title: miRNA expression profiles in the serum of Doberman Pinschers

status: Public on Mar 22 2013

city: Munich

first: Karin

last: Weber

address: Veterinärstr. 13

department: Medizinische Kleintierklinik

country: Germany

institute: Zentrum für klinische Tiermedizin

summary: Background: Dilated cardiomyopathy (DCM) is the most common acquired heart disease in large- and giant-breed dogs with Doberman Pinschers representing one of the most frequently affected breeds. MicroRNAs (miRNAs) are short non-coding RNAs which play important roles in gene regulation. Different miRNA expression patterns have been described for human DCM and might represent potential diagnostic markers. There are no studies to date investigating miRNA expression profiles in canine DCM.  Goals: The goals of this study were to screen the miRNAs expression profile of canine serum by using a miRNA microarray platform and to compare the miRNA expression patterns of a group of Doberman Pinschers with DCM and healthy controls.  Results: Although total RNA concentrations were very low in canine serum samples, 421 different miRNAs were detectable with sufficient signal intensity on the miRNA microarrays. About 30 miRNAs were differentially expressed in the two groups, but did not reach statistical significance. No significant differences were found using specific miRNA PCR assays.   Conclusions: More than 400 miRNAs can be detected in canine serum samples. Changes in expression levels of various miRNAs between healthy and DCM dogs could be detected, but the results did not reach statistical significance most probably due to the small group size. miRNAs are potential new circulating biomarkers in veterinary medicine and should be investigated in larger patient groups and additional canine diseases

overall_design: Blood was drawn from two groups of Doberman Pinschers: 4 healthy dogs and 4 dogs suffering from dilated cardiomyopathy. After clotting, samples were centrifuged and total mRNA was extracted from serum. These 8 serum samples were analyzed and the groups were compared

first: Stefan

last: Bauersachs

first: Gerhard

last: Wess

first: Carola

last: Steudemann


title: Profiling livers from LPS-treated rats

city: West Point

first: I-Ming

last: Wang

state: PA

address: 770 Sumneytown Pike

department: Genetics and Pharmacogenomics

country: USA

institute: Merck Research Lab

summary: This program addresses the gene signature associated with LPS-treated liver in rat. Specifically, which genes are differentially expressed in livers of the Sprague Dawley rats treated with LPS?

overall_design: The LPS-treated liver profiling data was analyzed by identifying genes that were up- and down-regulated at selected p value and fold change in livers of the Sprague Dawley rats treated with LPS compared to the corresponding non-treated controls.

first: Bin

last: Zhang


title: Profiling whole lung from lung-specific IL-1b-Tg mice

summary: This program aims at identifying the lung gene signature associated with inflammation and emphysema in IL-1b-Tg mouse COPD model to facilitate understanding of the disease mechanism and therapeutic compound testing

overall_design: The lung profiling data was analyzed by identifying genes that were up- and down-regulated at selected p value and fold change in the lungs of IL-1b-Tg mice treated with doxycycline (to induce IL-1b transgene) compared to the corresponding water-treated controls.


title: Profiling muscle from aged rat model for sarcopenia

summary: This program aims at identifying a muscle gene signature associated with aging in rat sarcopenia model

overall_design: The profiling data was analyzed by identifying genes that were up- and down-regulated at selected p value and fold change in the muscle of aged rats compared to the young controls.


title: Identification of differentially expressed genes in equine endometrium at day 16 of early pregnancy

status: Public on Mar 31 2013

city: Lindau

middle: Michael

state: Zurich

address: Eschikon 27 EHB 23.1

department: Department for Farm Animals

country: Switzerland

institute: University of Zurich

summary: In order to systematically analyze the maternal, i.e. the endometrial, changes in the equine endometrium underlying the complex embryo-maternal dialogue during early pregnancy, a transcriptome study of endometrium samples from mares at day 16 of pregnancy and  day 12 cyclic mares was performed. Results were compared to a previous study of samples from day 12 of pregnancy and day 12 cyclic controls.

overall_design: Endometrial biopsies were taken from six wormblood mares at day 16 of early pregnancy after embryo recovery and day 12 cyclic controls. 8 samples were analyzed: one pregnant sample and the corresponding control sample of every mare each at a time.

first: Maximiliane

last: Merkl

first: Susanne

last: Ulbrich

first: Christiane

last: Otzdorff

first: Rüdiger

last: Wanke

first: Eckard

last: Wolf

first: Johannes

last: Handler


title: Profiling adipose tissue (eWAT) from obese ob/ob and lean control ob/+ mice

summary: This program addresses the molecular basis of beta-cell failure associated with the development of type 2 diabetes in the db/db mice. Specifically, which genes are differentially expressed in pancreatic islets of the db/db mice compared to the control db/+ mice?

overall_design: The db/db mice islets profiling data was analyzed by identifying genes that were up- and down-regulated at selected p value and fold change in the islets of db/db mice compared to the corresponding db/+ controls.


title: TLS-CHOP Fusion Oncoprotein Regulates MicroRNA-486 in Human Myxoid Liposarcoma

status: Public on Mar 23 2013

city: Sinjuku-ku

first: Masami

last: Tanaka

state: Tokyo

address: Sinjuku 6-1-1

country: Japan

institute: Tokyo Medical University

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

summary:
MicroRNAs (miRNAs, miRs) are small noncoding RNAs, which control or are controlled by the dysregulation of multiple protein-coding oncogenes or tumor suppressor genes, play important roles in carcinogenesis. Myxoid liposarcomas (MLS) are characterized by t(12;16)(q13;p11) translocation and expression of TLS/CHOP chimeric transcripts (various types) which encode different oncogenic proteins.  TLS-CHOP is important for the molecular mechanisms in the development of MLS, but the involvement in microRNA expression still remain poorly understood.
Thus we explored the target microRNA of TLS-CHOP influence cell-proliferation or cell death with microarray.
MicroRNAs (miRNAs, miRs) are small noncoding RNAs, which control or are controlled by the dysregulation of multiple protein-coding oncogenes or tumor suppressor genes, play important roles in carcinogenesis. Myxoid liposarcomas (MLS) are characterized by t(12;16)(q13;p11) translocation and expression of TLS/CHOP chimeric transcripts (various types) which encode different oncogenic proteins.  TLS-CHOP is important for the molecular mechanisms in the development of MLS, but the involvement in microRNA expression still remain poorly understood.  In this study, we have found that miR-486-5p (miR-486) expression level was downregulated by ectopic expression of TLS-CHOP fusion gene in mouse fibroblast cells (NIH3T3). In addition, we found overexpression of miR-486 inhibited the cell growth in the 2645/94 cells and in situ hybridization of miR-486 showed MLS tissues had lower signal intensity compared with non-tumor tissues.
Thus we explored the target genes of miR-486 influence cell-proliferation or cell death with microarray.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design:
We compared the microRNA profiles of cells treated with TLS-CHOP or empty vector about NIH-3T3 cell-line.
We compared the whole mRNA profiles of cells transfected with miR-486 oligonucleotides or control oligo about myxoid liposarcoma cell-line.

first: Nariso

last: Brojigin

first: Shinichiro

last: Ohno

first: Tanaka

last: Masami

first: Weihong

last: Wu

first: Suzuki

last: Rieko

first: Koji

last: Fujita

first: Masakatsu

last: Takanashi

first: Masahiko

last: Kuroda


title: MicroRNA regulations during differentiation of mouse mammary stem cell-like cells

status: Public on Mar 29 2013

city: Houston

first: Eylem

last: Aydogdu

state: TX

address: 3605 Cullen Blvd SERC Bldg. #545

institute: University of Houston

summary: MicroRNAs are likely to play pivotal roles in both stem cells and cancer, and are further promising candidates for future therapeutic purposes. To understand the involvement of microRNAs throughout mammary cell differentiation, and the association between microRNAs, stem cells and cancer we profiled the expression of all known microRNA in different stages of mammary cell differentiation.

overall_design: MicroRNA microarray analysis was based on hybridization between the microRNA and its corresponding probes. RNA sequences were labeled with an affinity tag which allowed detection of microRNAs after hybridization to the chip. Dual color microarray assays were carried out such that each sample (stem cell-like and fully-differentiated) was labeled with either Cy3 or Cy5 dye. Errors introduced by differential labeling were adjusted using dye-swap replicates.

first: Cecilia

last: Williams


title: Profiling whole lung from Ovalbumin (OVA)-challenged and control BALB/c mice

first: I-Ming

last: Wang

summary: This program aims at identifying the lung gene signature associated with OVA-challenged mouse asthma model to facilitate understanding of the disease mechanism and therapeutic compound testing

overall_design: The OVA-challenged profiling data was analyzed by identifying genes that were up- and down-regulated at selected p value and fold change in the lungs of OVA-challenged mice compared to the corresponding PBS-treated controls.

first: Bin

last: Zhang


title: Profiling fibrotic lung in TGFb1-Tg mice

summary: Transgenic (Tg) mice over-expressing TGFb1 in a lung-specific manner display airway inflammation and fibrosis, phenotypes relevant to human COPD and asthma. This model system provides a platform for identifying and validating genes/pathways involved in these disease pathogeneses.

overall_design: The TGFb1-Tg mice lung profiling data was analyzed by identifying genes that were up- and down-regulated at selected p value and fold change in the lung of TGFb1-Tg mice compared to the corresponding wild type controls.


title: Profiling pancreatic islets from obese db/db and lean control db/+ mice


title: Zebrafish 22 hpf embryos: WT vs. MO-grnA injected

status: Public on Mar 28 2013

city: Taipei

first: gen

middle: hwa

last: lin

state: Nankang

address: 128,section2,academia road

department: Institute of Cellular and Organismic Biology

country: Taiwan

institute: Academia Sinica

summary: Transcriptional profiling of zebrafish embryos comparing wild type untreated embryos with embryos injected with morpholino of zf-grna. This assay is used for the determination of expression profiling at 22 hpf under GRN-A deficiency.

overall_design: Two-condition experiment: wild type vs. MO-grnA treated cells. 3 biological replicates: each group contains 200 embryos.

first: Yen-Hsing

last: Li

first: Ya-Wen

first: Gen-Hwa

last: Lin

first: Jen-Leih


title: MiRNA expression profile in murine early atherosclerotic plaque compared with un-diseased arterial tissue

status: Public on Mar 27 2013

first: Andreas

last: Schober

state: Bavaria

address: Pettenkoferstr. 9

department: Institute for Cardiovascular Prevention

institute: Ludwig-Maximilians-University

summary: Aberrantly expressed miRNAs contribute to developmental abnormalities and diseases such as cancer, diabetes, and cardiovascular disorders, by hybridizing to specific mRNA targets and repressing their translation into proteins. Although miRNA expression signature is characterized in the process of neointimal thickening during proliferative vascular diseases such as atherosclerosis, so far global miRNA expression profiling in the different stages of atherosclerosis is completely unknown. We explored stage-specific microRNA signatures in the progress of atherosclerosis in hyperlipidemia mouse model, which may help to identify the critical miRNAs contributing atherosclerotic development and stabilization.

