title: Alpha-amylase overproduction in Streptomyces lividans

status: Public on Jul 23 2015

city: Cantoblanco

first: Juan

middle: Carlos

last: Oliveros

state: Madrid

address: Darwin 3

country: Spain

institute: CNB, CSIC

summary: The gene aml encoding alpha-amylase in Streptomyces lividans was cloned in the multicopy plasmid pIJ486, generating plasmid pAMI11. Plasmid pAMI11 and pIJ486 were propagated in S. lividans TK21 to obtain S. lividans TK21(pAMI11) and its isogenic strain S. lividans TK21(pIJ486). Transcriptional profiling of the bacterium that overproduces alpha-amylase mainly resulted in the upregulation of genes involved in the biogenesis and function of ribosomes, together with the upregulation of the genes involved in the redox processes, the ABC transporters, the central carbon, aminoacid and purine /pyrimidine metabolism.  Moreover, some genes involved in oxidative stress were upregulated. The number of genes downregulated was much lower than the upregulated ones. Therefore, bacteria respond by favouring alpha-amylase overproduction that apparently does not cause damage to the cell.

overall_design: All microarray analyses were performed with RNA samples obtained from three independent cultures grown under identical conditions. The cDNA obtained from each RNA preparation of the alpha-amylase overproducer strain was hybridised with the cDNA obtained from the equivalent RNA preparation of the isogenic strain (S. lividans TK21 [pIJ486]).

first: Sonia

last: Gullón

first: Rafael

middle: P

last: Mellado


title: Agarase overproduction in Streptomyces lividans

summary: The gene dagA encoding agarase in Streptomyces coelicolor was cloned in the multicopy plasmid pIJ486 generating plasmid pAGAs5. Plasmid pAGAs5 and pIJ486 were propagated in S. lividans TK21 to obtain S. lividans TK21(pAGAs5) and its isogenic strain S. lividans TK21(pIJ486). Transcriptional profiling of the bacterium that overproduces agarase mainly resulted in the downregulation of the genes involved in the biogenesis and function of ribosomes, together with the downregulation of the genes involved in nitrogen, aminoacids, purine/pyrimidine and central carbon metabolism as well as ABC transporters, redox processes and fatty acids biosynthesis. The number of genes upregulated in the agarase overproducer strain is lower than in the downregulated ones. Almost 50% of the dowregulated genes have been described as forming part of the stringent response in streptomycetes. Therefore, the overproduction of agarase may lead to a condition of nutrient depletion that triggers the stringent response.

overall_design: All microarray analyses were performed with RNA samples obtained from three independent cultures grown under identical conditions. The cDNA obtained from each RNA preparation of the agarase overproducer strain was hybridised with the cDNA obtained from the equivalent RNA preparation of the isogenic strain (S. lividans TK21 [pIJ486]).


title: Gene expression patterns in responding versus non-responding AB1-HA tumors from mice during immunotherapy

status: Public on Jul 22 2015

city: Subiaco

first: Anthony

last: Bosco

state: WA

address: 100 Roberts Road

country: Australia

institute: Telethon Kids Institute

summary:
Balb/c mice were inoculated subcutaneously with AB1-HA cells on both flanks on day 0. The mice were then treated with anti-CTLA-4 on day 5 or 6.
7 days later, one tumor was removed for gene expression studies, and the other was left in situ to monitor tumor growth and determine if the eventual outcome was progression or regression.

overall_design: The study design consisted of three experimental groups; (i) untreated mice; (ii) anti-CTLA-4 treated responders; (iii) anti-CTLA-4 treated nonresponders. There were 10 animals in each group.


title: Gene expression profiling of bovine muscle samples upon experimental treatment with dexamethasone and dexamethasone/Clenbuterol combination

status: Public on Jul 27 2015

city: Mölndal

first: Ramy

last: Elgendy

state: Göteborg

address: Pepparedsleden 1

country: Sweden

institute: AstraZeneca

summary: In the present study, Bovine transcriptome was characterized in order to identify a set of candidate genes potentially useful for rapid detection of illegal use of some growth promoters (GPs) as dexamethasone (DEX) alone or in combination with the B2-agonist clenbuterol (CLEN). A bovine oligo microarray platform (GPL7053) was used to profile gene expression from twelve (12) bovine biceps brachii samples. Isolated and purified total RNAs were individually hybridized to the Agilent bovine V1 4x44k DNA microarray. The comparison of untreated and treated bovine transcriptomes revealed a set of differentially expressed genes. After functional analysis and qPCR validation, 16 genes were found to be differentially expressed among groups (15 downregulated genes & 1 upregulated gene between CTR and DEX and CTR and DEX CLEN groups, respectively).

overall_design: A total of 24 animals was used in this study. Animals were randomly divided into three groups of 8 animals each. The first group was used as a control (CTRL), the second was treated with dexamethasone (DEX)  administered via feed 0.75 mg per capita for 42 days (group DEX), and the third one was treated with an increasing dose of Clenbuterol (CLEN) via feed 2 mg per capita during the first week, 4 mg per capita during the second week, and 6 mg per capita during the third and the fourth weeks (28 days in total), in combination with DXM 0.66 mg per capita for 21 days (group DEX+ CLEN).Twelve samples (4/group) out of the 24 were chosen for the microarray analysis based on the highest isolated RNA quality.

first: Mery

last: Giantin

first: Mauro

last: Dacasto


title: Copy Number Data from Archival Leiomyosarcoma

status: Public on Jul 24 2015

city: Sheffield

first: Abdulazeez

middle: Temitope

last: Salawu

address: Beech Hill Road

department: Oncology

country: United Kingdom

institute: University of Sheffield Medical School

type: Genome variation profiling by genome tiling array

summary:
Soft tissue sarcomas (STS) often present a significant diagnostic challenge as many STS bear histologic resemblance, but are known to have very different clinical and biologic characteristics. Some STS subtypes are characterized by specific genetic abnormalities and this has helped in their classification, diagnosis and even treatment. However, a large majority of STS have no known specific genetic aberrations even though they almost always have highly aberrant karyotypes. We therefore hypothesize that the latter subgroup of STS bear genetic abnormalities that are sub-type specific, but as yet unidentified.

High-resolution mapping of copy number aberrations in cancer genomes is a valuable way of identifying recurrent genomic changes that could be of pathogenetic significance. Traditionally, this has been done using high quality DNA obtained from fresh frozen tissue or cells and archived tissue is generally regarded as unsuitable because of the degradative effects of formalin fixation on DNA. Utility of archival tumour material for such molecular genetic analysis is vital, especially for rare cancers like STS but recent efforts to accomplish this have produced variable results.

We therefore set out, in addition to optimize a protocol for obtaining genomic copy number data from formalin-fixed, paraffin-embedded (FFPE) STS material that is comparable to that from fresh frozen (FF) material. Microarray-based Comparative Genomic Hybridization (aCGH), a high- resolution, genome-wide method was used to identify somatic copy number aberrations (SCNAs) in primary STS samples (fresh frozen and archival FFPE), using an optimized protocol for labeling DNA. Findings were confirmed using Conventional Cytogenetics and Fluorescence in-situ Hybridization (FISH). Data obtained from paired samples (FF and FFPE) of the same tumours showed similar results and array results were consistently of good quality.

On-going analysis of the recurrent SCNAs in combination with expression data and clinical correlates may serve to identify specific patterns that can serve as diagnostic markers, characterize subgroups with prognostic implication or identify potential therapeutic targets.

overall_design:
To identify common CNAs among LMS fresh and FFPE.
25 samples in total: 22 individual FFPE cases; 3 cases also obtained fresh.  Reference DNA was obtained from same patient when possible, otherwise commercial genomic DNA was used [Promega® UK with Cat Nos.  G1471 (male) and G1521 (female)].

first: Karen

last: Sisley


title: Identification of drought stress related genes in NatA depleted mutants

city: Mannheim

first: Carsten

last: Sticht

address: Theodor-Kutzer-Ufer

department: ZMF

country: Germany

institute: University Heidelberg

summary:
N-terminal protein acetylation is one of the most common protein modifications in eucaryotes and is catalyzed co-translationally by N-terminal aceytltransferases (Nats). Regarding the number of predictaed substrates, NatA is the main Nat complex in human and yeast and is composed of the catalytic subunit NAA10 and the auxilliary subunit NAA15. The down-regulation of NAA10 and NAA15 results in Arabidopsis in drought resistant plants. This study focus on the identification of altered gene expression leading to the drought resistant phenotype.
Microarray analysis was used to identify misregulated genes in the NatA depleted mutants responsible for the drought resistant phenotype

overall_design: Arabidopsis thaliana plants were grown on soil for 6 weeks under short-day conditions (8h light / 16h dark cycles) with normal watering and subsequently challenged with drought for 10 days. After 10 days of drought Arabidopsis leaf material was harvested and used for RNA extraction and hybridization on Affymetrix microarrays. Four biological replicates from each genotype and condition were analyzed.

first: Eric

last: Linster

first: Markus

last: Wirtz


title: Micro-array analysis of the anterior vaginal wall from premenopausal patients with Pelvic Organ Prolapse (POP)

status: Public on Jul 31 2015

city: Amsterdam

first: Manon

middle: Heleen

last: Kerkhof

state: Noord Holland

address: de Boelelaan 1118

department: Obstetrics & Gynaecology

country: Netherlands

institute: VU University Medical Centre

summary:
Pelvic organ prolapse (POP) is a common multifactorial disease in a heterogeneous population of women. Due to this heterogeneity, the underlying molecular mechanisms contributing to the pathogenesis of POP are still unclear. We sought to identify dysregulated pathways by comparing gene expression profiles of prolapsed and non- prolapsed anterior vaginal wall tissue within the same patient.
Biopsies were collected from 12 premenopausal women undergoing prolapse surgery (cystocele POP-Q stage ≥ 2). A full thickness anterior vaginal wall sample was taken from the POP site during anterior colporrhaphy. An additional sample was taken from the non-prolapsed apex of the anterior vaginal cuff. Micro-array analysis was performed using whole genome GE 4x44K microarrays. Beside a significance analysis of micro-array (SAM), also a visual cluster analysis was performed.

