title: Gene expression in developing fibrotic lesions in tracheas of chlorine-exposed mice

status: Public on Jan 19 2018

city: Louisville

last: Hoyle

state: KY

address: EOHS Lab 701 HSC-A

institute: University of Louisville

summary:
Chlorine is a widely used industrial chemical that is also considered a chemical threat agent.  Inhalation of chlorine gas can cause acute injury to the respiratory tract, including the death of airway epithelial cells.  Failure to efficiently repair the epithelial damage is associated with long-term respiratory abnormalities, including airway fibrosis.  We previously developed a model of airway injury in which mice exposed to chlorine gas exhibit epithelial damage and develop fibrosis in large airways.
In the present study, we measured gene expression in developing fibrotic lesions isolated from chlorine-exposed mice 4 days after exposure and compared to expression in corresponding areas from unexposed mice.  Mesenchymal tissue was isolated by laser-capture microdissection to limit the analysis to the developing fibrotic lesions.  The 4-day time point was chosen in an attempt to identify early profibrotic signaling events because at this time fibroblast proliferation has commenced but the fibrotic scar has not yet formed.

overall_design: Male FVB/NJ mice 9 weeks of age were exposed to 235 ppm chlorine for 1 hr.  Tracheas were collected from 5 chlorine-exposed mice 4 days after exposure and from 5 unexposed mice.  Laser-capture microdissection was used to collect mesenchymal tissue from frozen sections of tracheas.  RNA prepared from the isolated tissue was amplified, labeled, and hybridized to Affymetrix microarrays.

first: Kendall

last: Stocke


title: Transcriptomic analysis of Candida albicans cup9 deletion mutant

status: Public on Feb 01 2018

city: Würzburg

first: Tobias

last: Ludwig

address: Josef-Schneider-Straße 2

country: Germany

institute: Institute for Molecular Infection Biology

type: Expression profiling by high throughput sequencing

summary: Goal: We employed RNA-seq to identify targets of regulation of the Candida albicans transcription regulator CUP9. The cup9 deletion mutant strain displays increased fitness in a mouse model of oropharyngeal candidiasis.

overall_design: Comparison of the transcriptome of Candida albicans wild-type reference strain vs. isogenic cup9 deletion mutant. One growth condition, two biological replicates per sample. RNA-seq data generated with Illumina HiSeq2500.

first: J

middle: C

last: Perez

first: Juliane

last: Meir


title: Identification of the tumour transition states occurring during EMT [ATAC-seq]

status: Public on Feb 15 2018

city: Brussels

first: Cédric

last: Blanpain

address: Route de Lennik 808

country: Belgium

institute: ULB

type: Genome binding/occupancy profiling by high throughput sequencing

summary: EMT (epithelial-mesenchymal transition) in cancer has been associated with tumour stemness, metastasis and resistance to therapy. It has recently been proposed that, rather than being a binary process, EMT occurs through distinct intermediate states. However,direct in vivo evidence supporting this possibility is still lacking. By screening a large panel of cell surface markers, we identified the existence of multiple tumour subpopulations associated with different EMT stages from epithelial to completely mesenchymal states passing through intermediate hybrid states in skin and mammary primary tumours. Although all EMT subpopulations presented similar tumour propagating cell capacity, they displayed different, invasiveness and metastatic potential. Their transcriptional and epigenetic landscapes defined by RNA-seq and ATAC-seq identified the underlying gene regulatory networks, transcription factors and signalling pathways that control these different EMT transition states. Finally, these tumour subpopulations are localized in different niches that differentially regulateEMT transition states.

overall_design: ATAC sequencing on the different intermediate states of EMT

first: Ievgenia

last: Pastushenko

first: Audrey

last: Brisebarre

first: Panagiota

last: Sotiropoulou


title: RNA-SEQ analysis of a C. albicans rim101-/- disrupted strain, a strain overexpressing RIM101 and a reference strain at both alkaline (7.6) and acidic (4) pH

status: Public on Jan 18 2018

city: Grenoble Cedex 9

first: Cécile

last: Garnaud

country: France

institute: CHU Grenoble Alpes

summary: The aim of the study was to compare the RNA-SEQ profiles of a wild type C. albicans strain (SC5314), a rim101-/- mutant strain (DAY25) and a strain overexpressing RIM101 (CGY1) at both alkaline (7.6) and acidic (4) pH, in order to identify Rim-dependent genes involved in tolerance to antifungals

overall_design: Samples were collected after growth at pH 4 (Rim pathway inactivated) and pH 7.6 (Rim pathway activated), in triplicates. RNAs were extracted, prepared, and sequenced using standard RNA-Seq methods and Illumina technology.

first: Encar

last: García-Oliver

first: Yan

last: Wang

first: Danièle

last: Maubon

first: Sébastien

last: Bailly

first: Quentin

last: Despinasse

first: Morgane

last: Champleboux

first: Jérôme

last: Govin

first: Muriel

last: Cornet


title: Identification and differential expression of microRNAs in the testis of chicken with high and low sperm motility

status: Public on Jan 13 2018

city: Yangzhou

first: Yifan

last: Liu

address: No.58 Cangjie road

country: China

institute: Institute of Poultry Science, Chinese Academy of Agricultural Science

type: Non-coding RNA profiling by high throughput sequencing

summary: Sperm motility is one of the most important indicator for evaluating roosters’ fecundity. However, the molecular regulation underlying chicken sperm motility is not yet clear. MicroRNA (miRNA) plays epigenetic roles in reproduction. In this study, we compared the testicular miRNAs of Beijing-you roosters with high (HS) and low (LS) sperm motility using Solexa sequencing. Length distribution analysis showed that the dominant size of the small RNAs detected in the testis was 24~28 nt. In total, 518 known and 106 novel miRNAs were identified. A number of 23 miRNAs were found differentially expressed (P < 0.05, |log2fold change| ≥ 1) between the HS and LS, including 18 known and five novel miRNAs. Function enrichment of predicted target genes of the differential miRNAs indicated that the differentially expressed miRNAs were involved in the pathways of GnRH signaling, MAPK signaling, and Wnt signaling. The miRNA-gene interaction network revealed two key candidate miRNA-gene pairs that may affect chicken sperm motility viz gga-miR-155/KCNA1 and gga-miR-7480-5p/AHI1. qRCR was also used to further validate their expression. The results here provide deep insight into the expression of miRNA in the testis of chicken and suggest their roles in sperm motility regulation.


title: Estrogen protects neurotransmission transcriptome during status epilepticus

status: Public on Dec 06 2017

city: Prairie View

first: Dumitru

middle: Andrei

last: Iacobas

state: TX

address: Ann Preston St

department: Undergraduate Medical Academy

country: USA

institute: Prairie View A&M University

summary: Epilepsy in women is often accompanied by hormonal disturbances including irregular cycles and premature onset of menopause. Decline in estrogen levels results in increased risk for neurodegenerative diseases, with strong participation of chronic inflammation. We have shown that estradiol (EB) has neuroprotective effects against seizure-induced damage in the sensitive hilar region of hippocampal dentate gyrus associated with neuropeptide Y (NPY) upregulation. Here, we quantify the alterations caused by kainic acid-induced status epilepticus in the glutamatergic, GABAergic, dopaminergic, cholinergic and serotonergic synapse transcriptomes of dentate gyrus of ovariectomized female rats and the recovery effects of the EB replacement. Our data indicate that the EB replacement reduces the number of significantly regulated genes in seizured ovariectomized female rats by about 45%. The new measure Pathway Restoration Efficiency (PRE) indicates the dopaminergic synapse to be the most protected (65%) and the GABAergic synapse the least protected (37%) by the EB replacement.

overall_design: Two-conditions (AE = beta-estradiol replacement vs AO = oil) in seizured ovariectomized female rats experiment. Biological replicates: 4AE, 4AO.

middle: A

first: Sanda

first: Tamar

last: Chachua

first: Libor

last: Velíšek

first: Jana

last: Velíšková


title: Hepatic transcriptomic profiles in zebrafish exposed to surface water with pollution gradients and different industrial discharge - Part2

status: Public on Dec 19 2017

city: Dalian

first: Zhou

last: Zhang

state: Liaoning

address: Linggong Road 2

department: Environmental Science and Technology

institute: Dalian University of Technology

summary: To assess the impact of surface water across the Hun River, several sampling sites located in the mainstream and the tributary were selected representative of pollution gradient and different pollution source. Male adult zebrafish were exposed to surface water from seven sites for 4 days. The obiectives of the study was to evaluate the ability of transcriptomic profiles exposed to surface water to determine the potential biological effects, to differentiate different pollution source, and to identify the toxic components.

overall_design: Gene expression in zebrafish liver was measured after 96h exposure to surface water from the Hun River. Pooled liver tissues from five zebrafish were used for total RNA extraction.