overall_design: Female apoe-/- mice (6-8 weeks, Jackson Laboratory) were fed a high fat diet (HFD, 21% crude fat, 0.15% cholesterol and 19.5% casein, Altromin, Germany) for 3 or 10 months (N=3-4). Serial sections (20 µm thick) of aortic roots and carotid arteries from these mice were mounted on membrane mounted metal frame slides (MMI), deparaffinized under RNase-free conditions, and completely dried. Laser capture microdissection (LCM) was performed with a laser microdissection system (MMI cellcut plus, Molecular Machines and Industries, Switzerland) assembled onto an inverted microscope (Olympus IX71). Plaque tissue or morphologically normal vessel wall of at least 40 sections per mouse were collected. RNA was isolated using RecoverAll total nucleic acid isolation kit (Applied Biosystems) according to the manufacturer’s instructions.

first: Malihe

middle: N

last: Jahantigh

first: Yuanyuan

last: Wei


title: MiRNA expression profile in murine advanced atherosclerotic plaque compared with un-diseased arterial wall


title: Profiling liver from 5LO KO and WT B6 mice

summary: To understand the effects of knocking out the 5-LO gene on gene expression in key metabolic target tissues liver.

overall_design: The 5LO KO mouse liver profiling data was analyzed by identifying genes that were up- and down-regulated at selected p value and fold change in the liver of 5LO KO mice compared to the corresponding WT B6 controls.


title: An innate fear response in domestic chicks: screening for short copy number variations associated with tonic immobility

city: Kyoto

first: Hideaki

last: Abe

state: Kyoto

address: 2-24 Tanaka-Sekiden-cho, Sakyo

department: Wildlife Research Center

institute: Kyoto University

type: Genome variation profiling by genome tiling array

summary: We performed aCGH analysis among domestic chicks (Gallus gallus) with different sensitivity in the tonic immobility (TI) to identify the copy number aberrants within genes or regions responsible for innate fear responses.

overall_design: Four samples (high fear) were compared with a reference sample (low fear)

first: Miho

last: Inoue-Murayama


title: microRNA changes during pDC activation

status: Public on Mar 25 2013

city: Shanghai

last: Shen

address: 145 Shan Dong Middle Road

department: Department of Rheumatology

country: China

institute: Renji Hospital, JiaoTong University School of Medicine

summary: To identify microRNA changes during plasmacytoid dendritic cell (PDC) activation, we stimulated human primary PDCs with 10ug/ml R837 (Invivogen, San Diego, CA, USA) for 4 hours.

overall_design: Purified human pDCs were divided into two parts: one was cultured with medium alone, another was cultured with R837. 4 hours later, cells were collected and total RNA was extracted for the TaqMan® Human MicroRNA Arrays. The experiment was duplicated (sample1 and sample2).


title: Profiling brain cortex from tMCAO rat stroke model

summary: This program addresses the gene signature associated with brain (cortex) in the tMCAO rat model for stroke.

overall_design: The tMCAO stroke model profiling data was analyzed by identifying genes that were up- and down-regulated at selected p value and fold change in brain cortex of the Sprague Dawley rats following middle cerebral artery occlusion compared to the sham-operated controls.


title: Transcriptomic profile of human preadipocyte treated by macrophages from adipose tissue

city: Paris

first: Danièle

last: Lacasa

address: 15 rue de l'Ecole de Médecine

country: France

institute: INSERM

summary:
Obesity is characterized by a chronic auto-inflammation of the hypertrophied white adipose tissue (WAT) associated with metabolic and vascular complications. WAT of obese subjects produces inflammatory factors like cytokines (IL6, TNF-alpha) and chemokines (CCL2 and IL-8) originating mainly from the accumulated macrophages. WAT macrophages profoundly affect adipose cell biology leading in particular to the inflammation of the adipocytes and altered differentiation of their precursors, the pre-adipocytes.
We previously showed that conditioned media from WAT macrophages (ATM CM) induced inflammation in human pre-adipocytes. We performed pangenomic cDNA microarrays analysis to compare gene expression profiles between control and ATM CM treated preadipocytes. By a functional analysis, we identified the biological themes that best characterized the proinflammatory preadipocytes. The most significantly overrepresented GO Cellular Component categories were "cytokine-cytokine receptor interaction" and "chemokine signaling pathway", emphasizing the importance of cytokine and chemokine production by the inflammatory preadipocyte. The chemokines acting  in concert to recruit leukocytes in inflamed tissues, still need to be more precisely identified in human WAT. Thus, our data lead to the identification of new chemokines involved in attraction of immune cells in inflamed human WAT.

overall_design:
The transcriptomic profile of human preadipocytes was compared to that of preadipocyes treated by macrophages isolated from human adipose tissue.
Two-condition experiment,human control preadipocyte vs preadipocyte treated by macrophages from adipose tissue. 5 biological replicates (with a dye-swap design).

first: Christine

last: Rouault

first: Daniele

first: Corneliu

last: Henegar

first: Aurélie

last: Cotillard

first: Karine

last: Clément


title: Profiling skin from Carrageenan (CGN) rat model for inflammation pain

first: I-Ming

summary: This program aims at identifying a skin gene signature associated with inflammation pain in rat CGN model

overall_design: The profiling data was analyzed by identifying genes that were up- and down-regulated at selected p value and fold change in the skin of rats treated with CGN (to induce pain) compared to the corresponding non-treated controls.

first: Bin


title: Profiling epididymal white adipose tissue (eWAT) from obese db/db and lean control db/+ mice

summary: This program addresses the gene signature associated with the development of type 2 diabetes in the db/db mice. Specifically, which genes are differentially expressed in adipose tissue of the db/db mice compared to the control db/+ mice?

overall_design: The db/db mice eWAT profiling data was analyzed by identifying genes that were up- and down-regulated at selected p value and fold change in the eWAT of db/db mice compared to the corresponding db/+ controls.


title: Profiling Chung rat model for neuropathic pain

summary: This program addresses the gene signature associated with DRG in the Chung rat model for neuropathic pain.

overall_design: The Chung neuropathic pain profiling data was analyzed by identifying genes that were up- and down-regulated at selected p value and fold change in DRG of the Sprague Dawley rats following spinal nerve ligation compared to the sham-operated controls.


title: Genome array of hair follicle genes in lamp skin with different patterns

status: Public on Mar 26 2013

city: China yangzhou

first: nirong

last: nirong

address: Yangzhou city,yangzhou university  wenhui road

institute: yangzhou nuiversity

summary: Differentially expressed genes in the skin tissue of newborn Hu sheep were screened using an Agilent gene chip and RT-PCR. Differential expression analysis revealed 3 groups of large waves and small waves; 1067, 2071, and 3879 differentially expressed genes; and 137 genes common to all 3 groups. Differentially expressed genes were classified using gene ontology. They were found to be mainly involved in cell differentiation, proliferation, apoptosis, growth, immune response, and ion transport. RT-PCR results of 4 differentially expressed genes were consistent with gene chip results. Combined with related literature, our results suggest that BMP7, MMP2, SNAI1, SFXN1, CDKNIC, MT3, and POU1F1 may have important effects on the formation of large-wave and small-wave hair follicles.

overall_design: The samples collected with three full-sib individual and they borned at two days, what's more they were from the same paternal, each pair of big wave and small wave individuals from the same female parent.

first: W

last: Sun

first: R

last: Ni

first: J

middle: F

last: Yin

first: Hassan

middle: H

last: Musa

middle: T

last: Ding

first: L

last: Chen


title: MiRNA expression profile in murine advanced atherosclerotic plaque compared with early atherosclerotic plaque

first: Andreas

last: Schober

first: Malihe

last: Jahantigh

first: Yuanyuan


title: Expression of Human DAMPmiRs

city: Doha

first: Francesco

middle: Maria

last: Marincola

address: Al Nasr Tower, AL Corniche Street, PO Box 26999

country: Qatar

institute: Sidra Medical and Research Center

summary: Endogenous damage associated molecular pattern molecules (DAMPs) released from necrotic, damaged or stressed cells are associated with an inflammatory response. Whether the microRNA expression signature of this response is different from that of a PAMP-stimulated inflammatory response is unknown. We report here that miR-34c and miR-214 are significantly expressed in fresh human PBMCs exposed to DAMPcontaining freeze-thaw lysates, or to conditioned media from serum-starved and glucose-deprived cells (p<6x10-4 and p<3.7x10-3), respectively. Interestingly, only miR-34c expression was differentially expressed in PBMCs exposed to freeze-thaw lysates or conditioned media from HMGB1+/+ mouse embryonic fibroblast (MEF) cells, when compared to cultures exposed to lysates or conditioned media from HMGB1-/- MEFs. miR-155 expression in these cultures was negligible, but was significantly higher in PBMCs stimulated with LPS or most other TLR ligands, making it the prototypic PAMPmiR. Exposure to a damaged human colorectal carcinoma cell line lysate (HCT116) similarly resulted in increased miR-34c and miR-214 levels. When PBMCs were pre-transfected with anti-miR-34c and then exposed to lysate, expression levels of IKKgamma mRNA, a putative target of miR-34c, increased, while protein levels of IKKgamma in cultures transfected with a pre-miR-34c were abrogated. Levels of miR-34c expression (as well as pro-inflammatory cytokines, IL-1beta and TNFalpha) decreased when PBMC cultures were briefly pre-incubated with the K+ channel (inflammasome) inhibitor, glybenclamide, suggesting that miR-34c is involved in the inflammasome pathway in response to DAMPs. Our findings suggest that a specific microRNA expression signature is associated with the inflammatory response to damaged/injured cells and carries implications for many acute and chronic inflammatory disorders.

overall_design: Human PBMC (peripheral blood mononuclear cells) were exposed to 4 conditions for 48 hours. In the first condition, PBMCs were exposed to conditioned media from serum-starved and glucose-deprived and heat shocked HMGB1-/- MEF cells (mouse embryonic fibroblast cells). In the second condition, PBMCs were exposed to conditioned media from serum-starved and glucose-deprived and heat shocked HMGB1+/+ MEF cells (mouse embryonic fibroblast cells). In the third condition, PBMCs were exposed to LPS (Lipopolysaccharide). In the fourth condition, the PBMCs where left untreated. Four biological repeats were done for each condition for a total of 16 samples.


title: Identification of direct target genes of the tomato fruit-ripening regulator RIN by promoter ChIP-chip

city: Tsukuba

first: Yasuhiro

last: Ito

state: Ibaraki

address: 2-1-12 Kannondai

department: Food Biotechnology Division

institute: National Food Research Institute

type: Genome binding/occupancy profiling by genome tiling array

summary: The tomato (Solanum lycopersicum) MADS-box transcription factor RIN, one of the earliest-acting fruit-ripening regulators, is required for both ethylene-dependent and -independent regulatory pathways for fruit ripeing.  Here, we performed chromatin immunoprecipitation coupled with a DNA microarray (ChIP-chip) for the putative promoters of whole tomato predicted genes (ITAG2) for the genome-wide identification of the direct RIN targets. The ChIP-chip with anti-RIN antibody resulted in detection of 1,046 RIN-binding sites, each of which was assigned a significantly high peak score (FDR≤0.05) in at least two of the three biologically independent analyses. Using the information about genomic position of the RIN-binding sites, we found 1,200 genes as potential direct RIN targets that carried one or more RIN-binding sites in the transcription regulatory region (2-kb upstream putative promoter) or in other gene regions, such as exons, introns or a downstream region from the translation termination site (1-kb), where the promoter region of a neighbor gene are overlapped.

overall_design: Three biologically independent samples (chromatin-immunoprecipitated DNA and input DNA) recovered from the ripening tomato fruits.

