title: Differentially expressed miRNAs between Alzheimer's disease and control mice's hippocampus

status: Public on Sep 19 2013

city: Beijing

first: Subi

last: Wei

state: Beijing

address: Xueyuan Load

department: Medical Systems Biology Research Center

country: China

institute: Tsinghua university

summary: MicroRNAs influence restorative physiological or degenerative pathological processes in several neurological disorders, yet their role in Alzheimer’s disease remains unclear. Here we compared microRNAs expression in the period of AD pathogenesis when mice first begin to have detectable extracellular Aβ deposition. Tg2576 mice aged 9-10 months and their wild type littermates, as well as a double transgenic model of AD, APP/ PS1M146V/+  and wild type C57BL/6J mice both at 3-4 age months (n=3) were used. Hippocampus tissue miRNAs were detected by hybridization to microarrays having 924 mammalian miRNA probes.The result indicated that some of the deregulated miRNAs in AD mice have been implicated in amyloid beta production.

platform_organism:
Homo sapiens
Mus musculus
Rattus norvegicus

overall_design: AD mice vs. control mice

first: Kai

last: Gong


title: Steady-state samples of Methanococcus maripaludis MM901:del_fruA (MMP1382)-del_frcA (MMP0820)

status: Public on Sep 16 2013

city: Seoul

first: Sung Ho

last: Yoon

address: 120 Neungdong-ro, Gwangjin-gu

department: Department of Bioscience and Biotechnology

country: South Korea

institute: Konkuk University

type: Expression profiling by genome tiling array

summary: Effects of fruA (MMP1382) and frcA (MMP0820) on physiology and regulation of methanogenesis in Methanococcus maripaludis

overall_design: The strain was grown by continuous culture in a one-liter fermenter (New Brunswick Scientific, Edison, NJ) at 37°C (FEMS Microbiol Lett 238: 85-91, 2004). Medium and gas compositions were modified from those for non-limiting conditions (BMC Microbiol 9: 149, 2009). The standard gassing regime was 110 mL/min H2, 40 mL/min CO2, 35 mL/min Ar, and 15 mL/min H2S/Ar mixture (1:99). Hydrogen limited condition was 22 mL/min H2. After the OD increased above 0.6 (24 h), the medium flow was turned on at 0.083 L/h. Medium was either phosphate limiting (0.12 mM K2HPO4) or phosphate excess (0.8 mM K2HPO4). Culture samples (1.5 mL) were rapidly removed from the vessels by syringe and cell pellets collected by microcentrifugation, immediately frozen in an ethanol-dry ice bath, and stored at -80°C.  Total RNA from each sample was compared against a reference RNA pool that was generated in bulk from a mid-log phase culture of MM901. Total RNA from samples and reference were directly labeled with Cy3 or Cy5, and were hybridized to the tiling array. After hybridization and washing according to array manufacturer's instructions, the arrays were scanned by Microarray Scanner (Agilent Technologies, Santa Clara, CA). Dye-flip experiments were done for each sample.

first: Sung-Ho

first: June

last: Burn

first: Min

last: Pan

first: John

middle: A

last: Leigh

first: Nitin

middle: S

last: Baliga


title: Expression analysis of Yarrowia lipolytica Y4184 snf1 mutant

status: Public on Sep 25 2013

city: Wilmington

first: Seung-Pyo

last: Hong

state: DE

address: Experimental Station, E328/B47B

department: BCS&E

country: USA

institute: DuPont Central Research and Development

summary: Investigation of whole genome gene expression level changes in a Yarrowia lipolytica Y4184 snf1 mutant, compared to the Y4184U+.  The Y4184 is an engineered strain to produce eicosapentaenoic acid (EPA) via expression of a Δ9 elongase/Δ8 desaturase pathway, and is derived from Yarrowia lipolytica ATCC#20362.

overall_design: A six chip study using total RNA recovered from three separate cultures of Yarrowia lipolytica Y4184Ura+ strains and three separate cultures of Y4184 snf1 mutant strains in which YlSNF1 gene is deleted entirely.  Each chip measures the expression level of 6708 genes from Yarrowia lipolytica ATCC#20362 with fourteen 24-mer probe pairs (PM/MM) per gene, with three-fold technical redundancy.

last: Seip

first: Hongxian

last: He

first: Raymond

last: Jackson

first: Quinn

last: Zhu


status: Public on Sep 23 2013

city: Tsukuba

first: Nobutaka

last: Mitsuda

state: Ibaraki

address: Central 6 Higashi 1-1-1

department: Bioproduction Research Institute

country: Japan

institute: National Institute of Advanced Industrial Science and Technology

summary: Antirrhinum R2R3 MYB transcription factor MIXTA is known to regulate epidermal cell outgrowth in petal. Arabidopsis has three MIXTA-like proteins NOECK(NOK)/MYB106, MYB16 and MYB17 and nok mutant exhibits over-branched trichomes in rosette leaves. On the other hand, Arabidopsis AP2/ERF transcription factor WAX INDUCER1/SHINE1 is well known to induce cuticle development. Here, we report the transcriptional cascade of MYBs-WIN/SHNs coordinately regulates the epidermal cuticle development.  The constitutive expression of MYB106 chimeric repressor, in which strong repression domain was fused with MYB106 (35S:MYB106SRDX), induced cuticle deficiency characterized by organ adhesion, reduction of epicuticular wax crystals and staining by toluidine blue in broad region of aerial parts in addition to the over-branched trichomes. Most these phenotypes were partially reproduced in T-DNA knockout plants and also similarly induced by the chimeric repressors of WIN1/SHINE1(SHN1), SHN2 and SHN3, which are AP2/ERF transcription factors previously shown as positive regulators of cutin. Microarray experiments revealed that MYB106SRDX and WIN1SRDX plants have similar transcriptomes, in which the expression of wax and cutin biosynthetic genes was suppressed. Conversely, VP16-fused MYB106 which has high activation ability induced ectopic production of cutin nanoridges in the transgenic plants and enhanced the reporter driven by promoters of WIN1 and wax-related genes in transient expression assay. These results suggest that  MIXTA-like proteins regulate cutin biosynthesis partially via WIN1 and directly regulate wax accumulation as well as their known roles in epidermal cell differentiation.

overall_design: Transcriptomes of 35S:MYB106SRDX, 35S:WIN1SRDX and wild-type Arabidopsis seedling were compared.

first: Oshima

last: Yoshimi

first: Mitsuda

last: Nobutaka

first: Ohme-Takagi

last: Masaru


title: Transcriptomes of 35S:WIN1 and vector-control Arabidopsis seedling

overall_design: Transcriptomes of 35S:WIN1and vector-control Arabidopsis seedling were compared.


title: Expression data of Xrx1 gain and loss of function experiments from early Xenopus laevis embryos (stage 13)

city: Pisa

first: Massimiliano

last: Andreazzoli

address: SS.12 Abetone e Brennero, 4

country: Italy

institute: University of Pisa

summary:
Eye development is a multistep process that requires specific inductive signals and precise morphogenetic movements, starting early during development in the eye-field, a well-definite region of the anterior neural plate. It has been demonstrated that a gene network of eye field transcription factors (EFTFs) contributes to specify the neural and retinal fate of the eye field. Among these EFTFs, Xrx1 is involved in proliferation and neurogenesis in the eye field and is necessary for the correct development of the retina.
By means of Affymetrix microarrays, a high throughput screening was performed, looking for genes that can mediate the function of Xrx1, by comparison of the expression profiles of whole embryos in which the Xrx1 function was either overexpressed or abolished by use of morpholino antisense oligonucleotides.

overall_design: Xenopus laevis embryos were harvested soon after fertilization. 50ng of capped Xrx1 mRNA or 0.5pmol of MoXrx1 antisense oligonucleotides were coinjected with 400ng of GFP synthetic mRNA as a tracer, in both dorsal blastomeres of 4-cells stage embryos. Embryos were let to develop until stage 13, in which the eye field induction steps are active, and selected for correct injection site by fluorescence topographic assessment. RNA was extracted from each single embryo and control PCRs were performed to assess the correct molecular signature of Xrx1 loss- and gain- of function.

first: Guido

last: Giudetti


title: SAGE analysis reveals variation in midgut transcriptomes of dengue-2 susceptible and refractory Aedes aegypti mosquitoes

status: Public on Sep 30 2013

city: NOTRE DAME

first: David

last: Severson

state: IN

address: 138 GALVIN LIFE SCIENCE CENTER

department: Department of Biological Sciences

institute: University of Notre Dame

summary: Oral susceptibility of Aedes aegypti mosquitoes to dengue viruses varies between different Aedes species and strains. However, the midgut-specific transcriptional profile that may produce this variation is presently obscure and was the subject of our investigation. The variation in active expression between dengue-2 susceptible (SUS) and refractory (REF) mosquitoes was investigated during the first critical 96 hours after infection Transcriptional profiles were mined from respective guts using the serial analysis of gene expression technique (SAGE) and libraries constructed from midguts obtained from mosquitoes that received a dengue-2 infected blood meal (DENV-2), a non infected blood meal (naive) or a 5% sucrose meal (SM). Here we report that variation between DENV-2 infected libraries versus respective naïve libraries revealed very few transcripts that were common and statistically significant in DENV-2 infected libraries. In addition, the expression profiles among libraries displayed up regulation of antisense transcripts especially in the SUS strain. A strong proclivity towards strain-specificity in differential expression was observed, which suggested an exclusive transcription that is likely up-regulated after DENV-2 infection

overall_design: Thirty Aedes aegypti female mosquitoes aged 4-5 days were transferred to 500 ml paper cups and offered a 5% sucrose meal (SM), a naïve blood meal or a dengue-2 (JAM 1409 strain) infectious blood meal, using standard artificial membrane feeders. Fully engorged females were isolated and maintained on a 5% sucrose solution ad libitum at 26oC and relative humidity till dissection

first: Irene

middle: N

last: Kasumba

first: Adam

last: Iwanicki

first: Neil

last: Lobo

middle: W


title: microRNA expression profile in human gliomas

status: Public on Sep 18 2013

city: Messina

first: Alfredo

last: Conti

state: Sicily

address: via La Farina 15

institute: Alfredo

summary: To investigate the regulatory mechanisms governing the malignant signature of different gliomas we analyzed microRNA expression profiles in human tumor samples of world health organization (WHO) grade I (benign tumors), II (low grade tumors) and IV (high grade tumors) and from primary cultures obtained from tumor samples of grade II and IV.     Patients   This study included tumor samples histologically verified as astrocytic gliomas obtained from patients who had undergone craniotomy for microsurgical tumor removal. According to the revised WHO classification, tumors were diagnosed as: grade I or pilocytic astrocytomas; grade II or diffuse fibrillary astrocytomas; grade IV or glioblastoma multiforme. Primary cell cultures from grade II and grade IV gliomas were also obtained and miRNA expression in these cultures were analyzed     RNA extraction  Total RNA, including small RNA, was isolated from tissue samples using the mirVanaTM miRNA Isolation Kit (Ambion) following the standard protocol. The quantity and quality of the purified RNA was evaluated by spectrophotometric analysis and electrophoresis on denaturing gel of acrylamide.   Multiplex Real-Time Quantitative Reverse-Transcriptase Polymerase Chain Reaction (RT-PCR)  The miRNAs were first converted to cDNA using Multiplex RT for TaqMan Array Human MicroRNA Panel. The RT Master mix included 100 mM each of dNTPs , 50 U/ml MultiScrabe reverse transcriptase (Applied Biosystems), 20 U/µl RNase inhibitor (Applied Biosystems) and 10X RT Buffer. The 10 µl reactions, including 7 µl of RT master mix, 2 µl of purified microRNA and 1 µl of Multiplex RT Human primer pool (Applied Biosystem), were incubated in ice for 5 min and then in a thermal cycler for 30 min at 16°C, 30 min at 42°C, 5 min at 85°C, and then hold at 4°C. miRNA levels were normalized to the expression of small nucleolar RNAs, RNU44, RNU48 and RNU6B. All reverse transcriptase reactions, including no-template controls and RT controls, were run in duplicate.   Real-time PCR was performed using a standard TaqMan PCR kit procedure on an “Real Time Fast 7900 HT” PCR System (Applied Biosystems). The 100 µl PCR included 50 µl RT product (before diluited 1:60) and 50 µl TaqMan Universal PCR Master Mix (2X) (Applied Biosystems). The total volume were loaded into Card TaqMan Low Density Array Human MicroRNA Panel (Applied Biosystem) including a total of 384 human microRNAs publicated on databases www.sanger.ac.uk. The reaction cards was runned at 50°C for 2 min and 95°C for 10 min, followed by 40 cycles of 97°C for 30s and 59,7°C for 1 min. All reactions were run in triplicate.   Analysis of data was performed using the SDS 2.3 software using the 2-∆∆Ct (relative quantitative) method . The ∆Ct of every miRNA was determined in relation to the endogenous control RNA U6 that was invariably expressed in all samples. The ∆∆Ct   value was determined in relation to the calibrator, namely the normal brain tissue. Resulting data were grouped according to the tumor grading e selectioned using a cut-off value of 3. Results were expressed as “fold change” over normal brain tissue.

