title: Prefrontal cortex microRNA expression profiling in major depression

city: Vancouver

first: Paul

last: Pavlidis

state: British Columbia

address: 177 Michael Smith Laboratories 2185 East Mall

department: Centre for High-Throughput Biology / Psychiatry

institute: University of British Columbia

summary: To gain insight into the potential role of miRNA in major depressive disorder, in this study we assessed global expression of miRNAs in the ventrolateral prefrontal cortex (PFC) of depressed individuals in comparison to psychiatrically healthy controls. Our screening pointed to miR-1202, a miRNA specific to primates and enriched in the human brain. We validated our findings using quantitative real-time PCR and identified target genes of the differentially expressed miRNAs using bioinformatics analysis. MiR-1202 interacts with and regulates the expression of the metabotropic glutamate receptor 4 (GRM4) gene, and it responds to antidepressant treatment. These results suggest that miR-1202 is associated with the pathophysiology of depression, and is a potential target for novel antidepressant treatments.

overall_design: We assessed the global expression pattern of miRNAs in the ventrolateral PFC of depressed individuals (n = 14) in comparison with psychiatrically healthy controls (n = 11) using the Agilent human miRNA microarrays. Statistical analysis after multiple test correction identified miR-1202 as the most significantly dysregulated miRNA, with levels down-regulated in depressed brains. We validated the microarray miR-1202 findings by qRT-PCR using TaqMan probes, and found consistent results across the two expression analysis methods.

first: Juan

last: Lopez

first: Raymond

last: Lim

first: Gustavo

last: Turecki


title: Trophoblast giant cell underrepresentation (CGH)

status: Public on May 29 2014

city: Stanford

first: Roberta

middle: L

last: Hannibal

state: CA

address: 300 Pasteur Drive

department: Genetics

country: USA

institute: Stanford University

type: Genome variation profiling by genome tiling array

summary: We characterized regions of underrepresentation that are specific to mouse polyploid trophoblast giant cells.

overall_design: We performed array Comparative Genomics Hybridization (aCGH) to examine copy number variation (CNV) in mouse polyploid trophoblast giant cells (TGCs).  We performed the following experiments in duplicates to examine CNV during various stages of in vivo and in vitro TGC development: e9.5 TGCs vs. embryonic controls, e11.5 TGCs vs. embryonic controls, e13.5 TGCs vs. embryonic controls, e16.5 TGCs vs. embryonic controls, as well as TGCs cultured 3, 5 and 7 days vs. 2N trophoblast stem cells.  We also performed the following controls to show that underrepresentation is only found in polypoid trophoblast giant cells and not in either 2N placental cell types nor in other types of polyploid cells: 2N placenta disk vs. embryonic controls, 2N trophoblast stem cells vs. embryonic stem cells, and polyploid Megakaryocytes vs. embryonic controls.  When possible, we performed arrays with the test and control samples of opposite sex (F-female, M-male), as an internal control for the array.

first: Edward

middle: B

last: Chuong

first: Julie

middle: C

last: Baker


title: Expression data from skin of bovines infested with ticks

status: Public on May 23 2014

city: Bagé

first: Robert

last: Domingues

state: Rio Grande do Sul

address: Av. General Osório 1737/302

department: Animal health

country: Brazil

institute: Embrapa

summary:
The aim of this work was to access the early immune response triggered by R. microplus larvae attachment in previously selected resistant and susceptible animals in a bovine F2 population derived from Gyr (Bos indicus) × Holstein (Bos taurus) crosses.
We used microarray data both to access the changes in gene expression over the course of the first 48 hours after tick infestation as constrasting the phenotypically diferent groups.

overall_design: From a bovine F2 population, six tick-resistant (R) and seven tick-susceptible (S) animals were used in this experiment.  Skin biopses were taken at the feeding sites before infestation (0 hour), 24 and 48 hours after tick infestation in each animal.

first: Wanessa

middle: A

last: Carvalho

first: Marcia

last: Prata

first: Marcos

middle: V

last: Silva

first: Guilherme

last: Oliveira

first: Simone

middle: E

last: Guimarães

first: Marco

last: Machado


title: UPC2 Is universally essential for Azole antifungal resistance in Candida albicans

status: Public on May 24 2014

city: Memphis

first: Erin

last: Vasicek

state: TN

address: 881 Madison Ave

institute: University of Tennessee Health Science Center

summary: In Candida albicans, the transcription factor Upc2 is central to the regulation of ergosterol biosynthesis. UPC2-activating mutations contribute to azole resistance, whereas disruption increases azole susceptibility. In the present study, we investigated the relationship of UPC2 to fluconazole susceptibility, particularly in azole-resistant strains. In addition to the reduced fluconazole MIC previously observed with UPC2 disruption, we observed a lower minimum fungicidal concentration (MFC) for a upc2Δ/Δ mutant than for its azole-susceptible parent, SC5314. Moreover, the upc2Δ/Δ mutant was unable to grow on a solid medium containing 10 µg/ml fluconazole and exhibited increased susceptibility and a clear zone of inhibition by Etest. Time-kill analysis showed higher fungistatic activity against the upc2Δ/Δ mutant than against SC5314. UPC2 disruption in strains carrying specific resistance mutations also resulted in reduced MICs and MFCs. UPC2 disruption in a highly azole resistant clinical isolate containing multiple resistance mechanisms likewise resulted in a reduced MIC and MFC. This mutant was unable to grow on a solid medium containing 10 µg/ml fluconazole and exhibited increased susceptibility and a clear zone of inhibition by Etest. Time-kill analysis showed increased fungistatic activity against the upc2Δ/Δ mutant in the resistant background. Microarray analysis showed attenuated induction by fluconazole of genes involved in sterol biosynthesis, iron transport, or iron homeostasis in the absence of UPC2. Taken together, these data demonstrate that the UPC2 transcriptional network is universally essential for azole resistance in C. albicans and represents an attractive target for enhancing azole antifungal activity.

overall_design: We examined the genome-wide gene expression profiles of the wild-type parent strain SC5314 and its upc2Δ/Δ derivative in response to fluconazole in order to identify genes whose expression in response to fluconazole is influenced by Upc2.

middle: M

first: Elizabeth

last: Berkow

first: Stephanie

last: Flowers

first: Katherine

middle: S

last: Barker

first: P

middle: D

last: Rogers


title: Non-circadian expression masking clock-driven weak transcription rhythms in U2OS cells

city: Heidelberg

first: Anton

last: Shostak

address: Im Neuenheimer Feld 328

department: Circadian Rhythms and Molecular Clocks

country: Germany

institute: Heidelberg University Biochemistry Center (BZH)

summary:
U2OS cells harbor a circadian clock but express only a few rhythmic genes in constant conditions. We identified 3040 binding sites of the circadian regulators BMAL1, CLOCK and CRY1 in the U2OS genome. Most binding sites even in promoters do not correlate with detectable rhythmic transcript levels. Luciferase fusions reveal that the circadian clock supports robust but low amplitude transcription rhythms of representative promoters. However, rhythmic transcription of these potentially clock-controlled genes is masked by non-circadian transcription that overwrites the weaker contribution of the clock in constant conditions. Our data suggest that U2OS cells harbor an intrinsically rather weak circadian oscillator. The oscillator has the potential to regulate a large number of genes. The contribution of circadian versus non-circadian transcription is dependent on the metabolic state of the cell and may determine the apparent complexity of the circadian transcriptome.
Analysis of temporal expression profiles of 5708 expressed genes in synchronized U2OS cells.

overall_design: A 60k customized microarray was designed for 6356 genes, which corresponds to roughly one fourth of the human genome. 1373 genes were assigned to circadian regulator binding sites (CRBSs), 1503 genes were specifically selected in addition to a set of 3480 random genes. For each gene 10 independent probes in two microarray replicates were performed to increase reliability of the data.

first: Julia

last: Hoffmann

first: Laura

last: Symul

first: Tamás

last: Fischer

first: Felix

last: Naef

first: Michael

last: Brunner


title: Transcriptional patterns associated with PC-3 cells in response to osteopontin-c splicing isoform overexpression

city: Rio de Janeiro

first: Tatiana

middle: Martins

last: Tilli

address: Andre Cavalcanti, 37 - Centro

institute: Instituto Nacional de Câncer

summary:
We previously demonstrated that the osteopontin-c (OPNc) splice variant activates several aspects of the progression of prostate cancers. The goal of the present study was to develop cell line model to determine the impact of OPNc overexpression on main cancer signaling pathways and thus obtain insights into the mechanisms of OPNc pro-tumorigenic roles.

Methods: PC-3 cells were stably transfected to overexpress OPNc. Transcriptomic profiling was performed on these cells and compared to controls, to identify OPNc overexpression-dependent changes in gene expression levels and pathways by qRT-PCR analyses;

Results: Of 84 genes tested by using a multiplex real-time PCR Cancer Pathway Array approach, among then 16 were differentially expressed between PC-3 OPNc-overexpressing cells in relation to control clones. Differentially expressed genes are included in all main hallmarks of cancer, and several interacting proteins have been identified using an interactome network analysis.

Conclusions: Overall, the present study elucidated transcriptional changes of prostate cancer cells in response to OPNc overexpression, which provides an assessment for predicting the molecular mechanisms by which this splice variant promotes tumor progression features.

overall_design:
Cell Culture, OPN Plasmids and Transfection; As a model to examine the signaling pathways modulated by OPNc overexpression in prostate carcinoma, we used PC-3 cell line, which were provided by ATCC. The open reading frame of OPNc was cloned into the pCR3.1 mammalian expression vector as previously described [Tilli et al., 2012].
Transfections were performed using LipofectamineTM 2000 (Invitrogen, CA). Our previous data demonstrated that PC-3 stably transfected cells contain higher levels of protein and the mRNA OPNc splicing isoform in relation to their endogenous levels in empty vector-transfected cells. PC-3 transfected with empty vector (EV) were used as a negative control in these assays.
Human Cancer Pathway Finder PCR Array The Human Cancer Pathway Finder SuperArray (PAHS-033A; Qiagen) was used to determine changes in the specific genes encoding proteins related to the main hallmarks of cancer in response to OPNc overexpression. The assay design criteria ensure that each qPCR reaction will generate single, gene-specific amplicons and prevent the co-amplification of non-specific products. The qPCR Assays used in PCR Arrays are optimized to work under standard conditions enabling a large number of genes to be assayed simultaneously. Their specificity is guaranteed by SABiosciences when RT2 SYBR Green qPCR Master Mixes are used as part of the complete PCR Array System protocol. Simultaneous gene expression analyses require similar qPCR efficiencies for accurate comparison among genes. RT2 qPCR Primer Assays are designed with an amplicon size ranging from 100 to 250 bp and with PCR efficiencies uniformly greater than 90%. Overall, more than 10 thermodynamic criteria are included in the design of each RT2 qPCR Primer Assay to ensure the most reliable and accurate results for pathway-based gene expression analysis in the PCR Array System.   We analyzed mRNA levels of 84 genes related to cell cycle control, apoptosis and cell senescence, signal transduction molecules and transcription factors, adhesion, angiogenesis, invasion and metastasis; and also 5 housekeeping genes and genomic DNA contamination controls. The PCR plates were run using the CFX96 Real-Time System cycler (BioRad, Hercules, CA), following a superarray two-step cycling PCR protocol, in which each plate ran one cycle for 10 minutes at 95°C, as well as 40 cycles of 95°C for 15 seconds and 60°C for 1 minute. After the superarray protocol was run for each plate, RT-PCR data analysis was performed using the website:http://www.SABiosciences.com/pcrarraydataanalysis.php, in order to compare gene expression of OPNc-overexpressing cells and empty vector transfected cells. Total RNA quality control, cDNA synthesis and the quantitative real-time RT-PCR (qRT-PCR) array were performed as recommended by the manufacturer (Qiagen). Data analysis of gene expression was performed using Excel-based PCR Array Data Analysis Software provided by manufacturer (Qiagen). Fold-changes in gene expression were calculated using the ΔΔCT method, and five stably expressed housekeeping genes (β2 microglobulin, hypoxanthine phosphoribosyltransferase 1, ribosomal protein L13a, GAPDH and β-actin) were used to normalize the level of expression. The statistical analysis was performed to compare the gene expression values for the OPNc-overexpressing cells and those transfected with empty vector. P<0.05 was considered statistically significant. Only genes showing a 1.5-fold or greater change were considered for further analysis.

