title: Paternal poly(ADP-ribose) metabolism modulates retention of inheritable sperm histones and early embryonic gene expression [PJ34_sperm_MNaseb]

status: Public on Aug 30 2014

city: Logan

first: Ralph

last: Meyer

state: UT

address: 4700 Old Main Hill

department: School of Veterinary Medicine

institute: Utah State University

summary: To achieve the extreme nuclear condensation necessary for sperm function, most histones are replaced with protamines during spermiogenesis in mammals.  Mature sperm retain only a small fraction of nucleosomes, which are, in part, enriched on gene regulatory sequences, and recent findings suggest that these retained histones provide epigenetic information that regulates expression of a subset of genes involved in embryo development after fertilization.  We addressed this tantalizing hypothesis by analyzing two mouse models exhibiting abnormal histone positioning in mature sperm due to impaired poly(ADP-ribose) (PAR) metabolism during spermiogenesis and identified altered sperm histone retention in specific gene loci genome-wide using MNase digestion-based enrichment of mononucleosomal DNA.  We then set out to determine the extent to which expression of these genes was altered in embryos generated with these sperm.  For control sperm, most genes showed some degree of histone association, unexpectedly suggesting that histone retention in sperm genes is not an all-or-none phenomenon and that a small number of histones may remain associated with genes throughout the genome.  The amount of retained histones, however, was altered in many loci when PAR metabolism was impaired.  To ascertain whether sperm histone association and embryonic gene expression are linked, the transcriptome of individual 2-cell embryos derived from such sperm was determined using microarrays and RNA sequencing.  Strikingly, a moderate but statistically significant portion of the genes that were differentially expressed in these embryos also showed different histone retention in the corresponding gene loci in sperm of their fathers.  These findings provide new evidence for the existence of a linkage between sperm histone retention and gene expression in the embryo.

overall_design: Mnase sensitivity of sperm DNA, indicating nucleosomal, not protamine, packaging was altered in mice by manipulating poly(ADP-ribose) metabolism in adult males using a specific PARP inhibitor for 6 weeks. Abnormal sperm nucleosomal organization of males analyzed by these tiling arrays was compared with differential gene expression in 2 cell embryos fathered by these males analyzed by separate gene expression arrays and RNA sequencing.

first: Motomasa

last: Ihara

first: Mirella

middle: L

last: Meyer-Ficca

first: N

last: Leu

first: Shilpa

last: Rao

first: Fan

last: Li

first: Brian

middle: D

last: Gregory

first: Irina

last: Zalenskaya

first: Richard

last: Schultz


title: High density and limiting nitrogen response in rice

status: Public on Aug 24 2014

city: Guelph

first: Max

last: Misyura

state: ON

address: 50 stone rd

department: Department of Cellular and Molecular Biology

country: Canada

institute: University of Guelph

summary: Physiological changes underlying high density stress were examined in Oryza sativa plants over the course of a life cycle by assessing differences in gene expression.  Moreover, the nitrogen limitation was examined in parallel with high density stress to gain a better understanding of physiological responses specific to high density stress.

overall_design: RNA was extracted from 21 and 31 days old plants.  The plants were grown under four conditions: sufficient nitrogen (10mM N) and low density (six plants per bin), limiting nitrogen (3mM N) and low density, sufficient nitrogen and high density (40 plants per bin), limiting nitrogen and high density.  Three biological replicates were sampled from each growth condition.

first: M

first: D

last: Guevara

first: S

last: Subedi

last: Hudson

first: P

last: McNicholas

first: J

last: Colasanti

middle: J

last: Rothstein


title: The G-protein Alpha Subunit Gsα Is A Tumor Suppressor In Sonic Hedgehog-driven Medulloblastoma [Copy number analysis]

city: Cincinnati

last: Lu

state: OH

address: 3333 Burnet Ave

department: CBDI

country: USA

institute: Cincinnati Children's Hospital Medical Center

type: Genome variation profiling by genome tiling array

summary: Medulloblastoma, the most common malignant pediatric brain tumor, is highly heterogeneous with distinct molecular subtypes and cellular origins. Although current treatments improve survival rates, patients suffer severe treatment-related side effects and often relapse of tumors carrying resistance mutations, underscoring an urgent need for alternative targeted therapies. Currently, the genetic alterations underlying this disease are not fully understood. Here we identify GNAS, encoding the G-protein Gs-alpha, as a potent tumor suppressor gene in medulloblastoma. GNAS specifically defines a subset of aggressive Sonic Hedgehog (Shh)-group medulloblastomas. Gnas loss-of-function in distinct lineage progenitors of the developing hindbrain suffices to initiate medulloblastoma. We find that Gs-alpha is highly enriched at primary cilia of granule neuron precursors and suppresses Shh signaling not only by regulating classic cAMP-dependent pathway but also controlling ciliary trafficking of Smoothened. Concurrent cAMP elevation and Smoothened inhibition robustly arrests tumor cell growth in Gnas mutants. We further reveal oligodendrocyte progenitors as a novel cellular origin for anatomically-distinct Shh-associated medulloblastomas. Together, we identify a previously unrecognized tumor suppressor function of Gs-alpha in medulloblastoma partially mediated through inhibiting Shh signaling, and uncover Gs-alpha as a molecular link across disparate cells of origin among Shh-group medulloblastomas, pointing to G- protein modulation as a potential therapeutic avenue.

overall_design: We isolated genomic DNAs from the cerebellum of adult wildtype mice and tumor tissue from individual GFAP-Gnas or Olig1-Gnas mutants and performed the Copy number variation analysis.


title: Microarray experment to identify genes differentially expressed in the DDT resistant 91R strain of Drosophila

status: Public on Aug 31 2014

city: Salt Lake City

first: Carl

last: Thummel

department: Human Genetics

institute: University of Utah

summary: Transcriptional profiling of mature adult 91R males compared to 91C males.

overall_design: RNA was extracted from mature adult 91R or 91C strain of Drosophila melanogaster and subjected to micraoarray analysis.

middle: R

last: Misra

first: C

middle: S

first: G

last: Lam


title: A genetic approach of wine yeast fermentation capacity in nitrogen-starvation reveals the key role of nitrogen signaling.

status: Public on Sep 12 2014

city: Montpellier cedex1

first: Jean-Luc

last: Legras

address: 2, place Viala

department: UMR1083, Science pour l'Oenologie

country: France

institute: INRA

summary:
In conditions of nitrogen limitation, Saccharomyces cerevisiae strains differ in their fermentation capacities, due to differences in their nitrogen requirements. A population of 133 individuals from the F2 segregant population from a cross between two strains with different nitrogen requirements for efficient fermentation has been analyzed for their fermentation capacities. Two groups of 15 strains were defined, one group of High and one of Low Nitrogen requirement. These two groups are compared in order to detect genomic regions involved in the differences of nitrogen requirement.

We used a custom isothermal array that has been designed for the detection of SNP at 6317 position on RM11.1a genome sequence
http://www.broadinstitute.org/annotation/genome/saccharomyces_cerevisiae.3/Home.html)
and obtained from the comparison with the genome sequence of strain Saccharomyces P3-D5.

overall_design:
Each parental strain and each pool of segregant (Low Nitrogen Requirement LNR and High Nitrogen Requirement HNR) are hybridized in duplicates on the array (8*15k from Agilent). Each DNA pool is labeled with Cy3. A pool of both parental strains, labeled in Cy5, is used as a reference for each hybridization.

Please note that the array is built on pairs of probes, with each probe specific to one parent. S o that we calculate the hybridization differences between each probes in a pair which is proportional to the allele frequencies. The manner the probes used for the analysis are coded such as:
SACE-rm11-Chr03_1000412_1000394_1000422_r_P3
SACE-rm11-Chr03_1000412_1000395_1000422_f_RM11
where SACE-rm11 is the reference genome, Chr03_1000412 the SNP location, 1000394_1000422 the coordinates of the probe, and P3 or RM11 the name of the ancestral allele.

The processed_data.txt contains the further-processed log ratio data between the P3 specific probe and the RM11 specific probe along with the data description.

first: Claire

last: Brice

first: Isabelle

last: Sanchez

first: Frédéric

last: bigey

first: Jean-luc

first: Bruno

last: Blondin


title: Regulation of Activation-Associated mRNA and MicroRNA Accumulation Rates during Monocyte-to-Macrophage Differentiation

status: Public on Aug 21 2014

city: Iowa City

first: Joel

last: Graff

state: IA

address: 400 EMRB

department: Internal Medicine

institute: University of Iowa

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

overall_design: Refer to individual Series


title: Regulation of Activation-Associated Transcripts Accumulation Rates during Monocyte-to-Macrophage Differentiation

summary: We profiled macrophage activation-associated transcripts using TaqMan assays in a Fluidigm 48.48 Gene Expression Array to identify transcripts with expression levels that were affected by differences in culturing conditions during monocyte-to-macrophage differentiation.

overall_design: 48 samples: 12 sample types for 4 different human donors


title: NRSF mediated epigenetic mechanisms of ion channel dysfunction in experimental temporal lobe epilepsy [Control vs. Kainate, scrambled ODNs]

status: Public on Aug 12 2014

city: Irvine

first: Shawn

last: McClelland

state: CA

address: 19182 Jamboree

department: Anatomy & Neurobiology

institute: UC Irvine

summary: Oligodeoxynucleotides used to prevent NRSF binding to NRSE containing genes were utilized to prevent many kainate induced status epilepticus changes in gene expression.

overall_design: Total RNA recovered from CA1 of hippocampus of rats receiving scrambled, and saline(controls) or kainate injections (induced status epilepticus)

first: Tallie

middle: Z

last: Baram


title: The G-protein Alpha Subunit Gsα Is A Tumor Suppressor In Sonic Hedgehog-driven Medulloblastoma [Microarray expression]

first: Richard

summary:
Medulloblastoma, the most common malignant pediatric brain tumor, is highly heterogeneous with distinct molecular subtypes and cellular origins. Although current treatments improve survival rates, patients suffer severe treatment-related side effects and often relapse of tumors carrying resistance mutations, underscoring an urgent need for alternative targeted therapies. Currently, the genetic alterations underlying this disease are not fully understood. Here we identify GNAS, encoding the G-protein Gs-alpha, as a potent tumor suppressor gene in medulloblastoma. GNAS specifically defines a subset of aggressive Sonic Hedgehog (Shh)-group medulloblastomas. Gnas loss-of-function in distinct lineage progenitors of the developing hindbrain suffices to initiate medulloblastoma. We find that Gs-alpha is highly enriched at primary cilia of granule neuron precursors and suppresses Shh signaling not only by regulating classic cAMP-dependent pathway but also controlling ciliary trafficking of Smoothened. Concurrent cAMP elevation and Smoothened inhibition robustly arrests tumor cell growth in Gnas mutants. We further reveal oligodendrocyte progenitors as a novel cellular origin for anatomically-distinct Shh-associated medulloblastomas. Together, we identify a previously unrecognized tumor suppressor function of Gs-alpha in medulloblastoma partially mediated through inhibiting Shh signaling, and uncover Gs-alpha as a molecular link across disparate cells of origin among Shh-group medulloblastomas, pointing to G- protein modulation as a potential therapeutic avenue.
Transgenic medulloblastoma mouse models were analyzed by Affymetrix Mouse Gene 1.1 ST Array in order to determine their molecular subgroup.

overall_design: Tumors extracted from hGFAP:GnasCKO and Oligo1:GnasCKO transgenic mice were analyzed in 8 replicates each, together with normal mouse cerebellum.