first: M

last: Fujisawa

first: T

last: Nakano

first: Y

last: Shima


title: Profiling aorta from high fat diet (HFD)-fed ApoE KO and wild type C57BL6 mice

last: Wang

summary: This program aimed to understand gene expression changes in aorta during atherosclerotic lesion progression with an objective to identify genes that may present new opportunities for drug intervention

overall_design: The HFD-fed ApoE KO mice aorta profiling data was analyzed by identifying genes that were up- and down-regulated at selected p value and fold change in comparison to the HFD-fed WT C57BL6 controls.

last: Zhang


title: MiRNA expression profile in murine un-diseased arterial tissue on 3 month high fat diet vs 10 month high fat diet

last: Wei


title: MiRNA expression profile in murine

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

overall_design: Refer to individual Series


title: Various mice and rat tissues subjected to various treatments

sample_organism:
Mus musculus
Rattus norvegicus

platform_organism:
Mus musculus
Rattus norvegicus


title: A central role for TFIID in the pluripotent transcription circuitry [PP003]

status: Public on Mar 21 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: Pluripotent stem cells can be isolated from early embryos or induced by cell fusion, somatic nuclear transfer, or expression of a selected set of transcription factors. Embryonic stem (ES) cells are characterized by an open chromatin configuration and high transcription levels achieved via autoregulatory and feed-forward transcription factor loops. How the general transcription machinery is involved in pluripotency is unclear. Here, we show that TFIID knockdown affected the pluripotent circuitry in ES cells and inhibited reprogramming of fibroblasts. TFIID and pluripotency factors form a feed-forward loop to induce and maintain a stable transcription state. Strikingly, transient expression of TFIID subunits greatly enhanced reprogramming by Oct4, Sox2, Klf4 and c-Myc reaching efficiencies upto 50%. These results show that TFIID is a critical and selective component for transcription factor-mediated reprogramming. We anticipate that by creating plasticity in gene expression programs, basal transcription complexes such as TFIID assist reprogramming into different cellular states.

overall_design: Three iPS lines, iPS#1, iPS#4, and iPS#5 were used in duplicate for microarray analysis against a pool of RNA from ES-cells.

middle: P

last: Pijnappel

first: Daniel

last: Esch

first: Marijke

last: Baltissen

first: Guangming

last: Wu

first: Nikolai

last: Mischerikow

first: Atze

middle: J

last: Bergsma

first: Dong

middle: W

last: Han

first: Hermann

last: vom Bruch

first: Sören

last: Moritz

first: Dik

last: van Leenen

first: A

middle: M

last: Altelaar

first: Katrin

last: Sameith

first: Albert

last: Heck

first: Frank

middle: C

last: Holstege


title: A central role for TFIID in the pluripotent transcription circuitry


title: AURATUS goldfish environmental genomics projects: dopamine depletion in hypothalamus and telencephalon

status: Public on Mar 20 2013

city: Ottawa

first: Jason

middle: T.

last: Popesku

state: ON

address: 20 Marie Curie

department: Biology

country: Canada

institute: University of Ottawa

summary:
Sexually mature (mid-May) adult female goldfish received a single injection of 1-methyl-4-phenyl-1,2,3,6-tetrahydropyridine (MPTP; 50 ug/g body weight at 5 uL/g body weight) or 0.6% saline on day 0 and a single injection of alpha-methyl-p-tyrosine (aMPT;  240 ug/g body weight at 5 uL/g body weight) or 0.6% saline on Day 5 with the goal of severely deplete catecholamine (dopamine and norepinephrine) levels.
Hypothalamus tissue was extracted on Day 6.
Telencephalon tissue was extracted on Day 6.
The objective of this study was to examine gene expression changes in the neuroendocrine brain in response to catecholamine depletion.

platform_organism:
Carassius auratus
Cyprinus carpio

overall_design:
A common reference design was used for both the hypothalamus and telencephalon groups:

Hypothalamus: 3 independent groups of hypothalami from sexually mature female goldfish treated with 50 ug/g MPTP + 240 ug/g aMPT hybridized against a common vehicle control.  An additional group was used for a dye-swap.
Slides 4, 17, 21, 52.

Telencephalon: 3 independent groups of telencephali from sexually mature female goldfish treated with 50 ug/g MPTP + 240 ug/g aMPT hybridized against a common vehicle control. An additional group was used for a dye-swap.
Slides 28, 34, 43, 48.

first: Chris

last: Martyniuk

first: Vance

middle: L

last: Trudeau


title: AURATUS goldfish environmental genomics projects: SCH 23390 in the telencephalon

summary:
Sexually regressing female goldfish were administered 2 i.p. injections:
1) 40 ug/g SCH 23390 in 0.1% DMSO and 0.6% saline, and;
2) 0.6% saline

Tissues were harvested 5h post-injection.

overall_design:
A common reference design was used:
4 independent groups of telencephali from sexually regressing female goldfish treated with 40 ug/g SCH 23390 hybridized against a common vehicle control.
Slides 3, 19, 36, 41


title: AURATUS goldfish environmental genomics projects: sulpiride in the hypothalamus

summary:
Sexually regressing female goldfish were administered 2 i.p. injections:
1) 6 ug/g sulpiride in 0.1% DMSO and 0.6% saline, and;
2) 0.6% saline
Tissues were harvested 5h post-injection.

overall_design:
A common reference design was used:
4 independent groups of hypothalami from sexually mature female goldfish treated with 6 ug/g sulpiride hybridized against a common vehicle control.
Slides 6, 15, 28, 44.


title: A central role for TFIID in the pluripotent transcription circuitry [PP002]

first: Marian

last: Groot Koerkamp

overall_design: Two Taf5 knockdown cell lines and two control knockdown lines were each grown in duplicate and analysed on microarray against a pool of RNA from the parental ES-cells

first: W

last: Pijnappel


title: A Distinct Reactive Oxygen Species Profile confers Chemoresistance in Glioma-Propagating Cells and Associates with Patient Survival Outcome

status: Public on Mar 13 2013

city: Cambridge

first: Felicia

last: Ng

address: Wellcome Trust/MRC Building, Addenbrooke's Hospital, Hills Road

country: United Kingdom

institute: Cambridge Institute for Medical Research

summary: Aims: We explore the role of elevated O2-:H2O2 ratio as a prosurvival signal in glioma-propagating cells (GPCs). We hypothesize that depleting this ratio sensitizes GPCs to apoptotic triggers. Results: We observed that elevated O2-:H2O2 ratio conferred enhanced resistance in GPCs, and depletion of this ratio by pharmacological and genetic methods sensitized cells to apopotic triggers. We established the ROS Index as a quantitative measure of normalized O2-:H2O2 ratio and determined its utility in predicting chemosensitivity. Importantly, mice implanted with GPCs of reduced ROS Index demonstrated extended survival. Analysis of tumor sections revealed effective targeting of CD133- and nestin-expressing neural precursors. Furthermore, we established the Connectivity Map to interrogate a gene signature derived from varied ROS Index for patterns of association with individual patient gene expression in 2 clinical databases. We showed that patients with reduced ROS Index demonstrate better survival. These data provide clinical evidence for the viability of our O2-:H2O2-mediated chemosensitivity profiles. Innovation and Conclusion: Gliomas are notoriously recurrent and highly infiltrative, and have been shown to arise from stem-like cells. We implicate elevated O2-:H2O2 ratio as a prosurvival signal in GPC self-renewal and proliferation. The ROS Index provides quantification of O2-:H2O2-mediated chemosensitivity, an advancement in a previously qualitative field. Intriguingly, glioma patients with reduced ROS Index correlate with longer survival and the Proneural molecular classification, a feature frequently associated with tumors of better prognosis. These data emphasize the feasibility of manipulating the O2-:H2O2 ratio as a therapeutic strategy.

overall_design: Total RNA from primary neurosphere culture of brain tumor specimens treated with DPI and DDC as well as non-treated CD133+ and CD133- fractions were compared.  Specimens were obtained from 3 patients and replicate arrays were performed for all 3 neurosphere cultures.

first: Lynette

last: Koh

first: Geraldene

middle: S

first: Tan-Boon

last: Toh

first: Mark

last: Phong

first: Greg

last: Tucker-Kellogg

first: Oi-Lian

last: Kon

first: Shazib

last: Pervaiz

first: Beng-Ti

last: Ang

first: Carol

last: Tang

first: Edwin

last: Sandanaraj

first: Chong

last: Yuk Kien

first: Ng

last: Wai Hoe

last: Ivan Hua-Bak

first: Clement

last: Marie-Veronique


title: AURATUS goldfish environmental genomics projects: SCH 23390 in the hypothalamus

first: Jason

last: Popesku

summary:
Sexually regressing female goldfish were administered 2 i.p. injections:
1) 40 ug/g SCH 23390 in 0.1% DMSO and 0.6% saline, and;
2) 0.6% saline
Tissues were harvested 5h post-injection.

overall_design:
A common reference design was used:
4 independent groups of telencephali from sexually regressing female goldfish treated with 40 ug/g SCH 23390 hybridized against a common vehicle control.
Slides 16, 24, 30, 35

first: Vance

last: Trudeau


title: Isw2 and Ume6 ChIP-chip in transcription factor deletion (Δume6, Δnrg1, Δcin5, and Δsok2) and DNA-looping deficient (sua7-1) cells

status: Public on Mar 14 2013

city: Seattle

first: Toshio

last: Tsukiyama

state: WA

address: 1100 Fairview Ave N

department: Basic Science

institute: Fred Hutchinson Cancer Research Center

summary: The sequence-specific transcription factors Ume6, Nrg1, Cin5, and Sok2 and the general transcription factor TFIIB mediate the genome-wide targeting of the ATP-dependent chromatin remodeling enzyme Isw2.

overall_design: At least two biological replicates comparing Isw2-ChIP (Isw2-K215R ChIP DNA competitively hybridized against WT Isw2 ChIP DNA) in WT and Δume6, Δnrg1, Δcin5, Δsok2, and sua7-1 strains or Ume6-ChIP (ChIP DNA competitively hybridized again Input DNA) in WT and sua7-1 strains

first: Adam

last: Yadon


title: AURATUS goldfish environmental genomics projects: sulpiride in the telencephalon

summary:
Sexually regressing female goldfish were administered 2 i.p. injections:
1) 6 ug/g sulpiride in 0.1% DMSO and 0.6% saline, and;
2) 0.6% saline

Tissues were harvested 5h post-injection.

overall_design:
A common reference design was used:
4 independent groups of telencephali from sexually regressing female goldfish treated with 6 ug/g sulpiride hybridized against a common vehicle control.
Slides 12, 26, 37, 48


title: AURATUS goldfish environmental genomics projects: quinpirole in the telencephalon

summary:
Sexually mature female goldfish were administered 2 i.p. injections:
1) 0.1% DMSO in 0.6% saline, and;
2) 0.6% saline OR quinpirole (2 ug/g) dissolved in 0.6% saline.

overall_design:
A common reference design was used:
4 independent groups of telencephali from sexually mature female goldfish treated with 2 ug/g quinpirole hybridized against a common vehicle control.
Slides 8, 16, 24, 40.

first: Chris

last: Martyniuk

first: Susanna

last: Wiens


title: Defining a molecular roadmap of cellular reprogramming into iPS Cells [DNA methylation]

status: Public on Mar 18 2013

city: Boston

first: Ben

middle: S.