first: Etel

middle: R

last: Gimba


title: Transcriptional patterns associated with OvCar-3 and PC-3 cells in response to osteopontin-c splicing isoform overexpression

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

overall_design: Refer to individual Series


title: Loss of nuclear TDP-43 in ALS causes altered expression of splicing machinery and widespread dysregulation of RNA splicing in motor neurons [LCM]

status: Public on Jun 01 2014

city: Sheffield

first: Paul

middle: Roy

last: Heath

state: S. Yorks

address: SITraN, 385a Glossop Road

department: Academic Neurology Unit

country: United Kingdom

institute: University of Sheffield

summary:
Aims: Loss of nuclear TDP-43 characterises sporadic and most familial forms of amyotrophic lateral sclerosis (ALS). TDP-43 (encoded by TARDBP) has multiple roles in RNA processing. We aimed to determine whether 1) RNA splicing dysregulation is present in lower motor neurons in ALS and in a motor neuron-like cell model, and 2) TARDBP mutations (mtTARDBP) are associated with aberrant RNA splicing using patient-derived fibroblasts.
Methods: Affymetrix exon arrays were used to study mRNA expression and splicing in lower motor neurons obtained by laser capture microdissection of autopsy tissue from individuals with sporadic ALS and TDP-43 proteinopathy. Findings were confirmed by qRT-PCR and in NSC34 motor neuronal cells following shRNA-mediated TDP-43 depletion. Exon arrays and immunohistochemistry were used to study mRNA splicing and TDP-43 expression in fibroblasts from patients with mtTARDBP-associated, sporadic and mutant SOD1-associated ALS.
Results: We found altered expression of spliceosome components in motor neurons and widespread aberrations of mRNA splicing that specifically affected genes involved in ribonucleotide binding. This was confirmed in TDP-43 depleted NSC34 cells. Fibroblasts with mtTARDBP showed loss of nuclear TDP-43 protein and demonstrated similar changes in splicing and gene expression, that were not present in fibroblasts from patients with sporadic or SOD1-related ALS.
Conclusion: Loss of nuclear TDP-43 is associated with RNA processing abnormalities in ALS motor neurons, patient-derived cells with mtTARDBP, and following artificial TDP-43 depletion, suggesting that splicing dysregulation directly contributes to disease pathogenesis. Key functional pathways affected include those central to RNA metabolism.

overall_design: RNA was extracted from lower motor neurons obtained by laser capture microdissection from autopsy material from neurologically healthy controls (n=6) and cases of sporadic ALS (n=3) and ALS due to C9ORF72 mutations (n=3).

first: J

last: Highley

first: Janine

last: Kirby

first: Joeri

last: Jansweijer

first: Philip

last: Webb

first: Channa

last: Hewamadduma

first: Adrian

last: Higginbottom

first: Rohini

last: Raman

last: Ferraiuolo

first: Scott

middle: P

last: Allen

first: Jonathan

last: Cooper-Knock

first: Christopher

middle: J

last: McDermott

first: Stephen

last: Wharton

first: Pamela

last: Shaw

middle: G

last: Ince


title: Transcriptional patterns associated with OvCar-3 cells in response to osteopontin-c splicing isoform overexpression

last: Tilli

summary:
We previously demonstrated that the osteopontin-c (OPNc) splice variant activates several aspects of the progression of ovarian cancers. The goal of the present study was to develop cell line model to determine the impact of OPNc overexpression on main cancer signaling pathways and thus obtain insights into the mechanisms of OPNc pro-tumorigenic roles.

Methods: OvCar-3 cells were stably transfected to overexpress OPNc. Transcriptomic profiling was performed on these cells and compared to controls, to identify OPNc overexpression-dependent changes in gene expression levels and pathways by qRT-PCR analyses;

Results: Of 84 genes tested by using a multiplex real-time PCR Cancer Pathway Array approach, 34, were differentially expressed between OvCar-3 OPNc-overexpressing cells in relation to control clones. Differentially expressed genes are included in all main hallmarks of cancer, and several interacting proteins have been identified using an interactome network analysis.

Conclusions: Overall, the present study elucidated transcriptional changes of ovarian cancer cells in response to OPNc overexpression, which provides an assessment for predicting the molecular mechanisms by which this splice variant promotes tumor progression features.

overall_design:
Cell Culture, OPN Plasmids and Transfection; As a model to examine the signaling pathways modulated by OPNc overexpression in ovarian carcinoma, we used OvCar-3 cell line, which were provided by ATCC. The open reading frame of OPNc was cloned into the pCR3.1 mammalian expression vector as previously described [Tilli et al., 2012].
Transfections were performed using LipofectamineTM 2000 (Invitrogen, CA). Our previous data demonstrated that OvCar-3 stably transfected cells contain higher levels of protein and the mRNA OPNc splicing isoform in relation to their endogenous levels in empty vector-transfected cells. OvCar-3 transfected with empty vector (EV) were used as a negative control in these assays.
Human Cancer Pathway Finder PCR Array The Human Cancer Pathway Finder SuperArray (PAHS-033A; Qiagen) was used to determine changes in the specific genes encoding proteins related to the main hallmarks of cancer in response to OPNc overexpression. The assay design criteria ensure that each qPCR reaction will generate single, gene-specific amplicons and prevent the co-amplification of non-specific products. The qPCR Assays used in PCR Arrays are optimized to work under standard conditions enabling a large number of genes to be assayed simultaneously. Their specificity is guaranteed by SABiosciences when RT2 SYBR Green qPCR Master Mixes are used as part of the complete PCR Array System protocol. Simultaneous gene expression analyses require similar qPCR efficiencies for accurate comparison among genes. RT2 qPCR Primer Assays are designed with an amplicon size ranging from 100 to 250 bp and with PCR efficiencies uniformly greater than 90%. Overall, more than 10 thermodynamic criteria are included in the design of each RT2 qPCR Primer Assay to ensure the most reliable and accurate results for pathway-based gene expression analysis in the PCR Array System.   We analyzed mRNA levels of 84 genes related to cell cycle control, apoptosis and cell senescence, signal transduction molecules and transcription factors, adhesion, angiogenesis, invasion and metastasis; and also 5 housekeeping genes and genomic DNA contamination controls. The PCR plates were run using the CFX96 Real-Time System cycler (BioRad, Hercules, CA), following a superarray two-step cycling PCR protocol, in which each plate ran one cycle for 10 minutes at 95°C, as well as 40 cycles of 95°C for 15 seconds and 60°C for 1 minute. After the superarray protocol was run for each plate, RT-PCR data analysis was performed using the website:http://www.SABiosciences.com/pcrarraydataanalysis.php, in order to compare gene expression of OPNc-overexpressing cells and empty vector transfected cells. Total RNA quality control, cDNA synthesis and the quantitative real-time RT-PCR (qRT-PCR) array were performed as recommended by the manufacturer (Qiagen). Data analysis of gene expression was performed using Excel-based PCR Array Data Analysis Software provided by manufacturer (Qiagen). Fold-changes in gene expression were calculated using the ΔΔCT method, and five stably expressed housekeeping genes (β2 microglobulin, hypoxanthine phosphoribosyltransferase 1, ribosomal protein L13a, GAPDH and β-actin) were used to normalize the level of expression. The statistical analysis was performed to compare the gene expression values for the OPNc-overexpressing cells and those transfected with empty vector. P<0.05 was considered statistically significant. Only genes showing a 1.5-fold or greater change were considered for further analysis.


title: Temperature dependent Transcriptome of L. monocytogenes EGDe in minimal medium

city: Freising

first: Stefanie

last: Müller-Herbst

address: Weihenstephaner Berg 3

department: ZIEL and Chair for Microbial Ecology

institute: Technical University Munich

summary:
Comparison of transcriptome of L. monocytogenes EGDe at 24°C and 37°C
L. monocytogenes EGDe cells used in this study were grown either at 24°C or 37°C  to an OD600 = 0.82-0.87 and the transcriptome of these two conditions was compared

overall_design: Six biologically independent cultures of each at 24°C and 37°C grown L. monocytogenes EGDe were used for total RNA isolation (six RNA sets). Three array experiments were performed with Cy5-labelled cDNA derived from at 24°C grown Listeria and Cy3-labelled cDNA derived from at 37°C grown cells. For the three other RNA sets a dye swap was performed, that means the three other array experiments were performed with Cy3-labelled cDNA derived form at 24°C grown Listeria and Cy5-labelled cDNA from at 37°C grown cells. As all oligonuceotides are spotted twice on an array, technical duplicates were performed for each experiment. The overall design results in 12 data points for the expression of each gene.

first: Daniela

last: Kaspar

last: Eder

first: Claudia

last: Held

first: Armin

last: Ehrenreich

first: Siegfried

last: Scherer


title: Hypoxia regulates alternative splicing of HIF and non-HIF target genes

status: Public on May 14 2014

city: Aurora

first: Cheng-Jun

last: Hu

state: CO

address: E. 17th Ave

department: Craniofacial Biology

institute: University of Colorado Denver

summary:
Alternative RNA splicing analysis in Hep3B cell cultured under 21% (N1,3,5) or 1.2% (H2,4,6) oxygen
Hypoxia is a common characteristic of many solid tumors. The hypoxic microenvironment stabilizes hypoxia-inducible transcription factor 1α (HIF1α) and 2α (HIF2α) to activate gene transcription, which promotes tumor cell survival. 95% of human genes are alternatively spliced, producing RNA isoforms that code functionally distinct proteins. Thus, effective hypoxia response requires increased HIF target gene transcription as well as proper RNA splicing of these HIF target genes. However, it is unclear if and how hypoxia regulates RNA splicing of HIF target genes. This study determined the effects of hypoxia on alternative splicing (AS) of HIF and non-HIF target genes in Hep3B cells and characterized the role of HIF in regulating AS of HIF induced genes. The results indicated that hypoxia generally promotes exon inclusion for hypoxia-induced, but reduces exon inclusion for hypoxia reduced genes. Mechanistically, HIF activity, but not hypoxia per se is found to be necessary and sufficient to increase exon inclusion of several HIF target genes including pyruvate dehydrogenase kinase 1 (PDK1). PDK1 splicing reporters confirmed that transcriptional activation by HIF is sufficient to increase exon inclusion of PDK1 splicing reporter. In contrast, transcriptional activation of the PDK1 minigene by other transcription factor in the absence of endogenous HIF target gene activation fails to alter PDK1 RNA splicing, demonstrating a novel role of HIF target gene(s) in regulating RNA splicing of HIF target genes.     Implications:This study demonstrates a novel function of HIF in regulating RNA splicing of HIF target genes.

