title: Gene expression changes following demethylation by 5-aza-2'-deoxycytidine（decitabine, DAC）in mouse T cell lymphoma EL4 cells

status: Public on Feb 15 2013

city: Beijing

first: Li-Xin

last: Wang

address: Fuxing Road

department: Hematology

country: China

institute: Chinese PLA General Hospital

summary: Our study had shown that DAC treatment enhanced immunogenecity of EL4 cells. To explore the mechanisms of DAC-induced tumor immunity, we carried out cDNA microarray analyses to compare the differential expression of genes between DAC and PBS treated EL4 cells.

overall_design: Two-condition experiment, PBS treated EL4  vs. Decitabine treated EL4 cells. Biological replicates: 3 PBS treated, 3 Decitabine treated, independently treatment and harvested. One replicate per array.

first: Li

last: Yu


title: Glucose catabolism via a partially cyclic pentose phosphate pathway in Gluconobacter oxydans 621H: a combined fluxomics and transcriptomics analysis

status: Public on Feb 13 2013

city: Juelich

first: Tino

last: Polen

state: NRW

address: Wilhelm-Johnen-Str 1

department: IBG-1: Biotechnology

country: Germany

institute: Forschungszentrum Jülich GmbH

summary: In this study, the distribution and regulation of periplasmic and cytoplasmic carbon fluxes in Gluconobacter oxydans 621H with glucose were studied by 13C-based metabolic flux analysis (13C-MFA) in combination with transcriptomics and enzyme assays. For 13C-MFA, cells were cultivated with specifically 13C-labeled glucose and intracellular metabolites were analyzed for their labeling pattern by LC-MS. In growth phase I, 90% of the glucose was oxidized periplasmatically to gluconate and partially further oxidized to 2-ketogluconate. Of the glucose taken up by the cells, 9% was phosphorylated to glucose 6-phosphate, whereas 91% was oxidized by cytoplasmic glucose dehydrogenase to gluconate. Additional gluconate was taken up into the cells by transport. Of the cytoplasmic gluconate, 70% was oxidized to 5-ketogluconate and 30% was phosphorylated to 6-phosphogluconate. In growth phase II, 87% of gluconate was oxidized to 2-ketogluconate in the periplasm and 13% was taken up by the cells and almost completely converted to 6-phosphogluconate. Since G. oxydans lacks phosphofructokinase, glucose 6-phosphate can only be metabolized via the oxidative pentose phosphate pathway (PPP) or the Entner-Doudoroff pathway (EDP). 13C-MFA showed that 6-phosphogluconate is catabolized primarily via the oxidative PPP in both phase I and II (62% and 93%) and demonstrated a cyclic carbon flux through the oxidative PPP. The transcriptome comparison revealed an increased expression of PPP genes in growth phase II, which was supported by enzyme activity measurements and correlated with the increased PPP flux in phase II. Moreover, genes possibly related to a general stress response displayed increased expression in growth phase II.

overall_design: The transcriptome comparisons of G. oxydans growth phase II vs. growth phase I were repeated independently three times in biological replicates resulting in 3 hybridizations as termed by sample 1 to 3.

first: Tanja

last: Hanke

first: Katharina

last: Nöh

first: Stephan

last: Noack

first: Stephanie

last: Bringer

first: Hermann

last: Sahm

first: Wolfgang

last: Wiechert

first: Michael

last: Bott


title: Expression profiles of human primary osteoblasts (HOB) and MET transformed osteoblast clones

status: Public on Feb 28 2013

city: Torino

first: Raffaele

middle: A

last: Calogero

state: To

address: Via Nizza 52

department: Molecular Biotechnology Center

country: Italy

institute: University of Torino

summary: We studied MET-transformed human primary osteoblasts (MET-HOBs), which we previously turned into osteosarcoma cells by LV driven over-expression of MET oncogene. We obtained distinct MET transformed HOB clones  derived from independent events of transgene integration. To characterise the phenotype of the MET-HOB clones we used oligonucleotide microarrays. Expression profiles of MET-HOBs and parental HOBs were compared.

first: Nadia

last: Dani

first: Martina

last: Olivero

first: Katia

last: Mareschi

first: MarjanMarja

last: vanDuist

first: Silvia

last: Miretti

first: Sara

last: Cuvertino

first: Salvatore

last: Patané

first: Riccardo

last: Ferracini

first: Franca

last: Fagioli

first: MariaFlavia

last: DiRenzo


title: Chip-chip from human ES cells (H1), iPS cells (iPSC38), astrocytes (HA) and aortic endothelial cells (HAEC) with H3K9me2 antibody

status: Public on Feb 17 2013

city: Baltimore

first: Andrew

last: Feinberg

state: MD

address: 855 N. Wolfe Street

department: Center for Epigenetics and Department of Medicine

country: USA

institute: Johns Hopkins University

type: Genome binding/occupancy profiling by genome tiling array

summary: Histone modification H3K9me2 is associated with gene silencing and forming large heterochromatin domains. But the micro-structure within large H3K9me2 domains and their relationship with DNA methylation remains unclear. This dataset was generated to compare with genome-wide DNA methylation data.

overall_design: Genome-wide distribution of H3K9me2 in human fibroblasts was mapped using ChIP-chip.

first: Bo

last: Wen

first: Hao

last: Wu

middle: P


title: Genome-wide transcriptional responses to benzo[a]pyrene and clofibrate in the tunicate Oikopleura dioica

status: Public on Feb 05 2013

city: Bergen

first: Fekadu

last: Yadetie

address: Thormøhlensgt. 55

country: Norway

institute: Sars International Centre for Marine Molecular Biology

type: Expression profiling by genome tiling array

summary: Animals have developed extensive mechanisms of response to xenobiotic chemical attacks. Although recent genome surveys have suggested a broad conservation of the chemical defensome across metazoans, global gene expression responses to xenobiotics are not known in most invertebrates. Here, using high density tiling arrays with over 2 million probes, we explored genome-wide gene expression in the tunicate Oikopleura dioica in response to two model xenobiotic chemicals – the carcinogenic polycyclic aromatic hydrocarbon benzo[a]pyrene (BaP) the pharmaceutical compound Clofibrate (Clo). The genotoxic compound BaP induced xenobiotic biotransformation and oxidative stress responsive genes, as in vertebrates. Notable exceptions were genes of the aryl hydrocarbon receptor (AhR) signaling pathway. Clo also affected the expression of many biotransformation genes and markedly repressed genes involved in energy metabolism and muscle contraction pathways. Oikopleura appears to have basic defensome toolkit consisting of phase I, phase II and phase III biotransformation genes.

overall_design:
Exposure of about 130 four-days-old animals in 1L seawater in glass beakers. Pooled animals used, no replicates.  DMSO Treatments:   -Clofibrate (Clo) (Sigma-Aldrich, St. Louis, MO): 1 µM and 5 µM.   -Benzo[a]pyrene (BaP (Sigma-Aldrich):  0.2 µM and 1 µM  - Controls  received 1 ml Dimethyl sulfoxide (DMSO).    -The animals kept at room temperature and harvested after 10 hrs and frozen.   -Total RNA was isolated from the pooled animals using the RNeasy Mini Kit according to manufacturer’s protocols (QIAGEN, Hilden, Germany).  - 5 µg total RNA was converted to dscDNA using SuperScript Double-Stranded cDNA Synthesis Kit (Invitrogen, Carlsbad, CA), and dscDNA samples were submitted for microarray analysis. BaP and Clo treated samples were labeled using Cy3-coupled random nonamers and DMSO controls were labeled using Cy5-coupled random nonamers.

Total 4 hybridizations for the 8 samples (single hybridization for each treatment and DMSO control pair), no replicates.

first: Stephen

last: Butcher

first: Hilde

middle: E

last: Førde

first: Coen

last: Campsteijn

first: Jean-Marie

last: Bouquet

first: Odd-Andre

last: Karlsen

first: France

last: Denoeud

first: Raghu

last: Metpally

first: Eric

middle: M

last: Thompson

first: John

middle: R

last: Manak

first: Anders

last: Goksøyr

first: Daniel

last: Chourrout


title: Transcriptional profiling of experimental CD8+ lymphocyte depletion in rhesus macaques infected with SIVmac239

status: Public on Feb 08 2013

city: Atlanta

first: Gregory

middle: K

last: Tharp

state: GA

address: 954 Gatewood Dr

department: Developmental and Cognitive Neuroscience

institute: Yerkes National Primate Research Center

summary: CD8+ T-cells inhibit virus replication in SIV-infected rhesus macaques (RM). However, it is unclear to what extent the viral suppression mediated by CD8+ T-cells reflects direct killing of infected cells as opposed to indirect, non-cytolytic mechanisms. In this study, we used functional genomics to investigate potential mechanisms of in vivo viral suppression mediated by CD8+ lymphocytes. Eight chronically SIVmac239-infected RMs underwent CD8+ lymphocyte depletion, and RNA from whole blood was obtained prior to depletion, at the nadir of CD8+ lymphocytes (5 days post-depletion), and during the repopulation phase (11 days post-depletion). Principal components analysis demonstrated that overall gene expression during the nadir of CD8+ T-cells was highly divergent from other intervals. Conversely, the genomic signature of samples from the CD8+ cell rebound phase was similar to that of pre-depletion samples. During CD8+ lymphocyte depletion we detected a strongly significant decrease in the expression of the genes encoding CD8α and CD8β chains, consistent with the near complete CD8+ T-cell depletion measured by flow cytometry. Of note, we observed significant down-regulation of the expression of genes encoding for factors that can suppress SIV replication, including the CCR5-binding chemokine CCL5/Rantes, several retroviral restriction factors (TRIM10, TRIM15, APOBEC3G/H) and defensins. Reduced expression of various genes related to T cell activation and proliferation was also observed. Collectively, these data indicate that depletion of CD8+ lymphocytes in SIV-infected RMs is associated with the establishment of a pattern of gene expression that may result in increased intrinsic permissivity to virus replication.

overall_design: A total of 60 RNA samples were hybridized on to Rhesus Affymetrix 3' Expression arrays. The study was composed of 8 replicate rhesus macaques subjected to SIVmac239 infection and followed over infection, during subsequent treatment with monocloncal antibody OKT8F to deplete CD8+ T lymphocytes, antiretroviral therapy to suppress virus. Samples were taken at various time points during acute and chronic infection, after CD8+ cell depletion, after CD8+ cell reconstition, and during ART suppression of virus.

first: Steven

last: Bosinger

first: Simon

last: Jochems

first: Kathryn

last: Folkner

first: Nichole

last: Klatt

first: Guido

last: Silvestri


title: A key role for neuropeptide Y in lifespan extension and cancer suppression by dietary restriction

city: Nagasaki

first: Isao

last: Shimokawa

address: 1-12-4 Sakamoto

department: Basic Medical Science

country: Japan

institute: Nagasaki University Graduate School of Biomedical Sciences

summary: Key molecules that modulate the effect of dietary restriction (DR), a well-known laboratory intervention for longevity in organisms, remain elusive in mammals. We evaluated neuropeptide Y (Npy), which is involved in the physiological adaptation to energy deficits, for its role in the effects of DR.

overall_design: At 12 weeks of age, Npy-/- and WT mice were divided into the AL (ad libitum) and DR groups. The DR groups received a food allotment consisting of 70% of the mean daily food intake of the AL groups. Two replicates per genotype per feeding group.