first: Xuelian

last: He

first: Ying

last: Chen

first: Fanghui

first: Haibo

last: Wang

first: Liguo

last: Zhang

first: Yang

last: Yu

first: Yaqi

last: Deng

first: Tom

last: Hu

first: Yong

last: Xia

first: Yiping

last: Hou

first: Dennis

middle: K

last: Burns

first: Marc

last: Remke

first: David

last: Shih

first: Xiaochong

last: Wu

first: Lee

last: Weinstein

first: Scott

last: Pomeroy

last: Gilbertson

first: Joshua

middle: B

last: Rubin

first: Robert

last: Wechsler-Reya

first: Michael

last: Taylor

first: Q


title: Alanine scan of potential linear epitopes of Klebsiella pneumoniae MGH 78578

status: Public on Aug 22 2014

city: Potsdam

first: Sebastian

last: Hoppe

address: Am Mühlenberg 13

department: Bioanalytics and Biosensorics

country: Germany

institute: Fraunhofer Institute for Cell Therapy and Immunology

summary: Sequences of 11 amino acids belonging to the KPN_00363 protein and KPN_00459 protein from Klebsiella pneumoniae MGH 78578 which was previously identified as potentially immunogenic was analyzed via alanine scanning to narrow down the significant amino acid residues within the sequence.

overall_design: 26 peptides, two representing the original sequences, 22 peptides with each residue replaced by alanine (or glycin, if the original sequence contained alanine) as well as two related peptides were synthesized on microarrays by JPTs Pepstar Technology. For each microarray, nine replicates for each peptide were spotted. The microarray was seperated into three incubation chambers by the ProPlate 3-well module (Grace Biolabs) to allow for incubation with different antibodies in parallel. For specific interaction rabbit polyclonal IgG to K. pneumoniae (Abcam ab20947) was used, while non-specific binding to the epitope sequences was checked using rabbit polyclonal IgG to E. coli (Abcam ab137967) and S. enterica (Abcam ab35156).


title: Paternal poly(ADP-ribose) metabolism modulates retention of inheritable sperm histones and early embryonic gene expression [Parg(110)_KO_sperm_MNase]

first: Ralph

middle: G

last: Meyer

type: Genome binding/occupancy profiling by genome tiling array

overall_design: Mnase sensitivity of sperm DNA, indicating nucleosomal, not protamine, packaging was altered in mice by manipulating poly(ADP-ribose) metabolism in adult males using Parg gene disruption (Parg(110)-/-). Abnormal sperm nucleosomal organization of males analyzed by these tiling arrays was compared with differential gene expression in individual 2 cell embryos fathered by these males analyzed in separate expression microarrays.

first: Motomasa

last: Ihara

first: Mirella

last: Meyer-Ficca

first: N

middle: A

last: Leu

first: Shilpa

last: Rao

first: Fan

last: Li

first: Brian

last: Gregory

first: Irina

last: Zalenskaya

first: Richard

middle: M

last: Schultz


title: Response to drought and salt stress in leaves of poplar (Populus alba × P. glandulosa): Expression profiling by oligonucleotide microarray analysis

city: Suwon

first: seokyung

last: yoon

address: Onjeong-ro

country: South Korea

institute: KFRI

summary: We performed that comprehensive identification of genes responsible for stress tolerance by analyzing the whole-genome expression profiles of poplar (Populus alba × P. glandulosa) leaves exposed to drought and salt stresses. Examination at the molecular level how this tree species responds to drought and salt stresses by regulating the expression of genes involved in signal transduction, transcriptional regulation, and stress responses.

overall_design: Genome-wide analysis was conducted in poplar leaves exposed to drought and salt stresses.The plants were acclimated in soil and grown for 6 weeks in controlled conditions in a growth room (16 h light; light intensity, 150 μmol m-2sec-1; 24°C). Plants with a height of about 15 cm were separately exposed to either drought or salt stress. Up- and down-regulated genes were identified, and their putative functions are discussed.

first: Seo-Kyung

last: Yoon

first: Eung-Jun

last: Park

first: Young-Im

last: Choi

first: Eun-Kyung

last: Bae

first: Joon-Hyeok

last: Kim

first: So-Young

first: Kyu-Suk

last: Kang

first: Hyoshin

last: Lee


title: Meta-Analyses of Dehalococcoides mccartyi Strain 195 Transcriptomic Profiles Identify a Respiration Rate-Related Gene Expression Transition Point and Interoperon Recruitment of a Key Oxidoreductase Subunit

status: Public on Aug 11 2014

city: Ithaca

first: Cresten

last: Mansfeldt

state: NY

address: 220 Hollister Hall

institute: Cornell University

summary:
A cDNA-microarray was designed and used to monitor the transcriptomic profile of Dehalococcoides mccartyi strain 195 (in a mixed community) respiring various chlorinated organics, including chloroethenes and 2,3-dichlorophenol. The cultures were continuously fed in order to establish steady-state respiration rates and substrate levels. The organization of array data into a clustered heat map revealed two major experimental partitions. This partitioning in the data set was further explored through
principal component analysis. The first two principal components separated the experiments into those with slow (1.6 plus or minus 0.6 M Cl- per h) and fast (22.9 plus or minus 9.6 M Cl- per h) respiring cultures. Additionally, the transcripts with the highest loadings in these principal components were identified, suggesting that those transcripts were responsible for the partitioning of the experiments. By analyzing the transcriptomes (n = 53) across experiments, relationships among transcripts were identified, and hypotheses about the relationships between electron transport chain members were proposed. One hypothesis, that the hydrogenases Hup
and Hym and the formate dehydrogenase-like oxidoreductase (DET0186–DET0187) form a complex (as displayed by their tight clustering in the heat map analysis), was explored using a nondenaturing protein separation technique combined with proteomic sequencing. Although these proteins did not migrate as a single complex, DET0112 (an FdhB-like protein encoded in the Hup operon) was found to comigrate with DET0187 rather than with the catalytic Hup subunit DET0110. On closer inspection of the genome annotations of all Dehalococcoides strains, the DET0185-to-DET0187 operon was found to lack a key subunit, an FdhB-like protein. Therefore, on the basis of the transcriptomic, genomic, and proteomic evidence, the place of the missing subunit in the DET0185-to-DET0187 operon is likely filled by recruiting a subunit expressed from the Hup operon (DET0112).

overall_design: 53 arrays total: 3 biological replicates of PCE High, 2 biological replicates of PCE High Inhibited, 3 biological replicates of PCE Low, 3 biological replicates of PCE Half Butyrate, 2 biological replicates of PCE Lactate, 2 biological replicates of PCE Butyrate, 2 replicates of hydrogen control, 2 biological replicates of PCE hydrogen, 2 biological replicates of PCE + no donor, 2 biological replicates of PCE + yeast extract, 2 biological replicates of PCE + fermented yeast extract, 2 biological replicates of each 3 feed rates for PCE (6 total), 2 biological replicates of each 3 feed rates for TCE (6 total), 2 biological replicates of each 3 feed rates for dCE (6 total), 3 biological replicates for dCE 10, 2 biological replicates for 2 feed rates for Chlorophenols (4 total), and 3 decay samples.

first: Annette

last: Rowe

first: Gretchen

last: Heavner

first: Ruth

last: Richardson


title: Multinodality vaccination against clade C SHIV: partial protection against mucosal challenges with a heterologous tier 2 virus

status: Public on Aug 14 2014

city: Atlanta

first: Siddappa

last: Byrareddy

address: 101 Woodruff circle

department: Pathology & Laboratory Medicine

institute: Emory Univeristy

summary: We sought to test whether vaccine-induced immune responses could protect rhesus macaques (RMs) against upfront heterologous challenges with an R5 simian-human immunodeficiency virus, SHIV-2873Nip. We immunized the RMs with recombinant Env proteins heterologous to the challenge virus. For induction of immune responses against Gag, Tat, and Nef, we explored a strategy of immunization with overlapping synthetic peptides (OSP). The immune responses against Gag and Tat were finally boosted with recombinant proteins. The vaccinees and a group of ten control animals were given five low-dose intrarectal (i.r.) challenges with SHIV-2873Nip. All controls and seven out of eight vaccinees became systemically infected; there was no significant difference in viremia levels of vaccinees vs. controls. Prevention of viremia was observed in one vaccinee which showed strong boosting of virus-specific cellular immunity during virus exposures.  The protected animal showed no challenge virus-specific neutralizing antibodies in the TZM-bl or A3R5 cell-based assays and had low level ADCC activity after the virus exposures. Microarray data strongly supported a role for cellular immunity in the protected animal. Our study represents a case of protection against heterologous tier 2 SHIV-C by vaccine-induced, virus-specific cellular immune responses.

overall_design: For the protected RM, blood was collected before vaccination, on the day of first virus exposure and six weeks after last virus challenge. Lymph node and rectal pinch biopsies were performed before vaccination and six weeks after last virus challenge. Blood was collected in tempus tubes and processed immediately according to the manufacturer’s instructions and stored at -80C. The biopsy specimens were cut into small pieces and immediately placed into RNAlater solution (Qiagen, Valencia, CA) and also stored at -80C. Total RNA from blood, lymph node and rectal biopsies was extracted using RNAeasy extraction kits (Qiagen, Valencia, CA). cDNA labeling, hybridization, staining and scanning were performed according to the manufacturer’s instructions (Affymetrix, Santa Clara, CA) for rhesus gene expression arrays.

first: Samir

last: Lakhashe

first: Girish

last: Hemashettar

last: Ruprecht


title: MicroRNA signature predict chemotherapy response in patients with advanced colorectal cancer

city: Seville

first: Sonia

last: Molina-Pinelo

address: Avda. MAnuel Siurot s/n

country: Spain

institute: IBIS

summary: The aim of our study was to evaluate the ability of miRNA expression patterns to predict chemotherapy response in a cohort of 39 patients with metastatic colorectal carcinoma

overall_design: To define miRNA signature, samples were obtained from tumor tissue samples of 39 patients . Patients were divided into responders or non-responders according to tresponse treatment with a chemotherapy regimen that included fluoropyrimidines and either oxaliplatin or irinotecan .Tumor response was evaluated by conventional methods according to the standard RECIST 1.0 criteria: a complete response (CR) was defined as the disappearance of all measurable and evaluable evidence of disease; a partial response (PR) was defined as a > 30% decrease in the sum of the longest diameters of target lesions;  stable disease (SD) was considered if the tumor burden decreased less than 30% or increased less than 20%; and progressive disease (PD) was indicated by a >20% increase in the sum of the longest diameters of target lesions or the appearance of any new lesion.   Patients were classified according to best response to chemotherapy in two groups: those that achieved an objective response (Responders [R]: CR + PR) and those that did not (Non-responders [NR]: SD + PD). Mature human miRNA expression was detected and quantified using the TaqMan® Low Density Arrays (TLDA). The Human MicroRNA Card Set v2.0 array is a two card set containing a total of 384 TaqMan® MicroRNA Assays per card to enable accurate quantification of 667 human microRNAs, all catalogued in the miRBase database. Expression of target miRNAs was normalized in relation to the expression of MammU6.  Cycle threshold (Ct) values were calculated using the SDS software v.2.3 using automatic baseline settings and a threshold of 0.2. Relative quantification of miRNA expression was calculated by the 2−ΔCt method (Applied Biosystems user bulletin no. 2 (P/N 4303859)).

