title: Expression data from chick embryonic midbrain over-expressing constitutively active integrin-beta 1 in a hetergenous manner.

city: Edinburgh

first: Katherine

last: Long

address: 5 Little France Drive

department: Centre for Regenerative Medicine

institute: The University of Edinburgh

summary: Integrins have long been known to have a role in adhesion of neural stem cells within the neuroepithelium, but little is known about their role in regulating stem cell behaviour through signalling.  We aimed to investigate the effect of integrin-beta 1 signalling (itgb1) on these cells by transfection of a constitutively active itgb1.  This creates a heterogenous pattern of expression allowing the study of cell-autonomous and non-cell autonomous effects.

overall_design:
Chick embryonic midbrains were electroporated with the CA*b1 construct at E2, onset of neurogenesis, creating a hetergenous pattern of expression.  At E4, cells were FACS sorted into expressing and non expressing and sent for microarray analysis of gene expression.  5-8 embryos were pooled for each replicate.
Contributor: ARK Genomics, Roslin Institute, University of Edinburgh

first: Charles

last: ffrench-Constant


title: Adaptive Evolution and Regulation of a Stress-Activated Transposon in Arabidopsis

status: Public on Jan 31 2016

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 an effect of an ONSEN insertion for a gene network, a genome wide gene expression on the ONSEN inserted lines was analyzed by a microarray. The microarray analysis identified 6,520 and 7,262 significant different expressed genes (3/2 fold or 2/3 fold, FDR < 0.05) in 13-7 and 19-4 respectively under ABA stress.

overall_design: Two of ONSEN inserted lines (13-7, 19-4),  parent line (nrpd1), and wild-type plants (Arabidopsis thaliana ecotype Columbia) were grown on MS medium with and without 2μM ABA for 7 days. Total RNA was extructed from the plants, using  TRI Reagent (Sigma T9424). 100 ng of the isolated tatal RNAs were used for the expresion profiling using the custom array.

first: Hidetaka

last: Ito

first: Maho

last: Tanaka

first: Kei

last: Iida

first: Motoaki

last: Seki


title: miRNA from leukemia cells

status: Public on Jan 20 2016

city: Memphis

first: William

last: Evans

state: TN

address: 262 Danny Thomas Place

department: Pharmaceutical Sciences

country: USA

institute: St Jude Children's Research Hospital

summary: In primary leukemia cells there is a significant over-representation of positively correlated microRNA and mRNA expression (see GSE66708) for genes containing sequences favoring microRNA-duplex DNA triplex formation, suggesting this as a mechanism by which microRNA may enhance gene transcription.

platform_organism:
Homo sapiens
Mus musculus
Rattus norvegicus
Human alphaherpesvirus 1
Human alphaherpesvirus 2
Human betaherpesvirus 5
Murid betaherpesvirus 1
human gammaherpesvirus 4
JC polyomavirus
Human immunodeficiency virus 1
Murid gammaherpesvirus 4
Human gammaherpesvirus 8
Merkel cell polyomavirus
Mus musculus cytomegalovirus 2
Betapolyomavirus hominis
Betapolyomavirus macacae

overall_design: RNA was extracted from fresh leukemic blasts and hybridized to a panel of miRNA probes.

first: Evans

last: William

first: Paugh

last: Steve

first: Bonten

last: Erik


title: Gene expression of human peripheral blood cells of patients with rheumatoid arthritis

status: Public on Dec 31 2015

city: Birmingham

first: S

middle: Louis

last: Bridges

state: Al

address: University Blvd

department: Rheumatology

institute: UAB

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

overall_design: Refer to individual Series


title: Detection of aberrant DNA methylation in undifferentiated and differentiated mouse ES cells compared to normal tissues

city: Jerusalem

first: Deborah

last: Nejman

address: Ein Kerem

country: Israel

institute: Hebrew University

type: Methylation profiling by genome tiling array

summary: Embryonic stem cells can be differentiated in vitro to produce a variety of somatic cell types. We have employed the mDIP method combined with hybridization to a CpG islend microarray .  We show that this differentiation is accompanied by an intrinsic process of extensive aberrant CpG island de novo methylation that includes developmental and cancer target genes.

overall_design: CpG-methylated genomic DNA was enriched using a methyl-DNA immunoprecipitation (mDIP) assay. DNA from the input and bound (enriched) DNA for each sample were labeled and hybridized on the array to define the methylation state of each region.

first: Howard

last: Cedar


title: Gene expression of human peripheral blood cells of patients with rheumatoid arthritis [dataset 2]

summary: Factors responsible for radiographic severity of rheumatoid arthritis (RA) in African-Americans are poorly understood.  We sought to examine genes whose expression in peripheral blood mononuclear cells (PBMCs) is associated with radiographic severity of RA.

overall_design: 20 control samples (from individuals without RA) were compared with 10 early mild, 10 early severe, 10 late mild, and 10 late severe RA samples. All samples were obtained from African-American individuals.

first: Xiangqin

last: Cui


title: ofr1 regulates white-to-opaque switching and mating of Candida albicans (MTLa/α)

status: Public on Dec 29 2015

city: Montreal

first: Yuan

last: Sun

state: Quebec

address: 7141 Sherbrooke Street West

department: Biology Department

country: Canada

institute: Concordia University

summary:
It has been proposed that the ancestral fungus was mating competent and homothallic. However, many mating competent fungi were initially classified as asexual because their mating capacity was hidden behind layers of regulation. For efficient in vitro mating, the essentially obligate diploid ascomycete pathogen C. albicans has to homozygose its mating type locus from MTLa/α to MTLa/a or MTLα/α, and then undergo an environmentally controlled epigenetic switch to the mating competent opaque form. These requirements greatly reduce the potential for C. albicans mating. Deletion of the YciI domain gene OFR1 bypasses the need for C. albicans cells to homozygose the mating type locus prior to switching to the opaque form and mating, and allows homothallic mating of MTL heterozygous strains. This bypass is carbon source dependent and does not occur when cells are grown on glucose. Transcriptional profiling of ofr1 mutant cells shows that in addition to regulating cell type and mating circuitry, Ofr1 is needed for proper regulation of histone and chitin biosynthesis gene expression. It appears that OFR1 is a key regulator in C. albicans, and functions in part to maintain the cryptic mating phenotype of the pathogen.
Distruption of OFR1 gene which encodes a Yci1 related domain in Candida ablicans (MTLa/α) is shown to have white-opaque switching related and mating related gene expression. The expression of histone genes are also positively regulated in some conditions.

overall_design: Four-condition experiment, ofr1 null mutant (MTLa/α) vs. wild type (MTLa/α) on glucose medium; ofr1 null mutant (MTLa/α) vs. wild type (MTLa/α) on GlcNAc medium; ofr1 null mutant (MTLa/α) opaque cells vs. ofr1 null mutant (MTLa/α) white cells on glucose medium; ofr1 null mutant (MTLa/α) opaque cells vs. ofr1 null mutant (MTLa/α) white cells on GlcNAc medium. One replica per array.

first: Sun

last: Yuan

first: Whiteway

last: Malcolm


title: Spitz tumors and melanomas with MET fusion

status: Public on Dec 01 2015

city: San Francisco

first: Iwei

last: Yeh

state: California

address: 1701 Divisadero St. Ste 280

department: Dermatology

institute: UCSF

type: Genome variation profiling by genome tiling array

summary: Oncogenic gene fusions have been identified in many cancers and many serve as biomarkers or targets for therapy. Here we identify six different melanocytic tumors with genomic rearrangements of MET fusing the kinase domain of MET in-frame to six different N-terminal partners. These tumors lack activating mutations in other established melanoma oncogenes. We functionally characterize two of the identified fusion proteins (TRIM4-MET and ZKSCAN1-MET) and find that they constitutively activate the mitogen-activated protein kinase (MAPK), phosphoinositol-3 kinase (PI3K), and  phospholipase C gamma 1 (PLCγ1) pathways. The MET inhibitors cabozantinib (FDA-approved for progressive medullary thyroid cancer) and PF-04217903 block their activity at nanomolar concentrations. MET fusion kinases thus provide a potential therapeutic target for a rare subset of melanoma for which currently no targeted therapeutic options currently exist.

overall_design: The UCSF dermatopathology array comparative genomic hybridizaton database consists of copy number profiles of difficult to classify tumors obtained in the course of clinical practice. These cases were noted to have either a copy number transition within MET with relative gain of the 3' end of the gene or gain of the distal portion of chromosome 7q. There are 6 cases in this series, with one replicate each.

first: Boris

middle: C

last: Bastian


title: Gene expression of human peripheral blood cells of patients with rheumatoid arthritis [dataset 1]

summary: Factors responsible for radiographic severity of rheumatoid arthritis (RA) in African-Americans are poorly understood. We sought to examine genes whose expression in peripheral blood mononuclear cells (PBMCs) is associated with radiographic severity of RA.


title: To screen miRNA expression of SP and MP cells in mutiply myeloma by miRNA array

city: Shanghai

first: Juan

last: Du

state: Shanghai

address: NO.415 Fengyang Road

country: China

institute: Changzheng Hospital

summary: To better understand the molecular mechanisms of SP cells, we screened the miRNAs expression patterns in the SP compared with the MP cells. MiRCURY™ LNA array analysis of sorted SP and MP cells from two relapsed myeloma patients with more than 70% bone marrow plasma cells were performed.

overall_design: In order to identify the miRNA patten between SP and MP cells, the samples were labeled using the miRCURY™ Hy3™/Hy5™ Power labeling kit (Exiqon) and hybridized on the miRCURY™ LNA Array (v.16.0).


title: Gene expression profiling of Human Hepatocellular Carcinoma tissues

status: Public on Nov 04 2015

first: Huiyong

last: Yin

address: 320 Yueyang Road, Xuhui District

institute: Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences

summary:
Hepatocellular carcinoma (HCC) is the fifth most common malignancy of cancer-related deaths worldwide, and prognosis of patients with HCC still remain unsatisfactory. Therefore, more reliable biomarkers for predicting the disease and understanding the mechanisms underlying cancer development need to be found out urgently.
In this study, we explored the clinical significance and role of ALDOB, G6PD in HCC pathogenesis. Here we show that low ALDOB expression with high G6PD expression lead to patients' poor survival and prognosis by remodeling metabolic pathway and increasing tumor proliferation and metastasis. Stat5a regulates ALDOB expression positively but negatively to G6PD expression in mRNA level, simultaneously, ALDOB inhibits G6PD enzymatic activity by protein-protein interaction and we have found one of their interaction sites in ALDOB. These data suggest that ALDOB and G6PD could be potential biomarkers for HCC.

overall_design: We analyzed tissues from 5 hepatocellular carcinoma patients using the GeneChip PrimeView Human Gene Expression Array. Affymetrix microarray assays were performed according to the manufacturer's directions on total RNA isolated from patients' tissues. Array data was processed by Affymetrix Exon Array Computational Tool. No techinical replicates were performed.

