title: Custom array CGH of Oral Squamous Cell Cancer

status: Public on Feb 28 2015

city: Omaha

first: Hamid

last: Band

state: Nebraska

address: 42nd and Emile

department: Eppley

country: USA

institute: University of Nebraska Medical Center

summary: Over last decade several studies on oral cancer patients from eastern India have identified alterations in copy numbers in many regions of the chromosome such as 3p21.3, 8q24.21, 9p21, 9p22, 11q13, 11q21-24. However, all these studies employed microsatellite markers to map these CNV regions. This resulted in large map intervals (10-12 megabases) between the adjacent markers studied. As these regions contain a large number of genes, a high resolution CNV map of these regions was necessary to precisely identify novel genes affected by the amplifications and deletions. We thus used custom made Agilent 4X44K oligonucleotide array CGH platform to map the identified CNV regions in a resolution of 3 Kb in oral cancer patients from eastern India.

overall_design: Twenty-nine defined genomic intervals of ten male and two female oral cancer patients were compared with a normal male and normal female sample, respectively, by Agilent's custom oligo CGH array of 4X44K format.

first: Mondal

last: Pinaki

first: Maiti

middle: G

last: Prasad

first: Panda

middle: C

last: Kumar

first: Roychoudhury

last: Susanta


title: Yeast zeta-crystallin: An AU-Rich Element Binding Protein Involved in the Nutritional Stress Response

status: Public on Feb 27 2015

city: Badalona

first: Lauro

last: Sumoy

state: Barcelona

address: Ctra. Can Ruti, Camí de les escoles s/n

department: High Content Genomics and Bioinformatics

country: Spain

institute: IGTP

summary: The yeast ζ-crystallin Zta1p interacts specifically with RNA sequences rich in adenine and uracil (AU-rich element). We have looked for possible targets of Zta1p through a comparative transcriptional analysis of the yeast defective in ZTA1 (Δzta1) versus the wild-type by microarray. This revealed that a group of genes implicated on amino acid biosynthesis are affected by the lack of ZTA1. The effect on one of the targets ARG4 was studied in more detail, revealing a clear positive correlation between ZTA1 and ARG4 expression at the mRNA level. We demonstrate that Zta1p is able to bind specifically to the 3’UTR AU-rich elements of ARG4 mRNA in vitro, suggesting that the mechanism by which ZTA1 modulates the expression of ARG4 is probably mediated by this mRNA binding ability. Moreover, the expression of ZTA1 is also under the control of the TOR pathway, and under Gcn4p, which regulates genes implicated in the response to nutrient availability and the general amino acid control (GAAC). In summary, our results shed light on the functional role of the ζ-crystallin family as stress response proteins, with a conserved functional role, from yeast to humans, in the post-transcriptional regulation of genes that need to be rapidly activated for cell defense.

overall_design: Triplicate biological replicate experiments were performed, where the two strains, ∆zta1 and wild-type, were grown in the presence or absence of hydrogen peroxide. The experimental design was defined to directly compare the ∆zta1 versus the wild-type strain in either of the two hydrogen peroxide treatment conditions (i.e. treated ∆zta1 versus treated wt, or untreated ∆zta1 versus untreated wt). A duplicate hybridization on a separate array with dye swapping was performed in each case to correct for dye bias effects. Thus, a total of 12 array data sets were produced as a result of processing three experimental pairs of samples, for each of two treatment conditions, with dye swap duplicates.

first: Eva

last: Crosas

first: Josep-Antoni

last: Biosca

first: Xavier

last: Pares

first: M-Rosario

last: Fernández


title: MiRNAinU118_Cells_Inactive_vs_ active_ Adar2

city: Roma

first: Carlo

last: Presutti

state: Italia

address: Via dei Sardi 70

department: Biology and Biotechnology

country: Italy

institute: University Sapienza

summary: MicroRNA expression profile of NB U118 cells transfected with a plasmid directing an inactive Adar2 vs an active Adar2 - 3 biological replicates

overall_design: 1 Condition experiment, 3 biological replicates, 2 replicates/array

first: Sara

last: Tomaselli

first: Federica

last: Galeano

first: Shahar

last: Alon

first: Susanna

last: Raho

first: Silvia

last: Galardi

first: Vinicia

middle: A

last: Polito

last: Vincenti

first: Eli

last: Eisenberg

first: Franco

last: Locatelli

first: Angela

last: Gallo


title: Genomic characterization of clones derived from a murine acute myeloid leukemia cell line for the description of genes involved in immunogenicity (dataset 1)

status: Public on Feb 25 2015

city: lille

first: frédéric

last: leprêtre

address: Boulevard du Pr Leclercq

department: CHU of Lille, CBP

country: France

institute: Lille University

type: Genome variation profiling by genome tiling array

summary: The goal of this study was to determine the effects of gene deletions and duplications on acute myeloid leukemia cells immunogenicity. The Clones were derived from the C1498 AML cell line. Lymphocytes were isolated from the C57BL/6 mouse strain.

overall_design: Genome profiling of mouse single cell clones originating from an acute myeloid leukemia cell line compared to control T lymphocytes from the same murine strain.

first: Carine

last: Brinster


title: Gene expression of ultra violet irradiation of silk worm Bombyx mori larvae

status: Public on Feb 26 2015

city: Mishima

first: Hiromasa

last: Ono

state: Shizuoka

address: National Institute of Genetics, Yata 1111

department: Database Center for Life Science (DBCLS)

country: Japan

institute: Research Organization of Information and Systems

summary: 3 day of fifth instar larvae were treated with ultra-violet (UV) rays using UVL-56 (1350μW/cm2, UVP) for 6 and 12 hours (29.2 and 58.32 J/cm2). Since, larvae of each group rare on artificial diet for 24 hour and dissected fatbody. We examined gene expression profile in these groups.

overall_design: Gene expression was measured in 3 day of fifth instar larvae of ultra violet irradiation.

first: Hiroko

last: Tabunoki

first: Yuki

last: Nakamura

first: Yoshitaka

last: Suetsugu

first: Hidemasa

last: Bono

first: Takeru

last: Nakazato

first: Kimiko

last: Yamamoto


title: Study of the role of AMP-activated protein kinase (AMPK) in heart

status: Public on Feb 24 2015

city: CHATENAY-MALABRY

first: Claudine

last: DELOMENIE

address: 5, rue Jean-Baptiste Clément

department: Transcriptomique

institute: University Paris Sud 11

summary: Transcriptional profiling of mouse ventricular tissue comparing WT control mice with mice invalidated (KO) for AMPK-alpha 2 gene. Goal was to identify new biological targets of AMPK in heart, through a global gene expression approach.

overall_design: Two-condition experiment, KO vs. Control WT mice. Biological replicates: 6 WT (AMPK alpha2 +/+) control mice, 6 KO (AMPK alpha2 -/-) mice.

last: Deloménie

first: Anne

last: Garnier


title: Genomic characterization of clones derived from a murine acute myeloid leukemia cell line for the description of genes involved in immunogenicity

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

overall_design: Refer to individual Series


title: The effects of putative lipase and wax ester synthase/acyl-CoA:diacylglycerol acyltransferase gene knockouts on triacylglycerol accumulation and transcriptome expression in Gordonia sp. KTR9.

status: Public on Feb 14 2015

city: Vicksburg

first: Dawn

middle: E

last: Hancock

state: Mississippi

address: 3909 Halls Ferry Road

department: Engineer Research and Development Center

institute: DEPARTMENT OF DEFENSE Army Corps of Engineers

summary:
Gene disruption of KTR9_0186 resulted in a 2-fold increase in TAG content in nitrogen starved cells. Lipase mutants subjected to carbon starvation, following nitrogen starvation, retained 75% more TAGs and retained pigmentation. Transcriptome expression data confirmed the deletion of KTR9_0186 and identified the up-regulation of key genes involved in fatty acid degradation, a likely compensatory mechanism for reduced TAG mobilization.
The Gordonia sp. KTR9 strain used in this study has been previously described (PMID 16332812)

overall_design: A 12 x 135K array study using total RNA recovered from triplicate cultures of KTR9 under carbon starvation and triplicate cultures of KTR9 0186 Mutant under carbon starvation.

first: Karl

middle: J

last: Indest

first: Jed

middle: O

last: Eberly


title: ChIP-chip analysis of CspC binding in Salmonella enterica serovar Typhimurium strain SL1344

city: Dublin

first: Shane

last: Dillon

address: Trinity College

department: Department of Microbiology

country: Ireland

institute: Moyne Institute of Preventive Medicine

type: Genome binding/occupancy profiling by array

summary: We performed Chromatin Immunoprecipitation (ChIP) and microarray hybridization analysis of CspC binding in Salmonella Typhimurium strain SL1344 which has been genetically engineered to express a 3xFLAG tagged CspC protein.

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

overall_design: Chromatin samples were prepared from SL1344 CspC 3xFLAG grown to exponential phase (OD600nm = 0.2). CspC FLAG ChIP and mock normal mouse IgG ChIP reactions were carried out. The purified ChIP DNA samples were hybridized to SL1344 tiling microarrays.

first: Matthew

last: Dorman

first: Charles


title: Adult zebrafish: cornea vs dermis

status: Public on Feb 19 2015

city: Kalrsruhe

first: Masanari

last: Takamiya

address: Hermann-von-Helmholtz-Platz 1

department: Institute of Toxicology and Genetics

country: Germany

institute: Karlsruhe Institute of Technology

summary: Transcriptional profiling of adult zebrafish cornea against dermis as a reference.

overall_design: Three biological repeats with dye swap (6 chips of 1x22k for 6 data sets).

first: Uwe

last: Straehle


title: Oxidative stress in E. coli K-12 and O157

status: Public on Feb 22 2015

city: BIRMINGHAM

first: Martin

middle: D.

last: Goldberg

address: Edgbaston

department: School of Chemical Engineering

country: United Kingdom

institute: University of Birmingham

summary:
Escherichia coli O157 presents a number of specific problems in terms of food safety and public health. It has been found that E. coli O157 is more resistant to a number of the stresses encountered during food production such as heat, pH and osmotic shock. This greater resistance is thought to contribute to the low infectious dose of E. coli O157 (<100 organisms). Moreover, E. coli O157 is associated with debilitating conditions such as haemorrhagic colitis and haemoytic uraemic syndrome, particularly in children and the elderly.

We have been studying the stress responses of E. coli O157:H7 (Sakai) and comparing with a commensal strain of E. coli K-12, MG1655. We found that E. coli O157 (Sakai) is more sensitive to oxidative stress than MG1655. A microarray study of these strains treated with sub-lethal concentrations (0.5mg/ml) of menadione revealed big differences in their responses. In E. coli O157 (Sakai), 540 genes responded significantly to the treatment compared to 121 genes in MG1655. One surprising finding from the microarray data was the observation that many iron-transport genes were up-regulated in E. coli O157 (Sakai) whereas relatively few were induced in MG1655 despite the fact that the bacteria were grown in a medium containing ample iron. We speculated that the induction of iron transport genes in an iron-rich medium might have contributed to the enhanced killing of E. coli O157 (Sakai) through triggering of a Fenton reaction.