first: Rocio

last: Suarez

first: Purificación

last: Estevez

first: Maria

last: Pastor

first: Amancio

last: Carnero

first: Luis

last: Paz-Ares

first: Rocío

last: García Carbonero


title: Coordinated regulation of photosynthesis in rice increases yield and tolerance to environmental stress.

city: Fayetteville

first: Andy

last: Pereira

state: Arkansas

address: 115 Plant Science Building

department: Crop, Soil and Environmental Sciences

institute: University of Arkansas

summary:
Plants capture solar energy and atmospheric carbon dioxide (CO2) through photosynthesis, which is the primary component of crop yield, and needs to be increased considerably to meet the growing global demand for food. Environmental stresses, which are increasing with climate change, adversely affect photosynthetic carbon metabolism (PCM) and limit yield of cereals such as rice (Oryza sativa) that feeds half the world. To study the regulation of photosynthesis, we developed a rice gene regulatory network and identified a transcription factor HYR (HIGHER YIELD RICE) associated to PCM, which on expression in rice enhances photosynthesis under multiple environmental conditions, determining a morpho-physiological program leading to higher grain yield (GY) under normal, drought and high temperature stress conditions. We show HYR is a master regulator, directly activating photosynthesis genes, cascades of transcription factors and other downstream genes involved in PCM and yield stability under drought and high temperature environmental stress conditions.
To assess the role of increased HYR expression in rice, whole-genome microarrays were used to generate gene expression profiles of rice cultivar Nipponbare transformed with an overexpression construct of the HYR gene (Loc_Os03g02650) under control of the CaMV 35S promoter, along with control wild-type (WT) lines.

overall_design: Two biological replicate samples each from the HYR and WT-control lines were profiled using rice whole-genome microarrays.

first: Arjun

last: Krishnan


title: Translational profiling through biotinylation of tagged ribosomes in zebrafish

status: Public on Aug 07 2014

city: Bad Nauheim

first: Michael

middle: Patrick

last: Housley

state: Hessen

address: Ludwigstr. 43

department: Developmental Genetics

institute: Max Planck Institute

summary: Phenotypic heterogeneity within a population of cells of the same cell type is a common theme in metazoan development. Apprehending complex developmental and physiological processes critically relies on our ability to probe the expression profile of these genetically defined cell sub-populations. Current strategies rely on cell enrichment based on tandem or simultaneous evaluation of multiple intersecting markers starting from a heterogeneous cellular suspension. The extensive tissue manipulations required for single-cell suspension generation, as well as the complexity of the required equipment, inherently complicates these approaches. Here, we propose an alternative methodology based on a genetically encoded system in the model organism Danio rerio (zebrafish). In transgenic fish, we take advantage of the combinatorial biotin transfer system where polysome-associated mRNAs are selectively recovered from cells expressing both a tagged ribosomal subunit, Rpl10a and the bacterial biotin ligase, BirA. We have applied this technique to skeletal muscle development, identifying genes with novel regulation and have developed tools for highly specific gene expression profiling during vertebrate development.

overall_design: Translational profiling of zebrafish skeletal muscle during 4 time points (21, 24, 27, 34 hours post fertilization)

middle: P

first: Benoit

last: Vanhollebeke


title: Standing at the gateway to Europe - the genetic structure of Western Balkan populations based on autosomal and haploid markers

city: Tartu

first: Mait

last: Metspalu

address: Riia 23

country: Estonia

institute: Estonian Biocentre

type:
Genome variation profiling by SNP array
SNP genotyping by SNP array

summary: Here we present genome-wide high-coverage genotyping data on a panel of 75 human samples from Western Balkan region, Europe, that are used in addition to public data in studing the genetic variation of Southern Europe that was sequenced to the avwerage depth of 1X.

overall_design: 70 samples were analysed with the Illumina platform Human660W-Quad v1.0 Genotyping BeadChip and are described herein.

first: Richard

last: Villems

first: Lejla

last: Kovacevic

first: Damir

last: Marjanovic

first: Kristiina

last: Tambets

first: Tuuli

last: Reisberg


title: Telomeric ORFs (TLOs) in Candida spp. encode Mediator subunits that regulate distinct virulence traits

status: Public on Aug 06 2014

city: Dublin

first: Gary

middle: P.

last: Moran

address: Lincoln Place

department: Dental Science

country: Ireland

institute: Trinity College Dublin

summary:
Analysis of the interaction of Candida dubliniensis protein Tlo1p with DNA by ChIP-chip
HA-tagged Tlo1p in Candida dubliniensis was used to identify Tlo1 interacting regions of DNA in global ChIP-chip analysis

overall_design: Experiment was carried out on cells grown at 30˚C in YEPD broth


title: MNase-chip of maize B73

city: Tallahassee

first: Daniel

last: Vera

state: FL

address: 319 Stadium Drive

department: Biological Science

institute: Florida State University


title: MNase-chip of maize B73 immature ears and seedlings

summary: The eukaryotic nuclear genome is organized into the fundamental units of chromatin, nucleosomes. The positions and biochemical states of nucleosomes on DNA can regulate protein-DNA interactions, and in turn influence DNA-templated events. Despite the increasing number of genome-wide maps of nucleosome position, how global changes in nucleosome position relate to changes in gene expression is poorly understood. Using micrococcal nuclease (MNase) to map nucleosome positions, we show that in the maize genome, nucleosome occupancy signals are remarkably uniform between different tissues, whereas particular genomic regions are highly susceptible to variation. We demonstrate that much of this variation is associated with the degree to which chromatin is digested with MNase. Using high-density DNA microarrays, we exploited this digestion-linked variation to identify protein footprints in the maize genome that are hypersensitive to MNase digestion, a method we term Differential Nuclease-Sensitivity profiling (DNS-chip). Hypersensitive footprints were enriched at the 5’ and 3’ ends of genes, associated with gene-expression levels, and significantly overlapped with conserved noncoding sequences and the binding sites of the homeobox transcription-factor Knotted1, suggesting a functional role in genome regulation. We also found that the tissue-specific regulation of gene expression was linked to tissue-specific hypersensitive footprints in gene promoters. These results demonstrate the value of DNS-chip for revealing biochemical features of nucleosome organization that correlate with gene expression levels and colocalize with functional DNA elements. This approach to chromatin profiling should be broadly applicable to other species and should shed light on how chromatin organization might influence protein-DNA interactions and genome regulation.

overall_design: Comparison of buffers and concentrations of Mnase in immature ears and seedlings

first: Hank

middle: W

last: Bass


title: Regulation of Activation-Associated MicroRNA Accumulation Rates during Monocyte-to-Macrophage Differentiation

first: Joel

last: Graff

summary: We profiled miRNA expression using TaqMan TLDA assays to identify miRNAs with expression levels that were affected by differences in culturing conditions during monocyte-to-macrophage differentiation.

overall_design: 9 samples: 3 sample types for 3 different human donors


title: MNase-chip of maize B73 immature ears, seedling shoots, and seedling roots

overall_design: Comparison of two to three different concentrations of Mnase in immature ears, seedling shoots, and seedling roots.


status: Public on Aug 02 2014

city: Leiden

first: Jeroen

last: Corver

address: Albinusdreef 2

department: Medical Microbiology

country: Netherlands

institute: LUMC

summary: Transcriptional profiling of an HtrA proteases knock-out compared to wild type on two different time points; logarithmic growth phase and stationary growth phase

overall_design: 3 Biological replicates per time point, two arrays

first: W

last: Smits

first: D

last: Bakker

first: Anne

last: de Jong

first: Oscar

last: Kuipers

first: Ed

last: Kuijper

first: Gillian

last: Douce

first: Anthony

last: Buckley


title: Genome-wide DNA methylation changes in skeletal muscle between young and middle-aged pigs

city: Ya'an

first: long

last: jin

state: Sichuan

address: Ya’an, Xinkang Road #46 Sichuan

country: China

institute: Sichuan Agricultural University

summary:
Background
Age-related physiological, biochemical and functional changes in mammalian skeletal muscle have been shown to begin at the mid-point of the lifespan. However, the underlying changes in DNA methylation that occur during this turning point of the muscle aging process have not been clarified. To explore age-related genomic methylation changes in skeletal muscle, we employed young (0.5 years old) and middle-aged (7 years old) pigs as models to survey genome-wide DNA methylation in the longissimus dorsi muscle using a methylated DNA immunoprecipitation sequencing approach.

Results
We observed a tendency toward a global loss of DNA methylation in the gene-body region of the skeletal muscle of the middle-aged pigs compared with the young group. We determined the genome-wide gene expression pattern in the longissimus dorsi muscle using microarray analysis and performed a correlation analysis using DMR (differentially methylated region)-mRNA pairs, and we found a significant negative correlation between the changes in methylation levels within gene bodies and gene expression. Furthermore, we identified numerous genes that show age-related methylation changes that are potentially involved in the aging process. The methylation status of these genes was confirmed using bisulfite sequencing PCR. The genes that exhibited a hypomethylated gene body in middle-aged pigs were over-represented in various proteolysis and protein catabolic processes, suggesting an important role for these genes in age-related muscle atrophy. In addition, genes associated with tumorigenesis exhibited aged-related differences in methylation and expression levels, suggesting an increased risk of disease associated with increased age.

Conclusions
This study provides a comprehensive analysis of genome-wide DNA methylation patterns in aging pig skeletal muscle. Our findings will serve as a valuable resource in aging studies, promoting the pig as a model organism for human aging research and accelerating the development of comparative animal models in aging research.

overall_design:
We collected the longissimus dorsi muscles tissue from Jinhua pigs which aged 0.5 year and seven years and study the genome-wide DNA methylation difference and the genome-wide gene expression profile between the two age periods.

This submission represents transcriptome component of study.

first: Long

last: Jin


title: MicroRNA profile of tumorigenic cells during formation of pulmonary adenocarcinoma

city: chongqing

first: guo

middle: zhen

last: zhao

address: Cancer Institute of PLA, Xinqiao Hospital, Third Military Medical University, Chongqing, China

summary: Study designed to obtain microRNA profile of tumorigenic Sca-1+CD34+ cells during the formation of pulmonary adenocarcinoma. After intranasal infection with adenovirus CRE (Ad-Cre), lung adenocarcinoma was identified pathologically in Lox-stop-lox Kras (LSL-Kras) G12D mice. Sca-1+CD34+ cells were sorted by flow cytometry and tested for the tumor-initiating ability to undergo self-renewal and differentiation. MiRNA profile was obtained from the microarray and further confirmed by qRT-PCR.The function of miRNAs was predicted bioinformatically, and miR-294 was verified to explore its relationship with tumor migration and invasion.

platform_organism:
Mus musculus
Murid betaherpesvirus 1
Murid gammaherpesvirus 4

overall_design: We taken lung tissues from the LSL-Kras G12D mouse on the 0, 15th, 30th days, and defined as Group A, B, C respectively. These 3 samples were analyzed. Each kind of probe has 4 repeat spots on the microarray. Total RNA are harvested using TRIzol (Invitrogen) and RNeasy mini kit (QIAGEN). All processing conducted at the Kang Cheng Biological chip Company Limited.  Microarray was synthesized using μParafloTM microfluidic chip technology, and the information of miRNA probe sequence of each region was obtained from the database of Sanger miRBase version 11.0.