first: Yongzhen

last: Tao


title: Exploring transcriptomic diversity in muscle revealed that cellular signaling pathways mainly differentiate five Western porcine breeds

status: Public on Nov 24 2015

city: Castanet tolosan

first: Laurence

last: Liaubet

address: chemin de borde rouge

department: Animal Genetic

country: France

institute: INRA

summary:
Background
Among transcriptomic studies, those comparing species or populations can increase our understanding of the impact of the evolutionary forces on the differentiation of populations. A particular situation is the one of short evolution time with breeds of a domesticated species that underwent strong selective pressures. In this study, the gene expression diversity across five pig breeds has been explored in muscle. Samples came from: 24 Duroc, 33 Landrace, 41 Large White dam line, 10 Large White sire line and 39 Piétrain. From these animals, 147 muscle samples obtained at slaughter were analyzed using the porcine Agilent 44K v1 microarray.
Results
A total of 12,358 genes were identified as expressed in muscle after normalization and 1,703 genes were declared differential for at least one breed (FDR < 0.001). The functional analysis highlighted that gene expression diversity is mainly linked to cellular signaling pathways such as the PI3K (phosphoinositide 3-kinase) pathway. The PI3K pathway is known to be involved in the control of development of the skeletal muscle mass by affecting extracellular matrix - receptor interactions, regulation of actin cytoskeleton pathways and some metabolic functions. This study also highlighted 228 spots (171 unique genes) that differentiate the breeds from each other. A common subgroup of 15 genes selected by three statistical methods was able to differentiate Duroc, Large White and Piétrain breeds.
Conclusions
This study on transcriptomic differentiation across Western pig breeds highlighted a global picture: mainly signaling pathways were affected. This result is consistent with the selection objective of increasing muscle mass. These transcriptional changes may indicate selection pressure or simply breed differences which may be driven by human selection. Further work aiming at comparing genetic and transcriptomic diversities would further increase our understanding of the consequences of human impact on livestock species.

overall_design: A total of 147 individuals were sampled, and came from 5 breeds:  24 Duroc (DU), 33 Landrace (LR), 41 Large White dam line (LWF), 10 Large White sire line (LWM) and 39 Piétrain (PI). These animals were castrates in all breeds except females in PI, and were reared in 10 different batches. Further details can be found in Rohart et al (2012). From these animals, 147 muscle samples obtained at slaughtering  around 100kg and were analyzed using the porcine Agilent 44K v1 microarray.

first: Magali

last: SanCristobal

first: Florian

last: Rohart

first: Christine

last: Lascor

first: Marcel

last: Bouffaud

first: Lidwine

last: Trouilh

first: Pascal

last: Martin

first: Thierry

last: Tribout

first: Thomas

last: Faraut

first: Marie-Jose

last: Mercat

first: Denis

last: Milan

first: Yannick

last: Lippi


title: Five Omic Technologies Are Concordant in Differentiating the Biochemical Characteristics of the Berries of Five Grapevine (Vitis vinifera L.) Cultivars

status: Public on Nov 12 2015

city: Reno

first: Grant

last: Cramer

state: Nevada

address: 1664 N. Virginia St

department: Biochemistry & Molecular Biology

institute: University of Nevada, Reno

summary:
Background: Grape cultivars and wines are distinguishable by their color, flavor and aroma profiles. Omic analyses (transcripts, proteins and metabolites) are powerful tools for assessing biochemical differences in biological systems.

Results: Berry skins of red- (Cabernet Sauvignon, Merlot, Pinot Noir) and white-skinned (Chardonnay, Semillon) wine grapes were harvested near optimum maturity from the same experimental vineyard and ˚Brix-to-titratable acidity ratio. Identical sample aliquots were analyzed for transcripts by grapevine whole-genome oligonucleotide microarray and RNA-seq technologies, proteins by nano-liquid chromatography-mass spectroscopy, and metabolites by gas chromatography-mass spectroscopy and liquid chromatography-mass spectroscopy. Principal components analysis of each of five Omic technologies showed similar results across cultivars in all Omic datasets. Comparison of the processed data of genes mapped in RNA-seq and microarray data revealed a strong Pearson's correlation (0.80). The exclusion of probesets associated with genes with potential for cross-hybridization on the microarray improved the correlation to 0.93. The overall concordance of protein with transcript data was low with a Pearson's correlation of 0.27 and 0.24 for the RNA-seq and microarray data, respectively. Integration of metabolite with protein and transcript data produced an expected model of phenylpropanoid biosynthesis, which distinguished red from white grapes, yet provided detail of individual cultivar differences.

Conclusions: The five Omic technologies were consistent in distinguishing cultivar variation. There was high concordance between transcriptomic technologies, but generally protein abundance did not correlate well with transcript abundance. The integration of multiple high-throughput Omic datasets revealed complex biochemical variation amongst five cultivars of an ancient and economically important crop species.

overall_design: Vitis vinifera L. cv. Cabernet Sauvignon, Chardonnay, Merlot, Pinot Noir, Semillon berries were harvested from Nevada Agricultural Experiment Station Valley Road Vineyard, Reno, NV, USA. Whole-genome microarray analysis was used to assess the transcriptomic response of berry skins at harvest, approximately 24 °Brix (2011 vintage). Vines were grown under water deficit and well-watered conditions. At least two clusters harvested from non-adjacent vines were used for each of five experimental replicates.

first: Ryan

last: Ghan

first: Steven

last: Van Sluyter

first: Uri

last: Hochberg

first: Asfaw

last: Degu

first: Daniel

middle: W

last: Hopper

first: Richard

last: Tillet

first: Karen

last: Schlauch

first: Aaron

last: Fait

first: Paul

middle: A

last: Haynes

middle: R


title: Microbial Biogeography Across a Full-Scale Wastewater Treatment Plant Transect: Evidence for Immigration Between Coupled Processes

status: Public on Nov 03 2015

city: Evanston

first: George

middle: F

last: Wells

state: Illinois

address: 2145 Sheridan Road, Tech A236

department: Civil & Environmental Engineering

institute: Northwestern University

summary: Wastewater treatment plants use a variety of bioreactor types and configurations to remove organic matter and nutrients.  Little is known regarding the effects of different configurations and within-plant immigration on microbial community dynamics.  Previously, we found that the structure of ammonia-oxidizing bacterial (AOB) communities in a full-scale dispersed growth activated sludge bioreactor correlated strongly with levels of NO2- entering the reactor from an upstream trickling filter (Wells et al 2009).   Here, to further examine this puzzling association, we profile within-plant microbial biogeography (spatial variation) and test the hypothesis that substantial microbial immigration occurs along a transect (raw influent, trickling filter biofilm, trickling filter effluent, and activated sludge) at the same full-scale wastewater treatment plant. AOB amoA gene abundance increased >30-fold between influent and trickling filter effluent concomitant with NO2- production, indicating unexpected growth and activity of AOB within the trickling filter. Nitrosomonas europaea was the dominant AOB phylotype in trickling filter biofilm and effluent, while a distinct ‘Nitrosomonas-like’ lineage dominated in activated sludge.  Prior time series indicated that this ‘Nitrosomonas-like’ lineage was dominant when NO2- levels in the trickling filter effluent (i.e., activated sludge influent) were low, while N. europaea became dominant in the activated sludge when NO2- levels were high.  This is consistent with the hypothesis that NO2- production may co-occur with biofilm sloughing, releasing N. europaea from the trickling filter into the activated sludge bioreactor. Phylogenetic microarray (PhyloChip) analyses revealed significant spatial variation in taxonomic diversity, including a large excess of methanogens in the trickling filter relative to activated sludge and attenuation of Enterobacteriaceae across the transect, and demonstrated transport of a highly diverse microbial community via the trickling filter effluent to the activated sludge bioreactor.  Our results provide compelling evidence that substantial immigration between coupled process units occurs and may exert significant influence over microbial community dynamics within staged bioreactors.

sample_organism:
uncultured bacterium
uncultured archaeon

platform_organism: Bacteria Archaea

overall_design: Samples described in this study were obtained at the Palo Alto Regional Water Quality Control Plant (PARWQCP) in Palo Alto, CA on 12 November 2008.  Sampling along a transect within the PARWQCP occurred on 12 November 2008.  Upon temporary shutdown of the rotating distributor arm in one of the trickling filters, a surface PVC media module (0.9 m deep) was removed from the reactor, and 1-3 g biofilm samples were obtained with a sterile spatula, placed in sterile 1.5 ml tubes, weighed, and stored at -20oC.  Concurrently, samples of influent, trickling filter effluent, and activated sludge were obtained.  Activated sludge samples represented a 24-h composite from the combined outlet of all four aeration basins using a Sigma 900 refrigerated automatic sampler (Hach, Loveland, CO). Eight 1.5 ml activated sludge samples were centrifuged onsite for 5 min at 5000 g, decanted, and stored at -20oC.  Raw influent and trickling filter effluent samples were transported on ice to the laboratory, vacuum filtered in 10 ml aliquots onto 0.22 μm Hydrophilic Durapore PVDF filters (25 mm diameter, Millipore, Billerica, MA), and archived at -20oC.  PhyloChip analyses were performed on biological triplicate samples from trickling filter biofilm, trickling filter effluent, and activated sludge, and biological duplicate samples (due to biomass limitations) from the plant influent.

first: Cindy

middle: H

last: Wu

first: Yvette

middle: M

last: Piceno

first: Brad

last: Eggleston

first: Eoin

middle: L

last: Brodie

first: Todd

middle: Z

last: DeSantis

first: Gary

last: Andersen

first: Terry

last: Hazen

first: Christopher

last: Francis

first: Craig

middle: S

last: Criddle


title: The zinc finger protein Mig1 regulates mitochondrial function and azole drug susceptibility in the pathogenic fungus Cryptococcus neoformans

status: Public on Dec 17 2015

city: Lynchburg

first: Michael

last: Price

state: VA

address: 1971 University Blvd.

department: Biology & Chemistry

institute: Liberty University

summary: The opportunistic pathogen Cryptococcus neoformans causes fungal meningoencephalitis in immunocompromised individuals.  In previous studies, we found that the Hap complex in this pathogen represses genes encoding mitochondrial respiratory functions and TCA cycle components under low-iron conditions. The orthologous Hap2/3/4/5 complex in Saccharomyces cerevisiae exerts a regulatory influence on mitochondrial functions and Hap4 is subject to glucose repression via the carbon catabolite repressor Mig1.  In this study, we explored the regulatory link between a candidate ortholog of the Mig1 protein and the HapX component of the Hap complex in C. neoformans.  This analysis revealed repression of MIG1 by HapX and activation of HAPX by Mig1 in low iron conditions, and Mig1 regulation of mitochondrial functions including respiration, tolerance for reactive oxygen species, and expression of genes for iron-consuming and iron-acquisition functions. Consistent with these regulatory functions, a mig1Δ mutant had impaired growth on inhibitors of mitochondrial respiration and ROS inducers.  Furthermore, deletion of MIG1 provoked a dysregulation in nutrient sensing via the TOR pathway and impacted the pathway for cell wall remodeling.  Importantly, loss of Mig1 increased susceptibility to fluconazole thus further establishing a link between azole antifungal drugs and mitochondrial function.  Mig1 and HapX were also required together for survival in macrophages, but Mig1 alone had a minimal impact on virulence in mice.  Overall, these studies provide novel insights into a HapX/Mig1 regulatory network and reinforce an association between mitochondrial dysfunction and drug susceptibility that may provide new targets for the development of antifungal drugs.

overall_design: In this study, transcription profiles of WT and mig1D mutant strains of Cryptococcus neoformans were compared in a dye-swap experiment following 6hr exposure to Low Iron Medium (LIM) or LIM + 100mM FeCl3.

first: Melissa

last: Caza

first: Guanggan

last: Hu

first: John

last: Perfect

first: James

last: Kronstad


title: Genome wide DNA methylation profiling of hyperplasias, primary endometrial cancer and metastases

status: Public on Sep 01 2015

city: London

first: Andrew

middle: E

last: Teschendorff

address: 72 Huntley Street

department: UCL Cancer Institute/Institute for Women's Health

country: United Kingdom

institute: University College London

summary: The Illumina Infinium 450k Human DNA methylation Beadchip was used to obtain DNA methylation profiles across approximately 480,000 CpGs in a total of 96 samples, including  8 hyperplasias, 33 endometrial cancers and 53 metastases, as well as 2 cell-lines.

