title: wt expression changes in deletion strain-conditioned media

status: Public on May 14 2014

city: UTRECHT

first: PHILIP

last: LIJNZAAD

address: HEIDELBERGLAAN 25

department: Single Cell Facility

summary: Alteration of growth condition or disruption of gene function are commonly used strategies to study cellular systems. Although widely appreciated that such experiments may result in indirect effects, these frequently remain uncharacterized. Here, genome-wide expression reanalysis of functionally unrelated Saccharyomyces cerevisiae deletion strains reveals a common expression signature. One property shared by these strains is slower growth, with increased presence of the signature in more slowly growing strains. The slow growth signature is highly similar to the environmental stress response, an expression response common to diverse environmental perturbations. Both environmental and genetic perturbations result in growth rate changes. These are accompanied by a change in the distribution of cells over different cell cycle phases. Rather than representing a direct expression response, the slow growth signature is a consequence of the redistribution of cells over different cell cycle phases, primarily characterized by an increase in the G1 population. The findings have implications for any study of perturbation that is accompanied by growth rate changes. Strategies to counter these effects are presented and discussed. This series shows the absence of media effects by growing wt strains in filtered medium in which slow-growing strains were grown previously.

overall_design: Two channel microarrays were used. RNA isolated from a large amount of wt yeast from a single culture was used as a common reference. Two independent cultures were hybridized on two separate microarrays. For the first hybridization the Cy5 (red) labeled cRNA from the deletion mutant is hybridized together with the Cy3 (green) labeled cRNA from the common reference. For the replicate hybridization, the labels are swapped.

first: Eoghan

last: O'Duibhir

first: Philip

last: Lijnzaad

first: Frank

last: C.P. Holstege


title: wt yeast expression changes in low phosphate conditions

state: Utrecht

country: Netherlands

institute: Princess Maxima Center for Pediatric Oncology

summary: Alteration of growth condition or disruption of gene function are commonly used strategies to study cellular systems. Although widely appreciated that such experiments may result in indirect effects, these frequently remain uncharacterized. Here, genome-wide expression reanalysis of functionally unrelated Saccharyomyces cerevisiae deletion strains reveals a common expression signature. One property shared by these strains is slower growth, with increased presence of the signature in more slowly growing strains. The slow growth signature is highly similar to the environmental stress response, an expression response common to diverse environmental perturbations. Both environmental and genetic perturbations result in growth rate changes. These are accompanied by a change in the distribution of cells over different cell cycle phases. Rather than representing a direct expression response, the slow growth signature is a consequence of the redistribution of cells over different cell cycle phases, primarily characterized by an increase in the G1 population. The findings have implications for any study of perturbation that is accompanied by growth rate changes. Strategies to counter these effects are presented and discussed. This series shows the effect of phosphate limitation on gene expression

overall_design: Two channel microarrays were used. RNA isolated from a large amount of wt yeast from a single culture was used as a common reference. Two independent cultures were hybridized on two separate microarrays. For the first hybridization the Cy5 (red) labeled cRNA from the test sample is hybridized together with the Cy3 (green) labeled cRNA from the common reference. For the replicate hybridization, the labels are swapped. In the statistical analysis, factor levels are compared using the common reference as an intermediate.


title: Contribution of CBX4 to cumulus oophorus cell phenotype in mice, and attendant effects in cumulus cell cloned embryos

status: Public on Apr 29 2014

city: East Lansing

first: Uros

last: Midic

state: MI

address: 474 S. Shaw Lane

department: Animal Sciences

country: USA

institute: Michigan State University

summary: Cumulus oophorus cells play an essential role in oocyte development. CBX4 is a member of the Polycomb complex, which plays a role in regulating cellular differentiation.

overall_design: We used siRNA mediated knockdown of Cbx4 expression followed by Affymetrix array analysis to evaluate the role of CBX4 in cumulus cell differentiated state.

first: Keith

middle: E

last: Latham

first: Lanping

last: Hao

first: Judith

last: Garriga


title: Polysome profiling of Huh7.5 cells expressing HCV NS5A

status: Public on May 01 2014

city: HYDERABAD

first: KRISHNAN

middle: HARINIVAS

last: HARSHAN

address: HABSIGUDA

country: India

institute: CENTRE FOR CELLULAR AND MOLECULAR BIOLOGY

type:
Expression profiling by array
Other

summary: Hepatitis C Virus protein NS5A was found to upregulate assembly of cap binding initiation complex eIF4F in Huh7.5 cells. NS5A also was found to associate with translation machinery. To understand consequences of NS5A mediation in host translation, we analyzed mRNA associated with polysome fractions of NS5A expressing Huh7.5 cells and compared them with the corresponding fractions from control cells.

overall_design: Agilent-027114 Genotypic Technology designed Custom Human Whole Genome 8x60k Microarray

first: Dhiviya

last: Vedagiri

first: Swarupa

last: Panda

first: Soundara

last: Viveka

first: Harinivas

middle: H

last: Krishnan


title: SNP data from 76 adrenocortical carcinomas

status: Public on Apr 07 2014

city: Paris

first: Nabila

last: Elarouci

address: 14 rue Corvisart

department: Recherche

country: France

institute: Ligue Nationale contre le Cancer

summary: SNP array data from 76 adrenocortical carcinomas were used to detect recurrent copy number alterations.

overall_design: 76 tumors were analyzed with Illumina HumanCore-12v1 BeadChip.

first: Eric

last: Letouze

first: Aurelien

last: de Reynies

first: Windy

last: Luscap

first: Barreau

last: Olivia

first: Guillaume

last: Assie

first: Jerome

last: Bertherat


title: Whole genome SNP array data from myelodysplastic syndromes (MDS) patients

status: Public on May 22 2014

city: Shanghai

first: Zhaohui

last: Gu

state: Shanghai

address: 197 Rui Jin Road II

department: School of Medicine

country: China

institute: Shanghai Jiao Tong University

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

summary:
With the whole genome SNP array information obtained from tumor and matched normal control, we could evaluate the acquired copy number variations (CNVs) and uniparental disomies (UPDs) .
Seven MDS patients in a whole genome sequencing project were included in this experiment.

overall_design: To detect acquired CNVs and UPDs in MDS patients, we genotyped both CD34+ cell from bone marrow and matched skin tissue.

first: Zhu

last: Chen

first: Saijuan


title: SNP data from 45 adrenocortical carcinomas

summary: SNP array data from 45 adrenocortical carcinomas were used to detect recurrent copy number alterations.

overall_design: 7 tumors were analyzed with Illumina Human610-Quad v1.0 BeadChip. 38 tumors were analyzed with Illumina HumanOmniExpress BeadChip.

last: Letouzé

first: Aurélien

last: de Reyniès

first: Olivia

last: Barreau

last: Assié

first: Jérome


title: Differential expressions of microRNAs under normoxic and hypoxic conditions

status: Public on Apr 18 2014

city: Daegu

first: You Mie

last: Lee

address: 80, Daehak-ro

country: South Korea

institute: Kyungpook National University

summary: Outcome prediction classifiers were successfully constructed through expression profiling of a total of 1,329 miRNAs in MKN1, gastric cancer cell line under normoxic and hypoxic conditions.

overall_design: In the study presented here, MKN1 under normoxic and hypoxic conditions was used to acquire expression profiles of a total 1,329 unique miRNAs.

first: You

first: Min

last: Kim


title: Phosphorylation of Bacillus subtilis gene regulator AbrB modulates its DNA-binding properties

status: Public on Apr 11 2014

city: Jouy-en-Josas

first: Olivier

last: Delumeau

address: Domaine de Vilvert

institute: INRA

type: Expression profiling by genome tiling array

summary: AbrB is a global gene regulator involved in transition phase phenomena in Bacillus subtilis. It participates in a complex regulatory network governing the expression of stationary phase functions. AbrB was previously found to be phosphorylated on serine 86 located close to its C-terminal oligomerization domain. Here we report that AbrB can be phosphorylated by three B. subtilis serine/threonine kinases expressed during the transition and stationary phase: PrkC, PrkD and YabT. Our in vitro findings suggest that AbrB phosphorylation impedes its DNA binding and abolishes binding cooperativity. In vivo we established that a phospho-mimetic mutation abrB S86D leads to a significant loss of AbrB control over several key target functions: exoprotease production, competence development and sporulation. A wider transcriptome analysis of abrB S86D and S86A mutant strains revealed deregulation of a large number of target genes. We therefore propose that AbrB phosphorylation serves as an additional input for fine-tuning the activity of this ambiactive gene regulator.

sample_organism: Bacillus subtilis subsp. subtilis str. 168

overall_design: A 6 arrays study of the transcriptome profiles of B. subtilis strain 168, abrB-S86A and abrB-S86D mutant strains. Compared to the wild-type strain the mutant strains were used to test the effect of the phosphorylation of AbrB on ser-86 (using a phosphomimetic of AbrB (abrB-S86D strain) or its absence (abrB-S86A strain) on transcript profiles.

first: Ahasanul

last: Kobir

first: Sandrine

last: Poncet

first: Vladimir

last: Bidnenko

first: Carsten

last: Jers

first: Samira

last: Zouhir

first: Rosa

last: Grenha

first: Sylvie

last: Nessler

first: Philippe

last: Noirot

first: Ivan

last: Mijakovic


title: Identification of the 5' end of the pig miRNA by the RAKE technology

status: Public on Mar 31 2014

city: Padova

first: Gerolamo

last: Lanfranchi

address: Via U. Bassi, 58/B

department: CRIBI - Biotechnology Center and Biology Department

country: Italy

institute: University of Padova

summary: We applied a new computational approach to predict specie-specific and conserved miRNAs, than experimentally confirmed by a modified RNA-primed Array-based Klenow Extension (RAKE) method. We identified 489 conserved and 1,178 pig-specific novel miRNAs increasing our tally of confirmed miRNAs to 1,667 novel miRNAs. In addition, RAKE allowed the identification of miRNA isoforms (isomiRs) that we demonstrated to be differentially expressed across tissues suggesting that subtle variability in isomiR expression is regulated and biologically meaningful.