overall_design: 12 women with POP: 12 biopsies anterior vaginal wall (POP site) versus 12 biopies precervical anterior vaginal wall ( non POP site)

middle: H

first: Saskia

last: Vosslamber

first: Alejandra

middle: M

last: Ruiz-Zapata

first: Behrouz

middle: Z

last: Doulabi

first: Theo

last: Smit

first: Hans

middle: A

last: Brolmann

first: Marco

middle: N

last: Helder


title: Alternative splicing fine-tunes transcriptome and translatome in photomorphogenic Arabidopsis [array]

status: Public on Jul 26 2015

city: Taipei

first: Chiung-Swey

middle: Joanne

last: Chang

address: 128 Sec. 2, Academia Rd, Nankang,

department: Institute of Plant and Microbial Biology

country: Taiwan

institute: Academia Sinica

summary: Light is a pivotal signal for plants’ growth and survival.  The promptly responses are required and achieving by sophisticated transcriptomic adjustments, the promptly translation enhancement, and effective protein surveillance.  However, the global role of alternative splicing regulations in response to the light is unknown.  Through global surveys of alternative splicing profile and frequency calculation for individual events normalized to transcriptomic changes, we identify nearly half of transcript present at this stage are alternatively spliced.  Through the unbiased event comparison in D and L4h mRNA, we reveal a clear impact of splicing control on 2,961 genes during early photomorphogenesis.  Intron retention is the most frequently event under controls of light as discovered in other developmental tissues and stages of Arabidopsis.  Cryptic exon is the most abundant event preserved only in the dark-grown Arabidopsis.  Genes underlying the splicing and transcriptional control mostly not overlapped indicate the distinct impacts of two regulatory mechanisms.  Through confirmation with a homemade microarray for their responsiveness of light, we conclude 1,792 genes as biological validated candidates.  Through functional study for genes underlying light-mediated splicing controls, we explore new light-signaling components which mainly responsive in isoform abundance but steady state mRNA.  Among examination both positive (RPR39, KH-RBP, RRM and RRC1) and negative (PIF4, AMI1, DNAJ, UKL3, TF-IIs-like, and ubknown-Golgi protein) factors are controlled by splicing.  Through predictions for example isoform structures, PIF4-IR4, AMI1-IR7-IR8, and DNAJ-IR1 both possess PTC and possibly produce truncated coding protein.  PIF4-IR4 becomes best illustration for the dysfunction for the negative regulator by light.  Above PTC+ isoforms together with one third of retained introns translate that evident for NMD-insensitive retained introns and supplements for protein levels.  The event identities and cis-motif signatures associated with light regulations confirm a given uniqueness for the gene expression regulation during Arabidopsis photomorphogenesis.

overall_design: mRNA and polysome-associated mRNA of 4 days old Arabidopsis seedling grown under the dark or with 4 h light-treatment were isolated and the transcriptome and splicing events profiles were surveyed by mRNAseq.  Independent 3 biological replicates of dark and L4h mRNA were applied for two-color-microarray using custom designed alternative-splicing array from Agilent Technologies.

middle: J

first: Shu-Hsing

last: Wu


title: Gene Expression in Taxol Resistance SKOV3 Cells (primary)

status: Public on Jul 16 2015

city: Kwei-San

first: Ching-Kuey

middle: Chuck

last: Chao

state: Tao-Yuan

address: 259, Wen-Hwa 1 Rd

department: Biochemistry and Molecular Biology

institute: Chang-Gung University

summary: To investigate the differences in gene expression between parental SKOV3 cells and the two taxol-resistant cell lines SKOV3/Tx50 and SKOV3/Tx600.

overall_design: Two Taxol resistant cell lines were established by stepwise increasing Taxol concentration. RNA from these resistant lines and its parental SKOV3 cells were labeled with Cy5 and were hybridized to oligo DNA array. Signals were scanned and analyzed to find out the candidate genes involved in Taxol resistant mechanism.

first: S

middle: L

last: Huang

first: N

middle: K

last: Sun

first: H

last: Lu

first: C

middle: C


title: Identification of MicroRNAs Targeting to a Specific mRNA Loci

status: Public on Jul 17 2015

city: Shanghai

first: Xiaoping

last: Su

address: 800 Xiangyin Road

country: China

institute: National Key Laboratory of Medical Immunology & Institute of Immunology

summary: Purification of human mRNAs encoding cyclin-dependent kinase inhibitor 1A (CDKN1A), also known as p21Cip1/Waf1 and signal transducer and activator of transcription 3 (STAT3) identified many miRNAs using multiplex miRNA array in HepG2 and PC-3 cells.

overall_design: To investigate the miRNAs targeting to one specific gene in vivo, we developed a protocol miRIP to affinity purify the miRNAs from an endogenous segment of mRNA using nucleic acid hybridization and use multiplex miRNA array to identify the associated miRNAs.

first: Xuetao

last: Cao


title: Genome-wide analysis of long noncoding RNA expression profile in papillary thyroid carcinoma

city: Shenyang

first: Xiabin

last: Lan

state: Liaoning Province

address: No. 155, Nanjing Bei Street, Heping District

department: Department of Thyroid Surgery

institute: The First Hospital of China Medical University

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

summary: Long noncoding RNAs (lncRNAs) have been proved to play important roles in cancer biology. To understand their expression profile and potential functions in papillary thyroid carcinoma (PTC), we investigated the lncRNA and mRNA expression in PTC and paired adjacent noncancerous thyroid tissues using microarray analysis.

overall_design: Five PTC specimens and their paired adjacent noncancerous thyroid tissue samples were obtained from the Department of Thyroid Surgery, the First Affiliated Hospital of China Medical University. All tissue samples were snap-frozen in liquid nitrogen immediately after surgical resection, and were transferred to the freezer at −80℃ before use. The diagnosis of PTC was confirmed pathologically. Five pairs of samples were used for microarray study. None of the patients had received preoperative radiotherapy, chemotherapy or any other cancer treatment.

first: Hao

last: Zhang


title: Gene Expression in Taxol Resistance SKOV3 Cells (II)


title: Gene expression profiles in liver of Sprague-Dawley rat using two types of anesthesia.

city: Kitakatsushika-gun

first: Hiroshi

last: Matsumoto

state: Saitama

address: 1600 Shimotakano, Sugito-machi

country: Japan

institute: Chemicals Evaluation and Research Institute, Japan

summary: To reveal influence of anesthesia in toxicogenomics study, gene expression analysis of liver of Sprague-Dawley rat after isoflurane anesthesia or CO2/O2 anesthesia was performed. The liver samples were excised from each rat after isoflurane anesthesia or CO2/O2 anesthesia. The gene expression profiles in liver were measureed by Agilent microarray.

overall_design: In animal study, corn oil was administrated for three days in  Sprague-Dawley rats of 9-week-old. Rats were killed after isoflurane anesthesia (n=3) or CO2/O2 anesthesia (n=3). Microarray analysis was performed one replicate per array.

first: Kyosuke

last: Yamashita

first: Fumiyo

last: Saito

first: Masahiro

last: Takeyoshi


title: Genetic heritage of the Balto-Slavic speaking populations: a synthesis of autosomal, mitochondrial and Y-chromosomal data

status: Public on Jul 18 2015

city: Tartu

first: Mait

last: Metspalu

address: Riia 23

country: Estonia

institute: Estonian Biocentre

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

summary: Here we present genome-wide genotyping data of 70 human samples from Europe (Balto-Slavic speakers, Greeks) that are used in addition to public data in a study of genetic heritage of the Balto-Slavic populations.

overall_design: 70 samples were analysed with the Illumina platforms HumanHap650Yv3 (HumanHap650Yv3_A) and Human660W-Quad v1.0 Genotyping BeadChip and are described herein.

first: Alena

last: Kushniarevich

first: Olga

last: Utevska

first: Oleg

last: Balanovsky

first: Richard

last: Villems


title: A Tumor Suppressor Function of LncRNA-X in Bcr-Abl-induced Tumorigenesis

status: Public on Jul 20 2015

city: Beijing

first: Guijie

last: Guo

address: NO.1 Beichen West Road, Chaoyang District

institute: Institute of Microbiology, Chinese Academy of Sciences (CAS)

summary:
Aberrant long noncoding RNA (lncRNA) expression has been described in many human malignancies, including leukemia. Philadelphia-positive (Ph+) chronic myeloid leukemia (CML) is a stem cell disease induced by Bcr-Abl hybrid gene. Here we attempt to identify lncRNAs associated with CML by analyzing lncRNA expression profiles in K562 cells when Bcr-Abl gene silenced. LncRNA microarray analysis revealed a group of lncRNAs that exhibit Bcr-Abl-dependent expression. In this study, we focused on lncRNA-X that was downregulated by Bcr-Abl, suggesting that lncRNA-X might have a function of tumor suppression. We showed that lncRNA-X over-expression delays Bcr-Abl-induced tumorigenesis in vivo, maybe through its effect on cell survival by modulating STAT5-dependent expression of anti-apoptotic Bcl-XL protein. We also demonstrated that lncRNA-X may affect tumor formation behavior of Bcr-Abl-transformed cells by regulating signaling pathways associated with leukemia stem cells of CML. Together, these results suggest that lncRNA-X suppresses Bcr-Abl-induced tumorigenesis, and the tumor suppressor function of lncRNA-X may be of significance for exploring novel therapeutic strategies for treating CML.
This microarray was performed to identify lncRNAs associated with Bcr-Abl-induced chronic myeloid leukemia (CML).

overall_design: Total RNAs were isolated from three independent groups of K562 cells treated with anti-Bcr-Abl or anti-luciferase shRNAs respectively, using TRIzol reagent (Invitrogen, Carlsbad, CA). Samples were amplified and labeled using a NimbleGen One-Color DNA Labeling Kit.

first: Qingzheng

last: Kang

first: Jing

last: Ouyang

first: Song

last: Wang

first: Yuhai

last: Chen

first: Ji-Long


title: miRNA profiling of Terc-/- mice plasma samples: in selenium deprivation or supplementation at young or old ages

city: Mississippi State

first: Wen-Hsing

last: Cheng

state: Mississippi

address: 945 Stone Blvd.

department: Food Science, Nutrition and Health promotion

country: USA

institute: Mississippi state university

summary: This study describes a circulating miRNA signature of selenium deprivation or supplementation at young or old Terc-/- mice, which may indentify the candidate miRNAs related to systemic changes at different stages.

overall_design:
Plasma samples were taken from mice under selenium deprivation or supplementation at 12 month-old or 18 month-old. The plasma samples from three mice in each group were used for miRNA profiling.

**Please note that [1] the normalized data matrix includes the result after filtering out all miRNA not presenting in all, and normalized as well [2] Although the results from Card A and Card B can identify up to 762 miRNA, the Raw_Ct.txt lists 315 out of 762 excluding those not detectable or below the threshold.

first: Kenneth

middle: W

last: Witwer

first: Ryan

middle: T

last: Wu


title: Effect of furan on transcriptomic and gene-specific DNA methylation changes in the livers of Fischer 344 rats in a two-year carcinogenicity study

city: Jefferson

first: Volodymyr

last: Tryndyak

address: 3900 NCTR Rd

department: Division of Biochemical Toxicology

institute: US-FDA National Center for Toxicological Research

summary: The carcinogenic effect of furan, a potent hepatotoxicant and rodent liver carcinogen, has been attributed to genotoxic and non-genotoxic, including epigenetic, changes in the liver; however, the mechanisms of the furan liver tumorigenicity are still unclear.  The goal of the present study was to investigate the role of transcriptomic and epigenetic events in the development of hepatic lesions in Fischer (F344) rats induced by furan treatment in a classic two-year rodent tumorigenicity bioassay.  Male F344 rats were distributed randomly into control and experimental groups.  Rats from the experimental groups were treated by gavage 5 days/week with either 0.92 or 2.0 mg furan/kg body weight (bw) in corn oil for 104 weeks.  Rats from control group received corn oil only.  High-throughput whole genome microarray analyses demonstrated distinctive dose-dependent alterations in gene expression in the furan-induced liver lesions.  A total of 2073 and 2422 genes was found to be differentially expressed in the furan-induced liver lesions in rats treated with 0.92 and 2.0 mg furan/kg bw, respectively, as compared to normal liver tissue.  Approximately 60% (1340) of the differentially expressed genes were common to both treatment groups.  In silico analysis of the common differentially expressed genes revealed the presence of CpG island in 51% (679) of the genes, suggesting that they may be epigenetically regulated.  Promoter methylation analysis of individual differentially expressed CpG island-containing genes demonstrated dose-dependent gene-specific methylation changes that were highly correlated with gene expression.  Our findings illustrate that gene-specific DNA methylation changes have functional consequences and may contribute to the development of furan-induced pathologic liver lesions.