overall_design: We analyzed two samples of grade I, two samples of grade II, two samples of grade IV gliomas. Four samples form norma brain were used as norma control. Primary cell cultures form grade II and grade IV samples were used for the analysis. All reverse transcriptase reactions, including no-template controls and RT controls, were run in triplicate.

first: AnnaMaria

last: Cama

first: M'hamed

last: Aguennouz


title: Differential expression of Dictyostelium discoideum AX2 upon infection with wt L. pneumophila JR32 vs. uninfected 6h p.i. (timecourse experiment)

city: Cologne

first: Ludwig

last: Eichinger

address: Joseph-Stelzmann-Strasse 52

country: Germany

institute: Institute for Biochemistry 1

summary: Differential gene expression of Dictyostelium discoideum after infection with Legionella pneumophila in comparison to uninfected cells was investigated using DNA microarrays. Investigation of a 48 h time course of infection revealed several clusters of co-regulated genes, an enrichment of preferentially up- or downregulated genes in distinct functional categories and also showed that most of the transcriptional changes occurred 24 h after infection. Functional annotation of the differentially regulated genes revealed that apart from triggering a stress response Legionella apparently not only interferes with intracellular vesicle fusion and destination but also profoundly influences and exploits the metabolism of its host. For some of the identified genes, e.g. rtoA involvement in the host response has been demonstrated in a recent study, for others such a role appears plausible. The results provide the basis for a better understanding of the complex host-pathogen interactions and for further studies on the Dictyostelium response to Legionella infection.

overall_design: The bacterial strain used in this study was L. Pneumophila Philadelphia I JR32. The strain was grown on buffered charcoal yeast extract agar (BCYE) at 37°C with 5% CO2 atmosphere for 3 days. The D. discoideum wild-type strain AX2 was grown at 23°C in 75 cm2 cell-culture flasks with 10 ml HL5 medium. For infection, Dictyostelium cells were harvested, resuspended in a 1:1 solution of HL5 medium and Soerensen buffer. Fifteen millilitres of a 1×10e6 cells/ml suspension were seeded into a 75 cme2 cell culture flask and the amoebae were inoculated with 10e7 bacteria/ml. After different time intervals of incubation (1, 3, 6, 24, and 48 h) the RNA was isolated from 1.5×10e7 Dictyostelium cells. Usually two or three parallel cultures for the experiment and the control were inoculated per infection. The percentage of infected cells was determined by in situ hybridization with Legionella-specific 16S rRNA probes. The average from three independent determinations was 34, 42, 42, 57 and 82% of infected Dictyostelium cells after 1, 3, 6, 24 and 48 h, respectively.

first: Patrick

last: Farbrother

first: Roman

last: Konertz


title: Differential expression of Dictyostelium discoideum AX2 upon infection with wt L. pneumophila JR32 vs. uninfected 48h p.i. (timecourse experiment)


title: Differential expression of Dictyostelium discoideum AX2 upon infection with wt L. pneumophila JR32 vs. uninfected 3h p.i. (timecourse experiment)


title: Control of RNA stability by NrrF, an iron-regulated small RNA in Neisseria gonorrhoeae.

status: Public on Sep 27 2013

city: Oklahoma City

first: Lydgia

last: Jackson

state: OK

address: 975 NE 10th Street

department: Micorbiology and Immunology

institute: OUHSC

summary: Regulation of gene expression by small non-coding RNAs (sRNAs) plays a critical role in bacterial response to physiological stresses.  NrrF, a trans-acting sRNA in Neisseria meningitidis and Neisseria gonorrhoeae, has been shown in the meningococcus to indirectly control, in response to iron (Fe) availability, the transcription of genes encoding subunits of succinate dehydrogenase, a Fe-requiring enzyme.  Given that in other organisms sRNAs target multiple mRNAs to control gene expression, we used a global approach to examine the role of NrrF in controlling gonococcal transcription.  Three strains, including N. gonorrhoeae FA1090, an nrrF deletion mutant and a complemented derivative were examined using a custom CombiMatrix microarray to assess the role of this sRNA in controlling gene expression in response to Fe availability.  In the absence of NrrF, mRNA half-lives increased for 12 genes in Fe-depleted growth conditions, compared to FA1090.  Biological functions for the 12 genes controlled by NrrF included energy metabolism, oxidative stress, antibiotic resistance, amino acid synthesis and a regulatory protein whose functions are not fully understood, in addition to hypothetical proteins.

overall_design: 18 samples. Three separate biological replicates for both growth conditions (Fe deplete and Fe replete) were done for all each isolate (6 samples per isolate); FA1090 wild type strain; NrrF_mutant strain LJ001; NrrF_complemented strain LJ002

first: Jingcao

last: Pan

first: Michael

last: Day

last: Dyer


title: Steady-state samples of Methanococcus maripaludis MM901:del_frcA (MMP0820)

first: Sung Ho

last: Yoon

summary: Effects of frcA (MMP0820) on physiology and regulation of methanogenesis in Methanococcus maripaludis

overall_design: The strain was grown by continuous culture in a one-liter fermenter (New Brunswick Scientific, Edison, NJ) at 37°C (FEMS Microbiol Lett 238: 85-91, 2004). Medium and gas compositions were modified from those for non-limiting conditions (BMC Microbiol 9: 149, 2009). The standard gassing regime was 110 mL/min H2, 40 mL/min CO2, 35 mL/min Ar, and 15 mL/min H2S/Ar mixture (1:99). Hydrogen limited condition was 21 mL/min H2. After the OD increased above 0.6 (24 h), the medium flow was turned on at 0.083 L/h. Medium was either phosphate limiting (0.12 mM K2HPO4) or phosphate excess (0.8 mM K2HPO4). Different nitrogen sources of NH4Cl and alanine was used (10mM). Culture samples (1.5 mL) were rapidly removed from the vessels by syringe and cell pellets collected by microcentrifugation, immediately frozen in an ethanol-dry ice bath, and stored at -80°C.  Total RNA from each sample was compared against a reference RNA pool that was generated in bulk from a mid-log phase culture of MM901. Total RNA from samples and reference were directly labeled with Cy3 or Cy5, and were hybridized to the tiling array. After hybridization and washing according to array manufacturer's instructions, the arrays were scanned by Microarray Scanner (Agilent Technologies, Santa Clara, CA). Dye-flip experiments were done for each sample.

first: Sung-Ho

first: June

last: Burn

first: Min

first: John

last: Leigh

first: Nitin

last: Baliga


title: Steady-state samples of Methanococcus maripaludis MM901 grown on N14 or N15

summary: Effects of hydrogen on physiology and regulation of methanogenesis in Methanococcus maripaludis

overall_design: The strain was grown by continuous culture in a one-liter fermenter (New Brunswick Scientific, Edison, NJ) at 37°C (FEMS Microbiol Lett 238: 85-91, 2004). Medium and gas compositions were modified from those for non-limiting conditions (BMC Microbiol 9: 149, 2009). The standard gassing regime was 110 mL/min H2, 40 mL/min CO2, 35 mL/min Ar, and 15 mL/min H2S/Ar mixture (1:99). Hydrogen limited condition was 21 mL/min H2. After the OD increased above 0.6 (24 h), the medium flow was turned on at 0.083 L/h. Medium was either phosphate limiting (0.12 mM K2HPO4) or nitrogen limiting (3 mM NH4Cl). Culture samples (1.5 mL) were rapidly removed from the vessels by syringe and cell pellets collected by microcentrifugation, immediately frozen in an ethanol-dry ice bath, and stored at -80°C.  Total RNA from each sample was compared against a reference RNA pool that was generated in bulk from a mid-log phase culture of MM901. Total RNA from samples and reference were directly labeled with Cy3 or Cy5, and were hybridized to the tiling array. After hybridization and washing according to array manufacturer's instructions, the arrays were scanned by Microarray Scanner (Agilent Technologies, Santa Clara, CA). Dye-flip experiments were done for each sample.


title: Comparative Transcriptional Analysis of Canine and Human Diffuse Large B cell Lymphoma (DLBCL). Molecular Signatures of NF-κB Pathway Activation and Sub-Classification of Canine DLBCL.

status: Public on Sep 26 2013

city: Glasgow

first: Manikhandan

middle: A V

last: Mudaliar

state: Scotland

address: Room B528, Sir Graeme Davies Building, 120 University Place

department: College of Medical, Veterinary and Life Sciences

country: United Kingdom

institute: University of Glasgow

summary:
In this study, we present the first comparison of global transcriptional changes taking place in canine lymphoma and human diffuse large B-cell lymphoma (DLBCL), with particular reference to the nuclear factor-kappaB (NF-κB) pathway. Microarray data generated from lymph nodes diagnosed with canine DLBCL and healthy lymph nodes were used for differential expression analysis, co-expression analysis and pathway analysis, and compared with analysis of publicly available microarray data from human healthy and DLBCL lymph nodes. The comparisons between species at gene level were performed by mapping the probesets in canine microarrays to orthologous genes in humans and vice versa.
A considerable number of differentially expressed genes between canine lymphoma and healthy lymph node samples were also found differentially expressed between human DLBCL and healthy lymph node samples. Principal component analysis (PCA) using a literature derived 120 NF-κB target gene set mapped to 199 orthologous canine array probesets and 259 human array probesets clearly separated the healthy and cancer samples in both canine and human datasets.
The analysis demonstrated that for both human and canine DLBCL there is activation of the NF-κB/p65 canonical pathway rather than the alternative pathway. This has therapeutic implications for the use of specific pathway inhibitors for the treatment of DLBCL for both species and also indicates that naturally occurring canine lymphoma could be used as a model to study therapeutic strategies for human lymphoma.  The model was further validated by the identification of molecular signatures that could sub-classify canine DLBCL into activated B-cell-like (ABC) or germinal centre B-cell-like (GCB) types equivalent to human subtypes.