overall_design: 12K microarray was hybridized with a pool of small RNAs from 20 different tissues (superior vena cava, adipose tissue, lung, spleen, stomach, liver, intestine, kidney, descending aorta, left atrium, left ventricle, skeletal muscle, pulmonary aorta, skin, tongue, ascending aorta, arterial white cells blood, venal white cells blood, coronary valve, lymph node). Same experiment was replicated three times to grant the reliability of the identified 5’ end of miRNAs and microarray slides were scanned three times at low, medium and high PMT to improve microarray dynamic range.

first: Stefano

last: Cagnin

first: Gabriele

last: Sales

first: Paolo

last: Martini

first: Alessandro

last: Gandaglia

first: Filippo

last: Naso

first: Mattia

last: Brugiolo

first: Cristiano

last: De Pitta’

first: Gino

last: Gerosa

first: Michele

last: Spina

first: Chiara

last: Romualdi


title: Evaluation of miRNA expression in 14 different tissues by the RAKE technology

summary: The short length of miRNAs results in a high dynamic range of melting temperatures and therefore impedes a proper selection of detection probes or optimized PCR primers. While miRNA microarrays allow for massive parallel and accurate relative measurement of all known miRNAs, they have so far been less useful as an assay for absolute quantification. Here we developed a new method based not only to the hybridization process that presents the limits before described, but integrating the hybridization to an enzymatic reaction. Moreover we introduced spike-in in the hybridization-enzymatic reaction allowing the quantification of miRNAs respect to them, canceling biases related to sequence, labeling, or hybridization. An alternative method for the absolute miRNA quantization was recently proposed by Bissels (Absolute quantification of microRNAs by using a universal reference. RNA). It was based on the Absolute quantification of microRNAs by using a universal reference consisting of 954 synthetic human, mouse, rat, and viral miRNAs, with each individual oligoribonucleotide present in equimolar concentrations with tested miRNAs. Thereby, any single miRNA detected on a microarray can be quantified by directly comparing its signal intensity with the one obtained by the same miRNA sequence present in the universal reference adjusting for biases related to sequence, labeling, hybridization, or signal detection. Our method allowed the detection of a comparable concentration of miRNA (10-18 moles to 10-14 moles in a linear range) (see Figure), but allows controlling the hybridization quality and reproducibility basing on the results of the interpolation of the spike-in dependent curve. Moreover, our method does not influenced by phenomena imputable to different labeling process due to different sequences because labeling was due only to the incorporation of biotin-d(A) if the hybridized miRNA acted as primer for the klenow enzyme.  This method allowed the discussion of miRNA genes expression in 14 different tissues relating it with tissue anatomical proximity and functional similarity.

overall_design: 2K microarray was hybridized with small RNAs from 14 different tissues (Atrium Sinister; Skin; Liver; W_B_A: White Blood Cells from Arteriosum blood; W_B_V: White Blood Cells from Venosum blood; Lymph Node; Tongue; Spleen; Skeletal Muscle; Lung; Kidney; Stomach; Adipose Tissue; Ventricle Sinister). Each experiment was replicated to have 28 experiments and miRNA gene expression was correlated with mRNA gene expression in the same samples.


title: Heatshock-Coldshock

first: PHILIP

last: LIJNZAAD

summary: Alteration of growth condition or disruption of gene function are commonly used strategies to study cellular systems. Although widely appreciated that such experiments may result in indirect effects, these frequently remain uncharacterized. Here, genome-wide expression reanalysis of functionally unrelated Saccharyomyces cerevisiae deletion strains reveals a common expression signature. One property shared by these strains is slower growth, with increased presence of the signature in more slowly growing strains. The slow growth signature is highly similar to the environmental stress response, an expression response common to diverse environmental perturbations. Both environmental and genetic perturbations result in growth rate changes. These are accompanied by a change in the distribution of cells over different cell cycle phases. Rather than representing a direct expression response, the slow growth signature is a consequence of the redistribution of cells over different cell cycle phases, primarily characterized by an increase in the G1 population. The findings have implications for any study of perturbation that is accompanied by growth rate changes. Strategies to counter these effects are presented and discussed. In this series, the effects, over time, of heatshock (shifting cells from 30 to 37 C) or the reverse (cold 'shock') are studied.

first: Eoghan

last: O'Duibhir

first: Philip

last: Lijnzaad

first: Frank

last: C.P. Holstege


title: Identification of the 3' end of the pig miRNA by the RAKE technology [platform 2: 9003179]

overall_design: 90K microarray was hybridized with a pool of small RNAs from 20 different tissues (superior vena cava, adipose tissue, lung, spleen, stomach, liver, intestine, kidney, descending aorta, left atrium, left ventricle, skeletal muscle, pulmonary aorta, skin, tongue, ascending aorta, arterial white cells blood, venal white cells blood, coronary valve, lymph node). Same experiment was replicated four times to grant the reliability of the identified 3’ end of miRNAs and microarray slides were scanned three times at low, medium and high PMT to improve microarray dynamic range.


title: Identification of responsive probes for mRNA transcripts of the pig (S. scrofa) genome

summary: Pig mRNAs Ensembl transcripts (Ver. 56) and UniGene (Ver. 38) sequences were used to produce a dedicated microarray platform to analyze mRNAs gene expression. Based on sequence similarity we rejected UniGene features that overlapped more than 40% with an Ensembl transcript. After this filter we obtained 40,267 UniGene clusters and 19,603 Ensembl transcripts (protein coding + pseudogenes + retrotransposed elements). Starting from these sequences, the microarray probes were computed using 6 different algorithms (YODA, Picky, ArrayOligoSelector, OligoPicker, OligoFaktory, CommOligo). Two probes in the most 3’ end was tested for their specificity and performance. For any transcript with a replicated tested probe, we used the most responsive and specific in an hybridization trial with a pool of mRNAs from 20 tissues to construct the definitive gene expression microarray for the pig. Definitive 90K Combimatrix gene expression microarrays were composed by 17,048 replicated probes and 963 not replicated specific for the Ensembl transcripts, 11,363 replicated probes specific for the UniGene clusters of length comprised between 778 nt and 1,348 nt, and 28,790 single probes specific for the remaining UniGene clusters (GEO: GPL13259).

overall_design: Microarray was probed with a pool of RNAs from 20 different tissues (superior vena cava, adipose tissue, lung, spleen, stomach, liver, intestine, kidney, descending aorta, left atrium, left ventricle, skeletal muscle, pulmonary aorta, skin, tongue, ascending aorta, arterial white cells blood, venal white cells blood, coronary valve, lymph node). Moreover each tissue sample was performed by a pool of 3 different adult pigs because they was not inbred.


title: Transcriptional profiling of Mycobacterium tuberculosis H37Rv in whole blood from HIV- and HIV+ individuals

city: New York

first: Suman

last: Laal

state: NY

address: 423 Esat 23rd Street, 18N

department: Pathology

institute: VA/NYU

summary: Mycobacterium tuberculosis (M. tb), the cause of tuberculosis (TB), utilizes the blood circulation to spread systemically and establish infection, and the risk of developing active TB (pulmonary and extrapulmonary) is significantly increased in individuals infected with human immunodeficiency virus (HIV). In this work, we have used DNA microarray analysis to investigate the transcriptome of M. tb replicating in human whole blood from both HIV-negative and HIV-positive donors compared to M. tb grown in Middlebrook 7H9 broth media in order to identify M. tb adaptations to this host environment as well as M. tb mechanisms/factors contributing to increased active and disseminated TB during M. tb/HIV co-infection.

overall_design: We compared  the global gene expression of M. tb H37Rv replicating in whole blood from 6 HIV- and 6 HIV+ individulas at 96 hr to M. tb grown to log phase in Middlebrook 7H9 media.

first: Krishna

middle: K

last: Singh

first: Michelle

middle: B

last: Ryndak

first: Susan

last: Zolla-Pazner

first: Zhengyu

last: Peng

first: Meng

last: Lu


title: 2D and 3D Madin-Darby Canine Kidney Cell Type II cell line response to hepatocyte growth factor

city: Philadelphia

first: Maria

middle: Fernanda

last: Chacon-Heszele

state: Pennsylvania

address: 415 Curie Blvd - 411 CRB

institute: University of Pennsylvania

summary:
Analysis of 2D (transwell) and 3D (collagen type I) cultured MDCK cells and HGF (a MAPK activator). Traditional 2D cultures are fast and inexpensive but do no mimic natural niche/cell environment as well as the more laborious and costly 3D-cultures. 3D cultures, arguably, are better models for the study of developmental processes, such as tubulogenesis.
Epithelial organs (such as kidney) develop via tubulogenesis, a process, at least in part, regulated by MAPK signaling. Therefore, 2D and 3D cells also treated with HGF plus MAPK inhibitors. Results provide insights into differential response to HGF-induced tubulogenesis depending on cell culture conditions (2D vs. 3D).

overall_design: 29 samples total: 2D and 3D control (untreated) in quadruplicate, respectively; 2D and 3D + HGF in quadruplicate, respectively; 2D + HGF + PD-98059 in quadruplicate; 3D +  HGF + PD-98059 in triplicate; 2D + HGF + U0126 in triplicate; and 3D + HGF + U0126 in triplicate.

middle: F

first: Xiaofeng

last: Zuo

first: Nathan

last: Hellman

first: Sarah

last: McKenna

first: Soo

middle: Y

last: Choi

first: Liwei

last: Huang

first: John

middle: W

last: Tobias

first: Kwon

middle: M

last: Park

first: Joshua

last: Lipschutz


title: Identification of the 3' end of the pig miRNA by the RAKE technology [platform 1: 9003467]

first: Gerolamo

last: Lanfranchi

first: Stefano

last: Cagnin

first: Gabriele

last: Sales

first: Paolo

last: Martini

first: Alessandro

last: Gandaglia

first: Filippo

last: Naso

first: Mattia

last: Brugiolo

first: Cristiano

last: De Pitta’

first: Gino

last: Gerosa

first: Michele

last: Spina

first: Chiara

last: Romualdi


title: The Mycobacterium tuberculosis Rv2745c Plays an Important Role in Responding to Redox Stress

status: Public on Mar 25 2014

city: San Antonio

first: Deepak

last: Kaushal

state: TX

address: 8715 W Military Dr

department: HPI

institute: Texas Biomedical Research Institute

summary: The Rv2745c (clgR) gene encodes a Clp protease gene regulator that is induced in response to a variety of stress conditions and potentially plays a role in Mtb pathogenesis. The isogenic Mtb:ΔRv2745c mutant is significantly more sensitive to in vitro redox stress generated by diamide, relative to wild-type Mtb, implicating a role for ClgR in the management of intraphagosomal redox stress. Redox stress led to dysregulation of the σH regulon in the isogenic mutant, Mtb:ΔRv2745c. Induction of clgR in Mtb and Mtb:ΔRv2745c (comp) did not lead to Clp protease induction, indicating that clgR has additional functions that need to be elucidated. Disruption of genes involved in sulfate assimilation also occurred in the knock out, implicating clgR as a possible regulator of downstream signaling cascades that facilitate Mtb survival.

