title: The transcriptional response of ovarian cancer cells to treatment with cisplatin (CDDP)

status: Public on Dec 31 2013

city: Torino

first: Raffaele

middle: A

last: Calogero

state: To

address: Via Nizza 52

department: Molecular Biotechnology Center

country: Italy

institute: University of Torino

summary:
The transcriptional response to CDDP of three ovarian cancer cell lines was studied. These lines show different genetic profiles and display different susceptibilities to CDDP. The time and doses that resulted in the apoptotic death of each cell line was identified and used to study the expression profiles associated to CDDP-induced cell death in each cell line.
CDDP: cis-diamminedichloroplatinum(II)

overall_design: In order to elucidate the mechanism of CDDP dependent cell susceptibilities to drugs, the transcriptional response of the three ovarian cancer cell lines to CDDP were studied by microarray based transcription profiling

first: Simona

last: Pavan

first: Martina

last: Olivero

first: Davide

last: Corà

first: MariaFlavia

last: DiRenzo


title: Comparative analysis of Papaver somniferum genotypes having contrasting latex and alkaloid profiles

status: Public on Dec 30 2013

city: Lucknow

first: Ashutosh

middle: K

last: Shukla

state: Uttar Pradesh

address: P.O. CIMAP

department: Biotechnology Division

country: India

institute: CSIR-Central Institute of Medicinal and Aromatic Plants

summary: Sampada and Sujata are two contrasting genotypes of Papaver somniferum that are contrasting in terms of their latex and alkaloid profiles. The major objective of the present study was to use a small-scale (750 target genes) microarray of P. somniferum for identification of genes that are differentially expressed in the capsule walls of the two contrasting genotypes, Sampada and Sujata. Nidarshana Chaturvedi and Mridula Singh made equal contribution as first authors to this data.

overall_design: The experiment aimed at studying the expression levels of target genes in P. somniferum. A dual channel procedure with dye-swap arrangement was adopted in the study on two samples - Sampada and Sujata. The interest was to compare the expression levels of target genes in Sujata against Sampada. The expression data was generated on 1,569 probes, which includes controls and target probes.

first: Nidarshana

last: Chaturvedi

first: Mridula

last: Singh

first: Ajit

last: Shasany

first: Suman

last: Khanuja


title: Global gene profiling of glutamate-induced neuronal death

city: Hobart

first: Minghui Jessica

last: Chen

state: Tasmania

address: Menzies Research Institute, University of Tasmania, Private Bag 24

department: Neuroscience group

country: Australia

institute: Menzies Research Institute

summary: Glutamate, a major neurotransmitter in the mammalian nervous sytem, has been involved in the mediation of excitotoxicity commonly observed in the pathogenesis of stroke. Current study focused on gaining an insight into the molecular mechanisms of glutamate-induced neuronal death

overall_design: A total of 15 RNA samples were analyzed. There is one treatment conditions of 250uM glutamate. 3 replicates were collected for each of the selected time-points (5h, 15h and 24h) in addition to 6 replicates of shared vehicle control.

first: Nam

middle: S

last: Cheung

first: Minghui

middle: J

first: Zhao

middle: F

last: Peng

first: Jayapal

last: Manikandan


title: Real-time quantitative PCR analysis of human leukemic B-cells.

city: Lodz

first: Ida

last: Franiak-Pietryga

address: Pabianicka 62

country: Poland

institute: Copernicus Memorial Hospital in Lodz

summary:
Fresh blood samples were collected from 10 CLL (chronic lymphocytic leukemia) previously untreated patients before and after 2 weeks of the first cycle of CCR (cladribine, cyclophosphamide, rituximab) treatment. Peripheral blood mononuclear cells (PBMNCs) were separated from EDTA blood by layering on the Histopaque 1077 and centrifuging on a density gradient. Mean B-cell CD19+ purity was ≥95% as measured by flow cytometry (FC).
Microarray analysis was performed using 0.5 microgram of RNA transcribed to cDNA. Prepared cDNA samples were subjected to RT-PCR in duplicate in the TaqMan 7900HT Sequence Detection System (Applied Biosystems).

overall_design: qPCR gene expression profiling. Intensity of gene expression in CLL cells collected from particular patient before treatment was compared with the gene expression signals in CLL cells from the same patient after 2 weeks of treatment.

first: Aleksandra

last: Salagacka


title: Locust flight muscle: Tibetan Plateau population vs. North China Plain population

status: Public on Dec 24 2013

city: New Haven

first: Dejian

last: Zhao

state: CT

address: 333 Cedar St

department: Genetics

country: USA

institute: Yale School of Medicine

summary: Background: Responses to hypoxia have been investigated in many species; however, comparative study between conspecific geographical populations in different altitude regions is rare, especially for invertebrates . The migratory locust, Locusta migratoria, is widely distributed both on high-altitude Tibetan Plateau (TP) and on low-altitude North China Plain (NP). TP locusts have inhabited Tibetan Plateau since Quaternary glaciations events and thus probably have evolved superior capacity to deal with hypoxia. Results: Here we compared the hypoxic responses of TP and NP locusts from morphological, behavioral and physiological perspectives. We found that TP locusts were more tolerant of extreme hypoxia than NP locusts, with a lower proportion exhibiting stupor, a faster recovery time, and higher respiration rates. We compared the transcriptional profiles of field TP and NP locusts and found that their differences were possibly attributed to a combination of multiple factors, e.g. oxygen, UV radiation, temperature and nutrition. To evaluate why TP locusts respond to extreme hypoxia differently from NP locusts, we subjected them to extreme hypoxia and compared their transcriptional responses. We found that the aerobic metabolism was more active in TP locusts than in NP locusts. RNAi disruption of PDHE1b, an entry gene from glycolysis to TCA cycle, increased the ratio of stupor in Tibetan locusts and decreased the ATP content of Tibetan locusts in hypoxia, confirming the significant importance of this metabolic branch for TP locusts to conquer hypoxia. Conclusions: Here we show that TP locusts are better tolerant of hypoxia than NP locusts and the better capacity to modulate primary metabolism in TP locusts contributes to their superior tolerance of hypoxia compared to NP locusts.

overall_design: FIELD POPULATION: TP locusts vs. NP locusts;direct comparison on 6 separate microarrays; each microarray compares one biological replicate; each biological replicate contains 10 individuals. LAB POPULATION: hypoxia-treated TP locusts vs TP locusts in normoxia; hypoxia-treated NP locusts vs NP locusts in normoxia; direct comparison on 6 separate microarrays; each microarray compares one biological replicate; each biological replicate contains 10 individuals.

first: Le

last: Kang

first: De-Jian


title: Global gene profiling of (-)-Epigallocatechin-3-gallate (EGCG)-induced neuronal death

summary: Alzheimer’s disease (AD) is the most common form of adult-onset dementia with severe intellectual deterioration and is characterised by the accumulation of the amyloid-β (Aβ) peptides and the presence of hyperphosphorylated microtubule- associated protein, tau. (-)-Epigallocatechin-3-gallate (EGCG) – a polyphenolic catechin found in green tea leaves, not only acts as a proteasome inhibitor, it is also involved in neuroprotection.

overall_design: A total of 7 RNA samples were analyzed. Cultured murine primary cortical neurons were treated with 1uM EGCG for 24h (n=3) in addition to the vehicle control (n=4).


title: Serotyping of Streptococcus pneumoniae based on capsular genes polymorphisms

city: Quebec City

first: Frederic

last: Raymond

state: Quebec

address: 2440 Bd Hochelaga Suite 1710

department: École de nutrition

country: Canada

institute: Université Laval

summary:
Diagnostic primer extension assay to serotype Streptococcus pneumoniae. Assay validation.
Background: Monitoring of Streptococcus pneumoniae serotype epidemiology is essential since serotype replacement is a concern when introducing new polysaccharide-conjugate vaccines. To simplify S. pneumoniae serotyping, a novel PCR-based automated microarray assay was developed to assist in the tracking of the serotypes.  Results: Autolysin (lytA), pneumolysin (ply) and eight genes located in the capsular operon (cps) were amplified using multiplex PCR. This step was followed by a tagged fluorescent primer extension step targeting serotype-specific polymorphisms. The tagged primers were then hybridized to a microarray. Results were exported to an expert system that transforms genetic typing data into capsular serotype identification.   The assay was validated on 166 cultured S. pneumoniae samples from 63 different serotypes as determined by the Quellung method. In addition, the assay was tested on clinical specimens including 43 cerebrospinal fluid samples from patients with meningitidis and 59 nasopharyngeal aspirates from bacterial pneumonia patients. The assay presented with no cross-reactivity for 24 relevant bacterial species found in these types of samples. The limit of detection for serotyping and S. pneumoniae detection was 100 genome equivalent per reaction.   Conclusion: This automated assay is amenable to clinical testing and does not require any culturing of the samples. The assay will be useful for the evaluation of serotype prevalence changes after new conjugate vaccines introduction.

overall_design: 166 quellung serotyped strains and two negative controls

first: Frédéric

first: Nancy

last: Boucher

first: Robin

last: Allary

first: Lynda

last: Robitaille

first: Brigitte

last: Lefebvre

first: Cécille

last: Tremblay

first: Jacques

last: Corbeil

first: Alain

last: Gervaix


title: Global gene profiling of alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid (AMPA)-induced neuronal death

first: Minghui Jessica

summary: AMPA receptors are involved not only in neuronal plasticity but also in excitotoxicity, mediated largely by the influx of Ca2+ (Choi et al., 1988). Their implication has been highlighted in animal models of ischemia and epilepsy. Studies of ischemic rodent models featured that prior to cell death, hippocampal CA1 pyramidal cells exhibit an increased AMPA receptor-mediated Ca2+ influx and decreased GluR2 and GluR3 mRNA and protein levels (Gorter et al., 1997; Heuerteaux et al., 1995).

overall_design: A total of 15 RNA samples were analyzed. Cultured murine primary cortical neurons were treated with 300uM AMPA over a time-course of 5h, 15h and 24h (n=3) in addition to the vehicle control (n=6).

first: Nam

first: Minghui


title: Positive emotion-specific changes in gene expression profile in brain and peripheral tissues of the tickled rats

status: Public on Dec 28 2013

city: Tsurumi-ku, Yokohama

first: Katsuyuki

last: Hayashi

state: Kanagawa

address: 1-1-43, Suehiro-cho

department: Business Development

country: Japan

institute: DNA Chip Research Inc

summary:
The changes of mRNA expression levels were analyzed in striatum, salivary glands , and peripheral leukocyte of the juvenile rat stimulated by tickling for 4 weeks as a positive stimulation.