overall_design: Canine DLBCL patients were recruited via the clinical oncology service of the University of Edinburgh Royal (Dick) School of Veterinary Studies (DJA), and the University of Wisconsin-Madison School of Veterinary Medicine (DMV).  Lymph node biopsy samples were taken, as part of normal diagnostic procedures, from dogs newly diagnosed with lymphoma (naïve) and samples from dogs that had relapsed following standard of care CHOP chemotherapy.   Only dogs with confirmed DLBCL after pathological grading were used in this study.  This included standard histopathological grading by two independent pathologists and CD3/PAX5 marker analysis. Normal lymph node samples were obtained from canines that were euthanized for non-lymphoma conditions. Microarray data were generated from 35 canine samples (25 DLBCL and 10 healthy) in total. However, data from 2 canine DLBCL samples did not meet our required quality and were removed from further analysis.  Only data from 33 (23 DLBCL and 10 healthy) samples were used for analysis. The generated data were used for differential expression analysis, co-expression analysis and pathway analysis, and compared with analysis of publicly available microarray data (GSE12195) from human healthy and DLBCL lymph nodes. The comparisons between species at gene level were performed by mapping the probesets in canine microarrays to orthologous genes in humans and vice versa.

first: Ross

middle: D

last: Haggart

first: Gino

last: Miele

first: Grant

last: Sellar

first: Kate

last: Tan

last: Goodlad

first: Elspeth

last: Milne

first: David

middle: M

last: Vail

first: Ilene

last: Kurzman

first: Daniel

middle: J

last: Crowther

last: Argyle


title: Differential expression of Dictyostelium discoideum AX2 upon infection with wt L. pneumophila JR32 vs. uninfected 24h p.i. (timecourse experiment)

first: Ludwig

last: Eichinger

first: Patrick

last: Farbrother

first: Roman

last: Konertz


title: Microarray Analysis of microRNA Expression during Notophthalmus viridescens (red-spotted newt) heart regeneration

status: Public on Sep 24 2013

city: Stockholm

first: Jamie

middle: Ian

last: Morrison

address: Svante Arrheniusväg 20C

department: Department of Molecular Biosciences, The Wenner-Gren Institute

country: Sweden

institute: Stockholm University

summary:
The adult vertebrate red spotted newt is a champion of regeneration, demonstrating an amazing ability to regenerate damaged organs and tissues back to an uninjured state without the formation of scar or reduction in function. By developing a novel cardiac resection strategy, our group recently demonstrated that newt hearts could morphologically and functionally regenerate, without scarring, within a period of 2-3 months following injury. MicroRNAs (miRs) have been widely publicized as essential post-transcriptional gene regulators in a variety of biological processes, including regeneration. We have conducted a microarray screen for vertebrate miRs, with several candidate miRs showing significant differential expression at important time-points following injury to the newt heart.
The newt microRNA expression between uninjured hearts and regenerating hearts, 7 and 21 days post-injury (dpi), was compared by microarray analysis.

platform_organism:
Danio rerio
Pipidae
Homo sapiens

overall_design: Three paired samples were analyzed: Uninjured, 7dpi and 21dpi newt hearts. Three arrays were hybridized comparing two-paired samples each time.

first: Nevin

last: Witman


title: Differential expression of Dictyostelium discoideum AX2 upon infection with wt L. pneumophila JR32 vs. uninfected 1h p.i. (timecourse experiment)


title: Differential expression of Dictyostelium discoideum AX2 upon infection with wt L. pneumophila JR32 vs. uninfected (timecourse experiments)

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

overall_design: Refer to individual Series


title: Molecular classification of mature aggressive B cell lymphoma using digital multiplexed gene expression on formalin-fixed paraffin-embedded biopsy specimens [Frozen tissue]

city: Regensburg

first: Christian

last: Kohler

state: Bavaria

address: Am BioPark 9

department: Institute of Functional Genomics

institute: University of Regensburg

summary: The most frequent mature aggressive B-cell lymphomas are diffuse large B-cell lymphoma (DLBCL) and Burkitt lymphoma (BL). Patients suffering from molecularly defined BL (mBL) but treated with a regimen developed for DLBCL show an unfavorable outcome compared to mBL treated with chemotherapy regimens for BL. Distinguishing BL from DLBCL by conventional histopathology is challenging in lymphomas that have features common to both diseases (aggressive B-cell lymphoma unclassifiable with features of DLBCL and BL [intermediates]). Moreover, DLBCL are a heterogeneous group of lymphomas comprising distinct molecular subtypes: the activated B-cell (ABC)-like, the germinal center B-cell-like (GCB) and the unclassifyable subtype as defined by gene expression profiling (GEP). Attempts to replace GEP with techniques applicable to formalin-fixed paraffin-embedded (FFPE) tissue led to algorithms for immunohistochemical stainings (IHS). Disappointingly, the algorithms yielded conflicting results with respect to their prognostic potential, raising concerns about their validity.  Furthermore, IHS algorithms did not provide a fully resolved classification:  They did not identify mBL; nor did they separate ABC from unclassified DLBCL.

overall_design:
29 diffuse large B-Cell lymphoma samples were hybridized to HGU133A Affymetrix GeneChips. In addition, this study contains 22 already published samples whereas 11 of them contribute to GSE22470, 6 contribute to GSE10172,  3 to GSE44164 and 2 to GSE4475. No re-normalisation of published samples was performed.

We used digital multiplexed gene expression (DMGE) with FFPE derived RNA to classify agressive B-cell lymphomas. Our assay comprised only 30 genes (10 for the detection of mBL and 20 for the detection of ABC and GCB). We chose these genes by reanalysis of the microarray data reported in a previous study. 39 samples from mature aggressive B-cell lymphomas were analyzed using DMGE (nCounter, NanoString Technologies Inc., Seattle, WA, USA) of FFPE- and fresh-frozen derived RNA. All cases were previously characterized by the Molecular Mechanisms of Malignant Lymphoma (MMML) consortium using the Affymetrix GeneChip technology (gold standard of classification).  Please note that there are total 40 FFPE-derived and 50 fresh-frozen derived samples, with 39 samples derived from both materials (allowing direct comparison).

first: Neus

last: Masque-Soler

first: Monika

last: Szczepanowski

first: Rainer

last: Spang

first: Wolfram

last: Klapper


title: Yuan- microRNAs upregulated in Ep300-overexpressing mouse heart

city: Coral Gables

first: Nanette

middle: Hahr

last: Bishopric

state: FL

address: 10 Edgewater Drive, Apt. 9A

department: Medicine

institute: Nanette Bishopric

summary: Objective: To characterize downstream effectors of p300 acetyltransferase in the myocardium.   Background: Acetyltransferase p300 is a central driver of the hypertrophic response to increased workload, but its biological targets and downstream effectors are incompletely known.  Methods and Results: Mice expressing a myocyte-restricted transgene encoding acetyltransferase p300, previously shown to develop spontaneous hypertrophy, were observed to undergo robust compensatory blood vessel growth together with increased angiogenic gene expression. Chromatin immunoprecipitation demonstrated binding of p300 to the enhancers of the angiogenic regulators Angpt1 and Egln3. Interestingly, p300 overexpression in vivo was also associated with relative upregulation of several members of the anti-angiogenic miR-17~92 cluster in vivo.  Confirming this finding, both miR-17-3p and miR-20a were upregulated in neonatal rat ventricular myocytes following adenoviral transduction of p300. Relative expression of most members of the 17~92 cluster was similar in all 4 cardiac chambers and in other organs, however, significant downregulation of miR-17-3p and miR-20a occurred between 1 and 8 months of age in both wt and tg mice. The decline in expression of these microRNAs was associated with increased expression of VEGFA, a validated miR-20a target. In addition, miR-20a was demonstrated to directly repress p300 expression through a consensus binding site in the p300 3’UTR. In vivo transduction of p300 resulted in repression both of p300 and of p300-induced angiogenic transcripts.  Conclusion: p300 drives an angiogenic transcription program during hypertrophy that is fine-tuned in part through direct repression of p300 by miR-20a.

overall_design: 4 littermates, 3 transgene-expressing and 1 wild-type were analyzed.  Samples were spotted in duplicate.

middle: H

first: Huijun

last: Yuan


title: Campylobacter jejuni transcriptomic response to benzylisothiocyanate

city: Rennes

first: Virginie

last: Dufour

address: 263 avenue du General Leclerc

country: France

institute: Université Rennes 1

summary:
Campylobacter jejuni is a widespread pathogen responsible for most of the food-borne gastrointestinal diseases in Europe. For pathogen control in the food industry, the use of natural antimicrobial molecules is a promising strategy to avoid antibiotic treatments. Isothiocyanates are natural antimicrobial compounds which also display anti-cancer activity. Several studies described the chemoprotective effect of isothiocyanates on eukaryotic cells, but the antimicrobial mechanism is still poorly understood.
We investigated the early cellular response of C. jejuni to benzylisothiocyanate (BITC) by both transcriptomic and physiological (respirometry, ATP content measurements and isolations of aggregated proteins).

sample_organism: Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819

overall_design: To characterize the transcriptomic early response to benzylisothiocyanate, C. jejuni NCTC11168 were grown in 100 ml flasks containing 25 ml of MEMα medium plus 20 mM sodium pyruvate. At mid-log phase, 2µg/mL benzylisothiocyanate in ethanol, or the same volume of ethanol (control) was added to the flasks for 10 or 15 min prior to total RNA extraction and purification. Samples were then processed for microarray hybridization. Microarray data was acquired from two (10 minutes assay) or three (15 minutes assay) independent biological replicates and 6 to 9 technical replicates for each biological replicate (total number of measurement per gene = 42).

last: DUFOUR

first: Martin

last: STAHL

first: Eric

last: ROSENFELD

first: Alain

last: STINTZI

first: Christine

last: BAYSSE


title: Real-time quantitative PCR analysis of human colon cancer cells for UPR related genes

city: sendai

first: yosuke

last: shimodaira

address: 1-1, seiryomachi, aoba-ku

institute: tohoku university

summary: human colon cancer cell line HT29 cells treated with 0.5μM thapsigargin 2.5hours. Compared with equal amount total RNA from nontreated control cells. qPCR gene expression profiling.

overall_design: one sample

first: Yosuke

last: Shimodaira


title: Real-time quantitative PCR analysis of human colon cancer cells for autophagy related genes

summary:
human colon cancer cell line HT29 cells treated with 0.5μM thapsigargin 2.5hours. Compared with equal amount total RNA from nontreated control cells. qPCR gene expression profiling.
one sample

overall_design: Yosuke,Shimodaira


title: Methanotrophic community microarray

status: Public on Sep 28 2013

first: Kyung-eun

last: Moon

address: 52, Ewhayeodae-gil, Seodaemun-gu

institute: Ewha womans university

summary: Transcriptional profiling of methanotrophic bacteria (pmoA gene) in methane oxidation biocover soil by depth

overall_design: Three-different depth condition in methane oxidation biocover soil: top, middle and botton layer soil: genomic DNA extract. Three replicate per array.