last: Wittner

state: MA

address: 149 13th Street

department: Center for Cancer Research

institute: Massachusetts General Hospital

type: Methylation profiling by genome tiling array

summary: Factor-induced reprogramming of somatic cells into induced pluripotent stem cells (iPSCs) is inefficient, complicating mechanistic studies. Here, we examined defined intermediate cell populations poised to becoming iPSCs by genome-wide analyses. We show that induced pluripotency elicits two transcriptional waves, which are driven by c-Myc/Klf4 (first wave) and Oct4/Sox2/Klf4 (second wave). Cells that become refractory to reprogramming activate the first but fail to initiate the second transcriptional wave and can be rescued by elevated expression of all four factors. The establishment of bivalent domains occurs gradually after the first wave, whereas changes in DNA methylation take place after the second wave when cells acquire stable pluripotency. This integrative analysis allowed us to identify genes that act as roadblocks during reprogramming and surface markers that further enrich for cells prone to forming iPSCs. Collectively, our data offer new mechanistic insights into the nature and sequence of molecular events inherent to cellular reprogramming.

overall_design: DNA methylation profiles obtained at different timepoints during reprogramming of somatic cells: Day 0, +3, +6, +9 and iPSC

first: Jose

last: Polo

first: Maria

middle: E

last: Figueroa

first: Konrad

last: Hochedlinger


title: AURATUS goldfish environmental genomics projects: SKF 38393 in the telencephalon

summary:
Sexually mature female goldfish were administered 2 i.p. injections:
1) 0.1% DMSO in 0.6% saline or SKF 38393 (40 µg/g) dissolved in 0.1% DMSO in 0.6% saline, and;
2) 0.6% saline.

overall_design:
A common reference design was used:
4 independent groups of telencephali from sexually mature female goldfish treated with 40 ug/g SKF 38393 hybridized against a common vehicle control.
Slides 7, 13, 30, 47.


title: CLP1 links tRNA metabolism to progressive motor-neuron loss

status: Public on Mar 12 2013

city: Bolzano

first: Johannes

last: Rainer

address: Via A. Volta 21

department: Institute for Biomedicine

country: Italy

institute: Eurac Researc

summary: CLP1 was the first mammalian RNA kinase to be identified. However, determining its in vivo function has been elusive. Here we generated kinase-dead Clp1 (Clp1K/K) mice that show a progressive loss of spinal motor neurons associated with axonal degeneration in the peripheral nerves and denervation of neuromuscular junctions, resulting in impaired motor function, muscle weakness, paralysis and fatal respiratory failure. Transgenic rescue experiments show that CLP1 functions in motor neurons. Mechanistically, loss of CLP1 activity results in accumulation of a novel set of small RNA fragments, derived from aberrant processing of tyrosine pre-transfer RNA. These tRNA fragments sensitize cells to oxidative-stress-induced p53 (also known as TRP53) activation and p53-dependent cell death. Genetic inactivation of p53 rescues Clp1K/K mice from the motor neuron loss, muscle denervation and respiratory failure. Our experiments uncover a mechanistic link between tRNA processing, formation of a new RNA species and progressive loss of lower motor neurons regulated by p53.

overall_design: RNA was extracted from spinal cord of 3 Clp1 knock-out mice and 3 wild type mice (15 days old, male, all samples age and sex matched) and submitted to differential splicing analysis using Affymetrix Exon microarrays. Differential splicing analysis was performed between the Clp1 KO and WT samles employing a custom CDF, that was based on a complete re-alignment of oligonucleotide probes to the genome and transcriptome (Ensembl 52, ASTD 1.1; further information on http://bioinfo.i-med.ac.at).

first: Toshikatsu

last: Hanada

first: Stefan

last: Weitzer

first: Barbara

last: Mair

first: Reiko

first: Shane

last: Cronin

first: Vukislav

last: Komnenovic

first: Adi

last: Minis

first: Hiromitsu

last: Mimata

first: Akihiko

last: Yoshimura

first: Reinhard

last: Kofler

first: Avraham

last: Yaron

first: Clifford

last: Woolf

first: Ruth

last: Herbst

first: Javier

last: Martinez

first: Josef

last: Penninger


title: Monitoring Homology Search during DNA Double-Strand Break Repair in vivo

city: Martinsried/Munich

first: Jörg

last: Renkawitz

address: Am Klopferspitz 18

department: Molecular Cell Biology

institute: Max Planck Institute of Biochemistry

summary: Homologous recombination (HR) is crucial for genetic exchange, accurate repair of DNA double-strand breaks and pivotal for genome integrity. HR uses homologous sequences for repair, but how homology search, the exploration of the genome for homologous DNA sequences, is conducted in the nucleus remains poorly understood. Here, we use time-resolved chromatin immunoprecipitations of repair proteins to monitor homology search in vivo. We found that homology search proceeds by a probing mechanism, which commences around the break and samples preferentially on the broken chromosome. However, elements thought to instruct chromosome loops mediate homology search shortcuts, and centromeres, which cluster within the nucleus, may facilitate homology search on other chromosomes. Our study thus revealed crucial parameters for homology search in vivo and emphasizes the importance of linear distance, chromosome architecture and proximity for recombination efficiency.

overall_design:
2 new custom ChIP-chip platforms used; both Nimblegen; differ in oligo density: (platform 1: 2006-07-18_Scerevisiae_ChIP_Stefan Jentsch MPI Biochemistry S.cerevisiae 385K Tiling Array Version 1) ( platform 2: 100304_Scer2_MS_Chip_Stefan Jentsch MPI Biochemistry S.cerevisiae 135K Tiling Array Version 2)
ChIP-chip profiling of DSB repair factors (Rad51, Rad52, RPA, gamma-H2A) upon single inducible DSBs in S.cerevisiae

first: Claudio

middle: A

last: Lademann

first: Marian

last: Kalocsay

last: Jentsch


title: AURATUS goldfish environmental genomics projects: dopamine antagonists

first: Jason

last: Popesku


title: Methylation profiling of Glioma Stem Cell lines vs GBM FFPE tissue biopsies and foetal Neural Stem Cell lines

status: Public on Mar 08 2013

city: Monza

first: Simona

last: Baronchelli

address: Via Cadore 48

institute: University of Milan-Bicocca

summary: The DNA methylation profiles of Glioma Stem Cell (GSC) lines were investigated in order to find the stem cell signature associated to glioblastoma (GBM). This goal was achieved through the comparison of GSC methylation data with FFPE-GBM biopsies and human foetal Neural Stem Cell (NSC) lines profiles.

overall_design: GSC lines: 3 (GBM2, G144, G166). FFPE-GBM biopsy pool: FFPE-GBM pool: 1 pool from 5 GBM biopsies. Human foetal NSC lines: 2 (CB660 from forebrain; CB660SP form spinal cord). Methylated DNA from each sample was enriched with the immunoprecipitation method using 5-methylcytosine antibody (Eurogentec). Immunoprecipitated DNA (IP-DNA) and total DNA were labeled and hybridized on Agilent Human CpG Island ChIP-on-Chip Microarray 244K. IP-DNA were labeled with Cy5 while the matching total DNA were labeled with Cy3.

first: Angela

last: Bentivegna

first: Serena

last: Redaelli

first: Gabriele

last: Riva

first: Valentina

last: Butta

first: Laura

last: Paoletta

first: Leda

last: Dalprà


title: miRNAs regulation by miR-145 in pancreatic cancer

status: Public on Mar 19 2013

city: Baltimore

first: Tai-Chung

last: Huang

state: MD

address: 733 N Broadway BRB R560

department: Institute of Genetic Medicine

institute: Johns Hopkins University School of Medicine

summary: miR-145 is a tumor suppressor miRNA in various malignancies including pancreatic cancer. How miR-145 regulates expression of other miRNAs could provide a panoramic view of the development of pancreatic cancer. Therefore, in this project, we aimed to characterize how other miRNAs are affected by miR-145 in hope for understanding proteomic changes that are not explained by miR-145 alone.

overall_design: miRNA microarray was used to compare expression of all miRNAs 48 hr after transfection of miR-145 mimics or control scramble RNA in a pancreatic cancer cell line, Mia-PaCa2.

first: Tai

first: Yi

last: Yang

first: Akhilesh

last: Pandey


title: European eel immune response against Vibrio vulnificus challenge

status: Public on Mar 15 2013

city: Burjassot

first: Agnès

last: Callol Junyer

address: Dr. Moliner, 50

department: Microbiology & Ecology

country: Spain

institute: University of Valencia

summary: Vibriosis caused by Vibrio vulnificus on eels represents an important threat for this specie under culture conditions. Development of new transcriptomic tools is essential to increase the knowledge of eel biology, that nowadays is scarcer. Therefore, using previous results obtained by 454 sequencing of the eel immune-enriched transcriptome, an eel-specific custom microarray have been designed. Gills transcriptomic pattern were analyzed as a principal portal of entry for pathogens in fish after 1h of bath infection with Vibrio vulnificus to describe gill immune response. Moreover, two different strains were used, vibro vulnificus wild type (R99) and rtx double mutant (CT285), to asses the virulence of these pathogen caused by MARTX.

overall_design: Adult european eels were bath infected with two Vibrio vulnificus strains, the wild type and double Rtx mutant (CT285). After 0, 3, 12h post-infection eel gills were sampled. Three individuals per experimental point were sampled, including a Control group and a Handling control group. Obtaining a total of 24 samples. The transcriptomic profile was described for each individual sample.

last: Callol

first: Simon

last: Mackenzie

first: Carmen

last: Amaro

first: Sebastian

last: Boltaña


title: Functional profiling in yeast with the benzene metabolites hydroquinone, catechol and 1,2,4-benzenetriol

city: Berkeley

first: Chris

last: Vulpe

state: Ca

address: 119 Morgan Hall

department: Nutritional Sciences and Toxicology

institute: UC Berkeley

summary:
Benzene is a ubiquitous environmental contaminant and is widely used in industry. Exposure to benzene causes a number of serious health problems, including blood disorders and leukemia. Benzene undergoes complex metabolism in humans, making mechanistic determination of benzene toxicity difficult. We used a functional genomics approach to identify the genes that modulate the cellular toxicity of three of the phenolic metabolites of benzene, hydroquinone (HQ), catechol (CAT) and 1,2,4-benzenetriol (BT), in the model eukaryote Saccharomyces cerevisiae. Benzene metabolites generate oxidative and cytoskeletal stress, and tolerance requires correct regulation of iron homeostasis and the vacuolar ATPase. We have identified a conserved bZIP transcription factor, Yap3p, as important for a HQ-specific response pathway, as well as two genes that encode putative NAD(P)H:quinone oxidoreductases, PST2 and YCP4. Many of the yeast genes identified have human orthologs that may modulate human benzene toxicity in a similar manner and could play a role in benzene exposure-related disease.
Genome-Wide Functional Profiling Reveals Genes Required for Tolerance to Benzene Metabolites in Yeast. PLoS ONE 2011, 6(8):e24205 - PMID: 21912624.