platform_organism:
Mycobacterium tuberculosis CDC1551
Mycobacterium tuberculosis H37Rv

overall_design: At different time points, (30, 60 and 90 mins, t=30, t=60 and t=90) following the addition of diamide to M. tuberculosis CDC1551 cultures, RNA was extracted and labeled with Cy5. RNA was also extracted from pre-diamide addition (t=0) time points and labeled with Cy3. These samples were cohybridized on M. tuberculosis CDC1551 whole genome microarrays using biological triplicate samples (i.e. samples derived from three distinct cultures and treatments) and thus three unique datasets were generated for each of the three time points for Mtb. Similar experiments were performed for an isogenic Rv2745c (clgR) mutant in Mtb CDC1551 which was generated by allelic exchange and a complemented strain which was generated by trans-complementation of Rv2745c in the attB locus of the mutant strain, thus restoring the wild type regulation of Rv2745c.

first: Smriti

last: Mehra


title: miRNA profiling of H1 ES cells in neural induction timecourse

status: Public on Mar 22 2014

city: Seattle

first: Sherman

last: Ku

state: WA

address: Suite 200, 551 North 34th St

institute: Allen Institute for Brain Science

summary:
H1 ES cells were differentiated using a neural induction protocol. Biological triplicate samples were collected at five timepoints (d0, d3, d6, d9, d12) and analyzed by miRNA microarrays.
The goal of this experiment was to identify potential biases in Drosha processing of miRNAs dependent on biophysical properties and to identify differentially expressed miRNAs over the course of differentiation/neural induction.

overall_design: Using a robust differentiation protocol (described in the associated publication), H1 ES cells underwent differentiation/neural induction for 12 days. Samples were collected in biological triplicate every three days, beginning with day 0 and ending at day 12 for a total of five timpoints and fifteen samples. Total RNA was purified using the Qiagen miRNeasy Mini kit according to the manufacturer and submitted to LC Sciences according to their specifications. Raw data were received and were Lowess-normalized to allow cross-chip comparisons.


title: Discovering, evolution, biogenesis, expression and target prediction of porcine micro-RNAs: new regulatory gene expression network in different tissues.

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

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

overall_design: Refer to individual Series


title: Microarray expression profiling of C. elegans N2 L4 control (RNAi) vs. nhr-25 (RNAi) and N2 (Wt) vs. acs-3 (ft5) mutants

status: Public on Mar 21 2014

city: Santa Cruz

first: Jordan

middle: David

last: Ward

state: California

address: 1156 HIGH ST, UCSC THIMANN RECEIVING, SINSHEIMER 327

department: Molecular, Cell, and Developmental Biology

institute: University of California, Santa Cruz

summary: Acyl-coA synthases (ACSs) produce fatty acyl-CoAs that are used in metabolic and signaling pathways. Metazoans have a large number of ACS genes with differing expression patterns and substrate preferences, but the physiological roles of most ACS genes are unknown. Here, we focused on the C. elegans acyl CoA synthase, ACS-3, which is known to regulate fat uptake and de novo fat synthesis through the conserved nuclear hormone receptor, nhr-25. We performed microarray analysis of acs-3 mutants to elucidate the acs-3-regulated transcription program. This analysis revealed an enrichment among differentially regulated genes of those involved in lipid metabolism, pathogen and wounding responses, and sterol binding genes, among others. As the immunity genes were the most represented gene class, we performed pathogen sensitivity assays to test the phenotypic consequences of this immune gene regulation. Interestingly, acs-3 mutants were hypersensitive to the fungal pathogen D. coniospora, but only mildly sensitive to the bacterial pathogen P. aeruginosa. acs-3 mutation suppressed nhr-25 mutant sensitivity to P. aeruginosa, yet surprisingly microarray analysis of nhr-25(RNAi) animals revealed significant overlap with the acs-3 mutant transcriptome, with an enrichment of pathogen response genes. The upregulation of pathogen response genes in acs-3(ft5) mutants and following nhr-25 reduction-of-function (rf) does not appear to be due to a constitutive osmotic response or defective cuticle barrier, two potential explanations for the acs-3(ft5) and nhr-25(rf) expression of innate immunity genes in the absence of pathogen exposure. Together, these data indicate that ACS-3 promotes resistance to the fungal pathogen, D. coniospora and regulates innate immunity genes through an unknown mechanism. Potential roles for ACS-3 in innate immunity are discussed.

overall_design: We used two-color expression microarrays to compare the transcriptional profiles in two experimental conditions: 1) comparing wild-type (N2) L4 stage larval worms to acs-3(ft5) L4 larval mutant animals; and 2) animals grown to L4 larval stage on bacteria harboring vectors for either control or nhr-25 RNA-interference (RNAi). L4 stage was determined by morphology of the developing vulva. Three biological replicates were used for each experimental condition. Statistically significant changes in gene expression in each experimental were determined using “linear models for microarray data” (limma).

middle: D

first: Brendan

last: Mullaney

first: Benjamin

middle: J

last: Schiller

first: Le

last: He

first: Sarah

last: Petnic

first: Carole

last: Couillault

first: Nathalie

last: Pujol

first: Teresita

middle: U

last: Bernal

first: Marc

middle: R

last: Van Gilst

first: Kaveh

last: Ashrafi

first: Jonathan

last: Ewbank

first: Keith

last: Yamamoto


title: Messenger RNA transcript expression in the pig (S. scrofa)

first: Gerolamo

last: Lanfranchi

summary: 90K Combimatrix gene expression microarrays were composed by 17,048 replicated probes and 963 not replicated specific for the Ensembl (Ver. 56) Transcripts (protein coding + pseudogenes + retrotransposed elements), 11,363 replicated probes specific for the UniGene clusters (Ver. 38) of length comprised between 778 nt and 1,348 nt, and 28,790 single probes specific for the remaining UniGene clusters. These microarrays were used to study gene expression in 14 different pig tissues (Atrium Sinister; Skin; Liver; W_B_A: White Blood Cells from Arteriosum blood; W_B_V: White Blood Cells from Venosum blood; Lymph Node; Tongue; Spleen; Skeletal Muscle; Lung; Kidney; Stomach; Adipose Tissue; Ventricle Sinister). Gene expression was correlated with the micro-RNA expression in the same tissues.

overall_design: 14 different samples were analyzed. Each experiment with a different sample was replicate two times. We performed a total of 28 experiments and correlated them with 28 experiments of micro-RNA gene expression.

first: Stefano

last: Cagnin

first: Gabriele

last: Sales

first: Paolo

last: Martini

first: Alessandro

last: Gandaglia

first: Filippo

last: Naso

first: Mattia

last: Brugiolo

first: Cristiano

last: De Pitta

first: Gino

last: Gerosa

first: Michele

last: Spina


title: Folate Pathway Disruption Leads to Critical Depletion of Methionine Derivatives in Mycobacterium tuberculosis

status: Public on Mar 19 2014

city: RENTON

first: Tige

last: Rustad

state: WASHINGTON

address: 1700 DAYTON AVE NE

institute: Seattle BioMed

summary: In this study, screening efforts identified novel antifolates with potent, targeted activity against whole cell Mycobacterium tuberculosis.  Liquid chromatography-mass spectrometry analysis of antifolate-treated cultures revealed unique metabolic disruption, including decreased pools of methionine and S-adenosylmethionine.  Transcriptomic analysis highlighted up-regulation genes involved in the biosynthesis and utilization of methionine.  Supplementation with amino acids or methionine derivatives was sufficient to rescue cultures from MIC-level antifolate treatment.  Instead of the “thymineless death” that characterizes folate pathway inhibition in a wide variety of organisms, these data suggest that M. tuberculosis is vulnerable to a critical disruption of the biosynthesis of methionine-derived compounds.

overall_design: These arrays look at the expression profile triggered by exposure to three different anti-folates (WR99210, dimethyl and diethyl methotrexate) in three biological replicates and in a matched set of untreated samples.

first: David

last: Sherman


title: Acetylation at the lateral surface of the nucleosome at lysine 64 of H3 regulates chromatin dynamics and defines transcriptionally active chromatin

status: Public on Mar 18 2014

city: Basel

first: Fabio

last: Mohn

address: Maulbeerstrasse 66

country: Switzerland

institute: Friedrich Miescher Institute for Biomedical Research

type: Genome binding/occupancy profiling by genome tiling array

summary: Post-translational modifications of proteins have emerged as a major mechanism for regulating gene expression. Yet our understanding of how histone modifications directly affect chromatin function remains limited. Here, we investigate acetylation of histone H3 at lysine 64 (H3K64ac), a previously uncharacterized acetylation site on the lateral surface of the histone octamer. We show that H3K64ac regulates nucleosome dynamics by (i) destabilizing nucleosomes, and (ii) regulating chromatin remodelling. Both of these functions have the potential to regulate gene expression. In line with this, we show that the p300 co-activator acetylates H3K64 both in vitro and in vivo. H3K64ac is enriched at the transcriptional start sites (TSS) of active genes and defines transcriptionally active chromatin in ES cells. Moreover, we find that H3K64ac is dynamic during developmental reprogramming, and during mammalian spermatogenesis where H3K64 hyperacetylation precedes histone replacement. Consistent with a function in transcriptional activation, H3K64ac opposes its repressive counterpart H3K64me3. Our findings reveal an important role for a histone modification within the nucleosome core as a regulator of chromatin function in vivo and they demonstrate that lateral surface modifications can define functionally opposing chromatin states.