overall_design: Male F344 rats were treated by gavage 5 days/week with 0.92 and 2 mg furan/kg bw for 104 weeks.  Gene expression profiles in the livers from vehicle-treated rats and non-lesion liver tissue (NT), adjacent non-lesion liver tissue (ANT) and cholangiofibrotic liver tissue (TRT) of furan-treated rats were investigated.

first: Aline

last: de Conti

first: Frederick

last: Beland

first: Igor

last: Pogribny


title: Comparative analysis of gene expression profiles in prostate cancer cells after treatment by Dexamethasone or CpdA

status: Public on Jul 21 2015

city: Moscow

first: Ekaterina

last: Lesovaya

address: Kashirskoe shosse 24-15

department: Chemical Carcinogenesis

country: Russia

institute: N.N. Blokhin Cancer Research Center

summary: The project is directed to the development of selective glucocorticoid receptor agonists for anticancer therapy. Glucocorticoids (GC) are widely used in treatment of many types of cancer due to its ability to induce apoptosis in malignant cells (in blood cancer therapy) and to prevent nausea and emesis (in the chemotherapy of solid tumors). However, severe dose-limiting side effects occur, including osteoporosis, muscle wasting, diabetes and other metabolic complications.   Both beneficial and harmful effects of glucocorticoids are due to selective activation or repression of particular genes by glucocorticoid receptor (GR). GR regulates gene expression via transactivation that requires GR homodimer binding to gene promoters and transrepression mediated via negative interaction between GR and other transcription factors as well as binding with negative glucocorticoid response elements (nGRE) in genes. GR transactivation is linked to metabolic side effects, while GR transrepression underlies glucocorticoid therapeutic action. Novel selective GR agonist Compound A (CpdA) prevents GR dimerization and transactivation, specifically activates GR transrepression, and has fewer side effects compared to glucocorticoids. Here we compare the gene expression profiles in prostate cancer cells treated with glucocorticoid Dexamethasone (Dex) or CpdA

overall_design: LNCaP prostrate cancer cells were treated with Dexamethasone (1 uM), Compound A (1 uM) or solvent (Ethanol) for 16 h. Then cells were pelleted and total RNA was isolated with RiboPure kit (Ambion) according to manufacturer's protocol. The RNA samples were treated with TURBOTM DNase (Ambion). Quality control was performed with Agilent Bioanalyser.

first: Irina

last: Budunova


title: Expression profile of plasma microRNAs in esophageal cancer

city: Nanjing

first: Juan

last: Liao

state: Jiangsu

address: No.87, Dingjiaqiao, Gulou District

institute: Southeast University

summary: In order to detect the expression profile of plasma microRNAs, we have employed microRNA microarray expression profiling as a discovery platform to identify microRNAs with the potential to distinguish the different microRNA profiles from ESCC patients and healthy controls. Three pairs of plasma samples from ESCC patients and healthy controls without any digestive tract disease history were collected for microarray analysis.

overall_design: Six samples in total, including plasma from three ESCC patients and three healthy controls

first: Ran

last: Liu

first: Yajuan

last: Shi

first: Lihong

last: Yin

first: Yuepu

last: Pu


title: Time course of the response to ACTH in pig: biological and transcriptomic study

city: Castanet-Tolosan

first: Pierre

last: Mormède

address: 24 Chemin de Borde Rouge

country: France

institute: INRA

summary: To explore individual variation in the biological response to cortisol, the main stress hormone, in pigs, we have developed a microarray analysis to study the kinetics of the response to an ACTH injection measured at 4 time points. ACTH is a hormone secreted by the pituitary gland and triggering the release of cortisol by the adrenal glands in response to a stress. The objective was to identify genes up- or down-regulated during the stress response triggered by cortisol in the whole blood.

overall_design: To explore individual variation in the biological response to cortisol, whole blood from 30 juvenile Large White (LW) pigs was collected at 4 time point ( t = 0, +1 h, +4 h, +24 h) for a total of 120 samples. All pigs were females and were raised in two batches. Arrays were designed such that all observations of a sole individual were kept on the same array, with two individuals (one from each batch) on one array. This design secured the kinetics of the response for each individual and  prevented confounding effects between batch and array. After quality and control, 120 samples were kept for normalization and analyses (represented here).

first: V

last: Sautron

first: E

last: Terenina

first: L

last: Gress

first: Y

last: Lippi

last: Billon

first: C

last: Larzul

last: Liaubet

first: N

last: Villa-Vialaneix

first: P


title: Expression values from 6 time points during the regeneration of secondary vascular System (SVS)

first: Fang

last: Tang

state: Beijing

address: Xiangshan Road， Haidian district

institute: chinese Academy of Forestry

summary:
Secondary vascular system (SVS) development resulted from cambial growth is a currently not well understood process. Therefore, more studies are needed to shed more lights on the molecular mechanisms underpinning the cambial activity. The regeneration of SVS from debarked trunk that can mimic the vascular cambium-driven wood formation has developed and could be used to revealed a larger number of differentially expressed genes during the stages of cambium formation and xylem differentiation in Populus tomentosa.
We used microarrays to detail the global programme of gene expression in 6 time points during the regeneration of SVS.

overall_design: A 1-m strip of bark was peeled from 65 healthy P. tomentosa plants in a 4-year-old single clonal plantation (located in Tangshan, Hebei Province, China), starting 0.5 m from the tree base. Exposed tissue was wrapped with transparent plastic sheets to prevent desiccation. Samples were subsequently collected by scraping regenerating tissues from the whole surfaces of the trunks at the same daytime (between 10:00-11:00 am) at 7 days (D7), 10 days (D10), 12 days (D12), 16 days (D16), 18 days (D18), and 21 days (D21) after girdling (AG), and immediately frozen and stored in liquid nitrogen. Sampling was performed on three clonal trees at one time.

first: Shutang

last: Zhao

first: Mengzhu

last: Lu


title: Microarray analysis of miRNAs in atrial tissue from chronic AF patients

status: Public on Jul 15 2015

city: Madrid

first: Susana

last: Cañón

address: Darwin, 3

department: Dept. Immunology and Oncology

institute: CNB

summary: OBJECTIVES: This study aims to define a microRNA signature in chronic AF (CAF) and to unravel key target genes contributing to the atrial remodelling.  METHODS: Total RNA from atrial biopsies of 2 sinus rhythm (SR)  and 4 CAF patients was analyzed by microRNA(miR)-array. Expression of most deregulated miRs and their actions on specific targets were confirmed by qRT-PCR in human and ovine samples and validated in HL-1 cells and myocytes isolated from CAF patients. After bioinformatics prediction of targets and signaling, and through lentiviral miR-transduction or mimics-miR transfection of HL-1 cells, effects on main predicted regulatory pathways were analyzed.  RESULTS: 38 microRNAs showed significant changes in expression in CAF atrial samples (>2-fold) and among them, miR-208a and miR-208b were confirmed to be significantly upregulated (>2 and >5-fold, respectively). Bioinformatics analysis predicted 70 pairs of CAF-altered mRNAs/miR-208a/b interactions. We confirmed that miR-208a and b directly targeted muscle cardiac gene program and canonical Wnt-signaling receptors and seemed to repress indirectly CX43. L-type Ca(2+) channel genes (CACNA1C and CACNB2) and sarcoplasmic reticulum-calcium pump SERCA2 were repressed by miR-208b at transcriptional, posttranscriptional and functional levels.   CONCLUSION:In this work we report for the first time the role of miR-208b upregulation in the control of calcium balance in CAF.

overall_design: To determine the miRNA repertoires of human AF atrial tissue, we extracted total RNA from 4 AF patients, 2 SR patients and 2 control (no AF) patients,  after disruption and homogeneization of  small pieces of frozen atrial appendage biopses from AF and SR patients. Total  RNA, including miRNAs, was purified by Qiagen miRNeasy Mini Kit - catalog number 217004, following manufacturer instructions.Isolated RNA was accurately quantified using Bioanalyzer

first: Ricardo

last: Caballero

first: Marta

last: Pérez-Hernández

first: Begoña

last: López

first: Felipe

last: Atienza

first: Jose

last: Jalife

first: Eva

last: Delpón

first: Antonio

last: Bernad


title: The Jejunum Mucosa of Female Black-boned Chickens: Control vs. Heat-stressed Treatment

status: Public on Jul 28 2015

city: Changsha

first: Lili

last: Liu

state: Hunan

address: SchooI of AnimaI Science and Technologe, Hunan AgricuIturaI University, Changsha, Hunan Province,China.

institute: Hunan AgricuIturaI University

summary: Transcriptional profiling of the jejunum mucosa with 1.5 fold-change reporter genes in comparing control black-boned chickens under normal temperature (NT) conditon with heat-stress treated black-boned chickens under high temperature (HT) condition. Goal was to determine the differentially expressed genes (DEGs) in co-family black-boned chickens exposure to heat stress based on global chicken gene expression.

overall_design: Two-condition experiment, HT vs. NT Treatment.  Biological replicates: 3 control replicates, 3 heat stressed replicates.

first: Jianhua

last: He


title: Comprehensive microRNA profiling of Nasopharyngeal Carinoma Specimens

city: Toronto

first: Jeff

last: Bruce

state: Ontario

address: 101 College St.

country: Canada

institute: Princess Margaret Cancer Centre

summary:
Publication: Identification of a microRNA signature associated with risk of distant metastasis in nasopharyngeal carcinoma
Purpose  Despite significant improvement in locoregional control in the contemporary era of nasopharyngeal carcinoma (NPC) treatment, patients still suffer from a significant risk of distant metastasis (DM). Identifying those patients at risk of DM would aid in personalized treatment in the future. MicroRNAs (miRNAs) play many important roles in human cancers; hence, we proceeded to address the primary hypothesis that there is a miRNA expression signature capable of predicting DM for NPC patients.  Methods and results  The expression of 734 miRNAs was measured in 125 (Training) and 121 (Validation) clinically annotated NPC diagnostic biopsy samples. A 4-miRNA expression signature associated with risk of developing DM was identified by fitting a penalized Cox Proportion Hazard regression model to the Training data set (HR 8.25; p < 0.001), and subsequently validated in an independent Validation set (HR 3.2; p = 0.01). Pathway enrichment analysis indicated that the targets of miRNAs associated with DM appear to be converging on cell-cycle pathways.  Conclusions  This 4-miRNA signature adds to the prognostic value of the current “gold standard” of TNM staging. In-depth interrogation of these 4-miRNAs will provide important biological insights that could facilitate the discovery and development of novel molecularly targeted therapies to improve outcome for future NPC patients.

