title: Overall gene expression comparison between antimony resistant and sensitive Leishmania donovani

city: Kolkata

first: Syamal

last: Roy

state: West Bengal

address: 4, Raja SC Mullick Road

department: Infectious Disease and Immunology

institute: Indian Institute of Chemical Biology

summary: The mRNA expression of antimony resistant strains of Leishmania donovani was compared to the expression of the sensitive Leishmania donovani.

overall_design: The antimony resistant and sensitive Leishmania donovani were grown in complete M199 medium with 10% FCS and Penicillin streptomycin mixture. At stationary phase (5 day culture) cells were harvested in sterile Phosphate buffered saline and used for RNA isolation.

first: Rupkatha

last: Mukhopadhyay

first: Sandip

last: Mukherjee

first: Budhaditya

first: Shyam

last: Sundar

first: Jean

middle: C

last: Dujardin


title: Cholesterol chemostat M. smegmatis

status: Public on Jan 01 2016

city: Bronx

first: Michael

last: Berney

state: NY

address: 1301 Morris Park Avenue

department: Department of Microbiology and Immunology

country: USA

institute: Albert Einstein College of Medicine

summary: M. smegmatis grown on cholesterol or glycerol in continous culture at a dilution rate of 0.01 h-1.

overall_design: Two-condition experiment, cholesterol chemostat vs. glycerol chemostat. Biological replicates: 4, two dye swaps


title: Intestinal development in two divergent chicken lines (X and Y)

status: Public on Jan 14 2016

city: Wageningen

first: Dirkjan

last: Schokker

address: Droevendaalsesteeg 1

department: Wageningen Livestock Research

country: Netherlands

institute: Wageningen UR

summary:
The objective of this study was to investigate the impact of genotypic variation on both early microbial colonization of the gut and functional development of intestinal tissue.
From two genetically diverse chicken lines intestinal content samples were taken for microbiota analyzes and intestinal tissue samples were extracted for gene expression analyzes, both at three subsequent time-points (days 0, 4, and 16).

overall_design: 1-day-old chicks (Lines X and Y) were housed in a floor pen system in which the chicks had ad libitum access to feed and water. At days 0, 4 and 16, 80 birds of each line X and line Y were sacrificed for tissue sampling, in total 240 birds per line. Subsequently, samples from these 80 birds were pooled in 8 pools of ten birds.

first: S

middle: A

last: Vastenhouw

first: M

last: Smits

first: J

middle: M

last: Rebel


title: Gene expression profiling of the fat body of Bombyx mori exposed to phoxim insecticide

city: Suzhou

first: Zhi

middle: Ya

last: Gu

address: Renai Road

department: School of Basic Medicine and Biological Sciences

country: China

institute: Soochow University

summary: Transcriptional characteristics of genes in the fat body of domestic silkworms after 24 h exposure to phoxim through whole-genome oligonucleotide microarray.

overall_design:
Transcriptional profiling of fat body in the domestic silkworms comparing control untreated fat body with phoxim-treated fat body
Transcription profiling experiments, phoxim-treated fat body (samples) were analyzed. Dual-channel experiments, with test samples labeled by Cy5 and control samples labeled by Cy3. Three Biological replicate. No dye-swaps.

first: Z

middle: Y

first: F

last: Li


title: Microarray based gene expression for invasive lobular cancer samples (RATHER)

status: Public on Jan 05 2016

city: Amsterdam

first: Inès

last: Goossens-Beumer

address: Science Park 406

institute: Agendia NV

summary: As part of the RATHER (RAtional THERapy for breast cancer: individualized treatment for difficult-to-treat breast cancer subtypes) consortium, expression profiling of 144 untreated primary invasive lobular carcinoma (ILC) breast cancer tissues and 15 ILC cell lines was performed using microarray.

overall_design: Gene expression profiling of 144 ILC breast cancers and 15 ILC cell lines


title: Identification of a long non-coding RNA as a novel biomarker and potential therapeutic target for atrial fibrillation

city: Shanghai

first: Yingjia

last: Xu

address: No.241, Huaihai west Road,

institute: Shanghai Chest Hospital

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

summary: We identified 177 lncRNAs and 153 mRNAs that were differentially expressed (≥ 2-fold change), indicating that many lncRNAs are significantly upregulated or downregulated in AF. Among these, NONHSAT040387 and NONHSAT098586 were the most up-regulated and downregulated lncRNAs, and were selected for validation via quantitative PCR. GO analysis and KEGG pathway were applied to exploring potential lncRNAs function, identifying several pathways were alerted in atrial fibrillation pathogenesis.

overall_design: we investigated the expression patterns of lncRNAs and mRNAs from atrial fibrillation with Agilent Human lncRNA array V4.0 (4 × 180 K), which include 78,243 human lncRNAs and 30,215 coding transcripts.


title: Characterization of the gene expression profile of porcine iPS-like cells derived by two reprogramming techniques from translocated t(Y;14) fibroblasts

city: Castanet-Tolosan

first: Herve

last: Acloque

address: 24 chemin de Borde Rouge

department: Animal Genetics

country: France

institute: INRA

summary:
In the present study we compare the effect of integrative and non-integrative strategies on pluripotency during pig somatic cells reprogramming to pluripotency. Microarray analysis was used to compare the gene expression profile of non reprogrammed porcine embryonic fibroblasts (PEF) and of iPS-like cells obtained by cell reprogramming of control amniocytes (PB20) or fibroblasts from animals carrying a t(Y;14) translocation (I, NI).
We investigate the impact of different reprogramming techniques by using a first integrative method based on viral infection (PB20, I) and a second non-integrative method based on the use of Sendaï viruses (NI).
Moreover, we analyzed the changes in gene expression profile upon embryoïd formation in the NI-iPS-like cells (EB).

overall_design: We cultured one cell line of porcine embryonic fibroblast, one cell line of iPS-like cells derived from normal amniocytes (PB20), 2 cell lines derived from t(Y;14) fibroblast by the integrative technique (I3 and I4) both at early (ep) and late passages (lp), and three cell lines derived from t(Y;14) fibroblasts by the non-integrative method (NI12, NI13 and NI20). Embryoïd bodies from NI cell lines were obtained by 10 days of floating culture in a specific medium under low agitation (EB12, EB13 and EB20). Total RNA from cell pellets of each sample was extracted in triplicate using the Nucleospin RNA kit (Macherey-Nagel) and checked for quantity and quality. After the microarrays experimentation, quality control and normalization, 34 over 36 samples were conserved (represented here).

first: Annabelle

last: Congras

first: Hervé

first: Laurence

last: Liaubet

first: Olivier

last: Féraud

first: Ali

last: Thuran


title: A microRNA blueprint for early atrial remodeling in a porcine model of paroxysmal atrial fibrilation

city: La Coruña

first: Mario

last: Torrado

state: La Coruña

address: Campus de Oza, Edificio El Fortin

department: Institute of Health Sciences

country: Spain

institute: University of La Coruña

summary:
Spontaneous paroxysmal atrial fibrillation (PAF) is one of the very common heart rhythm disorders. The molecular mechanisms underlying PAF susceptibility and persistence are multiple and incompletely understood. To study the contribution of microRNAs (miRNAs) to the development and perpetuation of PAF, we used microarray/qPCR analyses to search for changes in miRNA expression in atrial myocardium upon pacing-induced PAF.  The miRNA microarray analysis was performed at LC Sciences (Houston, TX, USA). Following screening-microarray, several miRNAs were selected for detailed real-time qPCR assay.  Our results suggest that immediate-early miR remodeling of LAA underlies the development and persistence of PAF.
A closed-chest model of PAF was established in postnatal pigs via a rapid atrial electrical stimulation with a controlled ventricular response rate. A pacing catheter (delivered into the right atrium via femoral vein access under fluoroscopic guidance) was connected with an external pulse generator for programmed pacing rates. The burst-pacing stimuli were repeated several times, and the induced PAF occurrence rates and durations were recorded. Burst pacing was not performed in sham-operated group. Animals were euthanized 24 hours after cessation of pacing. Given that the right atrium might have been damaged by catheter insertion, we studied miRNA expression changes associated with PAF in the left atrial appendage (LAA) from paced vs control pigs.

overall_design: Six piglet were randomized in two groups, the PAF group (3 replicates) and the sham-control group (3 replicates)

first: Alexander

last: Mikhailov


title: Dynamic transcriptome analysis and volatile profiling of Gossypium hirsutum in response to the cotton bollworm Helicoverpa armigera

city: beijing

first: xinzheng

last: huang

address: No. 2 Yuanmingyuan West Road, Haidian District

institute: Institute of Plant Protection, Chinese Academy of Agricultural Sciences

summary:
Cotton seeds (Gossypium hirsutum cv. CCRI12) were grown in a growth chamber under 29/25°C temperature and a 16:8 h light:dark cycle, and water was added every two days. All plants were used in experiments at the 6-7 fully expanded true leaf stage, which occurred 5-6 weeks after sowing. Cotton bollworm (CBW; Helicoverpa armigera) larvae were reared on an artificial diet and maintained at 27 ± 2°C, 75 ± 10% relative humidity, and 14:10 h light:dark in the laboratory. For insect treatment, seven H. armigera larvae (third instars) were placed on a group of three plants, which were kept within plastic bags (30 × 40 cm), until time of harvest, with samples for each time point maintained separately. Undamaged plants maintained under the same conditions were used as controls. Cotton leaves from control plants and plants exposed to H. armigera were harvested at 6 h, 12 h, 24 h, and 48 h after onset of herbivory. For each treatment group and time point, cotton leaves were harvested from the three plants per treatment group and flash frozen in liquid nitrogen. For each time point, three replicate treatments and controls were performed.
For insect treatment, seven H. armigera larvae (third instars) were placed on a group of three plants, which were kept within plastic bags (30 × 40 cm), until time of harvest, with samples for each time point maintained separately. Undamaged plants maintained under the same conditions were used as controls. Cotton leaves from control plants and plants exposed to H. armigera were harvested at 6 h, 12 h, 24 h, and 48 h after onset of herbivory. For each treatment group and time point, cotton leaves were harvested from the three plants per treatment group and flash frozen in liquid nitrogen. For each time point, three replicate treatments and controls were performed.

platform_organism:
Gossypium barbadense
Gossypium hirsutum
Gossypium arboreum
Gossypium raimondii

overall_design: In this study we present dynamic transcriptome analysis and volatile profiling of cotton plants fed upon by larvae of a leaf-chewing herbivore CBW. Plant transcriptomic changes induced by CBW were analyzed using Affymetrix’s Cotton GeneChips. Samples from a time course of six hour to 48 hours following onset of CBW feeding were analyzed to identify target genes and key pathways involved in the activation of herbivory-induced indirect defense and to explore genetic basis of such defense. In addition, we monitored the accumulation of VOCs, which represent changes in cotton plant phenotype, following CBW infestation.

first: Xin-Zheng

last: Huang

first: Yong-Jun

last: Zhang


title: Expression data from in vitro HIV-1-infected macrophages responding to phagocytic stimuli

city: 91400 Orsay

first: Florent

last: Dumont

state: Ile de France

address: 17 avenue des sciences

institute: Université Paris-Saclay

summary: We used microarrays to detail the global programme of gene expression in human macrophages infected in vitro with HIV-1 and then subjected to phagocytic stimuli; we identified distinct classes of differentially regulated genes during this process

overall_design: Primary human macrophages from 3 different donors were infected with HIV-1ADA WT or mock-infected for 8 days. They were incubated or not (basal) with IgG-SRBCs (FcR) or Salmonella Typhimurium (4/74 strain) during 1 hour at 37°C, then lysed and RNA of each sample was analyzed with microarrays.