first: Takuya

last: Chiba

first: Yukari

last: Tamashiro

first: Daeui

last: Park

first: Tatsuya

last: Kusudo

first: Ryoko

last: Fujie

first: Toshimitsu

last: Komatsu

first: Sang

last: Kim

first: Seongjoon

first: Hiroko

last: Hayashi

first: Ryoichi

last: Mori

first: Hitoshi

last: Yamashita

first: Hae

middle: Y

last: Chung


title: Expression of C. albicans genes during GI tract colonization and influence of efg1, efh1 and cph1 mutations

city: Boston

first: Carol

last: Kumamoto

state: MA

address: 136 Harrison Ave

department: Molecular Biology and Microbiology

institute: Tufts University

summary: The goals of this study were to identify the Efg1p-regulon during GI tract colonization and to compare C. albicans gene expression during colonization of different organs of the GI tract. Our results identified significant differences in gene expression between cells colonizing the cecum and ileum.  In addition, during laboratory growth, efg1- null mutant cells grew to a higher density than WT cells.  The efg1- null mutant grew in depleted medium, while WT cells could only grow if the depleted medium was supplemented with carnitine, a compound that promotes the metabolism of fatty acids.  During colonization, efg1- null mutant cells expressed higher levels of genes involved in lipid catabolism, carnitine biosynthesis and carnitine utilization in comparison to colonizing WT cells.  This altered gene expression supports the ability of efg1- cells to hypercolonize naïve mice.

overall_design: C. albicans cells (WT, efg1-, efg1- efh1- or efg1- cph1-) were inoculated into antibiotic-treated BALB/c mice by oral gavage.  Contents of the cecum and ileum were collected and frozen in RNALater.  Reference cells (WT C. albicans) were grown in YPD medium at 37oC to exponential phase. Total RNA was extracted from both all samples.  Sample of C. albicans isolated from GI tract organs was compared to reference on microarray.  Between 4 and 7 microarray hybridizations, with dye swaps, were performed for each sample.

first: Jessica

middle: V

last: Pierce

first: Daniel

last: Dignard

first: Malcolm

last: Whiteway


title: Identification of genes regulated by early embryo in bovine oviduct epithelial cells

status: Public on Feb 14 2013

city: jouy en josas

first: barbara

last: schmaltz-barbara

address: domaine de vilvert

country: France

institute: INRA

summary: In this study, we focused on the changes of mRNA expression in bovine oviduct epithelial cells in vitro co-cultured with embryos during preimplantation development in order to identify genes, which might be involved in embryo-maternal communication. For this purpose, we used large-scale cDNA microarray hybridizations to identify the genes differentially regulated in bovine oviduct epithelial cells (Boec) during in vitro culture. The main objective was to identify genes which are differentially expressed due to the presence or absence of bovine embryos on cell monolayers.

overall_design: Global transcriptional profiling was performed using 13 days Bovine oviduct epithelial cells (Boec) cultured in vitro with SOF media RNA as control samples (BOEC_SOF_CTL, n=3) for comparison to the experimental samples taken at the same culture time (day 13) and stimulated by the presence of bovine embryos during the last 8 days of culture (BOEC_SOF+EMB, n=3).Gene expression analysis was carried out between Boec with or without stimulation of embryos representing a total of 6 slides (dye swap protocol).

first: Barbara

last: Schmaltz-Panneau

first: Pascal

last: Mermillod

first: Sophie

last: Dhorne-Pollet

first: Christelle

last: Hennequet


title: Genomic diversity of Bifidobacterium pseudocatenulatum group

status: Public on Feb 06 2013

city: Parma

first: Marco

last: Ventura

address: Viale delle Scienze 11/A

department: Dept. Life Sciences

institute: University of Parma

summary:
Bifidobacteria have been described as a key component of the human gut microbiota, and recently significant efforts have been made to investigate their genome contents and assess the genetic variability at inter- and intra-species level. In the current work we investigated genome diversity among representatives of bifidobacterial species, i.e., Bifidobacterium pseudocatenulatum. These analyses were performed with comparative genomic hybridization (CGH) experiments and they revealed the existence of a strictly conserved set of 685 gene families. Furthermore, CGH analyses showed that genetic regions of diversity included mobile elements and putative genomic life-style adaptation islands, such as loci that encode pili and capsular polysaccharides, and genes involved in carbohydrate metabolism.
CGH analysis was performed with microarrays that were based on the genome sequences of Bifidobacteriapseudocatenulatum DSM20438 (ABXX00000000.2). A total of 39,249 probes of 35 bp in length were designed using OligoArray 2.1 software. Oligos were synthesized in triplicate on a 2 × 40-k CombiMatrix array (CombiMatrix, Mulkiteo, USA). Replicates were distributed on the chip at random, non-adjacent positions. A set of 74 negative control probes designed on phage and plant sequences was also included on the chip. Seventeen micrograms of purified genomic DNA was labeled with Cy5-ULS using the Kreatech ULS array CGH Labeling kit (Kreatech Diagnostics) according to the supplier’s instructions. Hybridization of labeled test DNA to these microarrays was performed according to CombiMatrix protocols.

sample_organism: Bifidobacterium pseudocatenulatum DSM 20438 = JCM 1200 = LMG 10505

sample_organism: Bifidobacterium catenulatum DSM 16992 = JCM 1194 = LMG 11043

overall_design: We analysed ten strains belong to Bifidobacteriapseudocatenulatum and Bifidobacteriacatenulatum species. Replicates were distributed on the chip at random, non-adjacent positions.


title: Genomic diversity of Bifidobacterium adolescentis group

summary:
Bifidobacteria have been described as a key component of the human gut microbiota, and recently significant efforts have been made to investigate their genome contents and assess the genetic variability at inter- and intra-species level. In the current work we investigated genome diversity among representatives of bifidobacterial species, i.e., Bifidobacterium adolescentis. These analyses were performed with comparative genomic hybridization (CGH) experiments and they revealed the existence of a strictly conserved set of 685 gene families. Furthermore, CGH analyses showed that genetic regions of diversity included mobile elements and putative genomic life-style adaptation islands, such as loci that encode pili and capsular polysaccharides, and genes involved in carbohydrate metabolism.
CGH analysis was performed with microarrays that were based on the genome sequences of B. adolescentis ATCC15703 (NC_008618) . A total of 39,249 probes of 35 bp in length were designed using OligoArray 2.1 software. Oligos were synthesized in triplicate on a 2 × 40-k CombiMatrix array (CombiMatrix, Mulkiteo, USA). Replicates were distributed on the chip at random, non-adjacent positions. A set of 74 negative control probes designed on phage and plant sequences was also included on the chip. Seventeen micrograms of purified genomic DNA was labeled with Cy5-ULS using the Kreatech ULS array CGH Labeling kit (Kreatech Diagnostics) according to the supplier’s instructions. Hybridization of labeled test DNA to these microarrays was performed according to CombiMatrix protocols.

overall_design: We analysed seven strains belong to B. adolescentis species. Replicates were distributed on the chip at random, non-adjacent positions.


title: Aristaeus chip 1.0: an in situ synthesized oligonucleotide microarray for Ovis aries

city: Viterbo

first: Alessio

last: Valentini

address: via San Camillo de Lellis

department: IBAF

institute: University of Tuscia

summary:
Here we present a high-density in situ synthesized microarray for Ovis aries, named Aristaeus, designed by means of a pipeline of software instruments that, starting from non-annotated redundant EST sequences, selects oligonucleotides suitable for in situ generation on chip. The chip was tested by comparing the gene expression profiles of two sheep breeds with different phenotype, Sarda and Gentile di Puglia.
We carried out microarray experiments on liver and udder tissues from lactating individuals and identified a relevant number of differentially expressed genes, all involved in metabolism pathways. The results are consistent with literature knowledge, while selected differential gene expressions have been confirmed by quantitative real-time polymerase chain reaction analyses.

overall_design: Tissue samples of liver were collected from 4 lactating individuals of two sheep (Ovis aries) breeds, Gentile di Puglia and Sarda. Biopsies of liver tissue were taken at second lactation stage (first record, stage 01: 6 days after lambing; second record, stage 02: 44 days after lambing) in both breeds. Tissues from liver were immersed in RNAlater (Sigma) immediately after biopsy and stored at -20°C. Samples were pooled by breed and then reverse labeled (cy5 and cy3), resulting in four raw data sets.

first: Gianluca

last: Prosperini

first: Lorraine

last: Pariset

first: Susana

last: Bueno

first: Silvia

last: Bongiorni

first: Giovanni

last: Chillemi


title: Borrelia host adaptation Regulator (BadR) regulates rpoS to modulate host adaptation and virulence factors in Borrelia burgdorferi

status: Public on Feb 22 2013

city: San Antonio

first: Janakiram

last: Seshu

state: Texas

address: One UTSA Circle

department: Biology

institute: The University of Texas at San Antonio

summary:
Our study is the first to demonstrate BadR as a repressor of rpoS and thus facilitates spirochete’s transition back into ticks. BadR binds upstream and represses rpoS in unfed ticks.  GLcNA-6P, an abundant nutrient of blood and released by subsequent remodeling of the tick peritrophic membrane, relieves repression of BadR on rpoS facilitating vertebrate host adaptation.  BadR regulates chitobiose utilization genes and activates genes critical for spirochetes residence of ticks (lp28-4 genes)
badR-deficient strain (Gene BB0693) compared to B31-A3 parental wild-type B. burgdorferi strains

overall_design: Two separate but identically designed microarrays were performed and thus two chips were used. Each chip contained two replicates of B31-A3 WT and badR-deficient strains, and thus the overall array analysis of both chips corresponds to n=4 for both WT and badR-deficient strains. Hierarchical clustering and correlation analysis was used to verify quality of the normalized array data. The expression data from biological replicates 1 and 2 (chip 1 and 2) were both pooled and analyzed individually. We used LIMMA R package to test contrasts between WT and badR-deficient strain (Smyth GK.2004. Stat Appl Genet Mol Biol 3:Article3 .)

first: Christine

middle: L

last: Miller


title: Network analysis of wood properties, gene expression levels and genotypes of natural Populus trichocarpa accessions

status: Public on Feb 26 2013

city: Vancouver

first: Ilga

last: Porth

address: 2424 Main Mall

country: Canada

institute: University of British Columbia

summary: High-throughput approaches have been widely applied to elucidate the genetic underpinnings of industrially important wood properties. Each single wood trait was found to be highly polygenic in its nature. However, gene hierarchies need to be assessed with the most important gene variants controlling a specific trait within the complex network of interacting secondary cell wall characteristics that defines the overall wood phenotype. We tested the available genetic and genomic information in an integrative approach to effectively predict wood properties in Populus trichocarpa.Nine-yr-old natural P. trichocarpa trees including accessions with high contrasts in six traits related to wood chemistry and ultrastructure were profiled for gene expression on 49K Nimblegen array elements and for 28,831 polymorphic SNPs. Pre-selected transcripts and SNPs with high statistical dependency on the phenotypic trait were used in a Bayesian network learning procedure with stepwise K2 algorithm to infer phenotype-centric networks. Transcripts were pre-selected at much lower logBF threshold than SNPs and were not accommodated in the networks. Complexity of phenotype-centric networks with 100% predictive accuracy ranged from 7 (glucose) to 39 SNPs (alpha-cellulose). Pleiotropic gene actions were accommodated in genetic networks of correlated traits; such gene variants help to understand independent evolution of trait values, and they represent new tools to support the maximization of correlated response to selection.

overall_design: Developing xylem harvested at breast height from the north side of each tree stem from 17 genotypes with two biological replicates and from two additional genotypes without a second replicate previously identified as most extreme phenotypes in six wood traits was individually profiled for transcriptome analysis totaling 36 hybridizations to three NimbleGen 12-plex poplar arrays.