overall_design: Pools of homozygous diploid deletion mutants (n = 4,607 strains) were grown in rich media (YPD) at 3 concentrations of hydroquinone (HQ), catechol (CAT) and 1,2,4-benzenetriol (BT) for 5 and 15 generations (5g, 15g). Each strain has a deletion in a different gene. In each strain, the gene was replaced by a deletion cassette containing a antibiotic resistance gene and two BARCODES, up and down tags (Please see Giaever et al, 2002, Nature). These tags in the DNA are specific to each strain. We pool all deletion strains and grow them under a selective condition; extract DNA; amplify barcodes using universal primers and hybridize to arrays containing complemetary sequences to the up and down tags. In this way, we can look at growth of each of the strains. Our strategy is to analyze separately the up and down tags. Therefore, for each array (CEL file), we generate two data files, one for all ups and another one for all downs. In these files, the list of genes are the same but the data come from different set of probes, up or down. The values are log2 averages of replicate probes for the same tag. These pre processed files were used to identify strains with differential growth in benzene metabolites by comparing to the control arrays.

first: Matthew

last: North

first: Vickram

last: Tandon

first: Reuben

last: Thomas

first: Alex

last: Loguinov

first: Inna

last: Gerlovina

first: Alan

last: Hubbard

first: Luoping

last: Zhang

first: Martyn

last: Smith

middle: D


title: MMP14 knockdown at U87 brain tumor cells.Analyse of the genes responsible for cell division

city: Chicago

first: Ilya

last: Ulasov

address: 5841 S Maryland ave SBRO J339

institute: University of Chicago

summary: Compared to the Scramble U87 cells, MMP14 ablation induces G2M arrest

overall_design: SABioscience Cell cycle platform, human genes. U87 cells were infected separately with eithr lentivirus carry on Scramble or sh RNA against human MMP14 gene.Equla amount of mRNA was isolated prior RT-PCR  analyses


title: Anchoring ethinylestradiol induced gene expression changes with testicular morphology and reproductive function in the medaka

status: Public on Mar 06 2013

city: Durham

first: Hilary

last: Miller

state: NC

address: LSRC Science Drive Rm A305

institute: Duke University

summary: This study assessed the implications of a 14 day sub-chronic exposure of ethinylestradiol (EE2; 1.0 or 10.0 µg/L EE2) on male medaka fertility, testicular histology and testicular gene expression. The findings demonstrate that a 14 day exposure to EE2 induced impaired male reproductive capacity and time- and dose-dependent alterations in testicular morphology and gene expression. The average fertilization rate/day following the exposure for control, 1.0 and 10.0 µg/L EE2 was 91.3% (±4.4), 62.8% (±8.3) and 28.8% (±5.8), respectively. The testicular morphologic alterations observed include increased germ cell apoptosis, decreased germinal epithelium and thickening of the interstitium. The morphologic changes observed were highly associated with gene expression changes observed using a medaka-specific microarray. A pathway analysis of the differentially expressed genes emphasized genes and pathways associated with apoptosis, cell cycle and proliferation, collagen production/extracellular matrix organization, hormone signaling, male reproduction and protein ubiquitination among others.

overall_design: Six month old male medaka were exposed to ethinyl estradiol (EE2) for a 14 day time period. Treatment exposures were completed in triplicate including DMSO (vehicle control), 1.0 µg/L EE2, and 10.0 µg/L EE2. Fish were sampled for gene expression on days 1, 7 and 14 of exposure. Five male fish were placed in 2-liter beaker replicates for each treatment and sampling time point.

first: Bryan

last: Clark

first: David

last: Hinton

first: Andrew

last: Whitehead

first: Stan

last: Martin

first: Kevin

last: Kwok

first: Seth

last: Kullman


title: Involvement of miRNAs in the induced differentiation of glioblastoma multiforme brain tumor stem-like cells [Exiqon miRNA array]

status: Public on Mar 05 2013

city: Pamplona

first: Raquel

last: Malumbres

state: Navarra

address: Avenida Pio XII 55

department: Hemato-Oncology

institute: University of Navarra/ Clínica Universidad de Navarra

summary: Brain tumor neurospheres (BTCSs) are cancer cells with neural stem cell-like properties found in the fatal brain tumor glioblastoma multiforme (GBM). These cells account for less than 1% of total tumor cells, are poorly differentiated and are believed to be involved in tumor induction, progression, treatment resistance and relapse. Specific miRNAs play important roles in modulating the proliferation and differentiation of neural stem cells, therefore, we aimed to identify miRNAs controlling differentiation in GBM-BTSCs through high throughput screening miRNA array profiling. We compared the miRNA expression profiles at the neurosphere state and upon 4 and 14 days of differentiation by using LIMMA, finding 21 differentially expressed miRNAs : hsa-miR-103, hsa-miR-106a, hsa-miR-106b, hsa-miR-15b, hsa-miR-17, hsa-miR-19a, hsa-miR-20a, hsa-miR-25, hsa-miR-301a and hsa-miR-93 were found up-regulated upon differentiation, while hsa-miR-100, hsa-miR-1259, hsa-miR-21, hsa-miR-22, hsa-miR-221, hsa-miR-222, hsa-miR-23b, hsa-miR-27a, hsa-miR-27b, hsa-miR-29a and hsa-miR-29b were down-regulated. Expression of 11 of the 21 miRNAs was examined by qPCR and 7 of them were validated: hsa-miR-21, hsa-miR-29a, hsa-miR-29b, hsa-miR-221 and hsa-miR-222 increased their expression upon differentiation, while hsa-miR-93 and hsa-miR-106a were inhibited. Functional studies demonstrated that miR-21 over-expression induced the expression of glial and/or neuronal cell markers in the neurospheres, possibly due to SPRY1 targeting by miR-21 in these cells, while miR-221 and miR-222 inhibition at the differentiated state reduced the expression of those differentiation markers. On the other hand, miR-29a and miR-29b targeted MCL1 in the GBM neurospheres and increased apoptotic cell death.

platform_organism:
Homo sapiens
Mus musculus
Rattus norvegicus
Human alphaherpesvirus 1
Human alphaherpesvirus 2
Human betaherpesvirus 5
human gammaherpesvirus 4
JC polyomavirus
Human immunodeficiency virus 1
Murid gammaherpesvirus 4
Human gammaherpesvirus 8
Merkel cell polyomavirus
Mus musculus cytomegalovirus 2
Betapolyomavirus hominis
Betapolyomavirus macacae

overall_design: Five GBM cell lines at the neurosphere state or after 4 or 14 days of differentiation

first: Beatriz

last: Aldaz

first: Jose

last: Luna

last: Martinez-Climent

first: Elizabeth

last: Guruceaga


title: The Candida glabrata transcription factor Stb5p is a negative regulator of ATP-binding cassette transporters

status: Public on Mar 11 2013

city: Bethesda

first: Jason

last: Noble

state: Maryland

address: 10 Center Drive, Building 10, Room 11N228

department: NIAID

institute: National Institutes of Health

summary: The opportunistic yeast pathogen Candida glabrata is recognized for its ability to acquire resistance during prolonged treatment with azole antifungals. Resistance to azoles is largely mediated by the transcription factor PDR1, resulting in the upregulation of ATP-binding cassette (ABC) transporter proteins and drug efflux. Studies in the related yeast Saccharomyces cerevisiae have shown Pdr1p forms a heterodimer with another transcription factor, Stb5p. In C. glabrata the ORF designated CAGL0I02552g has 38.8% amino acid identity with STB5 (YHR178w), and shares an N-terminal Zn2Cys6 binuclear cluster domain and a fungal specific transcriptional factor domain, prompting us to test for homologous function and a possible role in azole resistance. Complementation of deltayhr178w (stb5) with CAGL0I02552g resolved the increased sensitivity to cold, hydrogen peroxide and caffeine of the mutant, for which reason we designated CAGl0I02552g as CgSTB5. Overexpression of CgSTB5 in C. glabrata repressed azole resistance, whereas deletion of CgSTB5 increased resistance, both by a mechanism independent of CgPDR1. Expression analysis found that CgSTB5 shares many of the same transcriptional targets as CgPDR1 but, unlike the later, is a negative regulator of pleiotropic drug resistance, including the ABC transporter genes CDR1,PDH1, and YOR1.

platform_organism:
Nakaseomyces glabratus
Nakaseomyces glabratus CBS 138

overall_design: The CgPDR1OE (n=5) arrays consisted of five technical repeats with one prepared using reciprocal labeling. The Cgstb5delta (n=4) and CgSTB5OE (n=4) arrays consisted of four technical repeats each with one prepared using reciprocal labeling.


title: Expression data from mouse lung treated with saline or bleomycin

city: Pittsburgh

first: Kazuhisa

last: Konishi

state: PA

address: 1212 Kaufmann Building  3471 Fifth Ave

department: Pulmonry, Allergy, and Critical Care Medicine

institute: University of Pittsburgh

summary: Lung fibrosis represents the final common pathway of a variety of lung injuries, and it is characterized, independently of etiology, by the expansion of the fibroblast/myofibroblast population and by the abnormal accumulation of extracellular matrix (ECM) replacing normal functional parenchyma. In general, there is no effective therapy, and currently the only helpful available treatment for advanced lung fibrosis is transplantation. In this study we aimed to document the time-related reversibility of bleomycin-induced lung fibrosis, and to determine the gene expression patterns associated with the initial progression and the subsequent regression of the fibrotic response by microarray in this bleomycin mouse model of lung fibrosis.

overall_design: Mice (C57BL/6 ) aging 8 to 10 weeks were instilled intratracheally with 0.10 U/10 g of bleomycin (Blenoxane, Bristol-Myers Squibb Co.) in 50 μl sterile saline. Control animals received an equal volume of sterile saline (9, 10). Mice were housed in specific pathogen-free conditions and provided with food and water ad libitum. All studies and procedures were approved by the Science and Ethic Committee at the National Institute of Respiratory Diseases and were performed according to the protocols and guidelines of the institutional animal care and use committee. Mice were sacrificed at 7 days and 1, 2, 3, and 4 months after bleomycin or saline treatment. For every variable, six control and six experimental mice were used.

first: Sandra

last: Cabrera

first: Thomas

last: Richards

first: Naftali

last: Kaminski

first: Moises

last: Selman

first: Annie

last: Pardo


title: Gene expression profiling and functional analysis in cerebral artery after experimental subarachnoid hemorrhage

city: Fukuoka

first: Satoshi

last: Matsuo

address: 3-1-1, Maidashi, Higashi-ku

department: Department of Neurosurgery

institute: Graduate School of Medical Sciences, Kyushu University

summary: The molecular mechanisms of cerebral vasopasm after SAH are not totally understood. In the present study, we analyzed gene expression profile in rabbit basilar artery after SAH using cDNA microarrays.

overall_design: Total RNA was extracted from rabbit basilar arteries (12 samples: day0 n=3, day3  n=3, day5 n=3, and day7 n=3). They  were analyzed by microarray.

first: Yuichiro

last: Kikkawa

first: Masaaki

last: Hokama

first: Ryota

last: Kurogi

first: Akira

last: Nakamizo

first: Tomio

last: Sasaki


title: Comparative expression analysis between PfmR (TTHB023) deletion mutant and wild-type of Thermus thermophilus HB8

city: Hyogo

first: Akeo

last: Shinkai

address: 1-1-1, Kouto, Sayo

department: SPring-8 Center

institute: RIKEN Harima Institute

summary: We observed the expression profile of the total mRNA of PfmR (TTHB023) deletion mutant of Thermus thermophilus HB8 strain grown in a rich (TT) medium at 70°C compared with that of wild type.