first: Audrey

last: Dumas

first: Florence

last: Niedergang


title: Molecular interaction of bifidobacteria with kefir grains

city: Parma

first: Marco

last: Ventura

address: Viale delle Scienze 11/A

department: Dept. Life Sciences

country: Italy

institute: University of Parma

summary: We got insights into the B. bifidum PRL2010 genes whose expression resulted to be affected when bacterial cells were cultivated on kefir and kefiran as the unique carbon source.

overall_design: In order to exploit the transcriptome of PRL2010 grown on kefir and hefiran we performed global transcription profiling using PRL2010 microarrays hybridized with cDNA from the RNA samples of B. bifidum PRL2010 cultivated on these substrates. We isolated mRNA from B. bifidum PRL2010 cells collected from a culture of kefir grains and from PRL2010 cultivated on MRS plus kefiran at upon 12 hours following inoculation.   Microarray analysis was performed with an oligonucleotide array based on the B. bifidum PRL2010 genome: a total of 8,130 oligonucleotide probes of 60bp in length were designed on 1707 ORFs using eArray5.0 (Agilent Technologies). 5 Oligos were designed for each gene on a 4x44k Agilent Microarrays(Agilent Technologies, Santa Clara, CA, USA). Replicates were distributed on the chip at random, non-adjacent positions.

first: Francesca

last: Turroni


title: Comparisons of toxicogenomic responses in zebrafish (Danio rerio) exposed to different sized AgNPs: The impact of size on global gene expression profiles

city: Daejeon

first: Jinjong

last: Bong

address: Daehak-ro

country: South Korea

institute: NEXBIO

summary: To investigate the patterns of global gene expression profiles modulated by the different sized AgNPs and to differentiate their modes of toxicity, zebrafish (Danio rerio) will be exposed to the AgNPs (50, and 150nm) and used for microarray analysis by Agilent Zebrafish Oligo Microarray system. 334 genes overlaped between AgNPs and Ag+ treatments in a total of 7,538 differential expressed genes. Immune response, antigen processing and presentation, response to estradiol stimulus and regulation of RNA metabolic process are most significant GO terms enriched in genes up regulated by four treatments. Neuroactive ligand-receptor interaction pathway was enriched among AgNP 50nm and AgNP 150nm activated genes, and specifically induced by AgNP 50nm include cell cycle and Toll-like receptor signaling pathways.

overall_design: The zebrafish larvae (72hpf) was exposed to AgNPs for 96hour. And then after total RNA extration from the each samples, the AgNPs related gene expression profiles identified using Agilent Zebrafish Oligo Microarray. Significant alterations in gene expression were found for all treatments and many of the gene pathways connected.

first: Jin

middle: S

last: Choi

first: Yongju

last: Lee

first: Sung-Kyu

first: June-Woo

last: Park


title: Transcriptome analysis of xylose metabolism in the methylotrophic yeast Hansenula polymopha

first: Oh Cheol

last: Kim

address: Gwahakro 125

institute: KRIBB

summary: The transcriptomes of H. polymorpha grown on xylose were compared with those of glucose-grown cells under both aerobic and microaerobic conditions

first: O

first: S

last: Suwannarangsee

first: D

middle: B

last: Oh

first: J

middle: W

last: Seo

first: C

middle: H

last: Kwon


title: INDUCED HYPER (T3) AND HYPO (PTU) THYROIDISM AFFECT TRANSCRIT PROFILE IMMUNE RESPONSES IN RAINBOW TROUT HEAD KIDNEY

city: Madrid

first: José María

last: Navas

state: Madrid

address: Crta de la Coruña Km 7.5

department: Environment

institute: INIA

summary:
In mammals, increasing data suggests that there exists a complex and bi-directional relationship between thyroid and immune systems. However the existence of such interactions in fish is unknown. Here, we administered the biologically active hormone 3.3′.5-triiodo-L-thyronine (T3) and the anti-thyroid drug, propilthiouracil (PTU) to juvenile rainbow trout and examined the head kidney expression profile with a custom-made microarray enriched in immune-related genes.
A seven day-experiment was performed. Fish were divided in 3 groups. First group received 20 µg/g fish feed of T3; second group received 5000 µg/g fish feed of PTU; third group served as control.

overall_design: After 7 days orally administering T3 or PTU, differentially expressed transcript levels from selected immune-related rainbow trout genes were studied in head kidney. Three groups were studied (T3-treated, PTU treated and control), each group having 4 biological replicates (each replicate consisting of 2 pooled fish).

first: Alba

last: Quesada-García

first: Ana

last: Valdehita


title: Yersinia pestis uses AHL-based quorum sensing to regulate metabolic functions likely to be important for flea colonization

city: Ames

first: Chris

last: Minion

state: IA

address: 1130 Vet Med

department: VMPM

institute: Iowa State University

summary: The etiologic agent of bubonic plague, Yersinia pestis, senses cell density-dependent chemical signals to synchronize transcription between cells of the population in a process named quorum sensing. Though the closely related enteric pathogen Y. pseudotuberculosis uses quorum sensing system to regulate motility, the role of quorum sensing in Y. pestis has been unclear. In this study we performed transcriptional profiling experiments to identify Y. pestis quorum sensing regulated functions. Our analysis revealed that acyl-homoserine lactone based quorum sensing controls the expression of several metabolic functions. Maltose fermentation and the glyoxylate bypass are induced by acyl-homoserine lactone signaling. This effect was seen to be temperature conditional. Metabolism is unresponsive to quorum sensing regulation at mammalian body temperature, indicating a potential role for quorum sensing regulation of metabolism specifically during colonization of the flea vector. It is proposed that utilization of alternative carbon sources may enhance growth and/or survival during prolonged flea colonization, contributing to maintenance of plague in nature.

overall_design: Six independent RNA samples from Y. pestis CO92 R114 AHL deficient cultures were paired with six independent RNA samples from control Y. pestis CO92 R88 cultures for hybridization to six two-color microarrays. For three arrays, the control RNA sample was labeled with Alexa 555 dye and the experimental RNA sample was labeled with Alexa 647 dye; the dyes were reversed for the other three arrays to account for any dye bias.

first: Jing

last: Yu


title: Transcriptional analysis of AHLs signal treatment at 30°C

summary: Yersinia pestis, the etiological agent of plague, is able to sense cell density by quorum sensing. The function of quorum sensing in Y. pestis is not clear. Here, the process of AHL quorum sensing was investigated by comparing transcript profiles when two AHL quorum-sensing signals are added in. The strain Δpgm (pigmentation-negative) mutant was called wild type. The two AHLs signals are N-(3-Oxooctanoyl)-L-homoserine lactone and N-Hexanoyl-DL-homoserine lactone.The control consisted of cells grown and treated under the same conditions without added signals.

overall_design: Six independent RNA samples from Y. pestis CO92 Δpgm cultures were paired with six independent RNA samples from two AHLs added cultures for hybridization to six two-color microarrays. A dye-swap design was used to remove the Cy5 and Cy3 dye bias.


title: Transcriptional analysis of ypeIR mutation in Yersinia pestis at  37°C

summary: The etiologic agent of bubonic plague, Yersinia pestis, senses cell density-dependent chemical signals to synchronize transcription between cells of the population in a process named quorum sensing. Though the closely related enteric pathogen Y. pseudotuberculosis uses quorum sensing system to regulate motility, the role of YpeIR quorum sensing in Y. pestis has been unclear. YpeIR is one of the AHL quorum sensing system in Y. pestis. In this study we performed transcriptional profiling experiments to identify Y. pestis YpeIR quorum sensing regulated functions at 37°C.

overall_design: Six independent RNA samples from Y. pestis CO92 Δpgm ΔypeIR cultures were paired with six independent RNA samples from control Y. pestis CO92 R88 cultures for hybridization to six two-color microarrays. For three arrays, the control RNA sample was labeled with Alexa 555 dye and the experimental RNA sample was labeled with Alexa 647 dye; the dyes were reversed for the other three arrays to account for any dye bias.


title: Global gene expression analysis of Yersinia pestis Ysp AHL quorum sensing at 37°C

summary: Quorum sensing is a cell to cell communication process that involves chemical signaling. Yersinia pestis, the agent of plague, has two functional AHL quorum sensing systems Ysp and Ype. For several reasons, it was not clear what effect AHL pathways have on virulence gene expression and survival in the two different hosts, flea and human. To investigate to what effect Ysp AHL quorum sensing has on gene expression, we conducted microarray studies comparing Yersinia pestis CO92 (∆pgm) to a single AHL mutant strain (∆pgm ΔyspI) at 37°C.

overall_design: Six independent RNA samples from Y. pestis CO92 Δpgm ΔyspI cultures were paired with six independent RNA samples from control Y. pestis CO92 R88 cultures for hybridization to six two-color microarrays. For three arrays, the control RNA sample was labeled with Alexa 555 dye and the experimental RNA sample was labeled with Alexa 647 dye; the dyes were reversed for the other three arrays to account for any dye bias.


title: Global gene expression analysis of Yersinia pestis Ysp AHL quorum sensing at 30°C

summary: Quorum sensing is a cell to cell communication process that involves chemical signaling. Yersinia pestis, the agent of plague, has two functional AHL quorum sensing systems Ysp and Ype. For several reasons, it was not clear what effect AHL pathways have on virulence gene expression and survival in the two different hosts, flea and human. To investigate to what effect Ysp AHL quorum sensing has on gene expression, we conducted microarray studies comparing Yersinia pestis CO92 (∆pgm) to a single AHL mutant strain (∆pgm ΔyspI) at 30°C.


title: Global gene expression analysis of Yersinia pestis Ype AHL quorum sensing at 30°C

summary: Quorum sensing is a cell to cell communication process that involves chemical signaling. Yersinia pestis, the agent of plague, has two functional AHL quorum sensing systems Ysp and Ype. For several reasons, it was not clear what effect AHL pathways have on virulence gene expression and survival in the two different hosts, flea and human. To investigate to what effect AHL quorum sensing has on gene expression, we conducted microarray studies comparing Yersinia pestis CO92 (∆pgm) to a double AHL mutant strain (∆pgm ΔypeIR) at 30°C.


title: MYBQKI overexpression in mouse NSC, and suppression of wild type Qk

status: Public on Dec 31 2015

city: Boston

first: Pratiti

last: Bandopadhayay

state: Massachusetts

address: 450 Brookline Ave

institute: Dana-Farber Cancer Institute

summary: Samples are mouse neural stem cells overexpressing eGFP, MYBtr, MYBQKI5, MYBQKI6 and MYBQKI6 with suppression of Qk (or LacZ)

overall_design: We overexpressed MYBQKI in mouse NSC, and then also suppressed wild type QKI in some samples

first: Keith

last: Ligon

first: Adam

last: Resnick

first: Rameen

last: Beroukhim


title: Global gene expression analysis of Yersinia pestis AHL quorum sensing at 37°C

summary: Quorum sensing is a cell to cell communication process that involves chemical signaling. Yersinia pestis, the agent of plague, has two functional AHL quorum sensing systems Ysp and Ype. For several reasons, it was not clear what effect AHL pathways have on virulence gene expression and survival in the two different hosts, flea and human. To investigate to what effect AHL quorum sensing has on gene expression, we conducted microarray studies comparing Yersinia pestis CO92 (∆pgm) to a double AHL mutant strain (∆pgm ΔypeIR ΔyspIR) at 37°C.