overall_design: Bisulphite converted DNA from the 96 samples were hybridised to the Illumina Infinium 450k Human Methylation Beadchip

first: Martin

last: Widschwendter

first: Helga

last: Salvesen


title: The long noncoding RNA expression profile of human gallbladder carcinoma identified by microarray analysis

status: Public on Oct 16 2015

first: Jiwen

last: Wang

state: State...

address: Fenglin Road 180

institute: Fudan University

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

summary: Gallbladder carcinoma (GBC) is the most common biliary tract cancer with poor prognosis. Increasing evidences have pointed out that long non-coding RNAs (lncRNAs) play important regulatory roles in cancer biology. The alteration of lncRNAs is associated with many kinds of cancers. However, the contribution of lncRNAs to GBC is still vague. In order to explore the potential lncRNAs involved in GBC, we described lncRNAs profiles in 3 pairs of human GBC tissues and the matched peri-carcinomatous tissues by microarray. Quantitative real-time polymerase chain reaction (qRT-PCR) was used for the validation of the microarray data. To understand potential functions, Gene Ontology (GO), KEGG (Kyoto Encyclopedia of Genes and Genomes) analysis and network analysis were employed to figure out significant pathways. With abundant RNA probes, we detected 1,758 lncRNAs and 1,254 mRNAs differentially expressed in the microarray. Compared with PCT (Para-carcinoma tissue), plenty of lncRNAs were significantly up-regulated or down-regulated in GBC. Our data showed that lncRNAs down-regulated in GBC were much more than those up-regulated. Among them, RP11-152P17.2-006 was the most up-regulated, while CTA-941F9.9 was the most down-regulated. The results of qRT-PCR agreed with the data from the microarray. Pathway analysis indicated that 5 pathways were corresponded to differentially expressed transcripts. The data showed that the expression of lncRNAs in GBC was significantly changed, and a series of new lncRNAs associated with GBC were identified. These results suggested that the functions of lncRNAs might be significant in GBC development and progression.

overall_design: Two-condition experiment, gallbladder cancer tissues vs. para-carcinoma gallbladder tissues. Biological replicates: 3 control replicates, 3 treated replicates.

first: Houbao

last: Liu


title: Effects of PLEKHA7 depletion on miRNA expression

status: Public on Aug 03 2015

city: Charleston

first: Antonis

last: Kourtidis

state: SC

address: 173 Ashley Avenue

department: Regenerative Medicine and Cell Biology

institute: Medical University of South Carolina

summary: Global  miRNAs expression profilling of Caco2 cells after shRNA-mediated knockdown of PLEKHA7

overall_design: Caco2 cells were infected and selected either with a non-target (NT) or with a PLEKHA7-targeting shRNA (shPLEKHA7). Total RNA was isolated from three independent sets of infections and was used to assess total miRNA expression using NanoString's nCounter Human v2 miRNA Expression Assay Kit

first: Jennifer

last: Carr

first: E

last: Thompson

first: Panos

last: Anastasiadis


title: Yeast Whole Genome Analysis - Wild-Type vs kap108∆ cells

status: Public on Jul 18 2015

city: Hamilton

first: Ken

last: Belanger

state: NY

address: 13 Oak Drive

department: Biology

institute: Colgate University

summary:
A total cellular RNA analysis was performed to determine differential gene expression between wild-type and kap108∆ S. cerevisiae cells under both normal and oxidative stress conditions.
Goal was to determine which genes are differentially expressed in the absence of the Kap108 importin, and to see how that differential expression changes with the addition of oxidative stress. This information can then be used to help elucidate the function and transport cargoes of Kap108, which are currently unknown.

overall_design: Two-Channel microarray analysis compared gene expression between wild-type and kap108∆ S. cerevisiae cells under four conditions: pre-oxidative stress, 10 min oxidative stress, 60 min oxidative stress, and 60 min oxidative stress followed by 60 min no oxidative stress. Three biological replicates were performed for each condition.

first: Kenneth

middle: D

first: Ahmet

last: Ay


title: Burkitt Lymphoma beyond MYC translocation:N-MYC and DNA methyl transferases dysregulation

status: Public on Aug 05 2015

city: Bologna

first: Fabio

last: Fuligni

address: Via Massarenti 9

department: Department of Experimental, Diagnostic, and Specialty Medicine Bologna University Medical School

country: Italy

institute: University of Bologna

summary: Identification of miRNA differentially expressed between MYC-translocation positive and and MYC-translocation negative Burkitt Lymphoma and their impact on gene expression profile

overall_design: Study of microRNA profile of MYC-translocation positive and MYC-translocation negative Burkitt Lymphoma cases in order to uncover possible differences at the molecular level

first: Giulia

last: De Falco

first: Maria

last: Ambrosio

first: Anna

last: Onnis

first: Cristiana

last: Bellan

first: Bruno

middle: J

last: Rocca

first: Mohsen

last: Navari

first: Maryam

last: Etebari

first: Lucia

last: Mundo

first: Sara

last: Gazaneo

last: Facchetti

first: Stefano

last: Pileri

first: Lorenzo

last: Leoncini

first: Pier

middle: P

last: Piccaluga


title: The expression profiles of angiogenesis-related genes in the presence or absence of the NUP160-SLC43A3 fusion gene as measured with PCR array

status: Public on Jun 11 2015

city: Kumamoto

first: Naoki

last: Shimozono

institute: Kumamoto university

summary: mRNAs from HDMECs transfected with the control vector or the fusion gene were prepared, and the mRNA expression profiles were evaluated using PCR arrays. The raw threshold cycle (Ct) was normalized using the values of housekeeping gene.

overall_design: For PCR array, first-strand cDNA was synthesized from RNA using RT2 First Strand Kit (Qiagen). cDNA was mixed with RT2 SYBR Green/Rox qPCR Master Mix (Qiagen), and the mixture was added to 96-well Human Angiogenesis PCR Array (Qiagen). Real-time PCR was performed on Takara Thermal Cycler Dice TP800 (Takara Bio, Shiga, Japan). The raw Ct data were normalized using the values of housekeeping gene.


title: Comparison of CD8+ memory T-cells from fresh and high density precultured PBMC.

status: Public on Jun 09 2015

city: Würzburg

first: Claus

middle: Juergen

last: Scholz

address: Josef-Schneider-Str. 2

department: Core Unit SysMed

country: Germany

institute: University Hospital Würzburg

summary:
High density cultured CD8+ memory T-cells from peripheral blood mononuclear cells (PBMC) were found to be more sensitive towards antigenic stimulation.
We used microarrays to detail the global programme of gene expression underlying differences in the cell density of human PBMC and identified genes that are significantly up- or downregulated dependent on the cell density of PBMC.

overall_design: Paired analysis of CD8+ memory T-cells from fresh and high density precultured PBMC from three healthy donors.

first: Julia

last: Wegner

first: Thomas

last: Hünig


title: Pichia pastoris Glucose/Methanol comparison

status: Public on Aug 31 2015

city: Wien

first: Alexandra

middle: Bettina

last: Graf

address: Muthgasse 18

department: Applied Biotechnology

country: Austria

institute: University of Natural Resources and Life Sciences, Vienna

summary: Comparison of transcription profile of Pichia pastoris cells grown on Glucose medium with Pichia pastoris cells grown on Methanol/Glycerol medium, the fermentations were done in a chemostat.

overall_design: 2 color experiment in reference design. Pichia pastoris reference mix [mixed pool of Pichia pastoris cells sampled from various conditions including cells grown on glycerine, glucose and methanol, on full andminimal medium, in stationary and exponential growth phase, and in different stress states]

first: Markus

last: Buchetics

first: Hannes

last: Rußmayer

first: Minoska

last: Valli

middle: B

first: Diethard

last: Mattanovich

first: Brigitte

last: Gasser


title: Single-cell transcriptome profiling for metastatic renal cell carcinoma patient-derived cells [aCGH]

status: Public on Sep 18 2015

city: Seoul

first: Kyu-Tae

last: Kim

address: Irwon-Ro 81

department: Samsung Genome Institute

country: South Korea

institute: Samsung Medical Center

summary: Clear cell renal cell carcinoma (ccRCC) initiated from the renal epithelium is the most prevalent histological type of adult kidney cancers. Dissecting intratumoral heterogeneity (ITH) of ccRCC has leveraged to extend our knowledge on how primary tumors harboring driver mutations evolve and spread to other sites. The cellular fractions within and across the primary (pRCC) and metastatic RCC (mRCC) are heterogeneous in both their genetic and biological features determining the variability in clinical aggressiveness and sensitivity to the therapy. To achieve sustainable therapeutic benefit with targeted agents in mRCC, the effective target should focus on signaling pathways that are related to driver mutations occurred early in the clonal evolution of the disease and thus should be common to primary tumor and metastatic sites. Considering that extensive genetic heterogeneity may result in drug response variability among patients and treatment resistance, the tailored strategies for metastatic RCC is urgently needed. Here, we analyze single-cell RNA-seq (scRNA-seq) data from a matched primary RCC (pRCC) and lung metastasis (mRCC) to dissect ITH at the highest resolution to date with the objective of discovering the better therapeutic regimen.

overall_design: In order to identify successful clonal propagation from patient to PDX samples and understand pathogenesis from primary to metastatic RCC, we performed whole-exome sequencing (WES, n=4) and matched aCGH (n=4) on bulk tumor samples. And we utilized single-cell RNA sequencing (scRNA-seq) to model and dissect functional heterogeneity acroass primary and metastatic RCC tumors. We checked whether of capturing live one cell, not more cells, in microfluidics by fluorescent microscopic observation. To construct RNA sequencing libraries, we performed further quality controls including adequate quantities and qualities of amplified transcriptomes respectively from single cells. Tumor cells from the parental mRCC (n=34), PDX-mRCC (n=36) and PDX-pRCC (n=46) were finally analyzed in this study after filtering out poor quality cells.

first: Hye

last: Lee

first: Hae-Ock

first: Kyeung

last: Joo

first: Woong-Yang

last: Park


title: Impact of red blood cells on genome-wide DNA methylation and expression analyses of cord blood hematopoietic cells

status: Public on Oct 02 2015

city: Vancouver

first: Wendy

last: Robinson

state: BC

address: 950 W 28th Ave

department: Medical Genetics

institute: University of British Columbia

summary: Genome-wide DNA methylation (DNAm) studies have been extremely useful to understand hematopoiesis in humans. For cell-specific epigenetic studies, fluorescence-activated cell sorting (FACS) is the gold standard technique to isolate homogeneous cell populations of interest. However, in cord blood, the DNAm signature of isolated hematopoietic cells may be significantly altered by heterotopic interactions with nucleated red blood cells (nRBCs) that go undetected during conventional cell sorting. Using the Illumina 450K array, genome-wide DNAm profiles of the following cell types were obtained: (1) T lymphocytes, monocytes, and nRBCs isolated using a “standard” strategy lacking exclusion for erythroid lineage markers; and (2) CD4 and CD8 T lymphocytes, B lymphocytes, Natural Killer (NK) cells, granulocytes, monocytes, and nRBCs isolated using a “stringent” strategy formally excluding erythroid lineage-specific markers. DNAm profiles of cord blood cells isolated by the standard sorting strategy showed significant heterotopic cross-contamination between cell populations, whereas the cord blood cells sorted by the stringent strategy displayed DNAm profiles more consistent with their expected hematopoietic lineage relationships.