first: Zhen-guo

last: Zhao

first: Jun-yu

first: An-mei

last: Zhang

first: Lu-Ping

first: Xin-xin

last: Wang

first: Jian-guo

last: Sun

first: Zheng-tang

last: Chen


title: Genome-wide promoter methylation analysis of human melanocytes and melanoma cell lines

status: Public on Aug 01 2014

city: Copenhagen

first: Christina

last: Dahl

address: Strandboulevarden 49

country: Denmark

institute: Danish Cancer Society

type: Methylation profiling by genome tiling array

summary: DNA methylation profiling of human melanocytes and melanoma cell lines. Goal was to identify hypermethylated gene promoters in melanoma

overall_design: Genomic DNA from 4 human melanoma cell lines and normal human epidermal melanocytes was subjected to methylated DNA immunoprecipitation (MeDIP) and hybridized to Agilent's G4489A Human Promoter ChIP-on-Chip Set 244K

first: Johanne

last: Lade-Keller

first: Rikke

last: Riber-Hansen

first: Torben

last: Steiniche

first: Per

last: Guldberg


title: A PU.1 suppressive target gene, metallothionein-1G, inhibits retinoic acid-induced NB4 cell differentiation

city: Sagamihara-City

first: Shinichiro

last: Takahashi

state: Kanagawa-Ken

address: 1-15-1, kitasato, minami-ku

country: Japan

institute: Kitasato University

summary: We recently revealed that myeloid master regulator PU.1 directly represses metallothionein (MT)-1G through its epigenetic activity, but the functions of MT-1G in myeloid differentiation remain unknown. To clarify this, we established MT-1G-overexpressing acute promyelocytic leukemia NB4 (NB4MTOE) cells, and investigated whether MT-1G functionally contributes to all-trans retinoic acid (ATRA)-induced NB4 cell differentiation. Real-time PCR analyses demonstrated that the inductions of CD11b and CD11c and reductions in myeloperoxidase and c-myc by ATRA were attenuated in NB4MTOE cells. Since G1 arrest is a hallmark of ATRA-induced NB4 cell differentiation, we observed a decrease in G1 accumulation, as well as decreases in p21WAF1/CIP1 and cyclin D1 inductions, by ATRA in NB4MTOE cells. Nitroblue tetrazolium (NBT) reduction assays revealed that the proportions of NBT-positive cells were decreased in NB4MTOE cells in the presence of ATRA. Microarray analyses showed that the changes in expression of several myeloid differentiation-related genes (GATA2, azurocidin 1, pyrroline-5-carboxylate reductase 1, defensin-4, C-X3-C motif receptor 3, matrix metallopeptidase -8, S100 calcium-binding protein A12, neutrophil cytosolic factor 2 and oncostatin M) induced by ATRA were disturbed in NB4MTOE cells. Collectively, overexpression of MT-1G disturbs the proper differentiation of myeloid cells. The present study provides evidence that expression analysis of MT-1G in acute promyelocytic leukemia patients may be a good prediction marker to estimate the efficacy of ATRA.

overall_design:
Cell culture and generation of MT-1G-overexpressing cells:   To generate MT-1G-overexpressing cells and their control cells, the MT-1G expression vector and its parental pcDNA 3.1/myc-His(-) version A vector (Invitrogen) were transfected using a CLB-Transfection device (Lonza, Basel, Switzerland). NB4 clones stably transfected with the vectors were isolated by limiting dilution and selection with 400 µg/ml of neomycin in RPMI (Gibco BRL, Rockville, MD) containing 10% heat-inactivated fetal bovine serum (HIFBS). Cells were cultured under 5% CO2 at 37°C in a humidified atmosphere.
Microarray analyses:   MT-1G-overexpressing (NB4MTOE) cells and their control cells were seeded at a density of 1×105 cells/ml and treated with 1 µM all-trans retinoic acid (ATRA). The cells were harvested after 72 h and total cellular RNA was isolated from control (NB4pcDNA4, 6, 7) cells and NB4MTOE (NB4MT22, 23, 25) cells using an RNA Mini Purification Kit (Qiagen, Miami, FL) according to the manufacturer’s protocol. Aliquots containing 10 µg of RNA from each sample of control cells were mixed and used as controls. Similarly, 10 µg of RNA from each sample of NB4MTOE cells were mixed and used as NB4MTOE cells. The samples were subjected to microarray analyses using a CodeLink Human 54K Whole Genome Bioarray (Filgen, Nagoya, Japan).

first: Naomi

last: Hirako

first: Hiroko

last: Nakano


title: Key hub and bottleneck genes differentiate the macrophage response to virulent and attenuated Mycobacterium bovis

first: David

middle: E

last: MacHugh

address: University College Dublin, Belfield

department: College of Agriculture, Food Science and Veterinary Medicine

institute: University College Dublin

summary: Mycobacterium bovis is an intracellular pathogen that causes tuberculosis in cattle. Following infection, the pathogen resides and persists inside host macrophages by subverting host immune responses via a diverse range of mechanisms. Here, a high-density bovine microarray platform was used to examine the bovine monocyte-derived macrophage transcriptome response to M. bovis infection relative to infection with the attenuated vaccine strain, M. bovis Bacille Calmette–Guérin. Differentially expressed genes were identified (adjusted P-value ≤ 0.01) and interaction networks generated across an infection time course of 2, 6 and 24 h. The largest number of biological interactions was observed in the 24 h network, which exhibited small-worldscale-free network properties. The 24 h network featured a small number of key hub and bottleneck gene nodes, including IKBKE, MYC, NFKB1 and EGR1 that differentiated the macrophage response to virulent and attenuated M. bovis strains, possibly via the modulation of host cell death mechanisms. These hub and bottleneck genes represent possible targets for immunomodulation of host macrophages by virulent mycobacterial species that enable their survival within a hostile environment.

overall_design: Affymetrix GeneChip® Bovine Genome Arrays were used to examine gene expression from a paired comparison of bovine monocyte-derived macrophages (MDM) after in vitro challenge with Mycobacterium bovis versus M. bovis BCG across a time series of 2 hr, 6 hr and 24 hr post-challenge.

first: Kate

last: Killick

last: Magee

first: Stephen

last: Park

first: Maria

last: Taraktsoglou

first: John

last: Browne

first: Kevin

last: Conlon

first: Nicolas

middle: C

last: Nalpas

first: Eamonn

last: Gormley

middle: V

last: Gordon

first: Karsten

last: Hokamp


title: Global gene expression during early differentiation of Xenopus (Silurana) tropicalis gonad tissues.

status: Public on Jul 31 2014

city: Duluth

first: Jonathan

middle: Thomas

last: Haselman

state: MN

address: 6201 Congdon Blvd.

department: ORD

institute: US EPA

summary: African clawed frog Xenopus sp. is used extensively for developmental biology and toxicology research.  Amid concerns of environmental pollutants disrupting endocrine systems and causing altered reproductive development in wildlife, eco-toxicology research has led to a focus on linking molecular initiating events to population-level effects.  As such, efforts to better understand reproductive development at the molecular level in these model species are warranted.  To that end, transcriptomes were characterized in differentiating Xenopus tropicalis gonad tissues at Nieuwkoop and Faber (NF) stage 58 (pro-metamorphosis), NF66 (completion of metamorphosis), one week post-metamorphosis (1WPM), and two weeks post-metamorphosis (2WPM).  Differential expression analysis between tissue types at each developmental stage revealed a substantial divergence of ovary and testis transcriptomes starting between NF58 and NF66; transcriptomes continued to diverge through 2WPM.  Generally, testis-enriched transcripts were expressed at relatively constant levels, while ovary-enriched transcripts were up-regulated within this developmental period.  Functional analyses of differentially expressed transcripts allowed linkages to be made between their putative human orthologues and specific cellular processes associated with differentiating gonad tissues.  In ovary tissue, genetic programs direct germ cells through meiosis to the diplotene stage when maternal mRNAs are transcribed and trafficked to oocytes for translation following fertilization.  In the testis, gene expression is consistent with connective tissue development, tubule formation, and germ cell support (Leydig and Sertoli cells).  This dataset exhibited remarkable consistency with transcript profiles previously described in gonad tissues across species, and emphasizes the universal importance of certain transcripts for germ cell development and preparation of these tissues for reproduction.

overall_design: Four developmental time-points were considered for global expression analysis: NF58 (pro-metamorphosis), NF66 (completion of metamorphosis), one week post-metamorphosis (1WPM), and two weeks post-metamorphosis (2WPM).  Gonad tissues were time-matched and stage-matched, so collection occurred on a single day for each developmental time-point and all animals used were from the same spawn.  For the 1WPM and 2WPM time-points, all animals reached NF66 on the same day and were separated from the rest of the spawn until sample collection one and two weeks later respectively.  On the day of tissue collection, animals were developmentally staged (Nieuwkoop and Faber, 1994) and euthanized by submersion in a lethal concentration of tricane methanesulfonate ([MS-222], Argent Chemical Laboratories, Redmond, WA, USA) buffered with sodium bicarbonate. Gonad tissues were then excised independently of any other tissues (i.e. “pure” gonad tissue) and transferred to a separate vial for each individual, homogenized in lysis buffer from an RNeasy micro kit (Qiagen Inc., Valencia, CA, USA), and immediately frozen on dry ice until samples could be moved to -80oC storage.  Tail or toe tissue was also collected from each individual for genetic sex determination using methods previously described by Olmstead et al. (2010).  Once genetic sex was determined for each individual, testes and ovaries were randomly assigned to pools of four individuals (eight gonads per pool) to make a total of five pools of testis tissue and five pools of ovary tissue at each developmental time-point, with the exception of NF58 which had four pools of testis tissue and four pools of ovary tissue (38 total sample pools).

middle: T

first: Allen

last: Olmstead

first: Sigmund

middle: J

last: Degitz


title: Human HepG2 cells: control DMSO vs. K7174-treated

city: Kamakura

first: Satoshi

last: Kondo

state: Kanagawa

address: Tebiro 6-10-1

department: New Projects Development Division

institute: Toray Industries,Inc.

summary: Transcriptional profiling of human HepG2 cells comparing control DMSO-treated cells with K7174-treated cell

overall_design: Two-condition experiment, DMSO-HepG2 vs. K7174-HepG2 cells. Biological replicates: 1 control, 1 treated, independently grown and harvested. One replicate per array.

first: Tohru

last: Fujiwara

first: Hideo

last: Harigae


title: Transcriptome signatures for robustness of Lactococcus lactis MG1363

city: Ede

first: Annereinou

last: Dijkstra

address: Kernhemseweg 2

institute: NIZO food research

summary: This study describes a transcriptome-phenotype matching approach in which the starter L. lactis MG1363 was fermented under a variety of conditions that differed in the levels of oxygen and/or salt, as well as the fermentation pH and temperature. Samples derived from these fermentations in the exponential phase of bacterial growth were analyzed by full-genome transcriptomics and the assessment of heat and oxidative stress phenotypes. Variations in the fermentation conditions resulted in up to 1000-fold differences in survival during heat and oxidative stress. More specifically, aeration during fermentation induced protection against heat stress, whereas a relatively high fermentation temperature resulted in enhanced robustness towards oxidative stress. Concomitantly, oxygen levels and fermentation temperature induced differential expression of markedly more genes when compared with the other fermentation parameters. Correlation analysis of robustness phenotypes and gene expression levels revealed transcriptome signatures for oxidative and/or heat stress survival, including the metC-cysK operon involved in methionine and cysteine metabolism. To validate this transcriptome-phenotype association we grew L. lactis MG1363 in the absence of cysteine which led to enhanced robustness towards oxidative stress.   Conclusions   Overall, we demonstrated the importance of careful selection of fermentation parameters prior to industrial processing of starter cultures. Furthermore, established stress genes as well as novel genes were associated with robustness towards heat and/or oxidative stress. Assessment of the expression levels of this group of genes could function as an indicator for enhanced selection of fermentation parameters resulting in improved robustness during spray drying. The increased robustness after growth without cysteine appeared to confirm the role of expression of the metC-cysK operon as an indicator of robustness and suggests that sulfur amino acid metabolism plays a pivotal role in oxidative stress survival.