overall_design: Seven wild-type and three mutant T. thermophilus HB8 strains were each pre-cultured at 70°C for 16 h in 4 ml of TT medium containing 0.8% polypeptone, 0.4% yeast extract, 0.2% NaCl, 0.4 mM CaCl2, and 0.4 mM MgCl2, which was adjusted to pH 7.2 with NaOH. The cells were inoculated into 1 liter of the same medium and then cultivated at 70°C. Cells were collected after 360 min, and then crude RNA was extracted. In order to compare mRNA expression in the PfmR deletion mutant with that of wild type, the expression of each mRNA was analyzed on a GeneChip.

first: Yoshihiro

last: Agari

first: Keiko

last: Sakamoto


title: Identification and differential expression of microRNAs during metamorphosis in the Japanese flounder (Paralichthys olivaceus)

status: Public on Mar 10 2013

city: Shanghai

first: Yuanshuai

last: Fu

address: Hu-Cheng-Huan Road

institute: Shanghai Ocean University

summary: The 987 probes  (Japanese flounder conserved miRNAs and candidates, fish conserved miRNAs, and contro) were hybridized with two stages during Japanese flounder metamorphosis by miRNA microarray. We validated 92 miRNAs using miRNA microarray in the 17 dph and 29 dph of Japanese flounder development, and obtained 66 differertially expressed miRNAs by comparison miRNA expression patterns of the two stages. These results indicate that miRNAs might play key roles in regulating gene expression during Japanese flounder metamorphosis.

overall_design: Using miRNA microarray, the flounder conserved miRNAs and candidates were identified, and 92 conserved miRNAs were detected in the 17 dph and 29 dph during metamorphosis. Meanwhile, 66 conserved  miRNAs were differertially expressed by comparison miRNA expression patterns of the two stages. We further identified flounder miRNAs during metamorphosis.

first: Zhiyi

last: Shi


title: miRNA expression data from rhesus macaque testes: time course

first: Zhao

last: Guodong

address: Yueyang Road

institute: PICB

type: Non-coding RNA profiling by high throughput sequencing

summary: Small RNA including microRNA (miRNA) and Piwi-interacting RNA (piRNA) play important roles in germline maintenance and maturation in wide variety of species. Relatively little however is known about role played by miRNA in male germline maturation in humans and closely related primate species. Here we focused on rhesus macaques as a model species closely related to humans to study small RNA expression in testis samples throughout postnatal development and maturation. We observe clear transition in miRNA and piRNA expression resulting in the overall increase of piRNA expression levels and corresponding decrease in miRNA expression. Unexpectedly, this transition takes place at approximately one year of age – far earlier then rhesus macaque sexual maturation occurring at 4-5 years of age. Notably, contradictory to the overall trend of expression decline, a group of 29 miRNA showed marked expression increase in macaque testis at approximately five years of age – the time interval associated with sexual maturation.  Keywords: miRNA  piRNA Age Series

overall_design: Rhesus macaque post-mortem testicle samples were collected. The age ranges of the indibiual in rhesus macaque covered the  whole life span fom newborn to death.

first: Guodong

last: Zhao

first: Philipp

last: Khaitovich


title: Differential miRNA expression in hippocampus of hBDNF Val66Met Knockin Mice

city: New York

first: Pei-Ken

last: Hsu

state: NY

institute: Columbia University

summary: miRNA expression profiling of adult (8 wk) hippocampus by comparing samples from Met/Met and Val/Val animals

overall_design: Two-genotype experiment, Met/Met vs. Val/Val. Biological replicates: 5 Met/Met, 5 Val/Val

first: Joseph

last: Gogos


title: Transcriptional response of confluent human umbilical vein endothelial cells to stimulation with the related cytokines interleukin-1b or interleukin-33.

city: OSLO

first: Guttorm

last: Haraldsen

state: OSLO

address: Sognsvannsveien 20

department: Department for Pathology

country: Norway

institute: Oslo University Hospital

summary: The similar response of endothelial cells to exogenous IL-33 or IL-1β prompted us to compare the genome-wide transcription profile of confluent human umbilical vein endothelial cell (HUVEC) cultures after 4 hours exposure to IL-33 or IL-1β. Analysis of these data revealed a striking similarity in the transcriptional response to the two cytokines.

overall_design: Pooled HUVEC from 10 donors were seeded 10.000 cells/cm2 and cultured for 4 days before stimulation for 4 hours with IL-1β 0.5 ng/ml or IL-33 50 ng/ml. Total RNA was isolated using the RNeasy Mini Kit (Qiagen) according to instructions of the manufacturer. Microarrays were performed using an Illumina Human6 v2 Expression Beadchip, and the raw data was pre-processed by Illumina’s BeadStudio software V2. The expression service was provided by Helse Sør-Øst/University of Oslo Microarray Core Facility, a member of the Norwegian Microarray Consortium supported by the functional genomics program (FUGE) at the Research Council of Norway.

first: Axel

last: Küchler

first: Johanna

last: Hol


title: Met synergizes with p53 loss to induce mammary tumors that possess features of claudin-low breast cancer (aCGH data).

status: Public on Mar 04 2013

city: St. Louis

first: Robert

last: Lesurf

state: MO

address: 4444 Forest Park Ave

department: McDonnell Genome Institute

institute: Washington University in St. Louis

summary: Transcriptional profiling of normal and tumorigenic mouse mammary tissue. Mouse genotypes consist of wildtype, MMTV-Met, MMTV-Met;Trp53fl/+;Cre, and Trp53fl/+;Cre.

overall_design: Two-color common reference design. Samples consist of 4 normal tissues, 8 MMTV-Met tumors, 10 MMTV-Met;Trp53fl/+;Cre tumors, and 8 Trp53;Cre tumors.

first: Jennifer

last: Knight

first: Dushanthi

last: Pinnaduwage

first: Ryan

last: Davis

first: Sadiq

last: Saleh

first: Dongmei

last: Zuo

first: Hong

first: Monica

last: Naujokas

first: Naila

last: Chugthai

first: Jason

middle: I

last: Herschkowitz

first: Aleix

last: Prat

first: Anna

last: Mulligan

first: William

last: Muller

last: Cardiff

first: Jeffrey

last: Gregg

first: Irene

last: Andrulis

first: Michael

last: Hallett

first: Morag

last: Park


title: microRNAs and their target proteins associated with characteristics of estrogen receptor-positive breast cancer (mRNA data)

city: Kamakura

first: Satoshi

last: Kondo

state: Kanagawa

address: Tebiro 6-10-1

department: New Projects Development Division

institute: Toray Industries,Inc.

summary: Recent analyses have identified heterogeneity in estrogen receptor (ER)-positive breast cancer. There are so-called luminal A and luminal B subtypes, and the characteristics, such as response to endocrine therapy and chemotherapy and prognosis, are different in these two subtypes of breast cancer. In this study, expression profiles of microRNAs (miRNAs) and mRNAs in ER-positive breast cancer tissues were compared between highly and incompletely endocrine responsive tumors by miRNA and mRNA microarrays. Unsupervised hierarchical clustering analyses revealed distinct expression patterns of miRNAs and mRNAs in these two groups. We identified one miRNA that was downregulated in highly endocrine responsive tumors and 8 miRNAs that were downregulated in incompletely endocrine responsive tumors, and target genes of these miRNAs were predicted using TargetScan and MiRanda. Protein expression patterns of the predicted target genes and the genes that were identified by mRNA expression profiling were analyzed in ER-positive breast cancer samples by immunohistochemistry. We identified a novel protein that might be associated with characteristics of ER-positive breast cancer.

overall_design: Expression profiles of mRNAs in highly and incompletely endocrine responsive tumors using 8 (4 tumors in each group) frozen human breast cancer tissues.

first: Hiroko

last: Yamashita

first: Yumi

last: Endo


title: C. tropicalis a/alpha white, opaque, tdh3-wor, wor1 mutants

status: Public on Mar 01 2013

city: Providence

first: Richard

last: Bennett

state: RI

address: 171 Meeting St

department: Molecular Microbiology and Immunology

institute: Brown University

summary: Transcriptional profiling of C. tropicalis a/alpha cells (CAY1511) in white state, opaque state, overexpressing Wor1, or wor1 mutants hybridized against a universal mixed reference sample from all 4 states.

overall_design: 4 condition experiment: white, opaque, tdh3-wor1, Δ/Δwor1; 4 biological replicates of each

first: Allison

last: Porman


title: CGH: IsoClark vs. Clark

status: Public on Mar 02 2013

city: Saint Paul

first: Robert

last: Stupar

state: MN

address: 1991 Upper Buford Circle

department: Agronomy and Plant Genetics

institute: University of Minnesota

summary:
Soybean near-isogenic lines (NILs) differing in iron deficiency chlorosis (IDC) tolerance were genotyped to determine differential genetic introgressions from the donor line T203 into the Clark background.
The CGH comparison reveals T203 loci that are differentially introgressed between the IsoClark sub-lines.

overall_design: Comparison of IsoClark soybean NILs to the recurrent parent Clark; the reported values show the log2 ratio of the normalized IsoClark hybridization signals (Cy3) over the normalized Clark hybridization signal (Cy5)

first: Adrian

middle: O

last: Stec


title: Gene expression profile of PBMCs in response to metreleptin treatment at different time points.

city: Tampere

first: Dario

last: Greco

address: Arvo ylpön Katu 34

department: Faculty of Medicine and Health Technology

country: Finland

institute: Tampere University

summary: we evaluated the modulation of gene expression profile in PBMCs from patients with hypotalamic amenorrhea. We have employed whole genome microarray expression profiling as a discovery platform to identify genes differentially expressed upon metreleptin treatment at different time points, week 12, 24 and 36.

overall_design: Gene expression profile induced by metreleptin treatment in  PBMCs from hypotalamic amenorrhea subjects.

first: Giuseppe

last: Matarese

first: Hyun-Seuk

last: Moon

first: Claudia

last: La  Rocca

first: Sharon

last: Chou

first: Francesco

last: Perna

first: Holly

last: Kilim

first: Chuanyun

last: Gao

first: Kalliope

last: Arampatzi

first: Mary

last: Brinkoetter

first: Christos

last: Mantzoros


title: microRNAs and their target proteins are associated with characteristics of estrogen receptor-positive breast cancer

first: Satoshi

last: Kondo

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

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

overall_design: Refer to individual Series


title: Transcriptional Modulation of Genes by Gut Microbiota in Germfree and Conventional Mice

first: Lei

last: Lu

state: Illinois

address: 900 E 57th Street

institute: University if Chicago

summary: To characterize the effect of microbiota on global gene expression in the distal small intestine during postnatal gut development we employed mouse models with experimental colonization by intestinal microbiota. Using microarray analysis to assess global gene expression in ileal mucosa at the critical stage of intestinal development /maturation associated with weaning, and asking how expression is affected by microbial colonization

overall_design: In the study presented here, preweaned and postweaned GF, SPF mouse small intestinal total RNAs were used. Also, 3-week-old gnotobiotic mouse as well as GF mouse small intestinal RNAs were used.


title: Ammonia oxidizing archaeal community composition in Gulf of Mexico sediments investigated with an amoA functional gene microarray

city: Boston

first: Silvia

last: Newell

state: Massachusetts

address: 675 Commonwealth Ave.

institute: Boston University

summary: Ammonia-oxidizing archaeal (AOA) amoA diversity and relative abundance in Gulf of Mexico sediments (0-2 cm) were investigated using a functional gene microarray; a two color array with a universal internal standard

sample_organism:
synthetic construct
uncultured ammonia-oxidizing archaeon

overall_design: Two color array (cy3 and cy5): the universal standard 20 bp oligo (fluoresced with cy5) is printed to the slide with a 70-mer. Environmental DNA sequences (fluoresced with Cy3) within 15% of the 70-mer will bind to it.  Signal is the cy3/cy5. Up to four arrays per sample, with two biological replicates made into two targets, each run on duplicate arrays.