overall_design: Bisulphite-converted DNA from 15 cord blood cell populations sorted by a standard FACS protocol with no erythroid exclusion (T cells, monocytes, and nucleated RBCs collected from 5 cord blood samples) and from 48 cord blood cell populations sorted by a stringent FACS protocol formally excluding erythroid lineage-specific marker CD235 (B cells, CD4 and CD8 T cells, granulocytes, monocytes, NK cells, and nucleated RBCs collected from 7 cord blood samples; CD8 T cells were not collected from one sample) were hybridized to the Illumina Infinium HumanMethylation450 BeadChip.

first: Olivia

last: de Goede

first: E

last: Price

first: Hamid

last: Razzaghian

first: Meaghan

last: Jones

first: Michael

last: Kobor

first: Pascal

last: Lavoie


title: The UBC-40 Urothelial Bladder Cancer Cell Line Index [copy number variation]

status: Public on Jun 19 2015

city: Madrid

first: Enrique

last: Carrillo de Santa Pau

address: C/ Melchor Fernández Almagro, 3

department: Cancer Cell Biology Programme

country: Spain

institute: Spanish National Cancer Research Centre (CNIO)

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

summary: This is a comprehensive genomic characterization of 40 urothelial bladder carcinoma (UBC) cell lines including information on origin, mutation status of genes implicated in bladder cancer (FGFR3, PIK3CA, TP53, and RAS), copy number alterations assessed using high density SNP arrays, uniparental disomy (UPD) events, and gene expression. Based on gene mutation patterns and genomic changes we identify lines representative of the FGFR3-driven tumor pathway and of the TP53/RB tumor suppressor-driven pathway. High-density array copy number analysis identified significant focal gains (1q32, 5p13.1-12, 7q11, and 7q33) and losses (i.e. 6p22.1) in regions altered in tumors but not previously described as affected in bladder cell lines. We also identify new evidence for frequent regions of UPD, often coinciding with regions reported to be lost in tumors. Previously undescribed chromosome X losses found in UBC lines also point to potential tumor suppressor genes. Cell lines representative of the FGFR3-driven pathway showed a lower number of UPD events. Overall, there is a predominance of more aggressive tumor subtypes among the cell lines. We provide a cell line classification that establishes their relatedness to the major molecularly-defined bladder tumor subtypes. The compiled information should serve as a useful reference to the bladder cancer research community and should help to select cell lines appropriate for the functional analysis of bladder cancer genes, for example those being identified through massive parallel sequencing.

overall_design: Copy Number Variations were assessed in 45 bladder cell lines, included in the UBC-40 Urothelial Bladder Cell Line Index, with Human1M-Duov3 DNA Analysis BeadChip platform

first: Julie

last: Earl

first: Daniel

last: Rico

last: Carrillo-de-Santa-Pau

first: Benjamín

last: Rodríguez-Santiago

first: Marinela

last: Méndez-Pertuz

first: Herbert

last: Auer

first: Gonzalo

last: Gómez

first: H

last: Grossman

first: David

middle: G

last: Pisano

first: Wolfgang

last: Schulz

first: Luis

last: Pérez-Jurado

first: Alfredo

last: Carrato

first: Dan

last: Theodorescu

first: Stephen

last: Chanock

first: Alfonso

last: Valencia

first: Francisco

middle: X

last: Real


title: Gene Expression During the First 28 Days of Axolotl Limb Regeneration

status: Public on Apr 20 2015

city: Lexington

middle: Randal

last: Voss

state: KY

address: 675 Rose Street

institute: University of Kentucky

summary: Here we report the results of a robust microarray experiment that examined the first 28 days of axolotl forelimb regeneration. At each of 20 post-amputation time points, we estimated gene expression for 10 replicate RNA samples that were isolated from 1m of heterogeneous tissue collected from the distal limb tip.

overall_design: The distal 1.0mm of heterogeneous tissue from regenerating limb tip were removed and used for RNA extraction.  10 samples were collected for each of 20 time points.

first: Antony

last: Athippozhy


title: Pax5 is a tumor suppressor in mouse mutagenesis models of acute lymphoblastic leukemia

status: Public on Apr 10 2015

city: Memphis

first: Charles

last: Mullighan

address: 262 Danny Thomas Place

department: Pathology

institute: St Jude Children's Research Hospital

summary: To examine the role of PAX5 alterations in leukemogenesis, we performed mutagenesis screens of mice heterozygous for a loss-of-function Pax5 allele. Both chemical and retroviral mutagenesis resulted in a significantly increased penetrance and reduced latency of leukemia, with a shift to B-lymphoid lineage. We observed a range of maturation of lymphoid tumors, and genomic profiling identified a high frequency of secondary genomic mutations, deletions and retroviral insertions targeting B-lymphoid development, including Pax5, and additional genes and pathways known to be mutated in ALL, including tumor suppressors, Ras and JAK-STAT signaling. These results support the notion that loss-of-function of PAX5 is a central event in leukemogenesis and contributes to the arrest in lymphoid maturation characteristic of this disease. Moreover, we validate the role of mutations in additional pathways and demonstrate that sequential acquisition of genetic alterations is required for establishment of leukemia.

overall_design: Mice haploinsufficient for PAX5 were analyzed

first: Jinjun

last: Dang

first: Lei

last: Wei

first: Jing

last: Ma


title: A novel lncRNA, LUADT1 promotes lung adenocarcinoma proliferation by epigenetic suppression of p27

status: Public on Mar 10 2015

city: Nanjing

first: Mantang

last: Qiu

state: Jiangsu

address: 42 Baiziting

department: Thoracic Surgery

institute: Cancer Institute of Jiangsu Province

summary: Long noncoding RNAs (lncRNAs) are known to regulate the development and progression of various cancers, however, few lncRNAs have been well characterized in lung adenocarcinoma (LUAD). Understanding the expression profile of lncRNAs and protein-coding genes is critical to develop new diagnosis and treatment strategies for LUAD and improving the prognosis of diagnosed patients.

overall_design: Five female LUAD patients with no smoking history were selected to profile lncRNA and protein-coding gene expression with microarrays. Paired tumor tissues and adjacent nontumor tissues were collected and confirmed by pathologists.

first: Rong

last: Yin

first: Lin

last: Xu


title: Gene expression biomarkers discovery for the Sini Decoction Pattern

status: Public on Mar 20 2015

city: Hsinchu

first: Chaang Ray

last: Chen

address: 101, Section 2, Kuang-Fu Road

department: Biomedical Engineering and Environmental Sciences

country: Taiwan

institute: National Tsing Hua University

summary: We aimed to investigate the syndrome of Sini decoction pattern. The Sini decoction was first mentioned in Shang Han Za Bing Lun, then was developed into Sini decoction pattern (SDP) by Sun Simiao’s Qian Jin Yi Fang. The syndromes of SDP were correlated with various extremely Yang deficiency related symptoms, but there does not exist common definition.

overall_design: Loop design, one kind of statistical microarray experimental design, was utilized to construct an optimal design. The basic principles of good design: balance among the factors, approximately equal sampling of varieties, and minimizing the distance between pairs of varieties. Samples from twenty four individuals were hybridized on 48 arrays based on the two loop designs that are presented in Figure 1.Individuals of sample L1A1, L1A2, L1A3, L1C1, L1C2, L1C3, L2A1, L2A2, L2A3, L2C1, L2C2 and L2C3 are diagnosed as SDP, and individuals of sample L1B1, L1B2, L1B3, L1D1, L1D2, L1D3, L2B1, L2B2, L2B3, L2D1, L2D2, and L2D3 are diagnosed as non-SDP. Each arrow indicates a microarray hybridization experiment. The arrow heads and tails represent samples labeled with Cy5(-3DNA Capture Reagent) and Cy3(-3DNA Capture Reagent) respectively. We used twelve individuals in Loop 1 experiments as the training set and the other twelve individuals in Loop 2 experiments as the test set.

first: Hung

middle: T

last: Cheng

first: Ian

middle: C

last: Hsu


title: Comparative genomic, microRNA, and tissue analyses reveal subtle differences between non-diabetic and diabetic foot skin [nanoString nCounter miR expression assay]

status: Public on May 01 2015

city: Miami

first: Horacio

middle: Adrian

last: Ramirez

state: Florida

address: 1600 NW10th Avenue RMSB room 2029A

department: Dermatology

institute: University of Miami

summary: Diabetes Mellitus (DM) is a chronic, severe disease rapidly increasing in incidence and prevalence and is associated with numerous complications. Patients with DM are at high risk of developing diabetic foot ulcers (DFU) that often lead to lower limb amputations, long term disability, and a shortened lifespan. Despite this, the effects of DM on human foot skin biology are largely unknown. Thus, the focus of this study was to determine whether DM changes foot skin biology predisposing it for healing impairment and development of DFU. Foot skin samples were collected from 20 patients receiving corrective foot surgery and, using a combination of multiple molecular and cellular approaches we performed comparative analyses of non-ulcerated non-neuropathic diabetic foot skin (DFS) and healthy non-diabetic foot skin (NFS). MicroRNA (miR) profiling of laser captured epidermis and primary dermal fibroblasts from both DFS and NFS samples identified 5 miRs de-regulated in the epidermis of DFS though none reached statistical significance. MiR-31-5p and miR-31-3p were most profoundly induced. Although none were significantly regulated in diabetic fibroblasts, miR-29c-3p showed a trend of up-regulation, which was confirmed by qPCR in a prospective set of 20 skin samples. Gene expression profiling of full thickness biopsies identified 36 de-regulated genes in DFS (>2 fold-change, unadjusted p-value ≤ 0.05). Of this group, three out of seven tested genes were confirmed by qPCR: SERPINB3 was up-regulated whereas OR2A4 and LGR5 were down-regulated in DFS. However no morphological differences in histology, collagen deposition, and number of blood vessels or lymphocytes were found. No difference in proliferative capacity was observed by quantification of Ki67 positive cells in epidermis. These findings suggest DM causes only subtle changes to foot skin. Since morphology, mRNA and miR levels were not affected in a major way, additional factors, such as neuropathy, vascular complications, or duration of DM, may further compromise tissue’s healing ability leading to development of DFUs.

overall_design:
foot skin biopsies obtained from diabetic and non-diabetic people were thoroughly washed in DMEM supplemented with 2× Penicillin/Streptomycin/Fungizone, and gentamicin (50mg/L). After, the epidermis was removed from specimens, the dermis was finely minced and placed in 12-well plates. For the establishment of fibroblast cultures, DMEM (Life Technologies) supplemented with 10% FBS, HEPES (1.9mg/ml), streptomycin (100 μg/ml), penicillin (100 U/ml), and Fungizone Antimycotic (0.25 µg/mL) was used. RNA was isolated from cells (passage 1 or 2) using miRNeasy Mini Kit (QIAGEN).
miR expression profiles of DFF and NFF fibroblasts were generated by nanoString nCounter miR Expression Assays (NanoString Technologies, Seattle, WA, USA) and analyzed using nSolver2.0 software following manufacturer's instructions. Data were normalized to gene controls included in the assays.