sample_organism: Lactococcus cremoris subsp. cremoris MG1363

overall_design: two connected loops, both containing samples derived on a single day (sample 1-6, sample 7-13)

middle: R

first: Wynand

last: Alkema

first: Marjo

last: Starrenburg

first: Jeroen

last: Hugenholtz

first: Sacha

last: van Hijum

first: Peter

last: Bron


title: Differential gene expression in the oxyntic and pyloric mucosa of the young pig

status: Public on May 14 2014

city: bologna

first: PAOLO

middle: o

last: BOSI

state: BOLOGNA

address: Viale Fanin, 46

department: DISTAL

country: Italy

institute: UNIVERSITY OF BOLOGNA

summary:
The stomach is often considered a single compartment, but morphological differences among different areas are well known. Oxyntic mucosa (OXY)  is primarily equipped for acid secretion, while it is not enough clear if gastric functional control are shared with other areas.
We used microarrays to detail the differential gene expression related to the different gastric part in the young pig.  After slaughtering OXY and pyloric (PYL) mucosa were obtained in 7 already weaned pigs.

overall_design: The analysis of whole mRNA transcript expression was done by Affymetrix©Porcine Gene 1.1 ST array strips, a Robust Multichip Analysis was performed on the CEL files, and Transcripts ID’s were associated to 13,406 Human gene names, based on Sus scrofa Ensemble

first: Michela

last: Colombo

first: Davide

last: Priori

first: Paolo

last: Trevisi

last: Bosi


title: Somatic copy number alterations associated with populations and clinical characteristics in ovarian clear cell adenocarcinoma

status: Public on Jun 10 2014

city: Tokyo

first: Mitsuyoshi

last: Urashima

address: Nishishimbashi 3-25-8, Minato-ku

institute: Jikei University School of Medicine

summary:
Background: Clinical characteristics of ovarian clear cell adenocarcinoma (CCC) include 1) higher incidence among Japanese, 2) association with endometriosis, 3) poor prognosis in advanced stage, 4) higher incidence of thrombosis as complication. We applied high resolution comparative genomic hybridization (CGH) array to screen somatic copy number alterations (SCNAs) associated with these clinical characteristics.
Methods: We conducted a prospective cohort study. DNA obtained from tumors was assayed by array comparative genomic hybridization using Agilent Whole Human Genome 244K.

overall_design: 117 tumor samples were analyzed by Agilent-G4411B Human Genome CGH Microarray Kit 244A. Log2 Ratio (tumor sample DNA/normal DNA) were compared between Japanese and non-Japanese, between patients with thrombosis and without thrombosis, between patients with endometriosis and without endometriosis, among patients sensitive to, intermediate to and resistant to the chemotherapy, among FIGO stages, between relapsed and not relapsed, between survived and not survived.

first: Aikou

last: Okamoto


title: aCGH data of 5 cases of Hepatosplenic T-cell lymphoma

status: Public on May 24 2014

city: Leuven

first: Julio

last: Finalet

address: Herestraat 49

country: Belgium

institute: KULeuven

summary: Hepatosplenic T-cell lymphoma (HSTL) is an aggressive lymphoma cytogenetically characterized by isochromosome 7q   [i(7)(q10)], of which the molecular consequences remain unknown. We report here results of an integrative genomic and transcriptomic (expression microarray and RNA-sequencing) study of six HSTL cases with i(7)(q10) and three cases with ring 7   [r(7)], a rare variant aberration. Using high resolution array CGH, we prove that HSTL is characterized by the common loss of a 34.88 Mb region at 7p22.1p14.1 (3506316-38406226 bp) and duplication/amplification of a 38.77 Mb region at 7q22.11q31.1 (86259620-124892276 bp). Our data indicate that i(7)(q10)/r(7)-associated loss of 7p22.1p14.1 is a critical event in the development of HSTL, while gain of 7q sequences drives progression of the disease and underlies its intrinsic chemoresistance. Loss of 7p22.1p14.1 does not target a postulated tumor suppressor gene but unexpectedly enhances the expression of CHN2 from the remaining 7p allele, resulting in overexpression of β2-chimerin and dysregulation of a pathway involving RAC1 and NFATC2 with a cell proliferation response. Gain of 7q leads to increased expression of critical genes, including RUNDC3B, PPP1R9A and ABCB1, a known multidrug resistance gene. RNA-sequencing did not identify any additional recurrent mutations or gene fusions, suggesting that i(7)(q10) is the only driver event in this tumor. Our study confirms the previously described gene expression profile of HSTL and identifies a set of 24 genes, including three located on chromosome 7 (CHN2, ABCB1 and PPP1R9A), distinguishing HSTL from other malignancies

overall_design: Total genomic DNA was isolated from fresh frozen lymphoma samples using standard procedures. Genomic profiling, following the manufacturer’s protocols, was performed using the Agilent 244k (www.agilent.com) (5 cases)

middle: F

last: Ferreiro

first: Leila

last: Rouhigharabaei

first: Helena

last: Urbankova

first: Jo-Anne

last: van der Krogt

first: Lucienne

last: Michaux

first: Shashirekha

last: Shetty

first: Laszlo

last: Krenacs

first: Thomas

last: Tousseyn

first: Pascale

last: De Paepe

first: Anne

last: Uyttebroeck

first: Gregor

last: Verhoef

first: Tom

last: Taghon

last: Vandenberghe

first: Jan

last: Cools

first: Iwona

last: Wlodarska


title: Verfication of immunogenic nature by microarray screening

status: Public on Feb 02 2014

city: Potsdam

first: Sebastian

last: Hoppe

address: Am Mühlenberg 13

institute: Fraunhofer Institute for Cell Therapy and Immunology

summary: Screening of 14 novel proteins derived from Klebsiella pneumoniae MGH 78578 identified prior via screening of cDNA libraries. The full-length proteins were attached using a specific HaloTag to their corresponding ligand surface, HaloLink. Screening was performed using two different polyclonal antibodies to Klebsiella pneumoniae (Acris AP00792PU-N and Abcam ab20947) and detection achieved by Goat polyclonal to rabbit IgG conjugated with Chromeo-546 (Abcam ab60317). In order to assess their potential immungenic nature and rank the proteins investigated, comparative analysis using already described antigens from K. pneumoniae were used in the assay.

overall_design: Each microarray was seperated into different incubation chambers using the 16-well ProPlate (Grace Biolabs) multi-well gaskets. As positive references ompA and mdh were used. For negative control gapA was used and the crude lysates of the expression host (Acella E.coli) and buffer were spotted as well.Samples and controls were spotted with five replicates each. Incubation was performed using different antibodies reactive to K. pneumoniae.


title: Identification of differentially expressed long non-coding RNAs in bladder cancer

status: Public on Feb 28 2014

city: Sheffield

first: Stefan

last: Peter

address: Beech Hill Road

department: Oncology

country: United Kingdom

institute: The University of Sheffield

summary: As various data suggest that lncRNAs are important in human cancer, we hypothesized that they play a role in urothelial carcinogenesis. To test this hypothesis we analysed 83 normal and malignant urothelial samples using NCode™ Human Non-coding RNA Microarrays for differentially expressed lncRNAs with potential regulatory functions in urothelial cell cancer (UCC). We identified global changes in lncRNA expression that reflect the disease phenotype. We then performed explorative analysis (siRNA gene knock-down and loss-of-function studies) of selected species and identified those with potential prognostic roles. Quantitative real-time PCR was used to validate the microarray findings.

overall_design: Total RNA was extracted from urothelial samples from 57 patients with UCC (23 low-grade NMI, 14 high-grade NMI and 20 invasive tumours) and from 26 disease free controls.

first: James

last: Catto


title: Gene expression in the whole brains of two spontaneously hypertensive rat strains at 3 and 6 weeks of age

status: Public on Jan 24 2014

city: Suita

first: Daisuke

last: Okuzaki

state: Osaka

address: Yamadaoka 3-1

department: Immunology Frontier Research Center

institute: Osaka univ.

summary: We examined gene expression profiles in the rat whole brains using genome-wide microarray technology, and determined gene expression profiles in 3 rat strains: normotensive WKY, spontaneously hypertensive rats (SHR), and stroke-prone SHR (SHRSP). To identify candidate genes involved in the genesis of hypertension in the SHR strains, we compared the gene expression levels at 3 and 6 weeks of age, isolated 407 genes showing a more than 4-fold increase or a less than 1/4-fold decrease.

overall_design: The rat whole brains derived from normotensive WKY, spontaneously hypertensive rats (SHR), and stroke-prone SHR (SHRSP) were　examined. Each strain was run in triplicate.

first: Yuko

last: Watanabe

first: Momoko

last: Yoshida

first: Kazunori

last: Shimada

first: Hiroshi

last: Nojima

first: Hiromichi

last: Yamanishi


status: Public on Aug 05 2014

city: Zunyi

first: Lin

last: Xu

state: Guizhou

address: 201 Dalian Road

department: Immunology

institute: Zunyi Medical College

summary: To detect the miRNA expression profile in CCR6+ regulatory T cells

overall_design: In this study, the total RNA was extracted from CCR6+ regulatory T cells and CCR6- regulatory T cells. Then, the expression profile of miRNA on these cells was detected by microarray.

first: Yongju

last: Li


title: Epitope Mapping of potential novel immunogenic proteins of Klebsiella pneumoniae MGH 78578

summary: A number of six proteins were selected during immunoscreening and further analyses. The proteins were divided in silico into overlapping 15-mer oligopeptides with an overlap of 11 residues. The microarrays were incubated with different antibodies to K. pneumoniae, C. jejuni and S. aureus.