first: Wei


title: Genomics and transcriptomics of boar taint in pigs

status: Public on Sep 25 2017

city: Kongens Lyngby

first: Haja

middle: N

last: Kadarmideen

address: Richard Petersens Plads, Building 324

department: Department of Applied Mathematics and Computer Science

country: Denmark

institute: Technical University of Denmark

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

overall_design: Refer to individual Series

first: Markus

last: Drag

first: Ruta

last: Skinkyté-Juskiené

first: Duy

last: Do

first: Lisette

middle: J

last: Kogelman


title: Hepatic transcriptomic profiles in zebrafish exposed to surface water with pollution gradients and different industrial discharge

status: Public on Apr 01 2017


title: Integrated analysis of long non-coding RNAs expression profiles in tumor and adjacent gastric  tissues

status: Public on Sep 01 2017

city: beijing

first: HUI

last: GUO

state: beijing

address: NO.5 Dong Dan San Tiao, Dongcheng District

department: Department of Biochemistry and Molecular Biology

institute: Peking Union Medical College & Chinese Academy of Medical Sciences

summary: In this study, we used microarray and bioinformatics analysis to find potential lncRNAs which may be useful in gastric cancer and then investigate their potential functions.

overall_design: Total RNA from gastric carcinoma tissues  and normal gastric adjacent tissues were extracted and analyzed , we employed Arraystar Human LncRNA Microarray v2.0  as a discovery platform to identify genes.

first: Juan

last: Shi


title: Transcriptomic analysis of Mtb H37Rrv and MtbΔwhiB4 upon treatment with 0.25 mM CHP

status: Public on Apr 24 2017

city: Bangalore

first: Amit

last: Singh

address: C V Raman Avenue

department: MCBL

country: India

institute: Indian Institute of Science

summary: WhiB4 regulates expression of anti-oxidant genes and its own expression was shown to be down-regulated upon exposure to oxidatants like CHP. Further MtbΔwhiB4 was shown to survive better under oxidaitve stress. Thus, we did microarray upon exposure to 0.25 mM CHP to study comprehensively the WhiB4 regulon under oxidative stress.

overall_design: Mtb H37Rv and MtbΔwhiB4 were grown till early log phase and exposed to 0.25 mM CHP for 2 hours at 37 degree at 150rpm. Four and two independent experiments were done for each of the strain, respectively.

first: Pankti

last: Parikh

first: Manbeena

last: Chawla

first: Mansi

last: Mehta


title: Transcriptome profile of ureter tissue originating from CAKUT patients and healthy kidney donors

status: Public on Nov 27 2017

city: Belgrade

first: Aleksandra

last: Stankovic

address: Mike Petrovica Alasa 12

department: Department of Health and Environment

country: Serbia

institute: VINCA Institute of Nuclear Sciences, University of Belgrade

summary: Identification and analysis of differentially expressed genes and detection of miR activity from gene expression data in human CAKUT.

overall_design: The intact ureter tissue of 19 CAKUT patients and 7 healthy kidney donors was homogenized in liquid nitrogen and total RNA was extracted by TRI Reagent® Solution (Ambion). Structural integrity and concentration of total RNA and cRNA was determined using Agilent RNA 6000 Nano Kit on agilent 2100 Bioanalyzer. Linear RNA amplification procedure and synthesis of biotin labeled cRNA was performed with 200ng of total RNA using TargetAmp™-Nano Labeling Kit for Illumina® Expression BeadChip® (Epicentre). The RNeasy MinElute Cleanup Kit (QIAGEN) was used for purification of synthesized cRNA. Hybridization of human samples was performed on Illumina Human-HT12 Version 4 and scanned by the Illumina iScan system.

first: Ivan

last: Jovanovic

first: Maja

last: Zivkovic

first: Dragan

last: Alavantic


title: Sporobolus stapfianus transcriptome: Insights into the unique adaptations of the resurrection grasses to the dehydration stress

status: Public on Mar 01 2017

city: Columbia

first: Abou

last: Yobi

state: Missouri

address: 214 Curtis Hall

department: Plant Genetics Unit

institute: USDA-ARS

summary:
Sporobolus stapfianus is a desiccation tolerant (DT) grass and a member of the Poaceae family alongside prominent crop and forage species. Despite the worldwide distribution of this family, most of its species are vulnerable to water loss within their vegetative tissues. As a DT species, S. stapfianus, could, therefore, serve as a model species for identifying the molecular changes that enabled such a rare occurrence of the DT phenotype in resurrection grasses and the implications of such a unique adaptation for agriculture.
A comprehensive gene expression profiling was performed in plants subjected to a dehydration/rehydration cycle using NimbleGen microarrays hybridization method. Our results showed that most transcripts were high in the hydrated state of S. stapfianus leaf tissues and that minor dehydration (> 60% relative water content; RWC) did not induce most transcripts, but did repress photosynthetic activity, which show the importance of curtailing the production of toxic elements to the DT phenotype. It took a loss of 40% RWC for induction of most transcripts. This shows that this species is pre-equipped to deal with mild dehydration, but requires stress-induced activation mechanisms to prepare for desiccation. In agreement with our transcriptomic data, a global metabolic analysis conducted in this species has shown that most metabolites accumulate to their highest levels below 45% RWC, which suggests the importance of those late stages of dehydration in preparing resurrection grasses for desiccation and for early stages of rehydration. In most cases, a 12-h rehydration was sufficient to reinstate pre-stress expression levels, which shows that only partial damage occurred during drying. Unlike during dehydration, our metabolomic data profiled after rehydration showed that there is no clear correlation between gene expression and metabolic abundance, which suggests that most of the compounds that are produced during rehydration are quickly utilized in active metabolism of restoration.
The findings of the paper show that S. stapfianus is primed to respond to mild dehydration, although severe dehydration require inducible response, with 40-30% RWC being the peak of gene expression. As for photosynthesis, this species cease its photosynthetic activity even at high water levels (85% RWC) alleviating the need to activate antioxidants activity during mild dehydration.

overall_design: Total RNA was extracted from the grass, Sporobolus stapfianus leaf tissues at six hydration levels (3.0, 2.0, 1.5, 1.0, 0.75, and 0.50 g water/ g tissue) as well as at 12 and 24 h after rehydration. Each treatment was conducted in triplicates; making a total of 24 samples. Each chip measures the expresion level of 50,690 genes with each gene model represented by 7x60 mer probes.

first: Bernard

middle: M

last: Wone

first: Richard

middle: L

last: Tillett

first: Won

last: Yim

first: Karen

last: Schaluch

first: John

last: Cushman

first: Melvin

last: Oliver


title: Comparison of miRNA expression profile between arterial plasma and venous plasma

status: Public on Nov 22 2016

city: Beijing

first: Yuan

last: Zhou

address: 38 Xueyuan Rd, Haidian District

department: Department of Biomedical Informatics and Department of Physiology and Pathophysiology, School of Basic Medical Sciences

institute: Peking University

summary: Circulating microRNAs (miRNAs) presented in venous plasma have recently been demonstrated as powerful biomarkers for the diagnosis and prognostic prediction of complex diseases like cancer. Nevertheless, those presented in arterial plasma have been ignored based on the assumption that the miRNA profiles in arterial and venous plasma would be identical. Here, we disputed this intuitive assumption by comparing arterial and venous plasma miRNA expression profiles from male rats using microarray technique. Though the microRNA profiles were largely similar, a considerable number of miRNAs showed significant differential expression, including 10 arterial highly expressed miRNAs and 14 venous highly expressed miRNAs. The differentially expressed miRNAs were validated by qRT-PCR. We performed computational analysis of the function enrichment and disease association of these miRNAs and their targets. Our analysis also suggested significant correlations between plasma miRNA expression and tissue miRNA expression. Four arterial highly expressed miRNAs showed enriched expression in specific tissues and thus could serve as novel biomarker candidates.

overall_design: Three healthy male rats were prepared. For each rat, one arterial plasma sample and one venous plasma sample were extracted. MiRNA expression profiles in three matched pairs of arterial/venous plasma samples were measured by using microarray.

first: Wenjing

last: Xu

first: Guoheng

first: Bin

last: Geng

first: Qinghua

last: Cui


title: Circulating long noncoding RNAs INHBA-AS1, MIR4435-2HG, CEBPA-AS1, and AK001058 in plasma serve as diagnostic markers for gastric cancer

status: Public on Jan 12 2017

first: Hanjiang

last: Fu

address: 27 Taiping Road

institute: Beijing Institute of Radiation Medicine

summary:
Background: suitable diagnostic markers for cancers are urgently required in clinical practice. Long noncoding RNAs, which have been reported in many cancer types, are a potential new class of biomarkers for tumor diagnosis.