We speculated that the difference in sensitivity to oxidative stress might be due to differences in the intracellular iron content of E. coli O157 and MG1655. We found that E. coli O157 contains ~50% more iron than MG1655 and believe that during oxidative stress, this iron is released by damaged proteins. The greater levels of free iron in E. coli O157 will trigger a greater Fenton reaction that can damage the ferric uptake regulator (Fur), resulting in unregulated iron transport. In MG1655, the lower iron content results in a smaller Fenton reaction, enabling the cellular protection systems to limit damage and protect Fur.

overall_design:
Overnight cultures of E. coli O157 (Sakai) and E. coli K-12 MG1655 were grown in Neidhardt's EZ Rich Defined Medium and diluted 1:100 in 50 ml fresh medium in 125 ml Ehrlenmeyer flasks. The cultures were shaken at 37C until the optical density (OD600) reached 0.4. Each culture was divided into 2 equal parts in identical flasks. One flask contained menadione bisulphite to a final concentration of 0.5 mg/ml; the other flask contained an equivalent  volume of distilled water. The flasks were shaken for a further 10 mins and then treated with RNAprotect™ to stabilise the mRNA.

The experiment was performed 3 times on different days. Six custom-made microarray slides were used in this study; each slide was hybridised with labelled cDNA made from mRNA taken from untreated and treated E. coli O157 (Sakai) or MG1655.

middle: D

first: Peter

last: Lund


title: Factors that promote H3 chromatin integrity during transcription prevent promiscuous deposition of CENP-A(Cnp1) in fission yeast

city: Stockholm

last: Ekwall

address: Alfred Nobels Alle 7

country: Sweden

institute: Karolinska Inst

type: Genome binding/occupancy profiling by genome tiling array

summary: Specialized chromatin containing CENP-A nucleosomes instead of H3 nucleosomes is found at all centromeres. However, the mechanisms that specify the locations at which CENP-A chromatin is assembled remain elusive in organisms with regional, epigenetically regulated centromeres. It is known that normal centromeric DNA is transcribed in several systems including the fission yeast, Schizosaccharomyces pombe. Here, we show that factors which preserve stable histone H3 chromatin during transcription also play a role in preventing promiscuous CENP-A(Cnp1) deposition in fission yeast. Mutations in the histone chaperone FACT impair the maintenance of H3 chromatin on transcribed regions and promote widespread CENP-A(Cnp1) incorporation at non-centromeric sites. FACT has little or no effect on CENP-A(Cnp1) assembly at endogenous centromeres where CENP-A(Cnp1) is normally assembled. In contrast, Clr6 complex II (Clr6-CII; equivalent to Rpd3S) histone deacetylase function has a more subtle impact on the stability of transcribed H3 chromatin and acts to prevent the ectopic accumulation of CENP-A(Cnp1) at specific loci, including subtelomeric regions, where CENP-A(Cnp1) is preferentially assembled. Moreover, defective Clr6-CII function allows the de novo assembly of CENP-A(Cnp1) chromatin on centromeric DNA, bypassing the normal requirement for heterochromatin. Thus, our analyses show that alterations in the process of chromatin assembly during transcription can destabilize H3 nucleosomes and thereby allow CENP-A(Cnp1) to assemble in its place. We propose that normal centromeres provide a specific chromatin context that limits reassembly of H3 chromatin during transcription and thereby promotes the establishment of CENP-A(Cnp1) chromatin and associated kinetochores. These findings have important implications for genetic and epigenetic processes involved in centromere specification.

overall_design: In total, 24 samples: 22 ChIP DNA files (10 different conditions), 2 Input files.

first: Eun

middle: S

last: Choi

first: Annelie

last: Strålfors

first: Sandra

last: Catania

first: Araceli

last: Castillo

first: J

middle: P

last: Svensson

first: Alison

middle: L

last: Pidoux

first: Robin

last: Allshire


title: microRNA signatures of iPSCs and endoderm-derived tissues

status: Public on Feb 20 2015

city: Pamplona

first: Xabier

last: Agirre

state: Navarra

address: Pio XII, 55

department: Oncology

institute: CIMA

summary: MicroRNAs (miRNAs), small non-coding RNAs that fine-tune gene expression, play multiple roles in the cell, including cell fate specification. We have analyzed the differential expression of miRNAs during fibroblast reprogramming into induced pluripotent stem cells (iPSCs) and endoderm induction in iPSCs upon treatment with high concentrations of Activin-A in reduced serum. During reprogramming, adult mouse fibroblasts are converted into cells that resemble embryonic stem cells (ESCs) according to standard molecular and functional assays for pluripotency. The reprogrammed iPSCs assume an ESC-like miRNA signature, marked by the strong induction of pluripotency clusters miR-290-295 and miR-302/367 and conversely the downregulation of the let-7 family. On the other hand, endoderm induction in iPSCs results in the upregulation of 13 miRNAs. Given that the liver and the pancreas are common derivatives of the endoderm, the comparison of the expression levels of these 13 upregulated miRNAs with those in hepatocytes and pancreatic islets suggests a trend of miRNA upregulation in the endoderm tending towards an islet phenotype rather than that of a hepatocyte. These observations provide insights into how differentiation may be guided more efficiently towards the endoderm and further into the liver or pancreas. Moreover, we also report novel miRNAs enriched for each of the cell types analyzed.

overall_design: Stemloop RT-qPCR gene expression profiling. REPROGRAMMING: Differentially expressed miRNAs were determined between iPSCs (n=5 clones) and parent tail-tip fibroblasts (n=5) using mESCs R1 (n=3) and D3 (n=3). DIFFERENTIATION: Differentially expressed miRNAs were also analyzed in two iPSC clones upon treatment with Activin-A (n=2 each), and between primary mouse hepatocytes (n=3) and pancreatic islets (n=3).

first: Angelo

last: Porciuncula

first: Natalia

last: Zapata

first: Elizabeth

last: Guruceaga

first: Miguel

last: Barajas

first: Felipe

last: Prosper


title: Age-dependent changes in phosphorylation of signaling molecules in brain tissues of Alzheimer's disease (AD) model mice

city: Mainz

first: Hyobin

last: Jeong

state: Germany

address: Richard shirrmann Str 12.

institute: IMB

summary: To demonstrate the utility of the newly developed dendron-coated phosphokinase antibody array(DPA) in which the antibodies are immobilized on a dendron-coated glass slide, the phosphorylation profiles of brain tissue samples obtained from Alzheimer's disease (AD) model mice were generated.

overall_design: The phosphorylation profiles were generated from four conditions of mice brain tissues; normal at the age of 2month, AD at the age of 2month, normal at the age of 6month and AD at the age of 6month. For each conditions, the profiling was done with three biological replicates (n=3).

first: Inhee

last: Mook-Jung

first: Daehee

last: Hwang

first: Joon

middle: W

last: Park

first: Ju-Won

last: Kwak

first: Sun-Ho

last: Han

first: Youngkyu

last: Kim

first: Sung

middle: M

last: Son


title: Expression data from Zea mays cultivars Tietar and DKC 6575

status: Public on Feb 23 2015

city: Parma

first: Mariolina

last: Gulli

address: Parco Area delle Scienze 11a

department: Life Sciences

institute: University of Parma

summary: Maize transgenic event MON810, grown and commercialised worldwide, is the only cultivated GM event in EU. Maize MON810, variety DKC6575, and the corresponding near-isogenic Tietar were studied in different growing conditions, to assess their behaviour in response to drought. Profiling gene expression in water deficit regimes and in generalised water stress showed an up-regulation of different stress- responsive genes. A greater number of differentially expressed genes was observed in Tietar rather than in DKC6575, with genes belonging to transcription factor families and genes encoding HSPs, LEAs and detoxification enzymes. Since these genes have been from literature, indicated as typical of stress responses, their activation in Tietar rather than in DKC6575 may be reminiscent of a more efficient water stress response. DKC6575 was also analysed for the expression of the transgene CryIAb (encoding for the delta-endotoxin insecticidal protein) in water limiting conditions. In all the experiments the CryIAb transcript was not influenced by water stress, but expressed at a constant level. This suggests that though a different pattern of sensitivity to stress, the transgenic variety maintains the same expression level for the transgene.

overall_design: The Maize Oligonucleotide microarray was used to measure differences in gene expression levels under drought stress in DKC6575 and in the near-isogenic variety Tietar growing in the field. The gene expression profile of each variety was evaluated at T1 and at T2 for samples fully irrigated and at T2 for samples with irrigation deficit.

last: Gullì

first: Nelson

last: Marmiroli


title: Comparison of the Global Gene Expression Profiles in the Bovine Endometrium between Summer and Autumn Seasons

city: Morioka

first: Keiichiro

last: Kizaki

state: Iwate

department: Vet. Med.

institute: Iwate University

summary: To examine the difference of the endometrial conditions in the cows between on summer and autumn seasons, gene expression profiles were compared. The expressions of 268 genes were significantly higher in the endometrium collected on summer than those on autumn, whereas 369 genes were lower (P<0.05 or lower). Transcripts of GP2 and NTS were more abundant in the endometrium of summer than those of autumn (P<0.05). In contrast, the mRNA expressions of CDH1 and HSPH1 were lower in the endometrium of summer seasons (P<0.1). Collectively, the different gene expression profiles may contribute to functional differences of endometrium between the summer and autumn seasons, and GP2 and NTS may have a relevance to endometrial deficiency that cause infertility of cows on summer seasons.

overall_design: Bovine endometrium were obtained from Japanese-Black cows (day 15 of the estrous cycle) by a biopsy methods on summer (early in September) and autumn (mid-November) of two consecutive years.

first: Ryosuke

last: Sakumoto


title: Identifying actionable targets through integrative analyses of GEM model and human prostate cancer profiling [Agilent]

city: New York

first: Jeffrey

last: Zhao

state: NY

address: 1275 York Avenue

department: Genomics Core

institute: Memorial Sloan Kettering Cancer Center

summary: Here we prolife prostate cancers derived from GEM models of prostate cancer representative of human prostate cancer

overall_design: Total DNA was isolated from established prostate cancers in 4 GEM models of prostate cancer - PB-MYC, Pten-/-, Pten-/- p53-/-, Pten-/- Rosa26-ERG, and 3 cell lines derived from GEM models including CaP8, MYC CaP, and MPC3 and normalized to wild-type prostate of litter-mate mice of same genetic background strain

first: Brett

last: Carver


title: Analysis of the evolutionary adaptation of an AraC-like global regulatory protein in the murine enteric pathogen Citrobacter rodentium

city: Parkville

first: Matthew

last: Wakefield

state: VIC

address: 1G Royal Parade

department: Bioinformatics

country: Australia

institute: Walter and Eliza Hall Institute

summary: An experiment to test the equivalence of the Citrobacter rodentium RegA and E.Coli SMS 3-5 homologue

overall_design: 8 Conditions (4 Genotypes by 2 treatments) in duplicate. Reference design without dye swaps.

first: Aimee

last: Tan

first: Nicola

last: Petty

first: Hans

last: Steinsland

first: Vicki

last: Bennet-Wood

first: Judyta

last: Praszkier

first: Ji

last: Yang

first: Marija

last: Tauschek

first: Roy

last: Robins-Browne


title: Transcriptome profiling of H. polymorpha in response to hydrogen peroxide exposure

city: daejeon

first: eun hye

last: kim

address: gwahangno 111

country: South Korea

institute: kribb

summary: To gain insight into the basic mechanism of Hydrogen peroxide detoxification in the methylotrophic yeast, H. polymorpha, we analyzed changes in transcriptional profiles in response to hydrogen peroxide exposure.

overall_design: Total RNA samples were collected from H. polymorpha cells after 30 min incubation with 0.5mM hydrogen peroxide. Using the RNA sample obtained prior to hydrogen peroxide addition as a reference, the differential fluorescence intensities of each RNA sample prepared at the indicated time was measured after labeling with Cy3 or Cy5 fluorochromes. For all analyses, we performed dye swapping experiments to avoid dye bias.