first: Jaroslav

last: Klápště

first: Oleksandr

last: Skyba

first: Michael

middle: C

last: Friedmann

first: Jan

last: Hannemann

first: Juergen

last: Ehlting

first: Yousry

last: El-Kassaby

first: Shawn

middle: D

last: Mansfield

first: Carl

middle: J

last: Douglas


title: Expression profiles osteosarcoma cell lines and MET transformed osteoblast clones

first: Raffaele

last: Calogero

summary: We studied MET-transformed human primary osteoblasts (MET-HOBs), which we previously turned into osteosarcoma cells by LV driven over-expression of MET oncogene. We obtained distinct MET transformed HOB clones  derived from independent events of transgene integration. To characterise the phenotype of the MET-HOB clones we used oligonucleotide microarrays. Expression profiles of MET-HOBs and osteosarcoma cell lines were compared.

first: Nadia

last: Dani

first: Martina

last: Olivero

first: Katia

last: Mareschi

first: MarjanMarja

last: vanDuist

last: Miretti

first: Sara

last: Cuvertino

first: Salvatore

last: Patané

first: Riccardo

last: Ferracini

last: Scotlandi

first: Franca

last: Fagioli

first: MariaFlavia

last: DiRenzo


title: Indel array-based genotyping of pupariation site preference among Drosophila sechellia backcross progeny

city: East Setauket

first: Deniz

last: Erezyilmaz

state: NY

address: CMM 440

department: Biochemistry

institute: Stony Brook University

type: Genome variation profiling by genome tiling array

summary:
We identified 6,975 insertion/deletion events of between 10 and 100 bp in length from the Drosophila simulans and Drosophila sechellia Mercator/MAVID genomic sequence alignment.
Replicate pure samples of Drosophila simulans and Drosophila sechellia gDNA were competitively hybridized to measure the expected relative hybridization intensity of alleles from each species. We used these measured intensities to assess the likelihood that the hybridization signal at each probe in an experimental animal reflected homozygosity or heterozygosity at that locus.

sample_organism: Drosophila sechellia x Drosophila simulans

overall_design: Indel array  Agilent-022089 sim-sech.v.1.3

first: David

last: Stern


title: Agilent custom 244K array CGH data for the HuRef individual

status: Public on Feb 12 2013

city: Toronto

first: Andy

last: Pang

state: ON

address: MaRS Centre - East Tower, 101 College Street, Room 14-701

institute: The Centre for Applied Genomics

summary: The ideal genome sequence for medical interpretation is complete and diploid, capturing the full spectrum of genetic variation.  Toward this end, there has been progress in discovery of single nucleotide polymorphism (SNP) and small (<10bp) insertion/deletions (indels), but annotation of larger structural variation (SV) including copy number variation (CNV) has been less comprehensive, even with available diploid sequence assemblies. We applied a multi-step sequence and microarray-based analysis to identify numerous previously unknown SVs within the first genome sequence reported from an individual.

overall_design: CGH experiments were performed with genomic DNA extracted from the HuRef and six HapMap lymphoblastoid cell lines, hybridized against the reference NA10851. A dye-swap experiment was performed for each experiment. The custom CGH microarray contains probes that target novel sequences that are not on the NCBI reference build 35. Instead, the probes target scaffold sequences that are unique to the Celera R27C assembly.

middle: W


title: Role of the Bacteroides fragilis EcfO regulon during oxidative stress.

city: Greenville

first: Charles

middle: Jeffrey

last: Smith

state: NC

address: 600 Moye Blvd.

department: Microbiology & Immunology

institute: East Carolina University

summary: Genome expression study of Bacteroides fragilis strain 638R comparing an ecfO null mutant with an empty vector to a reo (anti-ecfO) null mutant containing the ecfO gene on a plasmid under the control of an IPTG inducible promoter.

overall_design: Seven chip study with 8 technical replicates (i.e. Each probe replicated 8 times on the chip) on each chip comparing the ecfO overexpressing strain in a reo (anti-ecfO) mutant to an empty vector control in an ecfO null mutant.

first: C

first: Ivan

last: Ndamukong


title: Exposure time during postembryonic development influences persistent biological effects of the insecticide carbaryl in green frogs (Lithobates clamitans)

status: Public on Feb 21 2013

city: Victoria

first: Nik

last: Veldhoen

state: BC

address: PO Box 3055 STN CSC

department: Biochemistry & Microbiology

institute: University of Victoria

summary: The impact of pesticides on amphibian metamorphosis may vary depending on developmental stage of individuals during the exposure period. Some anurans experience increased rates of development when exposure to the insecticide carbaryl occurs later in larval development. We exposed developing northern green frog tadpoles (Lithobates clamitans) to a 3 day pulsatile exposure of 1 mg/L carbaryl at 16 weeks relative to the starting free-swimming Gosner stage 25 (Gosner, 1960) and examined treatment effects on brain mRNA abundance profiles of Gosner stage 46 metamorphs using an amphibian cDNA microarray.

platform_organism:
Xenopus laevis
Aquarana catesbeiana
Lithobates pipiens

overall_design: Five individuals from control non exposed tadpoles and six animals that had been exposed transiently for 3 days to carbaryl at week 16 and allowed to continue development until Gosner stage 46 were randomly selected for analysis of brain mRNA levels evaluated using the MAGEX DNA microarray.

first: Caren

last: Helbing

first: Michelle

last: Boone


title: Agilent custom 24M array CGH data for the HuRef individual

overall_design: Agilent array CGH experiment was performed according to the manufacturer's directions on DNA extracted from lymphoblastoid cell lines. HuRef genomic DNA was co-hybridized with female sample NA15510 from the Polymorphism Discovery Resource. No replicate nor dye swap was done. The Agilent 24 million features CGH array set was designed with 23.5 million 60-mer oligonucleotide probes tiled along the NCBI Build 36 assembly.


title: Transcriptomic response of the auxotrophic Mycobacterium avium subspecies paratuberculosis (MAP) leuD mutant under environmental stresses

status: Public on Feb 16 2013

city: Ithaca

first: Jenn-Wei

last: Chen

institute: Cornell University

summary: Comparing the transcriptomic responses between the Mycobacterium avium subspecies paratuberculosis (MAP) leuD mutant with the parent strain K-10 under different environmental stresses: nutrition, temperature, anaerobic conditions, high- and low- pH conditions.

platform_organism: Mycobacterium avium subsp. paratuberculosis K-10

overall_design: MAP wild type K-10 vs. leuD mutant, 6 different treatments. Two biological replicates with two technical replicates.

first: Joy

last: Scaria

first: Jenn

first: Yung

middle: F

last: Chang


title: Maternal Influence on Exonic CpG Island Methylation in the Developing Hippocampus [HELP]

status: Public on Feb 04 2013

city: New York

first: Miklos

last: Toth

address: 1300 York Ave. Room W-506

department: Department of Pharmacology

institute: Weill Cornell Medical College

type: Methylation profiling by genome tiling array

summary: Maternal 5-HT1A-receptor (R) is required for the timely development of the hippocampus and the establishment of emotional behaviors in Swiss-Webster (SW) mice.  A partial and/or complete loss of maternal 5-HT1AR results in delayed ventral dentate granule cell (v-DGC) development and subsequent anxiety-like phenotype in the wild-type offspring by a non-genetic, presumably epigenetic mechanism.  Here we tested v-DGCs for genome-wide DNA methylation changes elicited by the receptor deficient maternal environment.  We identified a set of hypomethylated regions in the offspring of receptor deficient mothers.  A significant fraction of these maternal-differentially methylated regions (m-DMRs) mapped to strong CpG islands, sequences that are typically not methylated or if methylated, resistant to environmental-induced changes.  Many m-DMRs mapped to exons and some were associated with expression changes.  Their hypomethylation was due to an arrest in de novo methylation and, to a lesser extent, to demethylation during postnatal life indicating that the perturbation in methylation coincides with the developmental delay in DGC maturation in the offspring of receptor deficient mothers.  Inhibiting methylation in differentiating neurons impaired their maturation further suggesting a link between de novo methylation and neuronal differentiation.  These data suggest that methylation at specific exonic CpG-islands may contribute to the mechanism through which maternal 5-HT1AR modulates hippocampal development and consecutively the level of anxiety in the SW offspring.  Reduced 5-HT1AR-binding has been reported in individuals, particularly in association with anxiety/depression, including peri/postpartum depression.  Therefore, maternal receptor deficit may contribute, via a non-genetic mechanism, to the high prevalence and heritability of anxiety disorders in human.

overall_design: Comparison of methylation patterns in ventral Dentate Gyrus cells of wild type mice versus 5HT1A receptor knockouts, as well as the effect of the maternal 5HT1A genotype

first: Ji-eun

last: Oh

first: Nyasha

last: Chambwe

first: Judit

last: Gal

first: Stuart

last: Andrews

first: Georgia

last: Gleason

first: Rita

last: Shaknovich

first: Ari

last: Melnick

first: Fabien

last: Campagne


title: Genomic diversity of Bifidobacterium adolescentis and pseudocatenulatum group

first: Marco

last: Ventura

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

overall_design: Refer to individual Series


title: CPEB inducible knock-down in a H.D. Myz cell line

status: Public on Feb 25 2013

city: barcelona

first: BELEN

last: MINANA

state: barcelona

address: dr aiguader 88

department: GENE REGULATION, STEM CELLS AND CANCER

country: Spain

institute: Center for genomic regulation

summary: Messenger RNA stability, localization, and translation are largely determined by sequences in their 3′ untranslated regions (3’UTRs), which recruit regulatory proteins and RNAs. More than half of the mammalian genes generate multiple mRNA isoforms differing in their 3′UTRs and therefore in their regulatory elements. The Cytoplasmic Polyadenylation Element Binding protein 1 (CPEB1) binds to cognate sites in 3’ UTRs and regulates translation. CPEB1 can shuttle to the nucleus and we report its co-localization with splicing factors. CPEB1 knock down leads to changes in alternative splicing, and we show that alternative 3’ splice site linked to alternative polyadenylation of the bub-3 pre-mRNA, important for cell proliferation, is regulated by CPEB1 at least in part by preventing 3’ splice site recognition by U2AF. RNA-Seq experiments reveal that CPEB1 mediates 3’ UTR shortening of hundreds of mRNAs, leading to changes in their translation efficiency.

overall_design: Three total RNA from three biological replicates were labeled and hybridized versus its own control in direct and dye-swap hybridizations.

first: Belen

last: Minana

first: Alessio

last: Bava

first: Raul

last: Mendez

first: Juan

last: Valcarcel


title: Impacts of Salmonella enteritidis Infection on Liver Transcriptome in Broilers

city: Ames

first: Derrick

middle: Jamaal

last: Coble

state: IA

address: 2254 Kildee Hall

department: Animal Science

institute: Iowa State University

summary: To provide insight into the systemic metabolic effects of S. enteritidis infection, liver samples were harvested 10 days post infection from broiler hens. Hepatic global gene expression levels were assessed using a chicken 44K Agilent microarray. Forty-four genes were differentially expressed at a significance level of q-value < 0.05. One hundred eighty-three genes were differentially expressed at a suggestive significance level of q-value < 0.1. A predominance of down-regulation existed among significantly differentially expressed genes. A cell morphology, cell cycle, organismal injury and abnormalities network and a metabolic disease, cardiovascular system development and function, and urological disease network were created from the differentially expressed genes. Apoptosis, electron transport, peptidase activity, vein constriction, cell differentiation, IL-2 signaling, Jak-Stat signaling, B-cell receptor signaling, GDP/GTP exchange, and cytokine suppression were among the functions of the differentially expressed genes that were down-regulated in response to S. enteritidis. The effects of S. enteritidis infection on the liver transcriptome profiles of broilers reflect a predominance of down-regulation of genes involved with metabolic, cell morphology, cell cycle, urological disease, and organismal injury functions. These results provide insight into important systemic metabolic mechanisms that are active in the chicken liver in response to S. enteritidis infection.