Method: LncRNA gene expression profiles were analyzed in two pairs of human gastric cancer  and adjacent non-tumor tissues by microarray analysis. Nine gastric cancer-associated lncRNAs were selected and assessed by quantitative real-time polymerase chain reaction in gastric tissues, and 5 of them were further analyzed in gastric cancer patients’plasma.

Results: Five lncRNAs, including AK001058, INHBA-AS1, MIR4435-2HG, UCA1 and CEBPA-AS1 were validated to be increased in gastric cancer tissues. Furthermore, we found that plasma level of these five lncRNAs were significantly higher in gastric cancer patients compared with normal controls. By receiver operating characteristic analysis, we found that the combination of plasma lncRNAs with the area under the curve up to 0.921, including AK001058, INHBA-AS1, MIR4435-2HG, and CEBPA-AS1, is a better indicator of gastric cancer than their individual levels or other lncRNA combinations. Simultaneously, we found that the expression levels of a series of MIR4435-2HG fragments are different in gastric cancer plasma samples, but most of them higher than that in healthy control plasma samples.

Conclusion: Our results demonstrate that certain lncRNAs, such as AK001058, INHBA-AS1, MIR4435-2HG, and CEBPA-AS1, are enriched in human gastric cancer tissues and significantly elevated in the plasma of patients with gastric cancer. These findings indicate that the combination of these four lncRNAs might be used as diagnostic or prognostic markers for gastric cancer patients.

overall_design: In the study, to explore the potential value of lncRNAs as prognostic biomarkers for gastric cancer (GC) , we conducted lncRNA and mRNA profiling in 2 pairs of human GC and adjacent normal tissue(NT) by microarry.

first: H

first: D

last: Ke


title: Expression profiling of long noncoding RNAs and mRNAs in human plasma across time points

status: Public on Dec 01 2016

address: 38 Xueyuan Road

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

summary: The stability of long noncoding RNAs (lncRNAs) and mRNAs in human plasma was identified through expression profiling of genes across different time points (0, 0.5 hour, 1 hour, 2 hours, 4 hours, and 6 hours).

overall_design: In the study presented here, we mixed the plasma of three young males and identified the genome-wide expression level of lncRNAs and mRNAs across six time points after extraction of the plasma.

first: Cui

last: Qinghua

first: Geng

last: Bin


title: Fbxl19 recruits Rnf20 to CpG Islands and promotes H2B mono-ubiquitination [Affymetrix]

status: Public on Oct 01 2016

city: Austin

first: Bum-Kyu

last: Lee

address: 2506 Speedway Stop A5000

institute: University of Texas at Austin

summary: Rnf20 catalyzes lysine 120 mono-ubiquitination of histone H2B (H2Bub1) that has been previously involved in normal differentiation of embryonic stem (ES) and adult stem cells. However, the mechanisms underlying by which Rnf20 is recruited to its target chromosomal loci to generate H2Bub1 are still elusive. Here, we reveal that Fbxl19, a CxxC domain-containing protein, physically interacts with Rnf20, guides it preferentially to CpG island-containing target promoters, and thereby promotes mono-ubiqutination of H2B. We first show that up-regulation of Fbxl19 induces the level of global H2Bub1, while down-regulation of Fbxl19 reduces the level of H2Bub1 in mouse ES cells. Our genome-wide target mapping unveils the preferential occupancy of Fbxl19 on CpG island-containing promoters, and we further show that the binding of Fbxl19 is essential for the recruitment of Rnf20 to its target genes and subsequent H2Bub1. Altogether, our results demonstrate that Fbxl19 plays critical roles in the H2Bub1 pathway by recruiting Rnf20 to CGI target genes specifically and selectively.

overall_design: We investigated the roles of  Fbxl19 in mouse embryonic stem (ES) cells by knocking down Fbxl19. Total RNAs were extracted from the ES cells upon KD  of Fbxl19 and then hybridized on Affymetrix Mouse GeneChip 430A 2.0. We monitored global gene expression changes upon KD of Fbxl19

first: Jonghwan

last: Kim


title: Transcriptomic fingerprint of the type B trichothecene mycotoxins on the intestine

status: Public on Aug 18 2017

city: Toulouse

first: Yannick

last: Lippi

address: 180 chemin de tournefeuille

department: GeT-TRiX facility

institute: INRAE

summary:
We employed whole genome gene expression analysis to characterize the intestinal exposure to 5 closely related food contaminants belonging to the type B trichocene mycotoxins groups
The few data available on fusarenon-X (FX) do no support derivation of health-based guidance values for this mycotoxin, although preliminary results suggest higher toxicity compared to other regulated trichothecenes. Using histo-morphological analysis and whole-transcriptome profiling, the present study was designed to get a global view of intestinal alterations induced by FX. The well-described trichothecene deoxynivalenol (DON) served as a benchmark. FX exposure induced more severe intestinal histological alterations compared to DON. Intestinal inflammation was the hallmark of the molecular toxicity of DON, but also of FX. The dose-response analysis for FX revealed that benchmark doses for up-regulation of key-inflammatory genes expression were 4 to 45-fold higher than the previously reported ones for DON. Transcriptome analysis revealed that both mycotoxins down-regulated PPAR and LXR-RXR signaling pathways controlling lipid metabolism. Interestingly, several pathways including VDR/RXR activation, ephrin receptor signaling, and GNRH signaling were specific to FX and thus, discriminate the intestinal transcriptomic fingerprint of the two mycotoxins. Altogether, these results demonstrate that FX induces a more potent intestinal inflammation than DON. This study also reveals specific FX-targeted pathways, indicating that the toxicity of DON cannot serve as a benchmark for FX, and that toxicity evaluation of each trichothecene should be conducted separately.

overall_design: Jejunal explants from 4 pigs were exposed to 2µM or 10 µM deoxynivalenol, nivalenol, fusarenon-x, 3-acetyldeoxynivalenol or 15-acetyl deoxynivalenol, to vehicle (DMSO).

first: Imourana

last: Alassane-Kpembi

first: Isabelle

last: Oswald

first: Claire

last: Naylies


title: Genome-wide analysis of gene expression patterns by osteosarcoma tumor cells with different mtDNA genotypes

status: Public on Dec 31 2016

city: Clayton

first: Justin

last: St. John

state: Vic

address: 27-31 Wright St

department: Centre for Genetic Diseases

country: Australia

institute: Hudson Institute of Medical Research

summary:
Analysis of gene expression patterns in 143B osteosarcoma tumors that formed from 143B cells that harbor different background of mtDNA or no mtDNA.
The hypothesis tested in this study was that mtDNA genotypes exert influence on chromosomal gene expression.

overall_design: Total RNA extracted from 143B osteosarcoma tumors that harbor mtDNA from human neural stem cells and glioblastoma multiforme (HSR-GBM1) cells compared to 143B tumors (with their own mtDNA) and 143B rho 0 tumors (without mtDNA)

first: William

last: St John


title: Effects of Oltipraz on Gene Expression in the Livers of Wild-Type and Nrf2-null Mice

status: Public on Aug 16 2016

city: Research Triangle Park

first: Christopher

last: Corton

state: NC

address: 109 TW Alexander Dr.

institute: US-EPA

summary: Oltipraz is an activator of Nrf2 but is also an activator of other pathways including those mediated by constitutive activated receptor (CAR).  To identify genes regulated by oltipraz that were Nrf2-dependent, we compared gene expression after exposure in wild-type and Nrf2-null mice.

overall_design: Wild-type or Nrf2-null mice were treated each day for 4 days with 75 mg/kg/day/day oltipraz in corn oil or corn oil alone.  There were 4 biological replicates used for each of the 4 genotype-treatment groups.  Gene expression in the livers of the mice was evaluated using Affymetrix mouse exon arrays (MoEx-1_0-st-v1).

first: Chris


title: Gene expression analysis between primary keratinocytes and primary dermal fibroblasts obtained from the same skin sample

status: Public on Sep 01 2016

city: La Jolla

first: Masakazu

last: KURITA

state: CA

address: 10010 N Torrey Pines Rd

department: Gene Expression Laboratoy

institute: Salk Institute for Biological Studies

summary: Gene expression profile was obtained from primary keratinocytes and primary dermal fibroblasts obtained from the same skin sample

overall_design: For the successive promotor analysis, human primary keratinocytes and human primary dermal fibroblasts are obtained from the same skin sample and gene expression were evaluated by DNA microarray


title: Gene expression signatures and pathway analysis of esophageal squamous cell carcinoma

status: Public on Jul 24 2016

city: Guangzhou

first: Weihua

last: Jia

state: Guangdong

institute: SYSUCC

summary: We identified a number of deregulated genes through transcriptome analysis on esophageal squamous cell carcinoma (ESCC) and adjacent normal tissues. Our pathway enrichment analysis suggested that deregulated genes were strongly enriched in multiple functionally linked pathways known to be important in tumor cell proliferation (e.g., the p53 pathway and the cell-cycle pathway) and migration (e.g., the Notch pathway, the Wnt/β-catenin pathway).