first: Eun-Hye

last: Kim

first: MinJeong

last: Sohn

first: Doo-Byoung

last: Oh

first: Ohsuk

last: Kwon


title: Lepidium sativum seed germination timecourse

city: Sutton Bonington

first: Simon

middle: Peter

last: Pearce

state: Leicestershire

address: Sutton Bonington Campus

department: Plant and Crop Sciences

institute: University of Nottingham

summary: This series analyses germinating Lepidium sativum seeds with both temporal and spatial detail. This is a cross species microarray normalisation on Arabidopsis thaliana chips. Performed as part of the vSEED project

overall_design: Lepidium seeds were dissected into four compartments at seven time points during seed germination. The compartments were the micropylar endosperm (CAP), the non-micropylar endosperm (NME), the radicle and lower hypocotyl (RAD) and the cotyledons (COT). At testa and endosperm rupture the seeds were split into pre- and post- ruptured populations.  Dry seeds were also sampled: as a whole seed (DRY), the radicle and endosperm part (DRYRC) and the dry seed part containing the non-micropylar endosperm and part of the cotyledons (DRYNMC).

first: Karin

last: Weitbrecht

first: Kerstin

last: Müller

first: Michael

last: Holdsworth

first: Gerhard

last: Leubner-Metzger


title: Identification of genes associated with the astrocyte-specific gene Gfap during astrocyte differentiation

city: Maebashi showa-machi

first: Kenji

last: Ito

department: Graduate school pf medicine

institute: Gunma university

summary:
Chromosomes and genes are non-randomly arranged within the mammalian cell nucleus. Clustering of genes is of great significance in transcriptional regulation. However, the relevance of gene clustering in their expression during differentiation of neural precursor cells (NPCs) into astrocytes remains unclear.
We performed a genome-wide enhanced circular chromosomal conformation capture (e4C) to screen genes associated with an astrocyte-specific gene, glial fibrillary acidic protein (Gfap), during astrocyte differentiation. We identified 13 genes that were specifically associated with Gfap and expressed in NPC-derived astrocytes. These results provide evidence for functional significance of gene clustering in transcriptional regulation during NPCs differentiation.

overall_design: comparison of NPCs vs LIF+ vs LIF- cells.

first: Akira

last: Aizawa

first: Takumi

last: Takizawa


title: OsHAP2E over-expression in rice

city: Matsuyama

first: Masamichi

last: Nishiguchi

address: 3-5-7 Tarumi

institute: Ehime University

summary: The goal is to know which kinds of gene are affected in rice leaves by OsHAP2E over-expression

overall_design: Transgenic rice with OsHAP2E driven by CaMV35S promoter was produced by Agrobacterium. The resultant two over-expressed lines were used for rice 44K microarray with two colors.

first: Mahfuz

last: Alam

first: Toru

last: Tanaka


title: A regulatory hierarchy controls the dynamic transcriptional response to extreme oxidative stress in archaea.

status: Public on Feb 18 2015

city: Durham

first: Amy

middle: K

last: Schmid

state: NC

address: 125 Science Dr.

department: Biology

institute: Duke University

summary: Previous work identified the winged helix-turn-helix DNA binding transcription factor (TF) RosR (encoded by VNG0258H gene), which dynamically regulates expression of more than 300 genes in response to oxidative stress in Halobacterium salinarum (Sharma 2012). RosR is required for survival of oxidants from multiple sources (e.g. H2O2 and paraquat), as deletion mutants are impaired for ROS outgrowth. Genes directly and indirectly controlled by RosR in response to ROS encode macromolecular repair functions. In the current study, we ask which of these genes are direct targets of RosR regulation. Dynamic chromatin immunoprecipitation combined with microarray (ChIP-chip) analysis validates that genes encoding these functions are direct targets of RosR binding and control. In addition, new RosR direct target genes are identified, including those encoding central cellular functions and a surprisingly high number of other TFs. The majority of the 252 sites throughout the genome are RosR-bound in the absence of stress and cleared of RosR binding in the presence of H2O2. However, binding is dynamic, with promoter-specific differences in the timing of RosR-DNA release and re-binding relative to ROS exposure.

overall_design: Halobacterium salinarum harboring VNG0258H(rosR)::myc was grown to mid-logarithmic phase (OD600 ~ 0.2 - 0.4) and either left untreated or exposed to 25 mM H2O2 for 10, 20, and 60 minutes. Transcription factor-chromatin complexes from each treated time point and untreated cultures were then cross-linked in vivo with 1% formaldehyde for 30 min at room temperature and subjected to immunoprecipitation (IP) by virtue of the myc epitope tag as described previously (Schmid et al. 2011). One µg of each IP sample was hybridized against matched, mock-treated controls on a custom 2 x 105,000 feature 60-mer oligonucleotide microarray (Agilent Technologies, AMADID 026819). On this high-resolution array, the entire H. salinarum genome was tiled every 30 bp in triplicate. Randomly selected regions of the genome were spotted in quadruplicate. Dye swaps were conducted to correct for bias in incorporation. Seven biological replicate experiments were conducted for VNG0258::myc in the absence of H2O2 and three in the presence of H2O2. Four biological replicate experiments in an H. salinarum strain harboring the empty vector control plasmid were conducted to detect background peaks resulting from technical aspects of the protocol. This yielded a total of at least 18 replicate intensity data points per 30-bp genomic region per condition. DNA fragments were directly labeled with Cy3 and Cy5 dyes (Kreatech) as described previously (Facciotti et al., 2007). Microarray slide hybridization and washing protocols were conducted according to the manufacturer’s instructions (Agilent technologies) with the exception that hybridization was conducted in the presence of 37.5% formamide at 68˚C to ensure proper stringency.

first: Peter

last: Tonner

first: Adrianne

last: Pittman


title: TWIST1-induced microRNA-424 drives an intermediate epithelial-to-mesenchymal transition that opposes metastasis

city: Aurora

first: David

last: Drasin

state: CO

department: Pharmacology

institute: University of Colorado AMC

summary: Using a TWIST1-inducible epithelial-to-mesenchymal transition (EMT) model in HMLE cells, miRNA changes were profiled at different time points during an active EMT.

overall_design: This experiment includes a total of 12 samples consisting of 2 experimental groups at 2 matching time points (day 4, day 12), each with 3 biological repeats: 3 control empty vector samples as controls and 3 inducible TWIST1 samples as the experimental condition.

first: Anna

last: Guarnieri

first: Deepika

last: Neelakantan

first: Jihye

last: Kim

first: Joshua

middle: H

last: Cabrera

first: Chu

last: Wang

first: Vadym

last: Zaberezhnyy

first: Pierluigi

last: Gasparini

first: Luciano

last: Cascione

first: Kay

last: Huebner

first: Aik

last: Tan

first: Heide

last: Ford


title: Genomic characterization of clones derived from a murine acute myeloid leukemia cell line for the description of genes involved in immunogenicity (dataset 2)

city: lille

first: frédéric

last: leprêtre

address: Boulevard du Pr Leclercq

institute: Lille University

summary: The goal of this study was to determine the effects of gene deletions and duplications on acute myeloid leukemia cells immunogenicity. The Clones were derived from the C1498 AML cell line. Lymphocytes were isolated from the C57BL/6 mouse strain.

overall_design: Genome profiling of mouse single cell clones originating from an acute myeloid leukemia cell line compared to control T lymphocytes from the same murine strain.

first: Carine

last: Brinster


title: Gene expression in invaded cells and the flanking cells of rice in response to the inoculation with rice blast fungus

city: Tsukuba

first: Eiichi

last: Minami

address: 2-1-2 Kannondai

institute: National Institute of Agrobiological Sciences

summary: Rice blast fungus was inoculated to susceptible and resistant lines of rice leaves and the invaded cells and their adjacent cells were collected by Laser Microdissection method.  The extracted RNA was amplified and analyzed by two color microarray.

overall_design: Two-condition experiment, incompatible (resistant) and compatible (susceptible) combination by using two isogenic lines of rice cv Nipponbare. Biological replicates: 3 replicates. Time course: 4 points.

first: Shigeru

last: Tanabe

first: Naoki

last: Yokotani

first: Toshifumi

last: Nagata

first: Yoko

last: Nishizawa


title: Identification of a novel NF-kB target gene in human triple-negative breast cancer cells

city: Kamakura

first: Satoshi

last: Kondo

state: Kanagawa

address: Tebiro 6-10-1

department: New Projects Development Division

institute: Toray Industries,Inc.

summary: Analysis of human triple-negative breast cancer cells (TNBCs) which have high NF-kB activity. Proteins derived from NF-κB target genes might be molecular targets for cancer therapy. Results provide new insights into tumor proliferation mechanisms.

overall_design: Exp. 1: Mock MDA-MB-436 cells vs. MDA-MB-436 cells infected with Adenovirus-IkBaSR; Exp. 2: MDA-MB-436 cells infected with Adenovirus-GFP vs. MDA-MB-436 cells infected with Adenovirus-IkBaSR.

first: Taku

last: Ito-Kureha

first: Naohiko

last: Koshikawa

first: Mizuki

last: Yamamoto

first: Kentaro

last: Semba

first: Noritaka

last: Yamaguchi

first: Motoharu

last: Seiki

first: Jun-ichiro

last: Inoue


title: Comparison of cornea to the surface tissues, dermis and epidermis, in adult zebrafish

city: Kalrsruhe

first: Masanari

last: Takamiya

institute: Karlsruhe Institute of Technology

summary:
The gene expression profile of the adult zebrafish cornea was assessed in comparison to those from closely associated surface tissues: the dermis and epidermis.

This SuperSeries is composed of the SubSeries listed below.

overall_design: Refer to individual Series


title: Adult zebrafish: cornea vs epidermis

summary: Transcriptional profiling of adult zebrafish cornea against epidermis as a reference.

overall_design: Four biological repeats with dye swap (2 chips of 4x44k for 8 data sets).

first: Uwe

last: Straehle


title: Exploring the mode of action of anti-mycobacterial activity of C17 diynes using microarray

city: Saint John

first: Haoxin

last: Li

state: New Brunswick

address: 100 Tucker Park Road

country: Canada

institute: University of New Brunswick

summary: The anti-mycobacterial activity of C17 diynes has been described previously, however, their mode of action remains unknown. Microarray techniques were used to explore the genetic regulation reponses of Mycobacterium smegmatis to treatment with the C17 diynes, falcarinol and panaxydol. Our analyses showed a distinct mode of action of the C17 diynes when compared with commonly used anti-mycobacterial drugs. In addition, geneset enrichment analysis, pathway enrichment analysis and PASS analysis revealed significant gene ontology terms, pathways and potential modes of action, respectively. Combing the results of the three analyses, we hypothesize that the C17 diynes inhibit fatty acid biosynthesis, specifically phospholipid synthesis in mycobacteira.

overall_design: Mycobacterium smegmatis MC2 155 was treated with 10 times of MIC90 of falcarinol, panaxydol, isoniazid, ethambutol and kanamycin for 6 hours with at least 6 independent biological replicates.

first: Andrew

last: Cowie

first: Christopher

last: Martyniuk

first: Duncan

last: Webster

first: John

last: Johnson

last: Gray


title: GENOMIC ANALYSIS OF FIBROLAMELLAR HEPATOCELLULAR CARCINOMA REVEALS A UNIQUE MOLECULAR PROFILE

status: Public on Feb 12 2015

city: Paris

first: Sandrine

last: Imbeaud

address: 15 rue de l'Ecole de Médecine

department: INSERM UMRS1138-EQUIPE 28, Sorbonne Université-Inserm-Université de Paris

institute: Centre de Recherche des Cordeliers

summary: Fibrolamellar hepatocellular carcinoma (FLC) is a rare primary hepatic cancer usually developed in non-cirrhotic livers of children and young adults with unknown etiology. Treatment is limited to surgical intervention. To date, molecular pathogenesis of FLC has been poorly characterized. A cohort of FLCs was analyzed through SNP-array. GISTIC algorithm identified chromosomal aberrations.