title: Identification and fine mapping of a novel, recurrent deletion in osteosarcoma

city: Bethesda

first: Yuelin

middle: Jack

last: Zhu

state: MD

address: 9000 Rockville Pike

department: Genetics Branch, Center for Cancer Research

institute: NCI

summary:
A custom high-density oligonucleotide array CGH (HD aCGH) was designed to facilitate the accurate mapping of the boundaries of the recurrent breakpoint at 3q13.31in 8 osteosarcoma tumors and cell lines

Keywords: Genetic analysis by HD aCGH

overall_design: 8 cell lines and 8 tumor specimens

first: Francesca

last: Scrimieri

first: Jack

first: Paul

last: Meltzer


title: High-resolution profiling of copy-number aberrations in osteosarcoma

summary: Osteosarcoma is a rare, highly malignant tumor of the bone that presents with a highly complex and abnormal karyotype. Only a few of the genes, which are targets of genetic alteration are known. An integrated genome-wide genomic and gene expression profiling analysis was performed on human osteosarcoma tissues and osteosarcoma cell lines in order to identify and map, in a high-resolution fashion, the most drastic chromosomal changes and point out genes which could contribute to tumorigenesis by having altered expression levels of critical oncogenes and tumor suppressors. Combined gene expression and aCGH analysis on the same samples enables direct comparison between DNA and mRNA level and offers a general strategy to identify and prioritize potential targets while the parallel analysis on cell lines offers a reliable models for further functional studies.

overall_design: An integrated genomewide DNA and RNA level data was performed to achieve more accurate information about the target genes involved in the region of gain and loss that present with a consistent expression pattern of variation. 40 osteosarcoma tumor specimens, 12 osteosarcoma cell lines, 1 osteoblast cell line


title: Effects of egg enrichment with glucocorticoid hormone, antagonist and receptor messenger in the modulation of gene expression in zebrafish (Danio rerio) embryos

city: Padua

first: Andrea

last: Celeghin

state: Veneto

address: Via Ugo Bassi 58 B

department: Biology

institute: University of Padua

summary: Several studies have shown the presence of large reservoirs of maternally contributed liposoluble hormones in the yolk of mature teleost oocytes, such as steroid, thyroid and retinoid hormones, as found in other oviparous vertebrates. This supports the idea that maternal hormones could play a major role in regulating developmental processes post-fertilization. The aims of this study were: A) to verify whether a cortisol treatment of zebrafish eggs affects the growth rate of the progenies as compared to controls in F1-F4 treated generations (ontogenetic programming). It was to be established whether: 1) this is due to a short-term effect of maternal cortisol, directly producing an initial growth retard that is not compensated later on in lifetime (short-term epigenetic effect); or 2) this is due to a long-term priming of growth rate by maternal cortisol that persists later on in lifetime (long-term epigenetic effect); B) to verify whether the ontogenetic programming is inheritable, being transmitted also to the untreated F4 generation. It was to be established whether the programmed genes are developmental and/or growth genes that are inhibited, or genes encoding hormones of the corticoid stress axis (hypothalamo-hypophyso-interrenal axis) that are amplified, or both gene clusters.

overall_design: Control embryos (treated with the vehicle ethanol only) were compared to cortisol-treated embryos at 5 hpf, 12 hpf and 24 hpf. Four replicates were performed for the 5 hpf samples, three biological replicates were carried out for the 12 hpf samples, and a single experiment was performed for the 24 hpf samples.

first: Md

middle: G

last: Rabbane

last: Benato

first: Tatjana

last: Skobo

first: Elisa

last: Colletti

first: Lorenzo

last: Colombo

first: Luisa

last: Dalla Valle


title: Global gene expression analysis of *Yersinia pestis* AHL quorum sensing

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

platform_organism:
Yersinia pestis
Yersinia pestis CO92

overall_design: Refer to individual Series


title: Osteosarcoma (expression, HD aCGH, aCGH)

type:
Genome variation profiling by array
Expression profiling by array


title: Towards clinical applications of blood-born miRNA signatures: The influence of the anticoagulant EDTA on miRNA abundance

city: Saarbrücken

first: Christina

last: Backes

address: Campus, Building E 2.1

department: Chair for Clinical Bioinformatics

country: Germany

institute: Saarland University

summary: Circulating microRNAs (miRNAs) from blood are increasingly recognized as biomarker candidates for human diseases. Clinical routine settings frequently include blood sampling in tubes with EDTA as anticoagulant without considering the influence of phlebotomy on the overall miRNA expression pattern. We collected blood samples from six healthy individuals each in an EDTA blood collection tube. Subsequently, the blood was transferred into PAXgeneTM tubes at three different time points, i.e. directly (0 min), 10 min, and 2 h after phlebotomy. As control blood was also directly collected in PAXgeneTM blood RNA tubes that contain a reagent to directly lyse blood cells and stabilize their content.  For all six blood donors at the four conditions (24 samples) we analyzed the abundance of 1,205 miRNAs by human Agilent miRNA V16 microarrays.

overall_design: Blood from 6 healthy individuals was collected in one PAXgeneTM blood RNA tube (Becton Dickinson, 2.5 ml blood) and one dipotassium EDTA blood tube (EDTA-KE Monovette, Sarstedt, 9 ml blood) per individual.  There was no known disease for any of the blood donors. A fixed volume of 2.5 ml blood from the EDTA tube was transferred at three different time points after blood withdrawal (0 min, 10 min, and 2 h) into fresh PAXgene blood RNA tubes to ensure stabilization of the RNA in the blood samples. All PAXgene blood tubes were stored at room temperature until at least 2 h after the last transfer of EDTA blood into PAXgene tubes, to ensure complete lysis of the blood cells, before they were stored at -20°C until RNA isolation.

first: Petra

last: Leidinger


title: Transcriptomic impact of AWR5 effector expression in S. cerevisiae

city: CERDANYOLA DEL VALLES

first: JOAQUIN

last: ARINO

state: Barcelona

address: ED. IBB

department: Biochemistry & Mol. Biol.

institute: UNIVERSITAT AUTONOMA BARCELONA

summary: The type III effector (T3E) AWR5 from the phytopathogen Ralstonia solanacearum causes disease in many plants relevant in agriculture. Heterologous expression in yeast of AWR5 from an integrated tetO promoter caused strong growth inhibition. In this series of experiments we investigate the possible changes in the transcriptional profile in a time-course (2, 4 and 6 h) response to AWR5 production.

overall_design: Yeast strains were grown overnight in rich YPD medium with doxycycline 15 µg/ml (repressing conditions), then normalized to OD600=0.05 and grown resumed in YPD+dox (non-inducing conditions) or YPD (inducing conditions). Samples were taken at  2, 4 or 6 hours for each condition. Two biological replicates were made for each time point.

first: Joaquin

last: Ariño

first: Crina

last: Popa

first: Sergio

last: Gil

first: Laura

last: Tatjer

first: M

last: Tabuchi

first: Núria

last: Coll

first: Marc

last: Valls


title: Expression profile of micro-RNAs and functional annotation analysis of their targets in human chorionic villi from early recurrent miscarriage

city: Lianyungang

first: Leilei

last: Wang

state: Jiangsu

address: No.10 Cangwu road

institute: Lianyungang maternal and child health hospital

summary: This study was designed to investigate the miRNA expression profilein human chorionic villi from early recurrent miscarriage. We identified 155 miRNAs exhibiting over 2-fold change in expression levels (P<0.05) by microarray,

platform_organism:
Homo sapiens
Human alphaherpesvirus 1
Human alphaherpesvirus 2
Cytomegalovirus
Lymphocryptovirus
Rhadinovirus
JC polyomavirus
Human immunodeficiency virus 1
Merkel cell polyomavirus
Betapolyomavirus hominis
Betapolyomavirus macacae

overall_design: Chorionic villi tissues collected from cases with  recurrent miscarriage and normal people were used to investigate the miRNA expression profile by microarray, which would be beneficial to understanding the etiology and pathophysiological mechanism of early recurrent miscarriage

first: Lisha

last: Tang


title: Genomic Run On (GRO): determination of the nascent transcriptional rates and mRNA levels in several yeast mutants (PUB1 and NGR1)

city: Burjassot

first: Jose

middle: E.

last: Perez-Ortin

state: Valencia

address: Dr. Moliner 50

department: Bioquimica y Biologia Molecular

institute: Universitat de Valencia

summary: We analyzed the effect of PUB1 and NGR1 on the transcription rates, mRNA stabilities and mRNA levels by doing GRO experiments in a deletion mutants comparing with a wild type in both glucose (YPD) and galactose (YPGal) media. Some data for the wt in YPGal are not included because were already in GEO database:  GSE1002 accession number.

overall_design: This study focus on the transcriptional activity of RNA pol II in yeast genes. S. cerevisiae cells grown in YPD or YPGal to exponential phase were subjected to Genomic Run On.  Data were normalized by the ArrayStat software. Home-made macroarrays containing 6035 ORF were used.

first: José

middle: E

last: Pérez-Ortín

first: Daniel

last: Medina

first: Helena

last: Orozco

last: García-Martínez

first: Paula

last: Alepuz


title: Expression Profiling in Human Osteosarcoma

first: Yuelin

last: Zhu

overall_design: Gene expression profiling analysis  was performed on 27 osteosarcoma tumors, 12 OS cell lines and 8 leiomyosarcoma tumors

first: Francesca

last: Scrimieri

first: Robert

middle: L

last: Walker

first: Paul

last: Meltzer


title: Gene expression profile at liver tissue of White Leghorn and four Korean native chickens

city: Seoul

first: Cheol-Koo

last: Lee

address: Korea University, Biotechnology #318 West building, Anam-dong, Seongbuk-gu

department: Biotechnology

institute: Korea University

summary: To characterize breed-specific difference among four Korean native chicken breeds and White Leghorn, we measured their transcriptomes at liver tissue using Affymetrix Chicken gene 1.0 ST array platform.

overall_design: To characterize breed-specific gene expression, we measured global gene expression profiles at liver tissue of male control breed (White Leghorn, WL) and four different male korean native chicken breeds including Yeonsan Ogye (Og), Hyunin Black (Bl), Hwangbong (Hw) and Hoengseong Yakdak (Ya) (n=3 in each breed).

first: Seung-Soo

last: Kim


title: Sublethal costs of salinity stress contribute to habitat limitation in an endangered estuarine fish

city: Davis

first: Lisa

last: Komoroske

state: CA

address: One Shields Ave

department: Wildlife, fish and conservation biology

institute: University of California, Davis

summary: We exposed adult delta smelt to treatments of increased salinities to quantify the transcriptomic responses involved in coping with osmotic stress

overall_design: 70 samples were run on 70 arrays, with 1-4 replicates for each treatment or control

first: Richard

last: Connon

first: Ken

last: Jeffries

first: Jason

last: Dexter

first: Nann

last: Fangue


title: miRNA expression in healthy carriers of heterozygous BRCA1 mutation and healthy WT controls

first: Tereza

last: Vaclova

address: C/ Melchor Fernández Almagro, 3

department: Human Cancer Genetics

institute: CNIO - Spanish National Cancer Research Centre

summary: In order to investigate whether carriers of BRCA1 heterozygous mutation show altered miRNA expression profiles, we established a panel of lymphoblastoid cell lines (LCLs) harboring either mutated or WT BRCA1 (control) and investigated their miRNA expression profiles. We were especially interested whether we find differences in miRNA expression between carriers of missense versus truncating mutation in BRCA1 gene.