overall_design: We analyzed total RNA from Hep3B cells cultured under 21% (N1,3,5) or 1.2% (H2,4,6) oxygen using the Affymetrix Human Exon 1.0 ST platform. Array data was processed by Altanalyze software version 2.0.7.  Techinical replicates were performed for Nx and Hx treated Hep3B cells

first: Johnny

last: Sena

first: Liyi

last: Wang

first: Lynn

last: Heasley


title: Transcriptional profile of pulsed AsxR in Escherichia coli O157:H7 str. TUV93-0

status: Public on May 22 2014

city: Sydney

first: Jai

middle: Justin

last: Tree

state: NSW

address: Rm s110 Bldg F25, UNSW, Gate 11 Botany St

department: School of Biotechnology and Biomolecular Sciences

country: Australia

institute: University of New South Wales

summary: Transcript abundance in Escherichia coli O157:H7 was determined in the presence or absence of pulsed expression of the small RNA, AsxR.

overall_design: AsxR was cloned under the control the arabinose inducible promoter Para. Escherichia coli O157:H7 str. TUV93-0 with pAsxR or empty vector was cultured in MEM-HEPES media to an OD600 of 0.8 and 0.2% arabinose added. 10min after addition of arabinose 10ml  of cells were harvested and and pellets resuspended in 1ml of Trizol and total RNA isolated. RNAs were labelled using the SuperScript Plus indirect cDNA labelling System. Triplicate control RNAs were pooled and hybridised to seperate AsxR test RNAs on three microarays. Arrays were hybridised using the Maui hybridisation platform and Scann using and Axon Autoloader Scanner. GenePix software was used to analyse images and GPR files were analysed using Genespring 7.3.1.

first: David

last: Gally

last: Tollervey


title: Response of  Bacillus pumilus to hydrogen peroxide

status: Public on May 17 2014

city: Greifswald

first: Birgit

last: Voigt

address: F.-L.-Jahnstr. 15

department: Institute for Microbiology

summary:
Reactive oxygen species such as hydrogen peroxide occur in all aerobically living organisms. Oxidative stress during fermentation can impair the fitness of the production host and the quality of the product. B. pumilus has been described as highly resistant to hydrogen peroxide.
The response of exponentially growing B. pumilus cells to hydrogen peroxide was studied.

overall_design: Two-condition experiment, unstressed versus hydrogen peroxide stressed cells, 3 biological replicates

first: Rebecca

last: Schroeter

first: Britta

last: Jürgen

first: Sacha

last: van Hijum


title: Gene expression analysis during adventitious root formation in petunia cuttings

city: Grossbeeren

first: Philipp

last: Franken

address: Theodor-Echtermeyer-Weg 1

institute: Leibniz Institute of Vegetable and Ornamental Crops - IGZ EV

summary:
In order to identify genes specifically induced during various developmental stages of Adventitious Root (AR) formation (described in Ahkami et al. 2009) in leafy cuttings of Petunia hybrida (line W115) and to describe the series of physiological processes during adventitious rooting, a microarray-based transcriptome analysis in the stem base of the cuttings was conducted. The microarray was described by Breuillin et al. (2010) and included a normalized cDNA library from different time points after taking the cuttings from mother plant.
Because physiological processes and molecular changes specifically involved in AR formation were considered as of major interest, rather than those associated with wound responses, a filtration approach was chosen to eliminate primarily wound-responsive genes. This study is mainly focused on changes in transcript abundances of genes related to specific metabolic pathways or cellular events including primary metabolism, membrane transport, cell division or signalling during various phases of AR formation.

overall_design: The overall design of the custom microarray used in this study is described in Breuillin et al. (2010). In brief, a database of 24,816 unigene sequences (including 4,700 ESTs from P. hybrida cutting base and all public available P. hybrida and P. axillaris sequences) was used for construction of a custom microarray.

first: Amir

middle: H

last: Ahkami

first: Uwe

last: Scholz

first: Burkhard

last: Steuernagel

first: Marc

last: Strickert

first: Klaus

middle: T

last: Haensch

last: Druege

first: Didier

last: Reinhardt

first: Eva

last: Nouri

first: Nicolaus

last: von Wirén

first: Mohammad

last: Hajirezaei


title: Global microRNA profiling of mouse hemopoietic stem cells (LSKs), promyelocytes, myelocytes and granulocytes.

city: Camperdown

first: Justin

last: Wong

address: Building 93 Royal Prince Alfred Hospital

institute: Centenary Institute

summary: This study sought to determine the dynamic changes of miRNA expression during mouse granulopoiesis. We not only performed analyses of miRNA expression levels in whole cells but also analyzed purified nuclear and cytoplasmic cell fractions to profile miRNA subcellular localization.

overall_design: qRT-PCR analysis of miRNAs was performed on whole cell, nuclear and cytoplasmic RNAs extracted from mouse hemopoietic stem cells (LSKs), promyelocytes, myelocytes and granulocytes. 100 ng of RNA was reversed transcribed using the Taqman miRNA Reverse Transcription Kit  and Megaplex RT Primers rodent pool A and B (Life Technologies). Complementary DNA (cDNA) was amplified using a TaqMan rodent microRNA A and B Array v2.0 (Life Technologies) with TaqMan Universal PCR Master Mix on an ABI 7900HT Sequence Detection System.

first: Jeff

last: Holst


title: Gene Expression Dynamics of Defined Cell Populations in Developing Drosophila Embryos and Larvae

status: Public on May 09 2014

city: San Francisco

first: Charlie

last: Kim

address: 1001 Potrero Ave

department: Medicine

institute: University of California, San Francisco

summary: Microarray profiling of GFP-marked neuronal and non-neuronal cellular populations isolated by FACS at 24h intervals across development of Drosophila larvae.

overall_design: Multiple independent replicates collected for each population/timepoint combination.  RNA isolated and amplified from FACS-sorted populations.  Hybridized as two-color experiment against a common pooled reference.

first: Charles

first: Jay

middle: Z

last: Parrish

first: Lamont

last: Tang

first: Sharon

middle: B

last: Bergquist

first: Joseph

middle: L

last: DeRisi

first: Lily

last: Jan

first: Yuh

middle: N

first: Graeme

last: Davis


title: MicroRNA expression profiling analysis on a group of 52 heredo-familial and sporadic breast cancer samples

city: Milan

first: Elisabetta

last: Crippa

address: Via Adamello 16

country: Italy

institute: IFOM-FIRC Institute of Molecular Oncology

summary: In this study, using microarray technology we did a transcriptome profiling of miRNAs on a group of 52 cases of familial (BRCA1- or BRCA2-mutated, or BRCAX, i.e. familial cases with no mutations in BRCA1 or BRCA2 genes) and sporadic breast cancers. Class comparison of different clinical characteristics of the samples identified miR-342 as the miRNA with the most significant association with estrogen receptor (ER) status (categorised as positive and negative) of the samples analysed. As ER is one of the bio-pathological features currently used in routine clinical practice to aid treatment decision in breast cancer, identification of this miRNA has been promising for finding new mechanisms involved in this tumour type as we had next demonstrated in a cellular model of breast cancer.

overall_design: In the study presented here, microRNAs expression profiling on a well defined cohort of 52 breast cancer cases, followed up for more than 5 years, was used for a class comparison analysis with some relevant clinical characteristics of this tumour type like estrogen, progesterone or epidermal growth factor 2 receptor status.

first: Manuela

last: Gariboldi


title: Route specific dermal responses to vaccinia virus infection

status: Public on May 13 2014

city: Gainesville

first: Richard

middle: W

last: Moyer

state: FL

address: 1600 SW Archer Rd

institute: University of Florida

summary:
Transcriptional profiles of rabbit skin infected via the intradermal or scarification route of infeciton assessing the early time post infection.
Transcriptional profiles were assessed at 4hrs, 24hrs, and 48hrs post infection for each route of infection. Transcript variation is as compared to normal, uninfected rabbit skin.

overall_design: Two condition, three time points per condition. 3 biological replicates per time point per condition. Normal rabbit skin was used as the control.

first: Amanda

last: Rice

first: Mathew

last: Adams

first: Scott

middle: F

last: Lindsey

first: Daniele

last: Swetnam

first: Brandi

last: Manning

first: Andrew

last: Smith

last: Burrage

first: Greg

last: Wallace

first: Amy

last: MacNeill


title: Aplysia pleural Ganglia 1 Hour After Long-Term Sensitization Training

status: Public on May 08 2014

city: River Forest

first: Robert

last: Calin-Jageman

state: IL

address: 7900 West Division

department: Psychology

institute: Dominican University

summary: We used a custom-designed microarray and qPCR to characterize the rapid transcriptional response to long-term sensitization training in the marine mollusk Aplysia californica.  Aplysia were exposed to repeated noxious shocks to one side of the body (4 ten-second shocks at 90mA, 30 min ISI), a procedure known to induce a transcription-dependent and long-lasting increase in reflex responsiveness that is restricted to the side of training.  One hour after training, pleural ganglia from the trained and untrained sides of the body were harvested; these ganglia contain the sensory nociceptors which help mediate the expression of long-term sensitization memory.   Microarray analysis from 8 biological replicates suggests that long-term sensitization training rapidly regulates at least 102 transcripts.  We used qPCR to test a subset of these transcripts and found that 86% were confirmed in the same samples, and 83% of these were again confirmed in an independent sample (n = 9 animals).  Thus, our new microarray design shows very strong convergent and predictive validity for analyzing the transcriptional correlates of memory in Aplysia.  Fully validated transcripts include some previously identified as regulated in this paradigm (ApC/EBP and ApEgr) but also include novel findings.  Specifically, we show that long-term sensitization training rapidly up-regulates the expression of transcripts which encode a C/EBP gamma, a glycine transporter, and a vacuolar-protein-sorting-associated protein.

overall_design: Within-subjects comparison of trained (Cy5) to untrained (Cy3) pleural ganglia with 8 biological replicates.  Each replicate is a trained sample from two animals (right and left trained) and each untrained sample is from the same two aniamls (right and left untrained)

first: Irina

middle: E


title: Diagnosis and early detection of CNS-SLE in MRL/lpr mice using peptide microarrays (GPL14921)

city: Phoenix

first: Phillip

last: Stafford

state: AZ

address: 1001 S. McAllister

department: Center for Innovations in Medicine

institute: Biodesign Institute

summary:
We investigated whether mouse serum autoantibody binding patterns on random-sequence peptide microarrays (immunosignaturing) can be used for diagnosing and predicting the onset of lupus and its central nervous system (CNS) manifestations.