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

overall_design: Each microarray was seperated into three individual incubation chambers using ProPlate 3-Well modules. Within each incubation chamber each peptide was spotted in triplicate with the controls spotted nine times each. The controls included Human-IgG, Rabbit-IgG, Mouse-IgG and Myelin Basal Protein. Each chamber was incubated independently using different polyclonal antibodies to K. pneumoniae and for specificity testing with antibodies to C. jejuni or S. aureus. Thus, samples 2_1, 2_2, 3_1 and 3_2 represent epitope mapping of three proteins and S2_5_1, S2_5_2, S2_6_1 and S2_6_2 epitope mapping of three different proteins with K. pneumoniae antibodies, while 4_1, 4_2, 5_1 and 5_2 represent specificity assays for the first set of proteins (using C. jejuni and S. aureus antibodies) and S2_1_1, S2_1_2, S2_2_1, S2_2_2 (C. jejuni AB) as well as S2_7_1, S2_7_2, S2_8_1, S2_8_2 (S. aureus AB) for the second set of proteins.


title: Comparative genomic hybridization in traditional fermentative Saccharomyces cerevisiae yeasts

status: Public on Dec 15 2013

city: Valencia

first: Clara

last: Ibáñez

address: Avenue Agustín Escardino, 7

institute: Institute of Agrochemistry and Food Technology

summary: We study the genetics, including microarray karyotyping using comparative genomic hybridization, to explore global changes in the genomic DNA of seven S. cerevisiae strains related to traditional fermentations of very different sources comparing to the sequenced S. cerevisiae laboratory strain (S288C). Our final goal is to determine the adaptive evolution of properties of biotechnological interest in Saccharomyces yeasts. Many copy number variations (CNVs) were observed, especially in genes associated to subtelomeric regions and transposon elements. Among the fermentation strains, differential CNV was observed in genes related to sugar transport and metabolism. An outstanding example of diverse CNV is the gen PUT1, involved in proline assimilation, which correlated with the adaptation of the strains to the presence of this nitrogen source in the media.

overall_design: Seven S. cerevisiae strains were obtained from natural environments and different fermentation processes. The S. cerevisiae strain S288C was used as a control for microarray hybridizations. All experiments were performed using duplicate arrays, and Cy5-dCTP and Cy3-dCTP dye-swap assays were performed to reduce dye-specific bias.

first: Roberto

last: Pérez-Torrado

first: Rosana

last: Chiva

first: Jose

last: Guillamón

first: Eladio

last: Barrio

first: Amparo

last: Querol


title: Role of an archaeal PitA transporter in the copper and arsenic resistance of Metallosphaera sedula an extreme thermoacidophile

status: Public on Jul 10 2014

city: Raleigh

first: Garrett

last: Wheaton

address: 840 Main Campus Dr. Rm 3304

department: Chemical Engineering

institute: North Carolina State University

summary: Thermomacidophilic archaea, such as Metallosphaera sedula, are lithoautotrophs that occupy metal-rich environments. In previous studies, a M. sedula mutant lacking the primary copper efflux transporter, CopA, became copper sensitive. In contrast, the basis for supra-normal copper resistance remained unclear in the spontaneous M. sedula mutant, CuR1. Here, transcriptomic analysis of copper-shocked cultures indicated that CuR1 had a unique regulatory response to metal challenge corresponding to up-regulation of 55 genes. Genome re-sequencing identified 17 confirmed mutations unique to CuR1 that were likely to change gene function. Of these, 12 mapped to genes with annotated function associated with transcription, metabolism or transport. These mutations included 7 non-synonymous substitutions, 4 insertions and 1 deletion. One of the insertion mutations mapped to pseudogene, Msed_1517, and extended its reading frame an additional 209 amino acids. The extended mutant allele was identified as a homolog of Pho4, a family of phosphate symporters that include the bacterial PitA proteins. Orthologs of this allele were apparent in related extremely thermoacidophilic species, suggesting M. sedula was naturally lacking this gene. Phosphate transport studies combined with physiologic analysis demonstrated M. sedula PitA was a low affinity high velocity secondary transporter implicated in copper resistance and arsenate sensitivity. Genetic analysis demonstrated spontaneous arsenate resistant mutants derived from CuR1 all underwent mutation in pitA and non-selectively became copper resistant. Taken together, these results point to archaeal PitA as a key requirement for the increased metal resistance of strain CuR1 and its accelerated capacity for copper bioleaching.

sample_organism:
Metallosphaera sedula
Metallosphaera sedula DSM 5348

overall_design: The study comprises 5 samples, described in detail below. WT_CuR1: Differential transcriptional response of Metallosphaera sedula DSM 5348, WT, to the supra-normal copper resistant spontaneous Metallosphaera sedula mutant, CuR1 under normal growth conditions. This experiment was done to analyze the differential transcription of WT cells compared with CuR1 cells at mid log phase. WT-15_CuR1-15: Differential transcription of Metallosphaera cells under sub-inhibitory copper challenge (2.0 mM). This experiment was done to analyze the differential transcription of Metallosphaera sedula WT and CuR1 15 minutes post copper challenge. The copper cultures were harvested 15 minutes after the shock. WT-60_CuR1-60: Differential transcription of Metallosphaera cells under sub-inhibitory copper challenge (2.0 mM). This experiment was done to analyze the differential transcription of Metallosphaera sedula WT and CuR1 60 minutes post copper challenge. The copper cultures were harvested 60 minutes after the shock. WT-15_WT-60: Differential transcription of Metallosphaera cells under sub-inhibitory copper challenge (2.0 mM). This experiment was done to analyze the differential transcription of Metallosphaera sedula WT 15 and 60 minutes post copper challenge. The copper cultures were harvested 15 and 60 minutes after the shock, respectively. CuR1-15_CuR1-60: Differential transcription of Metallosphaera cells under sub-inhibitory copper challenge (2.0 mM). This experiment was done to analyze the differential transcription of Metallosphaera sedula CuR1 15 and 60 minutes post copper challenge. The copper cultures were harvested 15 and 60 minutes after the shock, respectively.

first: Samuel

last: McCarthy

first: Chenbing

last: Ai

first: Rahul

last: Tevatia

first: Valerie

last: Eckrich

first: Robert

last: Kelly

first: Paul

last: Blum


title: Screening for novel immungenic proteins of Klebsiella pneumoniae MGH 78578

first: Sebastian

last: Hoppe

summary: The screening of a cDNA derived expression library of Klebsiella pneumoniae MGH 78578 expressed in E.coli using a fusion construct and specific HaloTag interaction to a modified surface is shown. Thus, 1536 different clones were screened including positive (ompA, mdh) and negative (pyrC, gapA) reference proteins. The goal of the screening was to identify potential novel immunogenic proteins from K. pneumoniae by selecting clones showing a high signal intensity in comparison to the known antigens used as positve markers. Afterwards, the most promising clones were sequenced to identify the gene and corresponding protein and these proteins were then investigated further. Consequently, 14 novel immunogenic proteins could be identified.

overall_design: In total 1536 (4 x 384) different lysates were spotted on different microarray slides. Each slides contained 3600 distinct spots, seperated into two compartments of 1800 spots each. Each compartment comprised quadruplicate replicates of each sample lysate with controls being analysed with more replicates. As controls we used: ompA1, ompA2 and mdh (3 x 40 replicates) as positive reference proteins, as they have been described as immunogenic before. gapA and pyrC (2 x 40 replicates) as negative reference proteins, additionally two sets of E.coli cell lysates without fusionprotein expressed, namely Acella electrocompetent cells (40 replicates) and KRX (32 replicates). Last but not least a buffer control (24 replicates) was included. Therefore, each set of replicate slides contained 376 different samples and 8 controls. Each screening was performed with three replicate slides. Consequently, a total number of 12 slides were screened (4 sets of samples x 3 replicates). For identification rabbit polyclonal antibody to K. pneumoniae (Acris AP00792PU-N) as primary and Goat polyclonal to Rabbit IgG conjugated with ChromeoTM-546 (Abcam ab60317) as secondary antibody were used. The top compartment was incubated first with primary antibody, while the bottom compartment was incubated with PBS at the same time. Afterwards both compartments were incubated with secondary antibody.


title: Chip-chip from HepG2 cells with EZH2, SUZ12 and H3K27me3

status: Public on Nov 13 2013

city: Xiamen

first: Shubin

last: Gao

address: Chengzhi building 110,Xiang'an South Road

department: Basic Medical Sciences

institute: Medical College,Xiamen University

summary:
Polycomb group (PcG) proteins including EZH2, SUZ12 and so on, which specifically catalyze trimethylation of histone 3 lysine 27 (H3K27me3), and methylated H3K27 can be recognized by other specific binding proteins to compress chromatin structure, leading to the transcriptional repression of the target genes.
To completely understand the epigenetic profile and molecular network of PcG in HCC, we performed ChIP-on-chip screens with EZH2, SUZ12 and H3K27me3 antibodies in HepG2 cells.

overall_design: Comparison of  ChIP-on-chip results from EZH2, SUZ12 and H3K27me3.

first: Bin

first: Shu-bin


title: Basonuclin-1 modulates epithelial plasticity and TGF-β1-induced loss of epithelial cell integrity [BNC1]

status: Public on Mar 01 2014

city: Oxford

first: Alexander

last: Feuerborn

address: South Parks Road

institute: Sir William Dunn School of Pathology

summary:
TGF-b1-stimulation induces an epithelial dedifferentiation-process, throughout which epithelial cell sheets disintegrate and gradually switch into fibroblastic-appearing cells (EMT-like transition). Several transcription factors, some of them being TGF-b1-responsive, are functionally involved in such a switch and affect epithelial differentiation and plasticity.
We used microarray-based gene expression profiling of mammary epithelial cells that actively undergo TGF-b1-induced epithelial dedifferentiation. Further, we determined gene expression changes in Basonuclin-1 knock-down cells in conjunction with TGF-b1-stimulation in order to determine a possible effect of Bnc1 on TGF-b1-responsive genes.

overall_design: Cells were transfected with non-silencing (control) siRNA or siRNA against Basonuclin-1 (Bnc1) for 24hrs. Subsequently, cells were treated with 5ng/ml TGF-b1 or left untreated for additional 24hrs. The experiments were performed as independent biological triplicate.

first: Daniel

last: Mathow

first: Prashant

last: Srivastava

first: Norbert

last: Gretz

first: Hermann-Josef

last: Gröne


title: Role of AHR in cardiac developmental toxicity of PAHs

status: Public on Nov 24 2014

city: Durham

first: Nishad

last: Jayasundara

state: NC

address: A346, Research Drive, LSRC

department: Nicholas School of the Environment

institute: Duke University

summary: Transcriptmic profiling of cardiac tissues in AHR2 knockdown and control zebrafish (Danio rerio) embryos exposed to BaP, FL amd BaP+FL at 2,6,12, and 18 hours post dosing

overall_design:
Two-condition experiment, AHR2 knockdown vs control knockdown, exposed to BaP, FL and BaP+FL. 3-4 replicates per time point, at four diferent time points (2,6,12 and 18 hpd)
11 raw data files were received truncated.

first: Elwood

last: Linney

first: Lindsey

last: Garner


title: Follicular lymphoma in situ and partial involvement by follicular lymphoma are clona lesions that carry the t(14;18) and lack genetic secondary alterations

status: Public on Nov 12 2013

city: Barcelona

first: Itziar

last: Salaverria

address: Rossello 153

institute: Hospital Clínic

summary: Follicular lymphoma (FL) is characterized by the t(14;18)(q32;q21), frequent numerical chromosomal alterations, and recurrent somatic mutations. However, no genetic studies are available for FL in situ (FLIS), a putative precursor lesion of FL. In this study, we analyzed cases of FLIS without manifest (m)FL, partial involvement by FL (PFL), and paired cases of FLIS and mFL to detect possible early chromosomal imbalances, as well as DNA-methylation patterns of genomic regions of selected genes. We demonstrated that paired FLIS and mFL cases are always clonally related.  FLIS and PFL have no or few secondary chromosomal imbalances detectable by copy number arrays and a lower level of gene methylation as compared to mFL. Additionally, EZH2 Tyr641 mutations were detected in a subset of both FLIS and PFL cases. In conclusion, this study provides evidence that FLIS represents a FL precursor lesion of long-lived clonal B-cells carrying the t(14;18) with no or few secondary genetic changes. The earliest secondary genetic alterations detected in FLIS are the EZH2 Tyr641 mutation and low levels of CNAs, as evidence of clonal evolution. Our data suggest that there may be more than one distinct lesion driving the progression from FLIS to manifest lymphoma.