Keywords: Stress response

overall_design: Twenty-one-day-old male Wistar rats　after weaning were used. All rats were separately maintained in the standard cages which were shielded with screens not to see each other during the study. The rats were then subjected to the following three conditions; tickling, light touch, and no stimulus. The stimulation was given to the rats once every weekday (Monday to Friday) for 4 weeks. Tickling stimulation was used as a mimic of the rough-and-tumble play of rats which induced a positive emotional response [50 kHz ultrasonic vocalization (USV)]. Light touch was a discriminative stimulation to tickling, and neither the rat with light touch nor with no stimulus showed such a response in general. Gene expression changes in striatum, salivary glands, and peripheral leukocyte of the tickled rats were comprehensively analyzed comparing with light touched and no stimulated rats using microarray techniques.   Biological replicates: 4 animals each condition. One replicate per array.

first: Miyo

last: Hori

first: Osamu

last: Urayama


title: Expression data for human retinal pigment epithelium (RPE)/choroid - early age-related macular degeneration (AMD) and control samples

status: Public on Dec 23 2013

city: Iowa City

first: S. Scott

last: Whitmore

state: IA

address: 375 Newton Road

department: The University of Iowa Institute for Vision Research

institute: The University of Iowa

summary: Purpose: Age-related degeneration (AMD) is a major cause of blindness in developed countries. The molecular pathogenesis of early events in AMD is poorly understood. We investigated differential gene expression in samples of human retinal pigment epithelium (RPE)/choroid from early AMD and control maculas using exon-based arrays. Methods: Gene expression levels in nine early AMD and nine control human donor eyes were assessed using Affymetrix Human Exon ST 1.0 arrays. Two controls did not pass quality control and were removed. Differentially expressed genes were annotated using DAVID, and gene set enrichment analysis (GSEA) was performed on RPE-specific and endothelium-associated gene sets. CFH genotype was also assessed and differential expression was analyzed with respect to high AMD risk (YH/HH) and low AMD risk (YY) genotypes. Results: Seventy-five genes were identified as differentially expressed (raw p-value < 0.01; >50% fold change, mean log2 expression level in AMD or control ≥ median of all average gene expression values); however, no genes were significant (adj. p-value < 0.01) after correction for multiple hypothesis testing. Of 52 genes with decreased expression in AMD (fold change < 0.5; raw p-value < 0.01), 18 genes were identified by DAVID analysis as associated with vision or neurological processes. GSEA of RPE-associated and endothelium-associated genes revealed a significant decrease in genes typically expressed by endothelial cells in the early AMD group compared to controls, consistent with previous histologic and proteomic studies. Analysis with respect to CFH genotype indicated decreased expression of ADAMTS9 in eyes with high-risk genotypes (fold change = -2.61; raw p-value = 0.0008). Conclusions: GSEA results suggest that RPE transcripts are preserved or elevated in early AMD, concomitant with loss of endothelial cell marker expression. These results are consistent with the notion that choroidal endothelial cell dropout occurs early in the pathogenesis of AMD.

overall_design: Using AltAnalyze (ver. 2.0.7 beta), we analyzed nine early AMD and nine control eyes using Affymetrix Human Exon ST 1.0 arrays. Following initial processing in AltAnalyze, two control arrays were identified as potential outliers by tests implement in arrayQualityMetrics, a package for R.

first: S

first: Terry

last: Braun

first: Jessica

middle: M

last: Skeie

first: Christine

last: Haas

first: Elliott

middle: H

last: Sohn

first: Edwin

last: Stone

first: Todd

middle: E

last: Scheetz

first: Robert

last: Mullins


title: Global transcriptomic profiling of oxygen-glucose deprivation (OGD)-mediated neuronal injury

last: Chen

summary: Oxygen-glucose deprivation (OGD) is a cellular phenomenon consistently observed upon occurrence of ischemic stroke which eventually results in neuronal death. Neuronal cell death after ischemia takes place via two distinct processes, necrosis and apoptosis. Apoptosis, programmed cell death, is denoted by chromatin condensation, nuclear blebbing, cellular shrinkage, and DNA fragmentation. Unlike apoptosis, cellular swelling and lysis is suggestive of necrosis. However, these two processes are related not only to the severity but also to the duration of ischemia.

overall_design: Microarray analysis was carried out using 20 Illumina mouse Ref8V1.1 genechip arrays. The assignment of the arrays was as follows: Controls (n=5); exposure to OGD for 10min, 5h, 8h, 15h and 24 h (n=3 respectively).

last: Cheung

first: Zhao

last: Peng

first: Jayapal

last: Manikandan


title: Small molecule inhibitors suppress expression of both type III secretion and amylovoran biosynthesis genes in Erwinia amylovora

city: Urbana

first: Frank

last: Zhao

state: IL

address: 1210 Gregory Dr.

department: Crop Sciences

institute: University of Illinois

summary: Microarray analysis of E. amylovora treated with compounds no. 3 and no. 9 identified a total of 588 significantly differentially expressed genes. Among them, 95 and 78 genes were, respectively, induced and suppressed by both compounds as compared to DMSO control. Majority of T3SS genes in E. amylovora including hrpL and avrRpt2 effector gene were suppressed by both compounds. Compound no. 3 also suppressed the transcription of amylovoran precursor and biosynthesis genes. On the other hand, both compounds significantly induced expression of glycogen biosynthesis genes and siderophore biosynthesis, regulatory and transport genes. Furthermore, many membrane, lipoprotein and exported protein encoding genes were also activated by both compounds.

overall_design: Erwinia amylovora WT strain treated with compound No. 3 and No. 9 and compared to DMSO control. Four biological replicates for each chemical treatment (two samples were combined) were hybridized to three arrays. Four biological replicates (two each combined) for DMSO treatment were hybridized to two arrays.

first: Youfu

first: Fan

last: Yang


title: Comparative global transcriptomic profiling of low and high concentration of lactacystin-mediated neuronal death

first: Minghui Jessica

summary: Inhibition of proteasome degradation pathway has been implicated in neuronal cell death leading to neurodegenerative diseases such as Parkinson’s disease and Alzheimer’s disease.  Pharmacological proteasomal inhibitors such as lactacystin can induce apoptosis in cultured mouse cortical neurons through the activation of caspase-3. However, Meiners et al., 2003 suggested that low dose of lactacystin induces a concerted expression of proteasome genes and de novo formation of proteasomes.

overall_design:
We discovered by microarray analysis that lactacystin treatment induces a dose-dependent biphasic modulation of both potentially neuroprotective as well as pro-apoptotic genes in neurons.
Microarray analysis was carried out using 24 Illumina mouse Ref8V1.1 genechip arrays. The assignment of the arrays was as follows: Controls (n=6); exposure to 1 μM (High) lactacystin for 5h, 8h, 15h and 24 h (n=3 respectively) and 0.1uM (Low) for 15h and 24h (n=3 respectively).

first: Nam

first: Minghui


title: TLR-mediated basophil production of IL-4 and IL-13 in human and mouse

city: Kamakura

first: Satoko

last: Takizawa

address: 6-10-1 Tebiro

department: New Frontiers Research Laboratories

institute: TORAY Industries, Inc.

summary:
It has been previously shown that airway exposure to Toll-like receptor ligands through lipopolysaccharide (LPS)-contaminated house dust or bacterial infections can exacerbate allergic inflammation; however, the underlying mechanism(s) controlling this response have not been fully elucidated. Here we report that basophils are the major source of Th2 cytokines that respond to TLR4 ligands, such as LPS and lipid A, in human PBMC and murine spleen cells. LPS activated human PBMCs to up-regulate mRNAs for not only pro-inflammatory cytokines such as IL-6 and chemokines such as CXCL8 (IL-8), CCL2 (MCP-1), but also Th2 cytokines such as IL-4 and IL13. Among PBMCs, we identified CD123+/BDCA4- basophils as the major source of IL-4 and IL-13 in response to LPS. Even in the absence of IgE, purified human basophils, as well as a basophilic cell line, were directly activated by LPS to produce IL-4 and IL-13. Moreover, LPS-stimulated IL-4 knockin mouse (4get mice) spleens identified the basophils as the major IL-4 producing cells in a TLR4-dependent manner. These results indicate that bacterial LPS may play a role in type-2 immunity through direct activation of basophils to produce IL-4 and IL-13.
Keywords: Cell type comparison

overall_design: TLR-mediated production of cytokines in human PBMCs-depleted basophils or basophils are detected.7 independent human PBMCs-depleted basophils samples and 5 independent human basophils samples are included in this series. 2-color analysis was recruited. In each experiment, PBMCs-depleted basophils or basophils are devided to control (Cy5) group and sample (Cy3) group, and sample group was stimulated with LPS, whereas control group was not stumulated. Total RNA was extracted from each of control and sample cells, and amplified. The amplified RNA was labeled with Cy3 or Cy5, and applied to DNA microarray, 3D-Gene.

first: Yuichi

last: Torii

first: Tomokatsu

last: Iwamura

first: Shizuo

last: Akira

first: Ken

last: Ishii


title: Combinatorial analysis of miRNA and mRNA expression in pancreatic ductal adenocarcinoma (PDAC)_miRNA

city: Rome

first: Teresa

last: Colombo

address: p.le A. Moro 7

department: Institute of Molecular Biology and Pathology (IBPM)

institute: Consiglio Nazionale delle Ricerche (CNR)

summary:
miRNAs are known to be involved in PDAC tumorigenesis, but only a few biologically relevant gene targets have been identified.
Here we show that three miRNAs (miR-21, miR-23a and miR-27a) act in concert for the cooperative suppression of several tumor suppressor genes of which we experimentally validated PDCD4, BTG2 and NEDD4L.
The synergistic inhibition of this triple miRNA combination is capable of reducing PDAC growth in a mouse model greater than inhibition of oncomiR-21 alone.

overall_design: Patients samples of normal pancreas (n=9) or pancreatic ductal adenocarcinoma (PDAC; n=9) were retrieved during surgery and placed in RNA Later stabilization fluid and then kept at minus 80 until required.

first: Adam

last: Frampton


title: Transcriptional profiling of Hepatitis C virus HCV core transgenic mice liver

city: Taoyuan

first: ML

last: Chang

address: 5 Fu-Shin Str.

country: Taiwan

institute: CGMH

summary: Transcriptional profiling of HCV core transgenic mice liver comparing nontransgenic mice liver or HCV core transgenic mice liver with various core expression levels.

overall_design: Exp I: Double transgenic mice DTM with high core vs single transgenic mice STM (triplicate); ExpII: DTM with modest core vs STM (triplicate); ExpIII: DTM with modest core vs DTM with high core (triplicate).

first: Ming-Ling


title: Escherichia coli planktonic cultures: mono-species culture vs. mixed-species culture

city: Ann Arbor

first: Dongjuan

last: Dai

state: MI

address: 109 Observatory St

department: Environmental Health Sciences

institute: University of Michigan

summary:
Transcription profile of Escherichia coli cells in mono-species pure planktonic cultures was compared to that of E. coli cells in E. coli-Stenotrophomonas maltophilia dual-species planktonic cultures
E. coli cells were separated from dual-species planktonic cultures before total RNA extraction to eliminate possible cross hybridization from S. maltophilia transcripts. The separation method was developed by combining the use of reagent RNAlater and immuno-magnetic separation. Pure E. coli planktonic cultures were processed with the same separation protocol before RNA extraction.

overall_design: Two condition experiments: E. coli mono-species pure planktonic culture vs E. coli in mixed-species planktonic cultures. Two biological replicates with independently grown and harvested planktonic cultures. Each biological replicate has two technical replicates of hybridization on microarray slides. Each slide has three built-in replicates for each probe.

first: Lutgarde

last: Raskin

first: Chuanwu

last: Xi


title: Escherichia coli biofilms vs planktonic culture

summary:
Transcription profile of Escherichia coli cells in biofilms under static batch culture was compared to that of E. coli cells in planktonic cultures.
Both E. coli biofilm and planktonic cultures were cultivated for 18 h in 10% Luria-Bertani broth at room temperature (20 degree Celsius). Biofilms were grown in static batch culture in petri dishes. Both planktonic culture and biofilms were homogenized and run through a separated protocol.

overall_design: Two condition experiments: E. coli biofilm vs E. coli planktonic cultures. Two biological replicates with independently grown and harvested biofilms or planktonic cultures. Each biological replicate has two technical replicates of hybridization on microarray slides. Each slide has three built-in replicates for each probe.