Submitter states "We have no processed data to submit.  We have no gpr files to submit."

overall_design: To identify possible predictive and diagnostic peptides of lupus and CNS-lupus, we carried out two studies and selected peptides in common across both studies.  In the first study we tested 3-6 MRL/lpr, MRL/mp and C3H/HeJ mice at four months of age.  For study two we tested 9-10 MRL/lpr and MRL/mp at 1.5 and 4 months of age.  In both studies the mice sera were diluted 1/500 and analyzed using microarray peptides from platform GPL14921.  We ran each sample in triplicate.  The MRL/lpr and MRL/mp are the autoimmune strains and the C3H/HeJ is the control strain.

first: Stephanie

middle: M

last: Williams

first: Steven

middle: A

last: Hoffman


title: microRNA profiles of exosomes from two nasopharyngeal carcinoma cell line and nasopharyngeal epithelial cells

status: Public on May 07 2014

city: Guangzhou

first: ping

last: lan

address: 651 Dongfend East Road

country: China

institute: Sun Yat-sen University Cancer Center

summary: microRNA profiles of exosomes :Exosomes from two nasopharyngeal carcinoma cell line TW03（EBV+）and TW03（EBV-） and Exosomes from nasopharyngeal epithelial cells NP69

platform_organism:
Homo sapiens
Mus musculus
Rattus norvegicus

overall_design: Two-condition experiment, Exosomes from two nasopharyngeal carcinoma cell line vs.one normal epithelium cell line. Biological replicates:1 Exosomes from nasopharyngeal carcinoma cell line TW03（EBV+）, 1 Exosomes from nasopharyngeal carcinoma cell line TW03（EBV-）,1 Exosomes from nasopharyngeal epithelial cells NP69.

first: Jiang

last: Li

first: Shubiao

last: Ye


title: Diagnosis and early detection of CNS-SLE in MRL/lpr mice using peptide microarrays (GPL17600)

summary:
In addition to determining possible diagnostic and predictive peptides of lupus and CNS-lupus, we also used our microarray technology along with the Guitope computer program to determine possible natural protein match to five monoclonal autoantibodies that were created using one of the autoimmune MRL/lpr mouse.

Submitter states "We have no processed data to submit.  We have no gpr files to submit."

overall_design: Microarray analysis was performed on five monoclonal brain-reactive autoantibodies (F9, G10, G4, D1 and D9) that were created from one autoimmune mouse with altered behavior.  These samples were tested in duplicated along with a control sample on the GPL17600 platform.


title: Elucidation of Zymomonas mobilis physiology and stress responses by quantitative proteomics and transcriptomics

city: Golden

first: Shihui

last: YANG

address: 1617 Cole Blvd

department: National Bioenergy Center

institute: National Renewable Energy Lab

summary: Zymomonas mobilis is an excellent ethanologenic bacterium. Biomass pretreatment and saccharification provides access to simple sugars, but also produces inhibitors such as acetate and furfural. Our previous work has identified and confirmed the genetic change of a 1.5-kb deletion in the sodium acetate tolerant Z. mobilis mutant (AcR) leading to constitutively elevated expression of a sodium proton antiporter encoding gene nhaA, which contributes to the sodium acetate tolerance of AcR mutant. In this study, we further investigated the responses of AcR and wild-type ZM4 to sodium acetate stress in minimum media using both transcriptomics and a metabolic labeling approach for quantitative proteomics the first time. Proteomic measurements at two time points identified about eight hundreds proteins, or about half of the predicted proteome. Extracellular metabolite analysis indicated AcR overcame the acetate stress quicker than ZM4 with a concomitant earlier ethanol production in AcR mutant, although the final ethanol yields and cell densities were similar between two strains. Transcriptomic samples were analyzed for four time points and revealed that the response of Z. mobilis to sodium acetate stress is dynamic, complex and involved about one-fifth of the total predicted genes from all different functional categories. The modest correlations between proteomic and transcriptomic data may suggest the involvement of posttranscriptional control. In addition, the transcriptomic data of forty-four microarrays from four experiments for ZM4 and AcR under different conditions were combined to identify strain-specific, media-responsive, growth phase-dependent, and treatment-responsive gene expression profiles. Together this study indicates that minimal medium has the most dramatic effect on gene expression compared to rich medium followed by growth phase, inhibitor, and strain background. Genes involved in protein biosynthesis, glycolysis and fermentation as well as ATP synthesis and stress response play key roles in Z. mobilis metabolism with consistently strong expression levels under different conditions.

sample_organism: Zymomonas mobilis subsp. mobilis ZM4 = ATCC 31821

overall_design: A sixteen array study using total RNA recovered from wild-type cultures of Zymomonas mobilis subsp mobilis ZM4 and acetate-tolerant mutant AcR at different time points of 130, 148, 166, and 190h post-inoculation with 10g/L sodium acetate (NaAc) treatment were carried out to investigate the expression differences between ZM4 and AcR. Two biological replicates for treatment or control condition.

first: Chongle

last: PAN

first: Gregory

last: Hurst

first: Lezlee

last: Dice

first: Brian

last: Davison

middle: D

last: Brown


title: RNA helicases DDX5 and DDX17 dynamically orchestrate transcription, microRNA and splicing programs in cell differentiation

status: Public on May 06 2014

city: Lyon

first: Didier

last: Auboeuf

address: 28 rue Laennec

country: France

institute: INSERM - CNRS [CRCL]

summary: RNA helicases DDX5 and DDX17 are members of a large family of highly conserved proteins involved in gene expression regulation, although their in vivo targets and activities in biological processes like cell differentiation, that requires reprogramming of gene expression programs at multiple levels, are not well characterized. In this report, we uncovered a new mechanism by which DDX5 and DDX17 cooperate with hnRNP H/F splicing factors to define epithelial- and myoblast-specific splicing subprograms. We next observed that downregulation of DDX5 and DDX17 protein expression during epithelial to mesenchymal transdifferentiation and during myogenesis contributes to switching splicing programs during these processes. Remarkably, this downregulation is mediated by the production of microRNAs induced upon differentiation in a DDX5/DDX17-dependent manner. Since DDX5 and DDX17 also function as coregulators of master transcriptional regulators of differentiation, we propose to name these proteins “master orchestrators” of differentiation, that dynamically orchestrate several layers of gene expression.

overall_design: 6 samples of MCF7 cells exposed to different treatments were analyzed: 3 x siCTRL ; 3 x si(DDX5-17) AND 6 samples of MCF10 cells exposed to different treatments were analyzed: 3 x siCTRL ; 3 x si(DDX5-17)

first: Etienne

last: Dardenne

first: Micaela

last: Polay Espinoza

first: Laurent

last: Fattet

first: Sophie

last: Germann

first: Marie-Pierre

last: Lambert

first: Helen

last: Neil

first: Eleonora

last: Zonta

first: Hussein

last: Mortada

first: Lise

last: Gratadou

first: Mathieu

last: Deygas

first: Fatima

last: Chakrama

first: Samaan

last: Samaan

first: François-Olivier

last: Desmet

first: Léon-Charles

last: Tranchevent

first: Martin

last: Dutertre

first: Ruth

last: Rimokh

first: Cyril

last: Bourgeois


title: SDF-1 chemokine signaling modulates the apoptotic responses of clathrin-depleted DT40 cells

city: Cambridge

first: Antony

last: Jackson

state: Cambridgeshire

address: Tennis Court Road, Cambridge

department: Department of Biochemistry

institute: University of Cambridge

summary: The cell line DKO-S is derived form chicken B-Cell DT40 cells where the clathrin heavy-chain has been placed under  the control of a tetracycline-regulatable promoter (Tet-Off). The originally derived cell-line DKO-S underwent apoptosis when clathrin expression was repressed. A cell line, DKO-R, derived from DKO-S cells that was less sensitive to clathrin-depletion. This project explores the differnces in gene expression between DKO-R and DKO-S cells

overall_design: Duplicate samples ofDT40, DKO-S or DKO_R cells either with or without treatment with deoxycyclin are compared as is the expression between DKO-R and DKO-S cell lines

first: A

first: R

last: Talbot


title: Profiling of Lola-N genomic binding in Drosophila with DamID

city: London

first: Tony

middle: David

last: Southall

address: South Kensington Campus

department: Life Sciences

institute: Imperial College London

type: Genome binding/occupancy profiling by genome tiling array

summary: The ability to reprogram differentiated cells into a pluripotent state has revealed that the differentiated state is plastic and reversible. It is evident, therefore, that mechanisms must be in place to maintain cells in a differentiated state. Transcription factors that specify neuronal characteristics have been well studied but less is known about the mechanisms that prevent neurons from dedifferentiating to a multipotent, stem cell-like state. Here we identify Lola as a transcription factor that is required to maintain neurons in a differentiated state. We show that Lola represses neural stem cell genes and cell cycle genes in post-mitotic neurons. In lola mutants, neurons dedifferentiate, turn on neural stem cell genes and begin to divide, forming tumours. Thus, neurons rather than stem cells or intermediate progenitors are the tumour-initiating cells in lola mutants.

overall_design: 3 biological relicates were performed for Lola-N (with one dye-swap).

first: Andrea

last: Brand


title: Related insects show differing amounts of population differentiation and localization of transcribed genes in response to climate (Erynnis propertius)

status: Public on May 05 2014

city: Notre Dame

first: Jessica

last: Hellmann

state: IN

address: 100 Galvin Life Science Center

department: Biological Sciences

institute: University of Notre Dame

summary:
We used custom Nimblegen microarrays representing whole-larval transcriptomes for two species (Erynnis propertius [this submission] and Papilio zelicaon [submitted seperately]) to assess gene expression differences affecting tolerance to climatic regimes. Many individuals were sourced from populations from the northern periphery and center of the species' (shared) range; these were each divided into groups treated under peripheral and central climate regimes, resulting in 4 experimental groups for each species (Peripheral Source, Peripheral treatment; Peripheral Source, Central Treatment; Central Source, Peripheral Treatment; Central Source, Central Treatment). Using technical microarray replicates allowed us to use ANOVA to identify genes whose expression may underlie local adaptation to climate (i.e., those showing an interaction term between source and population).
Abstract: Population differences may determine geographic range shifts and adaptive evolution under climate change. Local adaptation in peripheral populations could preclude or slow range expansions, and populations with different genetic make-up could have distinct trajectories that produce complex spatial patterns of population change. To investigate the genetic extent of local responses to climate change, we exposed poleward-periphery and central populations of two Lepidoptera to reciprocal, common-garden climatic conditions and compared whole-transcriptome expression. We found significant expression differences between populations in both species. In addition, several hundred genes including genes involved in energy metabolism and oxidative stress responded in a localized fashion in the species that exhibits greater population structure and local adaptation. Expression levels of these genes are most divergent in the same environment in which we previously detected phenotypic divergence in metabolism. By contrast, we found no localized genes in the species with higher gene flow, reflecting the lack of previously observed local adaptation. These results suggest that population differences do not generalize easily, even for related species living in the same climate, but some taxa deserve population-level consideration when predicting the effects of climate change.