overall_design: In this study, 2 biological  replicate samples for H3K64ac ChIP and one sample of H3K9ac ChIP in mouse emryonic stem cells were analyzed using custom designed Nimblegen HD2.1oligonucleotide tiling arrays.

first: Vincenzo

last: Di Cerbo

first: Daniel

last: Ryan

first: Emilie

last: Montellier

first: Slim

last: Kacem

first: Philipp

last: Tropberger

first: Leslie

last: Horner

first: Celine

last: Ziegler-Birling

first: Angelika

last: Feldmann

first: Florian

last: Richter

first: Gerhard

last: Mittler

first: Maria-Elena

last: Torres-Padilla

first: Andrew

last: Bannister

first: Saadi

last: Khochbin

first: Robert

last: Feil

first: Dirk

last: Schübeler

first: Tom

last: Owen-Hughes

first: Sylvain

last: Daujat

last: Schneider


title: Expression analysis of evolved polygamous and monogamous Drosophila melanogaster

status: Public on Mar 17 2014

city: Columbia

first: Brian

last: Hollis

state: SC

address: 715 Sumter Street

department: Department of Biological Sciences

institute: University of South Carolina

summary:
Investigation of gene expression level changes in evolved polygamous and monogamous populations of Drosophila melanogaster.
The populations investigated are described in Hollis et al. 2011. Populations with elevated mutation load do not benefit from the operation of sexual selection. Journal of Evolutionary Biology 24: 1918-1926.

overall_design:
A study using total RNA extracted from male and female virgin 4-day old Drosophila melanogaster and then transcriptionally profiled with 12x135k Nimblegen arrays.

Also, transcriptional profiling of male and female heads from the same populations using Illumina RNA-Seq.


title: Severe Hypoxia Exerts Parallel and Cell-specific Regulation of Gene Expression and Alternative Splicing in Human Mesenchymal Stem CellsMesenchymal Stem Cells

status: Public on Mar 14 2014

city: Miami

first: Lina

middle: A

last: Shehadeh

state: FL

department: Medicine

institute: University of Miami

summary: To identify the effects of hypoxia on stem cell populations,  we subjected human mesenchymal stem cells to a pO2 of 4 mmHg and analyzed global gene expression and alternative splicing (AS) by genome-exon microarray.

overall_design: Hypoxia induced gene expression in human mesenchymal stem cells was measured at 24 hours after exposure to 0.5% oxygen or normal 21% oxygen.  Three independent experiments were performed per condition (Hypoxia or Normoxia).

first: Keith

last: Webster


title: a-CGH of Esophageal Cancer (70 cases)

status: Public on Mar 11 2014

city: shenzhen

first: Lin

last: Li

address: Beishan Industrial Zone

institute: BGI

type: Genome variation profiling by genome tiling array

summary: Esophageal cancer is one of the most aggressive cancers and the sixth leading cause of cancer death worldwide. Approximately 70% of the global esophageal cancers occur in China and over 90% histopathological forms of this disease are esophageal squamous cell carcinoma (ESCC). Currently, there are limited clinical approaches for early diagnosis and treatment for ESCC, resulting in a 10% 5-year survival rate for the patients. Meanwhile, the full repertoire of genomic events leading to the pathogenesis of ESCC remains unclear. Here we show a comprehensive genomic analysis in 158 ESCC cases, as part of the International Cancer Genome Consortium (ICGC) Research Projects (http://icgc.org/icgc/cgp/72/371/1001734). We conducted whole-genome sequencing in 17 ESCC cases and whole-exome sequencing in 71 cases, of which 53 cases and additional 70 ESCC cases were subjected to array comparative genomic hybridization (a-CGH) analysis.

first: Qimin

last: Zhan

first: Yongmei

last: Song

first: Yunwei

last: Ou

first: Zhibo

last: Gao


title: Analysis of the iron stimulon and fur regulon of Geobacter sulfurreducens [ChIP-chip]

status: Public on Mar 10 2014

city: La Jolla

first: Mallory

last: Embree

state: CA

address: PFBH/EBU3a, 9500 Gilman Drive Rm. 414

department: Bioengineering

institute: University of California, San Diego

summary:
Fur is a transcriptional regulator whose activity is dependent on Fe(II) concentrations.
Chromatin immunoprecipitation (ChIP) coupled to microarray analysis allowed for the identification of Fur binding sites within the G. sulfurreducens genome.

overall_design: Wild type G. sulfurreducnes was cultured on fresh water media (harvested during log phase), and ChIP was used to identify Fur binding regions.

first: Karsten

last: Zengler


title: Analysis of the iron stimulon and fur regulon of Geobacter sulfurreducens [expression]

summary: G. sulfurreducens was cultured on a variety of different iron concentrations and differential expression analysis was used to identify the iron stimulon.

overall_design: Wild type G. sulfurreducens was cultured on fresh water media with trace concentrations of iron (iron sufficient condition) as well as no trace iron (iron deficient condition). It was also cultured in ferric citrate (iron excess condition) media


title: Leptosphaeria maculans gene expression during in vitro growth after silencing of DIM5 or HP1, two genes involved in chromatin remodelling

status: Public on Mar 06 2014

city: Thiverval-Grignon

first: Isabelle

last: Fudal

address: avenue Lucien Bretignieres

summary: The transcriptome of Leptosphaeria maculans was analysed in mycelium of the wild type isolate v23.1.3 or in transformants silenced for DIM5 or HP1, two genes encoding enzymes involved in chromatin remodelling. The array probes were designed from gene models from the L. maculans whole genome annotation. The aim of this study was to characterise the effect of chromatin remodelling on gene expression during in vitro growth.

overall_design: We performed 9 hybridizations (NimbleGen) with samples derived from mycelium of a wild type isolate, v23.1.3, of a transformant silenced for HP1 and for a transformant silenced for DIM5. Three replicates each. All samples were labeled with Cy3.

first: Juliette

last: Linglin


title: AIP inactivation leads to pituitary tumorigenesis through defective Gαi-cAMP signaling

status: Public on Mar 05 2014

city: Helsinki

first: Miika

last: Mehine

address: P.O. Box 63 (Haartmaninkatu 8)

country: Finland

institute: University of Helsinki

summary: Gene-level expression profiles of 7 Aip knock-out (triplicates from each) and 9 Aip wild-type mouse embryonic fibroblast cell lines were studied using Affymetrix GeneChip Mouse Exon 1.0 ST Arrays

overall_design: All samples were quantile-normalized by the RMA method (Robust Multichip Average) using re-mapped gene annotations from Brainarray Custom CDF files (MoEx10stv1, Version 14.1.0, http://brainarray.mbni.med.umich.edu/Brainarray/default.asp). A 2-way ANOVA was constructed to identify genes that differentially expressed between KO and WT samples. False discovery rate control (FDR) with Benjamini and Hochberg method was used to correct for multiple testing

first: I

last: Tuominen

first: E

last: Heliövaara

first: A

last: Raitila

first: M-R

last: Rautiainen

first: M

first: R

last: Katainen

first: V

last: Aittomäki

first: H

last: Lehtonen

last: Ahlsten

first: J

last: Arola

first: S

last: Hautaniemi

last: Karhu


title: DNA damage signaling gene array on SMA mouse skeletal muscle

status: Public on Mar 03 2014

city: Baltimore

first: Saniya

last: Fayzullina

state: MD

address: 720 Rutland Avenue Ross Bldg., Room 558

institute: Johns Hopkins School of Medicine

summary: A commercially available gene array (SABiosciences array PAMM-029ZD-12) was used to assay gene expression in skeletal muscle of SMA mice and control littermates. The Taiwanese severe SMA mouse model was used (Hsieh-Li et al. 2000). The array included 84 genes associated with DNA damage detection, DNA repair, apoptosis, cell cycle, and other functions.

overall_design: SMA group (n=3) vs. control group (n=3) - single technical replicates, triple biological replicates

first: Lee

last: Martin


title: MYB87 chimera repressor suppresses longitudinal organ growth with aberrant expressions of cell wall related genes in Arabidopsis thaliana

city: Tsukuba

first: Nobutaka

last: Mitsuda

state: Ibaraki

address: Central 6 Higashi 1-1-1

department: Bioproduction Research Institute

country: Japan

institute: National Institute of Advanced Industrial Science and Technology

summary: Proper cell wall regulation is essential for growth and development in plants. Here we report that the constitutive expression of MYB87 chimera repressor causes the suppressed longitudinal organ elongation in almost all organs. Aberrant transversal growth is also observed in multiple organs which coincide with transversally expanded or swollen cells. Microarray analysis revealed the transcript levels of various primary cell wall related  enes are up- or down-regulated, and those of secondary wall related genes are down- regulated in the chimera repressor plants. These findings  ontribute to the further understanding of complex cell wall regulations and their roles in plant growth and development.

overall_design: Transcriptomes of 35S:MYB87-SRDX and wild-type Arabidopsis seedling were compared.

first: Sumire

last: Fujiwara

first: Yuko

last: Takiguchi


title: Changes in Gene Expression in the Larval Gut of Ostrinia nubilalis in Response to Bacillus thuringiensis Cry1Ab Protoxin Ingestion

status: Public on Mar 08 2014

city: College Station

first: jianxiu

last: yao

state: Texas

address: 422 Minne heep center

department: Entomology

institute: Texas A&M university

summary: This microarray was used to monitor gene expression in early third-instar larvae of Bt-susceptible O. nubilalis after 6-h feeding on diet with or without Bacillus thuringiensis (Bt) Cry1Ab protoxin.We identified 174 transcripts, for which the expression was changed more than 2-fold in the gut of the larvae fed Cry1Ab protoxin (p<0.05), representing 80 down-regulated and 94 up-regulated transcripts. Among 174 differentially expressed transcripts, 13 transcripts putatively encode proteins that are potentially involved in Bt toxicity, and these transcripts include eight serine proteases, three aminopeptidases, one alkaline phosphatase, and one cadherin.

overall_design: Cry1Ab protoxin ingestion induced gene expression was measured in O. nubilalis gut at 6 after Cry1Ab protoxin toxin exposure to doses of 0.25 μg/ml artificial diet.  three independent experiments were performed using three insect gut samples,and each sample was from five insects' gut pooled.