first: Fei-Fei


title: miRNA expression profiles in the serum of cats with hypertrophic cardiomyopathy compared to healthy cats

city: Munich

first: Karin

last: Weber

address: Veterinärstr. 13

department: Medizinische Kleintierklinik

institute: Zentrum für klinische Tiermedizin

summary: MicroRNAs negatively regulate gene expression and may serve as biomarkers for human cardiomyopathy. In the domestic cat, hypertrophic cardiomyopathy (HCM) represents the most common primary cardiomyopathy. In humans, the etiology of HCM is linked to mutations in genes of contractile muscle proteins, while in cats a clear proof for causal mutations is missing. The etiology of feline HCM is uncertain. Diagnosis is made by heart ultrasound examination and  measuring the serum level of N-terminal pro B-type natriuretic peptide. The purpose of this study was to investigate whether microRNA profiles in the serum of cats with HCM are different from the profiles of healthy cats and whether specific miRNAs can be detected to serve as potential biomarkers for feline HCM or may help in understanding the etiology of this disease

overall_design: Blood was drawn from two groups of cats: 12 healthy cats and 11 cats suffering from hypertrophic cardiomyopathy. After clotting, samples were centrifuged and total mRNA was extracted from serum. These 23 serum samples were analyzed and the groups were compared

first: Stefan

last: Bauersachs

first: Nadine

last: Rostert

first: Gerhard

last: Wess


title: cDNA array expression in cotton fiber secondary cell wall development from two germplasm lines that differ in fiber strength

city: Anyang

first: Lu

middle: You

last: Yuan

state: Henan

address: Huanghe Road 38#

department: Molecular Breeding

institute: Cotton Research Institute, Chinese Academy of Agricultyral Science

summary: Comparison of gene expression profiles in cotton fiber development (from 10 to 23 DPA) of two lines. Line 1 was excellent fiber strength, denoted with H; Line 2 was poor fiber strength, denoted withL.

overall_design: Analysis used H20 RNA as control samples for comparison to the experimental samples taken at 5, 10, 15 and 23 DPA. Indirect comparisons were made across multiple arrays with raw data pulled from different channels for data analysis and comparison to the control data.Cy3 and Cy5 dyes were used as follows:Set 1:H10-Cy5 vs H20-Cy3, Set 1(dye swap):H10-Cy3 vs H20-Cy5; Set 2:H15-Cy5 vs H20-Cy3,Set 2 (dya swap):H15-Cy3 vs H20-Cy5; Set 3:H23-Cy5 vs H20-Cy3, Set 3 (dya swap):H23-Cy3 vs H20-Cy5; Set 4:L10-Cy5 vs H20-Cy3, Set 4 (dya swap):L10-Cy3 vs H20-Cy5; Set 5:L15-Cy5 vs H20-Cy3, Set 5 (dya swap):L15-Cy3 vs H20-Cy5; Set 6:L20-Cy5 vs H20-Cy3, Set 6 (dya swap):L20-Cy3 vs H20-Cy5; Set 7:L23-Cy5 vs H20-Cy3, Set 7 (dya swap):L23-Cy3 vs H20-Cy5; Set 8:H20-Cy5 vs H20-Cy3.

first: Z

last: Ji

first: H

last: Shang

first: Y


title: Chip-SIP analysis of Monterey Bay surface waters incubated with organic carbon substrates

city: Livermore

first: Xavier

last: Mayali

state: CA

address: 7000 East Ave

department: Chemical Science

institute: Lawrence Livermore National Laboratory

summary:
October 2013 surface seawater collected from Monterey Bay was incubated with 1 micromolar 13C labeled glucose, starch, acetate, lipids, protein, or amino acids for 12 hours.
Community RNA was extracted and hybridized to a Roche Nimblegen microarray and analyzed by NanoSIMS to obtain isotope ratio data for all probe spots.

overall_design: Two Chips for fluorescence, and 15 Chips for different substrates from samples incubated for 12 or 36 hours.

first: Ryan

last: Mueller


title: Transcriptomic responses in Arabidopsis thaliana to PIPL3 peptide treatment

status: Public on Jul 10 2015

city: Trondheim

first: Per

last: Winge

address: Høgskoleringen 5e

department: Department of Biology

country: Norway

institute: Norwegian University of Science and Technology

summary: In order to investigate possible roles of IDL and PIP/PIPL peptides, the transcriptomic response of Arabidopsis seedlings to treatment with PIPL3 peptide was analysed. PIPL3 (At4g37295) was chosen, as no functional data was available for this peptide; furthermore, PIPL3 was expressed in leaf tissue during seedling stages. Transcriptomic responses to 3 hours PIPL3 peptide treatment suggested a role in regulation of biotic stress responses and cell wall modification.

overall_design: Two weeks old seedlings were treated either with 100 nM PIPL3 peptide (treated) or 100 nM mock peptide (control) and whole rosettes were harvested 3 hours after treatment. 4 biological replicates per treatment.

first: Ane

last: Vie

first: Javad

last: Najafi

first: Bin

first: Melinka

last: Butenko

first: Karina

middle: S

last: Hornslien

first: Robert

last: Kumpf

first: Reidunn

middle: B

last: Aalen

first: Atle

last: Bones

first: Tore

last: Brembu


title: Developmental expression profile of Dictyostelium discoideum: wild type (AX2) and polyketide synthase knock-out mutants

city: Pune

first: Bharat

middle: Ravi

last: Iyengar

address: Dr Homi Bhabha Road

department: Chemical Engineering and Process Development

country: India

institute: CSIR-National Chemical Laboratory

summary: Knockout mutants of polyketide synthase genes were generated (pks1, pks2, pks3, pks14, pks18, pks37) and compared to wild-type AX2 strain of Dictyostelium discoideum using Agilent custom microarrays. The Dictyostelium cells were harvested at eight developmental stages (Amoeboid, Intiation of starvation, loose aggregate, Streaming, Mound, Slug, early culminant,  Fruiting body) and subjected to microarray based expression profiling.

overall_design: Six pks mutant strains (pks1, pks2, pks3, pks14, pks18, pks37) were compared to a wild type strain.  Thus, seven strains were used in total.  Each strain was studied during eight developmental stages (Amoeboid, Starvation, Loose Aggregate, Streaming, Mound, Slug, Early Culminant, Fruiting Body) thus leading to 56 samples.

first: Rajesh

last: Gokhale


title: Microarray of four CSM strains

status: Public on Jul 14 2015

city: Beibei

first: Zhifeng

last: Xu

state: Chongqing

address: Tiansheng street 2#

institute: Southwest University

summary: The phenomenon of pesticide resistance is an important example of human induced evolution, and the factors governing the origin and spread of resistance-associated genes are of academic and practical importance. To identify such genes, RNA sequencing (RNA-seq) and a custom made microarray were utilized to compare transcription levels in four different Tetranychus cinnabarinus strains.

overall_design: Four samples,two replications. SS as a control, FeR, CyR and AbR as treatments.

first: Lin

last: He


title: Genome-wide expression of the leukemic cells with different sensitivity to AraC

city: Suzhou

first: wenjun

last: zhao

address: 199 Ren'ai Road

institute: Cyrus Tang Hematology Center

summary: To examine the molecular alterations in cells with different sensitivity, genome-wide expression of the leukemic cells was profiled, revealing that overall 366 and 212 genes became upregulated or downregulated, respectively, in the resistant cells. Many of these genes are involved in the regulation of cell cycle, cellular proliferation, and apoptosis.

overall_design: gene expression of myeloid leukemic cell


title: Cavin4/Murc is required for skeletal muscle development and function in zebrafish

city: Bad Nauheim

first: Michael

middle: Patrick

last: Housley

state: Hessen

address: Ludwigstr. 43

department: Developmental Genetics

institute: Max Planck Institute

summary: To understand the underlying cause of the swimming defect in Cavin4/Murcb deficient larvae, we isolated mRNA from mutant and sibling zebrafish at 72 hpf and subjected it to microarray analysis.

overall_design: RNA and gDNA were extracted from individual larvae at 72 hpf using Trizol (Life Technologies).  Following genotyping, the aqueous phases from at least 10 Trizol extractions were combined by genotype and purified over microspin columns (ZymoResearch).  RNA expression from heterozygous and mutant larvae was analyzed by single-color microarray (8x60K Zebrafish Array XS, Oaklabs, Germany).


title: Influence of Autoinducer-2 (AI-2) in Cell-Free Supernatant of Salmonella Typhimurium in Gene Expression of S. Typhimurium

city: Dallas

first: Palmy

middle: R

last: Jesudhasan

state: TX

department: Microbiology

institute: University of Texas Southwestern Medical Center

summary: Salmonella enterica serovar Typhimurium is known to synthesize and respond to the cell signaling molecule, autoinducer-2 (AI-2). The luxS gene is involved in the synthesis of AI-2. We have previously shown that luxS controls a variety of bacterial processes in S. Typhimurium. In this study we identified the genes regulated by AI-2 in the Cell-Free supernatant of S. Typhimurium using mRNA samples from isogenic luxS gene mutant of S. Typhimurium strain 87-26254 grown in LB media in the presence of S. Typhimurium wild type CFS / absence  AI-2 (mutant CFS of S. Typhimurium). In the presence of AI-2 in CFS, 758 genes were significantly regulated. Interstingly, AI-2 in CFS caused the down-regulation of 39 genes in Salmonella Pathogenicity Island-1 (SPI-1).

sample_organism: Salmonella enterica subsp. enterica serovar Typhimurium

overall_design: Purified cDNAs from the mutant supplemented with CFS containing AI-2 and mutant without AI-2 (Mutant CFS) were each labeled with Cy-3 mono-Reactive Dye and Cy-5 mono-Reactive Dye (GE Health Care, Piscataway, NJ) and were processed using a dye-swapping design. A total of 5 microarray arrays, each with duplicate spots for each gene.

first: Suresh

middle: D

last: Pillai


title: Influence of Autoinducer-2 (AI-2) in Salmonella Typhimurium Gene Expression

summary: Salmonella enterica serovar Typhimurium is known to synthesize and respond to the cell signaling molecule, autoinducer-2 (AI-2). The luxS gene is involved in the synthesis of AI-2. We have previously shown that luxS controls a variety of bacterial processes in S. Typhimurium. In this study we identified the genes regulated by AI-2 using mRNA samples from isogenic luxS gene mutant of S. Typhimurium strain 87-26254 grown in LB media in the presence/absence of in vitro synthesized AI-2. In the presence of in vitro synthesized AI-2, 536 genes were significantly (p<0.05) regulated. Interestingly, in vitro synthesized AI-2 caused the down-regulation of 39 genes in Salmonella Pathogenicity Island-1 (SPI-1) including the transcriptional regulators hilA, hilD, and invF.

platform_organism: Salmonella enterica subsp. enterica serovar Typhimurium

overall_design: Purified cDNAs from the mutant supplemented with AI-2 and mutant without AI-2 (PBS) were each labeled with Cy-3 mono-Reactive Dye and Cy-5 mono-Reactive Dye (GE Health Care, Piscataway, NJ) and were processed using a dye-swapping design. A total of eight microarray arrays, each with duplicate spots for each gene and used for mutant supplemented with AI-2.


title: Gene expression in response to low-intensity pulsed ultrasound treatment of bone marrow cells under osteogenic conditions in vitro

city: Nagoya

first: Daisuke

last: Yamaguchi

address: 2-11 Suemori-dori

institute: Aichi Gakuin University

summary:
We performed a comprehensive analysis of gene expression changes following low-intensity pulsed ultrasound (LIPUS) treatment of cultured bone marrow cells under bone formation conditions, using cDNA microarray analysis
Bone marrow cells were obtained from the femora of rats and were suspended in an osteogenic medium to make a cell culture. After cultures were established, test cultures were exposed to LIPUS via the base of the cell culture plates for 15 min/day on days 3–9  (LIPUS group). Control cultures (without LIPUS exposure) were otherwise treated identically to the LIPUS group. On day 10, total RNA was extracted from both sets of cultures and hybridized to microarray slides, the data sets were analysed. Markers for differentiated osteoblasts and osteocytes, as well as collagen-related genes, cell adhesion factors were up-regulated in LIPUS group on day 10.