overall_design: Previously we sequenced and assembled whole larval transcriptome ESTs sourced from pooled central-population individuals subjected to environmental stressors (see O'Neil et al., 2008). From these assemblies custom Nimblegen microarrays were designed (Nimblegen, Inc.), representing 34,609 putative gene sequences for E. propertius (this submission) and 25,735 putative gene sequences for P. zelicaon (submitted seperately). Probe designs sought 5 representative 60mer probes for E.propertius and 4 representative probes for P. zelicaon. Messenger RNA was was sampled from multiple individuals of each experimental group and pooled before being converted to cDNA and hybridized to technical replicate microarrays. Three technical replicates for each experimental group were used, for a total of 12 microarrays (per species). Microarray data were log2 transformed and quintile-normalized (Bolstad et al. 2003) on a per-species basis.

first: Shawn

last: O'Neil

first: Jason

middle: K

last: Dzurisin

first: Scott

last: Emrich

first: Neil

last: Lobo

first: Rory

last: Carmichael

first: Erliang

last: Zeng


title: Related insects show differing amounts of population differentiation and localization of transcribed genes in response to climate (Papilio zelicaon)

summary:
We used custom Nimblegen microarrays representing whole-larval transcriptomes for two species (Papilio zelicaon [this submission] and Erynnis propertius [submitted seperately]) to assess gene expression differences affecting tolerance to climatic regimes. Many individuals were sourced from populations from the northern periphery and center of the species' (shared) range; these were each divided into groups treated under peripheral and central climate regimes, resulting in 4 experimental groups for each species (Peripheral Source, Peripheral treatment; Peripheral Source, Central Treatment; Central Source, Peripheral Treatment; Central Source, Central Treatment). Using technical microarray replicates allowed us to use ANOVA to identify genes whose expression may underlie local adaptation to climate (i.e., those showing an interaction term between source and population).
Abstract: Population differences may determine geographic range shifts and adaptive evolution under climate change. Local adaptation in peripheral populations could preclude or slow range expansions, and populations with different genetic make-up could have distinct trajectories that produce complex spatial patterns of population change. To investigate the genetic extent of local responses to climate change, we exposed poleward-periphery and central populations of two Lepidoptera to reciprocal, common-garden climatic conditions and compared whole-transcriptome expression. We found significant expression differences between populations in both species. In addition, several hundred genes including genes involved in energy metabolism and oxidative stress responded in a localized fashion in the species that exhibits greater population structure and local adaptation. Expression levels of these genes are most divergent in the same environment in which we previously detected phenotypic divergence in metabolism. By contrast, we found no localized genes in the species with higher gene flow, reflecting the lack of previously observed local adaptation. These results suggest that population differences do not generalize easily, even for related species living in the same climate, but some taxa deserve population-level consideration when predicting the effects of climate change.

overall_design: Previously we sequenced and assembled whole larval transcriptome ESTs sourced from pooled central-population individuals subjected to environmental stressors (see O'Neil et al., 2008). From these assemblies custom Nimblegen microarrays were designed (Nimblegen, Inc.), representing 34,609 putative gene sequences for E. propertius (submitted separately) and 25,735 putative gene sequences for P. zelicaon (this submission). Probe designs sought 5 representative 60mer probes for E.propertius and 4 representative probes for P. zelicaon. Messenger RNA was was sampled from multiple individuals of each experimental group and pooled before being converted to cDNA and hybridized to technical replicate microarrays. Three technical replicates for each experimental group were used, for a total of 12 microarrays (per species). Microarray data were log2 transformed and quintile-normalized (Bolstad et al. 2003) on a per-species basis.

middle: J


title: Gene expression in closely-related species mirrors local adaptation: consequences for responses to a warming world

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

sample_organism:
Papilio zelicaon
Gesta propertius

platform_organism:
Papilio zelicaon
Gesta propertius

overall_design: Refer to individual Series


title: Expression data from laser microdissected murine intestinal epithelial cells

city: Freising

first: Jana

last: Hemmerling

state: Bavaria

department: ZIEL

institute: Technische Universität München

summary:
Microarray  analyses of laser microdissected murine intestinal epithelial cells under the control of maternal inflammation at 17.5 days post conception demonstrates that maternal inflammation differentially regulates 2174 (iWT) and 3345 (iARE) genes in fetal tissue, but these transcriptional profiles  were overwritten in the postnatal environment dominated by tissue inflammation at 8 weeks postnatal.
We isolated 50 ng total RNA out of laser microdissected fetal and adult intestinal epithelial cells from the distal ileum and performed microarrays to address whether maternal inflammation programs the fetal intestine towards TNF-driven pathology

overall_design: Conventionally raised heterozygous TnfΔARE/+ and Tnf+/+ wild type mice on C57BL/6 background were used for this study. Female Tnf+/+ wild type (WT) mice were bred with male TnfΔARE/+ (ARE) mice and vice versa, generating offspring from healthy WT dams (WT and ARE) and inflamed ARE dams (iWT and iARE). On day 17.5 post conception (dpc) and 8 weeks postnatal the fetuses and offspring were sacrificed.The gut was freshly frozen in  Optimal Cutting Temperature (O.C.T.) embedding compound (Sakura Finetek, Torrance, USA) on dry ice and stored at -80°C until laser microdissection.

first: Katharina

last: Heller

first: Gabriele

last: Hörmannsperger

first: Monika

last: Bazanella

first: Thomas

last: Clavel

first: George

last: Kollias

first: Dirk

last: Haller


title: Vibrio cholerae N16961 cpxA*

status: Public on May 03 2014

city: Boston

first: Matthew

last: Waldor

state: MA

address: 181 Longwood Ave

department: Division of Infectious Diseases

institute: HHMI/Brigham and Women’s Hospital

summary: Transcriptional profiling comparing a V. cholerae cpxA* mutant relative to WT at an OD600 of 1.

platform_organism: Vibrio cholerae O1 biovar El Tor str. N16961

overall_design: Three independent experiments with a technical replicate for each.

first: Leyla

last: Slamti


title: Transcriptome assembly and microarray construction for Enchytraeus crypticus, a model oligochaete to assess stress response mechanisms derived from soil conditions

status: Public on May 01 2014

city: Amsterdam

first: Tjalf

last: de Boer

address: Science Park 406

country: Netherlands

institute: MicroLife Solutions

summary: The soil worm Enchytraeus crypticus (oligochaete) is an ecotoxicology model species although without genome or transcriptome sequence information. The present research aimed at studying, via high-throughput pyrosequencing, the transcriptome of Enchytraeus crypticus, sampled from multiple test conditions, and the construction of a high-density microarray for functional genomic studies. A pyrosequencing run retrieved approximately 1.5 million reads representing 645 million bases. After assembly, 27,296 contigs and 87,686 singletons were obtained. from which 44% and 25% were annotated as protein-coding genes. We show that the high amount of orphan genes is not due to poor sequence or assemble quality: 84% of the contig sequences contains an open reading frame with a start codon and E. crypticus homologs were identified for 92% of the core eukaryotic genes. Moreover, 65 and 77% of the unknown singletons and contigs, respectively, showed transcriptional activity.  An Agilent 180K microarray platform was designed and validated by hybridizing cDNA from 3 day zinc- exposed E. crypticus to the concentration corresponding to 50% reduction in reproduction (EC50). Overall, 70% of all probes exerted a hybridization signal above background level. More specifically, the probes derived from contigs showed a wider range of average intensities when compared to probes derived from singletons. In total, 522 significantly regulated transcripts were identifying upon zinc exposure. Several significantly regulated genes exerted predicted functions (e.g. zinc efflux, zinc transport) associated with zinc stress. Unexpectedly, the microarray data suggest that zinc exposure alters retrotransposon activity in the E. crypticus genome. In conclusion, characterization of the presented E. crypticus transcriptome and associated microarray platform is a valuable and high quality resource that permits further functional genomics experiments examining gene expression patterns underlying distinct environmental stress conditions. We show that unknown sequences are not the result of technical errors but mostly represent functional genes that are actively transcribed.

overall_design: The data presented in our manuscript is part of a larger experiment which was performed in single, large loop design. The analysis presented here can be replicated only by including all raw data from the larger experiment (all raw files are included in the archive linked to this submission). A single channel, interwoven loop design was used to test animals exposed to zinc EC50 on reproduction as compared to untreated controls for 4 days. 4 biological replicates per condition were used containing 25 grams of soil and 5 - 7, adult old animals per replicate. T4_con stands for untreated control soil while T4_50 are the samples exposed to EC50 of zinc on reproduction.

first: Marta

middle: P

last: Castro-Ferreira

first: John

last: Colbourne

first: Riet

last: Vooijs

first: Cornelis

last: van Gestel

first: Nico

last: van Straalen

first: Amadeu

last: Soares

first: Mónica

last: Amorim

first: Dick

last: Roelofs


title: Israeli acute paralysis virus – what we have learned about the virus since mysterious disappearance of the US honey bees known as Colony Collapse Disorder (CCD) in 2006

status: Public on Apr 08 2014

city: Bethesda

first: WeiPing

last: Chen

state: MD

address: Bldg 8, Room 1A11, NIDDK/NIH

department: GCL

institute: NIDDK/NIH

summary: There were important gaps in our knowledge of Israeli acute paralysis virus (IAPV), when IAPV was tightly linked to bee Colony Collapse Disorder (CCD), the mysterious disease that, starting in 2006-2007, has been wiping out honey bees in the US.  To fill in these gaps we studied the molecular basis of transmission, pathogenesis, and genetic diversity of IAPV infection in honey bees.  We investigated the impact of IAPV infection on colony losses and host transcriptional response to IAPV infections, and exploited the potential of RNAi-based strategies for treating viral diseases in honey bees.  Our study clearly shows that IAPV has become established as a persistent infection and is highly prevalent in the honey bee population.  The existence of both horizontal and vertical transmission pathways of the virus likely accounts for the high prevalence of IAPV in bees.  While IAPV is probably not the only culprit responsible for CCD, its ability to cause increased mortality in honey bees is firmly demonstrated.  The phenotypic differences in pathology among different strains of IAPV may be due to their high level of standing genetic variation.   The JAK-STAT pathway, along with other signaling events such as mTOR and MAPK pathways, likely involves honey bees’ antiviral immune responses to the IAPV infection.   The identification of IAPV-encoded putative suppressor of RNAi and evidence that silencing the RNAi suppressor led to a significant reduction in IAPV replication in infected bees illustrates the therapeutic potential of targeting viral suppressor protein to reduce virus replication.  Our study gives direction for developing strategies to reduce colony losses due to viral diseases.

overall_design: Adult worker bees and brood were collected from colonies that were declining and identified with IAPV infections and its control with 6 replications per group.

first: Ai

last: Zhou

first: Barton

last: Smith

first: Dennis

last: vanEngelsdorp

first: Erica

last: Teixeira

first: Francis

last: Drummond

first: Gloria

last: DeGrandi-Hoffman

first: Gustavo

last: Palacios

first: Humberto

last: Boncristiani

first: Huo

middle: Q

last: Zheng

first: Jay

last: Evans

first: Jeffery

middle: S

last: Pettis

first: Ji

last: Li

first: Keith

last: Delaplane

first: Leellen

last: Solter

first: Li

middle: Y

last: Wu

first: Marla

last: Spivak

last: Kramer

first: Michele

middle: C

last: Hamilton

first: Miguel

last: Corona

first: Myeong-L

last: Lee

first: P

last: Visscher

first: Shao

last: Huang

first: W

middle: I

last: Lipkin

first: Xuan

last: Zhang

first: Yan

last: Zhao

first: Zhi

middle: G


title: Vibrio cholerae N16961 overexpression of CpxR

first: Matthew

last: Waldor

summary: Transcriptionnal profiling comparing a V. Choleare ∆cpxR mutant harboring either (pBAD33-cpxR) or empty (pBAD33) grown for 1h under inducing conditions.