title: Transcriptional response of ovarian cancer cell lines to HGF and CDDP

first: Raffaele

last: Calogero

summary: HGF sensitizes ovarian cancer cells to chemotherapeutics, e.g. cisplatin (CDDP), through a signaling cascade activated by its MET oncogene encoded receptor and transduced by the p38MAPK. This cascade results in the regulation of a common set of transcripts in three ovarian cancer cell lines, with different genetic profiles and susceptibility to drugs.

overall_design: In order to elucidate the mechanism of HGF dependent cell sensitization to drugs, the transcriptional response of the three ovarian cancer cell lines to HGF and CDDP were studied by microarray based transcription profiling

first: Annalisa

last: Lorenzato

first: Cosimo

last: Martino

first: Martina

last: Olivero

first: Yvonne

last: Oligshlager

first: Anna

last: Ferrero

first: Nicoletta

last: Biglia

first: MariaFlavia

last: DiRenzo


title: Identifying genes of Escherichia coli involved in interactions with Stenotrophomonas maltophilia in planktonic cultures and biofilms using transcriptomic analysis

summary:
Biofilm formation by Escherichia coli was significantly inhibited when co-cultured with Stenotrophomonas maltophilia in static systems. Genes of E. coli involved in species interactions with S. maltophilia were identified in order to allow the study of the mechanisms of inhibited E. coli biofilm formation in co-culture. A total of 89 and 108 genes were identified as differentially expressed in mixed species cultures when growing as biofilm and as planktonic cultures, respectively, compared to the counterpart of pure cultured E. coli. Differential expression of certain identified genes was confirmed using E. coli reporter strains combined with single-cell based flow cytometry analysis. Co-culture with S. maltophilia affected genes involved in metabolism, signal transduction, cell wall composition, and biofilm formation of E. coli. Several selected genes were further confirmed as affecting E. coli biofilm formation in mixed species cultures with S. maltophilia. The data suggest that these genes were involved in species interactions between E. coli and S. maltophilia.

This SuperSeries is composed of the SubSeries listed below.

overall_design: Refer to individual Series.


title: The Chimeric Oncoprotein TLS-CHOP Represses Expression of the Anticancer Cytokine MDA-7/IL-24 in Myxoid Liposarcoma Cells

status: Public on Dec 27 2013

city: Sinjuku-ku

first: Masami

last: Tanaka

state: Tokyo

address: Sinjuku 6-1-1

institute: Tokyo Medical University

summary:
The TLS-CHOP fusion protein is found in the majority of human myxoid liposarcomas (MLS), and is thought to have oncogenic functions.  Until now, however, the molecular function of TLS-CHOP for oncogenesis is still elusive.  In this report, we have revealed that knockdown of TLS-CHOP by specific siRNA in MLS-derived cell lines inhibits cell growth and leads to cell death.  Thus, TLS-CHOP may be a promising therapeutic target for MLS treatment.
Thus we explored the target genes of TLS-CHOP influence cell-proliferation or cell death with microarray.

overall_design: We compared the whole mRNA profiles of cells treated with TLS-CHOP siRNA or control oligo in two myxoid liposarcoma cell-line.

first: Kosuke

last: Oikawa

first: Shunji

last: Itoh

first: Masakatsu

last: Takanashi

first: Takashi

last: Ozaki

first: Yasuteru

last: Muragaki

first: Masahiko

last: Kuroda


title: Escherichia coli biofilm: mono-species culture vs. mixed-species culture

first: Dongjuan

last: Dai

summary:
Transcription profile of Escherichia coli cells in mono-species pure biofilms was compared to that of E. coli cells in E. coli-Stenotrophomonas maltophilia dual-species biofilms.
E. coli cells were separated from dual-species biofilms before total RNA extraction to eliminate possible cross hybridization from S. maltophilia transcripts. The separation method was developed by combining the use of reagent RNAlater and immuno-magnetic separation. Pure E. coli biofilms were processed with the same separation protocol before RNA extraction.

overall_design: Two condition experiments: E. coli mono-species biofilm vs E. coli in mixed-species biofilm. Two biological replicates with independently grown and harvested biofilms. Each biological replicate has two or three technical replicates of hybridization on microarray slides. Each slide has three built-in replicates for each probe.

first: Lutgarde

last: Raskin


title: Global gene profiling of kainate-induced neuronal death

first: Minghui Jessica

last: Chen

summary: It has long been established that in neurological disease models, KA is a potent excitotoxin, mediating acute limbic seizures and long-term morphologic changes in the hippocampus, which are hallmark characteristics seen in temporal lobe epilepsy (i.e. mossy-fiber sprouting, neuronal loss, and reactive gliosis; Ben-Ari and Cossart, 2000). Persuasive clinical evidence employing KA receptor agonists further substantiate the detrimental effects of kainate. For instance, domoic acid (a structural analogue of kainate) has been found to inflict detrimental damage the hippocampus through a real-life outbreak incident of toxic encephalopathy caused by ingestion of mussels contaminated with domoic acid (Pearl et al., 1990).

overall_design: A total of 15 RNA samples were analyzed. Cultured murine primary cortical neurons were treated with 100uM kainate over a time-course of 5h, 15h and 24h (n=3) in addition to the vehicle control (n=6).

first: Nam

last: Cheung

first: Minghui

first: Zhao

last: Peng

first: Jayapal

last: Manikandan


title: Systems analysis of the prostate tumor suppressor NKX3.1  substantiates roles in DNA repair and a transcriptional program that drives luminal cell differentiation

status: Public on Dec 25 2013

city: La Jolla

first: Roy

last: Williams

state: CA

address: 3030 Science Park Road

department: Regenerative Medicine

institute: The Scripps Research Institute

summary: NKX3.1 is an androgen-regulated, prostate-specific gene located on chromosome 8p21, a region frequently undergoing allelic loss in human prostate cancer. Mice deficient in NKX3.1 show signs of epithelial de-differentiation and develop dysplasia and prostatic intraepithelial neoplasia (PIN) that progresses to overt prostate cancer when combined with deletions of additional tumor suppressors such as PTEN or p27Kip1. Although NKX3.1 displays the typical features of an NK class homeobox transcription factor, mechanisms of NKX3.1-mediated tumor suppression remain insufficiently understood because neither the transcriptional program governed by NKX3.1 nor its interacting proteins have been comprehensively revealed.

overall_design: Adenoviruses were created that constitutively express either GFP alone,  or GFP and NKX3.1 (Ad-GFP and Ad-GFP-NKX3.1 viruses, respectively). PrEC LH cells were infected with these viruses and were harvested at 7h and 10h after infection. Using affinity purification and tandem mass spectrometry, we have established an extensive NKX3.1 interactome. In particular, we found that the transcription factor forms stable complexes with the DNA repair proteins Ku70, Ku80, and PARP, interactions that provide a molecular underpinning to previous reports implicating NKX3.1 in DNA repair. Transcriptomic profiling of immortalized human prostate epithelial cells acutely expressing NKX3.1 revealed a rapid and complex response that is a near mirror image of the gene expression signature of human PIN devoid of NKX3.1. Pathway and network analyses suggested that NKX3.1 actuates a fundamental cellular reprogramming toward luminal cell differentiation characterized by suppression of pro-oncogenic c-Myc and interferon-STAT signaling and activation of tumor suppressor pathways.

first: Chih-Cheng

last: Yang

first: Dieter

last: Wolf


title: Microarray analysis of the oocyte quality

city: Blacksburg

first: Fernando

last: Biase

state: VA

address: 175 West Campus Drive

department: School of Animal Sciences

institute: Virginia Tech

summary: Microarray analysis was performed in ooplast samples to identify gene expression profiles associated with the embryo capacity to develop to blastocyst stage

overall_design: A fraction of the cytoplasm from in vitro matured oocytes was collected and snap frozen. The oocytes were chemically activated and presumptive zygotes were in vitro cultured in individual medium microdrops. The embryo development was recorded and oocytes classified according to the stage of embryo development. Oocyte was considered of good quality if the development proceeded to blastocyst stage, whereas it was considered of bad quality if there was a development block between  8-16 cells stage and morula formation.

first: Robin

last: Everts

first: Rosane

last: Oliveira

first: Weruska

last: Santos-Biase

first: Giovana

last: Merighe

first: Lawrence

middle: C

last: Smith

first: Lúcia

last: Martelli

first: Harris

last: Lewin

first: Flávio

middle: V

last: Meirelles


title: microRNA Expression of mice corneal endothelia

city: Qingdao

first: Ye

last: Wang

address: No. 5 Yan'erdao Road

country: China

institute: Shandong Eye Institute

summary: MicroRNA profile comparison of the corneal endothelium of young and old mice: implications for senescence of the corneal endothelium

platform_organism:
Mus musculus
Murid betaherpesvirus 1
Murid gammaherpesvirus 4

overall_design: We collected the corneal endothelia from 30 mice aged 10-13 weeks and the corneal endothelia from 30 mice aged 2 years. The samples were pooled into six groups (y1, y2, y3 and s1, s2, s3). Each group comprised corneal endothelia from ten mice, and these six groups were used for a genome-wide microRNA microarray study.


title: Pax3 and Zic1 trigger the early neural crest gene regulatory network by the direct activation of multiple key neural crest specifiers [Xenopus_laevis]

city: Orsay

first: Anne-Helene

last: Monsoro-Burq

address: Bat 110

department: Université Paris Sud

country: France

institute: Institut Curie

summary:
Neural crest development is orchestrated by a complex and still poorly understood gene regulatory network. Premigratory neural crest is induced at the lateral border of the neural plate by the combined action of signaling molecules and transcription factors such as AP2, Gbx2, Pax3 and Zic1. Among them, Pax3 and Zic1 are both necessary and sufficient to trigger a complete neural crest developmental program. However, their gene targets in the neural crest regulatory network remain unknown. Here, through a transcriptome analysis of frog microdissected neural border, we identified an extended gene signature for the premigratory neural crest, and we defined novel potential members of the regulatory network. This signature includes 34 novel genes, as well as 44 known genes expressed at the neural border. Using another microarray analysis which combined Pax3 and Zic1 gain-of-function and protein translation blockade, we uncovered 25 Pax3 and Zic1 direct targets within this signature. We demonstrated that the neural border specifiers Pax3 and Zic1 are direct upstream regulators of neural crest specifiers Snail1/2, Foxd3, Twist1, and Tfap2b. In addition, they may modulate the transcriptional output of multiple signaling pathways involved in neural crest development (Wnt, Retinoic Acid) through the induction of key pathway regulators (Axin2 and Cyp26c1). We also found that Pax3 could maintain its own expression through a positive autoregulatory feedback loop. These hierarchical inductions, feedback loops, and pathway modulation provide novel tools to understand the neural crest induction network.
The transcriptomes of neural border samples (stage 14 and 18) were compared to the transcriptome of anterior neural fold (stage 18), early neural plate (stage 12), and animal cap explants (stage14) to identify genes expressed specifically in neural border samples.

overall_design: Tissue samples from Xenopus laevis embryos were dissected, then total RNA was extracted and hybridized on Affymetrix microarrays. Selected tissue samples encompass the neural crest at different stages of its induction (early neural plate at stage 12, neural border at stage 14, neural border at stage 18), as well as reference tissues (anterior neural fold at stage 18, a tissue that belongs to the neural border but does not produce neural crest, and animal cap grown until stage 14 that differentiates into epidermis).