overall_design: Gene expression in response to LIPUS treatment of bone marrow cells were measured on day 10 after cultures were established.  Experiments were performed at each conditions (LIPUS or Control).

first: Kazuo

last: Takeuchi

first: Hiroki

last: Furuta

first: Shi

last: Miyamae

first: Hiroshi

last: Murakami

first: Masami

last: Hattori


title: Changes in gene expression after epigentic targeted therapy in T-cell prolymphocytic leukemia (T-PLL)

status: Public on Jul 08 2015

city: Hershey

first: Penn State

last: COM

state: PA

address: 500 University Drive

department: Genome Sciences Facility

institute: Penn State College of Medicine

summary: Epigenetic therapy overcame alemtuzumab resistance in patients with relapsed T-cell prolymphocytic leukemia and induced the expression of treatment related genes. Method:  patient PBMCs from Ficoll, normal patient PBMCS enriched for CD3+/CD8+ or CD3+/CD8+/CD45RA+/CCR7- were extracted in Trizol.  Conclusion:  Gene expression profiles were changed by epigenetic therapy, likely activating treatment response genes silenced by carcinogenesis.

overall_design: Total RNA from patient Peripheral Blood Mononuclear Cells (PBMC)  or from normal negatively enriched CD3+/CD8+/CCR7-/CD45RA+(CD45RO-) blood

first: Zainul

last: Hasanali

first: Elliot

last: Epner

first: Thomas

middle: P

last: Loughran

first: Tom

last: Olson

first: Xin

last: Liu


title: Timecourse of Interferon-Gamma Treatment of Bone Marrow-Derived Macrophages (BMDMs)

city: Edinburgh

first: Nigel

last: Binns

address: The Chancellor's Building, 49 Little France Crescent

department: Division of Pathway Medicine

institute: The University of Edinburgh

summary: The systematic temporal gene expression analysis of primary macrophages activated under immune (interferon-gamma (IFN-g)) and productive viral infection with murine cytomegalovirus (mCMV). The primary objective of the study is to define, in an unbiased manner, cause-and-effect relationships in the program of gene activation in this cellular system. The even spacing and time intervals (every 30 minutes) makes this study amenable to modelling of gene networks in the system.

overall_design: A kinetic analysis of IFN-g treatment on the gene expression of murine (BALB/c) bone marrow-derived macrophages (BMDMs) over the first 12 hours, sampling every 30 minutes. Agilent mouse genome arrays were used to determine the differences in gene expression between mock and IFN-g treated. The 25 samples collected for the mock IFN-g treatment were pooled and treated as a pooled control. Pooled control was labelled with Cy3 dye and hybridised with every other sample (labelled with Cy5 dye) = 25 dual-dye array hybridisations. The reference channel of the dual-channel hybridisations was only used to normalise the expression of the test channel, rather than used to calculate ratio data. Thus, the normalised data represent log2 single-channel data.

first: Peter

last: Ghazal


title: Fitness of natural Saccharomyces cerevisiae strains

status: Public on Jul 07 2015

city: FLORENCE

first: DAMARIZ

last: RIVERO

state: FLORENCE

address: VIALE PIERACCINI 6

department: NEUROFARBA

country: Italy

institute: UNIFI

type:
Expression profiling by array
Genome variation profiling by array

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

overall_design: Refer to individual Series


title: Fitness of natural Saccharomyces cerevisiae strains [Expression]

summary: To characterize the ecological interactions among S. cerevisiae strains coming from the same geographical area, we examined the fitness of two natural isolates from San Giovese grapes, alone or in competition, in synthetic wine must (SWM). We performed genome-wide analyses in order to identify the genes involved in yeast competition and cooperation.

overall_design: 2 samples and 4 replicates.

first: Damariz

last: Rivero

first: Luisa

last: Berna

first: Enrico

last: Baruffini

first: Irene

last: Stefanini

first: Duccio

last: Cavalieri


title: P. falciparum Complicated Malaria: Modulation and Connectivity between Exportome and Variant Surface Gene Families

city: Pilani

first: Ashis

middle: Kumar

last: Das

state: Rajasthan

address: Vidya Vihar

department: Biological Sciences

institute: Birla Institute of Technology & Science,Pilani (Pilani Campus)

summary: In temperate and sub-tropical regions of Latin America, complicated malaria manifested as hepatic dysfunction or renal dysfunction is seen in all age groups. There has been a concerted focus on understanding the patho-physiological and molecular basis of complicated malaria in children, much less is known about it in adults. This can be attributed to many factors: one of which is the expression of clonally variant families of adhesion proteins: PfEMP1 on the iRBC surface. We report here, the analysis of data from a custom, cross strain microarray (Agilent Platform) using material from patient samples, showing hepatic dysfunction or renal failure. These are the most common manifestations seen in adults along with cerebral malaria. The data has been analyzed with reference to variable surface antigens, encoded by the var, rifin and stevor gene families. The differential regulation profiles of key genes (comparison of PFC and PFU) have been observed. The exportome has been analyzed using similar parameters. GO term based functional enrichment of differentially regulated genes identified, up-regulated genes stastically enriched (p<0.5) to critical biological processes. Systems network based functional enrichment of overall differentially regulated genes yielded a similar result. We are reporting here, up-regulation of var group A and B genes whose proteins are predicted to interact with CD36 receptor in the host as also the up-regulation of group A rifins and many of the stevors. This is contrary to most other reports from pediatric patients, with cerebral malaria where the up-regulation of var A group genes have been seen. A protein-protein interaction based network has been created and analysis performed. This co-expression and text mining based network has shown overall connectivity between the variable surface antigens and the exportome. The up-regulation of var group B and C genes encoding PfEMP1 with different domain architecture would be important for deciding strategies for disease prevention.

overall_design: Plasmodium falciparum isolates were collected from patients (n=12) with differing clinical conditions. The patients exhibited symptoms categorized as uncomplicated (n=5) or complicated malaria (n=7). Criteria for determination of complicated disease were based on World Health Organization year 2000 guidelines. Microarray array based transcriptional profiling was carried out to find out differentailly expressed genes in complicated malaria isolates (non-cerebral malaria) compared to un-complicated malaria isolates.

first: Amit

last: Subudhi

first: P

middle: A

last: Boopathi

first: Dhanpat

last: Kochar

first: Sanjay


title: Fitness of natural Saccharomyces cerevisiae strains [CGH]

overall_design: 2 samples and 2 replicates.


title: TREM2 regulates microglial cell activation in response to demyelination in vivo

status: Public on Jul 06 2015

city: Trieste

first: Danilo

last: Licastro

department: Genomica Funzionale

institute: CBM

summary: Microglia are phagocytic cells that survey the brain and perform neuroprotective functions in response to tissue damage, but their activating receptors are largely unknown. Triggering receptor expressed on myeloid cells 2 (TREM2) is a microglial immunoreceptor whose loss-of-function mutations in humans cause presenile dementia, while genetic variants are associated with increased risk of neurodegenerative diseases. In myeloid cells, TREM2 has been involved in the regulation of phagocytosis, cell proliferation and inflammatory responses in vitro. However, it is unknown how TREM2 contributes to microglia function in vivo. Here, we identify a critical role for TREM2 in the activation and function of microglia during cuprizone (CPZ)-induced demyelination. TREM2-deficient (TREM2(-/-)) mice had defective clearance of myelin debris and more axonal pathology, resulting in impaired clinical performances compared to wild-type (WT) mice. TREM2(-/-) microglia proliferated less in areas of demyelination and were less activated, displaying a more resting morphology and decreased expression of the activation markers MHC II and inducible nitric oxide synthase as compared to WT. Mechanistically, gene expression and ultrastructural analysis of microglia suggested a defect in myelin degradation and phagosome processing during CPZ intoxication in TREM2(-/-) microglia. These findings place TREM2 as a key regulator of microglia activation in vivo in response to tissue damage.

overall_design: Two STAGE (6weeks 12 weeks),

first: Laura

last: Piccio


title: Timecourse of mCMV Infection of Bone Marrow-Derived Macrophages (BMDMs)

summary: The systematic temporal gene expression analysis of primary macrophages activated under immune (interferon-gamma) and productive viral infection with murine cytomegalovirus (mCMV). The primary objective of the study is to define, in an unbiased manner, cause-and-effect relationships in the program of gene activation in this cellular system. The even spacing and time intervals (every 30 minutes) makes this study amenable to modelling of gene networks in the system.

overall_design: A kinetic analysis of mCMV infection on the gene expression of murine (BALB/c) bone marrow-derived macrophages (BMDMs) over the first 12 hours, sampling every 30 minutes. Agilent mouse genome arrays were used to determine the differences in gene expression between mock and mCMV infected. The 25 samples collected for the mock infected were pooled and treated as a pooled control. Pooled control was labelled with Cy3 dye and hybridised with every other sample (labelled with Cy5 dye) = 25 dual-dye array hybridisations. The reference channel of the dual-channel hybridisations was only used to normalise the expression of the test channel, rather than used to calculate ratio data. Thus, the normalised data represent log2 single-channel data.


title: Cataloguing of Potential HIV Susceptibility Factors during the Menstrual Cycle of Pigtail Macaques

city: Atlanta

first: Gregory

last: Tharp

state: GA

address: 954 Gatewood Dr

department: Developmental and Cognitive Neuroscience

institute: Yerkes National Primate Research Center

summary: Our earlier studies in pig-tailed macaques demonstrated varying SHIV susceptibility during the menstrual cycle, likely caused by cyclic variations in immune responses in the female genital tract.  There is concern that high-dose, long-lasting, injectable progestin-based contraception could mimic the luteal phase and predispose women to HIV-1 acquisition and transmission. In this study, we adopted a systems biology approach employing proteomics (tandem mass spectrometry), transcriptomics (RNA microarray hybridization), and other specific protein assays (enzyme-linked immunosorbent assays and multiplex chemokine-cytokine measurements) to characterize the effects of hormonal changes on the expression of innate factors and secreted proteins in the macaque vagina. Several antiviral factors and pathways (including acute phase response signaling and complement system) were overexpressed in the follicular phase. Conversely, during the luteal phase there were factors overexpressed (including moesins, syndecans, integrins, among others) that could play direct or indirect roles in enhancing HIV-1 infection. Thus, our study showed that specific pathways and proteins/genes might be working in tandem to regulate innate immunity, thus fostering further investigation and future design of approaches to help counter HIV-1 acquisition in the female genital tract.

overall_design: Samples were hybridized to Affymetrix GeneChip® Rhesus Macaque Genome Arrays. Vaginal pinch biopsies were collected from 12 pig-tailed macaques at both the follicular and luteal phases. The data from one animal suggested low RNA quality and was excluded.