platform_organism:
Homo sapiens
Mus musculus
Rattus norvegicus

overall_design: We evaluated the miRNA expression in a panel of 21 non-treated lymphoblastoid cell lines (LCLs). Among them, 6 LCLs with WT BRCA1, 5 LCLs carrying missense mutation in BRCA1, and 10 LCLs harboring truncating mutation in BRCA1 were included in this study.

last: Vaclová

first: Ana

last: Osorio

first: Javier

last: Benítez


title: Identification of gene expression patterns in lymphoma-prone SJL mice of different ages

first: Dong-Mi

last: Shin

address: 1 gwanak-ro

institute: seoul national university

summary: SJL mice spontaneously develop mature B cell lineage lymphomas. These studies were designed to evaluate significant gene expression differences between spleens of control mice that do not develop lymphomas compared to spleens from SJL mice of differeing ages

overall_design: 22 samples were tested from 4 groups of mice - 10 samples from one group and 4 samples each from the other three groups.  One sample per array

first: Herbert

last: Morse III


title: MtrA is involved in progression of Mycobacterium tuberculosis cell cycle

city: TYLER

first: Malini

last: Rajagopalan

state: Texas

institute: University of Texas Health Sciences Center at Tyler

summary: Synchronised cultures of Mycobacterium tuberculosis (M. tb H37Ra DnaAcos115) were used to determine the cell cycle dependent gene expression.

overall_design: Mycobacterium tuberculosis H37Ra DnaAcos115 strain was grown in Middlebrook 7H9 broth at 30C for 30h which arrests replication and later cultures were allowed to grow at 37oC for 30h. Samples were collected at 0, 2, 6, 12,18, 24 and 30 hours. Samples at 30oC for 30h were considered as '0' time point. A total of 18 samples, consisting of triplicates for 6 time-points were analyzed using microarray.

first: Murty

last: Madiraju

first: Emmanuel

middle: V

last: Pandeeti

first: Purushotham

last: Gorla

first: Erin

last: Maloney


title: miRNA expression profiles of pediatric medulloblastoma

first: Seung-Ki

last: Kim

address: Jonrro-gu

institute: Seoul National University

summary: The main cause of death in medulloblastoma is recurrence associated with leptomeningeal dissemination. Although the molecular basis of medulloblastoma has received considerable attention over the past decade, the role of microRNAs (miRNAs) in the acquisition of metastatic phenotype remains poorly understood. This study aimed to identify miRNA involved in leptomeningeal dissemination and to elucidate its target mechanisms. We analyzed miRNA expression profiles of 29 medulloblastomas according to the presence of cerebrospinal fluid (CSF) seeding. The differential expressed miRNAs (DEmiRNAs) were validated on 29 medulloblastoma tissues and three medulloblastoma cells. The biological function of the selected miRNA was evaluated using in vitro studies. A total of 12 DEmiRNAs were identified including miRNA-192 in medulloblastoma with seeding. The reduced expression of miRNA-192 was confirmed in tumor seeding group and the medulloblastoma cells. Overexpression of miRNA-192 inhibited cellular proliferation targeting dihydrofolate reductase (DHFR). MiRNA-192 decreased cellular anchoring via repression of integrin subunits (αV, β1, and β3) and CD47. Medulloblastoma with seeding showed specific DEmiRNAs compared with those without seeding. MicroRNA-192 suppresses leptomeningeal dissemination of medulloblastoma through modulating cell proliferation and anchoring ability.

overall_design: leptomeningeal dissemination in 29 pediatric medulloblastoma patients


title: Pathway analysis of microRNA expression profile during murine osteoclastogenesis

city: Farmington

first: Anne

last: Delany

state: CT

address: 263 Farmington Ave

department: Molecular Medicine

institute: UConn Health Center

summary: Osteoclasts are multinucleated cells specialized in degrading the mineralized bone matrix. Osteoclast differentiation and function are tightly regulated, to prevent excessive or insufficient bone resorption. Several control mechanisms participate in modulating osteoclastogenesis, and an increasing number of reports describe the role of microRNAs (miRNAs) in this process. Disrupting the expression of specific miRNAs can result in alterations of osteoclast formation and bone homeostasis. We and others have previously characterized 9 miRNAs whose levels change during osteoclast differentiation, and identified some of the target genes that mediate their function. However, little is known about changes in the miRNA expression profile during osteoclastogenesis. In this study, we isolated a murine primary bone marrow population enriched for osteoclast precursors, and used the Agilent microarray platform to analyze the expression of mature miRNAs after 1, 3, and 5 days of RANKL-driven differentiation. 93 miRNAs showed greater than 2 fold-change during these early, middle, and late stages of osteoclastogenesis. Many of these miRNAs were detected for the first time in osteoclasts, and we validated the expression of selected miRNAs by quantitative RT-PCR. We identified clusters of differentially expressed miRNAs, and performed computational analyses to predict functional pathways that may be regulated by these miRNAs. Several miRNAs were predicted to regulate genes involved in cytoskeletal remodeling, a crucial mechanism for the migration of osteoclast precursors, their maturation, and bone resorbing activity. Our results suggest that clusters of miRNAs differentially expressed during the course of osteoclastogenesis converge on the regulation of several key functional pathways. Overall, this study identified miRNAs expressed during early, middle and late osteoclastogenesis, contributing to understanding the molecular mechanisms regulating this complex differentiation process.

overall_design: Mouse primary bone marrow cultures were enriched for osteoclast precursors by depletion of B220/CD45R+ and CD3+ cells (B and T lymphocytes, respectively). Cells were differentiated with M-CSF and RANKL, and miRNA expression was analyzed at days 1, 3, and 5. Four biological replicates for each time point were used.

first: Tiziana

last: Franceschetti

first: Neha

last: Dole

first: Catherine

last: Kessler

first: Sun-Kyeong

last: Lee


title: Transcriptome analysis of annotated coding genes and sORF under elevated CO2

city: Iizuka

first: Kousuke

last: Hanada

state: Fukuoka

address: 680-4 Kawazu

department: Department of Bioscience and Bioinformatics

country: Japan

institute: Kyushu Institute Technology

summary: There are seedling samples (high CO2 exposure of 0h, 2h, 6h, 12h, 1d, 3d, 7d, 14d) with duplicates in two chambers.

overall_design: Arabidopsis WT (Col-0) seeds were plated on Murashige and Skoog plates and placed at 4°C in darkness for at least 2 d to synchronize germination. Plants were grown at 22C under long-day conditions (16-h light and 8-h dark) in two atmospheric CO2 environments: ambient (CO2: 390 μmol mol–1) or elevated (CO2: 780 μmol mol–1). Plants were grown in ambient atmospheric CO2 concentration and then exposed to elevated CO2 for 0 h, 2 h, 6 h, 12 h, 1 d, 3 d, 7 d and 14 d. 14-d-old seedlings were sampled at the same time. Treatments for elevated CO2 were carried out two times using two different chambers. Duplicate samples were collected from each chamber experiment. Totally, four biologically replicates were prepared in each condition.

first: Mieko

last: Higuchi-Takeuchi

first: Minami

last: Shimizu


title: Factors affecting the gene expression of in vitro cultured human preimplantation embryos

city: Amsterdam

first: Martijs

last: Jonker

address: Science Park 904

department: Microarray Department

institute: University of Amsterdam

summary:
Study question: What is the relative effect of common environmental and biological factors on transcriptome changes during human preimplantation development?

Summary answer: Developmental stage and maternal age had a larger effect on the global gene expression profile of human preimplantation embryos than the culture medium or oxygen concentration used in in vitro culture.

What is known already: Studies on mouse and bovine embryos have shown that different conditions in the in vitro culture of embryos can lead to changes in transcriptome profiles. For humans, an effect of developmental stage on the transcriptome profile of embryos has been demonstrated, but studies on the effect of maternal age or culture conditions are lacking.

Participants/materials, setting, methods: Embryos that developed to morula or blastocyst stage during these 2 days whose amplified mRNA passed our quality control criteria for microarray hybridization were individually examined for genome-wide gene expression (N = 37).

Main results and the role of chance: Based on the number of differentially expressed genes (DEGs), developmental stage (3519 DEGs) and maternal age (1258 DEGs) had a larger effect on the global gene expression profile of human preimplantation embryos than either tested culture medium (596 DEGs) or oxygen concentration (492 DEGs) used during in vitro culture. Interactions between the factors were found, indicating that culture conditions might have a different effect depending on the developmental stage or the maternal age of the embryos. Affected pathways included metabolism, cell cycle processes and oxidative phosphorylation.

Limitations, reasons for caution: Culture of embryos for only 2 days might have limited the effect on global gene expression by the investigated culture conditions. Earlier stages of development (Day 0 until Day 4) were not analyzed and these embryos might respond differently to the experimental conditions. The freezing and thawing procedures might have had an effect on gene expression. RT–PCR validation was not performed due to scarcity of the material.

Wider implications of the findings: Our results show that when studying gene expression in single human preimplantation embryos under various experimental conditions, one should take into account the confounding effect of biological variables, such as developmental stage and maternal age. This makes these experiments different from gene expression experiments where these variables can be tightly controlled, for example when using cell lines.

overall_design: Study design, size, duration: Donated, good quality, day 4 cryopreserved human preimplantation embryos (N = 89) were randomized to be cultured in one of two culture media (G5 medium or HTF medium) and one of two oxygen concentrations (5% or 20%), with stratification for maternal age. Next to these variables, developmental stage after culture was taken into account in the analysis.

first: E

last: Mantikou

first: M

middle: J

first: K

last: Wong

first: A

middle: P

last: van Montfoort

last: de Jong

first: T

last: Breit

first: S

last: Repping

last: Mastenbroek


title: Nutrigenomics and nutritional analysis of juvenile Asian seabass (Lates Calcarifer) fed five different commercial feeds

city: Singapore

first: Junhui

last: Jiang

address: 1 Research Link National University of Singapore

country: Singapore

institute: Temasek Life Sciences Laboratory

summary: In this study, the relative effect of consuming five different commercial feeds (Feed B-F) and and frozen fish (control; Feed A) for two months on our selected juvenile Asian seabass (77.3g ± 22.4g) were investigated. The growth performance, the biochemical analysis of their flesh, the histology of their midgut and the transcriptome of their midgut and liver were compared to each other and controls. Our customised agilent microarray platform (GPL17855), were used to investigate the liver transcriptomic expression of the different Groups fed with different Feeds. No differential expression were detected between commerical Feeds (B, C, E and F). A total of 397 differentially expressed transcripts (Foldchange cutoff: -1.5≤ or ≥1.5, Pvalue with FDR (<0.05) were detected between Feed D and control Feed A.

overall_design: Total: 24 samples (4 biological samples per Group; 6 Different Groups in total). Groups (A-F) were fed with Feeds (A-F) respectively for 61 days.

first: Si

last: Ngoh

first: Laszlo

last: Orban


title: Evaluation of ribonucleic acid amplification protocols for human oocyte transcriptome analysis

summary:
Objective: To develop a reliable, reproducible, and sensitive method for investigating gene-expression profiles from individual human oocytes.