first: Jean-Louis

last: Plouhinec

first: Daniel

middle: D

last: Roche

first: Caterina

last: Pegoraro

first: Ana-Leonor

last: Figueiredo

first: Frédérique

last: Maczkowiak

first: Lisa

last: Brunet

first: Jean-Philippe

last: Vert

first: Nicolas

last: Pollet

first: Richard

last: Harland

first: Anne


title: Ovarian Tumor Samples: mixed reference of 106 pooled ovarian samples vs.  individual patient ovarian sample

status: Public on Dec 26 2013

city: Santa Monica

first: Judy

last: Dering

address: 2825 Santa Monica Blvd. Suite 200

department: Medicine

institute: UCLA School of Medicine

summary: The goal of the study was to identify molecular subgroups that might predict clinical outcomes in serous epithelial ovarian cancer (EOC) patients.  A second objective was to identify potential therapeutic targets for serous EOC based on improved understanding of the molecular diversity of the disease.  Ovarian tissues and matched peripheral blood samples were prospectively obtained from sequential patients undergoing planned gynecologic surgery at Cedars-Sinai Medical Center between 1989 and 2005. All patients underwent surgery and received adjuvant chemotherapy with a contemporaneous standard-of-care regimen.

overall_design: Ovarian tissue samples (n=172) were compared to a reference pool of 106 ovarian samples. Mixed reference includes normal, benign, borderline, and malignant samples.

first: Dennis

last: Slamon

first: Beth

last: Karlan

first: Chuck

last: Ginther


title: Gene expression profiles in isolated proximal tubules and whole kidneys of rats after cisplatin-administration

city: Kyoto

first: Satohiro

last: Masuda

address: Shogoin

department: Pharmacy

institute: Kyoto University Hospital

summary: To clarify the effects of cisplatin (cis-diamminedichloroplatinum II, CDDP) on the gene expression profiles in renal proximal tubules, microarray analyses were carried out using total RNA samples isolated from microdissected proximal tubules and whole kidneys.  The molecular events underlying acute kidney injury (AKI) in the proximal tubules of rats with cisplatin-induced nephrotoxicity were successfully clarified with 17,000 transcripts.

overall_design: Renal proximal tubules were isolated under microscopy, and transcriptome data were collected with Rat Genome Survey Microarray® (Applied Biosystems)

first: Kumiko

last: Nishihara


title: microRNA Profiling in Wilms Tumors and Kidney Tissues

status: Public on Dec 22 2013

city: Heidelberg

first: Sven

last: Diederichs

address: Im Neuenheimer Feld 280

department: RNA Biology & Cancer

country: Germany

institute: German Cancer Research Center (DKFZ)

summary: The IGF2-intronic miR-483 selectively enhances transcription from IGF2 fetal promoters and enhances tumorigenesis.

overall_design: The expression levels of microRNAs were profiled in 20 human Wilms tumor samples (WT), 3 human normal adult kidney samples (AK) and 5 human fetal kidney samples (FK) using a Luminex bead platform.

first: Mingzhu

last: Liu

first: Anna

last: Roth

first: Min

last: Yu

first: Robert

last: Morris

first: Francesca

last: Bersani

first: Miguel

middle: N

last: Rivera

first: Jun

last: Lu

first: Toshihiro

last: Shioda

first: Shobha

last: Vasudevan

first: Sridhar

last: Ramaswamy

first: Shyamala

last: Maheswaran

last: Haber


title: Genome-wide expression profiling of the response to D-limonene in Saccharomyces cerevisiae

city: Wuxi

first: Jidong

address: 1800 Lihu Road

institute: Jiangnan university

summary: Metabolic engineering of Saccharomyces cerevisiae for efficient monoterpenes production was mostly restricted by the limited tolerance to these chemicals. Understanding of the molecular mechanisms underlying the tolerance of S. cerevisiae to monoterpenes was essential for the de novo biosynthesis these chemicals in S. cerevisiae. In this study, commercial oligonucleotide microarray assays were performed to investigate the global response of S. cerevisiae to typical monoterpene D-limonene under transcriptional level. Yeast cell treated with sublethal dose of D-liomonene, gene change profiles were investigated at transcription level and the microarry data were also verified with quantitative real time PCR.

overall_design: D-limonene induced gene expression in Saccharomyces cerevisiae at early logarithmic phase was measured at 2 hours after exposure to doses of 0.02% (v/v)  D-limonene. Three independent experiments were performed for each experiment (control or 2 hours).

first: Yibo

last: Zhu

first: Guocheng

last: Du

first: Byong

last: Lee

first: Jingwen

last: Zhou

first: Jian

last: Chen


title: Global transcriptional response of porcine intestinal epithelial cell lines to Salmonella enterica serovar Typhimurium and Choleraesuis: IPEC-J2 infected with S. choleraesuis

status: Public on Dec 20 2013

city: Malaga

first: Rocio

last: Bautista

address: Edificio de Bioinnovación, C/ Severo Ochoa, 34

country: Spain

institute: Plataforma Andaluza de Bioinformatica, Universidad de Malaga

summary:
The GeneChip Porcine Genome Array was used to identify the transcriptional response upon either Salmonella typhimurium (ST) or Salmonella choleraesuis (SC) infection in two porcine epithelial cell lines (IPEC-J2, from jejunum and IPI-2I, from ileum) during 2 and 4 hours post infection.

The objectives in this study were first, to identify the different response between the epithelial cell lines from different gut regions; second, to study how the Salmonella serotypes used could elicit a different host response; and third, to determine the effect of the time-points on the differentially gene expression.

overall_design: Epithelial cells were seeded into 6-well tissue culture plates and grown to confluence in 5% CO2 at 37ºC. Monolayers were infected for 1 h. with Salmonella typhimurium or Salmonella choleraesuis serotypes (MOI 1:10) or incubated with media alone (Control cells). Extracellular bacteria were removed, and cultures were further incubated during 2 and 4 h. in the presence of 50 µg/ml of the non-cell-permeant antibiotic gentamicin to kill remaining extracellular bacteria. The experiment was developed in triplicate in order to ensure a proper robustness in the microarray statistical analysis. An indirect ELISA was used to confirm cell activation by means of IL8 detection in cell culture medium. After each time-point, cells were lysed and RNA extracted.

first: Cristina

last: Arce

first: María

last: Ranírez-Boo

first: Rocío

first: M

middle: G

last: Claros

first: Diego

last: Llanes

first: Juan

last: Garrido


title: Microarray analysis of microbiota of gingival lesions in noma patients

city: Geneva

first: FRANCOIS

last: Patrice

state: Ge 4

address: Rue Gabrielle-Perret-Gentil, 4

department: Service of Infectious Diseases

country: Switzerland

institute: Genomic Research Laboratory

summary:
We used phylogenetic low-density microarrays targeting the 16S rRNA gene to characterize the gingival flora of acute noma and acute necrotizing gingivitis lesions, and compared them to healthy control subjects of the same geographical and social background.
Various types of samples were collected (column characteristics); patients from the same hospital without mouth infection (H), matched control populations (T), patients suffering gengivitis (Gengivitis), patient suffering NOMA (noma), patient suffering NOMA receiving antimicrobials (N-ATB). Sampled from patients were retrieved from both sides (column Description); healthy- or lesion-side of the mouth. All controls are matched with specific patients (see column patient category and number)

overall_design: We designed low-density 16S rDNA arrays representing 339 different phylotypes. We used an arbitrary cutoff of 1% of overall abundance to select from this dataset the most abundant sequences for probe design. Using this cutoff, the 132 most abundant 16S rRNA gene sequences were scanned for probes respecting defined physico-chemical properties (Tm = 65±5°C; probe length = 23–50 nt;  < -5.0 kcal/mol for hairpins; < -8.0 kcal/mol for self-dimers; and dinucleotide repeats shorter than 5 bp) using a commercial software (Array Designer TM 2.0 by Premier Biosoft). The 335 oligonucleotide probes were synthesized with a C6-linker with free primary amine (Sigma-Aldrich) and spotted on ArrayStrips microarrays (Clondiag GmbH, Jena, Germany).

first: Antoine

last: Huyghe

first: Patrice

last: François

first: Ignacio

last: Bolivar

first: Didier

last: Pittet


title: Regulation of NUMB alternative splicing by RBM5, RBM6 and RBM10 controls cancer cell proliferation

city: Budapest

first: Endre

last: Sebestyén

address: Üllői út 26.

department: 1st Department of Pathology and Experimental Cancer Research

country: Hungary

institute: Semmelweis University

summary: RBM5, a regulator of alternative splicing of apoptotic genes, and its close homologues, RBM6 and RBM10, are RNA binding proteins frequently deleted or mutated in lung cancer. We report that RBM5/6 and RBM10 antagonistically regulate the proliferative capacity of cancer cells and display distinct positional effects in alternative splicing regulation. We identify the Notch pathway regulator NUMB as a key target of these factors in the control of cell proliferation. NUMB alternative splicing, which is frequently altered in lung cancer, can regulate colony and xenograft tumor formation and its modulation recapitulates or antagonizes the effects of RBM5, 6 and 10 in cell colony formation. RBM10 mutations identified in lung cancer cells disrupt NUMB splicing regulation to promote cell growth. Our results reveal a key genetic circuit in the control of cancer cell proliferation.

overall_design: RNA from 3 biological replicates of knockdowns of RBM5, 6 and 10 and a control set were used. Changes between the control and knockdowns were measured based on using a splice-junction array (Affymetrix HJAY).

first: Elias

last: Bechara

first: Isabella

last: Bernardis

first: Eduardo

last: Eyras

last: Valcárcel


title: Global transcriptional response of porcine intestinal epithelial cell lines to Salmonella enterica serovar Typhimurium and Choleraesuis: IPI-2I infected with S. choleraesuis

overall_design: Epithelial cells were seeded into 6-well tissue culture plates and grown to confluence in 5% CO2 at 37ºC. Monolayers were infected for 1 h. with Salmonella typhimurium or Salmonella choleraesuis serotypes (MOI 1:10) or incubated with media alone (Control cells). Extracellular bacteria were removed, and cultures were further incubated during 2 and 4 h. in the presence of 50 µg/ml of the non-cell-permeant antibiotic gentamicin to kill remaining extracellular bacteria. The experiment was developed by triplicate in order to ensure a proper robustness in the microarray statistical analysis. An indirect ELISA was used to confirm cell activation by mean of IL8 detection in cell culture medium. After each time-point, cells were lysed and RNA extracted.


title: Global transcriptional response of porcine intestinal epithelial cell lines to Salmonella enterica serovar Typhimurium and Choleraesuis: IPI-2I infected with S. typhimurium


title: Global transcriptional response of porcine intestinal epithelial cell lines to Salmonella enterica serovar Typhimurium and Choleraesuis