first: S

last: Vishwanathan

first: A

last: Burgener

middle: E

last: Bosinger

first: G

last: Guenthner

first: N

last: Patel

first: K

last: Birse

last: Westmacott

first: T

last: Henning

first: D

last: Hanson

first: J

last: Radzio

middle: G

last: Garcia-Lerma

last: Ball

middle: M

last: McNicholl

first: E

middle: N

last: Kersh


title: Disseminated medulloblastoma in a child with germline BRCA2 6174delT mutation and without Fanconi anemia

city: Scottsdale

first: Michael

middle: Thomas

last: Barrett

state: AZ

address: 13400 East Shea Boulevard

department: Molecular Pharmacology and Experimental Therapeutics

institute: Mayo Clinic Arizona

summary: We describe an 8 year old child who had disseminated anaplastic medulloblastoma and a deleterious heterozygous BRCA2 6174delT germline mutation. Molecular profiling was consistent with Group 4 medulloblastoma. The posterior fossa mass was resected and the patient received intensive chemotherapy and craniospinal irradiation. Despite this, the patient succumbed to a second recurrence of his medulloblastoma, which presented eight months after diagnosis as malignant pleural and peritoneal effusions. Continuous medulloblastoma cell lines were isolated from the original tumor (CHLA-01-MED) and the malignant pleural effusion (CHLA-01R-MED). Here we provide their analyses, including in vitro and in vivo growth, drug sensitivity, comparative genomic hybridization and next generation sequencing analysis. In addition to the BRCA2 6174delT, the medulloblastoma cells had amplification of MYC, deletion at Xp11.2 and isochromosome 17, but no structural variations or overexpression of GFI1 or GFI1B. To our knowledge, this is the first pair of diagnosis/recurrence medulloblastoma cell lines, the only medulloblastoma cell lines with BRCA2 6174delT described to date, and the first reported case of a child with medulloblastoma associated with a germline BRCA2 6174delT who did not also have Fanconi anemia.

overall_design: Continuous medulloblastoma cell lines were isolated from the original tumor (CHLA-01-MED) and the malignant pleural effusion (CHLA-01R-MED). Here we provide their analyses, including in vitro and in vivo growth, drug sensitivity, comparative genomic hybridization with Agilent 400k CGH arrays and whole transcriptome RNASeq analysis.

first: Jingying

last: Xu

first: Ashley

last: Margol

first: Shahab

last: Asgharzadeh

first: Floyd

middle: H

last: Gilles

first: Mark

last: Krieger

first: Jonathan

middle: L

last: Finlay

first: Meraj

last: Aziz

first: Fergus

middle: J

last: Couch

first: Eric

last: Fung

first: Anju

last: Shukla

first: Anat

last: Erdreich-Epstein


title: Hereditary Breast Cancer Tumors

city: Santiago

first: Carolina

last: Alvarez

state: Santiago

address: Portugal 49

department: Cellular and Molecular Biology

country: Chile

institute: Pontificia Universidad Católica de Chile

summary: Genomic profile of  47 tumors from hereditary breast cancer cases by Array CGH, 7 of which were BRCA mutation carriers (4 in BRCA2 and 3 in BRCA1), previously analyzed for BRCA1 expression by immunohistochemistry. Our goal was to identify specific alterations for BRCA1 not expressing tumors

overall_design: DNA from 47 Tumors versus DNA pool from normal tissue. BRCA1 expression, Hierarchical clustering and overall survival analyses.

first: Carvallo

last: Pilar

first: Alvarez

last: Carolina


title: 4plex_tomato_2013_03: Effect of drought stress on the transcriptome of tomato leaves

status: Public on Jul 01 2015

city: Orsay

first: Stéphanie

last: Pateyron

address: Rue de Noetzlin _ Batiment 630

institute: IPS2_Institute of Plant Sciences Paris-Saclay

summary: 4plex_tomato_2013_03 - 4plex_tomato_2013_03 - What are the genes implied in drought resistance in tomato ?          - 2 strains of tomato (Cervil, a cherry tomato, and Levovil, an large fruited tomato) were cultivated under normal hydric conditions and drought stress. Young leaves were gathered 3 1/2 months after sawing for analysis.

overall_design: 4 dye-swap - genotype comparaison

first: Frederique

last: Bitton

first: Mathilde

last: Causse

first: Sandrine

last: Balzergue

first: Marie-Laure

last: Martin-Magniette


title: Characterization of differential gene expression profiles between wild-type Ler and proatcape1 mutant seedlings upon salt stress.

city: Taipei

first: Pei-Shan

last: Chien

address: 128 Academia Road, Section 2, Nankang

department: ABRC

institute: Academia Sinica

summary: To gain insight into how AtCAPE1 regulates salt response, we investigated the gene expression profiles of wild-type (Ler) and proatcape1 mutant seedlings in the presence and absence of 125 mM NaCl by microarray analysis.

overall_design: Ten seedlings were grown vertically on the mesh attached on 1/2 MS medium for 10 days. Seedlings with the mesh were transferred to a new petri dish and then covered by buffer-saturated filter papers with 1/2 MS liquid medium (Control) or with 125 mM NaCl (Salt). Salt-treated seedlings (n=10 for each treatment) were sampled after 12 h.  Three independent experiments were performed for the microarray analysis.

first: Yet-Ran

last: Chen


title: Genome-wide profiling of H3K56ac in Drosophila melanogaster Kc167 cell lines with Lz overexpression

city: Cambridge

first: Sarah

last: Bray

address: Downing Street

department: PDN

institute: University  of Cambridge

type: Genome binding/occupancy profiling by genome tiling array

summary: The conserved Notch pathway functions in diverse developmental and disease-related processes, requiring mechanisms to ensure appropriate target-selection and gene activation in each context. To investigate, we partitioned Drosophila chromatin into different states, based on histone modifications, establishing the preferred chromatin conditions for binding of CSL, the Notch pathway transcription factor and showing that a co-operating factor, Lozenge/Runx, can help establish these conditions. While most histone modifications were unchanged by CSL binding or Notch activation, rapid changes in H3K56 acetylation occurred at Notch regulated-enhancers. This modification extended over large regions, required the histone acetyl-transferase CBP and was independent of transcription. Such rapid changes in H3K56 acetylation are a conserved indicator of enhancer activation, also occurring at mammalian Notch-regulated Hey1 and at Drosophila ecdysone-regulated genes. This core histone modification may therefore underpin the changes in chromatin accessibility needed to promote transcription following signaling activation.

overall_design: H3K56ac profile of control cells (KP) and of Lz overexpression cells (KL). In total 3 samples,  H3K56ac ChIP in KP cells and 2 replicates of H3K56ac ChIP in KL cells.

first: Jinghua

last: Li

first: Bettina

last: Fischer


title: Genome-wide profiling of Su(H) in Drosophila melanogaster Kc167 cell lines

summary: The conserved Notch pathway functions in diverse developmental and disease-related processes, requiring mechanisms to ensure appropriate target-selection and gene activation in each context. To investigate, we partitioned Drosophila chromatin into different states, based on histone modifications, establishing the preferred chromatin conditions for binding of CSL, the Notch pathway transcription factor. While most histone modifications were unchanged by CSL binding or Notch activation, rapid changes in H3K56 acetylation occurred at Notch regulated-enhancers. This modification extended over large regions, required the histone acetyl-transferase CBP and was independent of transcription. Such rapid changes in H3K56 acetylation are a conserved indicator of enhancer activation, also occurring at mammalian Notch-regulated Hey1 and at Drosophila ecdysone-regulated genes. This core histone modification may therefore underpin the changes in chromatin accessibility needed to promote transcription following signaling activation.

overall_design: Su(H) profile of Kc cells transfected with GFP-Su(H). In total 6 samples,  3 replicates of anti-GFP ChIP and corresponding total input samples in Kc cells.

first: Gustavo

last: Cerda-Moya


title: Genome-wide profiling of H3K56ac in Drosophila melanogaster Kc167 cell lines with NICD overexpression

summary: The conserved Notch pathway functions in diverse developmental and disease-related processes, requiring mechanisms to ensure appropriate target-selection and gene activation in each context. To investigate, we partitioned Drosophila chromatin into different states, based on histone modifications, establishing the preferred chromatin conditions for binding of CSL, the Notch pathway transcription factor. While most histone modifications were unchanged by CSL binding or Notch activation, rapid changes in H3K56 acetylation occurred at Notch regulated-enhancers. This modification required the histone acetyl-transferase CBP and was independent of transcription. Such rapid changes in H3K56 acetylation are a conserved indicator of enhancer activation, also occurring at mammalian Notch-regulated Hey1 and at Drosophila ecdysone-regulated genes. This core histone modification may therefore underpin the changes in chromatin accessibility needed to promote transcription following signaling activation.

overall_design: H3K56ac profile of control cells (KP) and of NICD overexpression cells (KN). In total 6 samples, with 2 input files (from 2 different conditions) and 2 replicates of H3K56ac ChIP samples of each condition.

first: Robert

last: Stojnic


title: Genome-wide profiling of Su(H) in Drosophila melanogaster BG3 cell lines

overall_design: Su(H) profile of BG3 cells in control condition and EGTA treated condition. In total 8 samples,  4 replicates of Su(H) ChIP in hbss condition and 4 replicates of Su(H) ChIP in EGTA treated BG3 cells.

first: Lenka

last: Skalska


title: abaseed-ABA signaling in Arabidopsis seeds

city: evry

first: Soubigou-Taconnat

last: Ludivine

address: 2 rue gaston crémieux

department: URGV

institute: INRA

summary: ra14-04_nced - abaseed - Identification of abscisic acid (ABA) signaling factors and targets in Arabidopsis developing seeds by comparing ABA deficient and wild type genotypes. Transcriptome comparison of developing seeds harvested at 14 DAP from two ABA-deficient mutants (nced2 nced5 nced9 and nced2 nced5 nced6 nced9) and wild type (Columbia-0).

overall_design: 6 dye-swaps - gene knockout, genomic comparison.

first: Annie

last: Marion-poll

first: Ludivine

last: Taconnat

first: Marie


title: Chromatin signatures at Notch regulated enhancers reveal large-scale changes in H3K56ac upon activation

summary:
To investigate the influence of chromatin organization and dynamics on the response to Notch signaling, we partitioned Drosophila chromatin using histone modifications and established

This SuperSeries is composed of the SubSeries listed below.


title: Distinct regulatory programs for Sox9 in transcriptional regulation of the developing mammalian chondrocyte [expression array]

city: Los Angeles

first: Xinjun

last: He

address: 1425 San Pablo St

department: BROAD CIRM Center

institute: University of Southern California

summary: We compared Sox9-association at chondrocyte targets to a broad catalogue of regulatory indicators of chromatin organization and transcriptional activity to determine Sox9’s direct regulatory actions in normal developing chondrocytes. Sox9-associated regions resolve into two distinct regulatory categories. Class I regions closely associate with transcriptional start sites (TSSs). Their targets reflect general regulators of basal cell activities that Sox9 engages indirectly though a likely association with the basal transcriptional complex. In contrast, Class II regions outside of the local TSS domains highlight evolutionarily conserved, active enhancers directing expression of chondrocyte specific target genes, though DNA binding of Sox9-dimers at target sites with sub-optimal binding affinity. The level of associated chondrocyte gene expression correlates with the number of enhancer modules around the target gene and grouping into super-enhancer clusters. Comparison of Sox9 programs between neural crest and mesoderm-derived chondrocytes points to similar modes of chondrocyte specification in distinct chondrocyte lineages. These data provide the first insight into mammalian Sox family actions at the genome scale in the vivo setting. The resulting enhancer sets provide a key resource for further dissection of the regulatory programs of mammalian chondrogenesis.