overall_design: Sixteen broiler hens of approximately 5 months (8 challenged orally with 1x108 S. enteritidis on each of three sequential days and 8 mock-challenged with phosphate buffered saline) were used. Livers were harvested at 10 days post infection and stored in RNALater (Ambion).

first: Erin

last: Sandford

first: Tieming

last: Ji

first: Jason

last: Abernathy

first: Damarius

last: Fleming

first: Huaijun

last: Zhou

first: Susan

last: Lamont


title: MicroRNAs mediate rapamycin resistance in a myogenic tumor cell line

city: NY

first: Hana

last: Totary-Jain

address: 150, St. NICHOLAS AVE

institute: Columbia University

summary: The mammalian target of rapamycin (mTOR) is a central regulator of cell proliferation. Inhibitors of mTOR are being evaluated as anti-tumor agents. Given the emerging role of microRNAs (miRNAs) in tumorgenesis we hypothesized that miRNAs could play important roles in the response of tumors to mTOR inhibitors. Rapamycin resistant myogenic cells developed by long-term rapamycin treatment showed extensive reprogramming of miRNAs expression, characterized by up-regulation of the mir-17~92 and related clusters and down-regulation of tumor-suppressor miRNAs. Antagonists of oncogenic miRNA families and mimics of tumor suppressor miRNAs (let-7) restored rapamycin sensitivity in resistant tumor cells. This study identified miRNAs as new downstream components of the mTOR-signaling pathway, which may determine the response of tumors to mTOR inhibitors.

overall_design: Total RNA was extracted from rapamycin sensitive (RS) cells (BC3H1, mouse brain tumor cell line with myogenic properties, ATCC)  cultured in Dulbecco’s modified essential medium (DMEM) media supplemented with 20% fetal bovine serum (FBS), penicillin (100 U/ml) and streptomycin (100 mg/ml). Rapamycin resistant cells (RR1) were developed by culturing BC3H1 cells in the presence of 1 uM rapamycin for 6 months. Three samples in quadruplicate 1)RS cells treated with DMSO for 24 h(BC3H1, reference), 2) RS cells treated for 24 h with 100 nM rapamycin (BC3H1+R), 3) RR1 cells consantly treated with 1uM Rapamycion (RR1+R). For each experiment, 1 μM of total RNA was labeled with Hy3TM dye and a reference RNA pool (consisting of a mixture of equal amounts of total RNA from BC3H1, BC3H1+R and RR1+R cells) was labeled with Hy5TM dye using the miRCURYTM Labeling Kit. The samples were hybridized to Exiqon miRCURYTM LNA Arrays (V10.0).

first: Despina

last: Sanoudo

first: Iddo

middle: Z

last: Ben-Dov

first: Cula

middle: N

last: Dautriche

first: Paolo

last: Guarnieri

first: Steven

middle: O

last: Marx

first: Thomas

last: Tuschl

first: Andrew

last: Marks


title: MicroRNA expression in peripheral blood predicts poor and prolonged response to sunitinib.

status: Public on Feb 11 2013

city: Madrid

first: Juan Ángel

last: Fresno Vara

state: Madrid

address: Paseo de la castellana 261

department: INGEMM

institute: Hospital La Paz

summary: Peripheral blood samples were taken before initiation of therapy and 2 weeks later from patients with advanced renal cell carcinoma treated with sunitinib in first line. MicroRNA expression in peripheral blood was assessed using microarrays and several models predicting poor response and prolonged response to sunitinib were constructed and evaluated.

overall_design: Peripheral blood samples obtained before initiation of therapy with sunitinib and 14 days later were used to assess expression values of miRNAs.

first: Angelo

last: Gámez-Pozo

first: Iker

last: Sánchez-Navarro

middle: A

first: Enrique

last: Espinosa


title: Differential gene expression analysis for S.pyogenes SP-STK(-) mutant

city: Columbus

first: Vijay

last: Pancholi

state: OH

address: 420W 12th Ave, TMRF-288

department: Pathology

institute: Ohio State University

summary:
  This analysis revealed ~17.%  of all ORFs (292  out of a total 1697 ORFs)  differed by at least 1.5 fold (Log2 +0.6)  between the mutant and wild-type strains. Of these, ~45% of the ORFs (130 out of 292 ORFs) revealed at least 2-fold (Log2 +1) differences.  The complete spectrum of differentially expressed genes in the muatnt strain revealed almost equal number of genes up (143, 49%) or down-regulated (149, 51%). However, at a higher stringency (at least 2-fold), this distribution revealed slightly more leaning towards down-regulated genes (74 out of 130, 57%) indicating the lack of SP-STK results into down regulation of several genes. Amongst the genes belonging to different functional categories, the most notable genes that were affected by the absence of SP-STK were those correspond to Carbohydrate transport and metabolism  (57 out of 292, 20% at low stringency and 32 out of 130 ,~25% at high stringency), phage (28, ~10% at low stringency and 24, ~18% at high stringency), and virulence (5-6% irrespective of stringency level). Almost 20-25% of differentially expressed genes revealed at two stringencies were found to be either with unknown or undefined functions.
Keywords:  knockout mutant

overall_design: This analysis is based on a total of three independent prearations of total RNA from the wild-type S. pyogenes M1SF370 and the isogenic knockout mutant lacking SP-STK (SPy1625). First two preparations included dyeswap experiment and hence repeated twice (exp1-4). The third preparation done only one (Exp#5). Thus, the present analysis is based on five separate experiments


title: Arabidopsis transcriptional profile in response to chromate (K2CrO4)

city: Irapuato

middle: Ibarra

last: Laclette

state: Guanajuato

address: Km 9.6 Libramiento Norte Carretera Irapuato-León, A.P. 629

country: Mexico

institute: Laboratorio Nacional de Genomíca (LANGEBIO), Centro de Investigación y Estudios Avanzados del IPN (CINVESTAV)

summary: Transcriptional profiling of Arabidopsis thalina seedlings in response to high (140 µM) and low (20 µM) concentrations of chromate (K2CrO4). Low concentrations of chromate (e.g. 40 µM) promoted primary root growth, while high concentrations (e.g. 140 µM) repressed growth and increased formation of root hairs, lateral roots and adventitious roots.

overall_design: Three-condition experiment, high (140 µM) and low (20 µM) concentrations of chromate (K2CrO4) vs non-chromate added (Control). Four biological replicates, one replicate per array.

first: Miguel

last: Mártinez-Trujillo

first: José

last: López-Bucio

first: Alfonso

last: Méndez-Bravo

last: Ibarra-Laclette


title: NimbleGen 42M data for the HuRef individual

first: Andy

last: Pang

overall_design: The HuRef genomic DNA (from lymphoblastoid cell line) was co-hybridized with the female sample NA15510 (from lymphoblastoid cell line) from the Polymorphism Discovery Resources. The NimbleGen platform consists of 20 NimbleGen HD2 chips, each containing 2.1M probes, and each chip is further subdivided into 3 equal-sized subarrays containing about 726K probes. The probes target the NCBI Build 36 genome, with the exception that no homology filter was applied, allowing coverage of segmentally duplicated regions.


title: Transcript profiling of local and adjacent leaf responses in barley following inoculation with Pseudomonas syringae

status: Public on Jan 31 2013

first: PLEXdb Curator

middle: Sudhansu

address: 1023  Crop Genomes Informatics Lab (Iowa State University)

department: Virtual Reality Application Center

summary: Transcriptional changes were monitored in the barley cultivar Golden Promise 24 hours post inoculation (hpi) with the bacteria Pseudomonas syringae pv. tomato DC3000 avrRpm1 (PstavrRpm1) using the Affymetrix Barley genome array GeneChip®.      Seedlings of Golden Promise were grown to growth stage 12-13 (Zadoks et al., 1974) before inoculating with either PstavrRpm1 or water (for the mock inoculation control) by infiltration.  Plants were grown under a 18 °C / 16 h light period; 12 °C / 8 h dark period, with artificial lighting (100 µmol m-2 s-1) and a relative humidity of 75 – 85 %.      Leaf samples from three seedlings were collected 24 hpi for RNA extraction and transcriptomics analysis from the area infiltrated (local) and from the area next to the infiltrated region (adjacent) from three biological replicates.  Leaf tissue was ground under liquid nitrogen and total RNA extracted using the RNeasy miniprep kit (Qiagen), following the manufacturer’s instructions.  RNA was DNase treated using Turbo DNase (Ambion) according to the manufacturer instructions. RNA integrity was confirmed using the Agilent 2100 Bioanalyzer (Agilent).  The two cycle-target labeling method was used following the Affymetrix protocol.    Affymetrix GeneChip processing, including RNA quality control, microarray hybridisation and data acquisition was performed through contract research services by Cogenics (North Carolina, U.S.A.).  A total of twelve hybridisations were performed.   ****[PLEXdb(http://www.plexdb.org) has submitted this series at GEO on behalf of the original contributor,  Ellen Colebrook.  The equivalent experiment is BB92 at PLEXdb.]

overall_design: tissue type name: Local - treatment: Inoculated(3-replications);  tissue type name: Local - treatment: Control(3-replications);  tissue type name: Adjacent - treatment: Inoculated(3-replications);  tissue type name: Adjacent - treatment: Control(3-replications)

first: Ellen

last: Colebrook

first: Lesley

last: Boyd


title: Gene expression changes during mouse plasma cell differentiation

status: Public on Feb 03 2013

city: Parkville

first: David

middle: M

last: Tarlinton

state: Vic

address: 1G Royal Pde

country: Australia

institute: WEHI


title: Salmonella wild type and mutant sdiA in LB and 2mM indole

status: Public on Jan 30 2013

city: Norwich

first: Corinne

last: Appia-Ayme

state: Norfolk

address: UEA

department: BIO

country: United Kingdom

institute: University of East Anglia

summary: Transcriptional profiling of Salmonella Typhimurium SL1344 wild type and deletion of the sdiA regulator-encoding gene grown to OD600=1 in LB alone or in LB supplemented with 2mM indole. The goal is to determine Salmonella response to indole and to define the SdiA-regulated genes in these conditions.