overall_design: To identify the functional pathways playing important roles in the tumorigenesis of esophageal squamous cell carcinoma, pooled 10 ESCC tissues and pooled 10 adjacent normal tissues were analyzed using gene expression microarrays.


title: Replication timing program in 6 human model cell lines

status: Public on Jul 08 2016

city: Paris

first: Jean-Charles

last: Cadoret

address: 15 rue hélène Brion

institute: CNRS/ Université de Paris

summary: We present here the characterization of the replication timing program in 6 human cell lines : U2OS, RKO, 293T, HeLa, MRC5 and K562

overall_design: nascent-DNA from early S-phase versus nascent-DNA from late S-phase

first: Djihad

last: Hadjadj

first: Thomas

last: Denecker

first: Chrystelle

last: Maric

first: Fabien

last: Fauchereau

first: Giuseppe

last: Baldacci


title: Bladder cancer lncRNA expression profiling

status: Public on Jul 02 2016

first: Chong

last: Li

address: NO.15 Datun Road

institute: Institute of Biophysics, Chinese Academy of Sciences

summary: Using the highly sensitive lncRNA array, we screened the lncRNAs abundant in the human bladder cancer and Adjacent normal bladder tissues, and the function of differentially expressed lncRNAs were analyzed by bioinformatics.

overall_design: The Arraystar Human lncRNA Array (8x15K, Arraystar) and whole human mRNA Array (4x44K, Arraystar) and was used to profile differentially expressed lncRNAs and genes in bladder cancer vs. normal tissues following the manufacturer’s instructions. Briefly, extracted RNA template (1mg) was reversely transcribed into cDNA and digested into fragments with endonucleases. These fragments were labeled with DNA labeling reagent and labeled cDNAs were hybridized to the microarray via incubation at 45°C and rotated at 60 rpm for 17 h. Following washing and staining, the arrays were scanned using a GeneChip Scanner3000 with GeneChip Operating Software.


title: mRNA profiles in formalin-fixed and paraffin embedded (FFPE) breast cancer tissues

status: Public on Aug 01 2016

city: Duesseldorf

first: Silke

last: Schultz

address: Merowingerplatz 1A

department: Department of Obstetrics and Gynaecology

institute: University Hospital Duesseldorf

summary: we describe a mRNA profiling analysis of matched ductal carcinoma in situ and invasive duct carcinoma components of FFPE breast carcinomas with the purpose to identify potential prognostic markers

overall_design: mRNA extracted from 15 matched DCIS/IDC and 14 pure DCIS preparations was profiled using Illumina DASL platform

first: Hans

last: Neubauer

first: Karl

last: Sotlar

first: Michael

last: Bonin

first: Tanja

last: Fehm


title: Measuring lncRNAs in Exosomes from Prostate Cancer Cell Lines

status: Public on May 03 2016

city: Sydney

first: Nham

last: Tran

state: NSW

address: Jones

department: CHT/FEIT

institute: UTS

summary:
Long non-coding RNAs (lncRNAs) form the largest transcript class in the human transcriptome. These lncRNA are expressed not only in the cells, but they are also present in the cell-derived extracellular vesicles such as exosomes.
Our study examines the expression of lncRNAs in several prostate cancer cell lines but also measures the levels of these lncRNAs in the released exosomes. We show that specific lncRNAs are enriched in cancer exosomes and furthermore these sequences harbour miRNA seed regions and appear to be enriched for specific RNA binding motifs.

overall_design: A total number of four different prostate cancer cell lines and one normal cell line was used for this study. Total RNA was extracted from exosomes and the parent cell line. LncRNA expressions were then measured using a lncRNA arraystar array.

first: Alireza

last: Ahadi


title: Differential transcriptome expression in human nucleus accumbens as a function of loneliness

status: Public on Apr 27 2016

city: Stony Brook

first: Turhan

last: Canli

state: NY

address: Dept. of Psychology

department: Psychology

institute: Stony Brook University

summary: Loneliness is associated with impaired mental and physical health. Studies of lonely individuals reported differential expression of inflammatory genes in peripheral leukocytes and diminished activation in brain reward regions such as nucleus accumbens, but could not address gene expression in the human brain. Here, we examined genome-wide RNA expression in postmortem nucleus accumbens from donors (N = 26) with known loneliness measures. Loneliness was associated with 1 710 differentially expressed transcripts from 1 599 genes (DEGs; FDR p < 0.05, fold-change > |2|, controlling for confounds) previously associated with behavioral processes, neurological disease, psychological disorders, cancer, organismal injury, and skeletal and muscular disorders, as well as networks of upstream RNA regulators. Furthermore, a number of DEGs were associated with Alzheimer’s disease genes (which was correlated with loneliness in this sample, although gene expression analyses controlled for AD diagnosis). These results identify novel targets for future mechanistic studies of gene networks in nucleus accumbens and gene regulatory mechanisms across a variety of diseases exacerbated by loneliness.

overall_design: Gene expression in postmortem nucleus accumbens was examined as a function of loneliness. Twenty-six White, non-Hispanic individuals without a clinical diagnosis of depression (i.e., excluding individuals who were rated “probable” or “highly probable” to be depressed by a clinician) at baseline were selected out of a pool of 247 MAP participants with reported loneliness data by stratified random sub-sampling from a convenience sample from the top and bottom quartiles of loneliness scores (N=13 each), and matched for the number of females (N=6) in these quartiles.

first: Ruofeng

last: Wen

first: Xuefeng

last: Wang

first: Anatoly

last: Mikhailik

first: Lei

last: Yu

first: Debra

last: Fleischman

first: Robert

middle: S

last: Wilson

first: David

last: Bennett


title: CD54–NOTCH1 axis controls tumor initiation and cancer stem cell functions in human prostate cancer

status: Public on Apr 13 2016

summary: Using high sensitive ArrayStar Human, we detected differentially expressed genes and circRNAs, these part of data is the aberrent expressed genes.

overall_design: 12 Male NOD/SCID mice were obtained from the Animal Center of the Chinese Academy of Medical Science (Beijing, China). For xenograft generation, 1×10^6 LNCaP cells were subcutaneously injected into the backs of NOD/SCID mice (n=24). When tumors reached a diameter of 5 mm after 3 d, mice were randomly divided into two groups without castration (12 per group). Mice in the treatment group were administered with cisplatin at a dose of 5 mg/kg every 3 d for 30 d. Mice in the control group were treated with vehicle PBS. Tumors were taken out for microarray assay after 30 d.

first: Guoqing


title: Dissection of the cis-2-decenoic signaling network in Pseudomonas aeruginosa using microarray technique

status: Public on Mar 21 2016

city: Kermanshah

first: Hossein

last: Fallahi

state: Kermanshah

address: Bagh-e-Abrisham

department: Biology

country: Iran

institute: Razi University

summary: To identify the components of CDA signaling pathway in this pathogen, a comparative transcritpome analysis was conducted, in the presence and absence of CDA. Thereby, we identified 671 differentially expressed genes that were used to construct a gene regulatory network. GO analysis revealed that in P. aeruginosa, CDA mediates dispersion of biofilms through signaling pathways including enhanced virulence, persistence at different temperatures as well as multidrug and oxidative stress resistances.

overall_design: Two onditions; ±100 nmol CDA; One array with three hybridization blocks (3 technical repeats)

first: Azadeh

last: Rahmani-Badi


title: Development of gene expression in inflammatory bowel disease

status: Public on Feb 09 2016

first: Shenghong

last: Zhang

address: NO.58 Zhongshan Road 2

institute: Sun Yat-sen University

summary: To further development of gene expression in inflammatory bowel disease(IBD), we have employed whole genome microarray expression profiling as a discovery platform to identify genes with the potential to distinguish IBD patients and healthy volunteers. Colon biopsies were obtained from IBD patients and healthy volunteers during endoscopy. There were 353 genes that showed greater than 4-fold differential expression (285 upregulated and 68 downregulated) between IBD patients and healthy volunteers.

overall_design: Colon biopsies were obtained from 3 CD and age- ,sex- mathed healthy controlspatients and 3 healthy volunteers during endoscopy.

first: S

first: K

last: Chao

first: H

first: M

last: Chen

first: J

last: Hu


title: Knockdown of LIVE1 in HUVEC compared to universal negative control

status: Public on Jun 30 2015

city: Toronto

first: Philip

last: Marsden

address: 209 Victoria Street, Room 522

department: Medicine

country: Canada

institute: University of Toronto

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

summary: To profile changes in gene expression upon dsiRNA knockdown of LIVE1 lincRNA in HUVECs

overall_design: HUVECs were either subject to dsiRNA targeting LIVE1 or universal negative control, four distinct biological samples were used paired in each condition,  8 samples all together

first: Jenny


title: Transcriptome Analysis Of Human Rett Syndrome Brain

status: Public on Nov 24 2015

city: SYDNEY

first: Irina

last: VOINEAGU

address: High ST

institute: UNSW

summary: Transcriptome analysis of postmortem brain samples frrom frontal and temporal cortex of Rett Syndrome cases and matched controls. These data identify genes differentially expressed in postmortem brain tissue from Rett Syndrome cases.