overall_design: Incorportation of ChIP-seq data of Sox9 and histone modification marks for chromatin status together with microrarray gene expression profiling in neonatal mice chondrocytes to uncover Sox9 regulatory system

first: Shinsuke

last: Ohba

first: Hironori

last: Hojo

first: Andrew

last: McMahon


title: Genome-wide profiling of H3K56ac in Drosophila melanogaster BG3 cell lines

overall_design: H3K56ac profile of BG3 cells in control condition and EGTA treated condition. In total 4 samples,  2 replicates of H3K56ac ChIP in hbss condition and 2 replicates of H3K56ac ChIP in EGTA treated BG3 cells.


title: Genome-wide profiling of H3K56ac in Drosophila melanogaster Kc cell lines

overall_design: H3K56ac profile of Kc cells in control condition and EGTA treated condition. In total 4 samples,  2 replicates of H3K56ac ChIP in hbss condition and 2 replicates of H3K56ac ChIP in EGTA treated Kc cells.


title: Expression data of embryonic kidney from MWF E15.5 and SHR 16.0 rats

city: Berlin

first: Reinhold

last: Kreutz

address: Charitéplatz 1

institute: Charité

summary:
Defects in nephrogenesis can have detrimental effects on cardiovascular and renal health in adult life. This is confirmed by observations in the Munich Wistar Frömter (MWF) rat that exhibits a congenital nephron deficit and renal failure with age. We performed genome-wide transcriptome analysis in embryonic kidneys to identify candidate genes for the reduced nephron number in MWF. We compared MWF E15.5 with stage-matched spontaneously hypertensive rats (SHR) at E16.
Microarray analysis revealed 311 transcripts representing 253 known genes with differential expression between MWF and SHR (FC >+1.5 or <-1.5, FDR<0.05).

overall_design: 8 samples were analyzed, n=4 per group


title: Stretch-dependent genes in vascular smooth muscle cells

city: Mannheim

first: Carsten

last: Sticht

address: Theodor-Kutzer-Ufer

department: ZMF

institute: University Heidelberg

summary:
Vascular smooth muscle cells (VSMCs) respond to biomechanical stretch with specific changes in gene expression which govern the phenotype of these cells. The mechanotransducer zyxin is a
potential candidate for regulating the expression of such genes.  Using microarrays, we compared stretch-induced gene expression in wild type and zyxin-null VSMCs to define such changes in detail.

overall_design: Wild type (WT) and zyxin-null VSMCs were stretched at 10% cyclic elongation for 6 hours and the changes in gene expression were compared under static and stretched conditions. Up to 3 biological replicates were used for each of the 4 sample types.

first: Subhajit

last: Ghosh

first: Markus

last: Hecker


title: Primary CNS lymphoma B cell receptors recognize CNS proteins

city: Cologne

first: Manuel

last: Montesinos-Rongen

state: NRW

address: Kerpenerstr. 62

department: Institute for Neuropathology

institute: University Hospital Cologne

summary: Primary lymphoma of the central nervous system (PCNSL) is a diffuse large B cell lymphoma confined to the CNS. In order to elucidate its peculiar organ tropism, we generated recombinant antibodies (recAb) identical with the BCR of a series of 23 PCNSL from immunocompetent patients.  While none of the recAb showed self-reactivity upon testing with common autoantigens, they recognized 1547 proteins present on a large-scale protein microarray. Interestingly, proteins recognized by the recAb are physiologically expressed by CNS neurons (GRINL1A, centaurin-α, BAIAP2). Furthermore, 87% (20/23) of the recAb including all antibodies derived from IGHV4 34 using PCNSL recognized galectin-3, which was upregulated on microglia/macrophages, astrocytes, and cerebral endothelial cells upon CNS invasion by PCNSL. Thus, PCNSL Ig may recognize CNS proteins as self-antigens. Their interaction may contribute to BCR signaling with sustained NF-κB activation and, ultimately, may foster tumor cell proliferation and survival. These data may also explain, at least in part, the affinity of the tumor cells of PCNSL to the CNS.

overall_design: Recombinant antibodies (recAb) identical with the BCR of a series of 23 PCNSL from immunocompetent patients.


title: miRNA expression profiling of Human ES cell line (hESC) derived embryoid body (EB) treated with H3R17methylation inhibitor TBBD

city: Bangalore

first: Genotypic

last: technology

state: Karnataka

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

institute: Genotypic Technology

summary: H3R17 methylation inhibitor TBBD associated differential gene expression in embryoid bodies was assessed by microarray analysis treated with 10uM TBBD for 48 hours compared to DMSO control treated Ebs

overall_design: Agilent one-color experiment, Agilent Human miRNA 8x15k Arrays AMADID: 021827 [Agilent miRNA labeling reagent and Hybridization Kit Cat # 5190-0408]

first: Ruthrotha

last: Selvi

first: Amrutha

last: Swaminathan

first: Tapas

middle: K

last: Kundu


title: Microarray analysis to identify the differentially expressed genes induced by NROB

city: wuhan

first: Hong

middle: li

last: Yang

state: Hubei

address: xudong 2 road

department: Oil Crops Research Institute

institute: Chinese Academy of Agricultural Sciences

summary: Compared to wild type plants, overexpression of NROB results leaf early senescence, biomass and seeds yield decreased more than 70%. Microarray analysis the differential expression genes induced by NROB

overall_design: Young leaves of DAG 30 were harvested from WT and 35S: NROB #2 plants and frozen immediately in liquid nitrogen. Total RNA was extracted using the RNeasy plant mini kit (Qiagen) and was checked for a RIN number to inspect RNA integration by an Agilent Bioanalyzer 2100. Qualified and purified total RNA was amplified and labeled by Low Input Quick Amp Labeling Kit, Two-Color (Agilent technologies, US). Regulated genes were identified with a stringent significance threshold, namely a mean >2.0-fold change (transformants relative to WT control samples) and based on at least two replicates. Microarray analysis result was verified by real-time PCR

first: Hongli

first: Jing

last: Liu


title: miRNA expression of 3 prostate cell types from human normal donors

city: Pittsburgh

first: John

middle: Michael

last: Krill-Burger

address: Rm. WG21.3 Shadyside Hospital

institute: University of Pittsburgh Medical Center

summary: Prostate primary epithelial and stromal cells were isolated from normal donorhuman prostate tissue and patient prostate tumors (>Gleason 8) using in vitroselective media conditions and differential substrate adhesion properties.Tumor cells specific to the prostate epithelial cell component attached tomatrigel while epithelial cells from donors preferentially attached to gelatinsubstrate. The prostate tumor cells did not proliferate over time in culturebut cells of normal epithelial phenotype in comparison to the donor tissueeventually emerged from this cell compartment. The epithelial componentof both donor and tumor specimens produced stem cell colonies thatexpressed OCT4 in growth factor reduced media but subsequently formedembryoid bodies in hanging drop cultures which differentiated into multiplegerm line lineages under the influence of growth factors. To determineif prostate tumor-derived stem cells were capable of forming tumors invivo, we compared the behavior of the donor and tumor stem cells aftertransplantation as tissue recombinants under the renal capsule of SCID micein the presence of rat urogenital mesenchyme (rUGM). Stem cells from bothdonor and tumor sources produced glandular structures that secreted prostatespecific antigen (PSA) while no glandular structures were formed from tissue recombinants of normal epithelial or tumor epithelial cells plus rUGM or fromrUGM alone. Serial transplantation of the stem cell recombinants from tumor specimens yielded subrenal structures reflecting an abundance of glandswith morphological features typical of Prostatic Intraepithelial Neoplasia(PIN). In order to determine whether intrinsic differences existed amongthe donor-derived and tumor-derived stem cells, array based microRNAexpression profiling was performed on all cell types obtained after in vitro isolation.

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

overall_design:
Sample Labeling Key:
PC-Prostate Cancer
PD-Prostate Donor (Normal Tissue)
DNE-Donor Normal Epithelial
NS-Donor Normal Stem
TNE-Tumor Normal Epithelial
TE-Tumor Epithelial
(TNE and TE samples with corresponding numbers are matched pairs)
TS-Tumor Stem Cell
S-Stromal

PC 73 TNE was run in all 6 batches as a control for batch effect. The number in parentheses corresponds with the batch the sample was run in.

first: William

last: LaFramboise

first: Dean

last: Bacich

first: Patricia

last: Petrosko

first: Christin

last: Sciulli

first: Rajiv

last: Dhir


title: Differences in the transcriptomic response of human adult and neonatal dendritic cell subsets to TLR7/8 stimulation

status: Public on Jun 30 2015

city: Vancouver

first: Kathleen

last: Wee

state: BC

address: 938 W 28th Ave.

institute: University of British Columbia

summary: Previous studies have shown that purified dendritic cells (DCs) have cell-intrinsic, age-dependent differences in their response to TLR stimulation. To delineate which aspects of the age-dependent difference in innate immunity are cell intrinsic vs extrinsic, we searched for global differences to TLR7/8 stimulation in purified adult vs neonatal DC populations. We hypothesize that very few selected cell intrinsic differences in gene expression of key immune genes between these 2 age groups exist, and the bulk would be cell extrinsic differences. The results show that there are age-dependent differences in expression of several key genes involved in the immune response at baseline already. Upon stimulation, we identified a substantially larger fraction of age-dependent differentially expressed genes in conventional than plasmacytoid DCs. Bioinformatics analyses indicate that important immune pathways were significantly differentially expressed in DC subsets between the 2 age groups.

overall_design: Total RNA was isolated from purified human conventional and plasmacytoid dendritic cells from 6 adult and 6 cord blood donors that were stimulated with 3M-003 at a final concentration of 5 uM for 1 and 6 hr.

first: Edgardo

middle: S

last: Fortuno III


title: Expression profiles of Ewing family of tumors authenticate distinct molecular entities

city: Paris

first: Franck

last: Tirode

address: 26 Rue d'Ulm

department: Inserm U830

institute: Institut Curie

summary: The concept of Ewing family of tumors (EFT), characterized by FET-ETS fusions, has been recently challenged by the description of Ewing-like tumors with different gene fusions. Here we investigate the similarities and differences of FET-ETS, BCOR-CCNB3, CIC-DUX4 and EWSR1-NFATc2 tumors samples with a number of other sarcomas. Unsupervised clustering of gene expression profiles fully discriminates these four molecular entities. Specific gene signatures and pathways were further validated in model cell lines. While a clear inflammatory signature characterizes EWSR1-NFATc2 tumors, BCOR-CCNB3 and CIC-DUX4 exhibit high expression of homeobox and ETS protein families, respectively. We strongly suggest that abnormalities of chromatin remodeling may gather CIC-DUX4 and BCOR-CCNB3 tumors with rhabdoid tumors and synovial sarcomas.

overall_design: This dataset conains 14 CIC-DUX4 and 7 EWSR1-NFATc2 tumor samples as well as Human mesenchymal cell line expressing EWSR1-NFATc2 (duplicates) or mock treated (duplicates) and IB120 CIC-DUX4 cell line expressing an shRNA directed against CIC-DUX4 (4 replicates) or mock treated (duplicates).