first: Jianxiu

last: Yao

first: Kun

last: Zhu


title: Platform for Induction and Maintenance of Transgene-Free hiPSCs Resembling Ground State Pluripotent Stem Cells

city: San Diego

first: Bahram

last: Valamehr

address: 3535 General Atomics Court Tte 200

institute: Fate Therapeutics Inc.

summary: The purpose of this series of experiments is to identify copy number variations, duplications, deletions and regions of homozygosity in human induced pluripotent stem (hiPSC) cell lines.

overall_design: Genomic DNA of human induced pluripotent stem cell lines are extracted and hybridized to Agilent aCGH+SNP microarray, using genotyped Agilent Reference DNA as common reference. Differences and similarities between fibroblast and stem cell lines will be revealed.

first: Karen

last: Montgomery

first: Melodee

last: Patterson


title: a-CGH of Esophageal Cancer (53 cases)

first: Lin

last: Li

overall_design: We conducted whole-genome sequencing in 17 ESCC cases and whole-exome sequencing in 71 cases, of which 53 cases and additional 70 ESCC cases were subjected to array comparative genomic hybridization (a-CGH) analysis.

first: Qimin

last: Zhan

first: Yongmei

last: Song

first: Yunwei

last: Ou

first: Zhibo

last: Gao


title: Analysis of the iron stimulon and fur regulon of Geobacter sulfurreducens

first: Mallory

last: Embree


title: Listeria monocytogenes exposure to chlorine dioxide

status: Public on Mar 07 2014

city: West Lafayette

first: Aaron

middle: Mark

last: Pleitner

state: IN

address: 745 Agriculture Mall Drive

department: Food Science

institute: Purdue University

summary: Listeria monocytogenes strain 10403S has been studied extensively for stress response activity toward multiple stressors (acid, osmotic, cold, high temperature, etc.) as well as multiple stress regulons (SigB, CtsR, HrcA, etc.).  Here we aimed to determine the transcriptional response of Listeria monocytogenes in early log phase towards the strong oxidative stress imposed by ClO2.  The elucidation of such a response allows for further a more completel understanding of the mechanism of inactivation by sanitizers, specifically ClO2.

platform_organism:
Listeria monocytogenes
Listeria innocua

overall_design: Independent RNA isolations were performed for strain 10403S with and without exposure to ClO2 from cells grown to early log phase. Four biological replicates were used in competitive whole-genome microarray experiments. For each set of hybridizations, RNA from a control sample of Listeria monocytogenes was hybridized with RNA from a culture of L. monocytogenes following exposure to ClO2. Dye swapping was performed for the four replicates to mitigate any concerns of dye bias.

first: A

first: H

last: Oliver


title: MicroRNA expression profiles distinguish liposarcoma subtypes and implicate miR-145 and miR-451 as tumor suppressors (validation)

status: Public on Mar 01 2014

city: Rotterdam

first: Erik

last: Wiemer

address: Wytemaweg 80

department: Medical Oncology

institute: Erasmus University Medical Center

summary: Liposarcomas are rare, heterogeneous and malignant tumors that can be divided into five histological subtypes with different characteristics and clinical behavior. Treatment consists of surgery in combination with systemic chemotherapy, but nevertheless mortality rates are high. More insight into the biology of liposarcoma tumorigenesis is needed to devise novel therapeutic approaches. MicroRNAs (miRNAs) have been associated with carcinogenesis in many tumors and may function as tumor suppressor or oncogene. In this study we examined miRNA expression in an initial series of 57 human liposarcomas (including all subtypes), lipomas and normal fat by miRNA microarrays. Supervised hierarchical clustering of the most differentially expressed miRNAs (p<0.0002) distinguished most liposarcoma subtypes and control tissues. The distinction between well differentiated liposarcomas and benign lipomas was blurred, suggesting these tumor types may represent a biological continuum. MiRNA signatures of liposarcoma subtypes were established and validated in an independent series of 58 liposarcomas and control tissues. The expression of the miR-143/145 and miR-144/451 cluster members was clearly reduced in liposarcomas compared to normal fat. Overexpression of miR-145 and miR-451 in liposarcoma cell lines decreased cellular proliferation rate, impaired cell cycle progression and induced apoptosis. In conclusion, we show that miRNA expression profiling can be used to discriminate liposarcoma subtypes, which could aid in objective diagnostic decision making. In addition, our data indicate that miR-145 and miR-451 act as tumor suppressors in adipose tissue and show that re-expression of these miRNAs could be a promising therapeutic strategy for liposarcomas.

overall_design: 57 samples discovery set, 58 samples in validation set, subdivided in 5 liposarcoma subtypes plus lipomas and normal fat as control samples. Each sample was analysed on one array. All array probes are present in duplicate.

first: Caroline

last: Gits

first: Patricia

last: van Kuijk

first: Moniek

last: Jonkers

first: Marcel

last: Smid

first: Wilfred

last: van IJcken

first: Jean-Michel

last: Coindre

first: Fréderic

last: Chibon

first: Cornelis

last: Verhoef

first: Ron

last: Mathijssen

first: Michael

last: den Bakker

first: Jaap

last: Verweij

first: Stefan

last: Sleijfer

middle: C


title: Effects of  estradiol and growth hormone on liver transcriptome in hypothyroid-orquiectomized rats

status: Public on Feb 28 2014

city: Las Palmas de Gran Canaria

first: Leandro

last: Fernandez-Perez

state: Las Palmas

address: Campus of San Cristóbal

department: Clinical Sciences

country: Spain

institute: University of Las Palmas de Gran Canaria

summary: E2 and GH are critical regulators of growth and intermediate metabolism in mammals. Hypothyroidism causes endocrine and metabolic disturbances in the liver with features that mimic deficiencies of E2 or GH signalling. In this work, we used the hypothyroid-orchiectomized (TXOX) adult rat model to evaluate the influence of E2 and GH on the liver in terms of global changes in gene expression. This study shows the changes in hepatic transcriptome that were provoked by E2 benzoate (50 ug/kg; sc; 5 days per week x 27 days), intermittent GH administration (0.3 mg/kg/day;sc injection divided into two daily injections x 7 days) or the combination of E2 plus GH in TXOX rats. E2 influenced the liver transcriptome, particularly genes involved in metabolism of lipids and endo-xenobiotics, and the GH-regulated endocrine, metabolic, gender, and immune responses. E2 did not prevent the inhibitory effects of GH on urea and amino acid metabolism-related genes. Notably, the combination of E2 and GH caused deleterious effects on transcriptional immune response. These results highlight the role of E2 as a critical regulator of liver metabolism in mammals and provide insights into the functional interplay between E2 and GH in the liver.

overall_design: Groups=4;  Biological replicates = 4 per group; Samples=16; Reference samples=TXOX group. Adult (3 months old) male Sprague-Dawley rats (n=4 per group) were used throughout these experiments. The generation of TXOX was performed by adding methimazole (MMI; 0.05%) to the drinking water for 5 weeks starting on postnatal day (PND) 59 until sacrifice on PND94. Two weeks after starting MMI administration, male rats were castrated (OX) to make TXOX rats. Four days after OX, we began treatment with E2 benzoate (TXOXE2) or vehicle (TXOX) to TXOX rats for 20 days followed for 7 days by either vehicle plus GH (TXOXGH) or by E2 plus GH (TXOXE2GH). Twenty-four hours (in the case of E2) or twelve hours (in the case of GH) after the last injection, the animals were killed by exsanguinations. Portions of the liver were snap frozen in liquid nitrogen and stored at -80C until processed for mRNA analysis.

last: Fernández-Pérez


title: MicroRNA expression profiles distinguish liposarcoma subtypes and implicate miR-145 and miR-451 as tumor suppressors

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

overall_design: Refer to individual Series


title: Expression data from rhesus macaque jejunum

status: Public on Feb 27 2014

city: Davis

last: George

address: 451 Health Sciences Drive

department: Medical Microbiology and Immunology

institute: University of California, Davis

summary:
The mucosa that lines the gastrointestinal (GI) tracts is an important portal of entry for pathogens and provides the frontline of immune defense against HIV infection. Epithelial barrier dysfunction during HIV infection has largely been attributed to the rapid and severe depletion of CD4 T cells in the gastrointestinal (GI) tract. In this study, the poential role of small non-coding microRNA (miRNA) to contribute to epithelial dysfunction was investigated in the non-human primate SIV model and microarrays were utilized to determine changes in mucosal gene expression (non-miRNA) that could be correlated to  miRNA modulatiolns.
Microarrays were used to characterize changes in gene expression in the jejunal mucosa that occur during chronic SIV infection

overall_design: Jejunum tissues from healthy uninfected macaques and macaques with chronic stage SIV infection were used for RNA extraction and hybridization on Affymetrix microarrays.


title: MicroRNA expression profiles distinguish liposarcoma subtypes and implicate miR-145 and miR-451 as tumor suppressors (discovery)


title: Embelin induced differential gene expression in A549 lung cancer cells

status: Public on Jan 25 2014

city: Hyderabad

first: Shasi

middle: Vardhan

last: Kalivendi

state: Andhra Pradesh

address: Uppal Road, Tarnaka

department: Center for Chemical Biology

institute: CSIR - Indian Institute of Chemical Technology

summary: Embelin (15 uM) induced alterations in the gene expression profile was studied in A549 lung cancer cells during the initial stages of apoptosis  (4h following treatment)

overall_design: As embelin (15 uM) induces apoptosis as early as 4h time period, we performed  microarray analysis to study embelin-induced differential gene expression as early as 4h to identify the responsible pathways.

first: Deepa

last: Avisetti

middle: V


title: MeDIP-chip from dorsal root ganglia (DRG) tissue from wildtype mice, for 5-methyl-cytosine

city: London

first: Simone

last: Di Giovanni

address: DuCane Road W12 ONN UK

country: United Kingdom

institute: Imperial College

type: Methylation profiling by genome tiling array

summary:
Nerve injury in the peripheral  nervous system allows spontaneous regeneration, in contrast to injury of central nerves, which lead to a differential expression pattern of regeneration-associated genes and others. These genes might be regulated by promoter DNA methylation
As regeneration model, DRG tissue was analyzed for methyated gene promoters and CpG islands following both injury types. A differential methylation pattern could be identified, although most genes remained unmethylated.