overall_design: Total RNA was extracted from 100mg of postmortem brain tissue.

last: Voineagu

first: Peijie

last: Lin


title: HUVEC with/without VEGF-A treatment in 3D matrigel or 2D monoculture

summary: To profile changes in gene expression in human endothelial cells in response to VEGF-A165 and phenotypic changes during vascular network formation in vitro

overall_design: 16 samples of human umbilical vein endothelial cells were analysized, four distinct biological samples were used in each condition. The four conditions included: VEGF treatment in Matrigel culture, Mock treatment in Matrigel culture, VEGF treatment in 2D monolayer, and mock treatment in 2D monolayer.


title: The methyl binding domain 3 (MBD3) family proteins promote Tet2 enzymatic activity for mediating 5mC conversion [microarray]

status: Public on Mar 03 2016

city: Shanghai

first: Wei

last: Li

address: DongAn Road 130

institute: FuDan University

summary: Ten-eleven translocation (TET) proteins are key players involved in the dynamic regulation of cytosine methylation and demethylation. Inactivating mutations of TET2 are frequently found in human malignancies, highlighting the essential role of TET2 in cellular transformation. However, the factors that control TET enzymatic activity remain largely unknown. Here we found that MBD3 and its analogue MBD3L2 can specifically modulate the enzymatic activity of Tet2 protein, but not Tet1 and Tet3 proteins, in converting 5mC into 5hmC. Moreover, MBD3L2 is more effective than MDB3 in promoting Tet2 enzymatic activity via strengthening the binding affinity between Tet2 and the methylated DNA target. Further analysis revealed pronounced decreases in 5mC levels at MBD3L2 and Tet2 co-occupied genomic regions, most of which are promoter elements associated with either cancer-related genes or genes involved in the regulation of cellular metabolic processes. Our data add new insights into the regulation of Tet2 activity by MBD3 and MBD3L2 in modulating its target gene activities in cancer development and have important applications in understanding how dysregulation of TET2 may contribute to human malignancy.

overall_design: In order to investigate the biological function of MBD3L2 in regulating Tet2 enzymatic activity in mammalian cells, we extracted RNA and perform microarray profiling analysis to detect the genes regulated by Tet2 and MBD3L2.

first: Lina

last: Peng


title: Molecular karyotype analysis of 25 clinical-grade human embryonic stem cell lines

status: Public on May 05 2015

city: Edinburgh

first: Tilo

last: Kunath

address: 5 LIttle France Drive

department: Centre for Regenerative Medicine

country: United Kingdom

institute: University of Edinburgh

summary:
Clinical-grade human embryonic stem cells (hESCs) from 4 centres in the UK were cultured in self-renewal conditions
Genomic DNA was isolated from low passage hESCs and submitted for SNP analysis using Illumina HumanCytoSNP-12 v2.1 BeadChip arrays

overall_design: Evaluation of molecular karyotype of multiple clinical-grade hESC lines.

first: Maurice

last: Canham


title: LncRNA expression profiling for 6 human monocytes samples from Coronary Artery Disease patients and non Coronary Artery Disease patients

status: Public on Jun 05 2015

city: chongqing

first: Yue

last: Cai

address: Daping, Yuzhong District, the 10th branch of the Yangtze River

institute: Daping Hospital, Third Military Medical University, Cardiovascular Hospital, Chongqing Institute of Cardiovascular Disease

summary: The human LncRNA microarray analysis of the 6 monocytes samples  from Coronary Artery Disease patients and non Coronary Artery Disease

overall_design: 3 Coronary Artery Disease patients and 3 non-Coronary Artery Disease donors

first: Yujia

last: Yang


title: lncRNA and mRNA expression of cytokine treated MDA-MB-231 cells

status: Public on Mar 01 2015

first: Bodu

last: Liu

state: State...

address: School of Life Sciences, Sun Yat-sen U East Camp, High. Edu. Meg. Cntr.

summary: MDA-MB-231 cells were treated with PBS, LPS, IL1b, TNFa, IL6, and TGFb respectively and expression profile were assayed by Arraystar human lncRNA array 2.0

overall_design: We designed this experiment to screen for lncRNAs whose expressions are responsive to inflammatory stimuli.

first: Lijuan

last: Sun

first: Qiang

first: Chang

last: Gong

first: Yandan

last: Yao

first: Xiaobin

last: Lv

first: Ling

first: Herui

first: Fengxi

last: Su

first: Dangsheng

first: Musheng

last: Zeng

first: Erwei

last: Song


title: LncRNA expression profiling for 6 human plasma samples from Coronary Artery Disease patients and non Coronary Artery Disease patients

first: yujia

last: yang

summary: The human LncRNA microarray analysis of the 6 plasma samples  from Coronary Artery Disease patients and non Coronary Artery Disease

overall_design: Agilent Feature Extraction software (version 11.0.1.1) was used to analyze acquired array images. Quantile normalization was performed using Expander6 and subsequent data processing was performed using the GeneSpring GX v11.5.1 software package (Agilent Technologies). After low intensity filtering, LncRNAs and mRNAs that at least 2 out of 12 samples have flags in Present or Marginal (“All Targets Value”) were chosen for quantile normalization and further data analysis. Differentially expressed LncRNAs and mRNAs with statistical significance were identified through Volcano Plot filtering. Pathway analysis and GO analysis were applied to determine the roles of these differentially expressed mRNAs played in these biological pathways or GO terms. Finally, Hierarchical Clustering was performed to show the distinguishable LncRNAs expression pattern among samples.


title: PARTICLE - a triplex-forming long ncRNA regulates locus specific methylation in response to low dose irradiation

status: Public on Mar 19 2015

city: Neuherberg

first: Valerie

middle: B.

last: O'Leary

state: Bavaria

address: Ingolstädter Landstrasse 1

department: Institute of Radiation Biology

institute: Helmholtz Zentrum Munich

summary: Exposure to low dose irradiation causes transiently elevated expression of a long ncRNA PARTICLE (Gene PARTICL- 'Promoter of MAT2A-Antisense RadiaTion Induced Circulating LncRNA). PARTICLE affords both a cytosolic scaffold for the tumor suppressor methionine adenosyltransferase (MAT2A) and a nuclear genetic platform for transcriptional repression. In situ hybridisation discloses that PARTICLE-MAT2A associate together following irradiation. Bromouridine tracing and presence in exosomes indicate intercellular transport, and this is supported by ex-vivo data from radiotherapy-treated patients. Surface plasmon resonance indicates that PARTICLE forms a DNA-lncRNA triplex upstream of a MAT2A promoter CpG island. We show that PARTICLE represses MAT2A via methylation and demonstrate that the radiation-induced PARTICLE lncRNA interacts with the transcription repressive complex proteins G9a and SUZ12 (subunit of PRC2). The interplay of  PARTICLE with MAT2A, implicates this lncRNA in intercellular communication as well as a recruitment platform for gene silencing machineries through triplex formation in response to irradiation.

overall_design: Total RNA was isolated from T47D (ductal breast epithelial tumor), HUVEC (umbilical vein endothelial) and U2OS (osteosarcoma) human cell lines (using Ambion RNA Life Technologies, cat. # AM1560) 4 hr after 2.5 Gy γ-irradiation. RNA was amplified, transcribed into Cy3 labelled cDNA and hybridized onto the human lncRNA array V2 (representing lncRNA probes (n) = 33,045, ArrayStar).

middle: B

first: Natasa

last: Anastasov

first: Michael

last: Atkinson


title: Differential gene expression in human abdominal aortic aneurysm and atherosclerosis

city: Townsville

first: Erik

last: Biros

address: James Cook Drive

institute: James Cook University

summary: The aim of this study was to assess the relative gene expression in human AAA and AOD.

overall_design: Genome-wide expression analysis of  abdominal aortic aneurysm (AAA) and aortic occlusive disease (AOD) specimens obtained from 20 patients with small AAA (mean maximum aortic diameter=54.3±2.3 mm), 29 patients with large AAA (mean maximum aortic diameter=68.4±14.3 mm), and 9 AOD patients (mean maximum aortic diameter=19.6±2.6 mm). Relative aortic gene expression was compared with that of 10 control aortic specimen of organ donors.