overall_design: FLC tumors corresponding to 25 different patients. In all cases, tumor and corresponding non-tumor samples were frozen (-80°C) after hepatic resection at diagnosis. Comparative Genomic Hybridization analysis was done using Illumina HumanHap370CNV Genotyping BeadChip SNP array

first: Jessica

last: Zucman-Rossi

first: Gabrielle

last: Couchy


title: Transcriptional Response to C1 and methylated compounds in Pelagibacter HTCC1062

status: Public on Feb 11 2015

city: Corvallis

first: Jing

last: Sun

state: OR

address: 220 Nash Hall

department: Microbiology Department

institute: Oregon State University

summary: Recent studies have shown that Pelagibacter oxidize a wide range of one carbon (C1) and methylated compounds that are ubiquitous in the oceans. However, the metabolic pathways used to oxidize and assimilate these compounds are complex and have been only partly described. To understand the metabolism of these compounds in Pelagibacter and to identify candidate genes involved in these pathways, we used microarray to study changes in gene expression in response to five different compounds (trimethylamine N-oxide (TMAO), methylamine, dimethylsulfoniopropionate (DMSP), methanol, and glycine betaine (GBT)) in Pelagibacter strain HTCC1062.

platform_organism:
Candidatus Pelagibacter ubique HTCC1002
Candidatus Pelagibacter ubique HTCC1062
Candidatus Pelagibacter sp. HTCC7211

overall_design: This project will examine the transcriptional response of the marine microorganism Pelagibacter HTCC1062 to five methylated compounds. To do this, 18 flasks were innoculated with cells - 3 flasks without any methylated compounds and rest of 15 treated with different methylated compounds respectively (TMAO (trtmA), methylamine (trtmB), DMSP (trtmC), methanol (trtmD) and glycine betaine (trtmE)). Cells were all harvested at the same timepoint in the exponential phase.

first: Stephen

last: Giovannoni


title: Differentially expressed adipocyte-associated genes in Bone-marrow Mesenchymal stem cells under normal and hypoxic conditions

city: Changsha

first: Juanjuan

last: Xiang

address: 110 Xiangya Road

department: Cancer Research Institute

country: China

institute: Central South University

summary: To identify proteins involved in the regulation of adipogenic differentiation under hypoxic conditions, an RT2 Profiler PCR array was used to screen a panel of 84 genes associated with human adipogenesis in Bone-marrow Mesenchymal stem cells under normal and hypoxic conditions.

overall_design: Bone-marrow Mesenchymal stem cells were put in hypoxic chamber, set at an oxygen concentration of 0.2%. Cells under normoxia are considered as a control.


title: Transcriptome analysis of kidney cancer (CustomArray Inc)

status: Public on Feb 05 2015

city: Moscow

first: Maria

middle: Vladimirovna

last: Suntsova

address: Miklukho-Maklaya, 16/10

department: Department of Genetics and Postgenomic Technologies

country: Russia

institute: M.M. Shemyakin and Yu.A. Ovchinnikov  Institute of  bioorganic chemistry of the Russian Academy of Sciences

summary: The aim of this research was to explore activation/deactivation of signaling pathways during cancerogenesis.

overall_design: Tissue samples from malignant tumors were obtained from patients who had undergone surgery. Samples were formain fixed and embedded in paraffin. Tumors were evaluated by a pathologist to confirm the diagnosis and estimate the tumor cell numbers. All tumor samples used in this study contained at least 80% tumor cells.

middle: V

first: Alexander

last: Aliper

first: Elena

last: Ilnitskaya

first: Anton

last: Buzdin


title: Genetic characterization of T-PLL reveals two major biologic subgroups and JAK3 mutations as prognostic marker

city: Munich

first: Anna

last: Stengel

address: Max-Lebsche-Platz 31

institute: MLL Münchner Leukämielabor GmbH

summary: T-cell prolymphocytic leukemia (T-PLL) is a rare post-thymic T-cell neoplasm with aggressive clinical course and short overall survival. So far, due to the rareness of this disease, genetic data is available only from individual cases or small cohorts. In our study, we aimed at performing a comprehensive cytogenetic and molecular genetic characterization of T-PLL comprising the largest cohort of patients with T-PLL analyzed so far, including correlations between the respective markers and their impact on prognosis. Genetic abnormalities were found in all 51 cases with T-PLL, most frequently involving the TCRA/D locus (86%). Deletions were detected for ATM (69%) and TP53 (31%), whereas i(8)(q10) was observed in 61% of cases. Mutations in ATM, TP53, JAK1 and JAK3 were detected in 73%, 14%, 6%, and 21% of patients, respectively. Additionally, BCOR mutations were observed for the first time in a lymphoid malignancy (8%). Two distinct genetic subgroups of T-PLL were identified: A large subset (86% of patients) showed abnormalities involving the TCRA/D locus activating the proto-oncogenes TCL1 or MTCP1, while the second group was characterized by a high frequency of TP53 mutations (4/7 cases). Further, analyses of overall survival identified JAK3 mutations as important prognostic marker, showing a significant negative impact.

overall_design: 51 samples were processed; MLL Munich Leukemia Laboratory


title: miRNA expression profile in angiosarcoma

status: Public on Feb 06 2015

city: wuhan

first: yaobin

last: chen

address: Tongji Hospital, Wuhan,jiefang road 1095

institute: Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology,

summary: We first  use microRNA expression profiles to find miRNA expression signatures in 3 cases of human angiosarcoma and capillary hemangiomauman, then RT-PCR for large sample verification. Through the bioinformatics prediction of its target genes, we study its function and aim to find the new molecular markers and therapeutic targets.

overall_design: We identified the miRNA expression signatures in human angiosarcomas and capillary hemangiomas by using microRNA expression profiles

first: Y

middle: B

last: Chen

middle: Q

last: Duan

first: G

last: Wang


title: UV (UVC, 40J/m2) light irradiation effect on human hepatoma Hep3B cells

city: barcelona

first: BELEN

last: MINANA

state: barcelona

address: dr aiguader 88

department: GENE REGULATION, STEM CELLS AND CANCER

institute: Center for genomic regulation

summary:
human hepatoma Hep3B cells were treated with 40 J/m2 UV light versus untreated
Alternative pre-mRNA processing plays a key role in the response to DNA damage as well as in neoplastic transformation. We found that two Ewing Sarcoma (ES) cell lines exhibit different sensitivity to UV light irradiation, with Hep3B_UV_40J-N-MC cells being more sensitive than LAP-35 cells. RNA profiling during the response to low doses of UV light irradiation revealed genes differentially regulated between the two cell lines. In particular, UV light irradiation induced a novel isoform of the RNA helicase DHX9 which is targeted to nonsense-mediated decay (NMD) and therefore causes down-regulation of DHX9 in Hep3B_UV_40J-N-MC cells, but not in LAP-35 cells. DHX9 protein forms a complex with RNA polymerase II (RNAPII) and EWS-FLI1 to enhance transcription, and we found that down-regulation of DHX9 by UV light irradiation in Hep3B_UV_40J-N-MC cells impairs the recruitment of EWS-FLI1 to target genes and increases sensitivity to DNA damage. Notably, sensitivity of Hep3B_UV_40J-N-MC cells to irradiation correlated with enhanced phosphorylation and decreased processivity of RNAPII upon irradiation, which in turn causes inclusion of the novel DHX9 exon in Hep3B_UV_40J-N-MC cells exposed to UV light, an observation that could be recapitulated in LAP35 cells by pharmacological reduction of RNAPII processivity. Our data suggest that EWS-FLI1 oncogene activity could be targeted by modulation of DHX9 gene expression.

overall_design: Three biological replicates were labeled in direct and dye-swap microarray experiments and hybridized onto an Agilent custom splicing-sensitive microarray platform

first: Belén

last: Miñana

first: MariaPaola

last: Paronetto


title: Gene expression profiles of epithelial cells infected with microRNA-negative and -positive Epstein-Barr viruses

first: Satoshi

last: Kondo

summary: The Epstein-Barr virus (EBV) encodes its own microRNAs (miRNAs); however, their biological roles remain elusive. The commonly used EBV B95-8 strain lacks a 12 kb genomic region, known as BamHI A Rightward Transcripts (BART) locus, which encodes a number of viral miRNAs (BART miRNAs). These miRNAs are expressed abundantly in EBV-positive epithelial malignancies, suggesting that the 12 kb region somehow contributes to EBV-mediated epithelial carcinogenesis. Bacterial artificial chromosome (BAC) technology was used to generate an EBV B95-8 strain in which the 12 kb region was fully restored at its native locus (BART-restored virus). HEK293 and AdAH cells infected with either the parental BART-deleted virus or the BART-restored virus were established. The gene expression profiles of these cells were examined to identify cellular target genes of BART miRNAs.

overall_design: Total RNAs of 2 independent v-miRNA-positive HEK293 (or AdAH) cells and 2 independent v-miRNA-negative cells HEK293 (or AdAH) cells were processed for Microarray analysis using 3D-Gene human Oligo chip 25k (Toray, Tokyo, Japan).

first: Teru

last: Kanda


title: Genome-Wide Transcription Responses to Synchrotron Microbeam Radiotherapy

city: Parkville

first: Yuqing

last: Yang

state: Victoria

address: Royal Women's Hospital Level 7, 20 Flemington Rd

institute: University of Melbourne

summary: We hypothesized that gene expression changes in EMT6.5 tumors after Microbeam Radiotherapy (MRT) are different from those seen after broad beam (BB) at 4-48 h postirradiation. Our findings demonstrate molecular differences in the tumor response to MRT vs. BB and provide insight into the underlying mechanisms of MRT and BB.

overall_design: Total RNA obtained from isolated EMT6.5 tumours irradiated by MRT or BB at 4, 24 or 48 hours post-irradiation compared to unirradiated control tumours.

first: Carl

last: Sprung


title: ChIP-on-chip from multiple donors of BM-MSCs with H3K4me3 and H3K27me3

status: Public on Feb 09 2015

city: Silver Spring

first: Patrick

last: Lynch

state: MD

address: 10903 New Hampshire Ave.

institute: US Food and Drug Administration

summary:
Bone marrow-derived multipotent stromal cells (BM-MSCs) exhibit therapuetically valuable properties, including the capacity to differentiate into skeletal tissues and modulate immune system activity. These properties depend on proper regulation of dynamic gene expression in response to environmental  and developmental stimuli. This study used chromatin immunoprecipitation (ChIP) coupled with human promoter tiling microarray analysis (ChIP-on-chip) to profile histones H3K4me3 and H3K27me3 at promoters genome-wide.
The goal of the study was to identify gene promoters marked by H3K27me3 and H3K4me3 in BM-MSCs.

overall_design: ChIP-on-chip performed with antibodies to H3K4me3 and H3K27me3 on BM-MSCs from 3 different donors (labeled 1632, 167696, and 8F3560) and with technical replicates.

first: Kathleen

last: McGinnis

first: Elaine

middle: E

last: Thompson

first: Yazmin

middle: I

last: Rovira Gonzalez

first: Jessica

last: Lo Sordo

first: Steven

middle: R

last: Bauer

first: Deborah

middle: A

last: Hursh


title: Gene expression profile analysis of Staphylococcus aureus treated with nisin

status: Public on Feb 10 2015

city: Changchun

last: Guo

address: Xi’an Road 5333#

institute: Jilin University

summary:
Staphylococcus aureus (S. aureus) has already to be one of the most commonly identified bacteria that cause food poisoning. S. aureus colonization in humans can cause serious infections, toxinoses and life threatening diseases. The bacteriocin nisin has been extensively used as potential natural preservative in the food industry, but the overall transcriptional response mechanisms of S. aureus to nisin are still poorly understood.
To detect the possible molecular mechanism of nisin against S. aureus, Affymetrix GeneChips were used to determine the global comparative transcription of S. aureus cells triggered by treatment with sub-inhibitory concentrations of nisin.