Setting: University medical center and university microarray laboratory.
Patient(s): Couples undergoing intracytoplasmic sperm injection treatment were asked to donate their immature oocytes for research, and written informed consent was obtained in all cases. Seventy-nine human oocytes were used in total.
Intervention(s): None.
Main Outcome Measure(s): Amplification efficiency and microarray profiles.

Result(s): Two of the five protocols (WT-Ovation One-Direct and Arcturus RiboAMp HS Plus) resulted in sufficient yields and high success rates and were further validated for their performance in obtaining reliable, reproducible, and sensitive expression profiles from individual human oocytes. Evaluation of these two protocols demonstrated that they both displayed low technical variation and produced highly reproducible profiles (r R 0.95). One of them identified significantly more transcripts but also had a higher number of false discoveries.

Conclusion(s): Two protocols generated ample amounts of mRNA for (quantitative) polymerase chain reaction, microarray, and sequencing techniques. Further validation using a design that discriminates between biological and technical variation showed that both protocols can be used for gene-expression profiling of individual human oocytes.

overall_design: Design: Five commercially available protocols were investigated for their efficiency to amplify messenger RNA (mRNA) from 54 single human oocytes. Protocols resulting in sufficient yields were further validated using microarray technology. For the validation, mRNA was isolated from 25 human oocytes. To eliminate biological variation, RNA from 13 human oocytes was pooled together and split into 12 identical samples for further mRNA amplification. From 12 oocytes, mRNA was individually isolated.

first: Eleni

first: Oskar

last: Bruning

first: Sebastiaan

first: Sjoerd

first: Timo

first: Mark


title: Streptococcus suis 05ZY: control vs contact with hBMEC 3 h

city: Beijing

first: Huaijie

last: Hao

state: Beijing

address: NO. 20, Dongda Street, Fengtai District

institute: Institute of Microbiology and Epidemiology, Academy of Millitary Medicine Sciences

summary: The interactions of Streptocococcus suis (S.suis) with human microvascular endothelial cells (hBMEC) are important process for S.suis passage across human blood brain barrier (BBB). S.suis has evolved precise mechanisms to alter gene expression depending on the distinct challenges posed by particular disease sites. Herein, a whole-genome DNA microarray was used to investigate the change of gene expression profile of S.suis after contact with hBMEC 3 h. comparison of RNA isolated from hBMEC-associated S.suis with RNA derived from control bacteria revealed significant differential changes for 175 S.suis genes including 123 up-regulated genes and 52 down-regulated genes at 3 h post infection.

overall_design: A cDNA microarray imprinted with 2156 genes representing about 98% of Streptococcus suis serotype 2 genome was used for transcriptome analysis . For two-sample (reference vs. test) microarray hybridization, Two-condition experiment, control vs contact with hBMEC 3 h, four replicates (two biological replicates, two technical replicates) at each condition.

first: Qingyu

last: Lv

first: Xiaotao

last: Zeng

first: Yuling

last: Zheng

first: Yongqiang


title: Interleukin-10-anergized T-cell infusion provides immune reconstitution without severe graft-versus-host disease after haploidentical hematopoietic stem cell transplantation

status: Public on Dec 14 2015

city: Bergisch-Gladbach

first: Stefan

last: Tomiuk

address: Friedrich-Ebert-Str. 68

department: Bioinformatics

institute: Miltenyi Biotec GmbH

summary:
Regulatory T cells restore tolerance in preclinical models of immune-mediated diseases and are therefore a promising alternative to conventional immune-suppression for preventing graft-versus-host disease (GvHD) in patients receiving allogeneic hematopoietic stem cell transplantation (HSCT). Adaptive CD4+ Type 1 regulatory T (Tr1) cells specific for alloantigens are induced in vitro by interleukin-10 (IL-10). Therefore, we evaluated whether infusion of Tr1 cells could promote immune-competence to foreign antigens and long-term alloantigen-specific tolerance. In this phase 1-2 trial, we performed adoptive transfer with IL-10-induced alloantigen-specific Tr1 cells (IL-10-DLI), without immune-suppression, in patients with high-risk hematopoietic malignancies transplanted with CD34+ cells from haploidentical donors. Donor T cells, primed ex vivo with host antigen-presenting-cells and IL-10, are anergic towards host-HLA antigens and contain host-specific Tr1 cells but also memory T cells able to respond to pathogens.  Nineteen patients were enrolled in the trial. Twelve received IL-10-DLI. Seven were not evaluable because of early death/relapse, whereas five immune-reconstituted (>100/µl CD3+ T cells) at median day 28 after IL-10-DLI. T-cell counts and function progressively normalized in patients who received 105 CD3+ T cells/kg, whereas a higher dose (3x105 CD3+ T cells/kg) caused acute grade III GvHD in one patient. Four patients are alive, in disease remission and immune-suppression-free at a median follow-up of 3.3 years, three of them were analyzed by microarrays; their T-cell receptor repertoire and gene expression profiles are comparable to those of healthy subjects. Cell therapy with IL-10-DLI is feasible, safe, and provides immune-competence. This trial is the first step towards widespread use of Tr1 cells as adjuvant treatment in allogeneic HSCT (IS/11/6172/8309/8391).

Keywords: classification of clinical samples

overall_design: Whole blood samples of three healthy donors and three different patients collected at various time points after hematopoietic stem cell transplantation (HSCT) before and after the subsequent administration of IL-10 anergized T cells were analysed on a custom Agilent 8x15K 60mer oligonucleotide microarray encomprising 4610 probes in triplicates. The microarray is dedicated to transplantation research and was designed based on current literature and published and unpublished data provided by the RISET consortium. For the probe selection procedure we specially focused on the detection of multiple transcript variants of a gene, on optimized hybridization properties of the probes, and on the avoidance of crosshybridization. The RISET 1.0 platform (GPL10370) is a precursor of the RISET 2.0 microarray (GPL8136).

first: Rosa

last: Bacchetta

first: Barbarella

last: Lucarelli

first: Claudia

last: Sartirana

first: Patrick

last: Miqueu

first: Maria

middle: T

last: Stanghellini

first: Silvia

last: Gregori

first: Uwe

last: Janßen

first: Raffaella

last: Greco

first: Massimo

last: Bernardi

first: Elisabetta

last: Zappone

first: Silvano

last: Rossini

first: Alessandro

last: Ambrosi

first: Monica

last: Salomoni

first: Jacopo

last: Peccatori

first: Fabio

last: Ciceri

first: Maria-Grazia

last: Roncarolo


title: SYNTHESIS OF THE INTERSPECIES SIGNALING MOLECULE AUTOINDUCER-2 PLAYS AN IMPORTANT ROLE IN THE ANTI-MICROBIAL EFFECT OF BIFIDOBACTERIA

city: Cork

first: Mary

last: O'Connell Motherway

address: Western Road

department: Department of Microbiology and Alimentary Pharmabiotic Centre

country: Ireland

institute: University College Cork

summary: In the present study we show that a functional luxS gene is present in all members of the genus Bifidobacterium and that AI-2 production by Bifidobacterium breve UCC2003 is necessary to confer protection against Salmonella infection in Caenorhabditis elegans. Mutants carrying a disrupted luxS gene conferred less protection than the WT, whereas administration of a complemented strain, a LuxS-overexpression strain and the WT resulted in similar survival. Transcriptome data obtained for both the WT and the luxS-insertion mutant grown in vitro suggest that LuxS has a metabolic role that impacts on iron metabolism. In line with this, we demonstrated that the luxS mutant is significantly more susceptible to the ferrous ion chelator 2,2-dipyridyl than the WT strain. Furthermore, qRT-PCR shows that the iron regulated genes are upregulated under  in vivo conditions, while we also show that LuxS is required for colonization of BALB/c mice. Altogether, our findings provide detailed insights into the molecular mechanism underlying gut pathogen protection conferred by bifidobacteria.

overall_design: DNA-microarrays containing oligonucleotide primers representing each of the 1864 annotated genes on the genome of B. breve UCC2003  (O'Connell Motherway et al., 2011) were designed by and obtained from Agilent Technologies (Palo Alto, Ca., USA). Methods for cell disruption, RNA isolation, RNA quality control, complementary DNA synthesis and labeling were performed as described previously (Pokusaeva et al., 2009). Labeled cDNA was hybridized using the Agilent Gene Expression hybridization kit (part number 5188-5242) as described in the Agilent Two-Color Microarray-Based Gene Expression Analysis v4.0 manual (G4140-90050). Following hybridization, microarrays were washed in accordance with Agilent’s standard procedures and scanned using an Agilent DNA microarray scanner (model G2565A). Generated scans were converted to data files with Agilent's Feature Extraction software (Version 9.5). DNA-microarray data were processed as previously described (Garcia De La Nava et al., 2003). Differential expression tests were performed with the Cyber-T implementation of a variant of the t-test (Long et al., 2001). A gene was considered differentially expressed when p < 0.001 and an expression ratio of >3 or <0.33 relative to the control.

middle: O

last: Motherway

first: S

last: Christiaen


title: Staphylococcus aureus ST398 gene expression profiling during ex vivo colonization of porcine nasal epithelium

first: Martijs

last: Jonker

summary: Staphylococcus aureus is a common human and animal opportunistic pathogen. In humans nasal carriage of S. aureus is a risk factor for various infections. Methicillin-resistant S. aureus ST398 is highly prevalent in pigs in Europe and North America. The mechanism of successful pig colonization by MRSA ST398 is poorly understood. Previously, we developed a nasal colonization model of porcine nasal mucosa explants to identify molecular traits involved in nasal MRSA colonization of pigs. Here, we report the analysis of the transcriptome of MRSA ST398 strain S0462 during colonization on the explant epithelium. Major regulated genes were encoding metabolic processes and regulation of these genes represents metabolic adaptation to nasal mucosa explants. Colonization was not accompanied by significant changes in transcripts of main virulence associated genes or known human colonization factors. Here, we document regulation of two genes which have potential influence on S. aureus colonization; cysteine extracellular proteinase (scpA) and von Willebrand factor-binding protein (vwbp, located on SaPIbov5). Colonization with isogenic-deletion strains (Δvwbp and ΔscpA) did not alter the nasal S. aureus colonization compared to wild type. Our results suggest that nasal colonization with MRSA ST398 is a complex event that is accompanied with changes in bacterial gene expression regulation and metabolic adaptation.

overall_design: Number of the samples: 5 (timepoint 0 min, 30 min, 60 min, 90 min and 180 min) in 4 replicates. 4 control samples

first: Pawel

last: Tulinski

first: Jos

last: van Putten

first: Birgitta

last: Duim

first: Jaap

middle: A

last: Wagenaar

first: Floyd

middle: R

last: Wittink

first: Ad

middle: C

last: Fluit

first: Timo

middle: M

last: Breit


title: Transcriptomic analysis of dioxin like compounds

city: Barcelona

first: Eva

middle: Lima

last: Oliveira

address: Carrer Jordi Girona 18-26

department: Environmental Chemistry

institute: IDAEA CSIC

summary: We are presenting here the application of toxicogenomics in the evaluation of the toxic effects of three dioxin-like compounds, two Polycyclic aromatic hydrocarbons (PAHs), Benzo(a)pyrene, Benzo(k) fluoranthene and b-naphthoflavone on the developing zebrafish embryo. The main goal is to distinguish the pattern of action of the chemical compounds and their needs varying the times of exposure. The results suggest a variety of MoA for different dioxin-like compounds, probably related to the nature and number of benzene rings. About 5% genes were affected by the treatment. Gene ontology (GO) analyses show that these genes are involved in the oxidation-reduction process. Representatives of each GO functional groups were selected and quantified by real-time PCR to validate the microarray data and to differentiate the action of dioxin-like compounds studied.