first: Gabor

last: Gäbel

first: Jan

middle: H

last: Lindeman

first: Philip

last: Walker

first: Jonathan

last: Golledge


title: Long non-coding RNAs are differentially expressed in hepatocellular carcinoma cell lines with different metastatic potential

status: Public on Sep 03 2014

first: Fang

last: Tingting

state: Shanghai

address: 180 Fenglin Road, Xuhui

department: Liver Cancer Institute

institute: Zhongshan Hospital

summary: We describe the lncRNA expression profiles of two HCC cell lines, one with high potential for metastasis to the lung (HCCLM3) and the other to lymph nodes (HCCLYM-H2). The HCCLM3(LM3) and HCCLM6 cell lines were derived from the same parental cell line MHCC-97H. LM3 metastasizes to the lung, while HCCLM6 can metastasize to multiple organs in a mouse model. By subcloning HCCLM6, we established the HCCLYM-H2(H2) cell line, which showed stable and high metastatic potential specific to the lymph nodes. In the present study, we compared the expression profiles of HCC cell lines with a similar genetic background but different potential for lung or lymph node metastasis. We found that expression signatures comprising lncRNAs and protein-coding mRNAs were significantly associated with organ-specific HCC metastasis. To further validate microarray data, we selected six lncRNAs (CR613944, BC058547, RP5-1014O16.1, NCRNA00173, lincRNA-CALCA, lincRNA-TSPAN8) and two mRNAs (TSPAN8, CALCB) in the two HCC cell lines using qRT-PCR. Data obtained from qRT-PCR and the microarray was consistent.

overall_design: Differentially expressed lncRNAs between high lymphatic metastatic potential HCC cell H2 and high lung metastatic potiential HCC cell LM3 were identified by microarray and validated using quantitative real-time polymerase chain reaction.

first: Binbin

last: Liu

first: Tingting

last: Fang


title: Molecular signature in human cumulus cells related to embryonic developmental potential

status: Public on Apr 05 2014

city: Hefei

first: Dawei

last: Chen

state: Anhui

address: Huangshan Rd.

department: Life Sciences School

institute: USTC

summary:
The objective of the present study was to investigate gene expression profiles of human Cumulus cells isolated from oocytes at metaphase II  stage, under controlled ovarian stimulation (COS) cycle and to evaluate the relationship of embryo quality with molecular signatures in Cumulus cells. This study has been performed by microarray analysis in order to identify potential biomarkers related to oocyte developmental potential.
For each patient, the CCs were classified into two groups (good quality embryo group and bad quality embryo group) and pooled. From the total of 14 samples, total RNA was purified. After removal of rRNA, each sample was amplified and transcribed into fluorescent cRNA along the entire length of the transcripts without 3’ bias utilizing a random priming method. The amplified and labelled cRNA were pooled as good quality and bad quality group followed by hybridization, scanning and data analysis.Three independent repetitions were carried out, thus a total of 6 chips were employed in this study.

overall_design: the objective of the present study was to investigate gene expression profiles of human CCs isolated from oocytes at metaphase II  stage, under controlled ovarian stimulation (COS) cycle and to evaluate the relation of following embryo quality to molecular signatures in CCs.

first: Xiaofeng

last: Xu


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

status: Public on Apr 26 2014

city: Wuhan

first: BH

last: Wang

address: jiefang road 1095

institute: Tongji hospital

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

overall_design: lncRNA microarray were applied to evaluate the expression of HK-2 cells exposed to COM crystal for 0 and 24 hours.

first: Bohan

first: Xiao

last: Yu


title: Human gastric mucosa: 3 paired hTERT-negative para cancerous tissue (Control) vs. hTERT-positive gastric cancer tissue

status: Public on Jun 26 2014

city: Chongqing

first: Muhan

last: Lv

address: No.30 Gaotanyan Street, Shapingba District

institute: Southwest Hospital of Third Military Medical University

summary: The lncRNA expression profiles in three pairs of hTERT-positive gastric cancer tissue sand hTERT-negative para-cancerous tissues. The para-cancerous tissue is at least 5cm away from the cancer tissue. The expression of hTERT of identified by immunohistochemistry before RNA extraction for lncRNA assay.

overall_design: LncRNAs/mRNAs in 3 gastric cancer tissue and 3 paired para-cancerous tissue (Control) by microarray using Arraystar Human LncRNA Microarray v2.0

first: Y

last: Shiming

first: M

last: Lü


title: Murine Liver Tissues: Control vs. ErbB4 knocked out

status: Public on Sep 04 2014

city: Suzhou

first: Jianming

last: Li

address: 199 Renai Road

institute: Soochow University

summary: Transcriptional profiling of ErbB4-/- mouse liver tissues comparing controls.

overall_design: Two-condition experiment, ErbB4-/- vs. control mouse liver tissues. Biological replicates: 3 controls, 3 ErbB4-/- mice.

first: Yao


title: Role of calcium/calmodulin-dependent kinase type IV in podocyte function in lupus nephritis

status: Public on Aug 01 2014

city: Izumo

first: Kunihiro

last: Ichinose

address: 89-1 Enya-cho

department: Department of Rheumatology

country: Japan

institute: Shimane University Faculty of Medicine

summary: Kidney podocytes and their slit diaphragms contribute to prevent urinary protein loss. T cell from patients with systemic lupus erythematosus display increased expression of calcium/calmodulin kinase IV (CaMKIV).  Here we evaluated the functional role of CaMKIV in lupus nephritis (LN) using kidney biopsy specimens and human podocyte cell line (AB8/13). We found that exposure of podocytes to IgG from LN patients resulted in entry of IgG into the cytoplasm. CaMKIV expression was found to be increased in podocytes of LN kidney biopsy specimens and exposure to IgG from LN patients. IgG entered podocytes using the FcRn receptor because when podocytes where treated with FcRn siRNA less IgG was found in the cytoplasm. The DNA microarray studies of podocytes exposed to LN IgG revealed that genes that are related to the activation of immune cells or podocyte damage were upregulated. These genes included CD86, CaMKIV, PTPN22, PDE5A, CD47 and MALT1.   Interestingly, CD86 expression decreased after silencing CaMKIV in podocytes. Also, in situ hybridization experiments showed that the expression of CD86 was reduced in podocytes from MRL/lpr.camkiv−/− mice. IgG from LN patients may enter podocytes through the FcRn and causes the upregulation of a distinct set of genes which may alter podocyte function.  Upregulation of CaMKIV appears to precede that of genes known to be linked to podocyte damage such as CD86.  These findings may indicate that inhibition of CaMKIV may prove of clinical use in patients with LN.

overall_design: IgG Purification Kits (Dojindo Molecular Technologies, Inc.) are used for isolation and purification of immunoglobulin G of healthy and normal individual according to the manufacturer’s protocol. Flow through the column was used for non IgG binding samples. Cultured human podocytes with IgG purified from sera of normal individuals and LN patient for 24 hr were collected for RNA.

first: Kenichi

last: Miyoshi

first: Takeshi

last: Ushigusa

first: Ayako

last: Nishino

first: Yosikazu

last: Nakashima

first: Takahisa

last: Suzuki

first: Yoshiro

last: Horai

first: Tomohiro

last: Koga

first: Shin-ya

last: Kawashiri

first: Naoki

last: Iwamoto

first: Mami

last: Tamai

first: Kazuhiko

last: Arima

first: Hideki

last: Nakamura

first: Tomoki

last: Origuchi

first: Atsushi

last: Kawakami

first: George

last: Tsokos


title: miRNA expression profiling in PBMCs from kidney patiens with or without donor specific antibody

status: Public on Aug 31 2014

city: Nagoya

first: Kenta

last: IWASAKI

state: Aichi

address: 65 Tsurumai-cho, Showa-ku

department: Department of Transplant Immunology

institute: Nagoya University School of Medicine

summary: Investigation whether PBMCs miRNAs could be a predictable biomarker for chronic AMR (CAMR). A validation study (Study I) based on microarray profiling of total 435 mature human miRNAs using pooled samples of Group I-1 (Stable: n=11), Group I-2 (DSA: n=11) and Group I-3 (clinical CAMR: n=6)

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: To assess the relation between PBMC miRNA levels and the development of CAMR, we conducted a global miRNA expression analysis using pooled RNA isolated from PBMCs of patients in respective groups according to the stage of CAMR (Stable function, DSA production, and then renal dysfunction due to CAMR). A total of 435 mature human miRNAs were profiled.

last: Iwasaki

first: Takaaki

last: Kobayashi


title: The gene expression profiling of human Glioblastoma multiforme and normal brain tissues

status: Public on Sep 26 2013

city: shanghai

first: Yong

last: Yan

address: 415# of Fengyang street

department: neurosurgery

institute: changzheng hospital

summary: We used microarrays to investigate the whole genome gene expression level changes of LncRNAs in human Glioblastoma multiforme (GBM) and normal brain tissues, and try to find out some LncRNA associated with the tumorigenesis of GBM.