overall_design: Staphylococcus aureus planktonic cells were exposed for 60 minutes to nisin at concentration of 4 μg/ml (1/2× MIC). 2 samples including 2 control samples are analyzed.

first: Xingchen

last: Zhao

first: Rizeng

last: Meng

first: Ce

last: Shi

first: Zonghui

last: Liu

first: Yanjun

last: Huang

first: Ziwen

first: Lu

last: Yu


title: Tumor Suppressor IKZF1 Mediates Glucocorticoid Therapy Resistance in B Cell Precursor Acute Lymphoblastic Leukemia

status: Public on Feb 04 2015

city: Nijmegen

first: Rene

last: Marke

state: Gelderland

address: Philipps van Leijdenslaan 15

department: Kindergeneeskunde

country: Netherlands

institute: Radboudumc

summary:
Analysis of the effect of Prednisolone in mouse splenocytes with and without Ikzf1 at gene expression level. The hypothesis tested in the present study was that loss of Ikzf1 affects the induction and repression of the Glucocorticoid receptor target genes.
Results provide important information of the differentially expressed genes regulated by Ikzf1 upon Prednisolone treatment, explaining the resistance towards Glucocorticoid-induced apoptosis in splenocytes  harboring Ikzf1 loss.

overall_design: Total RNA was obtained from WT and Ikzf1+/- splenocytes subjected to 16 hours Prednsiolone treatment compared to untreated cells.

first: Jørn

last: Havinga

first: Jacqueline

last: Cloos

first: Marc

last: Demkes

first: Geert

last: Poelmans

first: Laurensia

last: Yuniati

first: Dorette

last: van Ingen Schenau

first: Edwin

last: Sonneveld

first: Roland

last: Kuiper

first: Peter

last: Hoogerbrugge

first: Gertjan

middle: J

last: Kaspers

first: Frank

middle: N

last: van Leeuwen

first: Blanca

last: Scheijen


title: The VELVET complex in the gray mold fungus Botrytis cinerea:  impact of BcLAE1 on differentiation, secondary metabolism and virulence

status: Public on Feb 01 2015

city: Palaiseau

first: Adeline

last: SIMON

address: 22 place de l'agronomie

institute: INRAE

summary: Full transcriptomes of the Botrytis cinerea wild-type strain B0510 and the null-mutants deltaBcVEL1 and deltaBcLAE1, cultured onto solid grape juice medium with cellophane overlays , were compared to identify BcVEL1  or/and BcLAE1-dependent genes.

overall_design: The Botrytis cinerea wild-type strain and the null-mutants deltaBcVEL1 and BcLAE1  were cultured for 48h onto solid grape juice medium with cellophane overlays. 4 replicates were performed. The 12 total-RNA samples (3 strains* 4 replicates) were used for hybridization on NimbleGen 4plex gene expression arrays (20,885 gene models from Botrytis cinerea with three 60-mer probes per gene).

first: Julia

last: Schumacher

last: Simon

first: Kim

middle: C

last: Cohrs

first: Stefanie

last: Traeger

first: Antoine

last: Porquier

first: Berengere

last: Dalmais

first: Muriel

last: Viaud

first: Bettina

last: Tudzynski


title: microRNA expression profiling of small intestine of Tlr3+/+ and Tlr3-/- mice after total body g-irradiation

first: Satoshi

last: Kondo

summary: Microarray was performed to comprehensively examine microRNA induction in murine small intestine after exposure to total body g-irradiation.

overall_design: Small intestines were collected from Tlr3+/+ and Tlr3-/- mice at 0 and 6 hr after exposure to 10 Gy of total body g-irradiation. Samples were pooled from 3 mice. Total RNA was extracted and subjected to microRNA microarray analysis.

first: Naoki

last: Takemura

last: Uematsu


title: Paradoxical neurobehavioral rescue by cues associated with infant trauma: Amygdala 5-HT and CORT

city: Philadelphia

first: Gordon

middle: A.

last: Barr

state: PA

address: 3615 Civic Center Blvd

department: Anesthesiology and Critical Care Medicine

institute: Children's Hospital of Philadelphia

summary: We show that infant trauma, as modeled by infant paired odor-shock conditioning, results in later life depressive-like behavior that can be modulated by learned infant cues (i.e., odor previously paired with shock). We have previously shown that this infant attachment odor learning paradigm results in the creation of a new artificial maternal odor that is able to control pup behavior and retain its value throughout development. Here, we assess the mechanism by which this artificial maternal odor is able to rescue depressive-like behavior and show that this anti-depressant like effect results in glucocorticoid and serotonin (5-HT) related changes in amygdala gene expression and is dependent on amygdala 5-HT. Furthermore, increasing amygdala 5-HT and blocking corticosterone (CORT) in the absence of odor mimics the adult rescue effects elicited by the artificial maternal odor, suggesting a mechanism by which odor presentation exerts its repair effects.

overall_design: There are three experimental groups: 1: pups with no infant shock and the adult forced swim test (FST)with no odor; 2. pups with infant odor-shock pairing and the adult forced swim test (FST) with no odor; 3. pups with infant odor-shock pairing and adult forced swim test with infant odor.

first: Millie

last: Rincón-Cortés

first: Kiseko

last: Shio

first: Sheilyn

last: Nunez

first: Regina

last: Sullivan


title: Expression data from Zeb1 knockdown NM18 cells

city: Oxford

first: Alexander

last: Feuerborn

address: South Parks Road

institute: Sir William Dunn School of Pathology

type:
Expression profiling by array
Third-party reanalysis

summary:
Differentiation of epithelial cells is strongly affected by transcription factors related to epithelial to mesenchymal-like progression.
We used gene expression profiling to identify genes that are differentially regulated upon repression of the transcription factor Zeb1 (deltaEF1/Areb6).

overall_design:
NM18 cells were transfected with non-silencing siRNA (ns-siRNA) or siRNA targeting Zeb1 (Zeb1 siRNA) for 48h. Experiments were performed as independent biological triplicate.
Three non-silencing siRNA samples (GSM1322708, GSM1322709, and GSM1322710) were originally deposited in Series GSE54715. The samples were reanalyzed with the Zeb1 siRNA samples and the data is linked at the bottom of the Series record.

first: Daniel

last: Mathow

first: Federica

last: Chessa

first: Sylvia

last: Kaden

first: Mariona

last: Rabionet

first: Richard

last: Jennemann

first: Roger

last: Sandhoff

first: Hermann-Josef

last: Groene


title: Real-time quantitative PCR analysis of the expression of neurotransmitter receptor and regulator genes in 4 week old male MeCP2 A140V mutant mouse brain cortex

city: Phoenix

first: Garilyn

last: Jentarra

state: AZ

address: 350 W. Thomas Rd

department: Neurology Research

institute: Barrow Neurological Institute

summary: The goal of this study was to identify brain cortex gene expression differences between mutant MeCP2 A140V mice and their wild type littermates.The PCR array used for these experiments was the Mouse Neurotransmitter Receptors and Regulators Array (Catalog# PAMM-060A) from SABiosciences. Mice used in this study were 4 week old males.

overall_design: Total RNA was extracted from the somatosensory/motor cortex of 4 week old male MeCP2 A140V hemizygous mutant mice and their wild type littermates. For this study, brain tissue from 3 mice of each genotype was used and RNA from the cortex of each mouse was analyzed separately (ie., triplicate biological replicates). The RNA was purified to remove genomic DNA and was then reverse transcribed for use in quantitative RT-PCR analysis of gene expression using the SABiosciences RT2 profiler PCR array system.  The PCR array used for these experiments was the Mouse Neurotransmitter Receptors and Regulators Array (Catalog# PAMM-060A).

first: Vinodh

last: Narayanan


title: Real-time quantitative PCR analysis of the expression of neurotransmitter receptor and regulator genes in 2 week old male MeCP2 A140V mutant mouse brain cortex

summary: The goal of this study was to identify brain cortex gene expression differences between mutant MeCP2 A140V mice and their wild type littermates.The PCR array used for these experiments was the Mouse Neurotransmitter Receptors and Regulators Array (Catalog# PAMM-060A) from SABiosciences. Mice used in this study were 2 week old males.

overall_design: Total RNA was extracted from somatosensory/motor cortex of 2 week old male MeCP2 A140V hemizygous mutant mice and their wild type littermates. For this study, cortical tissue from 3 mice of each genotype was used and RNA from the cortex of each mouse was analyzed separately (ie., triplicate biological replicates). The RNA was purified to remove genomic DNA and was then reverse transcribed for use in quantitative RT-PCR analysis of gene expression using the SABiosciences RT2 profiler PCR array system.  The PCR array used for these experiments was the Mouse Neurotransmitter Receptors and Regulators Array (Catalog# PAMM-060A).


title: Dendritic cell fate is determined by BCL11A

city: Bethesda

first: Louis

middle: M.

last: Staudt

address: 9000 Rockville Pike, Bldg 10, Rm 4N114

department: Lymphoid Malignancies Branch

institute: National Cancer Institute

summary: The plasmacytoid dendritic cell (pDC) is vital to the coordinated action of innate and adaptive immunity. pDC development has not been unequivocally traced, nor has its transcriptional regulatory network been fully clarified. Here we confirm an essential requirement for the BCL11A transcription factor in fetal pDC development, and demonstrate this lineage-specific requirement in the adult organism. Furthermore, we identify BCL11A gene targets and provide a molecular mechanism for its action in pDC commitment. Embryonic germ-line deletion of Bcl11a revealed an absolute cellular, molecular, and functional absence of pDCs in fetal mice. In adults, deletion of Bcl11a in hematopoietic stem cells resulted in perturbed yet continued generation of progenitors, loss of downstream pDC and B-cell lineages, and persisting myeloid, conventional dendritic, and T-cell lineages. Challenge with virus resulted in a marked reduction of antiviral response in conditionally deleted adults. Genome-wide analyses of BCL11A DNA binding and expression revealed that BCL11A regulates transcription of E2-2 and other pDC differentiation modulators, including ID2 and MTG16. Our results identify BCL11A as an essential, lineage- specific factor that regulates pDC development, supporting a model wherein differentiation into pDCs represents a primed "default" pathway for common dendritic cell progenitors.

overall_design: Raji cells were infected with retroviruses containing pXY-PURO (negative control vector) or pXY-BCL11A-XS. BJAB cells were infected with retroviruses containing pXY-PURO (negative control vector) or pXY-BCL11A-XL. Two arrays measured Raji BCL11A-XS expression and two arrays measured BJAB BCL11A-XL expression.


title: Real-time quantitative PCR analysis of the expression of chromatin modification enzyme genes in 2 week old male MeCP2 A140V mutant mouse brain cortex

summary: The goal of this study was to identify brain cortex gene expression differences between mutant MeCP2 A140V mice and their wild type littermates.The PCR array used for these experiments was the Mouse Epigenetic Chromatin Modification Enzymes Array (Catalog# PAMM-085A) from SABiosciences. Mice used in this study were 2 week old males.