first: Bess

last: Ward


title: microRNAs and their target proteins are associated with characteristics of estrogen receptor-positive breast cancer (miRNA data)

overall_design: Expression profiles of microRNAs in highly and incompletely endocrine responsive tumors using 8 (4 tumors in each group) frozen human breast cancer tissues.

first: Hiroko

last: Yamashita

first: Yumi

last: Endo


title: Gene expression profile of G93A-SOD1 mouse spinal cord, blood and muscle

city: Utrecht

first: C.

last: Saris

address: Heidelberglaan 100

department: Neurology

institute: UMC Utrecht

summary: To investigate the usefulness of gene expression as diagnostic biomarkers, we compared whole genome expression profiles of lumbar spinal cord with profiles of peripheral blood and tibialis anterior muscle in 16 mutant G93A-SOD1 mice and 15 wild type littermates.

overall_design: Total RNA obtained from blood, tibialis anterior muscle and lumbar spinal cord of G93A-SOD1 mice compared to wild type littermates.

first: Christiaan

middle: G

first: Leonard

middle: H

last: van den Berg


title: miRNA expression profile in GIST (gastrointestinal stromal tumor)

summary: To clarify aberrantly expressed miRNAs affecting the biology of GIST, miRNA array was performed in 19 cases of GIST.

overall_design: A series of 19 GISTs specimens were analyzed using 3D-Gene Human miRNA Oligo chips containing 904 human miRNAs and 107 viral miRNAs anti-sense probes printed in duplicate spots (Toray, Kamakura, Japan).

first: Hidetaka

last: Yamamoto


title: microRNA binding by wildtype Ago2 and mutant Ago2 in human cells

city: Nanjing

first: Yan

last: Zeng

state: Jiangsu

address: XuanWu District, No.1 WeiGang

institute: Nanjing Agricultural University

summary: Ago2 binds mature microRNAs (miRNAs) to regulate gene expression.  A mutant Ago2 is constructed to render it unable to bind miRNAs and inhibit mRNA translation.

platform_organism:
Caenorhabditis elegans
Drosophila melanogaster
Danio rerio
Homo sapiens
Mus musculus
Rattus norvegicus

overall_design: Human 293T cells were transiently transfected with a plasmid that encoded a FLAG-tagged wildtype human Ago2 or mutant Ago2.  FLAG IP was preformed, and assoicated RNA was isolated and subjected miRNA microarray analysis.


title: Expression data from Bifidobacterium longum strains exposed to hydrogen peroxide stress

status: Public on Feb 28 2013

city: Logan

first: Taylor

last: Oberg

state: UT

address: 8700 Old Main

department: NDFS

institute: Utah State University

summary:
Stress survival tactics in bacteria utalize the up- and down-regulation of stress response genes. In bacterial that lack classical stress response genes for oxidative stress, other cellular systems can be used for cell survival.
We used custom microarrays to study the regulation of genes in Bifidobacterium longum strains to oxidative stress to elucidate novel stress response mechanisms.

sample_organism:
Bifidobacterium longum NCC2705
Bifidobacterium longum

platform_organism:
Bifidobacterium longum
Bifidobacterium animalis subsp. lactis

overall_design: Bifidobacterium cells were grown to late log phase then harvested and exposed to a sub-lethal level of hydrogen peroxide. Samples were taken at 5 and 60 mins for RNA extraction and hybridization on Affymetrix microarrays. Controls were prepared for each time point which recieved no hydrogen peroxide treatment.

first: Jeff

middle: R

last: Broadbent


title: miRNA profiling of GFAP+ cells isolated from GBM and adjacent non-tumor glial brain tissues

first: Huibo

last: Wang

address: 300# Guangzhou Rd.

institute: First Affiliated Hospital of Nanjing Medical University

summary: To identify miRNAs expression changes in human gliomas, we conducted a comprehensive microarray analysis to compare miRNA expression profiles in primary cells obtained from matched pairs of GBM and adjacent non-tumor brain tissues from 6 patients.

overall_design: Paired primary glioma cells and astrocytes, isolated from GBM tissues andperipheral non-tumor glial brain tissues, respectively, with each pair prepared from a same patient, were established for primary culture. Total RNA was extracted and hybridized to microarrays overnight at 65°C.

first: Wanghao

last: Chen

first: Ning

last: Liu


title: Cav3.2 T-type calcium channel-dependent gene expression after retrieval of context-associated memory (right hippocampus)

city: Hualien

first: Ingrid

address: E411, 701, Section 3 Chung Yang Road

department: Molecular Biology and Human Genetics

institute: Tzu Chi University

summary: Among all voltage-gated calcium channels, the T-type Ca2+ channels encoded by the Cav3 genes are highly expressed in the hippocampus, which is associated with contextual, temporal and spatial learning and memory. However, the specific involvement of the Cav3.2 T-type Ca2+ channel in these hippocampus-dependent types of learning and memory remains unclear. To investigate the functional role of the 1H channel in learning and memory, we subjected Cav3.2 homozygous, heterozygous knockout and their wild-type littermates to hippocampus-dependent behavioral tasks, including trace fear conditioning (TFC), the Morris water-maze and passive avoidance. The Cav3.2-/- mice performed normally in the Morris water-maze and auditory trace fear conditioning tasks but were impaired in the context-cued trace fear conditioning, step-down and step-through passive avoidance tasks. Furthermore, long-term potentiation (LTP) could be induced for 180 minutes in hippocampal slices of WTs and Cav3.2+/- mice, whereas LTP persisted for only 120 minutes in Cav3.2-/- mice. To determine whether the hippocampal formation is responsible for the impaired behavioral phenotypes , we next performed experiments locally knock down function of the Cav3.2 T-type Ca2+ channel in the hippocampus. Wild-type mice infused with mibefradil exhibited similar behaviors as homozygous knockouts. Finally, microarray analyses indicated that Cav3.2-/- and WT mice presented distinct hippocampal transcriptome profiles. Taken together, our results demonstrate that retrieval of context-associated memory is dependent on the Cav3.2 T-type Ca2+ channel.

overall_design: After WT and Cav3.2 KO mice retrieval of context-associated memory, three right hippocampi of each group were dissected, pooled together and homogenized. The products of experimental and naive groups were used to acquire expression profiles of a total of 29,922 unique genes. Two replicates per group.

middle: Y

first: Chien-Chang

first: Chuan-Hsiung

last: Chang

first: Ni-Chun

last: Chung


title: Common bean (Phaseolus vulgaris) PvTIFY orchestrates global changes in transcript profile response to phosphorus deficiency

status: Public on Feb 27 2013

city: Cuernavaca

first: Gabriel

last: Guillen

state: Morelos

address: Av. Univeridad 2001

department: Biologia Molecular de Plantas

country: Mexico

institute: IBT-UNAM

summary: TIFY is a large plant-specific transcription factor gene family. A subgroup of TIFY genes named JAZ (Jasmonate-ZIM domain) has been identified as repressors of jasmonate (JA)-regulated transcription in Arabidopsis and other plants. JA signaling is involved in many aspects of plant growth/development and in the defense responses to biotic and abiotic stresses. Here we identified the TIFY genes (designated as PvTIFY) from the legume common bean (Phaseolus vulgaris) and functionally characterized PvTIFY10C as a transcriptional regulator. Twenty-three genes from the PvTIFY gene family were identified through whole genome sequence analysis. Most of these were induced upon methyl-JA elicitation. We selected PvTIFY10C as a representative JA-responsive PvTIFY gene for further functional analysis. Transcriptome analysis via microarray hybridization using the designed Bean Custom Array 90K was performed in transgenic roots of composite plants with modulated -RNAi-silencing or over-expression- PvTIFY10C gene expression. Data were interpreted using Mapman adapted to common bean. Microarray differential gene expression data were validated by real-time qRT-PCR expression analysis. Comparative global gene expression analysis revealed opposite regulatory changes in processes such as RNA and protein regulation, stress response and metabolism in silenced vs. over-expressing roots. These data point to transcript reprogramming -mainly repression- orchestrated by PvTIFY10C. In addition we found that several PvTIFY genes as well as genes from the JA biosynthetic pathway responded to P-deficiency. Relevant P-responsive genes that participate in carbon metabolic pathways, cell wall synthesis, lipid metabolism, transport, DNA, RNA and protein regulation, signaling, were oppositely-regulated in control vs. PvTIFY10C silenced roots. These data indicate that PvTIFY10C regulates, directly or indirectly, gene expression of some P-responsive genes something that could be mediated by JA-signaling.

platform_organism:
Glycine max
Phaseolus vulgaris

overall_design: Our work contributed to the functional characterization of PvTIFY transcriptional regulators in common bean, an agronomically important legume. Members from the large PvTIFY gene family are important global transcriptional regulators that could participate as repressors of the JA signaling pathway. In addition we propose that the JA-signaling pathway that involves PvTIFY genes might play a role in regulating the plant response / adaptation to P-starvation.

first: Roberto

last: Ferrarini

first: Francesca

last: Sparvoli

first: Bianca

last: Castiglioni

first: Paola

last: Cremonesi

first: Dario

last: Panzeri

first: Alessandra

last: Stella

first: Francesco

last: Strozzi

first: Georgina

last: Hernández

first: Rosaura

last: Aparicio-Fabre


title: Cav3.2 T-type calcium channel-dependent gene expression after retrieval of context-associated memory (left hippocampus)

overall_design: After WT and Cav3.2 KO mice retrieval of context-associated memory, three left hippocampi of each group were dissected, pooled together and homogenized. The products of experimental and naive groups were used to acquire expression profiles of a total of 29,922 unique genes. Two replicates per group.


title: Source-tracking fecal contamination by genomic analysis of Escherichia coli from human and animal hosts

city: Missoula

first: Frank

last: Rosenzweig

state: MT

address: 32 Campus Drive, HS 104

department: Division of Biological Sciences

institute: University of Montana

summary: The model prokaryote Escherichia coli can exist as a either a commensal or a pathogen in the gut of diverse mammalian hosts.  These associations, coupled with its ease of cultivation and genetic variability, have made E. coli a popular indicator organism for tracking the origin of fecal water contamination.  Source tracking accuracy is predicated on the assumption that E. coli isolates recovered from contaminated water present a genetic signature characteristic of the host from which they originated.  In this study, we compared the accuracy with which E. coli isolated from humans, bear, cattle and deer could be identified by standard fingerprinting methods used for library-based microbial source tracking (repetitive element PCR and pulsed-field gel electrophoresis) in relation to microarray-based analysis of genome content.  Our results show that patterns of gene presence or absence were more useful for distinguishing E. coli isolates from different sources than traditional fingerprinting methods, particularly in the case of human strains.  Host-associated differences in genome composition included the presence or absence of mobile IS1 elements as well as genes encoding the ferric dicitrate iron transporter (fec), E. coli common pilus (ECP), type 1 fimbriae and the CRISPR associated cas proteins.  Many of these differences occurred in regions of the E. coli chromosome previously shown to be “hot spots” for the integration of horizontally-acquired DNA.  PCR primers designed to amplify the IS1 and fec loci confirmed array results and demonstrated the ease with which gene presence/absence data can be converted into a diagnostic assay.   The data presented here suggest that, despite the high level of genetic diversity observed among isolates by PFGE, human-derived strains may constitute a distinct ecotype distinguished by multiple potential library-independent source tracking markers.