overall_design: comparison of DRG following either sciatic nerve axotomy (SNA) or dorsal column axotomy (DCA) - each 'real injury or sham' - at 1, 3 or 7 days post-injury vs. 'naive', Each sample was pooled from two mice, yielding an immunoprecipitated sample ('Test') and an input genomic DNA sample (Ref). altogether 33 microarrays were used for 13 conditions with triplicate arrays for 'real injury' or 'naive' samples, and duplicate arrays for 'sham' samples.

first: Ricco

last: Lindner


title: The persistent milk yield response to frequent milking during early lactation is associated with persistent changes in mammary gene expression

status: Public on Jan 01 2014

city: Burlington

first: Emma

middle: Hull

last: Wall

state: VT

address: 89 Beaumont Ave

institute: University of Vermont

summary:
BACKGROUND:
The lactating mammary gland responds to changes in milking frequency by modulating milk production. This response is locally regulated and, in dairy cows, the udder is particularly sensitive during early lactation. Relative to cows milked twice-daily throughout lactation, those milked four-times-daily for just the first 3 weeks of lactation produce more milk throughout that lactation. We hypothesized that the milk yield response would be associated with increased mammary cell turnover and changes in gene expression during frequent milking and persisting thereafter. Cows were assigned to unilateral frequent milking (UFM; left udder halves milked twice-daily; right udder halves milked four-times daily) on days 1 to 21 of lactation, followed by twice-daily milking for the remainder of lactation. Relative to udder halves milked twice-daily, those milked four-times produced more milk during UFM; the difference in milk yield declined acutely upon cessation of UFM after day 21, but remained significantly elevated thereafter. We obtained mammary biopsies from both udder halves on days 21, 23, and 40 of lactation.

RESULTS:
Mammary cell proliferation and apoptosis were not affected by milking frequency. We identified 75 genes that were differentially expressed between paired udder halves on day 21 but exhibited a reversal of differential expression on day 23. Among those genes, we identified four clusters characterized by similar temporal patterns of differential expression. Two clusters (11 genes) were positively correlated with changes in milk yield and were differentially expressed on day 21 of lactation only, indicating involvement in the initial milk yield response. Two other clusters (64 genes) were negatively correlated with changes in milk yield. Twenty-nine of the 75 genes were also differentially expressed on day 40 of lactation.

CONCLUSIONS:
Changes in milking frequency during early lactation did not alter mammary cell population dynamics, but were associated with coordinated changes in mammary expression of at least 75 genes. Twenty-nine of those genes were differentially expressed 19 days after cessation of treatment, implicating them in the persistent milk yield response. We conclude that we have identified a novel transcriptional signature that may mediate the adaptive response to changes in milking frequency.

overall_design: 36 samples from 6 cows; 3 timepoints

first: E

middle: H

first: J

middle: P

last: Bond

first: T

last: McFadden


title: Calcium deficient transcriptome analysis of rice

status: Public on Jan 17 2014

city: NEW DELHI

first: GIRDHAR

middle: KUMAR

last: PANDEY

state: DELHI

address: BENITO JUAREZ ROAD

department: Plant Molecular Biology

institute: Delhi University South Campus

summary:
Calcium is an essential macronutrient and plant requires it in large amounts for normal growth and development. This ion participated in innumerable processes and affects nearly all aspects of plant growth and development such as signal transduction, metabolism of lipids, proteins, and carbohydrates, cell growth, cell wall and membrane stabilization.
We used whole genome microarrays to determine the transcriptomic profile of rice seedlings exposed to short-term and long term Ca2+ deficiency followed by Ca2+ resupply.

overall_design: Calcium treated seedlings were used for for RNA extraction and hybridization on Agilent microarray platform. Three biological replicates of each sample were used for microarray analysis. We wanted to know the altered expression patterns of calcium-responsive genes majorly involved in metabolic processes, signal transdction pathways, transcriptional regulation, and transport of multiple molecules including Ca2+. Seeds of indica rice were surface sterilized and grown hydroponically in rice growing medium. Plants were grown in the rice growth room under the condition of 16 h light/8 h dark (28°C) photoperiod with 70 % humidity. After 5 days of normal growth, some of the seedlings were transferred to nutrient solution lacking CaCl2 (-Ca2+). After 5 and 14 days, calcium (0.798 mM CaCl2) was resupplied to the plants grown in -Ca2+ medium for 6 h.

first: Alka

last: Shankar

first: Ashish

middle: K

last: Srivastava

first: Akhilesh

last: Yadav

first: Manisha

last: Sharma

first: Amita

last: Pandey

first: Penna

last: Suprasanna

first: Girdhar


title: Intratumoral heterogeneity of prostate cancers

status: Public on Jan 18 2014

city: Seoul

first: Tae-Min

last: Kim

address: Seocho-Gu, Banpo-Dong

department: Dept of Medical Informatics

institute: The Catholic University of Korea, College of Medicine

summary:
Copy number analyses of regionally separated intratumoral biopsies of prostate cancers.
Intratumoral heterogeneity (ITH) leads to regional biases of the mutational landscape in a single tumor and may influence the single biopsy-based clinical diagnosis and treatment decision. To evaluate the extent of ITH in unifocal prostate cancers (PCAs) that had not been sought, we analyzed multiple regional biopsies from three PCAs using DNA copy number analyses. DNA copy number showed ITH including regional biases in the presentation of a well-known driver of TMPRSS2-ERG fusion.  Our analyses identified a substantial level of genetic ITH in unifocal PCAs at the genomic levels, which should be taken into account for the curation of biomarkers in the clinical setting.

overall_design: Four intratumoral biopsies were obtained per tumor for three prostate cancers. Radical prostatectomy tissue from three patients with prostate cancers were obtained.  Board-certified pathologists reviewed the hematoxylin&eosin stained sections and identified tumor-rich regions (> 80% purity).  We selected four different areas for biopsy that were at least 5mm apart and were comprised of the most common Gleason pattern (the most common histologic patterns with minimal histologic differences).  Copy number profiling was performed using Agilent 180K platform according to the manufacturer's protocol.


title: Gene expression changes in Nicd induced wing disc hyperplasia

status: Public on Dec 31 2013

city: Cambridge

first: Sarah

last: Bray

address: Downing Street

department: PDN

institute: University  of Cambridge

summary: The outcome of Notch proliferation on proliferation depends on the context. In Drosophila wing imaginal discs Notch activation causes hyperplasia despite having localized inhibitory effects on proliferation. To understand te underlying mechanisms we have used genomic strategies to identify the Notch-Su(H) target genes during wing discs hyperplasis. these data are the results from expression profiling the RNAs from hyperplastic wing discs overexpressing Nicd.

overall_design: Direct comparison of third instar lavae wing imaginal disc Nicd (abxUbxFLPase; Act>y>Gal4, UAS GFP; FRT82B tubGal80 with UAS-Nicd; FRT82B) vs control (abxUbxFLPase; Act>y>Gal4, UAS GFP; FRT82B tubGal80 with FRT82B ). 4 Biological replicates, the 2nd replicate was performed as a dye-swap.

first: Alexandre

last: Djiane

first: Alena

last: Krejci


title: Gene expression changes in Su(H) induced wing disc hyperplasia

summary: The outcome of Notch activation of proliferation depends on cellular context. In Drosophila wing discs Notch pathway overactivation results in hyperplasia. To understand the mechanisms we have used genomic strategies to indetify the Notch-S(H) target genes directly regulated in wing disc hyperplasia. These data are the results from expression profiling the RNAs from hyperplastic wing discs overexpressing Su(H).

overall_design: Direct comparison of Giant third instar lavae wing imaginal disc (UAS-GFP:Su(H) expressed by the patched[559.1]-Gal4 driver) vs control (UAS-NLS-GFP expressed by the patched[559.1]-Gal4 driver). 3 Biological replicates, the 3rd replicate was performed as a dye-swap.


title: Comparative Time Course Profiles of Phthalate Stereoisomers in Mice

status: Public on Dec 20 2013

city: RTP

first: Charles

last: Wood

state: NC

address: 109 TW Alexander Drive

institute: US EPA

summary: Analysis of gene expression level in a mouse tumorigenic phthalate, DEHP vs non-tumorigenic DNOP.  The hypothesis tested in the present study was to identify early key event thresholds related to tumor outcomes in a two-year carcinogenicity bioassay.  Our results highlight marked differences in the toxicity profiles of structurally similar phthalates and demonstrate quantitative relationships between early bioindicators and later tumor outcomes.

overall_design: Total RNA obtained from liver samples subjected to 30wk exposures of cont, DEHP, DNOP.  Samples processed with Illumina Mouse WG 8-v 2.0 beadarrays.  Gene profiles generated for the compounds support observed key events in mode-of-action for these phthalates.

first: Susan

last: Hester


title: Differentially expressed miRNAs in TGF-β1-knock down mice CT26 colorectal cancer cell lines vs controls

status: Public on Dec 16 2013

city: suzhou

first: shouli

last: wang

address: renai road 199, suzhou industrial park

department: pathology

institute: soochow university school of medicine

summary: To investigate the role of TGF-β1-regulated miRNAs in the progression of colorectal cancer,we performed comprehensive miRMA microarray analysis on RNA derived from CT26 cell lines and TGF-β1 knock-down  CT26 cell lines. We identified a novel set of TGF-β1-related miRNAs.

platform_organism:
Homo sapiens
Mus musculus
Rattus norvegicus

overall_design: Total RNA was isolated from TGF-β1-knock down CT26 cell lines and controls.Three-condition experiment: Locked nucleic acid microarray analyses to obtain miRNA expression profiles independently in TGFβ1-knocked down CT26 and control cell line at three different time (24hours, 48hours and 72hours).Biological replicates: 1 CT26 cells stably transfected with shRNA-TGF-β1- pSUPER gfp-neo for 24hours, 1 CT26 cells stably transfected with shRNA-TGF-β1- pSUPER gfp-neo for 48hours, 1 CT26 cells stably transfected with shRNA-TGF-β1- pSUPER gfp-neo for 72hours, 1 CT26 cells stably transfected with shRNA-Control- pSUPER gfp-neo for 24hours, 1 CT26 cells stably transfected with shRNA- Control- pSUPER gfp-neo for 48hours, 1 CT26 cells stably transfected with shRNA-Control- pSUPER gfp-neo for 72hours, independently grown and harvested. One replicate per array.