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

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

platform_organism: Salmonella enterica subsp. enterica serovar Enteritidis str. P125109

platform_organism: Salmonella enterica subsp. enterica serovar Typhimurium str. 14028S

overall_design: 4 different conditions tested (wild type in LB, wild type in LB + 2mM indole, sdiA mutant in LB, sdiA mutant in LB + 2mM indole), 4 replicates for each condition. The reference on each hybridisation is the chromosomal DNA of the wild type strain.

first: Gary

last: Rowley


title: Up-regulation of ERG11 is prevalent among azole-resistant clinical isolates of Candida albicans and is only partially explained by gain-of-function mutations in UPC2

city: Memphis

first: Katherine

middle: S

last: Barker

state: TN

address: 881 Madison Avenue, Room 305

department: Clinical Pharmacy

institute: University of Tennessee Health Science Center

summary: In Candida albicans, Upc2 is a zinc-cluster transcription factor that targets genes including those of the ergosterol biosynthesis pathway.  To date there have been three documented UPC2 gain-of-function (GOF) mutations recovered from fluconazole-resistant clinical isolates that contribute to an increase in ERG11 expression and decreased fluconazole susceptibility.  In a group of 62 fluconazole-resistant isolates, we found that 47 of these overexpressed ERG11 by at least two-fold over that of an average expression of 3 unrelated fluconazole susceptible strains. Of those 47 isolates, 29 contained a mutation in UPC2, whereas the remaining 18 isolates did not. Of the isolates containing mutations in UPC2, we recovered eight distinct mutations resulting in single putative amino acid substitutions: G648D, G648S, A643T, A643V, Y642F, G304R, A646V and W478C. Seven of these resulted in increased ERG11 expression, increased cellular ergosterol, and decreased susceptibility to fluconazole as compared to the wild-type strain. Genome-wide transcriptional analysis was performed for the four strongest Upc2 amino acid substitutions (A643V, G648D, G648S and Y642F).   Genes commonly upregulated in all four mutations included those involved in ergosterol biosynthesis, in oxidoreductase activity, the major facilitator efflux pump encoded by the MDR1 gene, and the uncharacterized ATP binding cassette transporter CDR11. These findings demonstrate that gain-of-function mutations in UPC2 are more prevalent than previously thought among clinical isolates, make a significant contribution to azole antifungal resistance, but do not account for ERG11 overexpression in all such isolates of C. albicans.

overall_design: We examined the expression of genes in response to the presence of 4 gain-of-function alleles of the zinc-cluster transcription factor Upc2. The global gene expression of each mutant Upc2 strain was compared to that of the wildtype strain SC5314.

first: Stephanie

last: Flowers

first: Elizabeth

last: Berkow

first: Geoffrey

last: Toner

first: Sean

middle: G

last: Chadwick

first: Scott

middle: E

last: Gygax

first: Joachim

last: Morschhäuser

first: P

last: Rogers


title: S-phase time-course of Lachancea kluyveri cells

status: Public on Feb 01 2013

city: Paris

first: AGIER

last: nicolas

address: 15 rue de l'école de médecine

department: microorganism genomic

institute: CNRS-UPMC

summary: Haploid cells of Lachancea kluyveri were arrested in G1 phase using Saccharomices cerevisiae alpha factor. After, release in a new media, cells go synchronously through S-phase. One sample is taken every five minutes. Microarrays are used to monitor the change of DNA copy number from 1 to 2, all along the genome during S-phase.

overall_design: Two-condition experiment, G1 cells vs. S-phase cells at different time points. Biological replicates: 3 biological replicates.

first: Nicolas

last: Agier

first: Gilles

last: Fischer


title: miRNA expression during in vitro mouse T cell activation (CD T cell timecourse)

status: Public on Jan 27 2013

city: San Francisco

first: Andrea

last: Barczak

state: CA

address: 1550 4th St Rock Hall 545

institute: UCSF Sandler Center Functional Genomics Core Facility

summary: Array of global miRNA expression during a time course of in vitro CD4 T cell activation

overall_design: 50 ng RNA isolated from mouse CD4 T cells, activated in vitro for a time course spanning 7 days and restimulated

first: Yelena

last: Bronevetsky

first: K

last: Ansel


title: MicroRNA profiling of human pancreatic alpha and beta cells

city: Miami

first: Ricardo

last: Pastori

state: FL

department: Diabetes Research Institute

institute: University of Miami

summary: MicroRNAs (miRNAs) are non-coding RNAs that play a fundamental role in regulation of gene expression affecting differentiation and development. In particular, miRNAs have been described to regulate genes important for pancreatic development and islet function. The aim of this work was to determine the miRNA expression signature in human pancreatic alpha and beta cells. miRNA stability to fixation allowed the study of microRNA in pure populations of human alpha and beta cells sorted by FACS after intracellular staining with glucagon and insulin, respectively. The determination of the specific group of miRNAs expressed in the human pancreatic alpha and beta cells may further the understanding of gene expression regulation of the islet differentiation process.

overall_design: The alpha and beta cells come from 6 different preparations of human pancreatic islets from donors. In this study we define expression profiles of a total of 665 miRNAs for pancreatic alpha and beta cells. For this purpose, cells were fixed with paraformaldehyde, 7AAD was applied to exclude dead cells. Then, cells were sorted after intracellular staining with C peptide to detect beta cells and glucagon to detect alpha cells. After sorting, we confirmed enriched beta cells have a purity of on average over 98%. Enriched alpha cells have a purity of on average over 98%. To determine the miRNA expression profiles, we used human miRNA TLDAs version 2.  For each sample card A and card B were run after cDNA synthesis and 12 cycles of preamplification according to the manufacturer protocol. Each TLDA card A contains 1 probe for the endogenous control RNU48 while each TLDA card B contains 4 replicates of the RNU48 probe. Analysis of these controls allows calculating the intra- and inter-assay variation. Quantitative values (RQ) were calculated measuring the ddCt between the Ct values of each miRNA and the Ct value of the small nucleolar RNU48 RNA comparing the target sample and the control sample.

first: Valia

last: Bravo-Egana

first: Samuel

last: Rosero


title: MDA-MB-231 cells: shMUC4 transfected vs. Control SCR

status: Public on Dec 31 2012

city: Omaha

first: Partha

last: Mukhopadhyay

state: Nebraska

address: 985870 Nebraska Medical Center

department: Biochemistry and Molecular Biology

institute: University of Nebraska Medical Center

summary: Identification of MUC4-associated expression of genes by comparing MUC4 knockdown (MDA-MB-231-shMUC4) and control (MDA-MB-231-SCR).

overall_design: Two-condition experiment, MUC4 knockdown cells vs. control. Biological replicates: 2 control, 2 sh-MUC4 transfected, independently grown and harvested. one replicate per array.

first: Subhankar

last: Chakraborty

first: Moorthy

middle: P

last: Ponnusamy

first: Maneesh

last: Jain

first: Imayavaramban

last: Lakshmanan

first: Priya

last: Pai

first: Lynette

last: Smith

first: Subodh

last: Lele

first: Surinder

middle: K

last: Batra


title: Gene expression of LNCaP cells grown in 2D cultures and polyethlene glycol-based hydrogels with the presence of synthetic androgen, R1881

city: Brisbane

first: Colleen

last: Nelson

state: Queensland

address: 199 Ipswich Road

department: Institute of Health and Biomedical Innovation; Vancouver Prostate Centre

institute: Queensland University of Technology; University of British Columbia

summary: Analysis of LNCaP cell molecular differences and their response to R1881 in 2D and 3D cultures. Androgen regulated genes were differentially expressed between 2D and 3D cultures. These results provide insights into factors that influence the expression of androgen regulated genes

overall_design: In this study, LNCaP cells cultured in tissue culture plastic (2D) and in the hydrogel (3D) were maintained up to 3 days and 24 days respectively in serum containing media before they were androgen-starved for 48 hours. Cells were either treated with 1nM R1881 or continued to be androgen-deprived (without R1881 with 0.008% ethanol) for another 48 hours prior to cell harvest for gene expression analysis. Biological triplicates were prepared for each condition.

first: Shirly

last: Sieh

first: Anna

middle: V

last: Taubenberger

first: Simone

middle: C

last: Rizzi

first: Martin

last: Sadowski

first: Melanie

middle: L

last: Lehman

first: Anja

last: Rockstroh

first: Judith

last: Clements

first: Dietmar

last: Hutmacher


title: Identification of the Bacteroides fragilis EcfO regulon 3

status: Public on Jan 01 2013

city: Greenville

first: Charles

middle: Jeffrey

address: 600 Moye Blvd.

institute: East Carolina University

summary: Genome expression study of Bacteroides fragilis strain 638R comparing a EcfO/anti-EcfO null mutant with an empty vector to a EcfO/anti-EcfO null mutant containing the EcfO gene on a plasmid under the control of a maltose inducible promoter.

overall_design: Two chip study with 8 technical replicates on each chip comparing the EcfO overexpressing strain in a EcfO/anti-EcfO mutant to an empty vector control in the same mutant background.

first: C

middle: J

first: Ivan

last: Ndamukong


title: LS001A: Aging/Early Degeneration Of The Intervertebral Disc Involves Downregulation Of Canonical Wnt Signaling and Caveolin-1 expression

city: Utrecht

first: Marian

last: Groot Koerkamp

state: Utrecht

address: Heidelberglaan 25

department: Research

country: Netherlands

institute: Princess Maxima Center for Pediatric Oncology

summary:
Objective: Aging and early degeneration of the intervertebral disc (IVD) involves the substition of notochordal cells (NCs) in the nucleus pulposus (NP) by chondrocyte-like cells (CLCs). This study investigated the gene expression profiles involved in this process using NP tissue from both non-chondrodystrophic and chondrodystrophic dogs, a species with naturally occuring IVD degeneration.
Methods: Dual channel DNA microarrays were used to compare 1) healthy NP tissue, 2) NP tissue with a mixed population of NCs and CLCs, and 3) NP tissue containing solely CLCs. Canonical Wnt-signaling was validated using qPCR of relevant Wnt target genes. Caveolin-1, a known regulator of canonical Wnt signaling, was investigated further in tissue sections using qPCR and immunohistochemistry, and in cultured NCs by qPCR and immunofluorescence. Also, the NP of 3-month-old caveolin-1 knock-out mice was histopathologically evaluated and compared with wild type mice of the same age.
Results: Early IVD degeneration involved significant regulations in numerous pathways, such as extracellular matrix remodeling, Bone Morphogenetic Protein- , and Wnt/beta-catenin-signaling. With regard to Wnt/beta-catenin signaling, axin2 gene expression was significantly higher in chondrodystrophic dogs compared with non-chondrodystrophic dogs. IVD degeneration involved significant downregulation of axin2 gene expression and caveolin-1 gene and protein expression. NCs showed abundant caveolin-1 expression in vivo and in vitro, whereas CLCs did not. The NP of 3-month-old WT mice were rich in viable NCs, whereas the NPs of 3-month-old caveolin-1 knock-out mice contained chondroid-like matrix with small, rounded cells, the majority of which showed morphological signs of apoptosis.
Conclusions: Aging and the onset of degeneration of the IVD involve significant downregulation of canonical Wnt signaling and caveolin-1, which appears to be essential in the physiology and preservation of NCs.

overall_design: DNA microarrays were used to compare nucleus palposus (NP) tissue of healthy and chondrodystrophic individuals. Furthermore, the situation of the tissue was divided into three stages: NCR: notochordal cell(NC) rich; CR: tissue containing solely chondrocyte-like-cells (CLC) and T: tissue with a mixed population of NCs and CLCs. Comparisons were analysed on a 2-color platform against a common reference sample, consisting of a multitude of canine organs, including liver, spleen, kidney, lung, hart, intestine and bone.

first: Lucas

last: Smolders

first: Björn

last: Meij

first: David

last: Onis

first: Frank

last: Riemers

first: P

last: Bergknut

first: Richard

last: Wubbolts

first: Guy

last: Grinwis

last: Houweling

first: Dik

last: van Leenen

last: Holstege

first: Herman

last: Hazewinkel

first: Laura

middle: B

last: Creemers

first: Louis

last: Penning

first: Marianna

last: Tryfonidou


title: Gene expression analysis of B cell differentiation using B cell blasts and developmentally arrested plasmablasts

last: Tarlinton

summary: In vitro generated blasts from B cells deficient in prdm1 were isolated according to whether they were attempting to express Blimp1, reported by a GFP cassette knocked into the prdm1 locus

overall_design: After four days stimulation with CD40L, IL4 and IL5, cells were FACS sorted into GFP+ and GFP- populations, RNA extracted and gene expression analysed by microarray. Data presented in Peparzak et al, 2013, Fig 3b.

