Xi'an Jiaotong University

type: Genome binding/occupancy profiling by genome tiling array

summary:
Histone 3 lysine 9 acetylation (H3K9ac) at transcription initiation sites is a well known marker for actively initiating and transcribing genes.The purpose of the present study was to investigate the association between H3K9ac and diverse progress of HBV infection.
We employed chromatin immunoprecipitation microarray (ChIP-chip) technology to profile and compare the variations of genes H3K9ac in CD4 T cells of the CHB patients at the different clinic phases. The results showed there were lots of different genes with H3K9ac among the study groups.

overall_design: Comparison of genomic H3K9ac status in CD4 T cells from CHB patients at the different clinic phases

first: Ke

last: Wang

first: Hongli

last: Liu

first: Yingli

last: He

first: Tianyan

last: Chen

first: Xiaohua

last: Ma

first: Li

last: Jin

first: Qian

last: Yang

first: Yingren

last: Zhao


title: Expression data from Chicken duodenum

status: Public on Aug 02 2012

city: Athens

first: Samuel

last: Aggrey

state: GA

address: 110 Cedar Street

department: Poultry Science

institute: University of Georgia

summary: The objective of this study was to decipher the molecular basis of feed efficiency in meat-type chicken using duodenum tissues from a chicken population divergently selected for residual feed intake (RFI). Residual feed intake is the deviation of expected feed intake from actual feed intake. Chickens that consume less feed than expected are efficient (LRFI) and chickens that consume more feed than expected are inefficient (HRFI). A divergent selection for RFI was undertaken using an unselected random bred chicken population. RFI at day 35-42 was used as a criterion for selecting low (LRFI) and high (HRFI) RFI. Duodenum tissues were collected from 16 male chickens under sterile conditions experimentation. Tissues were collected from 4 males at days 35 and 42 in each line.

overall_design: Duodenum at 35 and 42 days from a chicken population divergently selected for residual feed intake were utilized for RNA extraction and hybridization on Affymetrix microarrays.


title: Regulating the angiogenic balance in tissues

status: Public on Dec 03 2012

city: Princeton

first: Eric

middle: Jungwoo

last: Suh

state: NJ

address: 14 Washington Rd

department: Molecular Biology

institute: Princeton University

summary: A balance between angiogenesis inducers and inhibitors in the microenvironment controls the rate of new blood vessel formation. We hypothesized that fibroblasts, an important cellular constituent of the tissue stroma, secrete molecules that contribute to this balance. We further hypothesized that fibroblasts secrete molecules that promote angiogenesis when they are in a proliferative state and molecules that inhibit angiogenesis when they are not actively cycling (quiescent). Microarray analysis revealed that angiogenesis inducers and inhibitors are regulated as fibroblasts transition into a quiescent state and reenter the cell cycle in response to changes in serum. To assess whether changes in transcript levels result in changes in the levels of secreted proteins, we collected conditioned medium from proliferating and quiescent fibroblasts and performed immunoblotting for selected proteins. Secreted protein levels of the angiogenesis inhibitor pigment epithelium derived factor (PEDF) were higher in quiescent than proliferating fibroblasts. Conversely, proliferating fibroblasts secreted increased levels of the angiogenesis inducer vascular endothelial growth factor-C (VEGF-C). For the angiogenesis inhibitor thrombospondin-2, quiescent cells secreted a prominent 160 kDa form in addition to the 200 kDa form secreted by proliferating and restimulated fibroblasts. Using immunohistochemistry we discovered that fibroblasts surround blood vessels and that the angiogenesis inhibitor PEDF is expressed by quiescent fibroblasts in uterine tissue, supporting a role for PEDF in maintaining quiescence of the vasculature. This work takes a new approach to the study of angiogenesis by examining the expression of multiple angiogenesis regulators secreted from a key stromal cell, the fibroblast.

overall_design: mRNAs were analyzed by two color microarray from a human neonatal dermal fibroblasts cell line over a timecourse of serum starvation and serum restimulation.

first: Elizabeth

last: Pollina

first: Aster

last: Legesse-Miller

first: Erin

last: Haley

first: Tracy

last: Goodpaster

first: Julie

last: Randolph-Habecker

first: Hilary

last: Coller


title: miR-K12-9 expression and inhibition

status: Public on Nov 01 2012

city: Bethesda

first: Joseph

last: Ziegelbauer

address: 10 Center Dr. 6N110

institute: NIH / National Cancer Institute

summary:
Transcriptional profiling of BJAB cells expressing miR-K12-9 and BCBL cells treated with miR-K12-9 inhibitor.
To identify host RNA targets of KSHV miRNAs, we took advantage of the observation that RNAs targeted by miRNAs often display small reductions in their steady-state levels, perhaps as a result of their impaired translation. Accordingly, we examined cellular transcript accumulation by array-based expression profiling under four sets of conditions in which KSHV miRNAs were expressed or inhibited.

overall_design: Cells transfected with negative control miRNA compared to miR-K12-9 or negative miRNA inhibitor compared to miR-K12-9 inhibitor.

first: Don

last: Ganem


title: PPD stimulated PBMCs from tuberculosis patients, latent infectious individuals and healthy controls.

status: Public on Sep 19 2012

city: Shanghai

first: Chanyi

last: Lu

address: 220 Handan Rd

institute: Fudan University

summary: Comprehensively compare the transcriptional difference in PPD stimulated PBMCs from individuals with different tuberculosis infectious status: tuberculosis patients, latent infectious individuals and healthy controls using the microarray analysis.

overall_design: Two-condition experiment, PBMCs vs. PPD-PBMCs. 12 individuals: 4 TB patients, 4 latent infectious individuals and 4 healthy controls.

first: Wenhong

last: Zhang


title: Integrative genomic analysis of sporadic clear cell Renal Cell Carcinoma

status: Public on Dec 01 2011

city: Philadelphia

first: Vijay

last: Dondeti

address: 421 Curie Boulevard, 456 BRB II/III

institute: University of Pennsylvania School of Medicine

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

summary: Human clear cell renal cell carcinoma (ccRCC) is a common cancer of the kidney. We applied an integrated approach to identify important factors that influence carcinogenesis in ccRCC.

overall_design: 33 frozen ccRCC samples were subject to copy number analysis. The data was analyzed to identify factors affecting tumorigenesis. The samples were also stained for HIF-1alpha and HIF-2alpha expression. The tumors were subtyped based on HIF expression and investigated for differences in genetic aberrations.

first: Bradley

last: Wubbenhorst

first: Priti

last: Lal

first: John

middle: D

last: Gordan

first: Kurt

last: D'Andrea

last: Attiyeh

first: M

last: Simon

first: Katherine

middle: L

last: Nathanson