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

overall_design: Refer to individual Series


title: Global transcriptional response of porcine intestinal epithelial cell lines to Salmonella enterica serovar Typhimurium and Choleraesuis: IPEC-J2 infected with S. typhimurium


title: Canonical and non-canonical EcfG sigma factors control the general stress response in Rhizobium etli

city: Leuven

first: Kristof

last: Engelen

address: Kasteelpark Arenberg 20

country: Belgium

institute: KULeuven

summary:
A core component of the α-proteobacterial general stress response is the extracytoplasmic function (ECF) sigma factor EcfG, exclusively present in this taxonomic class. Half of the completed α-proteobacterial genome sequences contain two or more copies of genes encoding σEcfG-like sigma factors, with the primary copy typically located adjacent to genes coding for a cognate anti-sigma factor (NepR) and two-component response regulator (PhyR). So far, the widespread occurrence of additional, non-canonical σEcfG copies has not satisfactorily been explained. This work explores the hierarchical relation between Rhizobium etli σEcfG1 and σEcfG2, canonical and non-canonical σEcfG proteins, respectively. Contrary to reports in other species, we find that σEcfG1 and σEcfG2 act in parallel, as nodes of a complex regulatory network, rather than in series, as elements of a linear regulatory cascade. We demonstrate that both sigma factors control unique yet also shared target genes, corroborating phenotypic evidence. σEcfG1 drives expression of rpoH2, explaining the increased heat sensitivity of an ecfG1 mutant, while katG is under control of σEcfG2, accounting for reduced oxidative stress resistance of an ecfG2 mutant. We also identify non-coding RNA genes as novel σEcfG targets. We propose a modified model for general stress response regulation in R. etli, in which σEcfG1 and σEcfG2 function largely independently. Based on a phylogenetic analysis and considering the prevalence of α-proteobacterial genomes with multiple σEcfG copies, this model may also be applicable to numerous other species.
In this study, we investigate to which degree R. etli EcfG1 and EcfG2 regulation is interdependent. Furthermore, we demonstrate that both sigma factors control distinct regulons and pinpoint unique EcfG2 target genes. We also identify non-coding RNAs (ncRNAs) as novel targets of EcfG1 and EcfG2 and show that expression of at least one of these ncRNAs is under direct EcfG control. The presence of ncRNAs in the regulon of an EcfG type sigma factor has not been described previously and adds an extra level of complexity to the regulation of the general stress response in Alpha-proteobacteria. Moreover, considering the widespread existence of Alpha-proteobacterial genomes with multiple EcfG copies, the here presented results not only lead to a better understanding of the general stress response in R. etli, but also contribute to a conceptual paradigm for general stress response regulation by multiple EcfG proteins in Alpha-proteobacteria.

overall_design: Comparative transcriptome analyses were carried out on four samples: the parental strain (WT) and mutants in either sigma factor gene ecfG1, sigma factor gene ecfG2, and both genes combined.

first: Ann

last: Jans

first: Jan

last: Michiels


title: NCOA3 upregulates MUC4 and MUC1 transcriptionally and through post-translational stability during pancreatic cancer development

status: Public on Dec 19 2013

city: Omaha

first: Sushil

last: Kumar

state: NE

address: 985870 Nebraska Medical Center, DRC1

department: Biochemistry and Molecular Biology

institute: UNMC

summary:
Stable knock down of NCOA3 in PC cell lines resulted in significant downregulation of the two most differentially expressed MUCs in PC, MUC4 and MUC1.
NCOA3 creates pro-inflammatory conditions by up-regulating chemokines like CXCL1, 2, 5 and CCL20

overall_design: Stable Knock down of NCOA3 in CD18/HPAF cell line. RNA was isolated from control and stably transfected cells. Each group has three biological replicate.

first: Surinder

last: Batra


title: The peripheral blood transcriptome reflects variations in immunity traits in swine: toward identification of biomarkers

city: Jouy-en-Josas

first: Nuria

last: Mach

state: Ile de France

address: Rue de Vilvert

department: Animal Genetics and Integrative Biology (GABI)

institute: INRA

summary: Immune traits (ITs) are potentially relevant criteria to characterize individual’s immunocompetence. Thus, porcine ITs related to innate and adaptive immunity were studied by functional genomics approaches, with no initial focus on resistance to specific pathogens. Peripheral blood transcriptome was analysed in 60 days old Large White pigs (N=445) 3 weeks after vaccination against Mycoplasma hyopneumoniae. Groups of 4 to 10 animals classified in the extreme tails of CD4-/CD8+and TCRγδ+ cell counts, phagocytosis, in vitro production of IL2, IL10, TNF and IFNG, and anti-Mycoplasma antibodies distributions were selected for transcriptome studies with a porcine generic array enriched with immunity-related genes (SLA-RI/NRSP8-13K). Among the ITs studied, transcriptome analysis revealed differentially expressed genes for CD4-/CD8+cell counts, phagocytosis, and in vitro production of IL2 and IL10. A subset of these genes was confirmed by real time qPCR. Gene set enrichment analysis showed a significant over-representation of immune response functions. An independent set of 74 no overlapping animals was employed for validation and a total of 5 potential gene biomarkers were found for prediction of immunocompetence. These biomarkers performed with 79% sensitivity (95% CI 61% to 97%) and 86% specificity (95% CI 72% to 100%). Considering the observed transcriptome differences in animals with extreme ITs levels, we conclude that gene expression profiling appears promising as a tool for biological monitoring of genetic variance in pigs.

overall_design:
Test set: Two-condition experiment (High vs Low) for a total of 8 ITS. Three ITs were measured from total blood and referred to as in vivo ITs. They included the seric levels of IgG directed against Mycoplasma hyopneumoniae (IgG-Mh), and the cell counts for  αβ T lymphocytes CD4- CD8+ (CD4- CD8+, or γδ T lymphocytes (TCRγδ+)) . Additionally, five ITs were measured after in vitro tests, and were further referred to as in vitro ITs.  They include the phagocytosis capacity (PHAG), and the in vitro production of TNFα, IFNγ, IL2 and IL10 after in vitro stimulation of total blood diluted five times. For each IT included in the present report, pigs were selected at the higher and lower 10% of the Gaussian distribution in order to generate two extreme groups defined as High (H) and  Low (L). Groups of 4 to 10 animals classified in the extreme tails of different ITs were selected. A two-channel microarray experiments were carried out using a common reference hybridization design. The standard reference RNA sample was prepared by pooling of total RNAs from different porcine tissues. As the reference is common to all the arrays, this design allowed an indirect comparison between the conditions of interest (H vs L groups). Additionally, in order to provide potential gene biomarkers to produce new insight into pig immunocompetence, the top 50 genes most differentially expressed genes when comparing H vs L groups in CD4-/CD8+ cell counts, phagocytosis, and in vitro production of IL2 and IL10 phenotypes were assessed across 74 animals (experimental animals non included) that were analyzed with the same SLA-RI/NRSP8-13K microarray.
Validation set: A total of 74 animals were analyzed in order to validate potential gene biomarkers found in the following immune traits: CD4- CD8+ lymphocyte counts, phagocytosis capacity, IL2 and IL10 production.  As no differentially gene expressions were detected between animals with High and Low levels of gamma delta T lymphocyte counts, IgG-Mh, and in vitro production of TNF-alpha or IFN-gamma immune traits, some of them were used in the validation set (n=50). None of experimental animals with extreme CD4- CD8+ lymphocyte counts, phagocytosis capacity, IL2 and IL10 production levels were included were included in the validation set.

first: Yu

last: Gao

first: Gaëtan

last: Lemonnier

first: Jérôme

last: Lecardonnel

first: Jordi

last: Estellé

first: Claire

last: Rogel-Gaillard


title: Real-time quantitative PCR analysis of rat diaphragm before and after acute cervical spinal cord injury

status: Public on Dec 18 2013

city: Gainesville

first: Heather

last: Ross

state: FL

institute: University of Florida

summary: Male Sprague Dawley adult rats were subjected to a cervical hemisection at C2 (C2HS).  Costal diaphragm (both ipsilesional and contralesional sides) were assessed under control conditions (sham surgery) and at 1 and 7 days post-C2HS.   We used SA Biosciences Rat Skeletal Muscle Development and Disease RT2 Profiler PCR Array to quantitate gene expression of muscle atrophy and regeneration-relevant genes from the uninjured and injured tissues on the indicated sides and at the indicated timepoints post-lesion.

overall_design:
qPCR gene expression profiling.  Tissue was derived from the costal diaphragm from control animals, and from contralesional and ipsilesional sides at days 1 and 7 post-lesion.   RNA was extracted from flash-frozen tissue (TRIzol reagent) and quantitated via spectrophotometry.  Equal amount total RNA from each donor was pooled prior to gene expression analysis.
N=3 or 4 rats per condition.  Four genes in the array study appeared to undergo unphysiologic increases in expression following SCI:  Mmp9, Leptin, activin A and alpha actinin. For these genes, expression levels in control tissue were detectable but extremely low, thus fold-increases following SCI are numerically exaggerated.  Therefore, we cannot explicitly comment on the physiologic scale of this response

first: H

first: L

last: Gill

first: K

middle: Z

last: Lee

first: B

last: Dougherty

first: A

middle: R

last: Judge

first: D

last: Fuller


title: Switch Enhancer Elements Control Cell Fate in Human Embryonic Stem Cells (BeadChip)

city: Toronto

first: Tobias

middle: Andreas

last: Beyer

state: ONT

address: 600 University Ave

department: Lunenfeld-Tannenbaum Research Institute

institute: Mount Sinai Hospital

summary: A small toolkit of morphogens is used repeatedly to direct development, raising the question of how context dictates interpretation of the same cue. One example is the TGFβ pathway that in human embryonic stem cells fulfills two opposite functions: pluripotency maintenance and mesendoderm (ME) specification. Using proteomics coupled to analysis of genome occupancy, we uncover a regulatory complex comprised of transcriptional effectors of the Hippo pathway (TAZ/YAP/TEAD), the TGFβ   pathway (SMAD2/3) and the pluripotency regulator OCT4 (TSO). TSO collaborates with NuRD repressor complexes to buffer pluripotency gene expression, while suppressing ME genes. Importantly, the SMAD DNA binding partner FOXH1, a major specifier of ME, is found near TSO elements and upon fate specification we show that TSO is disrupted with subsequent SMAD-FOXH1 induction of ME. These studies define switch enhancer elements and provide a framework to understand how cellular context dictates interpretation of the same morphogen signal in development.

overall_design: Total RNA was isolated from human embryonic stem cells (WA09) 48h after siRNA transfection (siCntr, siTAZ/YAP, siTEAD1-4)

first: Jeffrey

middle: L

last: Wrana


title: Genes differentially expressed in Haloferax mediterranei strains, DF50 and ΔdeoR2,  with or without induction by fructose

city: Beijing

first: Lei

last: Cai

address: No.1 Beichen West Road, Chaoyang District,

institute: Institute of Microbiology, Chinese Academy of Sciences

summary: Transcriptional profiling of Haloferax mediterranei DF50 and ΔdeoR2 with induction by fructose comparing with the strains without this induction. Goal was to explore the effect of induction by fructose on Haloferax mediterranei.

overall_design: Total RNA from the Haloferax mediterranei DF50 and ΔdeoR2 with or without induction by fructose were used to generate target cDNA, and then hybridized to  Haloferax mediterranei genome array genechips, representing about 3800 genes.

first: Cai

last: lei


title: Effect of TetR family regulator SAOUHSC_02897 deletion in S. aureus NCTC8325

city: hefei

first: Yibo

last: You

state: Anhui

address: Huangshan street

department: School of Life Sciences

institute: University of Science and Technology of China

summary: To analyze function of TetR family regulator SAOUHSC_02897, we have employed whole genome microarray expression profiling to identify genes transcription changed in respective mutant strains. Target SAOUHSC_02897 was replaced by ermB gene.

sample_organism: Staphylococcus aureus subsp. aureus NCTC 8325

overall_design: Bacteria grown in the wells of biofilm formation at 12 hours, and the RNA level of wild type NCTC8325 and SAOUHSC-02897 mutant were compared.