first: Eun-hee

last: Lee

first: Tae-Gwan

last: Kim

first: Sun-ah

last: Choi


title: Steady-state samples of Methanococcus maripaludis MM901:del_mtd (MMP0372)

first: Sung Ho

last: Yoon

summary: Effects of mtd (MMP0372) on physiology and regulation of methanogenesis in Methanococcus maripaludis

overall_design: The strain was grown by continuous culture in a one-liter fermenter (New Brunswick Scientific, Edison, NJ) at 37°C (FEMS Microbiol Lett 238: 85-91, 2004). Medium and gas compositions were modified from those for non-limiting conditions (BMC Microbiol 9: 149, 2009). The standard gassing regime was 110 mL/min H2, 40 mL/min CO2, 35 mL/min Ar, and 15 mL/min H2S/Ar mixture (1:99). Hydrogen limited condition was 20 mL/min H2. After the OD increased above 0.6 (24 h), the medium flow was turned on at 0.083 L/h. Medium was either phosphate limiting (0.12 mM K2HPO4) or phosphate excess (0.8 mM K2HPO4). Culture samples (1.5 mL) were rapidly removed from the vessels by syringe and cell pellets collected by microcentrifugation, immediately frozen in an ethanol-dry ice bath, and stored at -80°C.  Total RNA from each sample was compared against a reference RNA pool that was generated in bulk from a mid-log phase culture of MM901. Total RNA from samples and reference were directly labeled with Cy3 or Cy5, and were hybridized to the tiling array. After hybridization and washing according to array manufacturer's instructions, the arrays were scanned by Microarray Scanner (Agilent Technologies, Santa Clara, CA). Dye-flip experiments were done for each sample.

first: Sung-Ho

first: June

last: Burn

first: Min

last: Pan

first: John

last: Leigh

first: Nitin

last: Baliga


title: Synbiotic impact of tagatose on viability of Lactobacillus rhamnosus strain GG mediated by the phosphotransferase system (PTS)

city: Jeonju

first: Younghoon

address: 567 Baekje-Daero, Deokjin-Gu

department: Department of Animal Science

institute: Chonbuk National University

summary:
The presence of tagatose in Lactobacillus rhamnosus strain GG caused induction of a large number of genes associated with carbohydrate metabolism including the phosphotransferase system.
In addition, these results indicate the tagatose enhanced the growth of Lactobacillus casei 01 and Lactobacillus rhamnosus strain GG and their probiotic activities by activating tagatose-associated PTS networks.

overall_design: Two-condition experiment, Lactobacillus rhamnosus GG with glucose vs. Lactobacillus rhamnosus GG with tagatose. For preparing the total RNA, Lactobacillus rhamnosus GG cells were grown at 37°C in prebiotic minimum medium supplemented with 2% glucose or tagatose for 24 h.

first: Ji

last: Koh

first: Seung

last: Park

first: Sae


title: Molecular classification of mature aggressive B cell lymphoma using digital multiplexed gene expression on formalin-fixed paraffin-embedded biopsy specimens [FFPE]

first: Christian

last: Kohler

first: Neus

last: Masque-Soler

first: Monika

last: Szczepanowski

first: Rainer

last: Spang

first: Wolfram

last: Klapper


title: Gene regulation by Pax6 in the lens placode - E10.25

city: Saint Louis

first: David

middle: Cy

last: Beebe

state: MO

address: 660 S. Euclid Ave.

department: Ophthalmology and Visual Science

institute: Washington University School of Medicine

summary: Wild type or Pax6 fx/fx; Le-Cre-positive surface ectoderm from E10.25 mouse embryos was laser micodissected from three embryos of each genotype. Total RNA was purified and reverse transcribed and amplified using a NuGEN kit. cDNA was biotinylated and hybridized to Illumina Mouse6 bead arrays.

overall_design: Three wild type and three knockout embryos were used. Each array used the cDNA obtained from the two prospective lens tissues from one embryo.

middle: C

first: Jie

last: Huang


title: HPV-related methylation in Oropharyngeal squamous cell carcinomas (OPSCC)

city: Heidelberg

first: Dr Efterpi

last: Kostareli

state: Baden-Wurtenberg

address: Im Neuenheimer Feld 280

institute: DKFZ

type: Methylation profiling by genome tiling array

summary: Using MCIp, we enriched highly methylated DNA from a normal mucosa control and from three OPSCC patient subgroups regarding the HPV status: group A, DNA-RNA- (Tu1-Tu5); group B, DNA+RNA- (Tu6-Tu10); group C, DNA+RNA+ (Tu11-Tu15).

overall_design: 3 groups of tumor biopsies, 5 samples each regarding HPV status: DNA-RNA-, DNA+RNA-, DNA+RNA+ and a control sample (normal mucosa from healthy individual): 15 tumor samples/ 1 control sample

first: Efterpi

first: Dieter

last: Weichenhan

first: Jochen

last: Hess


title: Hepatocellular carcinomas (HCC) in mice transduced in utero with feline immunodeficiency virus-based vectors (CGH)

status: Public on Sep 11 2013

city: Jerusalem

first: Reba

last: Condiotti

department: Goldyne Savad Institute of Gene Therapy

country: Israel

institute: Hadassah Medical Center

summary: Fetal mice (16 days gestation) were administered FIV-based lentiviral viral particles containing the gene encoding EGFP.  Six liver tumors developed in three mice (1 male, 2 females) between the ages of 273 and 484 days, each mouse developed 2 tumors. These tumors and non-tumorous liver tissue from the same animals were harvested and aCGH was performed on genomic DNA extracted from these samples. We were interested in investigating the link between lentiviral integration and chromosomal aberrations.

overall_design: Two tumors from each mouse (1 male, 2 females) were each compared to non-tumorous tissue surrounding the tumors.

first: Daniel

last: Goldenberg

first: Temima

last: Schnitzer-Perlman

first: Simon

last: Waddington

first: Suzanne

last: Buckley

first: Alina

last: Simerzin

first: Hilla

last: Giladi

first: Eithan

last: Galun

first: Michael

last: Themis


title: RNAPII CTD dataset

status: Public on Sep 13 2013

city: Utrecht

first: Marian

last: Groot Koerkamp

state: Utrecht

address: Heidelberglaan 25

department: Research

country: Netherlands

institute: Princess Maxima Center for Pediatric Oncology

summary: The C-terminal domain (CTD) of RNA polymerase II (RNAPII) is composed of heptapeptide repeats, which play a key regulatory role in gene expression. Using genetic interaction and mRNA expression analysis we found that truncating the CTD resulted in distinct changes to cellular function. Truncating the CTD altered RNAPII occupancy to not only cause decreases, but also increases in mRNA levels. The latter were largely mediated by promoter elements, and in part were linked to the transcription factor Rpn4. The mediator subunit Cdk8 was enriched at promoters of these genes, and its removal not only restored normal mRNA and RNAPII occupancy levels, but also reduced the abnormally high cellular amounts of Rpn4.  This suggested a positive role of Cdk8 in relationship to RNAPII, which contrasted with the negative role at the activated INO1 gene.  Here, loss of CDK8 suppressed the reduced mRNA expression and RNAPII occupancy levels of CTD truncation mutants.

overall_design: Two channel microarrays were used. RNA isolated from a large amount of wt yeast from a single culture was used as a common reference. This common reference was used in one of the channels for each hybridization and used in the statistical analysis to obtain an average expression-profile for each deletion mutant relative to the wt. Two independent cultures were hybridized on two separate microarrays. For the first hybridization the Cy5 (red) labeled cRNA from the deletion mutant is hybridized together with the Cy3 (green) labeled cRNA from the common reference. For the replicate hybridization, the labels are swapped. Each gene is represented twice on the microarray, resulting in four measurements per mutant. Using the Erlenmeyer growth protocol up to five deletion strains were grown on a single day. In the tecan platereader, up to eleven deletion strains could be grown on a single day. Wt cultures were grown parallel to the deletion mutants to assess day-to-day variance.

first: Maria

last: Aristizabal

first: Gian

middle: L

last: Negri

first: Joris

last: Benschop

first: Frank

last: Holstege

first: Nevan

last: Krogan

last: Kobor


title: Analysis of RNA quantitation in formaldehyde-fixed cells

status: Public on Sep 09 2013

city: Baltimore

first: Lucio

last: Gama

state: MD - EUA

address: 733 N Broadway St - BRB 831

department: Molecular and Comparative Pathobiology

institute: Johns Hopkins School of Medicine

summary: Fluorescence-activated cell sorting (FACS) is a sensitive and valuable technique to characterize cellular subpopulations and great advances have been made using this approach. Cells are often fixed with formaldehyde prior to the sorting process to preserve cell morphology and maintain the expression of surface molecules, as well as to ensure safety in the sorting of infected cells. It is widely recognized that formaldehyde fixation alters RNA and DNA structure and integrity, thus analyzing gene expression in these cells has been difficult. We therefore examined the effects of formaldehyde fixation on the stability and quantitation of nucleic acids in cell lines, primary leukocytes and also cells isolated from SIV-infected pigtailed macaques. We developed a method to extract RNA from fixed cells that yielded the same amount of RNA as our common method of RNA isolation from fresh cells. Quantitation of RNA by RT-qPCR in fixed cells was not always comparable with that in unfixed cells. In comparison, when RNA was measured by the probe-based NanoString system, there was no significant difference in RNA quantitation. In addition, we demonstrated that quantitation of proviral DNA in fixed cells by qPCR is comparable to that in unfixed cells when normalized by a single-copy cellular gene. These results provide a systematic procedure to quantitate gene expression in cells that have been fixed with formaldehyde and sorted by FACS.

overall_design: We compared RNA quantitation between unfixed and formaldehyde-fixed cells using the NanoString nCounter system. This analysis was performed using two cell lines, K562 and CEMx174, and human PBMCs. Three biological replicates were performed for each cell type. We also performed this comparison using human PBMCs sorted by FACS. For this analysis, we isolated PBMCs from two donors and performed two technical replicates for each donor sample.

first: Julia

last: Russell

first: Janice

middle: E

last: Clements


title: Differential expression of Dictyostelium discoideum AX2 upon infection with wt L. pneumophila JR32 vs. uninfected 24h p.i. (comparison experiment)

first: Ludwig

last: Eichinger

summary: Differential gene expression of Dictyostelium discoideum after infection with Legionella pneumophila was investigated using DNA microarrays. A detailed analysis of the 24 h time point post infection was performed in comparison to three controls, uninfected cells and co-incubation with Legionella hackeliae and L. pneumophila DeltadotA. One hundred and thirty-one differentially expressed D. discoideum genes were identified as common to all three experiments and are thought to be involved in the pathogenic response. Functional annotation of the differentially regulated genes revealed that apart from triggering a stress response, Legionella apparently not only interferes with intracellular vesicle fusion and destination but also profoundly influences and exploits the metabolism of its host. The results provide the basis for a better understanding of the complex host-pathogen interactions and for further studies on the Dictyostelium response to Legionella infection.

overall_design: The bacterial strains used in this study were L. pneumophila Philadelphia I JR32, L. pneumophila Philadelphia I JR32 LELA 3118 (dotA3118:Tn903 DLL LacZ) and L. hackeliae (ATCC 35250). The Legionella strains were grown on buffered charcoal yeast extract agar (BCYE) at 37°C with 5% CO2 atmosphere for 3 days. The D. discoideum wild-type strain AX2 was grown at 23°C in 75 cm2 cell-culture flasks with 10 ml HL5 medium. For infection, Dictyostelium cells were harvested, resuspended in a 1:1 solution of HL5 medium and Soerensen buffer. Fifteen millilitres of a 1×10e6 cells/ml suspension were seeded into a 75 square-cm cell culture flask and the amoebae were inoculated with 10e7 bacteria/ml. Three different pairs of infection were compared: 1. AX2 infected with L. pneumophila JR32 versus uninfected cells; 19 microarrays of seven independent infections; 2. AX2 infected with L. pneumophila JR32 versus AX2 infected with L. pneumophila JR32 delta DotA; 4 microarrays of two independent infections; 3. AX2 infected with L. pneumophila JR32 versus AX2 infected with L. hackeliae; 4 microarrays of two independent infections. 24h post infection the RNA was isolated from 1.5×10e7 Dictyostelium cells and microarray analysis was performed as described (Farbrother et al., 2006).