sample_organism: Vibrio cholerae O1 biovar El Tor str. N16961

overall_design: Two independent experiments with a technical replicate for each.

first: Leyla

last: Slamti


title: Genome wide transcriptional analysis of tissue macrophages and bone marrow derived macrophages (BMDMs)

status: Public on May 02 2014

city: New Haven

first: Yasutaka

last: Okabe

state: CT

address: 300 Cedar Street

department: Immunobiology

institute: Yale University School of Medicine

summary: Tissue macrophages from peritoneal cavity, lung, liver, spleen, small intestine and adipose tissue and M-CSF derived bone marrow derived macrophages (BMDMs) were determined for gene expression.

overall_design: Macrophages from six different tissues and BMDMs were compared for gene expression.

first: Ruslan

last: Medzhitov


title: Human sinonasal squamous cell carcinoma: Cell lines and corresponding primary tumors

status: Public on Apr 30 2014

city: Oviedo

first: Mario

last: Hermsen

state: Asturias

address: Celestino Villamil s/n

department: Otolaryngology

country: Spain

institute: Hospital Universitario Central de Asturias

summary: Genomic profiling of human squamous cell carcinoma cell lines cells and corresponding primary tumors

overall_design: Descriptive experiment, studying DNA copy number alterations in 6 newly established  human squamous cell carcinoma cell lines cells and corresponding 6 primary tumors.

first: Cristina

last: García-Inclán


title: Effect of choline kinase inhibitor hexadecyltrimethylammonium bromide on Plasmodium falciparum gene expression

status: Public on Feb 08 2014

city: Kuala Lumpur

first: Mohd Ridzuan

last: Mohd Abd Razak

address: Jalan Pahang

country: Malaysia

institute: Institute for Medical Research

summary:
Investigations on the fundamental of malaria parasite biology, such as invasion, growth cycle, metabolism and cell signalling have uncovered a number of potential antimalarial drug targets, including choline kinase, a key enzyme involved in the synthesis of phosphatidylcholine, an important component in parasite membrane compartment.
The effect on gene expression of Plasmodium falciparum K1 strain following 72 hours exposure to 2 μM (IC50 concentration) of the choline kinase inhibitor, hexadecyltrimethylammonium bromide (HDTAB) was evaluated by DNA microarray analysis.  Genes important in P. falciparum intra-erythrocytic life cycle, such as invasion, cytoadherance and growth were among those affected by at least 2-fold changes in their expression levels compared with non HDTAB-treated control.

platform_organism:
Plasmodium falciparum
Anopheles gambiae

overall_design: Two different cultures of P. falciparum was divided into two groups, untreated and HDTAB treated. The parasites were incubated for 72 hours and harvested for total RNA extraction. The expression profile was analysed by microarray.

first: M

middle: R

first: N

last: Abdullah


title: Expression analysis of Sphingomonas. sp A1 AlgO-deficient mutant grown in 0.5% alginate medium or 0.5% yeast extract medium

status: Public on Jan 28 2014

city: Uji

first: Wataru

last: Hashimoto

state: Kyoto

address: Gokasho

department: Graduate School of Agriculture

country: Japan

institute: Kyoto University

summary:
Investigation of whole genome gene expression level changes in Sphingomonas. sp A1 AlgO-deficient mutant grown on alginate compared with that on yeast extract
AlgO is a possble transcriptional factor described in J. Bacteriol. (2000) 182(14):3998-4004 by Momma K, Okamoto M, Mishima Y, Mori S, Hashimoto W, and Murata K.

overall_design: A two chip study using total RNA recovered from two cultures of Sphingomonas. sp A1 AlgO-deficient mutant grown in 0.5% alginate medium and 0.5% yeast extract medium.  Each chip measures the expression level of  genes from Sphingomonas. sp A1.

first: Chie

last: Hayashi

first: Yukie

last: Maruyama

first: Kousaku

last: Murata


title: Comparative Transcriptional Profiling of Human Merkel cells and Merkel Cell Carcinoma

status: Public on Jan 01 2014

city: Rennes

first: Nicolas

last: Mouchet

state: Bretagne

address: 2 Av du Professeur Leon Bernard

department: Institut genetique et developpement de Rennes

institute: CNRS UMR6290

summary: Merkel cell carcinoma is supposed to be derived from Merkel cells after infection by Merkel cell polyomavirus (MCPyV) and other poorly known events. A transcriptional profiling with cDNA microarrays was performed on cells from MCPyV(+) Merkel cell carcinomas and isolated normal Merkel cells. This microarray revealed numerous significantly upregulated genes and downregulated genes. The extensive list of genes identified in these experiments provides a large body of potentially valuable information of Merkel cell carcinoma carcinogenesis and could represent a source of potential targets for cancer therapy.

overall_design: Three-condition experiment: MCPyV(+), MCPyV(-) and Normal Merkel Cells. Biological replicates: 4 MCPyV(+) and 1 MCPyV(-)(Cy5), 1 control = pool of Normal Merkel cells from 3 liftings (Cy3).


title: Immunoprecipitation from rat kidney with 8-oxoguanine

status: Public on Jan 13 2014

city: Higashi-ku, Fukuoka

first: Minako

last: Yoshihara

state: Fukuoka

address: 3-1-1 Maidashi

department: Division of Bioinformatics

institute: Medical institute of Bioregulation, Kyushu University

summary: 8-oxoguanine (8-oxoG) is one of the most common DNA lesions generated by reactive oxygen species. Here we show the genome-wide distribution of 8-oxoG by coupling immunoprecipitation by antibodies specific for the DNA fragments containing 8-oxoG with microarray that covers rat genome. Genome-wide mapping of 8-oxoG in rat kidney reveals that 8-oxoG preferentially located at gene deserts and depleted in genic regions. We did not observe the difference in 8-oxoG level between highly- and lowly-expressed groups of genes, may be because of the low level of 8-oxoG in genic regions in general comparing to gene deserts. Rather, the distribution of 8-oxoG highly correlates with the distribution of lamina associated domains (LADs), suggesting that the spatial location of the genomic regions in the nucleus is the major determinant for the susceptibility to oxidative modifications. One possible explanation for the enrichment of 8-oxoG in LADs is that the nuclear periphery is more susceptible to the oxidative damage coming from outside the nucleus. Another explanation is that LADs take rather compact conformation, which might prevent  the recruitment of the repairing complex to the modified bases.

overall_design: Normal condition. Biological replicate 2

first: Mikita

last: Suyama

first: Shinya

last: Toyokuni


title: Effect of erythropoietin on primed leukocyte expression profile

status: Public on Dec 19 2013

city: Chieti

first: Mirko

last: Pesce

address: Via Vestini

institute: University G. D'Annunzio

summary:
Resistance to erythropoietin (EPO) treatment is observed in a considerable proportion of anemic patients with chronic kidney disease. Previous reports suggest that inflammation is one of the major independent predictors of this resistance, and pro-inflammatory cytokines have been shown to inhibit erythropoiesis. The aim of this study was to investigate EPO-induced modification to gene expression in primary cultured leukocytes.
Microarray experiments were performed on ex vivo Peripheral Blood Mononuclear Cells (PBMCs) from pooled ten healthy donors (n=9), primed or not with TNF-alpha, and treated with recombinant human erythropoietin alpha (EPO-alpha). Real-time PCR experiments were used to validate expression of the molecular targets considered most relevant for inflammation.
Data analysis suggested that EPO-alpha treatment mainly modulated genes involved in cell movement and cell-cell interaction in primed PBMCs. Notably, EPO-alpha exerts anti-inflammatory effects inhibiting the expression of pro-inflammatory cytokine IL-8 and its receptor CXCR2; by contrast, EPO-alpha further increases expression of genes relating to promotion of inflammation encoding for IL-1beta and CCL8, and induces de novo synthesis of IL-1alpha, CXCL1 and CXCL5 in primed PBMCs. MAPK p38alpha?reducing activity is involved in modulation of IL-1beta and IL-8 expression.
In conclusion, our findings confirm the anti-inflammatory role for EPO, but also suggest a plausible in vivo scenario, in which the positive correlation found between EPO-resistance and elevated levels of some pro-inflammatory mediators is due to treatment with EPO itself. One future objective will be to perform in vivo measurement of the molecular targets highlighted, in order to identify any additional markers involved in EPO-resistance among hypo-responsive patients.

overall_design: In this study, we analyzed the expression profiles of pooled blood PBMCs from 10 healthy donors primed or not with TNF-alpha and then treated with EPO-alpha. All RNAs from no stimulated PBMCs were hybridized against RNAs from PBMCs treated with TNF-alpha or TNF-alpha and EPO-alpha. We performed a total of 9 technical replicates.

first: Paolo

last: Felaco

first: Sara

last: Franceschelli

first: Lorenza

last: Speranza

first: Alfredo

last: Grilli

first: Maria

last: De Lutiis

first: Alessio

last: Ferrone

first: Vittorio

last: Sirolli

last: Bonomini

first: Antonia

last: Patruno


title: Gene expression comparison of L. reuteri DSM 17938 and pocR mutant

status: Public on Jan 24 2014

city: Houston

first: Toni-Ann

last: Mistretta

state: TX

address: 1 Baylor Plaza, BCM 315

department: Pathology

institute: Baylor College of Medicine

summary: Comparison of gene expression between L. reuteri DSM 17938  and L. reuteri DSM 17938::pocR mutant grown in semi-defined medium after 24h of growth at 37C in anaerobic condition.  PocR is an AraC-like transcriptional regulator, and changes in gene expression between mutant and wild-type strains would indicate genes involved in the PocR regulon.

overall_design: Includes 3 biological replicates and dye-swaps for DSM 17938  versus pocR mutant. One sample includes total RNA isolated from wildtype DSM 17938 labeled with either cy3 or cy5, and total RNA isolated from the pocR mutant labeled with the opposite dye.  Samples 1, 2, and 3 represent biological replicates.  Samples 4, 5, and 6 represent dye-swaps of the same biological replicates.