first: Ting

last: Xue

first: Haipeng

last: Sun


title: Dynamic Chromatin Modification Sustains Epithelial-Mesenchymal Transition following Inducible Expression of Snail-1 (ChIP-chip)

city: Boston

first: Ben

middle: S.

last: Wittner

state: MA

address: 149 13th Street

department: Center for Cancer Research

institute: Massachusetts General Hospital

type: Genome binding/occupancy profiling by genome tiling array

summary: Epithelial-Mesenchymal Transition (EMT) is thought to contribute to cancer metastasis, but its underlying mechanisms are not well understood. To define early steps in this cellular transformation, we analyzed human mammary epithelial cells with tightly regulated expression of Snail-1, a master regulator of EMT. Following Snail-1 induction, epithelial markers were repressed within 6 hours and mesenchymal genes induced at 24 hours. Snail-1 binding to its target promoters was transient (6-48 hours) despite continued protein expression and it was followed by both transient and long-lasting chromatin changes.

overall_design: To generate a potent reversible EMT-inducing stimulus, we created a Snail-1 retroviral expression construct, using a fused estrogen receptor (ER) response element to mediate regulation by exogenous 4-hydroxy-tamoxifen (4-OHT). Since Snail-1 protein stability and nuclear localization are suppressed by GSK3-beta-mediated phosphorylation, we substituted the six targeted amino acids (ER-Snail-1(6SA)), thus conferring constitutive activity to the induced protein (Zhou et al., 2004, Pubmed ID 15448698). Infection of non-transformed, immortalized human mammary epithelial MCF10A cells with ER-Snail-1(6SA), followed by treatment with 4-OHT, triggered morphological and biomarker characteristics of EMT. At 0, 6, 48 and 120 hours after beginning exposure to 4-OHT in ethanol (or, for controls, ethanol only) we ChIPed Snail-1 and 6 histone marks. We perfomed two replicates of each, except we only had one replicate of H3K27Me3 at 6 hours.

first: Sarah

last: Javaid

first: Jianmin

last: Zhang

first: Endre

last: Anderssen

first: Josh

last: Black

first: Ken

last: Tajima

first: David

middle: T

last: Ting

first: Gromoslaw

middle: A

last: Smolen

first: Matthew

last: Zubrowski

first: Rushil

last: Desai

first: Shyamala

last: Maheswaran

first: Sridhar

last: Ramaswamy

first: Johnathan

last: Whetstine

first: Daniel

last: Haber


title: Facing warm temperatures during migration – cardiac mRNA responses of two adult sockeye salmon Oncorhynchus nerka populations to warming and swimming challenges

status: Public on Dec 15 2013

city: Nanaimo

first: Shaorong

last: Li

state: British Columbia

address: 3190 Hammond Bay Road

department: Salmon and Freshwater Ecosystems Division

institute: Fisheries and Oceans Canada

summary: The main findings of the current study were that exposing adult sockeye salmon Oncorhynchus nerka to a warm temperature that they regularly encounter during their river migration induced an mRNA-level heat shock response that is exacerbated with swimming. Similar immune defense-related responses were also observed. Microarray analyses revealed that 347 genes were differentially expressed between the cold (12-13° C) and warm (18-19° C) treated fish (P < 0.01), with stress response (GO:0006950; P = 0.014) and response to fungus (GO:0009620; P = 0.003) elevated with warm treatment, while expression for genes involved in oxidative phosphorylation (GO:0006119; P = 0.0019) and electron transport chain (GO:0022900; P = 0.00043) increased in cold-treated fish. By studying single genes with RT-qPCR, warm treatment fish from the Chilko population of O. nerka  induced expression of heat shock protein (hsp) 90α, hsp90β and hsp30, as well as interferon-inducible protein (P < 0.05). A Nechako population of O. nerka with a narrower thermal tolerance window than the Chilko population showed even more pronounced responses to the warm treatment. In conclusion, it appears that during their once-in-the-lifetime migration these adult sockeye salmon encounter conditions that induce several cellular defense mechanisms. As river temperatures continue to increase, it remains to be seen whether or not these cellular defenses provide enough protection for all sockeye salmon populations.

platform_organism:
Oncorhynchus mykiss
Salmo salar

overall_design: Two condition experiment; cold treated fish vs. warm treated fish, n=4 in both group

first: Katja

last: Anttila

first: Erika

middle: J

last: Eliason

first: Karia

last: Kaukinen

first: Kristi

last: Miller

first: Anthony

middle: P

last: Farrell


title: Transformation of the Fallopian Tube Secretory Epithelium Leads to High-grade Serous Ovarian Cancer in BRCA/P53/PTEN Models

status: Public on Dec 17 2013

first: Sunita

last: Setlur

address: 221 Longwood Avenue

institute: Brigham and Women's Hospital

type: Genome variation profiling by genome tiling array

summary: Our study presents the first genetic models of de novo high-grade serous carcinomas (HGSC) that originate in fallopian tube secretory epithelial cells and recapitulate the key genetic alterations and precursor lesions characteristic of human invasive ovarian cancer.  Genomic copy number analysis, using array CGH, was performed on murine tumors in order to compare the overlap of copy number alterations between HGSC models and TCGA data.

overall_design: Array CGH was performed on genomic DNA isolated from murine HGSC tumors. Genomic DNA from three normal mouse fallopian tubes was pooled and used as the reference.

first: Daniela

last: Dinulescu

first: Ronny

last: Drapkin


title: Expression analysis of Edwardsiella ictaluri 93-146 wild type and mutant strains during catfish serum exposure.

city: Mississippi State

first: Attila

last: Karsi

state: MS

address: 240 Wise Center Drive

department: Department of Basic Sciences, College of Veterinary Medicine

institute: Mississippi State University

summary: Edwardsiella ictaluri is the causitive agent of enteric septicemia of catfish, one of the most important diseases impacting US catfish industry. The overall objective of this study is to identify E. ictaluri genes required for serum resistance.

overall_design: 4-plex array study using total RNA obtained from wild type and mutant Edwardsiella ictaluri exposed to heat-inactivated catfish serum and normal serum. Each treatment had four biological replica and each plex had two probe sets.

first: Mark

last: Lawrence

first: Jingjun

last: Lu


title: Expression analysis of Edwardsiella ictaluri 93-146 wild type and mutant strains during catfish fry encounter.

summary: Edwardsiella ictaluri is the causitive agent of enteric septicemia of catfish, one of the most important diseases impacting US catfish industry. The overall objective of this study is to identify E. ictaluri genes required for host encounter.

overall_design: 4-plex NimbleGen array study using total RNA obtained from wild type and mutant Edwardsiella ictaluri encountered with or without catfish fry. Each treatment had four biological replica and each plex had two probe sets.


title: The outcome of a competition for reproduction between fire ant queens is linked to their gene expression profiles

status: Public on Dec 14 2013

city: Lausanne

first: Yannick

last: Wurm

address: Biophore

department: Ecology and Evolution

institute: University of Lausanne

summary: In many animals living in groups the reproductivestatus of individuals is determined by their social status. In specieswith social hierarchies, the death of dominant individuals typicallyupheaves the social hierarchy and provides an opportunity for subordinateindividuals to improve their social status. Such a phenomenon occursin the monogyne form of the fire ant\emph{, Solenopsis invicta, }wherecolonies typically contain a single wingless reproductive queen, thousandsof workers and hundreds of winged non-reproductive virgin queens.Upon the death of the mother queen, many virgin queens shed theirwings and initiate reproductive development instead of departing ona mating flight. Workers progressively execute almost all of themover the following weeks. The workers base their collective decisionon pheromonal cues associated with the onset of reproductive developmentof the virgin queens which occurs after orphaning. To examine the factors that determine which virgin queens are executed and which survive, we set up artificial competitions between queens from different colonies. Using microarrays, we found that queens from winning colonies showed higher mitochondrial as well as organ development activities 24 hours after orphaning than did queens from colonies that lost the competitions. Furthermore, queens from colonies where queens shed their wings faster after orphaning were more likely to survive competitions. Finally, higher wing shedding speed is linked to higher mitochondrial activity.

overall_design: Eight competitions were initially conducted between queens form pairs of colonies. Six competitions clearly identified one winning colony and one losing colony. We thus have microarray data for six competitions (ie biological replicates), with one winning and one losing colony within each competition. Thus 12 colonies total. For each colony, RNA extracted from five queens was pooled, and hybridized against an unrelated common reference RNA that had been made from a pool of many S. invicta individuals of all castes and developmental stages.  Lab work was conducted in blocks (by competition) with randomized order within competition to avoid introducing bias. No technical replication was performed.

first: John

last: Wang

first: Kenneth

last: Ross

first: Laurent

last: Keller


title: hSETD1A cooperates with beta-catenin to regulate Wnt target genes and control colorectal tumor growth

first: Lei

last: Zhou

department: Molecular Genetics and Microbiology

summary: Glioblastoma multiforme (GBM) is the most prevalent type of adult brain tumor, and one of the deadliest tumors known to mankind. The genetic understanding of GBM is, however, limited, and the molecular mechanisms which facilitate GBM cell survival and growth within the tumor microenvironment are largely unknown. We applied digital karyotyping and single nucleotide polymorphism (SNP) arrays to screen for copy number changes in GBM samples and found that the most frequently amplified region is at chromosome 7p11.2. The high resolution of digital karyotyping and SNP arrays permits the precise delineation of amplicon boundaries and has enabled identification of the minimal region of amplification at 7p11.2, which contains two genes, EGFR and SEC61γ. SEC61γ encodes a subunit of a heterotrimeric protein channel located in the endoplasmic reticulum (ER). In addition to its high frequency of gene amplification in GBMs, SEC61γ is also remarkably overexpressed in 77% of GBMs, but not in lower-grade gliomas. The siRNA-mediated knockdown of SEC61γ expression in tumor cells led to growth suppression and apoptosis. Furthermore, we showed that pharmacological ER stress agents induce SEC61γ expression in GBM cells. Together, these results indicate that aberrant expression of SEC61γ serves significant roles in GBM cell survival, likely via a mechanism that is involved in the cytoprotective ER stress-adaptive response to the tumor microenvironment.

overall_design: hSETD1A was silenced in HCT116 cells using retrovirus harboring shRNA specifically against the hSETD1A gene.  10μg RNA was reverse transcribed to cDNA using the Applied Biosystems High Capacity cDNA Reverse Transcription kit according to the manufacturer’s instructions (Applied Biosystems). cDNA products were treated with 100ng RNaseA and then purified using the Qiagen PCR purification kit according to the manufacturer’s instructions. NimbleGen Human Gene Expression array was purchased from Roche Applied Sciences. cDNA samples were labeled, Cy3 hybridized, and processed at the FSU NimbleGen Microarray Facility at Florida State University.