first: Sarah

last: Watson

first: Virginie

last: Perrin

first: Karoly

last: Szuhai

first: Pancras

middle: C

last: Hogendoorn

first: Olivier

last: Delattre


title: Expression of Wigglesworthia glossinidia endosymbiont of Glossina morsitans morsitans genes (control vs self-cured)

city: Montpellier

first: Anne

last: Geiger

address: Laboratoire de Recherches et de Coordination sur les Trypanosomoses TA,A-17 / G Campus international de Baillarguet

institute: UMR 177 IRD-CIRAD

summary:
Transcriptome analysis of Wigglesworthia glossinidia endosymbiont derived from control samples with or without parasite contact at 10 days.
Expression profiling by array -  Wigglesworthia glossinidia endosymbiont of Glossina morsitans morsitans

overall_design: RNAs are a mix of Wigglesworthia, Sodalis and glossina. RNAs were extracted from 8 samples including 2 conditions (with 4 replicates per condition).


title: Profiling transcriptional and translational response to anoxia or hypoxia of genes in DNA damage response and repair pathways in human fibroblast and prostate cancer cells using NanoString nCounter.

city: Toronto

first: Kenneth

middle: Chung-kan

last: Chu

address: 101 College Street, Suite 800

institute: Ontario Institute for Cancer Research

summary: Identification of genes in DNA damage response and repair pathways differentially transcribed or translated under anoxia or hypoxia in GM05757 normal human fibroblast cells and DU145 human prostate cancer cells.

overall_design: Comparison of mRNA abundance and translation efficiency of genes in DNA damage response and repair pathways in selected anoxia/hypoxia-treated cells with those in normoxia-treated controls.

first: Emilie

last: Lalonde

first: Adrian

last: Ishkanian

first: Jenna

last: Sykes

first: Michael

last: Fraser

first: Nathalie

last: Moon

first: Gaetano

last: Zafarana

first: Kaisa

last: Luoto

first: Alice

last: Meng

last: Thoms

first: Michal

middle: R

last: Grzadkowski

first: Alejandro

last: Berlin

first: Cherry

last: Have

first: Varune

last: Ramnarine

first: Cindy

middle: Q

last: Yao

first: Chad

last: Malloff

first: Nicholas

last: Harding

first: Denise

middle: Y

last: Mak

first: Lauren

last: Chong

first: Dorota

last: Sendorek

first: Christine

last: P’ng

first: Omer

last: Ahmed

first: Colin

last: Collins

first: Jeremy

last: Squire

first: Igor

last: Jurisica

last: Cooper

first: Rosalind

last: Eeles

first: David

last: Neal

first: Bradly

last: Wouters

first: Mariane

last: Koritzinsky

first: Melania

last: Pintilie

first: Alan

middle: D

last: Pra

first: Wan

last: Lam

last: Milosevic

first: Theodorus

last: van der Kwast

first: Paul

last: Boutros

first: Robert


title: mRNA profiling of MEST knockdown in human adipocyte precursor cells at early stage (day 3) of adipocyte differentiation

status: Public on Jun 24 2015

city: Vienna

first: Michael

last: Karbiener

address: Benatzkygasse 2-6 / G

department: Global Pathogen Safety

country: Austria

institute: Takeda

summary: The Mesoderm-specific transcript homolog protein MEST is a member of the alpha/beta hydrolase fold family that is expressed in adipose tissue, adipocytes as well as their precursor cells. To get an idea about potential functions of MEST in adipocyte development, we knocked down MEST in human Multipotent Adipose-Derived Stem (hMADS) cells, induced adipocyte differentiation by a chemically defined medium and performed gene expression profiling at the early stage of adipocyte differentiation.

overall_design: Two-condition experiment, hMADS cells at day 3 after induction of adipocyte differentiation, comparison of cells transfected with an siRNA targeting MEST (siMEST) to cells transfected with a control siRNA (siC). Biological replicates: 3, indepently grown and harvested. On each array, one biological replicate of siMEST-transfected cells was directly compared to one biological replicate os siC-transfected cells (serving as reference sample). All hybridizations were repeated with reversed dye assignment (dye-swap) as technical replicates.

first: Marcel

last: Scheideler


title: Early dendritic cell molecular signature modelling predicts late vaccine-induced adaptive T-cell responses (Codelink)

first: Nicolas

last: Dérian

address: Bâtiment CERVI, 83 bvd de l'Hôpital

institute: UPMC

summary: Mice were vaccinated with AP205 bacteriophage based VLP vector-plaform or PBS. Transcriptomes of dendritic cells 6 hours after vaccination were used to build a model predictive of the vector-platform efficacy measured as the antigen-specific response 5, 7 and 10 days after the vaccination

overall_design: Groups of 7-week-old female C57BL/6 mice (Charles River, France and Germany) were immunized either intravenously or sub-cutaneously with a controlled quantity of vector particles as defined in CompuVac assay protocols (www.compuvac.eu). Control mice were injected with 100 µL of phosphate buffered saline solution (PBS).

first: Bertrand

last: Bellier

first: Hang-Phuong

last: Pham

first: Eliza

last: Tsitoura

first: Dorothea

last: Kazazi

first: Christope

last: Huret

first: Penelope

last: Mavromara

last: Klatzmann

first: Adrien

last: Six


title: Expression of miR-200c in claudin-low breast cancer alters stem cell functionality, enhances chemosensitivity and reduces metastatic potential

status: Public on Jun 22 2015

city: Chapel Hill

first: Charles

middle: M.

last: Perou

state: NC

address: 12-044 Lineberger Comprehensive Cancer Center CB# 7295

department: Professor of Genetics, and Pathology & Laboratory Medicine; Lineberger Comprehensive Cancer Center

institute: University of North Carolina at Chapel Hill

summary: Claudin-low tumors are a highly aggressive breast cancer subtype with no targeted treatments and a clinically documented resistance to chemotherapy. They are significantly enriched in cancer stem cells (CSCs), which makes claudin-low tumor models particularly attractive for studying CSC behavior and developing novel approaches to minimize CSC therapy resistance. One proposed mechanism by which CSCs arise is via an epithelial-mesenchymal transition (EMT), and reversal of this process may provide a potential therapeutic approach for increasing tumor chemosensitivity. Therefore, we investigated the role of the miR-200 family of microRNAs in regulating the epithelial state, stem-like properties, and therapeutic response in an in vivo primary, syngeneic p53null claudin-low tumor model that is normally deficient in miR-200 expression.  Using an inducible lentiviral approach, we expressed the miR-200c cluster in this claudin-low model and found that it changed the epithelial state, and consequently, impeded CSC behavior in these mesenchymal tumors. Moreover, these state changes were accompanied by a decrease in proliferation and an increase in the differentiation status. MiR-200c expression also forced a significant reorganization of tumor architecture, affecting important cellular processes involved in cell-cell contact, cell adhesion, and motility. Accordingly, induced miR200c expression also significantly enhanced the chemosensitivity and decreased the metastatic potential of this p53null claudin-low tumor model. Collectively, our data suggest that miR-200c expression in claudin-low tumors offers a potential therapeutic application to disrupt the EMT program on multiple fronts in this mesenchymal tumor subtype, by altering tumor growth, chemosensitivity, and metastatic potential in vivo.

overall_design: reference x sample

first: Jana

last: Knezevic

first: Adam

last: Pfefferle

first: Ivana

last: Petrovic

first: Stephanie

middle: B

last: Greene

first: Jeffrey

last: Rosen


title: The SLC36 Transporter Pathetic Supports Extreme Growth in Drosophila Sensory Neurons

status: Public on Jun 21 2015

city: San Francisco

first: Charlie

last: Kim

address: 1001 Potrero Ave

department: Medicine

institute: University of California, San Francisco

summary: Microarray profiling of amplified total RNA isolated from FACS-sorted class IV da neurons or body wall filets.

overall_design: 3 to 5 independent replicates collected from each sample group, RNA isolated and amplified. Hybridized as a one color experiment.

first: Kory

last: Luedke

first: Jay

middle: Z

last: Parrish


title: Post-transcriptional regulation of circadian rhythm by miRNA in mouse liver

city: ShangHai

first: Haifang

last: Wang

address: NO 320, Yueyang Road

department: functional genomics group

institute: PICB

summary: Gene regulatory circuit of circadian rhythm has been well studied at the transcriptional level. However, recent published Nascent-sequencing and proteomic data indicates that post-transcriptional mechanisms play essential roles in modulating temporal gene expression for proper circadian function. miRNAs are 19-25 nucleotides long small RNAs now well-known for their regulatory roles in the development and diseases through post-transcriptional and translational controls in a wide range of species.  We systematically analyzed the miRNAs in mouse liver by Agilent microarray. Then by combining our results with the published high-through liver circadian microarray data,  we identified nine mouse liver circadian miRNAs.

overall_design: ice were housed under a 12-h light/12-h dark regimen with food and water available ad libitum. ZT0 is defined as the time when the lights are turned on. Two mouse livers were collected every four hours in two consecutive days. Then the two samples for each time point were pooled together. The mouse liver RNAs were extracted according Agilent protocol. miRNA microarrays were manufactured by Agilent Technologies, and each contains probes for 670 mouse and miRNAs. Labeling and hybridization of total RNA were performed according to the manufacturer's protocol with no modification.

first: Jun

last: Yan


title: Insight into Vibrio parahaemolyticus CHN25 response to artificial gastric fluid stress by transcriptomic analysis

city: Shanghai

first: Lanming

last: Chen

address: 999 Hu Cheng Huan Road

department: College of Food Science and Technology

institute: Shanghai Ocean University

summary: Vibrio parahaemolyticus is the causative agent of food-borne gastroenteritis disease. Once consumed, human acid gastric fluid is perhaps one of the most important environmental stresses imposed on the bacterium. Herein, for the first time, we investigated Vibrio parahaemolyticus CHN25 response to artificial gastric fluid (AGF) stress by transcriptomic analysis. The bacterium at logarithmic growth phase (LGP) displayed lower survival rates than that at stationary growth phase (SGP) under a sub-lethal acid condition (pH 4.9). Transcriptome data revealed that 11.6% of the expressed genes in Vibrio parahaemolyticus CHN25 was up-regulated in LGP cells after exposed to AGF (pH 4.9) for 30 min, including those involved in sugar transport, nitrogen metabolism, energy production and protein biosynthesis, whereas 14.0% of the genes was down-regulated, such as ABC transporter and flagellar biosynthesis genes. In contrast, the AGF stress only elicited 3.4% of the genes from SGP cells, the majority of which were attenuated in expression. Moreover, the number of expressed regulator genes was also substantially reduced in SGP cells. Comparison of transcriptome profiles further revealed forty-one growth-phase independent genes in the AGF stress, however, half of which displayed distinct expression features between the two growth phases. Vibrio parahaemolyticus seemed to have evolved a number of molecular strategies for coping with the acid stress. The data here will facilitate future studies for environmental stresses and pathogenicity of the leading food-borne pathogen worldwide.

overall_design: When V.parahemolyticus CHN25 grown to log phase and stationary phase at 37°C in TSB-3% NaCl, different cultures were subsequently exposed to artificial gastric fluid at 37°C for 30 min. Two independent experiments were performed at each phase for microarray expreriments.

first: Xuejiao

last: Sun

first: Taigang

last: Liu

first: Xu

last: Peng