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

overall_design: Twelve isolates of E. coli ( 3 from bear, 3 from cattle, 3 from deer and 3 from humans) were isolated from feces and/or raw sewage.  Genome content for each strain was assessed in duplicate using comparative genome hybridization with E. coli K12 MG1655 as the reference for a total of 24 arrays.

first: Margie

last: Kinnersley

first: James

last: Gannon

first: William

last: Holben


title: A network model of the molecular organization of chromatin in Drosophila

status: Public on Feb 12 2013

city: Amsterdam

first: Bas

last: van Steensel

address: Plesmanlaan 121

department: division of Molecular Biology

institute: Netherlands Cancer Institute

summary: Chromatin governs gene regulation and genome maintenance, yet a substantial fraction of the chromatin proteome is still unexplored. Moreover, a global model of the chromatin protein network is lacking. By screening >100 candidates we identify 42 Drosophila proteins that were not previously associated with chromatin, which all display specific genomic binding patterns. Bayesian network modeling of the binding profiles of these and 70 known chromatin components yields a detailed blueprint of the in vivo chromatin protein network. We demonstrate functional compartmentalization of this network, and predict functions for most of the previously unknown chromatin proteins, including roles in DNA replication and repair, and gene activation and repression.

overall_design: All DamID experiments were done in Drosophila Kc167 cells in duplicate. Samples were hybridized to 380k NimbleGen arrays with 300 bp probe spacing. Every experiment was done in duplicate in the reverse dye orientation, where Dam-fusion material was hybridized over Dam-only material.

first: Joke

last: van Bemmel

first: Guillaume

middle: J

last: Filion

first: Arantxa

last: Rosado

first: Wendy

last: Talhout

first: Marcel

last: de Haas

first: Tibor

last: van Welsem

first: Fred

last: van Leeuwen


title: Identification of metastamirs as metastasis-associated microRNAs in clear cell renal cell carcinomas

status: Public on Feb 26 2013

city: Berlin

first: Hellmuth-A

last: Meyer

address: Charitéplatz 1

department: Department of Urology

institute: Charite

summary: Background/Objective: MicroRNAs (miRNAs) play a pivotal role in cancerogenesis and cancer progression, but their specific role in metastasis of clear cell renal cell carcinomas (ccRCCs) as so-called metastamirs is still limited. Based on microRNA microarray analyses from normal (n=12) and cancerous (n=12) samples of ccRCC specimens and from bone metastases (n=9) of ccRCC patients, we identified a set of 57 differentially expressed microRNAs between those three sample groups of ccRCC. A selected panel of 33 miRNAs, including miRNAs reported in the literature as differentially expressed in non-metastatic RCC, was validated by RT-qPCR on 57 clinical samples. 30 of the 33 examined miRNAs were confirmed to be deregulated. A stepwise down-regulated miRNA expression from normal over primary tumor to metastatic tissue samples was found to be typical.  23 miRNAs (miR-10b/-19a/-19b/-20a/-29a/-29b/-29c/-100/-101/-126/-127/-130/-141/-143/-145/-148a/-192/-194/-200c/-210/-215/-370/-514) were down-regulated in metastatic tissue samples in comparison to normal tissue. This down-regulated expression in metastatic tissue was also present in 21 miRNAs except for miR-127 and miR-370. The altered miRNA profiles including the newly identified metastasis-associated miRNAs, the compiled predicted miRNA-target interactions, and the significant correlations of miRNAs which were either lost or newly appeared in the studied sample groups afford a solid basis for further functional analyses of individual miRNAs.

overall_design: In this study, microarray-based profiling was performed from 9 bone metastatic tissue samples from 9 patients with clear cell renal cell carcinoma (ccRCC). For controls, 2 bone metastatic samples from two patients with prostate carcinoma and 5 total RNA pools (2 different pools of total RNAs isolated from malignant renal tissue samples derived from different ccRCC patients; 1 pool from non-malignant renal tissue of ccRCC patients; 2 pools of total RNA both from malignant and non-malignant prostate cancer tissue) were used. In addition, matched malignant (e.g., malignant NC2) and non-malignant (e.g., non-malignant NN1) samples from two independent 12 ccRCC sets were profiled (these samples were previously analyzed on a different Platform in GSE12105). The 2002 TNM System and the 2004 WHO classification was used for staging and grading.

first: Zofia

last: Wotschofsky

first: H

first: Monika

last: Jung

first: Ina

last: Wagner

first: Alexander

last: Disch

first: Klaus

last: Schaser

first: I

last: Melcher

first: Ergin

last: Kilic

first: Jonas

last: Busch

first: Steffen

last: Weikert

first: Kurt

last: Miller

first: Andreas

last: Erbersdobler

last: Mollenkopf


title: CGH: HiPro_v_LoPro

first: Robert

last: Stupar

summary:
Two soybean near-isogenic lines (NILs) differing in seed protein content were genotyped to determine differential genetic introgressions from the wild relative Glycine soja.
The CGH comparison reveals loci that are differentially introgressed between the two lines.

overall_design: Comparison of HiPro (LD0-15154) and LoPro (LD0-15146) soybean NILs; the reported values show the log2 ratio of the normalized HiPro hybridization signal (Cy3) over the  normalized LoPro hybridization signal (Cy5)

first: Yung-Tsi

last: Bolon


title: WT vs WTmitomycinC comparison

status: Public on Jan 31 2013

city: Louvain-La-Neuve

first: Pascal

last: Hols

address: Place Croix du Sud 5

department: Institut des Sciences de la Vie

country: Belgium

institute: Université catholique de louvain

summary:
Transcriptional profiling of S. thermophilus LMD-9 wild-type in the presence of mitomycin C.
Cells were grown in CDM medium  supplemented with lactose 1% (CDML), without or with mitomycin C 0.08 microg/ml, and sampled at OD600 = 0.4 for mRNA extraction.

overall_design: wild-type vs wild-type + mitomycin C, 2 WT biological replicates (one used as technical replicate for a dye swap), 2 WT + mitomycin C biological replicates (one used as technical replicate for a dye swap)

first: Céline

last: Boutry

first: Laetitia

last: Fontaine

first: André

last: Clippe


title: Genomic copy number alterations in human esophageal squamous cell carcinoma (ESCC) cell lines

city: Beijing

first: Jia-Jie

last: Hao

address: 17 Panjiayuan Nanli

institute: Cancer Hospital (Institute), Chinese Academy of Medical Sciences

summary: Characterization of copy number alterations and unbalanced breakpoints in human esophageal squamous cell carcinoma cell lines by array-based comparative genomic hybridization.

overall_design: Six cell lines

first: Ming-Rong

last: Wang


title: WT vs KO hdiR comparison

summary:
Transcriptional profiling of S. thermophilus LMD-9 wild-type compared to the isogenic mutant strain CB0082 (deletion of hdiR, STER_0918) for the identification of the HdiR regulon.
Cells were grown in CDM medium supplemented with lactose 1% (CDML) and sampled at OD600 = 0.4 for mRNA extraction

overall_design: wild-type vs  knockout, 2 WT biological replicates (one used as technical replicate for a dye swap), 2 KO biological replicates (one used as technical replicate for a dye swap)


title: miRNA 135b regulation of inflammation

city: Ottawa

first: Sarah

last: Labib

state: Ontario

address: 204b-50 Colombine

institute: Health Canada

summary: RT-PCR analysis of inflammatory cytokines and receptors in pEGP-miR-135b over-expressing cells compard to controls (pEGP-miR-null) using pathway-specific PCR arrays for the evaluation of mouse inflammatory cytokines and receptors (#PAMM-011D).

overall_design: qPCR array gene expression profiling. This experiment examined the transcriptional response of NIH3T3 cells over-expressing pEGP-miR-135b. Total RNA (n = 3 per group) was used with SABiosciences pathway-specific PCR arrays for inflammatory cytokines and receptors (#PAMM-011D).

first: Dongmei

last: Wu

first: Sabina

last: Halappanavar

first: Andrew

last: Williams

first: Jake

last: Nikota

first: Carole

last: Yauk

first: Martin

last: Stampfli


title: miRNA 135b regulation by Il1r1 during inflammation

summary: RT-PCR analysis of inflammatory cytokines and receptors following Il1alpha treatment of pEGP-miR-135b over-expressing cells compard to controls (pEGP-miR-null) using pathway-specific PCR arrays for the evaluation of mouse inflammatory cytokines and receptors (#PAMM-011D).

overall_design: qPCR array gene expression profiling. This experiment examined the transcriptional response of NIH3T3 cells over-expressing pEGP-miR-135b following IL1alpha treatment. Total RNA (n = 3 per group) was used with SABiosciences pathway-specific PCR arrays for inflammatory cytokines and receptors (#PAMM-011D).


title: Outer cell surface components essential for Fe(III) oxide reduction in Geobacter metallireducens

status: Public on Feb 18 2013

city: Amherst

first: Jessica

middle: Amber

last: Smith

state: MA

address: 203 Morrill Science Center IVN

department: Microbiology

institute: UMASS Amherst

summary: The ability of Geobacter species to readily donate electrons to extracellular electron acceptors makes the study of their physiology not only important for the understanding of environmental processes, but also for industrial applications such as bioelectronics and electrosynthesis. Studies in G. sulfurreducens have shown that outer surface components, such as c-type cytochromes and conductive type IV pili play an important role in direct electron transfer to extracellular electron acceptors such as Fe(III) oxides and electrodes. However, many of these thoroughly studied outer surface components, including c-type cytochromes, are not well conserved among Geobacter species. In order to better understand which components are involved in extracellular electron transfer in Geobacter species other than G. sulfurreducens, studies were conducted with its close relative G. metallireducens. Whole-genome microarray analysis revealed that 23 of the 91 putative c-type cytochromes encoded in the G. metallireducens genome were upregulated at least 2-fold in cells grown with Fe(III) oxide compared to cells in which Fe(III) citrate was provided as the terminal electron acceptor. Protein identification with liquid-chromatography/mass spectrometry detected 6 c-type cytochromes that were more abundant in the outer surface cell fraction of cells that were grown with Fe(III) oxide as the terminal electron acceptor compared to cells grown on Fe(III) citrate.  22 genes encoding c-type cytochromes were chosen for gene deletion. Deletion of 6 genes encoding for c-type cytochromes, a gene encoding for a lipopolysaccharide biosynthesis-associated protein, and a gene encoding for a NHL- repeat containing protein inhibited growth when Fe(III) oxide was provided as the electron acceptor. This study suggests that there are different roads for extracellular electron transfer in Geobacteraceae since homologous c-type cytochromes have different functions from one species to the other, and novel components not previously found to be essential for extracellular electron transfer were identified.

overall_design: An eight-chip study using total RNA recovered from four separate cultures of Geobacter metallireducens GS-15 grown with acetate (10mM)-Fe(III) oxide (100 mmol l-1) (experimental condition) or with acetate (10 mM)-Fe(III) citrate (55mM) (control condition) during exponential growth. Each chip measures the expression level of 3,627 genes from Geobacter metallireducens GS-15 with nine 45-60-mer probe pairs (PM/MM) per gene, with three-fold technical redundancy.

first: Pier-Luc

last: Tremblay

first: Derek

last: Lovley