first: Patrick

last: Farbrother

first: Roman

last: Konertz


title: The effect of endosulfan on gene expression in Homarus americanus using an oligonucleotide microarray

status: Public on Sep 08 2013

city: Charlottetown

first: Megan

last: Bauer

state: Prince Edward Island

address: 550 University Ave

country: Canada

institute: University of Prince Edward Island

summary: Gene expression profiles of Homarus americanus larvae exposed to five endosulfan concentrations were compared to the control to identify genes that showed significant changes in expression as a result of exposure.  There was a significant dose response effect during the endosulfan experiment and changes in gene expression were seen at high endosulfan concentrations that could caused developmental delays and mortality

overall_design: A six condition experiment: control vs 5 endosulfan concentrations. Biological replicates: 6. Array replicates: 1

first: Bauer

last: Megan

first: Greenwood

last: Spencer

first: Jackman

last: Paula

first: Clark

middle: K

last: Fraser

first: Fairchild

last: Wayne


title: Gene expression profiles in group G streptococci during infection

city: Tokyo

first: Shinya

last: Watanabe

address: 1-21-1 Toyama

department: Department of Infectious Diseases

institute: National Center for Global Health and Medicine

summary: Streptococcus dysgalactiae subsp. equeisimilis (SDSE) has Lancefield group G or C antigens. Recent epidemiological studies reveal that invasive SDSE infections have been increasing in Asia, Europe and US. Although SDSE possesses similar virulence factors to S. pyogenes including streptolysin S (SLS) and streptolysin O (SLO), some important S. pyogenes virulence factors including active superantigens, SpeB and a hyarulonic acids capsule are missing in SDSE genome. The mechanisms and the key virulence factors for causing invasive diseases by SDSE are poorly understood. Here, we analyzed the transcriptome of SDSE in vivo using the murine sepsis model, revealing the strategy of SDSE to destruct host tissues with the virulence factors and to scavenge depleted nutrients. The expression of SLO operon increased at relatively early stage of infection while the SLS and hyaluronidases upregulated after 4h post infection. Microarray data suggested that SDSE degraded host tissue polysaccharides by streptococcal-secreting poly/oligosaccharide lyases and simultaneously used the Entner-Doudoroff pathway to metabolize acquired carbohydrates. A global negative virulence gene regulator CsrRS of SDSE modulated the expressions of genes encoding SLS and the carbohydrate metabolism enzymes. Moreover, csrS deficient mutant induced sever systemic hemolysis in mice. The most frequently isolated stG6792 strains from invasive disease secreted abundant SLS and SLO rather than other SDSE emm types, indicating the relationship between the SLS and SLO productions and poor outcome by the stG6792 strain infection. Our findings suggest that the concomitant regulation of virulence factors destructing the host tissues and metabolic enzymes play an important role to produce invasive diseases by SDSE.

sample_organism: Streptococcus dysgalactiae subsp. equisimilis GGS_124

overall_design: To analyze gene expressions in group G streptococci with the murine infection model, we developed a custom microarray for Streptococcus dysgalactiae subsp. equisimilis (SDSE) based on the genome sequences of three SDSE strains; GGS_124, ATCC12923 and RE378. We intraperitoneally inoculated 10^8 CFU of GGS_124 stain and the csrS deficient mutant into ddY mice. Bacterial cells were collected from the abdominal cavity at 0, 2, 4 and 8 h post infection. GGS_124 cells were also collected from OD600=0.6 culture in brain heart infusion broth as a control.

first: Tohru

last: Miyoshi-Akiyama


title: Differential expression of Dictyostelium discoideum AX2 upon infection with wt L. pneumophila JR32 vs. L. hackeliae 24h p.i.

status: Public on Sep 07 2013

institute: Institute for Biochemistry 1

summary: Differential gene expression of Dictyostelium discoideum after infection with Legionella pneumophila was investigated using DNA microarrays. A detailed analysis of the 24 h time point post infection was performed in comparison to three controls, uninfected cells and co-incubation with Legionella hackeliae and L. pneumophila DeltadotA. One hundred and thirty-one differentially expressed D. discoideum genes were identified as common to all three experiments and are thought to be involved in the pathogenic response. Functional annotation of the differentially regulated genes revealed that apart from triggering a stress response Legionella apparently not only interferes with intracellular vesicle fusion and destination but also profoundly influences and exploits the metabolism of its host. The results provide the basis for a better understanding of the complex host-pathogen interactions and for further studies on the Dictyostelium response to Legionella infection.


title: Rat MeDIP Array, naïve, epileptic, and adenosine treated

status: Public on Sep 05 2013

city: Portland

first: Theresa

last: Lusardi

state: Oregon

address: 2720 SW Moody Avenue

department: Knight Cancer Institute

institute: OHSU

summary:
Epilepsy causes altered gene expression; transient adenosine treatment inhibits progression of epileptogenesis
Hippocampus of epileptic rat is hypermethylated compared to naïve; adenosine treatment causes hypomethylation

overall_design: Metylation state in epileptic rats (9 weeks post kainic acid induced status epilepticus) was compared to naïve (untreated) rats and epileptic rats treated with adenosine for 5 days

first: Detlev

last: Boison


title: Differential expression of Dictyostelium discoideum AX2 upon infection with wt L. pneumophila JR32 vs. the L. pneumophila delta DotA mutant 24h p.i.

city: Cologne

address: Joseph-Stelzmann-Strasse 52


title: Integral nuclear pore proteins bind to Pol III genes and are required for Pol III transcript processing in C. elegans [array]

city: Cincinnati

first: Kohta

last: Ikegami

state: OH

address: 240 Albert Sabin Way, Cincinnati, OH 45229

department: Division of Molecular Cardiovascular Biology

institute: Cincinnati Children's Hospital Medical Center

type: Genome binding/occupancy profiling by genome tiling array

summary: Nuclear pores associate with active protein-coding genes in yeast and have been implicated in transcriptional regulation. Here, we show that in addition to transcriptional regulation, key components of C. elegans nuclear pores are required for processing of a subset of small nucleolar RNAs (snoRNAs) and tRNAs transcribed by RNA Polymerase (Pol) III. Chromatin immunoprecipitation of NPP-13 and NPP-3, two integral nuclear pore components, and importin-ß IMB-1, provides strong evidence that this requirement is direct. All three proteins associate specifically with tRNA and snoRNA genes undergoing Pol III transcription. These pore components bind immediately downstream of the Pol III pre-initiation complex, but are not required for Pol III recruitment. Instead, NPP-13 is required for cleavage of tRNA and snoRNA precursors into mature RNAs, whereas Pol II transcript processing occurs normally. Our data suggest that integral nuclear pore proteins act to coordinate transcription and processing of Pol III transcripts in C. elegans.

overall_design: Genome-wide ChIP-seq and ChIP-chip were performed in mixed-stage C. elegans embryos for nuclear pore proteins NPP-13, NPP-3, IMB-1 and chromatin proteins Pol III (RPC-1), TBP-1, TFC-1 (SFC-1), TFC-4 (TAG-315), and Pol II (AMA-1). For RPC-1 and TBP-1 ChIP-seq, embryos depleted for NPP-13 were also used. Total RNAs from wild-type, NPP-13 RNAi, and IMB-1 RNAi embryos were analyzed by RNA-seq.

first: Jason

last: Lieb


title: Specifically-expressed genes of Bursaphelenchus xylophilus involved in the nematode’s early interaction with pine trees

status: Public on Sep 03 2013

city: Nanjing

first: Jianren

last: Ye

state: Jiangsu

address: Long Pan Road

institute: Nanjing Forestry University

summary: This study compared the different gene expression of Bursaphelenchus xylophilus in two growth conditions (growing on Botrytis cinerea and inoculating Pinus thunbergii). The goal was to analyze the specifically-expressed genes of the pine wood nematode involved in the early interaction between B. xylophilus and P. thunbergii and screen the pathogenesis related genes of B. xylophilus.

overall_design: Two-condition experiment, Growing on Botrytis cinerea  vs. Inoculating Pinus thunbergii . Biological replicates: 3 replicates.

first: Xiuwen

last: Qiu


title: Gene expression profiling of the effects of Cyclophosphamide on peripheral blood mononuclear cells

status: Public on Sep 02 2013

city: Roma

first: Federica

last: Moschella

address: Viale Regina Elena 299

department: Cell Biology and Neurosciences

institute: Istituto Superiore di Sanità

summary: Certain anticancer drugs, particularly cyclophosphamide (CTX), were shown to enhance the antitumor efficacy of immunotherapy through different immunomodulatory mechanisms. A better understanding of the cellular and molecular basis of CTX-mediated immunomodulation is needed to improve the efficacy of chemoimmunotherapy. Transcript profiling and flow cytometry were used to explore CTX immune-enhancing activity in patients with hematologic malignancies. A single high-dose treatment quickly (1-2 days) induced an extensive transcriptional modulation in peripheral blood mononuclear cells, leading to the reduction of cell cycle and biosynthetic/metabolic processes and to the augmentation of transcripts related to DNA damage and cell death (p53 signaling pathway, CDKN1A, CCND3, BAX, BBC3, BID, DDB2, SESN2), of scavenger receptors involved in the recognition of death (MARCO, CD68, CD163L1, SCARB2), of antigen processing/presentation mediators (CIITA, CTSC, CTSL1, CTSZ, GLA, GAA, TPP1, NEU1, SLC11A1, LAMP-2), of T cell activation markers (CD69, OX40) and, noticeably, of a type I interferon (IFN-I) signature (OAS1, CXCL10, BAFF, IFITM2, IFI6, IRF5, IRF7, STAT2, UBE2L6, UNC93B1, ISG20L1, TYK2). Moreover, the plasma levels of IFN-I-induced proinflammatory mediators (CXCL10, CCL2, IL-8, BAFF) were increased by treatment. Accordingly, CTX preconditioning induced both monocyte and lymphocyte activation, leading to the expansion of CD14+CD16+ monocytes, of HLA-DR+, IL8RA+, MARCO+ monocytes/dendritic cells and of CD69+, OX40+, IL8RA+ lymphocytes. Altogether, these data define for the first time the immunomodulatory factors induced by CTX in humans and indicate that preconditioning chemotherapy may stimulate immunity as a consequence of danger perception associated to its cytotoxic action on blood cells, through p53 and IFN-I-related mechanisms.

overall_design: Four-condition experiment, Untreated (10 Biological replicates) - Cyclophosphamide-treated 1 day (10 Biological replicates) - Cyclophosphamide-treated 2 days (8 Biological replicates) - Cyclophosphamide-treated 5 days (5 Biological replicates). Each sample labeled with Cy5 and co-hybridized with Cy3-labeled “reference” aRNA. One replicate per array.