overall_design: Four different treatments were performed in this study. Zebrafish fertlized eggs were exposed to dioxin like compounds during 48h and 96h . 3 biological replicates are included as each control sample.

first: Marta

last: Casado

first: Amadeu

last: Soares

first: Carlos

last: Barata

first: Benjamín

last: Piña


title: A western-style diet, with and without chronic androgen treatment, alters the number, structure and function of small antral follicles in ovaries of young adult monkeys.

status: Public on Dec 21 2015

city: Beaverton

first: Cecily

middle: Vauna

last: Bishop

state: OR

address: 505 NW 185th Ave

department: Division of Reproductive & Developmental Sciences

institute: Oregon National Primate Research Center

summary: This study examined the small antral follicles (SAFs) in ovaries of young adult rhesus monkeys following consumption of a western-style diet (WSD), with or without chronically elevated androgen levels since before puberty. Cholesterol or testosterone (T; n=6/group) implants were placed subcutaneously beginning at 1 yr of age, with addition of a WSD (high fat/fructose) at 5.5 yrs. Ovaries from treated females and age-matched controls were collected at 7 yrs of age. Compared to controls, consumption of a WSD, with and without T treatment, increased the numbers of SAFs per ovary (P<0.001), due to the presence of more atretic follicles (P<0.01). Immunostaining for the cellular proliferation markers (pRb and pH3) was greater in granulosa cells of healthy SAFs (P<0.01), while staining for the cell cycle inhibitor (p21) was higher in atretic SAFs (P<0.01).  Intense CYP17A1 staining was observed on the theca of SAFs from WSD+/- T groups, compared to controls. Microarray analyses of the transcriptome in SAFs isolated from a subgroup (n=3/grp) of WSD and WSD+T treated females and controls consuming a standard diet, identified mRNA levels for 1944 genes changed >2-fold (p<0.05) among the three groups. Pathway analyses identified several gene pathways altered by WSD and/or WSD+T associated with lipid, carbohydrate and lipid metabolism, plus ovarian processes. Alterations of several SAF mRNAs are similar to those observed in follicular cells from women with PCOS. These data indicate chronic exposure to a WSD in the presence and absence of chronically elevated T alters structure and function of SAFs within primate ovaries.

overall_design: Affymetrix Microarray analyses of the transcriptome in SAFs isolated from ovaries of WSD and WSD+T treated rhesus macaque females and controls consuming a standard diet. Presumptive healthy SAFs were chosen for transcriptome evaluation based on criteria similar to previous studies: the presence of a clear antrum lacking dark oocytes or granulosa cells. Isolated SAFs were pooled by female/ovary (3.7±0.3 SAFs/ovary, n=3 ovaries/group), cleaned of extraneous stroma using 30-gauge needles, ruptured, and entire cellular contents (follicle wall/granulosa cells and cumulous-oocyte complex) placed into lysis buffer for RNA isolation (Absolutely RNA Nanoprep Kit, Agilent Technologies, Inc. USA).

first: Richard

last: Stouffer

first: Jing

last: Xu

first: Jon

middle: D

last: Hennebold


title: Saccharomyces cerevisiae deletion collections chemogenomic screen with sr7575

status: Public on Dec 09 2015

city: Paris

first: Cosmin

last: Saveanu

address: 25-28 rue du docteur Roux

department: Genomes and Genetics

institute: Institut Pasteur

summary: Growth assay in the presence of a toxic chemical (sr7575) that uses the barcoded collections of yeast gene deletions (haploid, diploid, DamP) to identify deletion strains that are hypersensitive to the drug.

overall_design:
Two-condition experiment – growth of a pool of strains in the presence or absence of the drug. Two independent biological replicates for each collection (haploids - homozygous and diploids – heterozigous).

Data for the article: Shriya Raj, Karthik Krishnan, David S Askew, Olivier Helynck, Peggy Suzanne, Aureslien Lesnard, Sylvain Rault, Ute Zeidler, Christophe d'Enfert, Jean-Paul Latgé, Hélène Munier-Lehmann and Cosmin Saveanu. Toxicity of a novel antifungal compound is modulated by ERAD components. Antimicrobial Agents and Chemotherapy.

first: Shriya

last: Raj


title: Global Changes in Gene Expression in Mesorhizobium loti MAFF303099 upon an acidic shock

city: Evora

last: Laranjo

address: Apartado 94

department: ICAAM

country: Portugal

institute: Universidade de Evora

summary: Expression profiling of a total of 7281 transcripts was compared between control and acidic shock conditions.

overall_design: In the present study, RNA was extracted from three independent cell cultures for each treatment (control and acidic shock).

first: Ana

last: Alexandre

first: Solange


title: Acute psychological stress induces short-term variable immune response

status: Public on Dec 01 2015

city: La Jolla

first: Brinda

last: Rana

address: 9500 Gilman

department: Psychiatry

institute: UCSD

summary: Analysis of gene expression in leukocytes taken from 13 participants 1 week before or after the skydive (baseline), before boarding the airplane (pre-boarding), at landing and 1 h after the parachute jump (1 h landing). Results identify a subset of genes expressed by natural killer cells that are upregulated in leukocytes in response to acute psychological stress.

overall_design: This study evaluated gene expression in leukocytes taken prior to and after first-time tandem skydive from 13 healthy individuals to identify genes whose expression is modulated in response to acute psychological stress.

first: Michael

middle: S

last: Breen

first: Nadejda

last: Beliakova-Bethell

middle: K


title: Response of Pseudomonas strains PAO1 and FRD1 to 10 mM added calcium in planktonic and biofilm conditions.

status: Public on Dec 02 2015

city: Bozeman

first: Kerry

last: Williamson

state: Montana

address: 109 Lewis Hall

department: Microbiology and Immunology

institute: Montana State University

summary:
PAO1 and FRD1 were cultured planktonically and in biofilms with 10 mM calcium and no added calcium. The transcriptional response to calcium addition was determined for PAO1 cultured planktonically, for FRD1 cultured planktonically, for PAO1 cutured in biofilms, and for FRD1 cultured in biofilms.
Pseudomonas aeruginosa is an opportunistic human pathogen that causes severe, life threatening infections in patients with cystic fibrosis (CF), endocarditis, wounds, or with artificial implants. During CF pulmonary infections, P. aeruginosa often encounters environments where the levels of calcium (Ca2+) are elevated.  Previously, we showed that P. aeruginosa responds to externally added Ca2+ through enhanced biofilm formation, increased production of several secreted virulence factors, and by developing a transient increase in the intracellular Ca2+ followed by its removal to the basal sub-micromolar level.  However, the molecular mechanisms responsible for regulating Ca2+-induced virulence factor production and Ca2+ homeostasis are not known.  Here, we characterized the genome-wide transcriptional response of P. aeruginosa strains PAO1 and FRD1 to elevated [Ca2+] in both planktonic cultures and in biofilms.  Among the genes induced by CaCl2 in PAO1 was an operon containing the two-component regulator PA2656-PA2657 (here called carS and carR), while the closely related two-component regulators, phoPQ and pmrAB were repressed by CaCl2 addition.  To identify the regulatory targets of CarSR, we constructed a deletion mutant of carR, and performed transcriptome analysis of the mutant strain at low and high [Ca2+].  Among the genes regulated by CarSR in response to CaCl2 are the predicted periplasmic OB-fold protein, PA0320 and the inner membrane-anchored five-bladed -propeller protein, PA0327. Mutations in both PA0320 and PA0327 affected Ca2+ homeostasis, reducing the ability of P. aeruginosa to export excess Ca2+.  In addition, a mutation in PA0327 had a pleotrophic effect in a Ca2+-dependent manner, altering swarming motility, pyocyanin production, and tobramycin sensitivity. Overall, the results indicate that the two-component system CarSR is responsible for sensing high levels of external Ca2+, and responding through its regulatory targets that modulate Ca2+ homeostasis, surface-associated motility, and production of the virulence factor, pyocyanin.

overall_design: Two-condition experiment:  0 mM calcium vs. 10 mM calcium. For each of the four biological sample types, cells were grown with and without 10 mM added calcium, and co-hybridized to two color arrays. Dye swaps were performed on an additional array. Two independent biological replicates, grown on different days, were also co-hybridized on two additional arrays (dye swap). In this manner, four biological replicates were co-hybridized to four arrays, for four conditions, resulting in 16 two-color arrays deposited. Each array contained one biological growth condition at 0 at 10 mM calcium.

first: Manita

last: Guragain

first: Michelle

last: King

first: Ailyn

last: Pérez-Osorio

first: Tatsuya

last: Akiyama

first: Sharmily

last: Khanama

last: Franklin

first: Marianna

last: Patrauchan


title: Epigenome analysis of primary MCL

first: Pedro

last: Jares

address: c/ Villarroel 170

department: Genomics Unit

institute: IDIBAPS

summary: Genome wide DNA methylation profiling of primary MCL. The Illumina Infinium 27k Human DNA methylation Beadchip v1.2 was used to obtain DNA methylation profiles across approximately 27,000 CpGs.

overall_design: Bisulphite converted DNA from the 132 samples were hybridised to the Illumina Infinium 27k Human Methylation Beadchip v1.2

first: Anna

last: Enjuanes


title: Streptococcus suis 05ZY: control vs contact with hBMEC 1 h

first: Huaijie

last: Hao

summary: The interactions of Streptocococcus suis (S.suis) with human microvascular endothelial cells (hBMEC) are important process for S.suis passage across human blood brain barrier (BBB). S.suis has evolved precise mechanisms to alter gene expression depending on the distinct challenges posed by particular disease sites. Herein, a whole-genome DNA microarray was used to investigate the change of gene expression profile of S.suis after contact with hBMEC 1 h. comparison of RNA isolated from hBMEC-associated S.suis with RNA derived from control bacteria revealed significant differential changes for 219 S.suis genes including 131 up-regulated genes and 88 down-regulated genes at 1 h post infection.

overall_design: A cDNA microarray imprinted with 2156 genes representing about 98% of Streptococcus suis serotype 2 genome was used for transcriptome analysis . For two-sample (reference vs. test) microarray hybridization, Two-condition experiment, control vs contact with hBMEC 1 h, four replicates (two biological replicates, two technical replicates) at each condition.