overall_design: The human LncRNA microarray analysis of 10 samples (5 GBM and 5 normal brain tissues) were completed. Total RNA from each sample was quantified and RNA integrity was assessed using standard denaturing agarose gel electrophoresis. Total RNA of each sample was used for labeling and array hybridization. Array scanning using the Agilent Scanner G250C. Scanned images were then imported into NimbleScan software (version 2.5) for expression data analysis. Differentially expressed LncRNAs were filtered out for further study.

first: Ju

middle: X

last: Chen

first: Yi

last: Lu


title: Profiling of lncRNAs and protein-coding RNAs in colorectal cancer and of MYC-regulated lncRNAs and protein-coding RNAs

status: Public on Sep 20 2013

city: Columbus

first: Taewan

last: Kim

state: OH

institute: The Ohio State University

summary:
The Arraystar Human LncRNA Array v2.0 was designed for researchers who were interested in profiling both LncRNAs and protein-coding RNAs in human genome. 33,045 LncRNAs were collected from the authoritative data sources including RefSeq, UCSC knowngenes, Ensembl and many related literatures.
This experiment is to profile lncRNAs and protein-coding RNAs using Arraystar Human LncRNA Array v2.0.

overall_design: Identification of coding RNAs and lncRNAs that are diffrentially expressed in colorectal cancer by comparing sample A-E (normal colorectal cells) vs sample F-J (colorectal tumor cells) and c-MYC-regulating lncRNAs by comparing sample 1-3 (triplicate of HCT116 cells treated with control siRNA) vs sample 4-6 (triplicate of HCT116 cells treated with siRNA targeting MYC) and sample 7-9 (triplicate of RKO cells treated with control siRNA)  vs sample 10-12 (triplicate of RKO cells treated with siRNA targeting MYC) .


title: Expression profiling of long noncoding RNAs and mRNAs in uterine leiomyoma

status: Public on Aug 14 2014

city: Jinan

first: Zhaojian

last: Liu

state: Shandong

address: 44# Wenhua xi Road

department: Cell Biology

institute: Shandong University

summary: Global protein coding gene and miRNA expression profiling studies in uterine leiomyoma showed their aberrant expression and involvement in the pathogenesis of uterine leiomyoma. But the global expression patterns and potential clinical value of long noncoding RNA (lncRNA) in uterine leiomyoma have not been explored.In this study, we performed lncRNA expression profiles analysis of uterine leiomyoma using microarray(Arraystar Human LncRNA Array v2.0) to evaluate the genome-wide expression of lncRNAs and mRNAs and their potential role in the pathogenesis of uterine leiomyoma.

overall_design: Expression profiling analysis of the 15 samples including 5 large fibroids, 5 small fibroids and 5 matched myometrium by Arraystar Human LncRNA Array v2.0.

first: Changshun

last: Shao

first: Jian-jun

last: Wei

first: Haiyang

last: Guo

first: Xiyu

last: Zhang

first: Ruifen

last: Dong

first: Xiaolin

first: Yinuo

last: Li


title: Long non-coding RNAs and mRNAs regulated by TGF-β

status: Public on Feb 08 2014

first: shu-han

last: sun

address: 800 Xiang-Yin Road

institute: Second Military Medical University

summary: The role of TGF-β-induced epithelial-mesenchymal transition (EMT) in cancer cell dissemination is well established, but the involvement of lncRNAs in TGF-β signaling is still unknown. In this study, we observed that the lncRNA-Activated by TGF-β (lncRNA-ATB) was upregulated in hepatocellular carcinoma (HCC) metastases and associated with poor prognosis. lncRNA-ATB promotes the invasion-metastasis cascade, which suggest that lncRNA-ATB, a mediator of TGF-β signaling, could predispose HCC patients to metastases and may serve as a potential target for anti-metastatic therapies.

overall_design: SMMC-7721 hepatoma cells were continuously treated with 10 ng/ml of recombinant TGF-β1 for 21 days. Total RNA recovered from three untreated cells and three treated cells were used to acquire different expression profiles of mRNAs and lncRNAs.

first: Ji-hang

last: Yuan

first: Shu-han

last: Sun


title: Aberrantly expressed lncRNAs in Primary Varicose Great Saphenous Veins

status: Public on Oct 01 2013

first: xiaoyan

last: jiang

state: shanghai

address: No.1239 siping road

institute: tongji university

summary: LncRNAs are key regulatory molecules involved in a variety of biological process and human diseases. However, the pathological effects of lncRNAs on primary varicose great saphenous veins (GSVs) remain unclear. In this study, we aimed at identifying aberrantly expressed lncRNAs involved in the prevalence of GSV varicosities and exploring their potential regulating effects.

overall_design: 6 paired tissues of the varicose great saphenous vein patient were used to compare the expression differences between varicose veins (VVs) and adjacent normal segments of saphenous veins (NVs) in the study. The lncRNA and mRNA expression profile of 6 paired vein tissues were studied using the microarry.

first: Xiang

first: Xiao-Yan

last: Jiang

first: Yi-Han


title: In vitro and In vivo Evidence of Long Non-coding OR3A4 in Gastric Cancer Progression and Tumorigenicity

status: Public on Feb 11 2014

first: lei

last: guo

address: changhai road 225

institute: EHBH

summary:
LncRNA and mRNA expression profiling for 7 human gastric cancr samples (3 tumor tissues and 3 tumor lymph node and 1 normal tissue)
We have completed the metastasis-related Long Noncoding RNA expression profiling data microarray analysis of the 7 human gastric cancer related samples

overall_design: In the study presented here, a consecutively operated, well-defined cohort of  three gastric cancer tissues and three metastatic lymph nodes tissues compared with the normal tissues and lymph nodes tissues, followed up more than five years, was used to acquire expression profiles of a total of 1942 lncRNA and 1976 mRNA, leading to the successful construction of supervised

first: Xiaobo

first: Ziguo

last: Yang


title: LncRNAs Expression in Preeclampsia Placenta Reveals the Potential Role of LncRNAs Contributing to Preeclampsia Pathogenesis

status: Public on Sep 12 2013

city: Nanchang

first: xiaoju

last: He

address: Bayi Road 318#

department: Department of Obstetrics

institute: Jiangxi Maternal and Child Health Hospital

summary:
Background: Long non-coding RNAs (lncRNAs) are an important class of pervasive genes involved in a variety of biological functions. They are aberrantly expressed in many types of diseases. We want to study the lncRNAs profiles in preeclampsia. Preeclampsia has been observed in patients with molar pregnancy where a fetus is absent demonstrating that the placenta is sufficient to cause the condition. So we analyze the lncRNAs profiles in preeclampsia placentas. In this study, we described the lncRNAs profiles in 6 preeclampsia placentas (T) and 5 matched normal pregnancy placentas (N) tissues by microarray.
Methodology/Principal Findings: With abundant and varied probes accounting 33,045 LncRNAs in our microarray, the number of lncRNAs that expressed at a certain level could be detected is 28,443. From the data we found there were 738 lncRNAs that differentially expressed (≥1.5 fold-change) among preeclampsia placentas compared with matched controls. Up to 18,063 coding transcripts could be detected in placenta samples through 30,215 coding transcripts probes. Coding-non-coding gene co-expression networks (CNC network) were constructed based on the correlation analysis between the differential expressed lncRNAs and mRNAs. According to the GO-Pathway analysis of differential expressed lncRNAs/mRNAs, we choose three lncRNAs to analyze the relationship between lncRNAs and preeclampsia. LOC391533, LOC284100, CEACAMP8 were evaluated by qPCR in 40 of preeclampsia placentas and 40 of controls. The results showed three lncRNAs were aberrantly expressed in preeclampsia placentas compared with controls.
Conclusions/Significance: Our study is the first one to determine genome-wide lncRNAs expression patterns in preeclampsia placenta by microarray. The results displayed that clusters of lncRNAs were aberrantly expressed in preeclampsia placenta compared with controls, which revealed that lncRNAs differentially expressed in preeclampsia placenta may exert a partial or key role in preeclampsia development. Misregulation of LOC391533, LOC284100, CEACAMP8 might be associated with preeclampsia. Taken together, this study may provide potential targets for future treatment of preeclampsia and novel insights into preeclampsia biology.

overall_design: LncRNAs/mRNAs profiles in 6 preeclampsia placentas and 5 matched normal pregnancy placentas tissues by microarray using Arraystar v2.0.