first: Mara

last: Valentini


title: Dictyostelium transcriptional host cell response upon infection with Legionella

first: Ludwig

last: Eichinger

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

overall_design: Refer to individual Series


title: RIP-Chip of endogenous Staufen and GFP-tagged Staufen from 0-3 hour Drosophila embryos

city: Toronto

first: Howard

last: Lipshitz

state: ON

address: 1 King's College Circle

department: Molecular Genetics

institute: University of Toronto

summary: Staufen-associated mRNAs were identified in early Drosophila embryos by RNA-co-immunoprecipitation followed by microarray analysis (RIP-Chip), using two complementary approaches: RIP-Chip from wild-type embryos using a synthetic anti-Staufen antibody, and RIP-Chip from transgenic GFP-Staufen-expressing embryos using an anti-GFP antibody. Genome-wide transcript expression in whole embryos was also assessed for the wild-type and GFP-Staufen lines.

overall_design: There are 18 samples in total.  These include 3 replicates each of 1) gene expression profiling from total mRNA isolated from wild-type 0-3 hour embryos, 2) synthetic anti-Staufen antibody RNA co-immunoprecipitations of endogenous Staufen from wild-type 0-3 hour embryos, 3) control synthetic antibody RNA co-immunoprecipitations from wild-type 0-3 hour embryos, 4) gene expression profiling from total mRNA isolated from transgenic GFP-Staufen expressing 0-3 hour embryos, 5) anti-GFP RNA co-immunoprecipitations of GFP-Staufen from transgenic GFP-Staufen expressing 0-3 hour embryos, 6) anti-FLAG control RNA co-immunoprecipitations from transgenic GFP-Staufen expressing 0-3 hour embryos.

first: John

last: Laver

first: Kristin

last: Ancevicius

first: Xiao

last: Li

first: Quaid

last: Morris

first: J

middle: T

last: Westwood

first: Craig

last: Smibert


title: Clinical Utility of Circulating MicroRNA Signatures for Breast Cancer Diagnosis (RT-PCR)

status: Public on Sep 06 2013

city: Singapore

first: Maurice

last: Chan

address: 11 Hospital Drive

department: Division of Medical Sciences

country: Singapore

institute: National Cancer Centre

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

summary: Purpose: There is a quest for novel non-invasive diagnostic markers for the detection of breast cancer. The goal of this study is to identify circulating microRNA signatures using a cohort of Asian Chinese breast cancer patients, and to compare microRNA profiles between  tumour and serum samples.  Experimental design: MicroRNAs from paired breast cancer tumours, normal tissue and serum samples derived from 32 patients were comprehensively profiled using microarrays (1300 microRNAs against tumour and normal tissues) or LNA RT-PCR panels (742 microRNAs against serum samples). Serum samples from healthy individuals (n=22) were also employed as normal controls. Significant serum microRNAs, identified by logistic regression, were validated in an independent set of serum samples from patients (n=82) and healthy controls (n=53).  Results: The 20 most significant microRNAs differentially expressed in breast cancer tumours included miR-21, miR-10b, and miR-145, previously shown to be dysregulated in breast cancer. Interestingly, 16 of the 20 most significant microRNAs differentially expressed in serum samples were novel. MiR-1, miR-92a, miR-133a and miR-133b were identified as the most important diagnostic markers, and were successfully validated; receiver operating characteristic curves derived from combinations of these microRNAs exhibited areas under the curves of 0.944-0.946. Only seven microRNAs were overexpressed in both tumours and serum, suggesting that microRNAs may be released into the serum selectively.   Conclusion: The clinical employment of microRNA signatures as a non-invasive diagnostic strategy is promising, but should be further validated for different subtypes of breast cancers.

overall_design: Blood samples were collected in Becton Dickinson (Franklin Lakes, NJ) Vacutainer SST tubes. Serum was harvested by centrifugation at 2200g after allowing blood to clot for 30mins. 32 patient samples and 22 samples from healthy controls were obtained for profiling. Sera samples were stored at -80oC.


title: Expression profiling of FRG1 transgenic mice.

status: Public on Sep 04 2013

city: Trieste

first: Danilo

last: Licastro

department: Genomica Funzionale

institute: CBM

summary: RNA from skeletal muscle of mice over-expressing selectively in the skeletal muscle the gene FRG1, a candidate of facioscapulohumeral muscular dystrophy, was compared to RNA from skeletal muscle of WT mice.

overall_design: Total RNA obtained from isolated vastus lateralis muscles of 4 weeks old females WT mice and vastus lateralis muscles of 4 weeks old mice over-expressing FRG1, FSHD region gene 1.

first: Davide

last: Gabellini


title: Microarray analysis of genes involved in Streptolysin S immunity

status: Public on Sep 01 2013

city: Notre Dame

first: Erliang

last: Zeng

address: 384 Fitzpatrick Hall

institute: University of Notre Dame

summary: Group A Streptococcus (GAS) is one of the world’s most successful pathogens, causing a multitude of common infections such as pharyngitis, cellulitis, and impetigo. It is also responsible for more severe diseases such as rheumatic fever, necrotizing fasciitis, and toxic shock syndrome. Group A Streptococcus produces a powerful peptide toxin known as streptolysin S (SLS). Although recent advances have begun to uncover the structure of SLS, many questions remain as to its route of synthesis, export and function. A fundamental yet unanswered question about SLS is the mechanism employed by GAS to resist the effects of its own toxin. To address this question, we developed a unique microarray-based approach aimed at identifying bacterial genes involved in SLS immunity. We measured changes in gene expression in a non-SLS producing GAS strain (∆SLS) after exposure to active SLS, as well as to an inactive SLS isoform. Initial exposure of a non-SLS producing GAS to the native SLS toxin resulted in significant upregulation of several gene candidates.  Proteins encoded by these gene candidates were produced and tested for their ability to neutralize SLS toxin activity in vitro.  The protein encoded by the gene Spy_0787 decreased the cytolytic activity of wt SLS by 50%.  Bacterial immunity is still a relatively unknown and unexplained phenomena. Insights into how toxin-producing microorganisms achieve resistance against the effects of their own toxin could uncover important therapeutic targets to neutralize virulence factors such as SLS, as well as other related peptide toxins. The microarray technique described here can be leveraged to other microbial systems to understand how microorganisms in general react to antibacterial and cytotoxic compounds for which the mechanism of action is unknown.

overall_design: Supernatants containing wt and S39A forms of SLS secreted by GAS strains were collected from 50 ml of overnight cultures of each strain at 37 degrees C in Todd Hewett broth supplemented with 10 mg/ml of bovine serum albumin fraction V (Sigma chemicals) in order to stabilize the toxin. The supernatant was then isolated and subjected to filter sterilization. For SLS exposure conditions, bacterial pellets containing GAS ∆SagA mutants were incubated with 1. supernatants containing wtSLS; 2. supernatants containing SLS S39A isoform; or 3. sterile TH media with 10mg/ml of BSA. The bacteria pellets were quickly resuspended after which the bacterial pellets were recollected for RNA isolation.  A total of three exposure timepoints were used: 0h (immediately after exposure to SLS-containing supernatants), 3h post-exposure, and 6h post-exposure. The pellets were frozen at -80C until used for RNA extraction. Total RNA extraction and purification from the bacterial pellets were performed using the RNeasy isolation kit per manufacturer's instructions (Qiagen). RNA samples were processed following standard Roche NimbleGen gene expression analysis protocols.  Double-stranded cDNA was synthesized from 10 μg of total RNA using random hexamer primers with the SuperScript cDNA synthesis kit (Invitrogen).  One μg of cDNA was labeled with Cy3-random nonamers (Roche NimbleGen) for microarray hybridization.

first: Clayton

last: Thomas

last: Tan

first: Shaun

last: Lee


title: Expression profiles of colorectal cancer cell lines

city: Sendai

first: Yasufumi

last: Matsuda

state: Miyagi

address: 1-1 seiryouchou aobaku

department: Surgery

institute: Tohoku University Graduate School of Medicine

summary: We ortho-topically implanted 16 human colorectal cancer (CRC) cell lines onto the cecal walls of nude mice . To identify the genes possibly involved in EMT of CRC, we analyze the EMT related changes with the orthotopic implantation method in vivo in combination with that of gene expression profiles using a cDNA microarray in vitro.

overall_design: We analyzed 16 human colorectal cancer cell lines. For each cell line, the experiments were carried out twice.


title: Transcriptional analysis of quorum sensing deficient in Yersinia pestis CO92 at 37°C

city: Ames

first: Chris

last: Minion

state: IA

address: 1130 Vet Med

department: VMPM

institute: Iowa State University

summary: Yersinia pestis, the etiological agent of plague, is able to sense cell density by quorum sensing. The function of quorum sensing in Y. pestis is not clear. Here, the process of quorum sensing was investigated by comparing transcript profiles when three quorum-sensing synthase genes are knocked out. Two strains, ∆pgm (pigmentation-negative) mutant R88 as treatment and quorum sensing null strain R115 with mutations (∆pgm, ∆ypeIR, ∆yspIR, and ∆luxS) as control, are used in this analysis.

overall_design: Six independent RNA samples from R115 cultures were paired with six independent RNA samples from R88 cultures for hybridization to six two-color microarrays. A dye-swap design was used to remove the Cy5 and Cy3 dye bias.

first: Jing

last: Yu


title: Transcription analysis of AI-2 signal add in experiment in Yersinia pestis CO92 at 37°C

summary: Yersinia pestis, the etiological agent of plague, is able to sense cell density by quorum sensing. The function of quorum sensing in Y. pestis is not clear. Here, the process of autoinducer-2 (AI-2) quorum sensing was investigated by comparing transcript profiles when AI-2 quorum-sensing signal is added in. The strain ∆pgm(pigmentation-negative) mutant R88 was used as wild type. The control consisted of cells grown and treated under the same conditions without added signals.

overall_design: Six independent RNA samples from Y. pestis CO92 ∆pgm cultures were paired with six independent RNA samples from AI-2 signal added cultures for hybridization to six two-color microarrays. A dye-swap design was used to remove the Cy5 and Cy3 dye bias.


title: A large novel deletion downstream of PAX6 gene in a Chinese family with coloboma of iris

city: Chongqing

first: Hong

last: Guo

address: 30# Gaotanyan St. Shapingba District

department: Medical Genetics

institute: Third Military Medical University

type: Genome variation profiling by genome tiling array

summary: The paired box gene 6 (PAX6) is an essential transcription factor for eye formation. Genetic alterations in PAX6 can lead to various ocular malformations including aniridia. The purpose of this study was to identify genetic defects as the underlying cause of familial coloboma of iris in a large Chinese family. After linkage analysis was carried out in this family, all exons of PAX6 in the proband were sequenced by the Sanger sequencing technique. Then the genome of the proband was evaluated by a microarray-based comparative genomic hybridization (aCGH). Quantitative real-time PCR was applied to verify the abnormal aCGH findings. All patients presented bilateral partial coloboma of iris, severe congenital nystagmus, hyperpresbyopia and congenital posterior polar cataracts. Two-point linkage analysis in the autosomal dominant family showed loss of heterozygosity at the D11S914 locus. There was no pathogenic mutation in the exons of PAX6. The aCGH analysis revealed a 681 kb heterozygous deletion on chromosome 11p13. Quantitative real-time PCR verified the deletion in the patients and further confirmed this deletion cosegregation with the coloboma of iris phenotype in the family. The 681 kb large deletion of chromosome 11p13 downstream of PAX6 is the genetic cause of the familial coloboma of ocular in this large Chinese family. aCGH should be applied if there is a negative result for the mutation detection of PAX6 in patients with aniridia.