first: Qingyu

last: Lv

first: Xiaotao

last: Zeng

first: Yuling

last: Zheng

first: Yongqiang

last: Jiang


title: Leukocyte gene expression as a function of perceived social isolation (PSI): Year 5

status: Public on Nov 23 2015

city: Los Angeles

first: Steve

last: Cole

address: 11-934 Factor Bldg, UCLA

department: Medicine

institute: UCLA School of Medicine

summary: Individual differences in basal leukocyte gene expression profiles as a function of perceived social isolation (PSI)

overall_design: Gene expression profiling was carried out on peripheral blood mononuclear cell RNA samples collected from 98 adults in Year 5 of the Chicago Health Aging and Social Relations Study.  Participants were assessed for PSI using the UCLA Loneliness Scale, and were also classified as chronically high in PSI (1/0) based on UCLA Loneliness Scale scores during study years 1-5.  A 1-year lagged value of PSI is also included, and analyses additionally controlled for age at study entry, sex, race/ethnicity (dummy codes for Black and Hispanic), marital status, (log) household income, Body Mass Index (BMI), smoking history, heavy alcohol consumption, depressive symptoms (CESD), perceived stress (PSS), social support (SocSupp), circulating monocyte percentages, and RNA indicators of major leukocyte subsets (CD3E, CD3D, CD4, CD8A, CD19, FCGR3A/CD16, NCAM1/CD56, CD14).


title: In(1)BM2(reinverted) males: reared at room temperature vs. Cold shock treatment

status: Public on Nov 05 2015

city: Pune

first: Priyanka

last: Guru

address: Ganeshkind road

department: Interdisciplinary School of Health Sciences

country: India

institute: Savitribai Phule Pune University

summary: Cold exposure leads to alteration in the structure of the male sex chromosome of the mutant strain In(1)BM2(reinverted).  Genome wide expression profiling was used to identify candidate genes involved in the expression of this phenotype.  Adult male flies were exposed to cold shock at 12±1°C for 4 hours and the differentially expressed  genes in the strain was compared to similarly exposed wild type Oregon R males. The microarray data was further validated using real time PCR.

overall_design: Two-condition experiment, RT vs. CS flies. Biological replicates: 2 control replicates, 2 replicates exposed to cold shock.

first: Anita

last: Kar


title: miRNA expreesion file in FOXP3 positive and negative SZ4 cell lines

status: Public on Nov 28 2015

city: Shanghai

first: Bin

last: Li

address: 320 Yueyang Road, Xuhui District,

institute: Institut Pasteur of Shanghai, CAS

summary: The SZ-4 cell was originally identified in a Sezary disease patient and expresses FOXP3. There are different subclones of SZ4 cell which have different expression of FOXP3. Here, we used FOXP3 positive and negative SZ4 cell lines to do miRNA microarray.

overall_design: We performed microarrays with two samples: SZ4 FOXP3+ and SZ4 FOXP3-

first: Zhiyuan

first: Andy

last: Tsun

first: Chao

last: Kong


title: MicroRNA expression profiling of zebrafish heart regeneration

city: Orono

first: Benjamin

last: King

state: ME

address: 5735 Hitchner Hall

department: Molecular and Biomedical Sciences

institute: University of Maine

summary: Cardiovascular disease is the leading cause of morbidity and mortality in the Western world due to a limited regenerative capacity. In lieu of new muscle synthesis, the human heart replaces necrotic tissue with deposition of a non-contractile scar. In contrast, the adult zebrafish is endowed with a remarkable regenerative capacity, capable of de novo cardiomyocyte (CM) creation and scar tissue resolution when challenged with an acute injury. In these studies, we examined the contributions of the dynamically regulated microRNA, miR-101a, during adult zebrafish heart regeneration. We demonstrate that miR-101a expression is rapidly depleted within 3 days post-amputation (dpa) but is highly upregulated by 7-14 dpa, before returning to uninjured levels at the completion of the regenerative process. Employing heat-inducible transgenic strains and antisense oligonucleotides, we demonstrate that decreases in miR-101a levels at the onset of cardiac injury enhanced CM proliferation. Interestingly, prolonged suppression of miR-101a activity stimulates new muscle synthesis but with defects in scar tissue resolution. Upregulation of miR-101a expression between 7-14 dpa is critical to stimulate remodeling of the scar. Through a series of studies, we identified the proto-oncogene, fosab (cfos) as a potent miR-101a target gene, stimulator of CM proliferation, and inhibitor of scar tissue remodeling. Importantly, combinatorial depletion of fosab and miR-101a activity rescued defects in scar tissue resolution mediated by miR-101a inhibition alone. In summation, our studies indicate that the precise temporal modulation in the miR-101a/fosab genetic axis is critical for coordinating CM proliferation and scar tissue resolution during zebrafish heart regeneration.

overall_design: Pooled cardiac samples from uninjured and regenerating (6hpa) adult fish in biological triplicate.

first: Megan

last: Beauchemin

first: Ashley

last: Smith

first: Viravuth

last: Yin


title: Gene expression profiles of desmoid tumor cells treated with gamma-secretase inhibitor

status: Public on Nov 03 2015

city: Houston

first: Chad

last: Creighton

state: TX

address: One Baylor Plaza, Mail Stop: BCM305

department: Biostatistics, Ducan Cancer Center

institute: Baylor College of Medicine

summary: Desmoid tumors (DTs) are rare mesenchymal monoclonal lesions that have a high risk of local recurrence but lack metastatic potential. Since the Notch pathway appears to be   important in the carcinogenesis of several tumor types, in the past few years γ-secretase inhibitors (GSIs) have emerged as a potential therapeutic treatment by inhibiting cancer cell  Notch signaling through NICD cleavage blockade. To investigate the antitumor effect of PF-03084014, a γ-secretase inhibitor, in DT models, cells treated with PF-03084014 were characterized by gene  array analysis.

overall_design: Three cell strains of Desmoid tumors (Desm14, Desm27 and Desm39b) were subjected to either no treatment (control, called G-0) or treatment with 10μM of PF-03084014 (called G-10). The regimen for each treatment was ~8 days and ~30 days; multiple group comparison

first: Yiqun

last: Zhang


title: Leukocyte gene expression as a function of perceived social isolation (PSI): Year 8

overall_design: Gene expression profiling was carried out on peripheral blood mononuclear cell RNA samples collected from 93 adults in Year 8 of the Chicago Health Aging and Social Relations Study.  Participants were assessed for PSI using the UCLA Loneliness Scale, and were also classified as chronically high in PSI (1/0) based on UCLA Loneliness Scale scores during study years 1-5.  A 1-year lagged value of PSI is also included, and analyses additionally controlled for age at study entry, sex, race/ethnicity (dummy codes for Black and Hispanic), marital status, (log) household income, Body Mass Index (BMI), smoking history, heavy alcohol consumption, depressive symptoms (CESD), perceived stress (PSS), social support (SocSupp), circulating monocyte percentages, and RNA indicators of major leukocyte subsets (CD3E, CD3D, CD4, CD8A, CD19, FCGR3A/CD16, NCAM1/CD56, CD14).


title: Transcriptional effects of forced KLF15 over-expression in mouse muscle.

city: San Francisco

first: Saptarsi

last: Haldar

address: 1650 Owens St

institute: Gladstone Institute of Cardiovascular Disease

summary: Excessive or sustained glucocorticoid (GC) exposure causes muscle wasting. Paradoxically, moderate or transient GC exposure elicits ergogenic effects, evidenced by their widespread use as doping agents by endurance athletes and poorly understood efficacy in Duchenne muscular dystrophy (DMD), a genetic muscle wasting disease. While mechanisms underlying GC-mediated muscle wasting are well defined, the molecular basis for the latter remains unknown. In this arm of our studies, we compare expression profiles in quadriceps tissue from KLF15 transgenic (MTg) and non-Tg mice.

overall_design: Total RNA was isolated from the quadriceps of KLF15 non-Tg and MTg mice and hybridized to Affymetrix Mouse430A 2.0 arrays to determine transcriptional responses to forced, 5-6-fold overexpression of KLF15.

first: Alexander

last: Morrison-Nozik

first: Madeleine

last: Lemieux


title: Gene expression profiling of histone deacetylase inhibition in epithelioid sarcoma

summary: Epithelioid Sarcoma (ES) is a rare neoplasm uniquely comprised of cells exhibiting both mesenchymal and epithelial features. Having propensity for local and distant recurrence, it can pose a diagnostic dilemma secondary to pathologic complexity. Patients have dismal prognosis due to lack of effective therapy. HDAC inhibitors exhibit marked anti-tumor effects in various malignancies. Our studies demonstrate that pan-HDAC inhibitors constitute potentially novel therapeutics versus ES. Human ES cells (VAESBJ, HS-ES, Epi544) were studied in vitro to evaluate the effects of HDACi.

overall_design: Gene array analysis was used to identify the impact of HDACi on ES gene expression in three cell lines.

first: Dina

last: Lev

first: Raphael

last: Pollock

first: Gonzalo

last: Lopez


title: Mouse frozen liver: vehicle-control vs. CCl4+DEN treated

status: Public on Nov 01 2015

city: Austin

first: Grace

last: Chappell

address: 9390 Research Blvd, Bldg 2, Ste. #100

department: Health Sciences

institute: ToxStrategies, Inc.

type: Genome variation profiling by genome tiling array

summary: Hepatocellular carcinoma (HCC) is a prevalent human cancer with rising incidence worldwide. Human HCC is frequently associated with chronic liver inflammation and cirrhosis, pathophysiological processes that are a consequence of chronic viral infection, disturbances in metabolism, or exposure to chemical toxicants. To better characterize the pathogenesis of HCC, we used a human disease-relevant mouse model of fibrosis-associated hepatocarcinogenesis.  In this model, marked liver tumor response caused by a pro-mutagenic chemical N-nitrosodiethylamine in presence of liver fibrosis was associated with epigenetic events indicative of genomic instability. Therefore, we hypothesized that DNA copy number alterations (CNAs), a feature of genomic instability and a common characteristic of cancer, are concordant between human HCC and mouse models of fibrosis-associated hepatocarcinogenesis. We evaluated DNA CNAs and changes in gene expression in the mouse liver (normal, tumor and non-tumor cirrhotic tissues). In addition, we compared our findings to those in human HCC (tumor and non-tumor cirrhotic/fibrotic tissues). We observed that while fibrotic liver tissue is largely devoid of DNA CNAs, highly frequently occurring DNA CNAs are found in mouse tumors, which is indicative of a profound increase in chromosomal instability in HCC. When compared to CNAs in human HCC, we found that 33% of genes in these segments are similarly affected in the mouse tumors. Our results suggest that CNAs most commonly arise in neoplastic tissue rather than in fibrotic liver, and demonstrate the utility of this mouse model in replicating the molecular features of human HCC.

overall_design: Genomic DNA was extracted from frozen liver samples from vehicle-control and DEN+CCl4-treated mice using a DNEasy kit (Qiagen, Valencia, CA). Eighteen mouse tumor samples were included in the study, as well as 18 matched non-tumor samples taken from fibrotic, non-tumorous, surrounding liver tissue from the same mice. Liver DNA from 6 vehicle control-mice was pooled and used as the reference genome in the aCGH experiments.  Copy number alterations were identified using the normalized data.