first: Tal

last: Salz

first: Frederic

last: Kaye

first: Yi

last: Qiu

first: Suming

last: Huang

first: Guangyao


title: EH004: Lmx1a encodes a rostral set of mesodiencephalic dopaminergic neurons marked by the Wnt/b-catenin signaling activator Rspo2

status: Public on Dec 13 2013

city: Utrecht

first: Marian

last: Groot Koerkamp

state: Utrecht

address: Heidelberglaan 25

department: Research

country: Netherlands

institute: Princess Maxima Center for Pediatric Oncology

summary: Recent developments in molecular programming of mesodiencephalic dopaminergic (mdDA) neurons have led to the identification of many transcription factors playing a role in mdDA specification. LIM homeodomain transcription factor Lmx1a is essential for chick mdDA development, and for the efficient differentiation of ES-cells towards a dopaminergic phenotype. In this study, we aimed towards a more detailed understanding of the subtle phenotype in Lmx1a-dr/dr mice. Therefore, microarray analysis was performed, to elucidate the exact molecular programming underlying the neuronal deficits after loss of Lmx1a. Subsequent expression analysis confirmed that Nurr1 is regulated by Lmx1a, and additional downstream targets were identified, like Pou4f1, Pbx1, Pitx2, C130021l20Rik, Calb2 and Rspo2. In line with a specific, rostral-lateral loss of expression of most of these genes during development, Nurr1 and C130021l20Rik were affected in the SNc of the mature mdDA system. Interestingly, this deficit was marked by the complete loss of the Wnt/b-catenin signaling activator Rspo2 in this domain. Expression analysis in Rspo2-/- embryos revealed affected mdDA neurons, partially phenocopying the Lmx1a mutant. Together, in this study we reveal that Lmx1a is essential for a rostral-lateral subset of the mdDA neuronal field, where it might serve a critical function in modulating proliferation and differentiation of mdDA progenitors through the activation of the Wnt activator Rspo2.

overall_design: Microarray expression study comparing 4 samples of homozygous LMX1A dr/dr mice, midbrain E12.5 with a pooled sample of their wt/wt littermates. Two samples were analyzed in opposite dye orientation.

first: Elisa

last: Hoekstra

first: Lars

last: von Oerthel

last: van der Heide

first: Jesse

last: Veenvliet

first: Iris

last: Wever

first: Yong-Ri

last: Jin

first: Jeong

middle: K

last: Yoon

first: Annemarie

last: van der Linden

first: Frank

last: Holstege

last: Koerkamp

first: Marten

last: Smidt


title: Expression of mutant p53 in Mammary carcinomas in WAP-SV40 transgenic mice

city: Hamburg

first: Florian

last: Wegwitz

state: Hamburg

address: Martinistraße 52

department: Department of Tumor Biology

institute: University Medical Center Hamburg-Eppendorf

summary:
Upon induction, WAP-T mice express two synergistically acting SV40 early region encoded proteins, large (LT) and small (sT) tumor antigens in the mammary epithelium, recapitulating thereby the loss of p53 and Rb function and deregulation of PP2A-controlled mitogenic pathways in human breast cancer. In primiparous mice, WAP-promoter driven expression of SV40 proteins induces well and poorly differentiated (respectively low- and high-grade) mammary adenocarcinomas.
We here studied the postulated mutant p53 (mutp53) 'gain of function' during mammary tumor development, progression and metastasis by crossing WAP-T mice with mutant p53 transgenic WAP-mutp53 mice.

overall_design: This study includes gene expression analysis of 12 high grade mammary carcinoma samples. An alternative probe set mapping published by the AffyProbeMiner project (remapped transcript consistent cdf-file) was used to calculate probe set signals of 6 mono-trangenic WAP-T-NP8 samples from the dataset GSE29117 and 6 bi-transgenic WAP-T-NP8 x WAP-W10 (mutp53R245R) samples.

first: Wolfgang

last: Deppert

first: Genrich

last: Tolstonog


title: Expression of seaweed genes induced by perwinkle grazing

city: Bremerhaven

first: Carla

last: Flöthe

address: Am Handelshafen 12

institute: Alfred-Wegener-Institut Helmholtz-Zentrum für Polar- und Meeresforschung

summary: The aim of this study was to elucidate changes in gene expression related to the induced anti-herbivory response in the brown seaweed Fucus vesiculosus. Microarray hybridizations were used to identify genes differentially expressed in response to grazing by the periwinkle Littorina obtusata. This study shows that modifications in gene expression occur simultaneously to a reduced palatability and that defence induction entails reallocation of resources from primary to secondary metabolism with down-regulation of photosynthesis.

overall_design: Total RNA of Fucus vesiculosus pieces that were or were not previously grazed by Littorina obtusata for 3, 12, 15, 21, and 24 days (5 biological replicates each) was hybridized against pooled RNA from 5 F. vesiculosus pieces that were collected before onset of grazing (day 0).

first: Markus

last: Molis

first: Uwe

last: John


title: JeB001: Elucidation of the distal convoluted tubule transcriptome identified new candidate players in magnesium balance

last: Groot Koerkamp

summary: The distal convoluted tubule (DCT) plays a key role in the fine-tuning of renal Mg2+ reabsorption. In recent years, hereditary magnesium (Mg2+) transport disorders have helped to identify important players in DCT Mg2+ homeostasis. Here, we report the Mg2+-sensitive transcriptional expression of the DCT transcriptome using gene expression microarray analysis. Mice expressing eGFP under a DCT-specific promoter were subjected to Mg2+-deficient or Mg2+-enriched diets. Subsequently, the Complex Object Parametric Analyzer and Sorter (COPAS) allowed isolation of eGFP-positive DCT cells. RNA extracts were subjected to pair-wise microarray analysis, high vs. low Mg2+. Of all genes in the genome, 46 were shown to be differentially expressed with a minimal fold-change of 2. Several known magnesiotropic genes, such as Trpm6 and Parvalbumin, were upregulated in the low Mg2+ fraction. Moreover, new genes were identified that are potentially involved in renal Mg2+ homeostasis. To confirm that the selected candidate genes are regulated by dietary Mg2+ availability, the expression levels of Slc41a3, Pcbd1, Tbc1d4 and Umod were determined by RT-PCR analysis. Indeed, all four genes were shown to be significantly upregulated in mice fed the Mg2+-deficient diet. In conclusion, by elucidating the Mg2+-sensitive DCT transcriptome, new candidate players in renal Mg2+ homeostasis were identified.

overall_design: RNA samples were isolated from PV-eGFP-positive tubules from mice fed on a low (L-samples) or high (H-samples) magnesium diet. Littermate H and L samples were labeled and put on mouse microarrays together. Two of the four sample sets were analyzed in dye-swap to compensate for dye-biases.

first: Jeroen

middle: H

last: de Baaij

first: Femke

last: van Zeeland

first: Hans

last: Meijer

first: Rene

last: Bindels

first: Joost

last: Hoenderop


title: The YmdB phosphodiesterase is a global regulator of biofilm-specific mRNA levels in Bacillus subtilis

status: Public on Dec 11 2013

city: Jena

first: Akos

last: Kovacs

address: Neugasse 23

department: Institute of Microbiology

institute: Friedrich Schiller University of Jena

summary: Detailed description (other than provided below) of growth conditions, RNA preparation, cDNA synthesis and hybridization conditions can  be found in the submitted paper.

overall_design:
GSM956794-GSM956801: Bacillus subtilis 168 wild type and its ymdB derivative strain were grown in CSE-Glu medium and cells were harvested at mid exponential (OD600 ~0.8) and early stationary phase (OD600 ~2.2-2.4).  For both time points, 4 biological replicates were used, resulting 4 slides for both exponential and stationary phase. Dye swaps are included in both experiments.
GSM1011025-GSM1011032: Bacillus subtilis GP966 antibiotic tagged synthetic wild type and its ymdB E39Q point mutant strain GP969 were grown in CSE-Glu medium and cells were harvested at mid exponential (OD600 ~0.8) and early stationer phase (OD600 ~2.2-2.4).  For both time points, 4 biological replicates were used, resulting 4 slides for both exponential and stationer phase. Dye swaps are included in both experiments.

first: Joseph

last: Newman

first: Christine

last: Diethmaier

first: Mirjam

last: Boonstra

first: Cecilia

last: Rodrigues

first: Oscar

last: Kuipers

first: Jorg

last: Stulke

first: Richard

last: Lewis


title: Identification of the genes regulated by YvfI transcriptional factor

summary:
Genome-wide comparative transcriptome analysis of the Bacillus subtilis parent strain PY79 and its yvfI derivative with yvfI::T10::spc (TEK1) grown in PA medium
Detailed description of sample preparation and microarray conditions can be also found in Irigul et al to be submitted

overall_design: One condition design comparision of treated vs non treated control including a dye swap, 3 biological replicates

first: Oyku

last: İrigül-Sönmez

first: Ayten

last: Yazgan-Karataş


title: Changes in translational state from 1 day to 8 day after inoculation in Arabidopsis thaliana T87 cells

status: Public on Dec 10 2013

city: Ikoma

first: Kiyotaka

last: Ueda

state: Nara

department: Graduate School of Biological Science

institute: Nara Institute of Science and Technology

summary: We investigated genome-wide changes in mRNA translation in Arabidopsis thaliana T87 suspension cell cultures which thought to be one of the host materials for bioreactor. Global translational repression was observed in cells of 8 day after inoculation that is thought to be stressful condition by the nutrient deficiency and hypoxia. This suggested the negative effect of the global translational repression on transgene expression. On the other hand, previous study using heat stress showed that some mRNAs were actively translated under such stressful condition, suggesting the existence of mRNA that were actively translated in cells of 8 day after inoculations. To identify mRNAs that escape global translational repression on 8 day and its cis-elements would be the 1st step to make the system for higher transgene expression by the escaping global translational repression. To this end, we subjected polysomal RNA and non-polysomal RNA from sucrose gradient fractionated cell lysates to the co-hybridization on Agilent Arabidopsis 4 Oligo Microarrays. The ratio of signal intensities (polysomal RNA: total RNA) was used as an indicator of the translation state for each transcript.

overall_design: Experiment using two-fractionated mRNA,  Polysomal mRNA vs. total mRNA. Biological replicates: 1

first: Renya

last: Okawara

first: Ko

last: Kato


title: Time course gene expression profiling of five diffuse large B-cell lymphoma cell lines following JQ1 treatment

first: Björn

last: Chapuy

address: 450 Brookline Ave.

department: Medical Onology

institute: Dana-Farber Cancer Institute

summary: To understand the molecular curcuits perturbed by BET bromodoman inhibtion we obtained gene expression profiling of five DLBCL cell lines, SU-DHL6, OCI-Ly1, OCI-Ly4, Toledo and HBL-1, which were treated with either 500nM JQ1 or DMSO for 0,2,6,12,24 and 48hr.

overall_design: RNA samples from five DLBCL cell lines at baseline (time 0) or following treatment with 500nM of JQ1 or vehicle (DMSO) alone for 2, 6, 24 or 48 hours were profiled in triplicate on Affymetrix Human Gene 1.0 ST Array.

first: Bjoern

first: Michael

last: McKeown

first: James

middle: E

last: Bradner

first: Margaret

last: Shipp


title: Identification of nucleosome positions at hox TSSs during zebrafish embryonic development

status: Public on Dec 09 2013

city: Worcester

first: Steven

last: Weicksel

state: Massachusetts

address: 55 Lake Ave

department: BMP

institute: UMass Medical School

summary: Nucleosome arrangement in promoter regions has been shown to play an important role in gene regulation.  Genome wide studies in yeast, flies, worms, mammalian ES and transformed cell lines have found well positioned nucleosomes with an area of nucleosome depletion flanking transcription start sites.  This Nucleosome arrangement has been shown to be dependent on sequence (cis-regulatory factors), DNA binding factors (trans-regulatory factors) and ATP-dependant chromatin modifiers.  However, little is understood about how the nascent embryonic genome positions nucleosomes during development.  This is particularly intriguing since the embryonic genome undergoes a whole scale rechromatinization event upon fusion of sperm and oocyte.  Using four stages of early embryonic zebrafish development we map nucleosome positions at the promoter region of 34 zebrafish hox genes.  We find that nucleosome arrangement at the hox promoters is a dynamic process which happens over several stages.  We also find evidence that trans-regulatory factors play a greater role in nucleosome positioning over cis-regulatory elements.  Finally we provide evidence that transcriptional activation is the driving force behind the arrangement of nucleosomes at the promoters of hox gene during early development.