middle: A

first: Lisa

last: Liang

first: Irena

last: Pastar

first: Ashley

last: Rosa

first: Olivera

last: Stojadinovic

first: Thomas

middle: W

last: Zwick

first: Robert

last: Kirsner

first: Anna

last: Maione

first: Jonathan

last: Garlick

first: Marjana

last: Tomic-Canic


title: MicroRNA Expression in Cutaneous Squamous Cell Carcinoma

status: Public on Feb 28 2015

city: Columbus

first: Amanda

middle: Ewart

last: Toland

state: OH

address: 460 W. 12th Ave

department: MVIMG

institute: The Ohio State University

summary: Cutaneous squamous cell carcinoma (cSCC) is the second most commonly diagnosed cancer in the United States each year. Despite a generally good prognosis, metastatic cSCC results in over 3500 deaths annually. There are no specifically targeted therapies or biomarkers for metastatic cSCC. To determine whether aberrant microRNA expression occurs in metastatic cSCC which could provide novel targets for therapy or biomarkers for earlier diagnosis or prognosis, microRNA expression profiling was performed in 48 samples including normal skin, primary tumors and metastases. Multiple microRNAs showed differential expression; miR-4286, miR-200a-3p and miR-148-3p showed increased expression and miR-1915-3p, miR-205-5p, miR-4516 and miR-150-5p showed reduced expression in metastatic samples. Several microRNAs previously showing aberrant expressionshown to be aberrantly expressed in primary cSCCs were also observed in this study including miR-100, miR-135b, miR-145, miR-21, and miR-214. In summary, several microRNAs show differential expression between primary and metastatic cSCCs; these may be useful as biomarkers for metastasis or as targets for therapytherapeutic targets.

overall_design: RNA extracted from primary human tissues


title: miRNA expression profiles in Wilms tumor subtypes

status: Public on Feb 11 2015

city: Homburg

first: Nicole

last: Ludwig

address: Kirrberger Strasse

department: Human Genetics

institute: Saarland University

summary: The aim of the study was to identify differentially expressed miRNAs in different Wilms tumor subtypes.

overall_design: Comparison of miRNA expression profiles in Wilms tumor of different subtypes (total n=62) compared to normal kidney tissue (n=4)

first: Jana

last: Schmitt


title: Circulating microRNAs are candidate markers of heart failure and differentiate between heart failure with reduced vs preserved left ventricular ejection fraction.

status: Public on Feb 12 2015

city: Singapore

first: Kandiah

last: Jeyaseelan

address: 8 Medical Drive

department: Biochemistry

country: Singapore

institute: National University of Singapore

summary: In this study, we compared the expression profiles of circulating miRNAs in blood samples from controls and patients with heart ailment. Subject with no past history of heart failure/disease are considered as controls. The patients were classified according to the percentage of left ventricular ejection fraction. Patients were grouped as heart failure  with reduced (hfREF) and preserved (hfPEF) left ventricular ejection fraction. Employing miRNA microarray, we identified 'signature miRNAs' in peripheral blood samples that distinguished Heart failure from the non-heart failure controls, as well as those of hfREF and hfPEF groups.

overall_design: Total RNA (plus miRNAs) was isolated using a modification of the RiboPure™-Blood kit from Ambion (Austin,TX) according to the manufacturer’s protocol. The concentration of total RNA and integrity were determined by using Nano-Drop ND-1000 Spectrophotometry (NanoDrop Tech, Rockland, Del) and gel electrophoresis respectively.

first: Sugunavathi

last: Sepramaniam

first: Arunmozhiarasi

last: Armugam

first: DwiSetyowati

last: Karolina

first: KaiYing

last: Lim

first: Carolyn

middle: S

last: Lam

first: Mark

last: Richards


title: A Novel miRNA-Based Predictive Model for Biochemical Failure Following Post-Prostatectomy Salvage Radiation Therapy

status: Public on Jan 23 2015

first: Erica

middle: Hlavin

last: Bell

state: Ohio

address: 410 W 12th Ave

summary: Radical prostatectomy remains one of the more widely-used treatment options for men with prostate cancer. However, few molecular biomarkers have been established to predict patients who are at high risk of biochemical failure. To our knowledge, this is the first such report on miRNA profiling in radical prostatectomy tissue using Nanostring. In addition, this is the first report to look at the prognostic value of miRNAs in the setting of biochemical failure and salvage radiation therapy post-radical prostatectomy.

overall_design: RNA was extracted from tumor-enriched 1mm cores from 43 radical prostatectomy paraffin tissue blocks. 800 miRNAs were profiled using the NanoString nCounter human miRNA assay. mirNAs were then correlated to clinical outcomes.

middle: H

first: Simon

last: Kirste

first: Jessica

last: Fleming

first: Petra

last: Stegmaier

first: Vanessa

last: Drendel

first: Xiaokui

last: Mo

first: Martin

last: Werner

first: Anca

last: Grosu

first: Arnab

last: Chakravarti


title: Identification of microRNA profiling of human ovary in PCOS with insulin resistance (pilot study)

status: Public on Jan 12 2015

city: Guangzhou

first: Lin

last: Lin

state: Guangdong

address: No. 107, Yanjiang Road

department: Ob/Gyn

institute: Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University

summary: Polycystic ovary syndrome (PCOS) is the most common endocrine disorder in women of reproductive age. It has become increasingly evident that insulin resistance plays a significant role both as a cause and result of the syndrome. In an effort to investigate further the observed insulin resistance in the ovarian tissue of women with PCOS, we conducted array-based, global miRNA profiling.

platform_organism:
Homo sapiens
Mus musculus
Rattus norvegicus
Human alphaherpesvirus 1
Human betaherpesvirus 5
Murid betaherpesvirus 1
human gammaherpesvirus 4
JC polyomavirus
Human immunodeficiency virus 1
Murid gammaherpesvirus 4
Human gammaherpesvirus 8
Betapolyomavirus hominis
Betapolyomavirus macacae

overall_design: PCOS ovarian tissue vs. normal control ovarian tissue. 1 patient sample vs 1 normal control sample on one array (replicates every 3 lines (12 blocks) in one array).


title: miRNA profile of exosomes released from PC-3 cells compared to parent cells

city: Oslo

first: Nina

middle: Pettersen

last: Hessvik

address: Ullernchausseen 70

department: Department for Biochemistry

country: Norway

institute: The Norwegian Radium Hospital, Oslo University Hospital

summary: Exosomes are small extracellular vesicles released through fusion of multivesicular bodies with the plasma membrane. The aim of this study was to investigate whether there are any differences in miRNAs in exosomes secreted from the prostate cancer cell line PC-3 and in parent cells, as well as to investigate whether there are any differences in miRNAs in cell lysates from PC-3 cells and the non-cancerous prostate cell line RWPE-1.

overall_design: Exosomes isolated from media of PC-3 cells, RNA isolated from exosomes and parent cells, as well as from RWPE-1 cells. Using 3 biological replicates, 1 replicate per array

first: Kirsten

last: Sandvig

first: Alicia

last: Llorente


title: miRNA expression-based, individualized outcome prediction for SDT treatment in melanoma

status: Public on Jan 29 2015

city: Harbin

first: Zheng

last: Hu

address: 92 West Dazhi Street , Nan Gang District, Harbin

institute: Harbin Institute of Technology

summary: Individualized outcome prediction classifiers were successfully constructed through expression profiling of a total of 3100 capture probes, covering all human, mouse and rat microRNAs annotated in miRBase 18.0, in 8 melanoma samples divided into 4 groups (Control, ALA, US, and SDT group).

overall_design: In the study presented here, a consecutively operated, well-defined cohort of 8 melanoma cases was used to acquire miRNA expression profiles with Exiqon arrays based on miRBase 18.0.

first: Haixia

last: Fan

first: Guixiang

last: Lv

first: Qi

last: Zhou

first: Bin

last: Yang

first: Jinhua

last: Zheng

first: Wenwu

last: Cao


title: Identification of differentially expressed genes against WSSV infection in Penaeus monodon by microarray

status: Public on Jan 02 2015

city: Chennai

first: Shekhar

middle: M

last: S

state: Tamil Nadu

address: 75, Santhome High Road, R.A.Puram

department: Genetics and Biotechnology

country: India

institute: Central Institute of Brackishwater Aquaculture

summary: Microarray analysis of the gill tissues of WSSV infected shrimp (P. monodon) at different time intervals 6 hrs, 24 hrs, 48 hrs and  moribund stage of post WSSV infection was carried out to identify differentially expressed genes in response to WSSV infection. The shrimps in WSSV challenege experiment were challenged through intra muscular route with known concentration of virus. The important immune genes identified would be further characterized by sequence analysis and gene expression profile would be validated by real time PCR

overall_design: One-color experiment,Organism: Penaeus monodon, Custom Penaeus monodon (Black Tiger Shrimp) 8x60k designed by Genotypic Technology Private Limited (AMADID: 041733), Labeling kit: Agilent Quick-Amp labeling Kit (p/n5190-0442)

first: M

last: Shekhar

first: A

last: Gomathi

last: Ponniah


title: miRNA profiling in high-grade serous ovarian carcinoma

status: Public on Nov 14 2014

city: Jinan

first: Zhaojian

last: Liu

state: Shandong

address: 44# Wenhua xi Road

department: Cell Biology

institute: Shandong University

summary: In this study, we performed miRNA profiles analysis of high-grade serous ovarian carcinoma compared to normal fallopian tube fimbria using microarray (Exiqon, Denmark) to evaluate  their potential role in the pathogenesis of uterine leiomyoma.

overall_design: miRNA profiling analysis of the 10 samples including 5 high-grade serous ovarian carcinomas and 5 normal fallopian tube fimbria.

first: Ruifen

last: Dong

first: Beihua

last: Kong


title: Targeting of Super-Enhancer-Associated Oncogenic Transcription in MYCN-driven tumor cells by CDK7 inhibition [Gene Expression]

status: Public on Nov 21 2014

city: Boston

first: Rani

last: George

state: MA

address: 450 Brookline Ave

department: Pediatric Oncology

institute: Dana Farber Cancer Institute

summary: Global gene expression after CDK7 inhibition by THZ1

overall_design: Global gene expression after genetic knockdown or overexpression of MYCN

first: Edmond

last: Chipumuro

first: Eugenio

last: Marco

first: Nicholas

last: Kwiatkowski

first: Brian

last: Abraham


title: Transcriptomic analysis of the late stages of grapevine (Vitis vinifera cv. Cabernet Sauvignon) berry ripening indicates significant induction of ethylene signaling and flavor pathways in the skin.

status: Public on Nov 01 2014

city: Reno

first: Grant

last: Cramer

address: 1664 N. Virginia St

department: Biochemistry & Molecular Biology

institute: University of Nevada, Reno

summary:
Background: Grapevine berry, a nonclimacteric fruit, goes through three developmental stages, the last one called the ripening stage, when the berry changes color and dramatically increases in sugar. Flavors derived from terpenoid and fatty acid metabolism develop at the very end of this ripening stage. Whole-genome microarray analysis was used to assess the transcriptomic response of pulp and skin of Cabernet Sauvignon berries in the latter stages of ripening between 22 and 37 °Brix.  Grapevine berry, a nonclimacteric fruit, goes through three developmental stages, the last one called the ripening stage, when the berry changes color and dramatically increases in sugar. Flavors derived from terpenoid and fatty acid metabolism develop at the very end of this ripening stage. Whole-genome microarray analysis was used to assess the transcriptomic response of pulp and skin of Cabernet Sauvignon berries in the latter stages of ripening between 22 and 37 °Brix.
Results: There were approximatedly 18,000 transcripts whose abundance changed with °Brix level and tissue type. There were very broad changes in many gene ontology (GO) categories involving metabolism, signaling and abiotic stress. GO categories reflecting tissue differences were overrepresentation in photoysynthesis, isoprenoid metabolism and pigment biosynthesis. A more detailed analysis of the interaction of the skin and pulp with °Brix levels revealed that there were significantly higher abundances of transcripts changing with °Brix level in the skin that were involved in ethylene signaling, isoprenoid and fatty acid metabolism. Many of these transcripts were peaking around the optimal fruit stage for flavor production. The transcript abundance of approximately two-thirds of the AP2/ERF Superfamily of transcription factors changed during these developmental stages. The transcript abundance of a unique clade of ERF6-type transcription factors had the largest changes and clustered with other genes involved in ethylene, senescence, and fruit flavor production including ACC oxidase, terpene synthases, and lipoxygenases. The transcript abundance of other important transcription factors (i.e. SPL, RIN, etc.) involved in the regulation of fruit ripening was also higher in the skin.
Conclusions: A detailed analysis of the transcriptomic response of grapevine berries revealed that these berries went through massive changes in chemical signaling and metabolism in both the pulp and skin, particularly in the skin. The ethylene signaling pathway of this nonclimacteric fruit was significantly stimulated in the late stages of ripening when the production of transcripts for important flavor and aroma compounds were at their highest. Ethylene transcription factors known to play a role in leaf senescence also appear to play a role in fruit senescence. Ethylene may play a bigger role than previously thought in this non-climacteric fruit.