overall_design: One Case sample and one control sample

first: Yun

last: Bai


title: Expression data from HeLa cells treated with tocotrienols

city: Rome

first: Guido

last: Leoni

address: Via Pontina

department: Bioinformatics

institute: IRBM

summary:
We used microarrays to investigate the pattern of gene expression induced by tocotrienols treatment in HeLA cells
Our study demonstrates that treatment with γ- and δ-T3 is associated to specific Ca-dependent signals

overall_design: 3 treatments vs control

first: Raffaella

last: Comitato

first: Fabio

last: Virgili


title: Super Vs Non

city: Saskatoon

first: Fernanda

last: Dias

address: 52 Campus Dr

institute: University of Saskatchewan

summary: The main objective of superovulatory treatment is to achieve multiple ovulations and produce multiple embryos. The technique is intended to rescue a cohort of follicles within a follicular wave that would otherwise regress. Superstimulory treatments change the intra-follicular and systemic hormonal milieu, but it is not clear how and to what extent treatment alters gene expression of follicular cells. In this study, a genome-wide bovine oligo-microarray was used to compare the gene expression of granulosa cells from post-LH preovulatory dominant follicle with those from follicles of the same status after superstimulatory treatment. Cows were allocated randomly to two groups (superstimulation group and control group, n=6 cows per group). A new follicular wave was induced by transvaginal ultrasound-guided ablation of follicles ≥5 mm in diameter, and a progesterone-releasing device (CIDR) was placed in vagina. The superstimulation group was given eight doses of 25 mg FSH im at 12-h intervals starting from the day of wave emergence (Day 0), whereas the control group was not given any FSH treatment. Both groups were given prostaglandin F2α im twice, 12 h apart, on Day 3 and the CIDR was removed at the second injection; 25 mg pLH was given im 24 h after CIDR removal, and cows were ovariectomized 24 h later. Granulosa cells were collected for RNA extraction, amplification and microarray hybridization. To translate microarray results to a physiological context, a list of differentially expressed transcripts were biologically annotated. A total of 190 genes were down-regulated and 280 genes were up-regulated in superstimulated group when compared with the reference (non-superstimulated control) group.

overall_design: straight comparison of superstimulation group (the treatment; group 1) versus non-superstimulated ( the reference; group 4)  using 3 different aninals (biological replicates) in each group and performed dye swap. For example on array 1:  group1 cow 1 versus group 4 cow 1 (cy3 vs cy5) and on array 4 is the dey swap group 4 cow 1 versus group 1 cow 1 (cy3 vs cy5).

first: Fernand


title: Nitric oxide-fixation in plants: A new pathway enabling the use of nitric oxide as nitrogen source

city: Nueherberg

first: Gitto

middle: Thomas

last: Kuruthukulangarakoola

address: Ingolsteadter Landstrasse 1

department: Biochemical Plant Pathology

institute: Helmholtz Zentrum München

summary:
Of all the essential nutrients, nitrogen is the one most often limiting for plant growth. Nitrogen can be taken up by plants in two ways. One possibility is through ammonium and nitrate, which are the predominate inorganic forms of nitrogen in soils. The second possibility is the uptake of air-born nitrogen through plant-associated mircoorganisms in root nodules. The majority of plants able to form such nitrogen-fixing root nodules are in the legume family Fabaceae. Here we present a third possibility – a new pathway, termed as nitric oxide (NO)-fixation pathway, which allows plants to fix atmospheric NO and to use it for better growth and development.
We identified non-symbiotic hemoglobin class 1 (AtGLB1) and class 2 (AtGLB2) as key proteins of the NO-fixation pathway. In an NO enriched environment NO-fixation is enhanced considerably in plants overexpressing AtGLB1 or AtGLB2 genes. NO uptake resulted in four-fold higher nitrate levels in these plants compared to NO-treated wild-type plants. Correspondingly, the growth parameters like rosettes size and weight, vegetative shoot thickness and also seed yield were 25%, 40%, 30%, and 20% higher, respectively, in the overexpression lines in comparison to wild-type plants. Our results highlight the existence of a NO-fixing pathway in plants. We demonstrated that plant non-symbiotic hemoglobin proteins can fix atmospheric NO and convert it to nitrate, which is further introduced into the N-metabolism. We assume that our results might provide new insights into the field of crop science research and that the NO-fixation capability might serve as a new economically important breeding trait for enhancing biomass, fruit, and seed production. Modifying this pathway might be a promising approach for better and more environment-friendly supply of nitrogen. For example crop plant hemoglobin proteins could be improved for their NO-fixing capability and their expression levels could be increased.

overall_design: WT-Arabidopsis thaliana plants were fumigated with Ambient NO and 3 ppm NO air in three completely independent biological experiments. Total RNA was isolated from four-week old rosette leaves of these plants to determine the gene expression signature of each samples using Agilent one-color  microarray. Differences in the gene expression signatures between Ambient NO and 3 ppm NO treated samples were analyzed to see the effect of NO fumigation on the WT Arabidopsis plants at the transcript level.

first: Christian

last: Lindermayr


title: Transcriptional analysis of luxS-null strain in Yersinia pestis CO92 at 37°C

summary: Yersinia pestis, the etiological agent of plague, is able to sense cell density by quorum sensing. The function of quorum sensing in Y. pestis is not clear. Here, the process of autoinducer 2 (AI-2) quorum sensing was investigated by comparing transcript profiles when luxS gene was knocked out. The luxS gene encodes S-ribosylhomocysteinase which can produce DPD, a precursor of AI-2. The strain ∆pgm (pigmentation-negative) mutant R88 was called wild type. The ∆pgm ∆luxS mutant was called control.

overall_design: Six independent RNA samples from R88 were paired with six independent RNA samples from ∆pgm ∆luxS mutant cultures for hybridization to six two-color microarrays. A dye-swap design was used to remove the Cy5 and Cy3 dye bias.


title: Methylated DNA immunoprecipitation coupled with NimbleGen's array to identify methylated genes in pancreatic ductal adenocarcinoma

first: wentao

last: gao

address: 300 Guangzhou Road

department: Department of General Surgery

institute: the first affiliated hospital with nanjing medical university

summary: Pancreatic ductal adenocarcinoma (PDAC) is a highly invasive cancer with a poor prognosis. Using methylated DNA immunoprecipitation (MeDIP)-chip analysis, we found that 161 genes that were specifically hypermethylated in PANC-1 cells. Among them, miR-615-5p was hypermethylated in its putative promoter region, which silenced its expression in PDAC cell lines.

overall_design: Comparison between PANC-1 cell lines and normal pancreas tissue

first: Wentao

last: Gao

first: Yi

last: Miao


title: Transcriptional analysis of three quorum sensing signals add in experiment inYersinia pestis CO92  at 37°C

summary: Yersinia pestis, the etiological agent of plague, is able to sense cell density by quorum sensing. The function of quorum sensing in Y. pestis is not clear. Here, the process of quorum sensing was investigated by comparing transcript profiles when three quorum-sensing signals are added in. The strain ∆pgm (pigmentation-negative) mutant R88 was used as wild type. The three signals are AI-2, AHLs (N-(3-Oxooctanoyl)-L-homoserine lactone and N-Hexanoyl-DL-homoserine lactone).The control consisted of cells grown and treated under the same conditions without added signals.

overall_design: Six independent RNA samples from Y. pestis CO92 ∆pgm cultures were paired with six independent RNA samples from 3 signals added cultures for hybridization to six two-color microarrays. A dye-swap design was used to remove the Cy5 and Cy3 dye bias.


title: affy_sunflower_2011_02-Effect of frost on sunflower

city: evry

first: stephanie

last: huguet

address: 2 rue gaston cremieux

institute: inra

summary: affy_sunflower_2011_02 - affy_sunflower_2011_02 - The early sowing constitutes an alternative strategy to avoid drought occurring during flowering and post-flowering periods and responsible for decrease in sunflower production. In French cropping system, early sowing is associated to low temperature period and frost during first development stages in sunflower. Knowledge about metabolism of frost acclimation must be performed to supply tools for breeding programs in sunflower. The aim of our experiment is to unravel the transcriptional regulation underpinning frost tolerance in sunflower-5 genotypes of sunflower were grown in a growth chamber 1 (23°C day/18°C night, 63% air humidity, 14 hours day photoperiod). At the stage of 6 leaves well-developed, 12 plants of each genotype were subjected to cold acclimation (+4°C during 2 days) in another growth chamber 2. Then, these plants were subjected to 2 nights at -3°C (frost treatment). Chlorophylle fluorescence, Osmotic potential, Relative electrolyte leakage were then determined in the following conditions : - 6th October on 6 plants X 5 genotypes from growth chamber 1 (C1) - 6th October on 6 plants X 5 genotypes from growth chamber 2 (S1) - 11th October on 6 plants X 5 genotypes from growth chamber 1 (C2) - 11th October on 6 plants X 5 genotypes from growth chamber 1 (S2)

overall_design: 12 arrays - SUNFLOWER; treated vs untreated comparison

first: Gwenola

last: Gouesbet-Jan

first: Stephanie

last: Huguet

first: Philippe

last: Grieu

first: Sandrine

last: Balzergue

first: Marie-Laure

last: Martin-Magniette


title: AtHB17 Regulates Photosynthetic Capacity

city: Hayward

first: Don

middle: R

last: Maszle

state: CA

address: 3935 Point Eden Way

institute: Mendel Biotechnology, Inc.

summary: The transcriptional profiles of root quiescent center tissues from AtHB17 KO lines in Arabidopsis were compared to wild-type sibling lines.


title: miRNA expression changes in murine liver tumorigenesis

city: San Francisco

first: Andrei

last: Goga

address: 513 Parnassus Ave

department: Cell & Tissue Biology

institute: UCSF

summary: Hepatocellular carcinoma (HCC) is associated with poor survival for patients and few effective treatment options, raising the need for novel therapeutic strategies. MicroRNAs (miRNAs) play important roles in tumor development and show deregulated patterns of expression in HCC. Because of the liver’s unique affinity for small nucleic acids, miRNA based therapy has been proposed in the treatment of liver disease. There is thus an urgent need to identify and characterize aberrantly expressed miRNAs in HCC. In our study, we profiled miRNA expression changes in de novo liver tumors driven by MYC and/or RAS, two canonical oncogenes activated in a majority of human HCC.

platform_organism:
Populus trichocarpa
Oryza sativa
Caenorhabditis elegans
Homo sapiens
Mus musculus
Rattus norvegicus
synthetic construct

overall_design: RNA from normal liver (LT2) and tumor tissue (LT2/MYC, LT2/RAS, LT2/MYC/RAS) was extracted, enriched for miRNAs and biotin-labeled using Ambion’s miRVana, flashPAGE and miRVana miRNA labeling kits respectively. Samples (n=4) from each genotype were hybridized to a custom Affymetrix Genechip designed to miRNA probes derived from Sanger miRBase v9.2. This array contained a total of 14216 probes, of which 672 matched to 301 unique mouse miRNAs. For each probe, an estimated background value was subtracted that was derived from the median signal of a set of GC-matched anti-genomic controls. Detection calls were based on a Wilcoxon rank-sum test of the miRNA probe signal compared to the distribution of signals from GC-content matched anti-genomic probes and normalized according to the variance stabilization method described.Post-normalized data scale is reported as generalized log2 data. For statistical hypothesis testing, one-way ANOVA was applied and probes are considered significantly differentially expressed based on a default p-value of 0.05 and log2 difference >1 or <-1.

first: Lionel

last: Lim


title: Gene regulation by Pax6 in the lens placode - E9.5 (1)

city: Saint Louis

first: David

last: Beebe

address: 660 S. Euclid Ave.