first: Shouli

last: Wang

first: Yuting

last: Kuang


title: Differentially expressed miRNAs in TGF-β1-knock down human colorectal cancer cell lines vs controls

summary: To investigate the role of TGF-β1-regulated miRNAs in the progression of colorectal cancer,we performed comprehensive miRMA microarray analysis on RNA derived from typical human colorectal cancer cell lines and TGF-β1 knock-down  human colorectal cancer cell lines. We identified a novel set of TGF-β1-related miRNAs.

overall_design: Total RNA was isolated from TGF-β1-knock down colorecatl cancer cell lines and controls.Three-condition experiment: shRNA-TGF-β1/Lovo cells vs. shRNA-Control/Lovo cells, shRNA-TGF-β1/SW620 cells vs. shRNA-Control/ SW620 cells, and shRNA-TGF-β1/HT29 cells vs. shRNA-Control/HT29 cells. Biological replicates: 1 Lovo cells stably transfected with shRNA-TGF-β1- pSUPER gfp-neo, 1SW620 cells stably transfected with shRNA-TGF-β1- pSUPER gfp-neo, 1HT29 cells stably transfected with shRNA-TGF-β1- pSUPER gfp-neo, 1Love cells stably transfected with shRNA-Control- pSUPER gfp-neo, 1SW620 cells stably transfected with shRNA-Control- pSUPER gfp-neo, and 1HT29 cells stably transfected with shRNA-Control- pSUPER gfp-neo, independently grown and harvested. One replicate per array.


title: Differentially expressed miRNAs in colon cancer tissues vs normal colon tissues

summary: To investigate the role of miRNAs in the progression of colon cancer, we performed comprehensive miRMA microarray analysis on RNA derived from colon cancer tissues and normal colon tissues. We identified a novel set of colon cancer-related miRNAs.

overall_design: Total RNA was isolated from colon cancer tissues and normal colon tissues. Six-condition experiment: H normal tiss vs. H tumor tissue, S normal tiss vs. S tumor tissue, W1 normal tiss vs. W1 tumor tissue, M normal tiss vs. M tumor tissue, W2 normal tiss vs. W2 tumor tissue, and Y normal tiss vs. Y tumor tissue. Biological replicates: 1H normal tiss, 1H tumor tissue, 1S normal tiss，1S tumor tissue, 1W1 normal tiss，1W1 tumor tissue, 1M normal tiss，1M tumor tissue, 1W2 normal tiss，1W2 tumor tissue, 1Y normal tiss and 1Y tumor tissue, independently grown and harvested. One replicate per array.


title: Comparative transcriptional analysis of Desulfovibrio alaskensis G20 grown under various syntrophic and fermentative conditions on pyruvate relative to respiratory growth

status: Public on Dec 12 2013

city: Berkeley

first: Jennifer

last: Kuehl

address: 1 Cyclotron Road

department: Physical Biosciences

institute: Lawrence Berkeley National Laboratory

summary:
Pyruvate fermentation pathway and energetics of Desulfovibrio alaskensis strain G20 under syntrophic coculture and fermentative monoculture conditions
Expression data for Desulfovibrio alaskensis strain G20 grown in chemostats on pyruvate under respiratory conditions (sulfate-limited and pyruvate-limited monoculture, dilution rate 0.047 and 0.027 h-1), fermentative conditions (monoculture, dilution rate 0.036 h-1), and syntrophic conditions (coculture with Methanococcus maripaludis or Methanospirillum hungatei, dilution rate of 0.047 and 0.027 h-1)

overall_design: 2 replicates each for syntrophic coculture (M. maripaludis or M. hungatei pairing) and respiratory (sulfate- or pyruvate-limited) monoculture for both growth rates (0.027 and 0.047 h-1), and 4 replicates fermentative monoculture (gas flow rate through head space of bioreactor 10 ml/min (chemostats C91 and C93) or 1 ml/min (chemostats C92 and C94)

first: Birte

last: Meyer

first: Adam

last: Deutschbauer

first: Morgan

middle: N

last: Price

last: Arkin

first: David

last: Stahl


title: Loss of Bright/Arid3A reprograms MEFs to a pluripotent state

status: Public on Nov 25 2013

city: Austin

first: Bum-Kyu

last: Lee

address: 2506 Speedway Stop A5000

institute: University of Texas at Austin

summary:
Bright null mouse embryonic stem cells and spontaneously reprogrammed Bright null cells compared to WT mouse embryonic stem cells;Work further described in Popowski et. al 2013
Bright null mouse embryonic stem cells and wildtype mouse embryonic stem cells differentiated in embryoid bodies at day 6 and day 15

overall_design: Total RNA from each cell line using indicated replicates

first: Haley

last: Tucker

first: Vishy

last: Iyer


title: SABioscience mouse PCR array of  the ear tissues of Nickel allergy model

status: Public on Nov 19 2013

city: Tokushima

first: Naozumi

last: Ishimaru

address: 3-18-15 Kuramoto

department: Department of Oral Molecular Pathology

institute: Institute of Health Biosciences The University of Health Biosciences

summary: PCR array analysis was performed to investigate the expression of genes in the ear tissues of Ni allergy-induced miceand control mice.

overall_design: Ni model mouse n=3, control mouse n=3


title: miRNA expression differences between FFPE prostate cancer and adjacent normal  tissues using real-time quantitative PCR array analysis

status: Public on Nov 15 2013

city: Washington DC,

first: Deepak

last: Kumar

state: District of Columbia

address: 4200 Connecticut Avenue, NW

department: Biology

institute: University of the District of Columbia

summary: Laser Capture Microdissected cells from archival FFPE Prostate cancer and normal adjacent tissues from 10 patients (5 CA and 5 AA) were converted to cDNA and analysed by PCR array to identify differentially expressed miRNAs between the groups. Selected differentially expressed miRNAs were further validated in tissues from 40 prostate cancer patients. The miRNAs which were differentially modulated in PCa patients in the validation set were further analysed in 32 urine samples from PCa patients and compared with 12 healthy individuals. Differentially expressed miRNAs were explored to e used as non-invasive biomarker for PCa.

overall_design: qPCR miRNA expression profiling.  mRNA  from 10 Prostate Cancer patients  (5 Caucasian American and 5 African American) and their paired adjacent normal tissue were analysed to identify the differentially expressed miRNA between the groups. Equal amount small RNA from each group was pooled prior to gene expression analysis.

first: Anvesha

last: Srivastava

first: Alexander

last: Dimtchev

first: Catalin

last: Marian

first: Xin

last: Li


title: A microRNA-based primary tumor site classification of liver core biopsies

status: Public on Oct 19 2013

city: Copenhagen

first: Katharina

middle: Anne

last: Perell

address: Blegdamsvej

department: Dep. of Oncology

country: Denmark

institute: Copenhagen University Hospital

summary: To develop a classifier based on microRNAs for primary tumor site identification of liver core biopsies and to explore the influence of surrounding normal liver tissue on classification.

overall_design: Tissue samples from 333 patients, corresponding to one of the following ten assay classes, were obtained from archives of the pathology department, Copenhagen University Hospital, Rigshospitalet, Denmark: Lung cancer, breast cancer, gastric/cardia cancer, colorectal cancer, bladder cancer, pancreatic cancer, hepatocellular carcinoma, cholangiocarcinoma, squamous cell cancers of different origin, and normal liver tissue

first: Martin

last: Vincent

first: Ben

last: Vainer

first: Bodil

middle: L

last: Petersen

first: Birgitte

last: Federspiel

first: Anne

last: Møller

first: Mette

last: Madsen

first: Niels

last: Hansen

first: Lennart

last: Friis-Hansen

first: Finn

last: Nielsen

first: Gedske

last: Daugaard


title: Comparison of the translational program in oocytes from wild type and Areg KO mice

status: Public on Oct 02 2013

city: San Francisco

first: Courtney

last: Onodera

address: 1450 Third St, HD374

institute: University of California, San Francisco

summary:
The study tests the hypothesis that maternal mRNA translation in oocytes is sensitive to the environment in which the oocytes mature. Amphiregulin (AREG) is a critical signal for oocyte maturation but also for oocyte developmental competence. Here we have used a genome-wide approach to determine whether the oocyte translational program is affected when oocytes mature in vivo in the absence of AREG.
To this aim, polysome arrays were used to define patterns of transcript recruitment to the polysomes in oocytes derived from wild type mice and mice homozygous null for the Areg gene.

overall_design: Forty-eight hours (h) after PMSG injection, mice were stimulated with hCG for 0, or 14 h, and GV, and MII stage oocytes were collected. Polysome bound mRNAs were purified, reverse-transcribed and linearly amplified with WT-Ovation FFPE RNA Amplification System V2 (NuGEN). 5µg cDNA were fragmented and hybridized with Affymetrix Mouse Genome 430.2 array chips. Experiments were done using 3 independent sample sets.

first: Jing

last: Chen

first: Simona

last: Torcia

first: Fang

last: Xie

first: Chih-Jen

last: Lin

first: Hakan

last: Cakmak

first: Frederica

last: Franciosi

first: Kathleen

last: Horner

first: Jun

middle: S

last: Song

first: Marcelle

middle: I

last: Cedars

first: Miguel

last: Ramalho-Santos

first: Marco

last: Conti


title: Vitrification alters fetal development by profound differences during fetal placenta formation

status: Public on Sep 26 2013

city: Valencia

first: M. Desemparats

last: Saenz-de-Juano

state: Valencia

address: Camino de Vera s/n

department: Animal Science

institute: Universidad Politécnica Valencia

summary: Vitrification is replacing slow freezing as the most popular method for human embryo cryopreservation in clinics world-wide. Several studies demonstrated that cryopreservation alters gene expression of mammalian embryos, but none of them analysed what happen with those embryos that get implanted and follow with the gestation. The aim of this study was to evaluate the effect of vitrification technique on rabbit embryonic and fetal development by performing a transcriptomic analysis of 6 day old embryos and 14 days old fetal placentas.