overall_design: Vitis vinifera L. cv. Cabernet Sauvignon (clone 8 scion on 1130 Paulsen rootstock) berries were harvested from J. Lohr Vineyards & Wines, Paso Robles, CA, USA. Whole-genome microarray analysis was used to assess the transcriptomic response of pulp and skin of berries in the latter stages of ripening between 22 and 37 °Brix (2008 vintage).

middle: R

first: Ryan

last: Ghan

first: Karen

last: Schlauch

first: Hildegarde

last: Heymann

first: Sara

last: Zenoni

first: Mario

last: Pezzotti


title: Spatio-temporal transcriptional profiling of early embryogenesis in rice

status: Public on Nov 08 2014

city: Tokyo

first: Jun-ichi

last: Itoh

state: Tokyo

address: Bunkyo, Yayoi 1-1-1

institute: The University of Tokyo

summary: Embryogenesis in rice shows a non-stereotypic cell division pattern, the formation of dorsal-ventral polarity, and endogenous initiation of the radicle, which differs from most dicotyledonous plants. To reveal the transcriptional features associated with developmental events during early embryogenesis in rice, we obtained transcriptome data, including the spatial and temporal data sets, using microarray experiments combined with a laser microdissection. We could predict the spatial expression foci of each expressed gene in the globular embryo, which revealed that the expression bias along the apical-basal and dorsal-ventral axes was correlated with temporal changes in expression levels during early embryogenesis. The spatial expression patterns of transcripts was suggestive of a potential contribution of phytohormone-related genes to early embryogenesis and was a characteristic feature of transcription factor genes. We also analyzed the relationship between expression sites of the genes in the globular embryo and those in embryonic organs at later stages. Based on in silico prediction of gene expression sites, we developed potential marker genes expressed in specific domains of the early embryo. The results and database will provide a framework for spatio-temporal gene expression in rice embryogenesis and increase our understanding of developmental diversity of plant embryogenesis.

overall_design: We designed microarray experiments for two types of dataset; i.e., spatial and temporal datasets. For temporal datasets, the entire embryonic tissues at 2, 3 and 4 DAP were collected using laser microdissection. For spatial datasets, 3-DAP embryos were separated into half parts of the embryo along the A-B and D-V axis using LM, which resulted in four tissues derived from the apical, basal, dorsal and ventral regions of the embryo. In addition to the spatial datasets for early embryos, we obtained sub-spatial datasets from tissues of 7-DAP embryos. Embryo tissues closely associated with four embryonic organs; namely, the shoot, scutellem, root (radicle), and epiblast/coleorhizae, were separated and collected by LM. These 11 samples were obtained in triplicate and used to perform the 44K rice microarray.

first: Yutaka

last: Sato

first: Ken-ichiro

last: Hibara

first: Sae

last: Shimizu-Sato

first: Hiromi

last: Kobayashi

first: Nobukazu

last: Namiki

first: Kaori

last: Kamatsuki

first: Hisae

last: Kamakura

first: Hinako

last: Takehisa

first: Yoshiaki

last: Nagamura


title: MicroRNA expression changes in Bone Marrow Stromal Cells from Myeloma Patients vs Normal Patients, and From Normal Patients cultured with or without Myeloma cells in 3D culture

first: Michaela

last: Reagan

address: 77 Ave. Louis Pasteur

institute: Dana-Farber Cancer Institute

summary: The objectives of this study were to assess differences in Bone Marrow Derived  Menenchymal Stromal Cells (MSCs) during co-culture with myeloma cells, and to assess differences in myeloma patient MSCs compared to normal donor MSCs.

overall_design: In the study presented here, a Bone Marrow Derived Menenchymal Stromal Cells (MSCs) were analyzed  after FACS sorting from 2 week culture in osteogenic media lacking dexamethasone in 3D silk scaffold matrices either in co-culture with the multiple myeloma cell line GFP+Luc+MM1.S or Alone, as controls. Also, monocultures of MSCs grown in 2D, in MSC expansion media, from Normal Donor Controls (ND) or Multiple myeloma patients (MM) were analyzed. Analysis was done looking at microRNA expression in samples with the nanoString microRNA platform for 800 microRNAs.


title: Differential gene transcript expression profiles among human monocyte-derived dendritic cells infected with Leishmania major Friedlin V1 strain and Leishmania donovani 1S strain parasites at early infection time points

city: Notre Dame

first: Mary

middle: Ann

last: McDowell

state: Indiana

address: 210 Galvin Life Science Center

department: Biological Sciences

institute: University of Notre Dame

summary: Monocyte derived dendritic cells (MDDC) were infected with Leishmania major or Leishmania donovani parasites and collected at 4, 8, and 24 hours post-infection to analyze the differential effects those parasite species have on human host cell gene expression over time.

overall_design: Monocyte derived dendritic cells (MDDC) were generated from blood buffy coats collected from five anonymous healthy human donors and infected 10:1 (parasite to host cell) with Leishmania major Friedlin V1 strain or Leishmania donovani 1S strain parasites, where after 4, 8, or 24 hours total RNA was harvested from cells, cDNA generated, and hybridized to human gene transcipt expression arrays to assess differential host cell gene transcriptional expression differences relative to uninfected cells.

first: Nicholas

last: Geraci

first: Brent

last: Harker

first: Melissa

last: Stephens

first: Erliang

last: Zeng


title: Long non-coding RNAs and microRNAs involved in integrated co-regulation of neuronal maturation [microRNA expression]

status: Public on Oct 24 2014

first: Kandiah

last: Jeyaseelan

summary: Neurogenesis is a pro-survival process that comprises of dendritic and axonal growth, synaptogenesis, synaptic and neuronal pruning. These complex processes are determined by temporal gene expression during development, which is in turn tightly regulated by long non-coding RNAs and microRNAs. In this study, we investigated the processes implicated in the maturation of primary neuronal cultures based on RNA expression profiling. Correlation between neuron specific gene ontologies of mRNA and non-coding RNAs identified direct regulation of axonogenesis and dendritogenesis. Temporally regulated mRNA and their associated long non-coding RNAs were significantly overrepresented in proliferation and differentiation associated signalling, cell adhesion molecules and neurotrophin signalling pathways during neuronal maturation. Long non-coding RNAs associated with Axin2, Cntn1, Ncam1, Negr1, Ntrk2, Nrxn1 and Sh2b3 displayed an inverse expression profile to their mRNA whereas long non-coding RNA -mRNA pairs for Kit, Prkcb and Ralgds displayed similar expression profiles. These genes were also predicted targets of the altered miRNAs, miR-124, -128, -129-5p, -203, -218, -290-5p, -326, -329, -377 and -495. These microRNAs particularly regulate the cell adhesion molecules, Cntn1, Ncam1, Negr1 and Nrxn1 that determine axonogenesis and dendritogenesis, supporting the observed co-regulation of these biological processes by non-coding RNAs. Verification of expression of these long non-coding RNA-mRNA pairs in an in vitro model of ischemic-reperfusion injury showed an inverse expression profile, thus confirming their role(s) in maintenance of the neuronal structure and function. This neuronal transcriptome (mRNAs, lncRNAs, miRNAs) is in turn orchestrated by C/EBPα/β transcription factors and CTCF, thereby governing intricate control of neuronal development.

overall_design: microRNA expression profiling of maturing primary cortical neurons from E15 mouse embryos. Maturing neurons were harvested on Days 2, 4, 6 and 8.

first: K

first: A

last: Armugam

first: S

last: Sepramaniam

first: P

last: Kaur


title: Long non-coding RNAs and microRNAs involved in integrated co-regulation of neuronal maturation

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

overall_design: Refer to individual Series


title: MiRNA expression profiling in human medullary thyroid carcinoma

status: Public on Dec 15 2014

city: Valbonne - Sophia-Antipolis

first: Kevin

last: Lebrigand

address: 660 route des lucioles

institute: IPMC/CNRS

summary: This study aims to investigate the microRNA profile in human medullary carcinoma tissue by microarray analysis and RT-qPCR. Matched tumor and adjacent normal tissue were obtained from 24 patients and analysed using human microRNA Microarray Kit Agilent, Differentially expressed miRNAs were validated by RT-qPCR using 37 other tumors samples (validation set), Associations of microRNA expression with clinicopathological items were studied

overall_design: Matched tumor and adjacent normal frozen tissues were obtained from thyroid of 40 patients. Normal tissue (name with suffix S) and lesionnal tissue (name with suffix L) were hybridized on microarray.

last: Lassalle

last: Hofman

first: B

last: Mari

first: I

last: Henaoui

last: Barbry


title: Targeting Transcriptional Addictions in Small Cell Lung Cancer with a Covalent CDK7 Inhibitor (Affymetrix)

status: Public on Oct 23 2014

city: Cambridge

first: Richard

last: Young

address: 9 Cambridge Center

institute: Whitehead Institute for Biomedical Research

summary: Small cell lung cancer (SCLC) is an aggressive disease with high mortality. The identification of effective pharmacological strategies to target SCLC biology represents an urgent need. Using a high-throughput cellular screen of a diverse chemical library we observe that SCLC is sensitive to transcription-targeting drugs, and in particular to THZ1, a newly identified covalent inhibitor of cyclin-dependent kinase 7 (CDK7).  We find that expression of super-enhancer associated transcription factor genes including MYC family proto-oncogenes and neuroendocrine lineage-specific factors are highly vulnerability to THZ1 treatment. We propose that downregulation of these transcription factors contributes, in part, to SCLC sensitivity to transcriptional inhibitors and that THZ1 represents a novel treatment paradigm for targeted SCLC therapy.