last: Silva

first: Takeki

last: Uehara

first: Igor

last: Pogribny

first: Ivan

middle: I

last: Rusyn


title: Identification of four subtypes of Triple Negative Breast Cancer (TNBC) by genomic profiling

status: Public on Dec 25 2015

first: Suzanne

last: Fuqua

address: 1 Baylor Plaza

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

summary: The aggressive triple negative breast cancers (TNBCs), which lack estrogen receptor (ER), progesterone receptor (PR) and human epidermal growth factor receptor 2 (HER2), comprise a high-risk subset of human breast cancers which remain poorly characterized and lack effective treatments. While meta-analyses have recently suggested the complexity of these tumors, no robust phenotypes have been defined. We identified four distinct subtypes through gene expression analyses of 198 TNBCs (84 Discovery, 114 Validation). We then classified 221 publically available TNBCs profiled on the same mRNA expression array. All three sets supported stratification of tumors by cell cycle (Subtype 1 Luminal – FOXA1, LUM), DNA repair (Subtype 2, Mesenchymal – ADIPOQ, MES), downregulated immunological (Subtype 3, Basal-Like – SOX10/8, BL), and upregulated immunological (Subtype 4, Basal Immune – STAT1, BI) signaling pathways. Additional classified data sets demonstrate significantly lower risk of relapse and death with BI tumors, and highest risk with BL tumors, even after correction with known risk factors. DNA copy number profiling of our primary study set produced optimal differentiation of the LUM subtype from the remaining tumors, and drove expression of FGFR2 and CDK1 in BL and BI subtypes. Subtype-specific targets include MUC1 in LUM tumors, CTLA4 in BI tumors, and a potential dependence of MES tumors on NTRK2, DDR2, PDGFRA, TEK, and ADRB2, which, upon validation, could enable targeted treatment with tyrosine-kinase inhibitors and beta-blockers. These findings further define TNBCs and provide the rationale for studies targeting agents against these tumor subtypes, thereby enabling a higher potential for preventive efficacy in patients with TNBC.

overall_design: DNA profiling analysis was conducted on 142 TNBC tumors (ER-negativity defined as Allred Scale value ≤2) with >50% cellularity (discovery set: n=84; validation set: n=58).

first: Matthew

last: Burstein

first: Anna

last: Tsimelzon

first: Susan

middle: G

last: Hilsenbeck

first: Graham

last: Poage

first: Kyle

last: Covington

first: Jenny

last: Chang

first: C

last: Osborne

first: Gordon

middle: B

last: Mills

first: Ching

last: Lau

first: Powel

middle: H

last: Brown


title: Exon-expression profiling of CD4+ T cells derived from HTLV-1-infected individuals with or without malignancy

city: lyon

first: franck

last: mortreux

address: 46 allee d'Italie

institute: oncovirology and Biotherapies, UMR5239, LBMC

summary: T-cell clones were obtained by limiting dilution culture of PBMC of HTLV-1 carriers. Exon expression profiling was performed using Affymetrix exon array (Affymetrix Human Exon 1.0 ST Array) according to the manufacturer's instructions. Gene version of CEL files 01 to 12 are presented in GSE46518.

overall_design: The main objectives were to assess whether transcriptional and post-transcriptional modifications associate with HTLV-1 infection in vivo. To this end, T-cell clones, infected or not by HTLV-1, were obtained by limiting dilution culture of PBMC derived from HTLV-1 carriers. Tumor cells derived from patients with an acute form ATLL. Exon expression profiles of cloned T-cells and ATLL cells was analyzed using Affymetrix exon array (Affymetrix Human Exon 1.0 ST Array) according to the manufacturer's instructions. Given that T-cell activation is known to modify alternative exon usage, microarray analysis was carried-out with unstimulated and PHA-stimulated CD4+ T cell clones.

first: Morgan

last: Thenoz

first: Céline

last: Vernin

first: Franck

last: Mortreux


title: Leukocyte gene expression as a function of perceived social isolation (PSI): Year 7

first: Steve

last: Cole

overall_design: Gene expression profiling was carried out on peripheral blood mononuclear cell RNA samples collected from 62 adults in Year 7 of the Chicago Health Aging and Social Relations Study.  Participants were assessed for PSI using the UCLA Loneliness Scale, and were also classified as chronically high in PSI (1/0) based on UCLA Loneliness Scale scores during study years 1-5.  A 1-year lagged value of PSI is also included, and analyses additionally controlled for age at study entry, sex, race/ethnicity (dummy codes for Black and Hispanic), marital status, (log) household income, Body Mass Index (BMI), smoking history, heavy alcohol consumption, depressive symptoms (CESD), perceived stress (PSS), social support (SocSupp), circulating monocyte percentages, and RNA indicators of major leukocyte subsets (CD3E, CD3D, CD4, CD8A, CD19, FCGR3A/CD16, NCAM1/CD56, CD14).


title: Peripheral blood transcriptome profiles from an RNA Pilot Study within the United States Health and Retirement Study (HRS)

status: Public on Nov 15 2015

summary: Individual differences in peripheral blood transcriptomes in older adults as a function of demographic, socio-economic, psychological, and health history characteristics.

overall_design:
Gene expression profiling was carried out on peripheral blood RNA samples collected from 121 community dwelling older adults participating in the United States Health and Retirement Study.  In addition to basic demographic characteristics (age, sex, race/ethnicity), participants were also assessed on health-related characteristics (body mass index/BMI; history of smoking or heavy alcohol consumption; history of chronic illnesses such as diabetes, cardiovascular disease, cancer, stroke), household annual income (log transformed), and measures of loneliness (UCLA Loneliness Scale; Russell D, Peplau LA, Cutrona CE: The revised UCLA Loneliness Scale: concurrent and discriminant validity evidence. J Pers Soc Psychol 1980, 39:472-480; higher values indicate greater loneliness) and purpose in life (PWB_Purpose; Purpose scale of the Ryff Scales of Psychological Well-being; Ryff CD (1989) Happiness is everything, or is it?  Explorations on the meaning of psychological well-being. J. Pers Soc. Psychol 57: 1069-1081; higher values indicate greater experience of purpose in life).  Additional analyses examined measures of optimism and pessimism (6 items from the Life Orientation Test; Scheier MF Carver CS Bridges MW (1994) Distinguishing optimism from neuroticism (and trait anxiety, self-mastery, and self-esteem): A reevaluation of the Life Orientation Test. J Pers Soc Psychol 67:1063-1078; higher values indicating greater optimism or pessimism), anxiety symptoms (5 items from Beck Anxiety Inventory; Beck AT et al (1988) An inventory for measuring clinical anxiety: Psychometric properties. J Consult Clin Psychol 56:893-897; higher values indicating greater anxietn), depressive symptoms (CESD; Center for Epidemiologic Studies Depression Scale; Radloff LS (1977) The CES-D scale:  A self-report depression scale for research in the general population. Applied Psychol Meas 1:386-401; higher values indicating greater depression), life satisfaction (Diener E et al (1985) The Satisfaction With Life Scale. J Pers Assess 49:71-75; higher values indicate greater life satisfaction), and positive affect (PA) and negative affect (NA; Watson D et al (1988) Development and validation of brief measures of positive and negative affect:  The PANAS scales. J Pers Soc Psychol 54:1063-1070; higher values indicate greater positive or negative affect).
Binary characteristics are coded yes=1 and no=0.


title: Changes in the transcriptome of bovine ovarian cortex during follicle activation in vitro

status: Public on Oct 31 2015

city: ithaca

first: Ming

last: yang

address: 316 tower road

institute: Cornell

summary:
A key transition in ovarian follicular development is the activation of resting primordial follicles to the growing primary follicle stage.  The signals that regulate activation are still not well understood, especially in non-rodent species.
we combined a microarray approach with an in vitro system to gain insight into the regulation of follicle activation.  Genes and pathways identified in this study provide interesting candidates for further investigation of mechanisms underlying follicle activation.

overall_design: Fetal bovine ovarian cortical pieces enriched for primordial or primary follicles were obtained by culture with cotrol medium supplemented with TS+ (transferrin, selenous acid, BSA, and linoleic acid) or with insulin (ITS+), a factor that stimulate bovine follicle activation.  Total RNA was extracted.  Differences in global gene expression profiles between pieces enriched for primordial or primary follicles were determined by microcarray analysis.

last: Yang

first: Joanne

last: Fortune


title: MicroRNA expression abnormalities in pancreatic endocrine and acinar tumours are associated with distinctive pathologic features and clinical behavior

status: Public on Oct 30 2015

city: Sutton

first: Anguraj

last: Sadanandam

state: Surrey

address: 15 Cotswold Road

department: Molecular Pathology

country: United Kingdom

institute: Institute of Cancer Research (ICR), London

summary: We investigated the global microRNA expression patterns in normal pancreas, pancreatic endocrine tumours and acinar carcinomas to evaluate their involvement in transformation and malignant progression of these tumour types.

overall_design: A neoplastic cellularity higher than 90% was obtained by cryostat enrichment. RNA was extracted with Trizol (Invitrogen, Carlsbad, CA) from 10 20-μm thick cryostat sections, checking the cell composition of the sample every five sections. RNA integrity was confirmed using the Agilent 2100 Bioanalyzer (Agilent Technologies, Palo Alto, CA). microRNA microarray (Ohio State University Comprehensive Cancer Center, version 2.0) contains probes for 460 mature microRNAs spotted in quadruplicate (235 homo sapiens, 222 mus musculus, and three Arabidopsis thaliana) with annotated active sites. Often, more than one probe set exists for a given mature microRNA.

first: Aldo

last: Scarpa


title: Pancreatic endocrine tumours: expression profiling evidences a rold for AKT-mTOR pathway

summary: We investigated the global gene expression in a large panel of pancreatic endocrine tumours (PETs) aimed at identifying new potential targets for therapy and biomarkers to predict patient outcome.

overall_design: Total RNA was extracted from frozen tissue and hybridized on a custom 18.5K human oligo microarrays obtained from the Ohio State University Cancer Center.


title: modENCODE_White Lab: genome-wide ChIP data of Bcd from E8-16 on Illumina Genome Analyzer.

city: Chicago

first: Kevin

middle: P.

last: White

state: IL

address: 900 E. 57th STR. 10th FL.

department: Institute for Genomics and Systems Biology

institute: University of Chicago

type: Genome binding/occupancy profiling by high throughput sequencing

summary:
This is a dataset generated by the Drosophila Regulatory Elements modENCODE Project led by Kevin P. White at the University of Chicago. It contains genome-wide binding profile of the factor Bcd from E8-16 generated by ChIP and analyzed on Illumina Genome Analyzer.

For data usage terms and conditions, please refer to http://www.genome.gov/27528022  and http://www.genome.gov/Pages/Research/ENCODE/ENCODEDataReleasePolicyFinal2008.pdf

overall_design:
A validated dataset is comprised of three biological replicates for ChIP-chip experiments and two replicates for ChIP-seq and meet the modENCODE quality standards. The control sample is the chromatin Input used for ChIP. Most factors binding profiles are generated by using specific antibodies for the protein of interest. However, some factors have been tagged by GFP in a transgenic line. In that case, ChIP is generated using an anti-GFP antibody.

This submission represents the ChIP-seq component of the study.

first: Nicolas

last: Negre

first: Nicholas

last: Bild


title: modENCODE_White Lab: genome-wide ChIP data of Hnf4 from E16-24 on Illumina Genome Analyzer.

summary:
This is a dataset generated by the Drosophila Regulatory Elements modENCODE Project led by Kevin P. White at the University of Chicago. It contains genome-wide binding profile of the factor Hnf4 from E16-24 generated by ChIP and analyzed on Illumina Genome Analyzer.

For data usage terms and conditions, please refer to http://www.genome.gov/27528022  and http://www.genome.gov/Pages/Research/ENCODE/ENCODEDataReleasePolicyFinal2008.pdf

middle: P