first: Cam

last: Wellard

first: Victor

last: Peperzak


title: Identification of the Bacteroides fragilis EcfO regulon 1

first: Charles

last: Smith

summary: Genome expression study of Bacteroides fragilis ATCC25285 strain containing the EcfO gene constitutively expressed from plasmid pFD340

overall_design: Two chip study with 5 technical replicates on each chip comparing the EcfO overexpressing strain to an empty vector control in the wild type strain.

first: C

last: Ndamukong


title: Characterization of the EcfO regulon

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

sample_organism:
Bacteroides fragilis NCTC 9343
Bacteroides fragilis 638R

overall_design: Refer to individual Series


title: A small-cell lung cancer subtype with good prognosis found by a three miRNA signature

city: Koto-ku

first: Yuichi

last: Ishikawa

state: Tokyo

address: 3-8-31 Ariake

institute: Cancer Insitute

summary: Background  Neuroendcrine carcinoma (NEC) of lung consists of small-cell lung carcinoma (SCLC) and large cell neuroendocrine carcinoma (LCNEC).  Although long-term outcomes of SCLC patients are usually poor, a few patients achieve long-term survivals.  Prognostic factors in SCLC have not been fully elucidated.  microRNAs (miRNAs) are known to negatively regulate gene expression and to be relevant to tumorigenesis, tumor classification and prognosis.  Methods  63 samples (46 neuroendocrine carcinoma including 35 SCLC and 11 LCNEC, 4 adenocarcinoma, 5 squamous cell carcinoma and 8 normal lung) were obtained through surgical resection.  miRNA expression in each sample was comprehensively investigated using miRNA microarray.    Results  Unsupervised hierarchial clustering classified the all NEC into two subgroups, group 1 and 2.  Group 1 was felt into an independent branch that consisted of only NEC, whereas group 2 was included in a branch that contained both NEC and non-NEC.  Compared with SCLC of group 1 (SCLC 1), SCLC of group 2 (SCLC 2) was a distinct subgroup with surprisingly good prognosis (0% v 79% survived for 5 years; p=0.007).  Serum proGRP level was significantly lower in SCLC 2 than in SCLC 1 despite of similar tumor stages between the two groups.  Among 12 cases treated by presurgical chemotherapy, PR:NC ratio was 6:3 in SCLC 1 and 2:1 in SCLC 2, suggesting no apparent difference of chemosensitivity.  Histologically, distinction between both groups was difficult.  Cox regression analysis demonstrated that three miRNA signature was correlated with survival of SCLC patients.  These prognostic miRNAs were differentially expressed between SCLC 1 and 2, which were validated by quantitative real time RT-PCR.  Bioinformatics analysis predicted that these miRNAs targeted not only genes involving with tumorigenesis but also genes associated with neuroendocrine function.  Conclusion  miRNA expression profiling identified a distinct subgroup of SCLC with favorable prognosis.  This subgroup might have less neuroendocrine character than usual SCLC.

overall_design: All samples were tissue samples obtained by surgical resection. 35 samples of small-cell lung cancer were investigated. 11 samples of larege cell neuroendocrine cancer, 4 samples of adenocarcinoma, 5 samples of squamous cell carcinoma and 8 samples of normal lung were also included as reference.

first: Takehiko

last: Ohba

first: Hiroko

last: Nagano


title: Salmonella wild type in LB, 2mM indole until OD1 and 2mM indole for 15 minutes

first: Corinne

last: Appia-Ayme

summary: Transcriptional profiling of Salmonella Typhimurium SL1344 wild type grown to OD600=1 in LB alone or in LB supplemented with 2mM Indole, or with 2mM indole for 15 min (called shock). The goal is to determine Salmonella response to indole at different time points.

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

overall_design: Different conditions were tested. The reference on each hybridisation is the chromosome DNA of the wild type strain. 4 replicates each for LB and LB + Indole, 6 replicates for indole shock.

first: Gary

last: Rowley


title: Aberrant gene expression in Drosophila hybrids supporting faster-male evolution

status: Public on Feb 02 2013

city: college park

first: Carlos Alberto

last: Machado

state: MD

department: department of biology

institute: University of Maryland

summary: To explore the aberrant expression patterns between hybrid sexes, we compare the global gene expression of 7-day-old whole body adults of hybrids by sex in recently diverged  Drosophia pseudoobscura group

sample_organism: Drosophila pseudoobscura x Drosophila persimilis

sample_organism: Drosophila pseudoobscura pseudoobscura x Drosophila pseudoobscura bogotana

sample_organism: Drosophila persimilis x Drosophila pseudoobscura

sample_organism: Drosophila pseudoobscura bogotana x Drosophila pseudoobscura pseudoobscura

overall_design: 7-day-old virgin hybrid flies were assayed by sex. Reciprocal F1 hybrids were produced for D. pseudoobscura/D. persimilis and D. pseudoobscura/D. p. bogotana crosses by mass mating virgin flies. At least three isofemale inbred lines were used for each species (D. pseudoobscura; D. persimilis; D. pseudoobscura bogotana).Two separate labeling reactions per sample were pooled and hybridized to the Agilent single color (Cyanine 3-CTP dye) arrays. Three different replicates were hybridized for each hybrid and sex. Pure species data (collected the same time and deposited as GSE17192 ) and hybrid data were analyzed together to determine the misexpression differences between hybrid males and females.

first: Zifeng

last: Jiang

first: Carlos


title: Role of putative RNA-binding proteins in Campylobacter jejuni gene expression and virulence

first: Bruce

middle: MacKenzie

last: Pearson

address: Colney Lane

department: Food Safety

institute: Institute of Food Research

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


title: Study of Cj0667 function in Campylobacter jejuni

summary: In order to study the function of the Campylobacter jejuni Cj0667 gene, a series of experiments were carried out. Two strains were constructed: a Cj0667 knockout strain and a strain with a second copy over-expressing Cj0667 from an fdxA promoter. The transcriptomes of these were all compared to the wild-type strain. The arrays are all from RNA isolated in mid-exponential growth.

overall_design:
Batch cultures of Campylobacter jejuni NCTC 11168 were grown in 50 ml volumes of Brucella broth in 70cm tissue culture flasks. Microaerophilic conditions were generated using a MACS-VA500 microaerophilic work station (5% Oxygen, 10% Carbon dioxide, 85% Nitrogen) from Don Whitley Scientific, Ltd which also maintained the growth temperature at 37 ºC. RNA was extracted from C. jejuni cultures grown to an OD600 of approximately 0.4. Briefly, 0.1 volume of 5% phenol in ethanol was mixed with the broth culture, and after centrifugation RNA was isolated with Tri Reagent (Sigma) and chloroform. RNA was further purified using the RNeasy kit (Qiagen) according to the manufacturer’s instructions. The RNA was treated with Turbo DNA-free (Ambion) to remove any residual DNA according to the manufacturer’s instructions. RNA concentration was determined using the Nanodrop Spectrophotometer NS-1000 (Thermo Scientific).

RNA preparations of each sample type were labelled and hybridized to custom-designed Agilent microarrays. Equal quantities of RNA from test and control cultures were labelled by using nucleotide homologues of dUTP containing either Cy3 or Cy5 fluorescent dye (Perkin Elmer). For each microarray slide, the test strain was labelled with Cy3-dUTP, while the wild-type sample was labelled with Cy5-dUTP. RNA (15 µg) was primed with 5 µg pd(N)6 random hexamers (Amersham Biosciences). The Affinity Script kit (GE Healthcare) was used to produce cDNA, and hybridized (Agilent Hi-RPM Gene Expression Hybridization Kit) to the microarray slide according to the manufacturer’s instructions. Microarrays were scanned at 5 µm using an Axon 4000A scanner, and images were acquired using GenePix Pro 3.0 software (Axon).

Related analysis reference: Holmes K., Mulholland F., Pearson B. M., Pin C., McNicholl-Kennedy J., Ketley J. M., Wells J. M. (2005) Campylobacter jejuni gene expression in response to iron limitation and the role of Fur Microbiology-SGM 151 243-257 (PMID 15632442).

first: Johanna

last: Meier

first: Andre

last: Fischer

first: Francis

last: Mulholland

first: Ulf

last: Gobel

first: Arnoud

middle: H

last: van Vliet

first: Stefan

last: Bereswill

first: Markus

last: Heimesaat


title: Gene expression of human cancer cells co-cultured with mouse astrocytes and fibroblasts after series of cross co-culture

city: Houston

first: Sangbae

last: Kim

state: TX

address: 1 Baylor plaza

department: HGSC

institute: Baylor Colleage of Medicine

summary: Brain metastases are highly resistant to chemotherapy. Brain metastases are surrounded and infiltrated by activated astrocytes. To examine the genes whose expression is associated with chemo-resistance of brain-metastasized cancer cells, gene expression data were collected and analyzed from breast cancer cells and lung cancer cells co-cultured with astrocytes. Fibroblast cells were used as control.

overall_design: Human lung cancer cell PC14 was co-cultured with mouse astrocytes or fibroblasts for two rounds. Total RNAs were extracted from co-cultured cells and hybridized to human microarray.

first: Eun

last: Park

first: Ju-Seog

last: Lee

first: Isaiah

last: Fidler

first: Sun-Jin


title: Identification of the Bacteroides fragilis EcfO regulon 2

first: Charles

last: Smith

state: NC

department: Microbiology & Immunology

summary: Genome expression study of Bacteroides fragilis strain 638R comparing a EcfO null mutant with an empty vector to a anti-EcfO null mutant containing the EcfO gene on a plasmid under the control of an IPTG inducible promoter.

overall_design: Two chip study with 8 technical replicates on each chip comparing the EcfO overexpressing strain in an anti-EcfO mutant to an empty vector control in a EcfO null mutant.

first: C

first: Ivan

last: Ndamukong


title: Study of Cj1103 function in Campylobacter jejuni

summary: In order to study the function of the Campylobacter jejuni Cj1103 gene, a series of experiments were carried out. Three strains were constructed: a Cj1103 knockout strain, a strain where the Cj1103 knockout was complemented in trans, and a strain with a second copy over-expressing Cj1103 from an metK promoter. The transcriptomes of these were all compared to the wild-type strain. The arrays are all from RNA isolated in mid-exponential growth from independent biological replicates.

overall_design:
Batch cultures of Campylobacter jejuni NCTC 11168 were grown in 50 ml volumes of Brucella broth in 70cm tissue culture flasks. Microaerophilic conditions were generated using a MACS-VA500 microaerophilic work station (5% Oxygen, 10% Carbon dioxide, 85% Nitrogen) from Don Whitley Scientific, Ltd which also maintained the growth temperature at 37 ºC. RNA was extracted from C. jejuni cultures grown to an OD600 of approximately 0.4. Briefly, 0.1 volume of 5% phenol in ethanol was mixed with the broth culture, and after centrifugation RNA was isolated with Tri Reagent (Sigma) and chloroform. RNA was further purified using the RNeasy kit (Qiagen) according to the manufacturer’s instructions. The RNA was treated with Turbo DNA-free (Ambion) to remove any residual DNA according to the manufacturer’s instructions. RNA concentration was determined using the Nanodrop Spectrophotometer NS-1000 (Thermo Scientific).

Two or three independent RNA preparations (biological replicates) of each sample type were labelled and hybridized to custom-designed Agilent microarrays. Equal quantities of RNA from test and control cultures were labelled by using nucleotide homologues of dUTP containing either Cy3 or Cy5 fluorescent dye (Perkin Elmer). For each microarray slide, the test strain was labelled with Cy3-dUTP, while the wild-type sample was labelled with Cy5-dUTP. RNA (15 µg) was primed with 5 µg pd(N)6 random hexamers (Amersham Biosciences). The Affinity Script kit (GE Healthcare) was used to produce cDNA, and hybridized (Agilent Hi-RPM Gene Expression Hybridization Kit) to the microarray slide according to the manufacturer’s instructions. Microarrays were scanned at 5 µm using an Axon 4000A scanner, and images were acquired using GenePix Pro 3.0 software (Axon).