overall_design: Microarray expression in small cell lung cancer lines treated with DMSO or THZ1

first: Camilla

middle: L

last: Christensen

last: Kwiatkowski

first: Brian

middle: J

last: Abraham

first: Julian

last: Carretero

first: Fatima

last: Al-shahrour

first: Tinghu

last: Zhang

first: Edmond

last: Chipumoro

first: Grit

last: Hurter-Sprie

first: Esra

last: Akbay

first: Abigail

last: Altabef

first: Jianming

first: Takeshi

last: Shimamura

first: Marzia

last: Capalletti

first: Jakob

middle: B

last: Reibel

first: Jillian

last: Cavanaugh

first: Peng

last: Gao

first: Yan

last: Liu

first: Signe

last: Michaelsen

first: Hans

last: Poulsen

first: Amir

last: Aref

first: David

last: Barbie

first: James

middle: E

last: Bradner

first: Rani

last: George

first: Nathanael

last: Gray

first: Kwok

middle: K

last: Wong


title: NF-kB coordinates rapid, BRD4-dependent remodeling of proinflammatory super-enhancers [Affymetrix]

status: Public on Sep 29 2014

address: 450 Brookline

department: Medical Oncology

summary: Proinflammatory stimuli rapidly and globally remodel chromatin landscape, thereby enabling transcriptional responses. Yet, the mechanisms coupling chromatin regulators to the master regulatory inflammatory transcription factor NF-kB remain poorly understood.  We report in human endothelial cells (ECs) that activated NF-kB binds to enhancers, provoking a rapid, global redistribution of BRD4 preferentially at super-enhancers, large enhancer domains highly bound by chromatin regulators.  Newly established NF-kB super-enhancers drive nearby canonical inflammatory response genes. In both ECs and macrophages BET bromodomain inhibition prevents super-enhancer formation downstream of NF-kB activation, abrogating proinflammatory transcription. In TNFa-activated endothelium this culminates in functional suppression of leukocyte rolling, adhesion and transmigration.  Sustained BET bromodomain inhibitor treatment of LDLr -/- animals suppresses atherogenesis, a disease process rooted in pathological vascular inflammation involving endothelium and macrophages. These data establish BET-bromodomains as key effectors of inflammatory response through their role in the dynamic, global reorganization of super-enhancers during NF-kB activation.

overall_design: Gene expression analysis of human endothelial cells in resting state, treatment with TNFalpha or TNFalpha with the BET bromodomain inhibitor JQ1

first: Jonathan

middle: D

last: Brown

first: Charles

middle: Y

last: Lin

first: Qiong

last: Duan

first: J

last: Plutzky


title: miRNA and consolidation of cued fear memory

status: Public on Sep 30 2014

city: Atlanta

first: Brian

middle: George

last: Dias

state: GA

address: 954 Gatewood Rd NE

department: Psychiatry and Behavioral Sciences

institute: Emory University

summary:
miRNA profiling was carried out using the miRCURY LNA™ microRNA Array (6th gen - hsa, mmu & rno)
miRNA were profiled in amygdala brain tissue obtained from adult mice 30 mins after auditory fear conditioning and expression levels compared to tissue obtained from Home cage controls

overall_design: Adult male mice were fear conditioned using tone-shock pairings and brains were harvested 30 mins later. The brains of Home Cage controls and Fear Conditioned animals (n = 4/group) were then punched to collect amygdala tissue. miRNA were extracted using the Qiagen miRNeasy Kit, and then shipped to Exiqon. Exiqon performed labeling, hybridization and data analysis after use of the miRCURY LNA™ microRNA Array (6th gen - hsa, mmu & rno). https://www.exiqon.com/ls/Documents/Scientific/miRCURY-LNA-microRNA-Array-6th-gen-hsa-mmu-rno-manual.pdf

middle: G

first: Kerry

last: Ressler


title: miRNA expression profiling in human esophageal cancer

status: Public on Sep 18 2014

city: Chongqing

first: Kai

last: Wang

address: Sha pingba

institute: Third Military Medical University

summary: miRNAs comprise a family of small non-coding RNA molecules that have emerged as key post-transcriptional regulators of gene expression. Aberrant miRNA expression has been linked to various human tumors. This study was aimed to identify new aberrant expression miRNA in esophageal squamous cell carcinoma (ESCC) and invested the potential functions in this tumor.

overall_design: miRNA microarray analysis with 4 ESCC and adjacent non-tumor tissues was performed.

first: Yun

last: Bai

first: Kang

last: Yang


title: MicroRNA profiling of Human Breast Cancer

status: Public on Aug 26 2014

city: Hyderabad

first: Lekha

middle: Dinesh

last: Kumar

state: Andhra Pradesh

address: Uppal road, habshiguda

department: Cancer biology

institute: Centre for cellular and molecular biology

summary: Total RNA was isolated from epithelial tissues of different grades and stages of human breast cancer samples using mirVana kit and RNA integrity number (RIN) was determined in Agilent Bioanalyzer (2100) to assess the suitability for microarray assays. Sixteen samples were individually analyzed using miRCURY™ LNA arrays version 11.0 (Exiqon, Denmark). The LNA array slides were scanned using Agilent G2565BA Microarray Scanner System (Agilent Technologies, Inc., USA) and image analysis was carried out using ImaGene 8.0 software (BioDiscovery, Inc., USA). The quantified signals were background corrected (Normexp with offset value 10 14 and normalized using global Lowess (Locally Weighted Scatterplot Smoothing) regression algorithm.

overall_design: Three condition experiment Grade 2, stage II vs its adjacent normals (AN) and Grade 3, stage III vs it AN, Grade 2 vs Grade 3, Grade 2, stage II 5 biological replicates, Grade 3 stage III 5 biological replicates, AN 3 biological replicates each

first: Rekha

middle: A

last: Nair


title: Divergent influence of microRNA-21 deletion on murine colitis phenotypes [TNBS]

status: Public on Jul 23 2014

city: Charlottesville

first: Yong

last: Huang

state: VA

address: 1340 Jefferson Park Ave

department: Medicine

institute: University of Viginia

summary: Background:  MicroRNAs (miRNAs) acting as negative regulators of gene expression are differentially expressed in intestinal tissues of patients with inflammatory bowel disease (IBD). Assessing the functional role of miRNAs in murine models of colitis facilitates elucidating the role of specific miRNAs in human IBD.  The aim of this study was to determine the miRNA signature of murine models of colitis and to assess the influence of miR-21 on intestinal inflammation.   Methods: miRNAs expression was accessed by microarray for acute and chronic murine model of colitis induced by DSS or TNBS. miR-21-deficient mouse and littermates controls were assessed in the standard DSS, TNBS and CD4+ T cell transfer models of colitis. RNAs of mouse colon and CD4+CD45RBHigh cells were analyzed by miRNA and mRNA microarray, and quantitative RT-PCR. Th1 polarization was accessed by flow-cytometry and ELISA. Results:  Alterations of in miRNAs expression were identified for acute and chronic DSS colitis and TNBS colitis, receptively.  The Expression of miRs-21, -142-3p and -223 was were distinct between DSS and TNBS models while overlap of numerous miRNAs was seen. Importantly, miRs-19b, -192 and -215, that are decreased in IBD, were significantly decreased in all 4 models of colitis. miR-21, which is increased in IBD, was increased in TNBS colitis but not the DSS colitis models.  Further assessment of the miR-21-deficient 1-/- mice revealed that the deletion of miR-21 results in the exacerbation of both the TNBS and T cell-transfer models of colitis.  Conclusions:  miRNAs are differentially expressed in both human IBD and murine colitis, with overlap of several IBD-associated miRNAs.  The demonstration that miR-21 deletion exacerbated CD4+ T cell-mediated models of colitis provides further evidence that miRNAs play significant roles in the pathogenesis of IBD.

overall_design: miRNAs expression was accesed for acute and chronic murine model of colitis induced by DSS or TNBS.Total of 20 samples with duplicates were analyed in this study.

first: Feng

last: Wu

first: Fengshi

last: Dong

first: Nicholai

last: Arendovich

first: Jing

last: Zhan

first: John

last: Kwon


title: Divergent influence of microRNA-21 deletion on murine colitis phenotypes [DSS]


title: Transcriptome analysis, Paramecium tetraurelia ICL (as a control) vs. Rdr3 silencing

status: Public on Jul 15 2014

city: Saarbrücken

first: Martin

last: Simon

address: Campus A2 4

department: Centre for Human and Molecular Biology

institute: Saarland University

summary: Differential transcriptome of Paramecium tetraurelia strain 51 undergoing RNAi by feeding against ICL7a (as a control) and RDR3 for nine days.

overall_design: three biological replicates each, meaning three ICL and three RDR3  silecning cultures and cDNAs on two 3x720k Chips

first: D

last: Baranasic

first: T

last: Oppermann

first: M

last: Cheaib

last: Cullum

first: H

last: Schmidt


title: mRNA Expression data from AG 1522 human fibroblasts post X-ray radiation

status: Public on Jul 30 2014

city: Hefei

first: Wei

last: Han

state: Anhui

address: #155 Shushanghu Road

institute: Center of Medical Physics and Technology, Hefei Institutes of Physical Science, Chinese Academy of Sciences

summary:
Radioadaptive response (RAR) in mammalian cells refers to the phenomenon where a low-dose ionizing irradiation alters the gene expression profiles, and protects the cells from the detrimental effects of a subsequent high dose exposure.
We focused on mRNA microarray studies, and aimed to characterize the transcriptome for RAR in AG 1522 human skin fibroblasts and to examine the functional regulatory networks at the genetic level. AG 1522 cells were exposed at a specific time point to a challenging dose of 2 Gy in the RAR group, or a priming dose of 5 cGy in the low-dose group.

overall_design: We aimed to have a comprehensive investigation on the RAR induced in the AG 1522 human fibroblasts first exposed to 5 cGy (priming dose) and then followed by 2 Gy (challenge dose) of X-ray through comparisons to those cells which had only received a single 2 Gy dose.

first: Jue

last: Hou


title: Expression data from AG 1522 human fibroblasts post X-ray radiation


title: Targeting transcriptional dependencies in cancer using a covalent CDK7 inhibitor (expression)

status: Public on Jun 22 2014

first: Richard

last: Young

summary: Cyclin-dependent kinase 7 (CDK7) plays a critical role in the general regulation of RNA polymerase II-mediated transcription.  However, the absence of selective CDK7 inhibitors has hindered the ability to investigate the consequences of acute and prolonged inhibition of CDK7 under normal and pathological conditions.  Here we present the discovery and characterization of the first covalent CDK7 inhibitor, CDK7-IN-1, that has the unprecedented ability to target a unique cysteine residue located outside of the canonical kinase domain, providing an unanticipated means of achieving selectivity for CDK7 amongst the 20 known CDKs.  Cancer cell line profiling indicates that a subset of cancer cell lines, including T-cell acute lymphoblastic leukemia (T-ALL), exhibit 100-fold greater sensitivity to CDK7-IN-1 over other tumor and normal cell lines.  Genome-wide expression analysis in Jurkat T-ALL indicates that CDK7-IN-1 disproportionally affects RUNX1 as well as other components of the TAL1 transcriptional network and its targets, downregulating key regulators of transcription and apoptosis critical for the T-ALL state.   These oncogenes are encoded by short-lived mRNA transcripts, are associated with super-enhancers, and exhibit a strong dependency on continuous transcription for sustained expression.  Therefore, pharmacological modulation of CDK7 kinase activity may define a method for the identification and treatment of tumor types exhibiting extreme dependencies on transcription for maintenance of the oncogenic state.

overall_design: Jurkat, MM1S, Loucy, and HeLa (WT and Dox-inducible CDK7 mutant) cells were treated with various drugs including a covalent inhibitor of CDK7 (CDK7-IN-1), a reversible inhibitor of CDK7 (CDK7-IN-1), Flavopiridol, Actinomycin D, and DMSO controls.  Replicates are annotated.