overall_design: Total RNA was extracted from the somatosensory/motor cortex of 2 week old male MeCP2 A140V hemizygous mutant mice and their wild type littermates. For this study, cortical tissue from 3 mice of each genotype was used and RNA from the cortex of each mouse was analyzed separately (ie., triplicate biological replicates). The RNA was purified to remove genomic DNA and was then reverse transcribed for use in quantitative RT-PCR analysis of gene expression using the SABiosciences RT2 profiler PCR array system.  The PCR array used for these experiments was the Mouse Epigenetic Chromatin Modification Enzymes Array (Catalog# PAMM-085A).

middle: M


title: Coupling of cellular processes and their coordinated oscillations under continuous light in cyanothece sp. ATCC 51142, a diazotrophic unicellular cyanobacteria

status: Public on Feb 03 2015

city: East Lansing

first: Sandeep

middle: B.

last: Gaudana

state: MI

address: 612 Wilson Road

institute: Michigan State University

summary: Transcriptional profiling of  a unicelluar diazotrophic cyanobacterium Cyanothece sp. ATCC 51142 in constant light under nitrogen fixing condition. The controls comprised of equimolar pool of RNA from all time points.

overall_design: Cyanothece sp. ATCC 51142 was grown in BG-11 medium without nitrate. The culture was entrained under 12 h alternate light/dark cycles for 96 h and released in constant light (LL). Nine samples were for two consecutive cycles under LL, at times when the culture underwent transitions in its photosynthetic and respiratory phases, as indicated by the exit CO2 and O2 profiles. Two biological replicates, two technical replicates and a dye swap were analyzed for each sample from individual time points.

first: S

last: Krishnakumar

first: Xuan

last: Nguyen

first: Ganesh

last: Viswanathan

first: Madhu

last: Chetty

first: Pramod

middle: P

last: Wangikar


title: Real-time quantitative PCR analysis of gene expression in the cortex of MeCP2 A140V mutant mice

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

overall_design: Refer to individual Series


title: Real-time quantitative PCR analysis of the expression of cytoskeleton regulator genes in 2 week old male MeCP2 A140V mutant mouse brain cortex

summary: The goal of this study was to identify brain cortex gene expression differences between mutant MeCP2 A140V mice and their wild type littermates.The PCR array used for these experiments was the Mouse Cytoskeleton Regulators Array (Catalog# PAMM-088A) from SABiosciences. Mice used in this study were 2 week old males.

overall_design: Total RNA was extracted from the somatosensory/motor cortex of 2 week old male MeCP2 A140V hemizygous mutant mice and their wild type littermates. For this study, cortical tissue from 3 mice of each genotype was used and RNA from the cortex of each mouse was analyzed separately (ie., triplicate biological replicates). The RNA was purified to remove genomic DNA and was then reverse transcribed for use in quantitative RT-PCR analysis of gene expression using the SABiosciences RT2 profiler PCR array system.  The PCR array used for these experiments was the Mouse Cytoskeleton Regulators Array (Catalog# PAMM-088A).


title: Real-time quantitative PCR analysis of the expression of neurotransmitter receptor and regulator genes in 4 week-old male MeCP2 A140V mutant mouse cerebellum

summary: The goal of this study was to identify cerebellar gene expression differences between mutant MeCP2 A140V mice and their wild type littermates.The PCR array used for these experiments was the Mouse Neurotransmitter Receptors and Regulators Array (Catalog# PAMM-060A) from SABiosciences. Mice used in this study were 4 week old males.

overall_design: Total RNA was extracted from whole cerebella of 4 week old male MeCP2 A140V hemizygous mutant mice and their wild type littermates. For this study, cerebella from 3 mice of each genotype were used and RNA from the cerebellum of each mouse was analyzed separately (ie., triplicate biological replicates). The RNA was purified to remove genomic DNA and was then reverse transcribed for use in quantitative RT-PCR analysis of gene expression using the SABiosciences RT2 profiler PCR array system.  The PCR array used for these experiments was the Mouse Neurotransmitter Receptors and Regulators Array (Catalog# PAMM-060A).


title: 835np mutant vs wild-type

city: Gainesville

first: Sang-Joon

last: Ahn

state: FL

address: 1395 Center Dr.

department: Department of Oral Biology

institute: University of Florida

summary:
Transcriptional profiling of the Δ835np mutant vs the wild-type strain grown in BHI to OD600=0.5.
An intimate linkage between the regulation of biofilm formation, stress tolerance and genetic competence exists in the dental caries pathogen Streptococcus mutans. We previously reported that the rcrRPQ genes, which encode ABC exporters (RcrPQ) and a MarR-family transcriptional regulator (RcrR) that represses the expression of the rcr operon, play a dominant role in regulation of development of genetic competence and connect competence with stress tolerance and (p)ppGpp production in S. mutans. Here we identify the region required for efficient RcrR binding to the rcr promoter region using purified recombinant RcrR (rRcrR) protein in electrophoretic mobility shift and fluorescence polarization assays. DNA fragments carrying mutations in the binding region resulted in decreased binding of rRcrR. Direct binding of RcrR to the comX gene promoter in vitro revealed that RcrR has the potential to directly regulate competence development. Likewise, direct interactions of rRcrR with the promoter region of relP, encoding a (p)ppGpp synthase, show the potential for RcrR-dependent modulation of (p)ppGpp pools. Introduction of mutations into the RcrR binding sites in the rcrR promoter region in vivo demonstrated that optimal RcrR binding is essential for proper expression of competence genes and optimal transformation efficiency. Transcription profiling by RNA-seq and mircroarrays of strains with mutations in rcrR showed that genes in the competence pathway were those most differentially expressed. Thus, here and in a accompanying paper, we establish mechanisms by which the products of the rcrRPQ operon integrate com gene expression, genetic transformation, ppGpp metabolism and stress tolerance in S. mutans

overall_design: Two-condition experiment, Δ835np mutant vs the wild-type strain. Biological replicates: 4 per strain, independently grown and harvested. One replicate per array

first: Kinda

last: Seaton

first: Robert

last: Burne


title: Real-time quantitative PCR analysis of the expression of cytoskeleton regulator genes in 4 week old male MeCP2 A140V mutant mouse brain cortex

summary: The goal of this study was to identify brain cortex gene expression differences between mutant MeCP2 A140V mice and their wild type littermates.The PCR array used for these experiments was the Mouse Cytoskeleton Regulators Array (Catalog# PAMM-088A) from SABiosciences. Mice used in this study were 4 week old males.

overall_design: Total RNA was extracted from the somatosensory/motor cortex of 4 week old male MeCP2 A140V hemizygous mutant mice and their wild type littermates. For this study, brain tissue from 3 mice of each genotype was used and RNA from the cortex of each mouse was analyzed separately (ie., triplicate biological replicates). The RNA was purified to remove genomic DNA and was then reverse transcribed for use in quantitative RT-PCR analysis of gene expression using the SABiosciences RT2 profiler PCR array system.  The PCR array used for these experiments was the Mouse Cytoskeleton Regulators Array (Catalog# PAMM-088A).


title: Real-time quantitative PCR analysis of the expression of neurotransmitter receptor and regulator genes in 2 week-old male MeCP2 A140V mutant mouse cerebellum

summary: The goal of this study was to identify cerebellar gene expression differences between mutant MeCP2 A140V mice and their wild type littermates.The PCR array used for these experiments was the Mouse Neurotransmitter Receptors and Regulators Array (Catalog# PAMM-060A) from SABiosciences. Mice used in this study were 2 week old males.

overall_design: Total RNA was extracted from whole cerebella of 2 week old male MeCP2 A140V hemizygous mutant mice and their wild type littermates. For this study, cerebella from 3 mice of each genotype were used and RNA from the cerebellum of each mouse was analyzed separately (ie., triplicate biological replicates). The RNA was purified to remove genomic DNA and was then reverse transcribed for use in quantitative RT-PCR analysis of gene expression using the SABiosciences RT2 profiler PCR array system.  The PCR array used for these experiments was the Mouse Neurotransmitter Receptors and Regulators Array (Catalog# PAMM-060A).


title: Real-time quantitative PCR analysis of the expression of chromatin modification enzyme genes in 4 week old male MeCP2 A140V mutant mouse brain cortex

summary: The goal of this study was to identify brain cortex gene expression differences between mutant MeCP2 A140V mice and their wild type littermates.The PCR array used for these experiments was the Mouse Epigenetic Chromatin Modification Enzymes Array (Catalog# PAMM-085A) from SABiosciences. Mice used in this study were 4 week old males.

overall_design: Total RNA was extracted from the somatosensory/motor cortex of 4 week old male MeCP2 A140V hemizygous mutant mice and their wild type littermates. For this study, cortical tissue from 3 mice of each genotype was used and RNA from the cortex of each mouse was analyzed separately (ie., triplicate biological replicates). The RNA was purified to remove genomic DNA and was then reverse transcribed for use in quantitative RT-PCR analysis of gene expression using the SABiosciences RT2 profiler PCR array system.  The PCR array used for these experiments was the Mouse Epigenetic Chromatin Modification Enzymes Array (Catalog# PAMM-085A).


title: Real-time quantitative PCR analysis of the expression of cytoskeleton regulator genes in 4 week old male MeCP2 A140V mutant mouse cerebellum

summary: The goal of this study was to identify cerebellar gene expression differences between mutant MeCP2 A140V mice and their wild type littermates.The PCR array used for these experiments was the Mouse Cytoskeleton Regulators Array (Catalog# PAMM-088A) from SABiosciences. Mice used in this study were 4 week-old males.

overall_design: Total RNA was extracted from whole cerebella of 4 week old male MeCP2 A140V hemizygous mutant mice and their wild type littermates. For this study, cerebella from 3 mice of each genotype were used and RNA from the cerebellum of each mouse was analyzed separately (ie., triplicate biological replicates). The RNA was purified to remove genomic DNA and was then reverse transcribed for use in quantitative RT-PCR analysis of gene expression using the SABiosciences RT2 profiler PCR array system.  The PCR array used for these experiments was the Mouse Cytoskeleton Regulators Array (Catalog# PAMM-088A).


title: Real-time quantitative PCR analysis of gene expression in the cerebellum of MeCP2 A140V mutant mice


title: Real-time quantitative PCR analysis of the expression of cytoskeleton regulator genes in 2 week old male MeCP2 A140V mutant mouse cerebellum

summary: The goal of this study was to identify cerebellar gene expression differences between mutant MeCP2 A140V mice and their wild type littermates. The PCR array used for these experiments was the Mouse Cytoskeleton Regulators Array (Catalog# PAMM-088A) from SABiosciences. Mice used in this study were 2 week old males.

overall_design: Total RNA was extracted from whole cerebella of 2 week old male MeCP2 A140V hemizygous mutant mice and their wild type littermates. For this study, cerebella from 3 mice of each genotype were used and RNA from the cerebellum of each mouse was analyzed separately (ie., triplicate biological replicates). The RNA was purified to remove genomic DNA and was then reverse transcribed for use in quantitative RT-PCR analysis of gene expression using the SABiosciences RT2 profiler PCR array system.  The PCR array used for these experiments was the Mouse Cytoskeleton Regulators Array (Catalog# PAMM-088A).


title: Real-time quantitative PCR analysis of the expression of chromatin modification enzyme genes in 4 week-old male MeCP2 A140V mutant mouse cerebellum

summary: The goal of this study was to identify cerebellar gene expression differences between mutant MeCP2 A140V mice and their wild type littermates.The PCR array used for these experiments was the Mouse Epigenetic Chromatin Modification Enzymes Array (Catalog# PAMM-085A) from SABiosciences. Mice used in this study were 4 week old males.