overall_design: DNA from cases, 20 tumor samples (10 in situ Follicular lymphoma, 4 Partial infiltration folliculary lymphoma and 6 manifest FL) were analyzed with Agilent-014693 Human Genome CGH Microarray 244A platform for copy number alterations study. For cases 9-14 paired samples of in situ follicular lymphoma and manifest follicular lymphoma were analyzed. Agilent-014693 Human Genome CGH Microarray 244A arrays were performed according to the manufacturer's directions on DNA extracted from lymph nodes that were hybridized against a normal DNA (pool) of the same gender.

first: Andrea

last: Haake

first: Reiner

last: Siebert

first: Leticia

last: Quintanilla-Martinez


title: Real-time quantitative PCR analysis of 3T3-L1 cells treated with Interleukin-15 (IL-15)

status: Public on Nov 14 2014

city: Hamilton

first: Ali

last: Ashkar

state: Ontario

address: 1280 Main Street West

department: McMaster Immunology Research Center

institute: McMaster University

summary: Differentiated 3T3-L1 adipocytes were either treated 0ng/ml or 500ng/ml rmIL-15 for 24 hours (n=3/group)

overall_design: qPCR gene expression profilling performed in vitro using recombinant murine (rm)IL-15 treated (500ng/ml) and untreated (control) 3T3-L1 cells. Equal amounts of total RNA per subject were used in the assay.

first: Nicole

middle: G

last: Barra


title: Drug Synergy Screen and Network Modeling in Dedifferentiated Liposarcoma (DDLS) part 2

status: Public on Sep 24 2013

city: Cambridge

first: Martin

middle: L

last: Miller

address: Robinson Way

department: Cancer research UK, Cambridge Institute

institute: University of Cambridge

summary:
Analysis of DNA copy number variations in two DDLS tumor-derived cell lines DDLS8817 and LPS141 growing in culture in basal conditions
The goal of this DNA copy number analysis was to determine if genes used in signaling network modeling in DDLS were amplified or deleted

overall_design: Genomic DNA was isolated from asynchronously growing DDLS8817 and LPS141 cultures growing in basal conditions using the Qiagen DNAy kit.

first: Evan

last: Molinelli

first: Jayasree

middle: S

last: Nair

first: Tahir

last: Sheikh

first: Rita

last: Samy

first: Xiaohong

last: Jing

first: Qin

last: He

first: Anil

last: Korkut

first: Aimee

last: Crago

first: Samuel

last: Singer

first: Gary

middle: K

last: Schwartz

first: Chris

last: Sander


title: A Proneural to Mesenchymal Transition Mediated by NFkB Promotes Radiation Resistance in Glioblastoma

status: Public on Aug 15 2013

city: Austin

first: Brian

middle: D

last: Vaillant

state: TX

department: Neurology

institute: Seton Brain and Spine Institute

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

overall_design: Refer to individual Series


title: Copy number data from five primary human glioblastomas (frozen surgical resection)

status: Public on Aug 13 2013

city: SAN FRANCISCO

first: RAMAN

middle: PAUL

last: NAGARAJAN

address: 1450 3RD ST, ROOM HD200

department: NEUROSURGERY

institute: UCSF

summary:
DNA hypomethylation could lead to activation of alternate promoters in GBM. We profiled DNA methylation and H3K4me3 genome-wide, and also performed expression and copy number analysis on the same samples
In this dataset, we include all array CGH copy number data obtained for five GBMs. We used estimated copy number to normalize sequencing-based methylation data.

overall_design: Five total samples were analyzed.

first: Raman

middle: P

last: Nagarajan

first: Joseph

last: Costello


title: Expression and copy number data from five primary human glioblastomas


title: Cholangiocarcinoma tissues VS. corresponding normal bile duct tissues

status: Public on Jun 10 2013

city: Wuhan

first: Feng

last: Peng

state: Hubei

address: 1095 Jiefang Ave

department: Department of Biliary-Pancreatic Surgery

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

summary: To identify miRNAs differentially expressed in cholangiocarcinoma,3 human cholangiocarcinoma and their corresponding normal bile duct tissues were obtained from 3 patients after operation with postoperative pathological diagnosed perihilar or distal biliary cholangiocarcinoma

overall_design: miRNAs expression in human cholangiocarcinoma/normal bile duct samples was measured after operation.Three independent experiments were performed using different patients for each experiment.

first: Renyi

last: Qin


status: Public on Oct 31 2013

city: Berkeley

first: Morgan

middle: N

last: Price

address: 1 Cyclotron Road Mailstop 977-152

department: Physical Biosciences Division

institute: Lawrence Berkeley Lab

type: Expression profiling by genome tiling array

summary: High-resolution “tiling” expression data for Zymomonas mobilis ZM4 growing in rich and minimal media, heat-shocked, or at high ethanol

sample_organism: Zymomonas mobilis subsp. mobilis ZM4 = ATCC 31821

overall_design: One chip for each growth condition and one “genomic control” array hybridized to genomic DNA

first: Zhuchen

last: Xu

first: Jeff

middle: M

last: Skerker

first: Adam

last: Deutschbauer


title: Chip-chip from budding yeast cells with Sir3

status: Public on Jul 01 2013

city: MIAOLI COUNTY

first: GUNN-GUANG

last: LIOU

state: TAIWAN

address: 35 KEYAN ROAD, JHUNAN TOWN

department: INSTITUTE OF MOLECULAR AND GENOMIC MEDICINE

country: Taiwan

institute: NATIONAL HEALTH RESEARCH INSTITUTES

summary: Chromatin immunoprecipitation of Sir3 applied with tilling array chip ( ChIP on chip of Sir3) analysis demonstrated that Changes of conventional and dynamical Genome-wide localization of Sir3 in Saccharomyces cerevisiae during different growth stages

overall_design: comparison the genome-wide localization of Sir3 of logarithmic phase younger cells vs of stationary phase older cells

first: Gunn-Guang

last: Liou

first: Shu-Yun

last: Tung


title: Gene Expression Analysis of Fat Body of Drosophila melanogaster Subjected to Sir2 Overexpression or Dietary Restriction

status: Public on May 01 2013

city: Cologne

first: Julia

last: Hoffmann

address: Joseph-Stelzmann-Str. 9b

department: Partridge

institute: MPI for Biology of Ageing

summary: Sir2 is the most intensively discussed longevity gene in current aging research. Although the gene encoding for a NAD+-dependent histone deacetylase initially was found to extend lifespan of various organisms ranging from yeast to mammals, serious doubts regarding its role in longevity have been expressed recently. In this study, we tested whether tissue-specific overexpression of Sir2 in the adult fat body can extend lifespan when compared to genetically identical controls. We also wanted to elucidate the mechanisms by which fat body Sir2 promotes longevity by studying the phenotypic and transcriptional changes in the fat body. We found that moderate (3-fold) Sir2 overexpression in the fat body during adulthood only can promote longevity in both sexes by roughly 13 %. In addition, we obtained transcriptional profiles elicited by this overexpression and propose a role for Sir2 in lipid droplet biology especially under conditions of starvation. Furthermore, our data do not support the idea of Sir2 mediating the response to dietary restriction (DR) because transcriptional profiles of fat bodies after DR or Sir2 overexpression do not match. This study provides additional independent evidence for the concept of Sir2 as a longevity gene and as a promising pharmacological target to cure age-related diseases.

overall_design: 6 groups of sample types were included in the experiment: a) females overexpressing Sir2 in the fat body b) female controls c) males overexpressing Sir2 in the fat body d) male controls e) wildtype females subjected to DR f) wildtype females feeding on a normal diet. 3 biological replicates were included per group.

first: Thomas

last: Roeder


title: Decreased expression of key tumour suppressor microRNAs is associated with lymph node metastases in triple negative breast cancer

city: New Lambton Heights

first: Kelly

last: Kiejda

state: NSW

address: HMRI

country: Australia

institute: University of Newcastle

summary: Breast cancer is the most common malignancy that develops in women, responsible for the highest cancer-associated death rates. Triple negative breast cancers (TNBC) represent an important subtype that have an aggressive clinical phenotype, are associated with a higher likelihood of metastasis and are not responsive to current targeted therapies. miRNAs have emerged as an attractive candidate for molecular biomarkers and treatment targets in breast cancer, but their role in the progression of TNBC remains largely unexplored. This study has investigated miRNA expression profiles in 31 primary TNBC cases and in 13 lymph node metastases compared with 23 matched normal breast tissues to determine miRNAs associated with the initiation of this disease subtype and those associated with its metastasis. 71 miRNAs were differentially expressed in TNBC, the majority of which have previously been associated with breast cancer, including members of the miR-200 family and the miR-17-92 oncogenic cluster, suggesting that miRNAs involved in the initiation of TNBC are not subtype specific. However, the repertoire of miRNAs expressed in lymph node negative and lymph node positive TNBCs were largely distinct from one another. In particular, miRNA profiles associated with lymph node negative disease tended to be up-regulated, while those associated with lymph node positive disease were down-regulated and largely overlapped with the profiles of their matched lymph node metastases.

overall_design: miRNA expression profiles were examined in 31 primary TNBC cases and in 13 lymph node metastases compared with 23 matched normal breast tissues

middle: A

last: Avery-Kiejda

first: Stephen

last: Braye

first: John

last: Forbes

first: Rodney

last: Scott


title: Gene expression in the adrenal glands of two spontaneously hypertensive rat strains at 3 and 6 weeks of age

status: Public on Apr 16 2013

city: Suita

first: Daisuke

last: Okuzaki

institute: Osaka univ.

summary: We examined gene expression profiles in the rat adrenal glands using genome-wide microarray technology, and determined gene expression profiles in 3 rat strains: normotensive WKY, spontaneously hypertensive rats (SHR), and stroke-prone SHR (SHRSP). To identify candidate genes involved in the genesis of hypertension in the SHR strains, we compared the gene expression levels at 3 and 6 weeks of age, isolated 407 genes showing a more than 4-fold increase or a less than 1/4-fold decrease.

overall_design: The rat adrenal glands derived from normotensive WKY, spontaneously hypertensive rats (SHR), and stroke-prone SHR (SHRSP) were　examined. Each strain was run in triplicate.

first: Yuko

last: Watanabe

first: Momoko

last: Yoshida

first: Kazunori

last: Shimada

first: Hiroshi

last: Nojima

first: Hiromichi

last: Yamanishi


title: Genome-wide study of the adaptation of Saccharomyces cerevisiae to the proliferative stages of wine fermentation

status: Public on Apr 18 2013

city: Logroño

first: Ramon

last: Gonzalez

address: C. Madre de Dios, 51

department: Instituto de Ciencias de la Vid y del Vino

institute: Consejo Superior de Investigaciones Científicas

summary:
This work was designed to identify yeast cellular functions specifically affected by the stress factors predominating during the first stages of wine fermentation and genes required for optimal growth under these conditions. The main experimental method used was quantitative fitness analysis by means of competition experiments of whole genome barcoded yeast knock-out collections in continuous culture. This methodology allowed the identification of haploinsufficient genes and homozygous deletions resulting in growth impairment in synthetic must. However, genes identified as haploproficient or homozygous deletions resulting in fitness advantage were of little predictive power concerning optimal growth in this medium. The relevance of these functions for enological performance of yeast was assessed in batch cultures with single strains. Previous studies addressing yeast adaptation to winemaking conditions by quantitative fitness analysis, were not specifically focused on the proliferative stages, and their results were greatly dependent on the effects of gene deletions on yeast survival during stationary phase. Since biomass production has a great influence on the whole fermentation kinetics, focusing on the proliferative stages of the fermentation process has practical implications.
In some instances our results highlight the importance of genes not previously linked to winemaking. In other cases our results are complementary to those reported in previous studies concerning, for example, the relevance of some genes involved in vacuolar, peroxisomal, or ribosomal functions. Transport processes and glucose signaling seem to be negatively affected by the stress factors encountered by yeast in synthetic must. Vacuolar activity is important for continued growth during the transition to stationary phase. Finally, reduced biogenesis of peroxisomes also seems to be advantageous. However, in contrast to what was described for later stages, reduced protein synthesis is not advantageous for the first stages of the fermentation, when most cell proliferation takes place.