first: Nicholas

middle: P

last: Kwiatkowski

first: Tinghu

last: Zhang

first: Peter

last: Rahl

first: Brian

last: Abraham

first: Jessica

last: Reddy

first: Scott

last: Ficarro

first: Anahita

last: Dastur

first: Sridhar

last: Ramaswamy

first: Arnaud

last: Amzallag

first: Bethany

last: Tesar

first: Christopher

last: Jenkins

first: Nancy

last: Hannett

first: Douglas

last: McMillin

first: Takaomi

last: Sanda

first: Taebo

last: Sim

first: Nam

last: Kim

first: Thomas

last: Look

first: Constantine

last: Mitsiades

first: Andrew

last: Weng

first: Jennifer

last: Brown

first: Cyril

last: Benes

first: Jarrod

last: Marto

first: Nathanael

middle: S

last: Gray


title: Systematic Identification of Defined Conditions for Induction and Maintenance of Naive Human Pluripotency [expression]

status: Public on Jul 16 2014

first: Rudolf

last: Jaenisch

department: Biology

institute: MIT/Whitehead Institute

summary: Embryonic stem cells (ESCs) of mice and humans have distinct molecular and biological characteristics, raising the question whether an earlier ‘naive’ state of pluripotency may exist in humans. Here we took a systematic approach to identify small molecules that support autonomous self-renewal of naive human ESCs based on maintenance of endogenous OCT4 distal enhancer activity, a molecular signature of ground state pluripotency. Iterative chemical screening identified a combination of five kinase inhibitors that induces and maintains OCT4 distal enhancer activity when applied directly to conventional human ESCs. These inhibitors generate a homogeneous population of human pluripotent stem cells in which transcription factors associated with the ground state of pluripotency are highly upregulated. Comparison with previously reported naive human ESCs indicates that our kinase inhibitor cocktail captures a novel pluripotent state in humans that closely resembles mouse ESCs.

overall_design: Expression analysis was performed on two groups of human ESC samples: WIBR2 (P12 and P14), WIBR3 (P9) and WIN1 (P10) human ESCs derived in our optimized naive medium (5i/L/A or 6i/L/A, as indicated), and parental WIBR2 and WIBR3 human ESCs in primed human ESC medium.

first: Thorold

middle: W

last: Theunissen

first: Jessica

last: Reddy

first: Zi

last: Fan


title: Supplemental carnitine affects the microRNA expression profile in skeletal muscle of obese Zucker rats

status: Public on Jun 17 2014

city: Giessen

first: Janine

last: Keller

address: Heinrich-Buff-Ring 26-32

department: Inst. for Animal Nutrition

institute: JLU Giessen

summary: Background  In the past, numerous studies revealed that supplementation with carnitine has multiple effects on performance characteristics and gene expression in livestock and model animals. The molecular mechanisms underlying these observations are still largely unknown. Increasing evidence suggests that microRNAs (miRNAs), a class of small non-coding RNA molecules, play an important role in post-transcriptional regulation of gene expression and thereby influencing several physiological and pathological processes. Based on these findings, the aim of the present study was to investigate the influence of carnitine supplementation on the miRNA expression profile in skeletal muscle of obese Zucker rats using miRNA microarray analysis.  Results  miRNA expression profiling in skeletal muscle revealed a subset of 152 miRNAs out of the total number of miRNAs analysed (259) were identified to be differentially regulated (adjusted P-value ˂ 0.05) by carnitine supplementation. Compared to the obese control group, 111 miRNAs were up-regulated and 41 down-regulated by carnitine supplementation (adjusted P-value ˂ 0.05). 14 of these miRNAs showed a log2 ratio ≥ 0.5 and 7 miRNAs showed a log2 ratio ≤ -0.5 (adjusted P-value ˂ 0.05).    Conclusion  The present study shows for the first time that supplementation of carnitine affects a large set of miRNAs in skeletal muscle of obese Zucker rats suggesting a novel mechanism through which carnitine exerts its multiple effects on gene expression, which were observed during the past.

overall_design: For microarray analyses, six RNA samples each, for the obese control group (n = 6) and the obese carnitine group (n = 6), were prepared from skeletal muscle tissue.

first: Robert

last: Ringseis

first: Klaus

last: Eder


title: Analysis of miRNA expression profiling in 3 samples(normal, cigarette smoking and lung cancer population's serum)

city: Guangzhou

first: jinkun

last: huang

state: guangdong

address: 195 Dongfengxi Road, Guangzhou

department: school of public health

institute: Guangzhou Medical University

summary: Using the highly sensitive miRNA array, we determined the serum miRNAs profiles of 10 non-smokers, 10 smokers and 10 lung cancer patients by miRCURY LNA™ microRNA Arrays. Differential expressed miRNAs were further validated in a larger scale samples. We found that let-7i-3p and miR-154-5p were significantly downregulation in serum of smokers and lung cancer patients. The serum level of let-7i-3p and miR-154-5p is associated with smoking and smoking-related lung cancer.

overall_design: In this study,  we mix 10 samples with equal volume of each group(non-smoking control group,smoking group and lung cancer group ) and run RNA extractions. And then miRCURYTM LNA Array (v.16.0) was applied in the studying of miRNA expression profile and its alteration to gain the miRNA expression profile to compare the variety between each two groups respectively.

first: Jinkun

last: Huang

first: Yiguo

last: Jiang


title: microRNA profiles of exosomes: Exosomes from Pooled Healthy donors' serum vs. Exosomes from Pooled NPC Patients' serum

status: Public on May 06 2014

first: ping

last: lan

address: 651 Dongfend East Road

institute: Sun Yat-sen University Cancer Center

summary: microRNA profiles of Exosomes from  Pooled NPC Patients serum comparing Control  Exosomes from Healthy donors serum

overall_design: Two-condition experiment, Exosomes from Pooled Healthy donors serum vs. Exosomes from Pooled NPC Patients serum. Biological replicates: 1 Exosomes from Pooled Healthy donors serum, 1 Exosomes from Pooled NPC Patients serum,

first: Jiang

last: Li

first: Shubiao

last: Ye


title: Gene expression profile of cardiomyocyte-like cells derived from human foreskin and lung fibroblasts, and human ES cell-derived cardiomyocytes

status: Public on Mar 13 2014

city: San Francisco

last: Cao

state: CA

address: 1650 Owens Street

department: Department of Pharmaceutical Chemistry

institute: gladstone institute of cardiovascular disease

summary: Cardiomyocyte-like cells can be reprogrammed from somatic fibroblasts by combinations of genes, providing a new avenue for cardiac regenerative therapy. Here we show that functional cardiomyocytes can be rapidly and efficiently generated from human fibroblasts by specific combination small molecules. Microarray analysis has been used to compare the expression profile of cardiomyocyte-like cells derived from human foreskin and lung fibroblasts, and human ES cell-derived cardiomyocytes.

overall_design: Cardiomyocytes generated from different origins were metabolically purified under glucose-depleted and lactate-abundant conditions for RNA extraction and hybridization on Affymetrix microarrays.

first: Sheng

last: Ding


title: miR-638 promotes melanoma metastasis and protects melanoma cells from apoptosis and autophagy (microRNA)

status: Public on Jan 30 2014

city: Leipzig

first: Animesh

last: Bhattacharya

state: Saxony

address: Johannisallee 30, MBFZ, Room no B-214

department: Dermatology

institute: University of Leipzig, Medical Faculty

summary: MicroRNA (miRNA) expression profiling identified miR-638 as one of the most significantly overexpressed miRNAs in metastatic lesions compared with primary melanomas. miR-638 enhanced the tumourigenic properties of melanoma cells in vitro and lung colonization in vivo. mRNA expression profiling of miR-638 and antagomir-transduced cells identified new candidate genes as miR-638 targets, the majority of which is involved in p53-mediated apoptosis regulation. miR-638 depletion stimulated expression of p53 and its downstream target genes and induced apoptosis and autophagy in melanoma cells. miR-638 promoter analysis revealed transcription factor associated protein 2-α (TFAP2A) as a direct negative regulator of miR-638. Further analyses provided strong evidence for a double negative regulatory feedback loop between miR-638 and TFAP2A. Taken together, miR-638 may support melanoma progression by suppressing p53-mediated apoptosis pathways and by targeting the transcriptional repressor TFAP2A.

overall_design: TaqMan® low-density arrays (TLDA; human microRNA Cards A v2.1 & B v2.0, Applied Biosystems, Darmstadt, Germany) were used for measuring the expression of 667 human miRNAs in primary melanomas (PM, n=8), lymph node metastases (LNM, n=9) or distant cutaneous metastases (DCM, n=10).

first: Ulf

last: Schmitz

first: Yvonne

last: Raatz

first: Madeleine

last: Schönherr

first: Tina

last: Kottek

first: Marianne

last: Schauer

first: Sandra

last: Franz

first: Anja

last: Saalbach

last: Anderegg

first: Olaf

last: Wolkenhauer

first: Dirk

last: Schadendorf

first: Jan

middle: C

last: Simon

first: Thomas

last: Magin

first: Julio

last: Vera

first: Manfred

last: Kunz


title: Drosophila Embryos: Engrailed GooseberryNeuro double heterozygous vs Control Wild Type

status: Public on Jan 01 2014

city: Montpellier

first: Florence

last: Maschat

address: 141 rue de la cardonille

institute: IGF

summary: Transcriptional profiling of drosophila embryos (0-14h collection) comparing embryos double heterozygous for Engrailed and GooseberryNeuro with control wild type embryos

overall_design: Two conditions experiment, Double heterezygous Engrailed GooseberryNeuro vs Wild Type. Biological replicates: 3 control, 3 mutant conditions, independently selected. Triplicate per array

first: S

last: Colomb

first: F

first: N

last: Bonneaud


title: miRQC data for NanoString nCounter miRNA Expression Assays.

status: Public on Dec 30 2013

city: Seattle

first: Lucas

last: Dennis

state: WA

address: 530 Fairview Ave N

institute: NanoString Technologies

summary:
nCounter miRNA Expression Assay data for all profiled miRQC samples prepared by the miRQC Consortium.
In this study, we systematically compared 12 commercially available miRNA expression platforms by measuring an identical set of standardized positive and negative control samples, including human universal reference RNA, human brain RNA and titrations thereof, human serum samples, and synthetic spikes from miRNA family members with varying homology. We developed novel and robust quality metrics to objectively assess platform performance of very different technologies such as small RNA sequencing, RT-qPCR and (microarray) hybridization. We assessed reproducibility, sensitivity, accuracy, specificity, and concordance of differential expression.

overall_design:
miRQC Consortium multi-platform comparision.
*This represents the NanoString component only


title: DNA methylation profiling of serum DNA samples of the UKCTOCS cohort

status: Public on Jun 03 2014

city: London

first: Andrew

last: Teschendorff

address: 72 Huntley Street

department: UCL Cancer Institute/Institute for Women's Health

institute: University College London

summary: The Illumina Infinium 27k Human DNA methylation Beadchip v1.2 was used to obtain DNA methylation profiles across approximately 27,000 CpGs in serum DNA samples from a total of 282 healthy postmenopausal women of which 134 developed breast cancer within a 5-year follow-up period

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

first: Martin

last: Widschwendter


title: Expression data from human ESCs-derived neural precursors (NPs) and neurons

status: Public on Oct 01 2013

first: Albert

last: Cheng

address: Room 453, 9 Cambridge Center

institute: Whitehead Institute

summary: We performed microarray analyses on human ESCs-derived NPs and neurons carrying loss-of-function mutation in the MeCP2 gene.

overall_design: Neural precursors and differentiating neurons at 2 and 4-week were used for RNA extraction and affymetrix microarrays. We added ERCC RNA spike-in controls to normalize to cell number input.

first: Yun

last: Li

first: Rudolf

last: Jaenisch