department: Ophthalmology and Visual Science

institute: Washington University School of Medicine

summary: Wild type or Pax6 fx/fx; Le-Cre-positive (Pax6-/-) surface ectoderm from E9.5 mouse embryos was laser micodissected from three embryos of each genotype. Total RNA was purified and reverse transcribed and amplified using a NuGEN kit. cDNA was biotinylated and hybridized to Illumina Mouse6 bead arrays.

overall_design: Three wild type and three knockout embryos were used. Each array used the cDNA obtained from the two prospective lens tissues (left and right eyes) from each embryo.

first: Jie

last: Huang


title: IL-21 regulates the expression of chemokine genes in B-chronic lymphocytic leukemia

city: Milan

first: Loris

last: De Cecco

address: via Venezian 1

institute: IRCSS Istituto Nazionale Tumori

summary:
B-cell chronic lymphocytic leukemia (CLL) is a common type of leukemia, characterized by the progressive accumulation of CD5+ “mature” monoclonal B lymphocytes in peripheral blood, bone marrow and lymphoid tissues. Although circulating CLL cells are non-dividing cells, prone to spontaneous apoptosis, their progressive accumulation is the result of a dynamic balance between cell death and proliferation and a high turn-over rate has been related to a poor prognosis. Indeed, CLL cells are protected from apoptosis and proliferate in specific niches within the lymphoid tissues and the bone marrow.
CLL cells show variable expression of IL-21R that can be up-regulated by cell activation via CD40. CD40-activated CLL cells phosphorylate STAT-1 and STAT-3 and undergo apoptosis in response to IL-21 stimulation. By gene-expression profiling we found out that IL-21 modulates the expression of several genes including cytokine and chemokine genes and genes involved in cell survival and apoptosis in CD40-activated CLL cells.

overall_design: PBMCs were isolated from heparinized blood obtained from 13 untreated patients diagnosed with CLL on the basis of clinical and immunophenotypic criteria. PBMCs were isolated by Ficoll density gradient centrifugation and characterized by immunofluorescence and FACS analysis. When residual non B-cells exceeded 10%, B cells were enriched by negative selection with antibody-coated magnetic beads (CD2-beads, Dynal, Oslo, Norway) to obtain a >95% pure CD19+/CD5+ B cell population. B-CLL cells were pre-activated on adherent CD40L-transduced L cells for 48-36h and then stimulated with IL-21 or medium only for additional 18h. Total RNA was isolated from  samples using TriZol (Invitrogen) reagent.

first: L


title: miRNAs expressed in murine CD4+ T cells of splenocyte and lamina propria lymphocytes

city: Kamakura

first: Satoshi

last: Kondo

state: Kanagawa

address: Tebiro 6-10-1

department: New Projects Development Division

institute: Toray Industries,Inc.

summary: The levels of some murine mRNAs and proteins are expressed discrepantly between the central immune system and the gut immune system in murine colitis. It was possible that RNA interference would result in some of the discrepancy. Thus, we compared microRNAs that are expressed in CD4+ T cells of spleen (SP) and lamina propria (LP) using Il-10+/- mice (C57BL/6 background) in order to reveal the role of miRNAs in murine colitis.

overall_design: Using 10-week-old female Il-10+/- mice, we investigated the difference in miRNA expressions between CD4+ T cells of spleen and that of lamina propria.

first: Akira

last: Mukai

first: Hideki

last: Iijima


title: Mechanisms and rescue strategies of Calcineurin inhibitor mediated tolerance abrogation

city: Bergisch Gladbach

first: Bernhard

last: Gerstmayer

state: NRW

address: Friedrich-Ebert-Str. 68

department: Genomic Services

institute: Miltenyi Biotec

summary: To ensure safety tolerance induction protocols are accompanied by conventional immunosuppressive drugs IS. But IS such as calcineurin inhibitors CNI can interfere with tolerance induction. We investigated the effect of an additional CNI treatment on anti-CD4 mAb-induced tolerance induction upon rat kidney transplantation.   Additional CNI treatment induced deteriorated graft function and chronic rejection characterised by alloantibody production, intragraft plasma cells and C3d deposition. Microarray analysis revealed enhanced intragraft expression of the B cell chemokine CXCL13 upon additional CNI treatment. In contrast PNOC, a B cell-related gene highly expressed in operational tolerant kidney transplant recipients, was decreased in grafts of anti-CD4 mAb+CsA-treated recipients suggesting an altered balance of B regulatory genes.  Transient B cell depletion or transfer of Tregs three weeks after transplantation could inhibit intragraft B cell accumulation, alloantibody production and ameliorate chronic rejection.  These data represent unexpected findings and should be taken into consideration when designing new clinical trials. To safe the benefit of CNI in controlling memory T cell responses we need strategies for a therapeutic optimization. We show here that early B cell depletion or transfer of Tregs may be one approach to arrest B cell accumulation, activation and graft destruction.

overall_design: comparative analysis of different immunosuppressive regimens on renal allograft gene expression versus untreated allografts

first: Anja

last: Siepert

first: Sabine

last: Brösel

first: Katrin

last: Vogt

first: Stefanie

last: Ahrlich

first: Isabela

last: Schmitt-Knosalla

first: Christoph

last: Loddenkemper

first: Ria

last: Baumgrass

first: Stefan

last: Tomiuk

first: Markus

last: Tiedge

first: Ondrej

last: Viklický

first: Horst

last: Nizze

first: Manfred

last: Lehmann

first: Hans-Dieter

last: Volk

first: Birgit

last: Sawitzki


title: Aspergillus nidulans : Wild type Fructose x Xylose

status: Public on Aug 31 2013

city: Ribeirão Preto

first: Ana

middle: Cristina

last: Colabardini

state: São Paulo

address: Av do Café s/n Cidade Universitária

department: Ciências Farmacêuticas

country: Brazil

institute: FCFRP-USP

summary: Transcriptional profiling of A. nidulans comparing Xylose and Fructose grown on Wild type strain. The main objective was to identifiy genes related to Xylose transport. The experiment was further validated by real-time PCR.

overall_design: Three-condition experiment : A. nidulans strains grown during 16 h on fructose and transfered to xylose for 6, 12 and 24h.


title: Expression analysis of Lactococcus lactis NIAI712 and its plasmid cured variant

city: Tsukuba

first: Miho

last: Kobayashi

address: 2 Ikenodai

department: Animal Products Research

institute: National Institute of Livestock and Grassland Science

summary: L. lactis NIAI712 carries five different plasmids, including an 8.7-kb plasmid designated pAG6. In this study, genome-wide expression profiles of the pAG6-cured variant was compared to the wild-type strain.

overall_design: Two samples of total RNA recovered from a wild-type culture of L. lactis NIAI712 and a pAG6-cured variant were examined


title: Identification of candidate microRNAs in colorectal adenomas and adenocarcinomas

status: Public on Aug 30 2013

city: Brest

first: Laurent

last: Corcos

address: 22, Avenue Camille Desmoulins

department: Faculty of Medicine

institute: INSERM U1078-ECLA

summary: We showed that some microRNAs could be characteristic of the progression from adenoma to adenocarcinoma in colorectal cancer.

sample_organism:
Homo sapiens
synthetic construct

overall_design: 48 colorectal biopsy samples (28 adenomas, 15 adenocarcinomas and 5 normal mucosae) were analyzed. We generated three comparisons: adenomas versus. normal mucosae, adenocarcinomas versus. normal mucosae, and adenocarcinomas versus. adenomas.

first: Marine

last: Pesson

first: Brigitte

last: Simon


city: Heverlee

first: Jos

last: Vanderleyden

address: Kasteelpark Arenberg 20

department: Department of Microbial and Molecular Systems

country: Belgium

summary:
InvF ChIP-chip on Salmonella enterica serovar Typhimurium SL1344 using anti-Myc antibody against strain with chromosomally 9Myc-tagged InvF (IP samples) and wildtype strain (mock IP samples)
Salmonella enterica serovar Typhimurium causes a range of diseases from self-limiting gastroenteritis to life-threatening systemic infections. Its complex infection process is initiated by the invasion of the intestinal epithelial monolayer by means of a type three secretion system. InvF is one of the key regulators governing the invasion of epithelial cells. By mapping the InvF regulon, i.e. locating its direct target genes, the gene network underlying invasion can be further examined, including identifying possible new effector-encoding genes.  In order to map the InvF regulon, we performed chromatin immunoprecipitation combined with tiling microarray analysis (ChIP-chip) and compared expression of the identified target genes in an invF mutant and a wildtype strain. In addition, the promoter regions of these target genes were searched for the presence of an InvF recognition site. Finally, a query-driven biclustering method, combined with a microarray compendium containing publically available S. Typhimurium gene expression data, was applied as an in silico validation technique for functional relatedness between newly identified target genes and known invasion genes.  As expected, under invasion inducing conditions, InvF activates the expression of invasion chaperone encoding sicA and the effector-encoding genes sopB, sopE, sopE2 and sopA by binding their promoter region. Newly identified InvF targets are steB, encoding a secreted effector, and STM1239. The presence of an InvF recognition site in the promoter regions of these target genes further supports this observation. In addition, the query-driven biclustering method revealed similarities in expression profiles between STM1239 and known InvF regulated invasion genes over a range of experimental conditions. In conclusion, we here deliver the first evidence for direct binding of InvF to the promoter regions of sopA and sopE2, and associate genes encoding a secreted effector (steB) and a putative novel effector (STM1239) with the Salmonella invasion regulator InvF.

sample_organism: Salmonella enterica subsp. enterica serovar Typhimurium str. SL1344

platform_organism: Salmonella enterica subsp. enterica serovar Typhimurium str. LT2

overall_design: Three IP samples (from three biological replicates using anti-Myc antibody against Salmonella Typhimurium SL1344 strain encoding chromosomally 9Myc-tagged InvF) and three control mock IP samples (from three biological replicates using anti-Myc antibody against Salmonella Typhimurium SL1344 wildtype strain) were labeled with Cy5 and hybridized against a common genomic DNA reference, labeled with Cy3, on 6 S. Typhimurium LT2 whole genome tiling arrays

first: Inge

last: Thijs

first: Sigrid

last: De Keersmaecker

first: Michael

last: McClelland

first: Steffen

last: Porwollik

first: Fred

last: Long

first: Yipeng

last: Wang


title: Human B cell receptor light chain repertoire analysis in healthy individuals and SLE patients

city: Chicago

first: Nathan

last: Schoettler

state: IL

address: 924 E 57th Street, R402

institute: University of Chicago

summary: Determination of expression levels of light chain V genes in peripheral blood B cells after FACS sorting for two populations of B cells (CD20+CD138-IgKappa+IgLambda- and CD20+CD138-IgKappa-IgLambda+).  Analysis was performed on healthy individuals and SLE patients with analysis performed using several models.

platform_organism:
Homo sapiens
Mus musculus

overall_design: Dual channel hybridization with experimental samples detected on red channel and reference sample detected on green channel.  Two replicate hybridizations.

first: Martin

last: Weigert

first: Dongyao

last: Ni


title: Exposure of Bacillus VOCs vs. Control

city: Daejeon

first: Choong-Min

last: Ryu

address: 125 Gwahak-ro Yuseong

institute: KRIBB

summary: Transcription profiling of E. coli by exposure of VOCs- Bacillus VOCs vs control

sample_organism: Escherichia coli str. K-12 substr. MG1655

overall_design: Experiments of two-conditions with 3 different time points,  Exposure of Bacillus VOCs vs Control

first: Kwang-sun

last: Kim

first: Soohyun

last: Lee