Related analysis reference: Holmes K., Mulholland F., Pearson B. M., Pin C., McNicholl-Kennedy J., Ketley J. M., Wells J. M. (2005) Campylobacter jejuni gene expression in response to iron limitation and the role of Fur Microbiology-SGM 151 243-257 (PMID 15632442).


title: Cross species hybridization of human cancer cells co-cultured with mouse astrocytes and fibroblasts

platform_organism:
Homo sapiens
Mus musculus


title: Pseudomonas syringae B728a responses to environmental stresses and growth in and on bean leaves

status: Public on Jan 12 2013

city: Ames

first: Gwyn

middle: A

last: Beattie

address: 207 Science I

department: Dept of Plant Pathology & Microbiology

institute: Iowa State University

summary: Some strains of the foliar pathogen Pseudomonas syringae are adapted for growth and survival on leaf surfaces and in the leaf interior.  Global transcriptome profiling was used to evaluate if these two habitats offer distinct environments for bacteria and thus present distinct driving forces for adaptation.  Further transcriptome profiling was performed to understand the various environmental conditions that P. syringae cells encounter during their association with plants.   RNA was collected from P. syringae pv. syringae strain B728a cells that were exposed to seven treatments.  The treatments included five in vitro treatments, namely exposing cells to a basal medium, sodium chloride to confer an osmotic stress, hydrogen peroxide to confer an apoplastic growth, iron limitation, nitrogen limitation.  They also included two in planta treatments, namely recovering cells from epiphytic sites after surface inoculation and 72 h of growth on bean (Phaseolus vulgaris L.) leaves and recovering cells from apoplastic sites after infiltration and 48 h of growth in bean leaves.  The results suggested that B728a cells experience vastly different environments when growing on the surface versus the interior of leaves and identified distinct traits that are likely used for persistence and growth in these environments.

overall_design:
RNA was collected from B728a cells that were exposed to seven treatments, each with two biological replicates in each of three laboratories.  Experimental methods were standardized across the three laboratories.  For the in vitro treatments, exponential cells from two independent cultures were each exposed to the five treatments.  For each treatment, the cells originating from the two cultures were pooled and the RNA was extracted; this was repeated in its entirety and the two RNA pools were combined.  The resulting RNA representing four independent cultures served as a single biological replicate.  Two biological replicates for each treatment were generated in this manner in each of three separate laboratories.
Epiphytic B728a populations were established following spray inoculation onto bean leaves and subsequent incubation; the epiphytic cells recovered from 400 to 600 leaves inoculated at one time served as a biological replicate, and the procedure was repeated to provide two biological replicates.  Due to the availability of facilities, all of the epiphytic treatments were conducted at as single laboratory, with cultures provided from each of the other laboratories, and the cell pellets were returned to those laboratories for RNA extraction and analysis.
Apoplastic B728a populations were established following vacuum infiltration into bean leaves and subsequent incubation; the apoplastic cells recovered from 40 to 80 leaves inoculated at one time served as a biological replicate, and two biological replicates were generated at each of the three laboratories.
The RNA from all treatments was submitted to Roche Nimblegen, Inc where it was labeled and hybridized to an ORF-based microarray that included 5,071 ORFs and 61 putative sRNAs, with each ORF represented by 14 60-mer nucleotide probes.  The fluorescence intensity for each probe was measured and subjected to robust multiarray averaging, which included adjustment for the background intensity, log2 transformation, quantile normalization and median polishing, and a robust estimated mean value was determined for each ORF and putative sRNA on the array.

first: Xilan

last: Yu

first: Steven

last: Lund

first: Russell

last: Scott

first: Jessica

middle: W

last: Greenwald

first: Angela

last: Records

first: Dan

last: Nettleton

last: Lindow

first: Dennis

last: Gross


title: Study of Cj0138 function in Campylobacter jejuni

first: Bruce

last: Pearson

summary: In order to study the function of the Campylobacter jejuni Cj0138 gene, a series of experiments were carried out. Three strains were constructed: a Cj0138 knockout strain, a strain where the Cj0138 knockout was complemented in trans, and a strain with a second copy over-expressing Cj0138 from an fdxA promoter. The transcriptomes of these were all compared to the wild-type strain. The arrays are all from RNA isolated in mid-exponential growth from independent biological replicates.

first: Johanna

last: Meier

first: Andre

last: Fischer

first: Francis

last: Mulholland

first: Ulf

last: Gobel

first: Arnoud

last: van Vliet

first: Stefan

last: Bereswill

first: Markus


title: Differential expression analysis of HFF cells in G0 phase compared to cells in G1 [TileShuffle]

status: Public on Dec 18 2012

city: Leipzig

first: Kristin

last: Reiche

address: Perlickstr. 1

department: Diagnostics

institute: Fraunhofer Institute for Cell Therapy and Immunology

summary: Whole transcriptome differential expression analysis of HFF cells on Affymetrix Human Tiling 1.0 array set. Cells were synchronised by serum starvation and transcriptome-wide changes occurring at the transition from G0 phase to G1 phase detected. Expression data and fold changes were processed with our new permutation approach TileShuffle variant B.

overall_design: We analyzed one Affymetrix Human Tiling 1.0R set each for HFF cells in G0 phase and cells in G1 phase

first: Levin

last: Böhlig

first: Christian

last: Otto

first: Antje

last: Kretzschmar

first: Friedemann

last: Horn

first: Jörg

last: Hackermüller

first: Kurt

last: Engeland


title: Cross species hybridization of human cancer cells co-cultured with mouse astrocytes and fibroblasts (Illumina human-6)

first: Sangbae

last: Kim

overall_design: Total RNAs were extracted from co-cultured cells and hybridized to human microarray and mouse microarrays to detect human cell and mouse cell specific gene expression data.

first: Eun

last: Park

first: Ju-Seog

last: Lee

first: Isaiah

last: Fidler

first: Sun-Jin


title: Genotyping of paired samples of normal colon and colon adenocarcinoma to estimate copy-number alterations

city: Moscow

first: Vladimir

last: Naumov

address: Malaya Pirogovskaya 1a

department: Molecular Biology

country: Russia

institute: Research Institute of Physico-Chemical Medicine

summary: 22 pairs of normal colon\colon adenocarcinoma samples were genotyped using Illumina HumanOmni1-Quad BeadChip to estimate copy number alterations

overall_design: Genomic DNA of 22 colon adenocarcinoma samples and 22 corresponding normal colon samples were genotyped using Illumina HumanOmni1-Quad BeadChip to estimate copy number alterations.

first: Eduard

last: Generozov


title: DNA methylation data from human lymphoblasts [NimbleGen]

status: Public on Dec 28 2012

city: Iowa City

first: Jeffrey

last: Plume

address: 500 Newton Rd.

department: Psychiatry

institute: University of Iowa

summary: DNA methylation profiling of IAS subjects

overall_design: Lymphoblasts RNA isolated from Iowa Adoption Study participants to compare the relationship between DNA methylation and gene expression on a genome-wide scale

first: Robert

last: Philibert


title: Differential expression analysis of HFF cells in G0 phase compared to cells in G1 [TAS]

summary: Whole transcriptome differential expression analysis of HFF cells on Affymetrix Human Tiling 1.0 array set. Cells were synchronised by serum starvation and transcriptome-wide changes occurring at the transition from G0 phase to G1 phase detected. Expression data and fold changes were processed with Tiling Array Software (TAS).


title: Expression analysis of HFF cells in G1 phase [TileShuffle]

summary: Whole transcriptome expression analysis of HFF cells on Affymetrix Human Tiling 1.0 array set. Cells were synchronised by serum starvation and transcriptome-wide expression in G1 phase. Expression data were processed with our new permutation approach TileShuffle.

overall_design: We analyzed one Affymetrix Human Tiling 1.0R set


title: Expression analysis of HFF cells in G0 phase [MAT]

summary: Whole transcriptome expression analysis of HFF cells on Affymetrix Human Tiling 1.0 array set. Cells were synchronised by serum starvation and transcriptome-wide expression in G0 phase. Expression data were processed with MAT (Johnson et al., "Model-based analysis of tiling-arrays for ChIP-chip." Proc Natl Acad Sci USA, 103:12457-62, 2006.).


title: Expression analysis of HFF cells in G0 phase using TAS

summary: Whole transcriptome expression analysis of HFF cells on Affymetrix Human Tiling 1.0 array set. Cells were synchronised by serum starvation and transcriptome-wide expression in G0 phase. Expression data were processed with Tiling Array Software (TAS).


title: Expression analysis of HFF cells in G1 phase using TAS

summary: Whole transcriptome expression analysis of HFF cells on Affymetrix Human Tiling 1.0 array set. Cells were synchronised by serum starvation and transcriptome-wide expression in G1 phase. Expression data were processed with Tiling Array Software (TAS).


title: Coral thermal tolerance: tuning gene expression to resist thermal stress

status: Public on Nov 29 2012

first: Anthony

middle: John

last: Bellantuono

department: Biological Sciences

institute: Florida International University

summary: Thermal history plays a role in the response of corals to subsequent heat stress. Prior heat stress can have a profound impact on later thermal tolerance, but the mechanism for this plasticity is not clear. The understanding of gene expression changes behind physiological acclimatization is critical in forecasts of coral health in impending climate change scenarios. Acropora millepora fragments were preconditioned to sublethal bleaching threshold stress for a period of 10 days; this prestress conferred bleaching resistance in subsequent thermal challenge, in which non-preconditioned coral bleached. Using microarrays, we analyze the transcriptomes of the coral host, comparing the bleaching-resistant preconditioned treatment to non-preconditioned and control treatments.

overall_design: This experiment compared host gene expression of Acropora millepora across control, non-preconditioned, and preconditioned treatments. Fragments were sampled prior to preconditioning (Day 4), following 10 days of thermal preconditioning (Day 20), and after two (Day 23), four (Day 25), and eight days (Day 29) of 31°C thermal challenge. The analysis implements 45 arrays, representing 5 sampling points of three treatments (n=3).

first: Mauricio

last: Rodriguez-Lanetty


title: Identification of autoantigens recognized by the 2F5 and 4E10 broadly neutralizing HIV-1 antibodies

status: Public on Dec 03 2012

city: Durham

first: Guang

last: Yang

address: DUMC 3010

institute: Duke University

summary: Many human monoclonal antibodies that neutralize multiple clades of HIV-1 are polyreactive and bind avidly to mammalian autoantigens. Indeed, the generation of neutralizing antibodies to the 2F5 and 4E10 epitopes of HIV-1 gp41 in man may be proscribed by immune tolerance since mice expressing the VH and VL regions of 2F5 have a block in B-cell development characteristic of central tolerance. This developmental blockade implies the presence of tolerizing autoantigens that are mimicked by the membrane-proximal external region of HIV-1 gp41. Here we identify human kynureninase (KYNU) and splicing factor 3b subunit 3 (SF3B3) as the primary conserved, vertebrate self-antigens recognized by the 2F5 and 4E10 antibodies, respectively. 2F5 binds the H4 domain of KYNU which contains the complete 2F5 linear epitope (ELDKWA). 4E10 recognizes a conformational epitope of SF3B3 that is strongly dependent on hydrophobic interactions. Opossums carry a rare KYNU H4 domain that abolishes 2F5 binding, but retain all SF3B3 4E10 epitopes. Immunization of opossums with HIV-1 gp140 induced extraordinary titers of serum antibody to the 2F5 ELDKWA epitope but little or nothing to the 4E10 determinant. Identification of structural motif shared by vertebrates and HIV-1 provides direct evidence that immunological tolerance can impair humoral responses to HIV-1.