overall_design: Total RNA was extracted from whole cerebella of 4 week old male MeCP2 A140V hemizygous mutant mice and their wild type littermates. For this study, cerebella from 3 mice of each genotype were used and RNA from the cerebellum of each mouse was analyzed separately (ie., triplicate biological replicates). The RNA was purified to remove genomic DNA and was then reverse transcribed for use in quantitative RT-PCR analysis of gene expression using the SABiosciences RT2 profiler PCR array system.  The PCR array used for these experiments was the Mouse Epigenetic Chromatin Modification Enzymes Array (Catalog# PAMM-085A).


title: Microarray analysis of the white muscle transcriptome in feed deprived rainbow trout treated with insulin-like growth factor-I

city: Kearneysville

first: Beth

last: Cleveland

state: WV

address: 11861 Leetown Rd

institute: NCCCWA/ARS/USDA

summary: Treatment with insulin-like growth factor-I (IGF-I) during feed deprivation attenuates the weight loss response in both mammals and fish, therefore the reduction in plasma IGF-I concentrations during fasting likely serves as a signal that contributes to the catabolic response.  To better understand the physiological mechanisms responsible for this effect rainbow trout were administered IGF-I during a 2 wk period of feed deprivation and changes in gene expression in white muscle were determined using microarray analysis.  Weight loss was reduced by 15% (P<0.05) in IGF-I treated fish.  A total of 440 transcripts were identified as differentially regulated (P<0.05) between saline and IGF-I treated fish.  Genes related to protein degradation were down-regulated and included protease and peptidase genes and genes involved in ubiquitin-proteasome and cathepsin-mediated proteolytic pathways.  IGF-I increased expression of myosin binding protein H and coronin-1C, while decreasing expression of other myofibrillar and cytoskeleton-associated genes like troponin-C and parvalbumin-2.   Polyadenylate-binding protein 2, a transcription factor that positively regulates myoD and myogenin expression, was upregulated with IGF-I treatment.  Additional genes that were differentially regulated are associated with lipid and carbohydrate metabolism, mitochondrial biogenesis and electron transport, gene transcription, signal transduction and regulation of apoptosis.  In summary, these data suggest that IGF-I plays a central role in regulating protein degradation, especially via the ubiquitin-proteasomal pathway, and that reductions in protein degradation and the subsequent effects on other physiological systems are largely responsible for the IGF-I-induced reduction in weight loss.

platform_organism:
Oncorhynchus mykiss
Salmo salar

overall_design: Eight approximately 1-year old full-sibling rainbow trout families were housed in individual tanks, according to family, at the National Center for Cool and Cold Water.  Each fish was pit-tagged at 7-months of age.  At the beginning of the study, fish were anesthetized with tricaine methanesulfonate (MS-222), weighed, and an osmotic pump was surgically inserted into the peritoneal cavity of each fish (n=4 fish/family/treatment, N=16 fish).  The osmotic pump contained either recombinant human IGF-I, which released hormone at 25 ug/kg/day, or saline, which was the vehicle used to resuspend IGF-I.  Feed was withheld 2-days prior to surgery and for the experimental 2 week period.  Fish were harvested using as overdose of MS-222, weighed, and white muscle samples were removed, frozen in liquid N, and stored at -80 C until analysis.  Muscle RNA was isolated from muscle of the two families that exhibited the greatest difference in weight loss between  IGF-I and saline treatments; families 64 and 107.  Hybridizations were performed using a dye-swap design with an IGF-I and saline treated fish within the same family, therefore a total of 16 slides were hybridized using Alexa 647 and Alexa 555 dyes.

first: Cecelia

last: Castano-Sanchez

middle: L

last: Vallejo

first: Gregory

last: Weber

first: Caird

last: Rexroad

first: Jianbo

last: Yao


title: Identification of NUCKS1 as a putative oncogene and immunodiagnostic marker of hepatocellular carcinoma

status: Public on Jan 24 2015

city: Suwon

first: Jaeyoun

last: Cheong

address: 164 Worldcup-ro

institute: Ajou University School of Medicine

summary:
Purpose: Hepatocellular carcinoma (HCC) is one of the leading causes of cancer-associated mortality worldwide. Although the molecular mechanisms underpinning HCC are unknown, gene copy number and associated mRNA expression changes are frequently reported.

Experimental Design: Comparative genomic hybridization arrays spotted with 4,041 bacterial artificial chromosome clones were used to assess copy number changes in 45 HCC tissues to identify chromosomal regions associated with the pathogenesis of HCC. Seventy more HCC tissues were used to validate candidate genes by using western blots and immunohistochemistry.

Results: A total of 259 clones were associated with copy number changes that significantly differed between normal liver and HCC samples. The chromosomal region 1q32.1 containing the nuclear casein kinase and cyclin-dependent kinase substrate 1 (NUCKS1) gene was associated with tumor vascular invasion. Western blot analysis demonstrated that NUCKS1 was up-regulated in 37 of 70 (52.8%) HCC tissues compared with adjacent non-tumor tissues, and over-expressed in a vast majority of HCCs (44/52, 84.6%) as determined by immunohistochemical staining. Furthermore, immunostaining of both NUCKS1 and glypican-3 improved the diagnostic prediction of HCC. Knock-down of NUCKS1 by siRNA decreased the cell viability of the Hep3B cell line and reduced tumor formation in a xenograft mouse model. Functional enrichment analysis revealed the association of NUCKS1 with signal transduction, immunity and defense, and nucleotide metabolism pathways.

Conclusions: NUCKS1 was identified as a potential oncogene at chromosomal 1q32.1 in patients with HCC, and it might be a valuable immunodiagnostic marker for HCC.

overall_design: Comparative genomic hybridization arrays spotted with 4,041 bacterial artificial chromosome clones were used to assess copy number changes in 45 HCC tissues and 25 normal liver tissues to identify chromosomal regions associated with the pathogenesis of HCC

first: Junghoon

last: Woo

first: Sungwon

last: Cho

first: Kap-Seok

last: Yang


title: Genomic profiling of chromophobe renal cell carcinoma by array-based comparative genomic hybridization

status: Public on Jan 21 2015

city: Yufu-city

first: Keiko

last: Matsuura

address: hasama-cho, Idaigaoka

institute: Oita University

summary: In this study, we investigated CNAs of 4 tumor samples from 2 patients, including conventioanl chromophobe renal cell carcinoma(ChRCC), ChRCC with neuroendocrine differentiation and no-tumor region by 44k oligonucleotide-based array comparative genomic hybridization (array CGH).

overall_design: 2 cases of ChRCC(NOS) vs ChRCC with neuroendocrine differentiation

first: Chisato

last: Ohe

first: Naoto

last: Kuroda

first: Tomoki

last: Kai


title: Identification of FoxO target genes during C-26 cancer cachexia

status: Public on Dec 31 2014

city: Boston

first: Susan

last: Kandarian

state: MA

address: 635commonwealth ave, Rm444

department: Health Sciences

institute: Boston University

summary:
Forkhead BoxO (FoxO) transcription factors expressed in adult skeletal muscle promote muscle atrophy during various catabolic conditions.  We have identified the genome wide target genes and biological networks regulated by FoxO in skeletal muscle during Colon-26 (C-26) cancer cachexia.
In this dataset, we include the expression data obtained from the tibialis anterior muscles of control and severely cachectic Colon-26 mice in which FoxO-dependent transcription was either intact (AAV9-EV) or inhibited (AAV9-d.n.FoxO). These data were used to obtain 543 FoxO target genes during cancer. These target genes were identified as those genes whose expression was both differentially regulated in skeletal muscle in response to cancer (control AAV9-EV vs. C26 AAV9-EV), and differentially regulated in the presence of d.n.FoxO (C26 AAV9-EV vs. C26 AAV9-d.n.FoxO).

overall_design: For microarray analysis, a total of 16 RNA samples across four groups (n = 4/group) are included. The groups are as follows: Control, AAV9-EV; C26, AAV9-EV; Control, AAV9-dnFoxO; C26, AAV9-dnFoxO. We found one outlier from the C26 AAV9-EV group by PC2 and PC3 (Sample #15), thus, this sample was removed from further analysis.  To identify genes changed in response to C26, expression data from Control, AAV9-EV were compared to expression data of C26, AAV9-EV. Differentially expressed genes were identifed using -1.5 > fold change > 1.5 and q<0.01 cut-off. Expression values of these genes were subsequently compared between C26, AAV9-EV and C26, AAV9-d.n.FoxO to identify FoxO target genes using -1.5 > fold change > 1.5 and q<0.01 cut-off.

first: Sarah

last: Senf

first: Chia-Ling

last: Wu

first: Adam

middle: W

last: Beharry

first: Brandon

last: Roberts

first: Leonardo

middle: F

last: Ferreira

first: Andrew

last: Judge


title: Docetaxel-loaded solid lipid nanoparticles suppress breast cancer cells growth with reduced myelosuppression toxicity

city: Dalian

first: Ying

last: Ge

address: 9 Western Section, Lvshun South Street

institute: Dalian Medical University

summary: Docetaxel is an adjuvant chemotherapy drug widely used to treat multiple solid tumors, however its toxicity and side-effect limits its clinical efficacy. Herein, the docetaxel-loaded solid lipid nanoparticles (DSNs) were developed to reduce systemic toxicity while still keeping its anti-cancer activity. To evaluate its anti-cancer activity and toxicity and understand the molecular mechanisms of DSNs, different cellular, molecular and whole genome transcription analysis approaches were utilized. The DSNs showed lower cytotoxicity compared with the commercial formulation of docetaxel-Taxotere and induced more apoptosis at 24 h treatment in vitro. It can cause the treated cancer cells arrested at G2/M phase in a dose-depend manner as Taxotere. The DSNs can also suppress tumor growth very effectively in a murine breast cancer model. Systemic analysis of gene expression profiles by microarray and the following verification experiments suggested that both DSNs and Taxotere regulate expression of series genes and these genes functions involved in DNA replication, DNA damage response, cell proliferation, apoptosis and cell cycle regulation. Some of these genes expressed differentially at protein level although their transcription level was similar under TAX and DSNs treatment. Moreover, DSNs improved main side-effect of Taxotere by greatly lowering myelosuppression toxicity to bone marrow cells from mice. Taken together, our results expound the anti-tumor efficacy and the potential working mechanisms of DSNs in its anti-cancer activity and toxicity, which provide a theoretical foundation to develop and apply more efficient docetaxel formulation to treat cancer patients.

overall_design: Tumor tissues were obtained from tumor-bearing mice after treated with GLU, BSNs, TAX or DSNs. Total RNA was extracted from tumor tissues

first: Qing

last: Yuan

first: Wenshu

last: Cong

first: Xiaolin

last: Bi


title: Analysis  of transcriptomic diversitification of developing cumulus and mural granulosa cells in mouse ovarian follicles

city: Bar Harbor

first: Timothy

middle: Michael

last: Stearns

state: ME

address: 600 Main Street

department: Computational Sciences

institute: The Jackson Laboratory

summary: Cumulus cells and mural granulosa cells (MGCs) are spatially and functionally distinct cell types in antral follicles: cumulus cells contact the oocyte and most MGCs contact the basal lamina. For transcriptomic analyses, both cell types were collected from small and large antral follicles, before and after stimulation of immature mice with eCG, respectively. Both cell types underwent dramatic transcriptomic changes and the differences between them became greater with follicular growth. Although cumulus cells of both stages of follicular development are competent to undergo expansion in vitro, they were otherwise remarkably dissimilar with transcriptomic changes quantitatively equivalent to those of MGCs. Gene Ontology (GO) analysis showed that cumulus cells of small follicles were enriched in transcripts generally associated with catalytic components of metabolic processes while those from large follicles were involved in regulation of metabolism, cell differentiation, and adhesion. Upon contrasting cumulus cells versus MGCs, cumulus cells were enriched in transcripts associated with metabolism and cell proliferation while MGCs were enriched for transcripts involved in cell signaling and differentiation.