first: Jennifer

last: Spinler


title: Towards in vivo regulatory kinetics: PurR activation by PRPP during purine depletion in Lactococcus

status: Public on Dec 01 2013

city: Hørsholm

first: Christian

middle: Bille

last: Jendresen

address: Kogle Allé 6

country: Denmark

institute: Technical University of Denmark

summary:
Short-term adaptation to changing environments relies on regulatory elements translating changing metabolite concentrations into a specifically optimized transcriptome. So far the focus of analyses has been divided between regulatory elements identified in vivo and kinetic studies of small molecules interacting with the regulatory elements in vitro. Here we describe how in vivo Regulatory Kinetics can describe a regulon through the effects of the metabolite controlling it, exemplified by temporal purine exhaustion in Lactococcus lactis. We deduced a causal relation between the pathway precursor 5-phosphoribosyl-1-pyrophosphate (PRPP) and each individual mRNA levels, whereby  unambiguous and homogenous relations could be obtained for PurR regulated genes, thus linking a specific regulon to a specific metabolite. As PurR activates gene expression upon binding of PRPP, the pur mRNA curves reflect the in vivo kinetics of PurR PRPP binding and activation. The method singled out the xpt-pbuX operon as kinetically distinct, which was found to be caused by a guanine riboswitch whose regulation was overlaying the PurR regulation. The strategy outlined here can be adapted to analyze the individual effects of members from larger metabolomes in virtually any organism, for elucidating regulatory networks in vivo.
Agilent 8x15k custom microarrays

sample_organism: Lactococcus cremoris subsp. cremoris MG1363

overall_design: Fifteen samples from two cultures were taken in a time-course experiment.

middle: B

first: Peter

last: Dimitrov

first: Laurent

last: Gautier

first: Meng

last: Lui

first: Jan

last: Martinussen

first: Mogens

last: Kilstrup


title: Effects on expression profile of acute congestive heart failure (ACHF) patients monocytes by treatment with conventional drugs.

status: Public on Oct 31 2013

first: Mirko

last: Pesce

summary: Several studies have shown the importance of immune and inflammatory mediators in the pathogenesis of heart failure. In clinical practice has been observed that many conventional drugs can modulate circulating levels of these mediators. Despite, there is poor understanding of the precise mechanisms of these drugs in regulating immune and inflammatory systems. Blood monocytes were isolated from 6 hospitalized patients in Intensive Cardiology Care Unit (ICCU) with symptomatic acute congestive heart failure (ACHF) (NYHA Class III-IV) before and after treatment with conventional drugs (ARBs, ACEIs, diuretics, and beta-blockers). Gene expression analysis (n=11) using whole human genome microarray showed that pharmacological treatment abrogate inflammatory activation of monocytes. The inflammatory response network constructed with Ingenuity Pathway Analysis (IPA) indicates the “TNFR1 signaling” as the most significantly modulated after pharmacological treatment and the pro-inflammatory cytokine TNF-alpha associated with more than a fifth of genes considered.

overall_design: In this study, we analyzed the expression profiles of 6 biological replicates of blood monocytes from ACHF patients pre- and post-treatment with conventional drugs (ARBs, ACEIs, diuretics, and beta-blockers). All RNAs from pre-treatment monocytes were hybridized against RNAs from post-treatment RNAs. We performed a total of 11 technical replicates.

first: Sabina

last: Gallina

first: Graziano

last: Riccioni

first: Mario

last: Felaco


title: Expression array analysis of myotonic dystrophy type 2 (DM2) muscle biopsies versus controls

status: Public on May 04 2014

city: Helsinki

first: Mark

middle: Andrew

last: Screen

address: Biomedicum1, Haartmaninkatu 8

department: Dpt. of Medical Genetics

country: Finland

institute: Folkhälsan Institute of Genetics, University of Helsinki

summary: The hypothesis was that different genes are abnormally expressed in DM2 biopsies compared to controls.

overall_design: Total RNA was obtained from DM2 vastus lateralis biopsies and compared to vastus lateralis control biopsies.


title: Metabolic engineering of Corynebacterium glutamicum for L-arginine production

status: Public on Nov 26 2013

city: Daejeon

first: Hyun Uk

last: Kim

state: Republic of Korea

address: 291 Daehak-ro

country: South Korea

institute: KAIST

summary: Metabolically engineered Corynebacterium glutamicum strains were constructed for the enhanced production of L-arginine, and their gene expression profiles were investigated

overall_design: Gene expression profiles of two C. glutamicum strains AR2 and AR6 were examined for the 3043 genes twice.

first: Seok

middle: H

last: Park

first: Hyun

middle: U

first: Tae

first: Jun

first: Suok-Su

first: Sang

last: Lee


title: An Immunosignature system for diagnosis of cancer [Cancer immunosignaturing - test 1]

status: Public on Dec 15 2013

city: Phoenix

first: Phillip

last: Stafford

address: 1001 S. McAllister

institute: Biodesign Institute

summary: This dataset contains peptide array information from 120 patients from 5 different cancer types using classic blinded test/train method.  This array is library 1 (GPL17600).

overall_design: A 1:500 dilution of human serum is added to a peptide array (GPL17600).  This array is a two-up design, with 10420 peptides printed on the top and bottom of a standard glass microscope slide.  Samples were run in duplicate.  The average of the duplicates are listed here.  20 train and 20 blinded test samples were run.

first: Cichacz

last: Zbigniew

first: Stephen

last: Johnston


title: An Immunosignature system for diagnosis of cancer

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

overall_design: Refer to individual Series


title: Inhibition of the PI-PLC by U73122

status: Public on Sep 01 2013

city: evry

first: Soubigou-Taconnat

last: Ludivine

address: 2 rue gaston crémieux

department: URGV

institute: INRA

summary:
au13-01_pi-plc
What are the genes that are regulated by basal PI-PLC?
Arabidopsis thaliana cells in suspension (5-days old). Cultivated in environment (middle) Gamborg+2,4-D. Added inhibitors 4 hr before extraction of the RNAs.
We try to determine the role of phospholipases C ( PI-PLC) in the control of the basal expression of the genes of suspension of Arabidopsis thaliana. A first experience in which we used the edelfosine as inhibitor allowed us to identify numerous genes the basal expression of which is altered by this inhibition. We want to confirm these results with another inhibitor.

overall_design: 4 dye-swap - treated vs untreated comparison - treatment variations

first: Sandrine

last: Balzergue

first: Ludivine

last: Taconnat

first: Eric

last: Ruelland

first: Marie-Laure

last: Martin-Magniette


title: Epe1 recruits the BET family bromodomain protein Bdf2 to establish heterochromatin boundaries

status: Public on Sep 24 2013

city: New York

first: Songtao

last: Jia

state: NY

address: 1114, Fairchild center

institute: Columbia University

summary: Heterochromatin spreading leads to the silencing of genes within its path, and boundary elements have evolved to constrain such spreading. In fission yeast, heterochromatin at centromeres I and III is flanked by inverted repeats termed IRCs, which are required for proper boundary functions. However, the mechanisms by which IRCs prevent heterochromatin spreading are unknown. Here, we identified Bdf2, homologous to the mammalian BET family of double bromodomain proteins involved in diverse types of cancers, as a factor required for proper boundary function at IRCs. Bdf2 is enriched at IRCs through its interaction with the boundary protein Epe1. The bromodomains of Bdf2 recognize acetylated histone H4 tails and antagonize Sir2-mediated deacetylation of histone H4K16 to prevent heterochromatin spreading. Our results thus illustrate a mechanism of establishing chromosome boundaries at specific sites through the recruitment of a factor that protects euchromatic histone modifications. They also reveal a previously unappreciated function of H4K16 acetylation, which cooperates with H3K9 methylation to regulate heterochromatin spreading.

overall_design: Two samples, H4K16ac & Bdf2-Flag

first: Jiyong

last: Wang


title: An Immunosignature system for diagnosis of cancer [Cancer immunosignaturing - test 2]

summary: This dataset contains peptide array information from 1516 patients from 12 different cancer types, 2 infectious diseases, and healthy controls using leave one out cross validation.  This array is library 2 (GPL14921).

overall_design: A 1:500 dilution of human serum is added to a peptide array (GPL14921).  This array is a one-up design, with 10286 peptides printed in duplicate on a standard glass microscope slide.  1516 patients samples from 14 different diseases and 1 control cohort were analyzed


title: Comparing the transcriptome of SP cells with that of non-SP cells in rainbow trout

status: Public on Aug 06 2013

city: Minato-ku

first: Makoto

last: Hayashi

state: Tokyo

address: Konan 4-5-7

department: Department of Marine Biosciences

institute: Tokyo University of Marine Science and Technology

summary: In rainbow trout, type A spermatogonia can be split into SP cells and non-SP cells by the ability to exclude Hoechst 33342 dye (H33342). The H33342 fluorescence of SP cells are lower than that of non-SP cells, after H33342 staining. To investigate whether SP cells were transcriptomically distinct from non-SP cells, we compared the transcriptome of these cells. We used fluorescence-activated cell sorting (FACS) to isolate SP cells and non-SP cells from the type A spermatogonia in rainbow trout.

overall_design: To compensate unavailability of genetically uniform rainbow trout in independent sampling, SP cells and non-SP cells were collected at 3 times from 3 different parental fish groups. This experimental design allowed us to estimate effects specific to each parental fish genotype on mRNA expression in SP cells by a statistical modeling and to exclude the effects in subsequent analysis.

first: Masanao

last: Sato

first: Satoru

last: Kobayashi

first: Goro

last: Yoshizaki


title: Expression analysis of Kasumi-1 cells treated with or without FTY720

city: Shanghai

first: Junyan

last: Lu

state: Shanghai

address: 555 Zuchongzhi Road, Zhangjiang High Tech Park

department: Drug Discovery and Design Center

institute: Shanghai Institute of Materia Medica, Chinese Academy of Sciences

summary: The clinical outcomes of M2 subtype Acute Myeloid Leukemia (AML-M2) with t(8;21) are poor. Here we report that FTY720 (Fingolimod), a sphingosine analogue and an FDA approved drug for treatment of multiple sclerosis, showed great antitumorigenic activity against Kasumi-1 cell line, xenograft mouse model and  leukemic blasts isolated from AML-M2 with t(8;21) patients. Primary investigation indicated that FTY720 caused cell apoptosis through caspase and protein phosphatase 2A (PP2A) activation. Transcriptomic profiling further revealed that FTY720 treatment could upregulate AML1 target genes and interfere with genes involved in ceramide synthesis. FTY720 treatment led to the elimination of AML1-ETO oncoprotein and caused cell cycle arrest. More importantly, FTY720 treatment resulted in rapid and significant increment of pro-apoptotic ceramide levels, determined by HPLC-ESI-MS/MS (high-performance liquid chromatography-electrospray ionization tandem mass spectrometry) based lipidomic approaches. Additionally, structural simulation model indicated that the directly binding of ceramide to inhibitor 2 of PP2A (I2PP2A) could reactivate PP2A and cause cell death. This study demonstrates, for the first time, that accumulation of ceramide plays a central role in FTY720 induced cell death of AML-M2 with t(8;21). Targeting sphingolipid metabolism by using FTY720 may provide novel insight into drug development for AML-M2 treatment.

overall_design: A six chip study using total RNA recovered from three separate cultures of DMSO-treated Kasumi-1 cells and three separate cultures of FTY720-treated Kasumi-1 cells.Each chip measures the expression level of genes from DMSO-/FTY720-treated Kasumi-1 cells.