overall_design: The invitrogen protoarray that contains >9,400 recombinant human proteins was used to identify self-ligands that are recognized by broadly neutralizing HIV-1 antibodies 2F5 and 4E10. An isotype-matched human myeloma protein (151K, Southern Biotech) was used as control.

first: Garnett

last: Kelsoe


title: Response of quiescent human fibroblasts to miR-22 overexpression

status: Public on Dec 07 2012

city: Austin

first: Vishy

last: Iyer

address: 2500 Speedway Dr. MBB 3.212

department: Molecular Biosciences

institute: University of Texas at Austin

summary: Quiescent human fibroblasts (2091) were transfected with 100nM mature miR-22 RNA duplexes.  Cells were collected 24 hours after miR-22 transfection.

overall_design: 4 biological replicates were run, one for each of the 4 dual channel arrays.  Each biological replicate included a miR-22 transfection sample and a control transfection sample

first: Damon

last: Polioudakis

first: Akshay

last: Bhinge

first: Vishwanath


title: Differential expression analysis of HFF cells in G0 phase compared to cells in G1 [MAT]

first: Kristin

last: Reiche

summary: Whole transcriptome differential expression analysis of HFF cells on Affymetrix Human Tiling 1.0 array set. Cells were synchronised by serum starvation and transcriptome-wide changes occurring at the transition from G0 phase to G1 phase detected. Expression data and fold changes were processed with MAT (Johnson et al., "Model-based analysis of tiling-arrays for ChIP-chip." Proc Natl Acad Sci USA, 103:12457-62, 2006.).

first: Levin

last: Böhlig

first: Christian

last: Otto

first: Antje

last: Kretzschmar

first: Friedemann

last: Horn

first: Jörg

last: Hackermüller

first: Kurt


title: Expression analysis of HFF cells in G0 phase [TileShuffle]

summary: Whole transcriptome expression analysis of HFF cells on Affymetrix Human Tiling 1.0 array set. Cells were synchronised by serum starvation and transcriptome-wide expression in G0 phase. Expression data were processed with our new permutation approach TileShuffle.

last: Engeland


title: High-throughput microRNA (miRNAs) arrays in pancreatic cancer

status: Public on Nov 22 2012

city: Amsterdam

first: Elisa

last: Giovannetti

address: De Boelelaan 1117

department: Medical Oncology

institute: VUmc

summary:
Background: Only a subset of radically-resected pancreatic ductal adenocarcinoma (PDAC) patients benefit from chemotherapy, and identification of novel prognostic factors is warranted. Recently miRNAs emerged as diagnostic biomarkers and innovative therapeutic targets, while high-throughput arrays are opening new opportunities to evaluate whether they can also predict clinical outcome.   The present study evaluated whether comprehensive miRNA expression profiling correlated with overall survival (OS) in resected PDAC patients.

Methodology/Principal Findings: High-resolution miRNA profiles were obtained with the Toray’s 3D-GeneTM miRNA chip, detecting more than 1200 types of human miRNA. RNA was isolated from paraffin-embedded primary tumors of 26 radically resected stage-pT3N1 homogeneously treated patients (adjuvant gemcitabine 1000mg/m2/day, days-1/8/15, every 28days), carefully selected according to their outcome (OS<12 vs. OS>30 months, i.e. short/long-OS). Highly stringent statistics included t-test, distance matrix with Spearman-ranked correlation, and iterative approaches. Unsupervised hierarchical analysis revealed that PDAC specimens clustered according to their short/long-OS classification, while the feature selection algorithm RELIEF identified the top-4 discriminating miRNAs between the two groups. These miRNAs target more than 1500 transcripts, including 169 targeted by two or more of these miRNAs. MiR-211 emerged as the best discriminating miRNA, with significantly higher expression in long- vs. short-OS patients. The expression of this miRNA was subsequently assessed by quantitative-PCR in an independent cohort of laser microdissected tumors from 60 resected stage-pT3N1 PDAC patients treated with the same gemcitabine regimen. Patients with low miR-211 expression according to median value had a significantly shorter median OS (14.8, 95%CI=13.1-16.5, vs. 25.7 months, 95%CI=16.2-35.1, log-rank P=0.004). Multivariate analysis demonstrated that low miR-211 expression was an independent factor of poor prognosis (hazard ratio 2.3, P=0.03) after adjusting for all the factors influencing outcome.

overall_design: 19 samples, duplicated gene spots

first: Arjan

last: van der Velde

first: Niccola

last: Funel

first: Enrico

last: Vasile

first: Vittorio

last: Perrone

first: Leticia

last: Leon

first: Nelide

last: De Lio

first: Amir

last: Avan

first: Sara

last: Caponi

first: Luca

last: Pollina

first: Heelo

last: Sudo

first: Alfredo

last: Falcone

first: Daniela

last: Campani

first: Ugo

last: Boggi

first: Godefridus

last: Peters


title: Integrative analysis reveals relationships of genetic and epigenetic alterations in osteosarcoma [gene expression]

status: Public on Dec 06 2012

city: Oslo

first: Leonardo

middle: A.

last: Meza-Zepeda

address: Ullernchausseen 70

department: Dept. of Tumor Biology

institute: The Norwegian Radium Hospital

summary: Osteosarcomas are the most common primary malignant tumours of bone, and almost all conventional osteosarcomas are high-grade tumours showing complex genomic aberrations. We have integrated genome-wide genetic and epigenetic profiles from the EuroBoNeT panel of 19 human osteosarcoma cell lines based on microarray technologies. The cell lines showed complex patterns of DNA copy number changes, where copy number gains were significantly associated with gene-rich regions of the genome and losses with gene-poor areas. Integration of the datasets showed that the mRNA levels were regulated by either alterations in DNA copy number or DNA methylation. Using a recurrence threshold of 6/19 (> 30 %) cell lines, 348 genes were identified as having alterations of two data types (gain or hypo-methylation/over-expression, loss or hyper-methylation/under-expression). These genes are involved in embryonic skeletal system development and morphogenesis, as well as remodelling of extracellular matrix. Several genes were hyper-methylated and under-expressed compared to normal osteoblasts, and expression could be reactivated by demethylation using 5-Aza-2’-deoxycytidine treatment for all four genes tested. Globally, there was as expected a significant positive association between gain and over-expression, loss and under-expression as well as hyper-methylation and under-expression, but gain was also associated with hyper-methylation and under-expression, suggesting that hyper-methylation may oppose the effects of increased copy number for some genes. Integrative analysis of genome-wide genetic and epigenetic alterations identified mechanistic dependencies and relationships between DNA copy number and DNA methylation in terms of regulating mRNA expression levels in osteosarcomas, contributing to better understanding of osteosarcoma biology.

overall_design: Comparison of gene expression patterns in 19 osteosarcoma cell lines and 6 normal samples (osteoblasts and bones)

first: Stine

last: Kresse

first: Halfdan

last: Rydbeck

first: Magne

last: Skårn

first: Heidi

middle: M

last: Namløs

first: Ana

last: Barragan-Polania

first: Anne-Marie

last: Cleton-Jansen

first: Knut

last: Liestøl

first: Eivind

last: Hovig

first: Ola

last: Myklebost


title: A human genome-wide screen for regulators of clathrin-coated vesicle formation

status: Public on Dec 01 2012

city: Cambridge

first: Patrycja

last: Kozik

address: Hills Road

department: Cambridge Institute for Medical Research

institute: University of Cambridge

summary:
Clathrin-mediated endocytosis is essential for a wide range of cellular functions. We used a multi- step siRNA-based screening strategy to identify novel regulators of the first step of clathrin- mediated endocytosis, formation of clathrin-coated vesicles (CCVs) at the plasma membrane. A primary genome-wide screen identified 334 hits that caused accumulation of CCV cargo on the cell surface. A secondary screen identified 92 hits that inhibited cargo uptake and/or altered the morphology of clathrin-coated structures. The hits include components of four functional complexes: coat proteins, V-ATPase subunits, spliceosome-associated proteins, and acetyltransferase subunits. Electron microscopy revealed that V-ATPase depletion caused the cell to form aberrant non-constricted clathrin-coated structures at the plasma membrane. The V- ATPase knockdown phenotype was rescued by addition of exogenous cholesterol, indicating that the knockdown blocks clathrin-mediated endocytosis by preventing cholesterol from recycling from endosomes back to the plasma membrane.
The microarray analysis was performed to test whether the siRNA targets are expressed in the cell lines used in the screen.

overall_design: For the microarray analysis of gene expression, the two cell lines used in the study were analyzed in duplicate: HeLa-YXXΦ and HeLa-FXNPXY (Hela-M cells expressing a CD8-YXXΦ and CD8-FXNPXY constructs respectively). YXXΦ and FXNPXY are motifs for clathrin-mediated endocytosis.

first: Margaret

middle: S

last: Robinson


title: Recruitment of MYC to target genes in ramos and mutu3 cells

status: Public on Nov 27 2012

city: San Francisco

first: Huimin

last: Geng

address: 513 Parnassus Ave., MSB HSW 1201

department: Department of Laboratory Medicine

institute: UCSF

summary: Follicular lymphomas and diffuse large B-cell lymphomas have markedly different biological phenotypes and yet all originate from mature, germinal center B-cells. We hypothesized that alterations in DNA methylation patterning might help explain the clinical heterogeneity of these diseases. We report that intra- and inter-individual patient heterogeneity in cytosine methylation is associated with disease severity, and that methylation heterogeneity originates in germinal centers and is amplified during disease progression. Abnormal methylation patterns differ between chromosomal regions and depend on local gene density and the methylation status of neighboring genes. Lymphomagenic transcriptional regulators, such as BCL6, MYC and EZH2, perturb DNA methylation in a target gene-specific manner. Furthermore, aberrant epigenetic states – especially hypomethylation – tend to spread along DNA in a non-specific manner while insulator elements like CTCF inhibit such spreading. Our findings suggest mechanisms through which altered cytosine methylation contributes to the distinct phenotypes of tumors derived from mature B-cells.

overall_design:
Identification of MYC target genes in Burkitt lymphomas by ChIP-on-chip. MYC ChIP-on-chip was done in two Burkitt Lymphoma (BL) cell lines (ramos and mutu3) in duplicate.

This submission represents the ChIP-chip component of the study.

first: Subhajyoti

last: De

first: Rita

last: Shaknovich

first: Markus

last: Riester

first: Olivier

last: Elemento

first: Matthias

last: Kormaksson

first: Yanwen

last: Jiang

first: Bruce

last: Wollcock

first: Nathalie

last: Johnson

first: Jose

last: Polo

first: Randy

middle: D

last: Gascoyne

first: Ari

last: Melnick

first: Franziska

last: Michor


title: Expression analysis of HFF cells in G1 phase [MAT]

first: Kristin

last: Reiche

summary: Whole transcriptome expression analysis of HFF cells on Affymetrix Human Tiling 1.0 array set. Cells were synchronised by serum starvation and transcriptome-wide expression in G1 phase. Expression data were processed with MAT (Johnson et al., "Model-based analysis of tiling-arrays for ChIP-chip." Proc Natl Acad Sci USA, 103:12457-62, 2006.).

first: Levin

last: Böhlig

first: Christian

last: Otto

first: Antje

last: Kretzschmar

first: Friedemann

last: Horn

first: Jörg

last: Hackermüller

first: Kurt

last: Engeland