overall_design: Five tissue types: 2, 4, 6, and 9 hours post fertilzation embryos and ZF4 cell line. Three treatments: Untreated (WT), Retinoic Acid treated embryos (RA), DEAB treated embryos. Two biological replicates for DNA input samples.

first: Charles

last: Sagerstrom


title: Gene expression of non-typeable Haemophilus influenzae strain R2866 and R2866Δ0112 mutant grown in supplemented brain-heart infusion medium

city: Nijmegen

first: Jeroen

middle: Daniel

last: Langereis

address: PO Box 9101

department: Department of Pediatrics

institute: Radboud University Medical Centre

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

overall_design: Refer to individual Series


title: SMN MO, Gemin2 MO knockdown vs Control MO injected

status: Public on Dec 05 2013

city: Philadelphia

first: Kelvin

last: See

state: PA

address: 3400 Civic Center Blvd, Smilow Center for Translational Research

department: Medicine

institute: University of Pennsylvania

summary: Transcriptiome profiling of SMN MO injected, Gemin2 MO injected zebrafish embryos vs Control MO injected

overall_design: Two condition experiment : MO injected vs control. Biological replicates for SMN MO injected : 6, Biological replicates for Gemin2 MO injected: 7; Control MO injected from 6 independent batches pooled to serve as common control sample in all arrays.


title: microRNAs involved in regulating embolic stroke recovery following spontaneous reperfusion [miRNA]

city: Singapore

first: Kandiah

last: Jeyaseelan

address: 8 Medical Drive

department: Biochemistry

country: Singapore

institute: National University of Singapore

summary: To date, miRNA expression studies on cerebral ischemia in both human and animal models have focused mainly on acute phase of ischemic stroke. In this study, we present the roles played by microRNAs in the spontaneous recovery phases in cerebral ischemia using rodent stroke models.

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

overall_design: In this study presented here, Middle Cerebral Artery Occlusion stroke model was established by using embolus and the brain samples of stroke model were harvested at 0hrs, 3hrs, 6hrs, 12hrs, 24hrs, 48hrs, 72hrs, 120hrs and 168hrs. RNAs were extracted from these samples and microRNA array and mRNA array were performed.

first: Fu

last: Liu

first: Kai

middle: Y

last: Lim

first: Prameet

last: Kaur

first: Sugunavathi

last: Sepramaniam

first: Arunmozhiarasi

last: Armugam

first: Peter

last: Wong


title: Flagellar export apparatus protein, FliH, is involved in post-transcriptional regulation of FlaB, motility and virulence of the relapsing fever spirochete Borrelia hermsii

city: Hamilton

first: Dan

last: Sturdevant

state: MT

address: 903 S 4th street

department: NIAID

institute: NIH

summary:
Spirochetes are long, thin, motile, helical or flat wave bacteria that are unique among the prokaryotes by having flagella or axial filaments confined to an internal periplasmic space. These flagella are complex organelles that can play major roles in bacterial pathogenicity and are used as propellers allowing bacteria to move through liquids, viscous environments or along surfaces. While most bacteria species use transcriptional regulatory cascades to regulate the synthesis and assembly of their flagella, spirochetes employ an unusual post-transcriptional mechanism. Using next generation sequencing, we characterized a natural mutant of the relapsing fever spirochete Borrelia hermsii lacking the flagellar export apparatus protein FliH. The mutant was non-motile, uncoiled and straight compared to the wild-type spirochetes. The B. hermsii fliH mutant produced only a residual amount of the major flagellin protein FlaB, which was correlated with a reduced number of periplasmic flagella. The amounts of flaB transcript were comparable in the fliH mutant and the wild-type strain. The synthesis of FlaB, the motility and the infectivity of the fliH mutant were rescued by trans-complementation. This report reveals a new function for FliH, and we propose that this regulator of the flagellar export apparatus influences the post-transcriptional processing of the flagella, motility and virulence of the relapsing fever spirochete Borrelia hermsii.
Spirochetes are bacteria characterized in part by rotating periplasmic flagella that impart their flat-wave morphology and motility. While other bacteria rely on a transcriptional cascade to regulate the expression of motility genes, spirochetes employ posttranscriptional mechanism(s) that are only partially known. In the present study, we characterize a non-motile mutant of the relapsing fever spirochete Borrelia hermsii that was straight, non-motile and deficient in flagella. We used next generation DNA sequencing of the mutant’s genome, which when compared to the wild-type genome identified a 142 bp deletion in the chromosomal gene encoding the flagellar export apparatus protein FliH. Immunoblot and transcriptome analyses showed that the mutant phenotype was linked to the posttranscriptional deficiency in the synthesis of the major flagellar filament core protein FlaB. The turnover of the residual pool of FlaB produced by the fliH mutant was comparable to the wild-type spirochete while the amount of FlaA was similar to the wild-type level. The non-motile mutant was not infectious in mice and its inoculation did not induce an antibody response. Trans-complementation of the mutant with an intact fliH gene restored the synthesis of FlaB, a normal morphology, motility and infectivity in mice. Therefore, we propose that the flagellar export apparatus protein regulates motility of B. hermsii at the posttranscriptional level by influencing the synthesis of FlaB.

platform_organism:
Borrelia hermsii
Francisella tularensis
Coxiella burnetii
Rickettsia prowazekii
Burkholderia mallei
Brucella suis

overall_design: Borrelia hermsii wild type vs. motility mutant

first: Cyril

last: Guyard

first: Sandra

last: Raffel

first: Merry

last: Schrumpf

first: Eric

last: Dahlstrom

first: Daniel

first: Stacy

middle: M

last: Ricklefs

first: Craig

last: Martens

first: Stanley

middle: F

last: Hayes

first: Stephen

last: Porcella

first: Tom

last: Schwan


title: Inflammatory bowel disease risk loci overlap with DNA regulatory regions in immune cells and intestinal epithelium

status: Public on Dec 06 2013

first: Michal

last: Mokry

address: Lundlaan 6

institute: Wilhelmina Children's Hospital, University Medical Center Utrecht

type: Genome binding/occupancy profiling by high throughput sequencing

summary: Background & Aims: The contribution of genetics to the pathogenesis of inflammatory bowel disease (IBD) has been established by twin studies, targeted sequencing and genome-wide association studies (GWASs). This has yielded a plethora of risk loci with an aim to identify causal variants. Research on the genetic components of IBD has mainly focused on protein coding genes, thereby omitting other functional elements in the human genome i.e. the regulatory regions. Methods: Using acetylated histone 3 lysine 27 (H3K27ac) chromatin immunoprecipitation and sequencing (ChIP-seq), we identified tens of thousands of potential regulatory regions that are active in intestinal epithelium and immune cells, the main cell types involved in IBD. We correlated these regions with susceptibility loci for IBD. Results: We show that 45 out of 163 single nucleotide polymorphisms (SNPs) associated with IBD co-localize with active regulatory elements.  In addition, another 47 IBD associated SNPs co-localize with active regulatory element via other SNP in strong linkage disequilibrium. Altogether 92 out of 163 IBD-associated SNPs can be connected with distinct regulatory element. This is 2.5 to 3.5 times more frequent than expected from random sampling. The genomic variation in these SNPs often creates or disrupts known binding motifs - thereby possibly affecting the binding affinity of transcriptional regulators and altering the expression of regulated genes. Conclusions: We show that in addition to protein coding genes, non-coding DNA regulatory regions, active in immune cells and in intestinal epithelium, are involved in IBD.

overall_design: H3K27ac ChIP-seq (ab4729, Abcam) profile of 7 intestinal epithelial samples


title: Expression Profiles of HepG2 cells treated with 7µM of the genotoxic compound cisplatin

city: Maastricht

first: Linda

last: Rieswijk

address: Universiteitssingel 50

department: Toxicogenomics

institute: Maastricht University

summary: The transcriptomic changes induced in the human liver cell line HepG2 by 7µM of cisplatin after treatment for 12, 24 and 48h

overall_design: The study investigated differential gene expression in HepG2 cell line mRNA following 12,24 and 48 hours of exposure to 7µM of cisplatin and its solvent. Three biological replicates per compound/solvent. In total 18 arrays .


title: Comparison of microRNA expression with whole blood between ER positive breast cancer patients and normal controls

status: Public on Dec 12 2013

city: Goyangsi

first: In Hae

last: Park

address: 323 Ilsanro Madu 1 dong

country: South Korea

institute: National cancer center, Korea

summary:
Background   MicroRNA expression is frequently dysregulated in cancer and it could be used potentially as a disease classifier and a prognostic tool in cancer. It has been reported that the cancer associated specific microRNAs were stably detected in blood. The objective of this study was to discover a panel of circulating microRNAs as potential ER+/HER2- breast cancer biomarkers.   Methods  We compared levels of circulating microRNAs in blood samples from 11 ER+/HER2- advanced breast cancer patients with age-matched 5 control subjects by using microarray-based expression profiling. We validated the level of microRNAs by real-time quantitative polymerase cycle reaction (RT-qPCR) in 40 control subjects, 180 early breast cancer patients (EBC), and 52 metastatic breast cancer patients (MBC). Then, we assessed the association between the levels of microRNA and clinical outcomes of ER+/HER2- metastatic breast cancer.
Background   MicroRNA expression is frequently dysregulated in cancer and it could be used potentially as a disease classifier and a prognostic tool in cancer. It has been reported that the cancer associated specific microRNAs were stably detected in blood. The objective of this study was to discover a panel of circulating microRNAs as potential ER+/HER2- breast cancer biomarkers.   Methods  We compared levels of circulating microRNAs in blood samples from 11 ER+/HER2- advanced breast cancer patients with age-matched 5 control subjects by using microarray-based expression profiling. We validated the level of microRNAs by real-time quantitative polymerase cycle reaction (RT-qPCR) in 40 control subjects, 180 early breast cancer patients (EBC), and 52 metastatic breast cancer patients (MBC). Then, we assessed the association between the levels of microRNA and clinical outcomes of ER+/HER2- metastatic breast cancer.

overall_design: Controls: 5 cases; ER +/HER2- breast cancer patients : 11 cases

first: In

first: Jungsil

last: Ro


title: Directed differentiation of placode from human embryonic stem cells

status: Public on Dec 04 2013

city: New York

first: Jeffrey

last: Zhao

state: NY

address: 1275 York Avenue

department: Genomics Core

institute: Memorial Sloan Kettering Cancer Center

summary: Here we compare the transcriptional profile during the differentiation of hESC into neuroepithelial cells (NSB) (Chambers et. al 2009 Nature Biotechnology) with our new placode differentiation (PIP).

overall_design: Total RNA was isolated at day 1,3, 5 (NSB), 5 (PIP), 7 (NSB), 7 (PIP), 9 (NSB), 9 (PIP), 11 (NSB) and 11 (PIP) of differentiation using Trizol. Samples for each group in triplicate were processed for Illumina bead arrays (Illumina HT-12) by the MSKCC genomics core facility according to the specifications of the manufacturer.

first: Zehra

last: Dincer

first: Lorenz

last: Studer