first: Limin

last: Chen

first: Liu-Fei

last: Luo

first: Lianchun

last: Li

first: Yuan-Fang

last: Liu

first: Jiang

first: Hong

first: Heng

last: Song

first: Hualiang

last: Jiang

first: Cheng

first: Keqin


title: Going Wireless: Fe(III) Oxide Reduction without Pili in Geobacter sulfurreducens Strain JS-1

status: Public on Jun 18 2013

city: Amherst

first: Jessica

middle: Amber

last: Smith

address: 203 Morrill Science Center IVN

department: Microbiology

institute: UMASS Amherst

summary: The conductive pili of Geobacter sulfurreducens are essential for optimal extracellular electron transfer to Fe(III) and long-range electron transport through current-producing biofilms. The KN400 strain of G. sulfurreducens reduces poorly crystalline Fe(III) oxide more rapidly than the more extensively studied DL-1 strain. Deletion of the gene for PilA, the structural pilin protein, in strain KN400 inhibited Fe(III) oxide reduction. However, slow rates of Fe(III) reduction were detected after extended (> 30 days) incubation in the presence of Fe(III) oxide. After seven consecutive transfers the PilA-deficient strain adapted to reduce Fe(III) oxide as fast as the wild type. Microarray, proteomic, and gene deletion studies indicated that this adaptation was associated with greater production of the c-type cytochrome PgcA, which was released into the culture medium. It is proposed that the extracellular cytochrome acts as an electron shuttle, promoting electron transfer from the outer cell surface to Fe(III) oxides. The adapted PilA-deficient strain competed well with the wild-type strain when both were grown together on Fe(III) oxide. However, when 50% of the culture medium was replaced with fresh medium every three days, the wild-type strain out-competed the adapted strain. A possible explanation for this is that the necessity to produce additional PgcA, to replace the PgcA continually removed, put the adapted strain at a competitive disadvantage, similar to the apparent selection against electron-shuttling producing Fe(III) reducers in most soils and sediments. Despite increased extracellular cytochrome production, the adapted PilA-deficient strain produced low levels of current; consistent with the concept that long-range electron transport through G. sulfurreducens biofilms cannot be achieved without PilA-pili.

overall_design: An eight-chip study using total RNA recovered from four separate cultures of Geobacter sulfurreducens JS-1 (experimental condition) or Geobacter sulfurreducens KN400 (control condition) grown with acetate (10mM)-Fe(III) oxide (100 mmol l-1) exponential growth. Each chip measures the expression level of 3,328 genes from Geobacter sulfurreducens KN400 with nine 45-60-mer probe pairs (PM/MM) per gene, with three-fold technical redundancy.

middle: A

first: Pier-Luc

last: Tremblay

first: Kelly

last: Nevin

first: Derek

last: Lovley


title: Targeted inhibition of three human breast cancer cell lines as model systems of ERBB2-positive breast cancer

status: Public on Aug 22 2013

city: Heidelberg

first: Ulrike

last: Korf

address: Im Neuenheimer Feld 580

department: Molecular Genome Analysis

institute: German Cancer Research Center


title: Staphylococcus aureus SH1000 compared to SH1000 ΔthyA

status: Public on May 29 2013

city: Muenster

first: Jochen

last: Seggewiss

address: Roentgenstr. 21

department: Integrated Functional Genomics

institute: University of Muenster

summary: Staphylococcus aureus thymidine-dependent small-colony variants (TD-SCVs) are frequently isolated from patients with chronic S. aureus infections after long-term treatment with trimethoprim-sulfamethoxazole (TMP-SMX). In TD-SCVs, mutations of thymidylate synthase (thyA, TS), essential for DNA synthesis, occur. However, it has never been shown, that TMP-SMX is responsible for the induction and selection of TD-SCVs. Short-term exposure of TMP-SMX induced the TD-SCV phenotype morphologically as shown in transmission electron-microscopy and on the transcriptional level by qRT-PCR in wild-type S. aureus, while selection of TD-SCVs with thyA mutations occurred only rarely after long-term exposure. In reversion experiments with clinical TD-SCVs, all revertants revealed compensating mutations at the initially identified mutation site. Whole DNA microarray analysis of a thyA deletion mutant (∆thyA), which exhibited the typical TD-SCV phenotype, identified tremendous alterations compared to the wild-type. Important virulence regulators such as agr, arlRS, sarA and major virulence determinants including hla, hlb, sspA, sspB and geh were down-regulated, while genes associated with the colonization capacity like fnbA, fnbB, spa, clfB, sdrC and sdrD were up-regulated. The expression of genes involved in pyrimidine and purine metabolism as well as in nucleotide interconversion changed significantly. The ∆thyA-mutant was attenuated in virulence in both, a Caenorhabditis elegans killing model and an acute murine pneumonia model. Furthermore, competition experiments in vitro and in vivo (using a chronic pneumonia mouse model) revealed a survival and growth advantage of the ∆thyA-mutant under low thymidine conditions and TMP-SMX exposure. In conclusion, our results clearly show for the first time that TMP-SMX induces the TD-SCV phenotype after short-term exposure in S. aureus and that long-term exposure selects thyA mutations providing an advantage for TD-SCVs under specified conditions. Thus, our results help to understand the dynamic processes of induction and selection of S. aureus TD-SCVs during TMP-SMX exposure.

overall_design: 18 independent samples were analysed; for each isolate and time point 3 replicates were performed

first: Andre

last: Kriegeskorte

last: Seggewiß

first: Cathrin

last: Baum

first: Claudia

last: Neumann

first: Karsten

last: Becker

first: Georg

last: Peters

first: Barbara

last: Kahl


title: Gene expression profiles of tumor and paired normal lung tissues from primary non-small cell lung cancer (NSCLC) patients in Taiwan.

status: Public on May 15 2013

city: Tainan

first: Yi-Ching

last: Wang

address: No.1, University Road, Tainan 70101, Taiwan, R. O. C.

department: Department of Pharmacology, College of Medicine

country: Taiwan

institute: National Cheng Kung University

summary: Genome-wide expression profiling of NSCLC patients were done using Phalanx Human OneArray chip. The surgically resected tumor tissue and corresponding normal tissue were collected from 21 patients diagnosed with primary NSCLC admitted to Taipei Veterans General Hospital, Taiwan.

overall_design: In this study, we used cDNA microarray to detect gene expression profiling in tumor and corresponding normal samples from 21 NSCLC patients. There were 11 AD patients and 10 SQ patients. The patients consisted of 10 early stage patients (stages I and II) and 11 late stage patients (stages III and IV). Hybridization targets were prepared from total RNA and hybridized according to standard protocol using Phalanx Human OneArray chip (32,050 total features: 30968 human genome probes and 1082 experimental control probes).

first: Jer-Wei

last: Chang


title: Three-stage continuous culture system with a self-generated anaerobia to study the regionalized metabolism of the human gut microbiota

status: Public on May 07 2013

city: Clermont-Ferrand

first: william

last: tottey

address: 28 place Henry Dunant

institute: EA-CIDAM 4678

summary: A three-stage continuous fermentative system was developed to simulate and control physicochemical factors of the gut biology. Inoculation was of each reactor was performed from a human fecal sample which was initially amplified with a batch procedure. Samples from the initial feces, the batch and from the bioreactors media were collected to extract bacterial DNA. 16S PCR amplification was performed to assess the microbial diversity at the family level using the HuGChip. Amplified DNA was purified and labelled with either Cy3 or Cy5 dye and hybridized on the microarray.

overall_design: A 5 chip study was realized, each corresponding to hybridization with 250ng of labelled 16S rRNA gene amplicons from either the initial stool, the batch inoculum or fermentative medium different compartments of the simulated colon (Proximal, Transversal and Distal). Each probe (4441) was synthetized in three replicates.

first: David

last: Feria-Gervasio

first: William

last: Tottey

first: Nadia

last: Gaci

first: Monique

last: Alric

first: Jean-Michel

last: Cardot

first: Pierre

last: Peyret

first: Jean-Francois

last: Martin

first: Estelle

last: Pujos

first: Jean-Louis

last: Sebedio

first: Jean-François

last: Brugère


title: C. elegans gonad-ablated (Z1-,Z4-) animals versus intact animals, N2 strain

status: Public on Mar 01 2013

city: Ipswich

first: Amit

last: Sinha

address: 240 County Road

institute: New England Biolabs

summary: Transcriptional profiling of C. elegans germline-ablated worms versus unablated intact animals, N2 strain

overall_design:
One-condition experiment.
C. elegans gonad-ablated versus intact N2. 3 biological replicates, including 1 dye-swap.

first: Robbie

last: Rae


title: Dysregulation of pathways involved in the processing of cancer and microenvironment information in MCA+TPA transformed C3H/10T1/2 cells

status: Public on Apr 26 2013

city: Lucknow

first: Dr Sushil

last: Kumar

state: Uttar Pradesh

address: M G Marg

department: Environmental Carcinogenesis

country: India

institute: Indian Institute of Toxicology Research

summary:
The two-stage cell transformation assay is an in
vitro model cell culture system to identify the ability of
chemicals to act as initiators or promoters of cell transforma-
tion and also to study the cellular and molecular mechanisms
of chemically induced morphological and neoplastic cell
transformation. The global gene expression profiles of 3-
methylcholanthrene (MCA)+12-O-tetradecanoylphorbol-13-
acetate (TPA)-transformed C3H/10T1/2 cells are not known.
Therefore, we have investigated the global transcriptional
profile of MCA+TPA-transformed C3H10T1/2 cells using
an 8×60 k probe microarray. The study revealed a differential
regulation of pathways and gene expressions. Multifold
dysregulation was seen in pathways of cancer, phagosomal
activity, and tumor cell microenvironment information pro-
cessing systems, notably the neuroactive ligand–receptor in-
teraction, actin cytoskeleton regulation, tight junction, axon
guidance, and cell adhesion molecules. The genes FGF1,
EIF4E1B, MAGI1,and GRIA3 showed upregulation; these
encoded the pluripotent fibroblast growth factor, the transla-
tion initiation factor, the tight junction scaffolding protein, and
the antiapoptotic as well as the enhancer of proliferation and
migration, respectively. The genes CXCL7/CXCL5/CXCL12,
H2DMB1,and HSPA1A showed downregulation; these
encoded the chemotactic agent protein, the protein involved

overall_design:
Total mRNA was isolated from the control as well as the
MCA+TPA-transformed C3H/10T1/2 cells and complemen-
tary RNA (cRNA) was prepared from mRNA (1 μg). One-
color microarray processing was performed. Acceptable qual-
ity of the total RNA sample was ascertained by its electropho-
resis trace and integrity assay using a Bioanalyzer which
profiled RNA by RIN interpretation. The T7 promoter-based
linear amplification was used to generate labeled complemen-
tary RNA to amplify target material and incorporate cyanine
3-labeled CTP using Agilent’s low-input RNA linear amplifi-
cation kit one color (cat no. 5188-5339). The fluorescence-
labeled cRNA samples were hybridized onto a Genotypic-
designed Custom Whole Genome Mouse 8x60k slide
(AMADID no. 26986) in duplicate using Agilent’sinsitu
hybridization kit (no. 5184-3568). Hybridization was carried
out in Agilent’s Surehyb Chambers at 65°C for 16 h. The
hybridized slides were washed using Agilent Gene Expression
wash buffers (part no. 5188-5327). Fluorescence data were
collected using an Agilent Microarray Scanner (G2567AA)
and analyzed with program Gene Spring GX, version 11.5
(Agilent Technologies, Bangalore, India). Significantly
dysregulated genes were identified. Statistical t test p value
was calculated based on volcano plot using Gene spring GX
Software.

first: shivam

last: priya

first: sushil

last: kumar