overall_design: Competition experiments of the genome-wide collections of mutants were performed in triplicate using conditions that mimicked Phases I or II of a batch fermentation (equivalent to around 14 and 22 hours after inoculation of a batch fermentation, respectively), as well as on YPD (complete medium) for reference purposes. To this end, different feed formulations were used. One mL of either the homozygote or heterozygote pool stored at -80 ºC was added to 50 mL of YPD broth supplemented with 200 µg/mL G418 and incubated overnight at 28 °C and 150 rpm to serve as inoculum for the competition experiments. Samples were taken before the onset of the continuous culture as t=0 (preculture) references. Variations in pool composition were always estimated against the cognate preculture (most often a single preculture served as inoculum for several competitions). After 10 or 20 generations in continuous culture, samples of cells were used for the genomic DNA extraction. lification of the barcodes (uptags and downtags), hybridization, and scanning were performed according to the protocol described elsewhere [Pierce SE, Davis RW, Nislow C, Giaever G (2007) Genome-wide analysis of barcoded Saccharomyces cerevisiae gene-deletion mutants in pooled cultures. Nat Protocols 2: 2958-2974]. Slight modifications concerning the hybridization of Tag4 microarrays by using reagents and protocols from the GeneChip Hybridization, Wash and Stain Kit (Affymetrix) were made.

first: Maite

last: Novo

first: Ana

last: Mangado

first: Manuel

last: Quirós

first: Pilar

last: Morales

first: Zoel

last: Salvadó


title: A functional screen for copper homeostasis genes identifies a pharmacologically tractable cellular system

status: Public on May 23 2013

city: Palo Alto

first: Ulrich

last: Schlecht

address: 3165 Porter Drive

department: Biochemistry

institute: Stanford University

summary:
Copper is an essential component of cytochrome C oxidase (i.e. complex IV of the electron transport chain), and is thus critical for the survival of aerobic organisms. If copper is not properly regulated in the body however, it can be extremely cytotoxic and genetic mutations that compromise copper homeostasis result in severe clinical phenotypes. Understanding how cells maintain optimal copper levels is therefore highly relevant to human health.
We found that addition of copper to culture medium leads to increased respiratory growth of yeast, a phenotype which we then systematically and quantitatively measured in 5050 homozygous diploid deletion strains using microarrays.

overall_design:
In the yeast homozygous gene deletion collection, both copies of every non-essential gene are deleted in a diploid strain. Each strain contains unique 20-bp “barcode” sequences flanked by common priming sites, allowing the relative abundance of individual strains to be quantitatively monitored within a pool of competitively-grown strains. To identify genes that are important for Cu-dependent respiratory growth, we measured the fitness of 5050 homozygous deletion strains in parallel in rich media (i.e. Yeast Extract, Peptone) using either dextrose, ethanol, glycerol, or lactate as a carbon source, in the presence or absence of 500 µM CuSO4 for 9 generations. Each condition was tested in triplicate.

Please note that there is a large percentage of null-values (i.e. Not Available) in the respiration deficient-pool samples because the respiration deficient pool consists of only a small subset of the complete pool (represented by 331 barcodes instead of 9937). For our analysis we discarded the remaining barcodes by assigning the null-value to them.

first: Sundari

last: Suresh

first: Weihong

last: Xu

last: Aparicio

first: Angela

last: Chu

first: Michael

last: Proctor

first: Ronald

middle: W

last: Davis

first: Curt

last: Scharfe

first: Robert


title: Array CGH analysis in gastric gastrointestinal stromal tumors (GISTs)

status: Public on Jun 14 2013

city: Seoul

first: Kyoung-Mee

last: Kim

address: #50 Irwon-dong

institute: Samsung Medical Center

summary: To explore mechanisms underlying wild-type GISTs, array CGH was performed on 32 gastric GISTs (4 risk groups stratified by tumor size and mitotic counts comprised 8 cases each).

overall_design: 27 KIT-mutant, 1 PDGFRA-mutant and 4 wild-type GISTs

first: Eui-Jin

last: Lee

first: Guhyun

last: Kang

first: Shin-Woo

first: Kee-Taek

last: Jang

first: Jeeyun

first: Joon-Oh

last: Park

first: Cheol-Keun

first: Tae-Sung

last: Sohn

first: Sung


title: Basonuclin-1 modulates epithelial plasticity and TGF-β1-induced loss of epithelial cell integrity

first: Alexander

last: Feuerborn

first: Daniel

last: Mathow

first: Prashant

last: Srivastava

first: Norbert

last: Gretz

first: Hermann-Josef

last: Gröne


title: Biphasic functional regulation in hippocampus of rat with chronic cerebral hypoperfusion induced by permanent occlusion of bilateral common carotid artery

status: Public on Feb 14 2013

city: Daejeon

first: Bu-Yeo

address: 1672 Yuseongdae-ro, Yuseong-gu

department: Herbal Medicine Research Division

institute: Korea Institute of Oriental Medicine

summary: We measured temporal changes of gene expression in hippocampus of rat after BCCAo using time-course microarray analysis

overall_design: Total RNA from the hippocampus from each time point of 21, 35, 45, 55 and 70 days after the BCCAo were subject to microarray.


title: Genome scale analysis of host-virus mRNA differential expression in Helicoverpa zea insect cells infected by H. armigera baculovirus from early till late infection

status: Public on Mar 01 2013

city: Brisbane

first: Quan

middle: Hoang

last: Nguyen

state: Queensland

address: Queensland Bioscience Precinct (Building 80) The University of Queensland. 306 Carmody Road. St

department: Australian Institute for Bioengineering and Nanotechnology

institute: The University of Queensland

summary: A custom microarray, based on deep transcriptome sequencing ((GEO accession number: GSE34418), was used to simultaneously investigate expression of over 24,000 Helicoverpa zea insect transcripts and 134 H. armigera nucleopolyhedrovirus (HearNPV) genes throughout the infection process at 0, 12, 24 and 48 hours post infection

platform_organism:
Helicoverpa zea
Helicoverpa armigera

overall_design: A cutom 8x60,000 SurePrint Agilent expression slide (Agilent, Santa Clara, CA)  was used to analyzed eight samples, including biological replicates of HaSNPV-infected cultures at 0, 12, 24 and 48 hpi.The microarray probes included probes for 27,400 H. zea sequences that were validated previously (Nguyen et al., 2012. PLOS ONE, 7(5), e36324) and all 134 H. armigera single-capsid nucleopolyhedrovirus (HearNPV) genes (Accession: NC_002654).

middle: H

first: Leslie

middle: C

last: Chan

first: Steven

last: Reid

first: Lars

last: Nielsen


title: Myeloma in African Americans: Myeloma gDNA vs. Control gDNA

status: Public on Feb 25 2013

city: Phoenix

first: Angela

middle: Stewart

last: Baker

state: AZ

address: 445 N. Fifth Street

department: Division of Integrated Cancer Genomics

institute: Translational Genomics Research Institute

summary: Epidemiological data have suggested that African Americans (AA) are twice as likely to be diagnosed with multiple myeloma (MM) as compared to European Americans (EA).  Here, we have analyzed a set of cytogenetic and genomic data derived from AA and EA MM patients.  We have compared the frequency of IgH translocations in a series of data from 115 AA patients from three studies and EA patients from the Eastern Cooperative Oncology Group (ECOG) studies E4A03 and E9487.  We have also interrogated tumors from 45 AA and 196 EA MM patients for somatic copy number abnormalities associated with poor outcome.  In addition, 35 AA and 178 EA patients were investigated for a transcriptional profile associated with high-risk disease.  Overall, based on this cohort, genetic profiles were similar except for a significantly lower frequency of IgH translocations (40% vs. 52%; p=0.032) in AA patients.  Frequency differences of somatic copy number aberrations were not significant after correction for multiple testing. There was also no significant difference in the frequency of high-risk disease based upon gene expression profiling.  Our study represents the first comprehensive comparisons of the frequency and distribution of molecular alterations in MM tumors between AA and EA patients.

overall_design: This submission contains 27 of the 45 African American cases analyzed by aCGH. In addition, 196 samples from European American myeloma patients were also analyzed and compared to the 45 African American patients.

first: Esteban

last: Braggio

first: Susanna

last: Jacobus

first: Sungwon

last: Jung

first: Dirk

last: Larwon

first: Terry

last: Therneau

last: Dispenzieri

first: Scott

last: Van Wier

first: Gregory

last: Ahmann

first: Joan

last: Levy

first: Louise

last: Perkins

first: Seungchan

first: Kim

last: Henderson

first: David

last: Vesole

first: S

middle: V

last: Rajkumar

first: Diane

last: Jelinek

first: John

last: Carpten

first: Rafael

last: Fonseca


title: Effect of IUGR on postnatal day 14 pancreatic islets

status: Public on Jul 13 2013

city: Philadelphia

first: Lane

middle: Johanna

last: Jaeckle Santos

state: PA

address: 421 Curie Blvd, BRB II/III 1341

department: CRRWH

institute: University of Pennsylvania School of Medicine

summary:
IUGR is a common complication of pregnancy. We have created a rat model of IUGR which mimics placental insufficiency. Surgery is performed at embryonic day 18 and dams are allowed to deleiver spontaneously.
At postnatal day 14, we isolate pancreatic islets and have compared their gene expression with that of control (sham) surgery animals.

overall_design: Two-condition experiment, control vs IUGR pancreatic islets. Biological replicates: 4 control replicates, 4 IUGR replicates.

first: Rebecca

last: Simmons


title: RNA expression for ethanologenic E coli strains LY180, EMFR9 and EMFR35 in the absence and presence of 5mM and 15 mM furfural for 15 min

status: Public on Apr 29 2013

city: Gainesville

first: Ryan

last: Geddes

state: Florida

address: Building 981 Museum Road

department: Microbiology and Cell Science

institute: University of Florida

summary:
The data explore the transcriptional response of strains LY180 and EMFR9 to 5 mM furfural under anaerobic fermentation condition
The data explore the transcriptional response of strains LY180 and EMFR35 to 15 mM furfural under anaerobic fermentation condition
The expression differences of polyamine transporters in LY180 vs EMFR9 and EMFR35 are further described in RD Geddes,X Wang, LP Yomano, EN Miller, H Zheng, KT Shanmugam, and LO Ingram. 2013. Selected Polyamines and Polyamine Transporters Increase Furfural Tolerance (in preparation for submission to Appl Env Microbiol)

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

overall_design:
Total RNA was prepared from cultures of LY180, EMFR9 and EMFR35 immediately before and 15 min after addition of furfural (5mM and 15 mM). The Nimblegen TI83333 chip measures expression of 4,237 genes, with 5 replicates, and 18 probes average per gene.
The complete dataset comprising 8 samples is linked below as a supplementary file.

first: Xuan

last: Wang

first: Lonnie

middle: O

last: Ingram