overall_design: Cumulus cell-oocyte complexes (COCs) were isolated from the ovaries of 22-day-old B6SJLF1 mice that were either not stimulated with eCG or stimulated by IP injection of 5 IU equine chorionic gonadotropin 44 hours before obtaining the COCs. Only COCs completely enclosed by tightly packed cumulus oophorus were selected for analysis. Cumulus cells were stripped from oocytes by drawing them into a fine glass pipet with a diameter slightly smaller than the diameter of the oocytes, which were discarded. At the same time as collection of COCs, clumps of healthy MGCs having a rusty rather than brown color, which would indicated a less than healthy phenotype, were collected. Both cumulus cells and MGCs were lysed and prepared for micro-array. The cumulus cells from 200 COCs and a roughly equivalent mass of MGCs were collected from three groups of five pooled mice. Thus there were three biological replicates of each sample.

first: John

last: Eppig


title: Expression analysis of genetically enginering S. cerevisiae strains

status: Public on Jan 30 2015

city: Paris

first: Varun

last: Khanna

address: 25 28 Rue du Docteur Roux

department: Genomes and Genetics

institute: institut Pasteur

summary: Transcriptomes of transgenic strains and of evolved mutants bearing the macrotene chromosomes

overall_design: Four samples were used for comparison of the transcriptomes

first: Agnes

last: Thierry


title: mTORC1 regulates microRNA biogenesis in Hela cells

status: Public on Dec 11 2014

city: Washington

first: Yang

last: Liu

state: DC

address: 111 Michigan Ave NW

department: Center for Cancer and Immunology Research

institute: Childrens' National Medical Center

summary:
mTOR senses nutrient and energy status to regulate cell survival and metabolism in response to environmental changes.  Surprisingly, targeted mutation of Tsc1, a negative regulator of mTORC1, caused a broad reduction in miRNAs due to Drosha degradation.  Conversely, targeted mutation of Raptor, an essential component of mTORC 1, increased miRNA biogenesis.  mTOR activation increased expression of Mdm2, which is hereby identified as the necessary and sufficient ubiquitin E3 ligase for Drosha.  Drosha was induced by nutrient and energy deprivation and conferred resistance to glucose deprivation.  Using a high throughput screen of a miRNA library, we identified 4 miRNAs that were necessary and sufficient to protect cells against glucose deprivation-induced apoptosis.  These miRNA was regulated by glucose through the mTORC1-MDM2- Drosha axis.  Taken together, our data reveal an mTOR-Mdm2-Drosha pathway in mammalian cells that broadly regulates miRNA biogenesis as a response to alteration in cellular environment.
Knockdown of DROSHA or TSC1 caused a global decrease in both miRNA and pre-miRNA in Hela stable cell lines.

platform_organism:
Homo sapiens
Mus musculus

overall_design: To determine whether TSC1 regulates miRNA accumulation in human cells, we used shRNAs to silence TSC1 in HeLa cells and then compare the general profile of miRNA and pre-miRNA in Hela cells. We also used shRNAs against DROSHA as a positive control.

first: Peiying

last: Ye

first: Yu

first: Chong

last: Chen

first: Fei

last: Tang

first: Qi

first: Xiang

last: Wang

first: Chang-Gong

first: Xiuping

first: Runhua

first: Pan

last: Zheng


title: mTORC1 regulates microRNA biogenesis in mouse bone marrow hematopoietic stem and progenitor cells

summary:
mTOR senses nutrient and energy status to regulate cell survival and metabolism in response to environmental changes.  Surprisingly, targeted mutation of Tsc1, a negative regulator of mTORC1, caused a broad reduction in miRNAs due to Drosha degradation.  Conversely, targeted mutation of Raptor, an essential component of mTORC 1, increased miRNA biogenesis.  mTOR activation increased expression of Mdm2, which is hereby identified as the necessary and sufficient ubiquitin E3 ligase for Drosha.  Drosha was induced by nutrient and energy deprivation and conferred resistance to glucose deprivation.  Using a high throughput screen of a miRNA library, we identified 4 miRNAs that were necessary and sufficient to protect cells against glucose deprivation-induced apoptosis.  These miRNA was regulated by glucose through the mTORC1-MDM2- Drosha axis.  Taken together, our data reveal an mTOR-Mdm2-Drosha pathway in mammalian cells that broadly regulates miRNA biogenesis as a response to alteration in cellular environment.
Deletion of Raptor caused a global increase in both miRNA and pre-miRNA in mouse bone marrow hematopoietic stem and progenitor cells(HSPCs).

overall_design: Rptr(flox/flox) mice with conditional alleles for inactivating Raptor in C57BL/6 background were used for this study.  Age (10 weeks old) and sex (all female)-matched Ctrl (Mx1-Cre-, 3 mice) and cKO (Mx1-Cre+, 3 mice) littermates were treated with 400 μg polyinosinic:polycytidylic acid (pIpC, 2mg/ml in 1xDPBS, Sigma-Aldrich) 7 times every other day by intraperitoneal injection (i.p.) to induce targeted gene deletion. At 10 days post pIpC treatment, bone marrow HSPCs (Lin-cKit+) were isolated by Danabeads (Life Technologies) and c-Kit positive selection microbeads (Stemcell Technologies). Total RNA isolation was performed with TRIzol (Invitrogen) according to manufacturer’s instructions. RNA labeling and hybridization for miRNA expression profiling on miRNA microarray chips were performed as described (Liu, C.G., Calin, G.A., Volinia, S., and Croce, C.M. (2008). MicroRNA expression profiling using microarrays. Nat Protoc 3, 563-578).

last: Wu


title: Acquisition of the ability to assimilate mannitol by Saccharomyces cerevisiae through dysfunction of Tup1-Cyc8, a general corepressor

status: Public on Dec 04 2014

city: Uji

first: Shigeyuki

last: Kawai

state: Kyoto

address: Gokasyo

institute: Kyoto University

summary:
Saccharomyces cerevisiae normally cannot assimilate mannitol, a promising brown macroalgal carbon source for bioethanol production. To date, the molecular mechanisms underlying this inability remain unknown. Here, we found that cells acquiring mannitol-assimilating ability appeared from wild-type S. cerevisiae strain during prolonged culture in mannitol medium. Our microarray analysis revealed that genes for putative mannitol dehydrogenase and hexose transporters were up-regulated in cells acquiring mannitol-assimilating ability. Take account of our other results including complementation analysis and cell growth data, we demonstrated that this acquisition of mannitol-assimilating ability was due to the spontaneous mutation in the gene encoding Tup1 or Cyc8. Tup1-Cyc8 is the general corepressor complex involved in the repression of many kinds of genes. Thus, it is suggested that the inability of wild-type S. cerevisiae to assimilate mannitol can be attributed to the transcriptional repression of a set of genes involved in mannitol utilization by Tup1-Cyc8 corepressor. In other words, Tup1-Cyc8 is a key regulator of mannitol metabolism in S. cerevisiae. We also showed that S. cerevisiae strain which carries mutant allele of TUP1 or CYC8 produced ethanol from mannitol efficiently. Especially, strain carrying mutant allele of CYC8 showed high tolerance to salt, which is superior to other ethanologenic microorganisms. This characteristic is highly beneficial to produce bioethanol from marine biomass. Taken together, Tup1-Cyc8 can be an ideal target to develop a yeast-algal bioethanol production system.
To figure out how Mtl+ strains (cells acquiring ability to grow in mannitol medium) had acquired the ability to assimilate mannitol, we performed genome-wide analysis by using Nimblegen microarrays.

overall_design: Yeast Saccharomyces cerevisiae cells (wild-type BY4742 strain and two Mtl+ strains, MK3619 and MK3683) were grown at 30°C to the logarithmic phase in SC or SM media. Total RNA was purified and the 4 RNA samples (BY4742 cells in SC as control, MK3619 cells in SM, MK3683 cells in both SC and SM) were analyzed with Nimblegen microarrays.

first: Moeko

last: Chujo

first: Anri

last: Ota

first: Kousaku

last: Murata


title: Heavy metal-inducible gene expression in Hyphomonas neptunium

status: Public on Nov 24 2014

city: Marburg

first: Martin

last: Thanbichler

address: Hans-Meerwein-Straße 4

institute: Philipps University Marburg

summary: Hyphomonas neptunium proliferates by a unique budding mechanism in which daughter cells emerge from the end of a stalk‐like extension emanating from the mother cell body. Studies of this species have so far been hampered by the lack of a genetic system and of molecular tools allowing the regulated expression of target genes. Based on microarray analyses, this work identifies two H. neptunium promoters that are specifically activated by copper and zinc, respectively. Functional analyses show that they have low basal activity and a high dynamic range, thus meeting the requirements for use as a multi‐purpose expression system.

overall_design: Hyphomonas neptunium was exposed to 0.5 mM CuSO4 or 0.5 mM ZnCl2. Samples were taken before as well as  20 min and 60 min after addition of the heavy metal solution.

first: Alexandra

last: Jung


title: Influence of osmopriming on rape seeds germination

status: Public on Nov 23 2014

city: Poznań

first: Małgorzata

last: Garnczarska

state: wielkopolska

address: Umultowska 89

department: Plant Physiology

country: Poland

institute: Adam Mickiewicz University

summary:
Transcriptomic study of the impact of osmopriming on rape seeds (Brassica napus L.; cv 'Libomir') during priming process and after germination. The assays were replicated twice on two independent priming and germination experiments.
Seeds were osmoprimed in PEG solution (-1.2 MPa osmotic potential) during 7 days, dried to initial  moisture content and then germinated for 7 hours on water. The analysis during different phases of priming procedure (soaking and drying), after whole osmopriming process and germination were done.

overall_design:
10 samples, four condition experiment;
non dried primed seeds (Pnd) vs. dry unprimed seeds (UPd) (PEG soaking),
non dried primed seeds (Pnd) vs dry primed seeds (Pd) (drying after soaking),
dry primed seeds (Pd) vs. dry unprimed seeds (UPd) (full osmopriming process),
primed seeds imbibed on water (P7h) vs unprimed seeds imbibed on water (UP7h) (germination after osmopriming).
Biological replicates: 2 replicates for comparison PEG soaking, drying after soaking, full osmopriming process and germination after osmopriming.

first: Szymon

last: Kubala

first: Łukasz

last: Wojtyla

first: André

last: Clippe

first: Arkadiusz

last: Kosmala

first: Agnieszka

last: Żmieńko

first: Stanley

last: Lutts

first: Muriel

last: Quinet


title: Gene expression in the mammary gland of the tammar wallaby during the lactation cycle

status: Public on Nov 27 2014

city: Bundoora

first: Christy

last: Vander Jagt

address: 5 Ring Road, LaTrobe University

department: Computational Biology

institute: Department of Environment and Primary Industries

summary: In this study we use microarray technology to identify differentially expressed genes in the tammar wallaby mammary gland during the lactation cycle. We have focused on gene expression changes in the tammar mammary gland as it shifts from one lactation phase to the next.

overall_design: Three separate time-course microarray experiments were performed. Each experiment involved the comparison of two time-points spanning two phases of tammar lactation. The three comparisons were: pregnancy day 26 vs lactation day 2 (phase 1 vs phase 2A), lactation day 110 vs lactation day 151 (phase 2A vs phase 2B) and lactation day 151 vs lactation day 216 (phase 2B vs 3).

first: Jane

last: Whitley

first: Ben

middle: G

last: Cocks

first: Michael

last: Goddard