first: Xiaoju

first: Yinyan

first: Binrong

last: Xi

first: Jiusheng

last: Zheng

first: Xiaoming

last: Zeng

first: Qinhua

last: Cai

first: Yu

last: OuYang

first: Chen

last: Wang

first: Xiaofei

last: Zhou

first: Huiying

last: Huang

first: Wei

last: Deng

first: Siming

last: Xin

first: Qixiang

first: Huai


title: Differential expression for salt and drought stress

status: Public on Dec 31 2011

city: New Delhi

first: Vandna

last: Rai

state: Delhi

address: Pusa campus

department: Genomics

institute: NRCPB

summary: Leaf samples were used. We exposed young seedlings to NaCl and drought.

overall_design:
Expression study in 24hrs salt and drought condition.
Salt-sensitive and salt-tolerant strains of rice exposed to NaCl or control conditions.
Drought-sensitive and drought-tolerant strains of rice exposed to drought or control conditions.

first: Nagendra

middle: K

last: Singh


title: Profiling of lncRNA expression in human monocytic cells

status: Public on May 07 2013

city: Birmingham

first: Gang

last: Liu

state: Alabama

address: 901 19TH ST S

institute: University of Alabama at Birmingham

summary: By employing ArrayStar Human LncRNA Array V2.0, we have identified ～1100 differentially expressed lncRNAs (with >2-fold change) in LPS-treated THP-1 cells.

overall_design: To know the differential expression of lncRNA in LPS-treated human THP-1 cells.


title: Noncoding RNA expression profiling of cisplatin-resistant cells derived from the A549 lung cell line (lncRNA and mRNA)

status: Public on Jan 15 2013

city: Beijing

first: Yong

address: baijiazhuang street 8

institute: ccmu

summary: To determine the signaling networks that are dysregulated in cisplatin-resistant non-small cell lung cancer, noncoding RNA expression data were obtained from, and compared between, the lung adenocarcinoma cell line, A549, and its cisplatin-resistant derivative, A549/CDDP.

overall_design: Noncoding RNA expression data from a cisplatin-sensitive lung adenocarcinoma cancer cell line (A549) were collected and compared to noncoding RNA expression data from a cisplatin-resistant cell line (A549/CDDP). 3 independent experiments were completed for both the sensitive and resistant cell lines.

first: Hui

last: Li

first: Jie

first: Jun


title: Noncoding RNA expression profiling of cisplatin-resistant cells derived from the A549 lung cell line

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

platform_organism:
Homo sapiens
synthetic construct

overall_design: Refer to individual Series


title: DNA methylation and expression profiling study for bladder cancer [gene expression]

status: Public on May 03 2013

city: Daejeon

first: Seon-Kyu

last: Kim

address: 125 Gwahak-ro, Yuseong-gu, Daejeon 305-806, Korea

department: Personalized Genomic Medicine Research Center

country: South Korea

institute: Korea Research Institutue of Bioscience & Biotechnology

summary: The DNA methylation patterns associated with the development and progression of cancer. The aim of the present study was to identify novel methylation markers that can discriminate between normal and Non-muscle-invasive bladder cancer (NMIBC), and between good and poor prognosis using microarray analysis of DNA methylation and RNA expression patterns in NMIBC patients. From the 24 matched microarray-based DNA methylation and gene expression profiling data set, tumor specific hypermethylated genes were selected and clinical relevance of these genes were verified by quantitative PQS analyses. Methylation statues of several genes were significantly associated with decreased gene expression levels and aggressive clinicopathological characteristics. In multivariate regression analyses, hypermethylation of these genes were the independent predictors of recurrence and progression.

overall_design: For the integrated analysis of global methylation status and gene expression levels, we used the genome-wide human-6 v2.0 expression beadchip (Illumina Inc., San Diego, CA). Gene expression analysis was performed according to the manufacturer’s protocol. Five hundred nanograms of total RNA were used for labeling hybridization according to the manufacturer’s protocol. Arrays were scanned with an Illumina Bead Array Reader confocal scanner (BeadStation 500GXDW; Illumina Inc., San Diego, CA), according to the manufacturer's instructions. Initial microarray gene expression data were obtained using the gene expression analysis module of Bead Studio software (version 3.1.3, Illumina Inc., San Diego, CA). To export to gene expression data based on unique gene, we use Sample Gene Profile option of Illumina BeadStudio software.  Therefore, a total of 5553 probe data which have duplicated gene aggregated unique genes from the whole 48701 probes on the Human-6 beadChip ver. 2.

first: Hyung-Yoon

last: Yoon

first: Yong-June


title: A Novel Model of Common TLR4- and Injury induced transcriptional themes in Human Leukocytes (supported by NIH grant GM34695)

status: Public on Jun 11 2010

city: New Brunswick

first: Stephen

middle: F

last: Lowry

state: NJ

address: 125 Paterson St

department: Surgery

institute: UMDNJ

summary: Fifteen human volunteer subjects (18-40 years of age) and 5 Trauma patients were studied. One volunteer group (saline + LPS [n = 8]) received a 12 hour infusion a second  volunteer group (cortisol + LPS [n = 7]) received a 12 hour infusion of cortisol (3 µg/kg/min). After 6 hours of saline or cortisol infusion, intravenous lipopolysaccharide (2 ng/kg) was administered to all subjects. Blood samples were collected at 0 hours, 6 hours and 24 hours relative to LPS administration at 0 hours. Blood samples were drawn from a grounp of Trauma patients shortly (day1-5) after admission and later in their ICU stay (day 5-7). Leukocytes were isolated from these blood samples, total RNA extracted, and microarray analyses performed using Affymetrix Focus GeneChips® on samples yeilding sufficent quantity and quality RNA for analysis.

overall_design: Blood samples were collected at 0hr, 6hr, and 24hr in relation to the LPS infusion. For both saline and cortisol treated subjects, infusion was started at (-6) hr and continued to (+6) hr.

first: Beatrice

last: Haimovich


title: Effect of 11 xenobiotics on Sf9 cells and insect midgut

status: Public on Dec 13 2012

city: Sophia Antipolis cedex

first: frederique

last: hilliou

address: 400 route des chappes, BP167

department: SPE

institute: INRA


title: DNA methylation and expression profiling study for bladder cancer

type:
Expression profiling by array
Methylation profiling by array


title: long noncoding RNAs expression data from GM0637 with and without DNA damage

status: Public on Jan 17 2013

city: Houston

first: Guohui

last: Wan

state: TX

address: 7777 Knight Road

department: Cancer Biology

institute: The University of Texas M.D. Anderson Cancer Center

summary: GM0637 cell were treated with or without DNA damaging agent neocarzinostatin (NCS), and cells were harvested after 4 hours and 8 hours for the microarray analyses of whole-genome long noncoding RNAs.

overall_design: To examine how long noncoding RNAs are regulated in the DNA damage response, we assessed the genome-wide long noncoding RNA expression in GM0637 cells treated with or without DNA damage


title: Aberrant expression of lncRNAs in autistic brain

status: Public on Sep 10 2012

city: Bethesda

first: Mark

last: Ziats

state: Maryland

address: 49 Convent Drive, Bld 49, Room 2c08

institute: National Institute of Child Health and Human Development

summary: To assess for the potential contribution of dysregulated long non-coding RNA expression in autism pathogenesis, we profiled lncRNAs and mRNAs from post mortem brain tissue from autism patients and age/sex matched controls

overall_design: 4 brain tissue samples from autism patients (2 patients, 1 prefrontal cortex and cerebellum sample from each) were compared to 4 brain tissue samples from non-affected controls (2 patients, 1 prefrontal cortex and cerebellum sample from each)

first: Owen

last: Rennert


title: Gene expression analysis of lung adenocarcinoma and adjacent non-tumor tissues

status: Public on Mar 09 2017

city: FuZhou

first: Guo

last: Zheng

state: FuJian

address: No.1 Xue Yuan Road

department: Department of Bioinformatics

institute: Fujian Medical University

summary: Genome wide gene expression profiling of lung adenocarcinoma and non-tumor adjacent tissues. The Agilent microarray was used to obtain gene expression profiles. Samples included eight lung cancer and adjacent non-tumor tissues excised from a cohort of 8 patients with lung adenocarcinoma.

overall_design: Total RNA was extracted using Trizol reagent (Invitrogen) according to the manufacture's protocol. The purity and concentration of RNA was determined by Nano Drop ND-1000 spectrophotometer according to OD260/280 reading. Total RNAs were hybridized using mRNA + lncRNA Human Gene Expression Microarray

first: Fei

last: He

first: Zheng

last: Guo


title: Gene expression analysis of cancer stem cells with stem cells or cancer related cells

status: Public on Jun 29 2018

city: Okayama

first: Akimasa

last: Seno

state: Okayama

address: 1-1, Tsushima-Naka, 1-chome, Kita-Ku

department: Applied Chemistry and Biotechnology

institute: Okayama University

type:
Expression profiling by array
Third-party reanalysis

summary: RNA expression of human induced cancer stem cells and human induced pluripotent stem cells were analyzed.

first: Tomonori

last: Kasai