overall_design: Effect of vitrification on late blastocyst and fetal placenta transcriptome. Four indepent replicates were performed for each condition (control and vitrified) and for both tissues (embryo and fetal placenta).

first: M

middle: D

first: J

last: Vicente

first: F

last: Marco-Jiménez

first: V

last: Duranthon

first: B

last: Schmaltz-Panneau

first: L

last: Jouneau


title: Host reponse of silkworm, Control vs. Nb infected

status: Public on Sep 27 2013

city: Chongqing

first: Tian

last: Li

address: Beibei District Tiansheng Road #2

department: State Key Laboratory of Silkworm Genome Biology

institute: Southwest University

summary:
Microsporidia have attracted much attention because they infect a variety of species ranging from protists to mammals, including immunocompromised patients with AIDS or cancer. Aside from the study on Nosema ceranae, few works have focused on elucidating the mechanism in host response to microsporidia infection. Nosema bombycis is a pathogen of silkworm pébrine that causes great economic losses to the silkworm industry. Detailed understanding of the host (Bombyx mori) response to infection by N. bombycis is helpful for prevention of this disease.
The 23 K silkworm genome array was used to investigate host responses (i.e., Bombyx mori) occurring at 2, 4, 6 and 8 d post-infection by Nosema bombycis.We focused on elucidating the mechanism of the host response to microsporidia infection, especially for the investigation of host immune response .

overall_design: The third instar molted silkworm larvae were in oral infected by Nosema bombycis. In order to known the silkworm host response to Nosema bombycis infection at different time points, samples of infected larvae (i.e., the treatment set) and uninfected larvae (i.e., the control set) were collected at 2, 4, 6 and 8 dpi for RNA extraction and array hybridization. The obtained data were usd to investigate on the interplay of the genome-wide expression profile of hosts.

first: Zhengang

last: Ma


title: Association of childhood chronic physical aggression with a DNA methylation signature in adult human T cells

status: Public on Sep 30 2013

city: Montreal

first: Moshe

last: Szyf

state: Quebec

address: McIntyre Medical Building, 3655 Promenade Sir William Osler, Room 1309

department: Pharmacology

country: Canada

institute: McGill University

summary: Chronic physical aggression (CPA) is characterized by frequent use of physical aggression from early childhood to adolescence. Observed in approximately 5% of males, it is associated with early childhood adverse environments. DNA methylation, a covalent modification of DNA, regulates genome function and has been associated with early childhood adverse environments. We analyzed T cell DNA genome-wide promoter methylation profiles from two groups of adult males assessed annually for frequency of physical aggression between 6 and 15 years of age: a group with CPA and a control group. Whole genome methylation analysis was performed using MeDIP followed by hybridization to microarrays. We mapped the promoter regions of 20 000 genes and 400 microRNAs.

overall_design: The subjects were recruited from participants in two longitudinal studies of child development9,47. We recruited two groups of Caucasian males who were born in families with a low socioeconomic status and were living at the time of the present study within 200km from our laboratory. The first group had a history of high physical aggression from age 6 to 15 years (chronic physical aggression group, CPA). The second group was recruited from the same longitudinal studies but included only those who did not have a history of high physical aggression from age 6 to 15 (Control group). A total of 65 eligible subjects agreed to participate (8 CPA and 57 controls). Using custom-designed microarrays with 244K probes tiling the promoter regions of 20000 genes and 400 microRNAs, we obtained DNA methylation profiles by meDIP-chip.  Each profile was generated in triplicate.

first: Nadine

last: Provencal

first: Matthew

last: Suderman

first: Claire

last: Guillemin

first: Richard

middle: E

last: Tremblay


title: Genomic profiling of oral squamous cell carcinoma by array-based comparative genomic hybridization

status: Public on Sep 08 2013

city: Yufu-city

first: shunichi

last: yoshioka

address: Hasama-machi Idaigaoka 1-1

department: Depertment of Molecular Pathology

institute: Faculty of Medicine, Oita University

summary: In this study, we investigated CNAs of 40 tumor samples from 25 patients, including 15 metastatic primary tumor (MPT), paired neck lymph-node metastasis (LNM) and 10 non-metastatic primary tumor (NMPT), by 44k oligonucleotide-based array comparative genomic hybridization (array CGH).

overall_design: 15 MPT vs 15 LNM, 10 NMPT vs 15 LNM

first: Shunichi

last: Yoshioka

first: Yoshiyuki

last: Tsukamoto

first: Naoki

last: Hijiya

first: Chisato

last: Nakada

first: Tomohisa

last: Uchida

first: Keiko

last: Matsuura

first: Seto

last: Masao

first: Ichiro

last: Takeuti

first: Kenji

last: Kawano

first: Masatsugu

last: Moriyama


title: A Proneural to Mesenchymal Transition Mediated by NFkB Promotes Radiation Resistance in Glioblastoma (part 2)

status: Public on Aug 15 2013

first: Brian

last: Vaillant

state: TX

department: Neurology

institute: Seton Brain and Spine Institute

summary:
SUMMARY  Despite numerous genome-wide association studies involving glioblastoma (GBM), few therapeutic targets have been identified for this disease. Using patient derived glioma sphere cultures (GSCs), we have found that a subset of the proneural (PN) GSCs undergo transition to a mesenchymal (MES) state in a TNFa/NFkB dependent manner with an associated enrichment of CD44 sub-populations and radio-resistant phenotypes. To the contrary, MES GSCs exhibit constitutive NFkB activation, CD44 enrichment and radio-resistance. Patients whose tumors exhibit a higher MES metagene, increased expression of CD44, or activated NFkB were associated with poor radiation response and shorter survival. Our results indicate that NFkB activation mediated MES differentiation and radiation resistance presents an attractive therapeutic target for GBM.
SIGNIFICANCE  In this study, we show plasticity between the proneural (PN) and mesenchymal (MES) transcriptome signatures observed in glioblastoma (GBM). Specifically, we show that PN glioma sphere cultures (GSCs) can be induced to a MES state with an associated enrichment of CD44 expressing cells and a gain of radio-resistance, which we implicate as NFkB- dependent. Newly diagnosed GBM samples show a direct correlation between radiation response, higher MES metagene, CD44 expression, and NFkB activation. This correlation is also observed in the subset of GBM samples that do not exhibit IDH1 mutation, a favorable prognostic marker. Our results uncover a previously unknown link between subtype plasticity that is regulated by NFkB. Inhibition of NFkB activation can directly impact radio-resistance and presents an attractive therapeutic target for GBM.

overall_design: 4 treatments

first: Krishna

last: Bhat

first: Veerakumar

last: Balasubramaniyan

first: Ravesanker

last: Ezhilarasan

first: Karlijn

last: Hummelink

first: Faith

last: Hollingsworth

first: Khalida

last: Wani

first: Lindsey

last: Heathcock

first: Johanna

last: James

last: Goodman

first: Siobhan

last: Conroy

first: Lihong

last: Long

first: Nina

last: Lelic

first: Suzhen

last: Wang

first: Joy

last: Gumin

first: Divya

last: Raj

first: Yoshinori

last: Kodama

first: Aditya

last: Raghunathan

first: Adriana

last: Olar

first: Kaushal

last: Joshi

first: Christopher

last: Pelloski

first: Amy

last: Heimberger

first: Se

last: Kim

first: Daniel

last: Cahill

first: Ganesh

last: Rao

first: Wilfred

middle: A

last: denDunnen

first: Hendrikus

middle: M

last: Boddeke

first: Heidi

last: Phillips

last: Nakano

first: Frederick

middle: F

last: Lang

first: Howard

last: Colman

first: Erik

last: Sulman

first: Kenneth

last: Aldape


title: Comparative transcriptional analysis of Desulfovibrio alaskensis G20 and regulator proteins mutants

status: Public on Aug 03 2013

first: Jennifer

last: Kuehl

state: California

summary:
Expression data for Desulfovibrio alaskensis strain G20 and mutants in regulator proteins grown on lactate sulfate media. Pellets collected at mid-log growth phase.
We aimed to confirm or expand the predicted regulons of each of the transposon interrupted regulator mutants.

overall_design: 12 samples were collected: 10 regulator mutants, 1 mutant in a secretory protein (Dde_2365) and 1 control sample Desulfovibrio alaskensis G20. 1 replicate for each condition.

first: Morgan

last: Price

first: Adam

last: Deutschbauer

last: Arkin

first: Pavel

last: Novichkov

first: Dmitry

last: Rodionov


title: Effect of overexpression of the OsWRKY53 or phospho-mimicking mutant of OsWRKY53 in rice

status: Public on Aug 31 2013

city: Tokyo

first: Kazunori

last: Okada

address: 1-1-1, Yayoi, Bunkyo-ku

department: Biotechnology Research Center

institute: The University of Tokyo

summary: To see the effect of phosphorylation of OsWRKY53, we compared the gene expression profiles in the rice plants overexpressing native OsWRKY53 or a phospho-mimicking mutant of OsWRKY53.

overall_design: Expression profiling in wild-type, OsWRKY53- or phospho-mimicking mutated OsWRKY53-overexpressing rice leaves was analyzed using one-color method with four biological replicates.

first: Satoshi

last: Ogawa

first: Takafumi

last: Shimizu

first: Tetsuya

last: Chujo

first: Koji

last: Miyamoto

first: Eiichi

last: Minami

first: Hisakazu

last: Yamane

first: Hideaki

last: Nojiri


title: Tellurite-mediated cefotaxime (CTX) potentiation

status: Public on Sep 01 2013

city: Santiago

first: David

middle: Enrique

last: Loyola

state: Santiago

address: Avenida Libertador Bernardo O'Higgins 340

country: Chile

institute: OMICS Solutions, Centro Nacional de Genómica y Bioinformática

summary: Transcriptional profiling comparing Escherichia coli simultaneously exposed to tellurite and CTX with untreated control cells; Tellurite with control; CTX with control

overall_design: Three-condition experiment,  antibacterial (tellurite; CTX or tellurite/CTX)  vs. Untreated control cells. Biological replicates: 3 control, 3 toxicants exposed cells, independently grown and harvested. One replicate per array.

first: R

middle: C

last: Molina-Quiroz

first: D


title: Comparative transcriptional analysis of Desulfovibrio alaskensis G20, a choline utilization regulator and LysX

middle: V

summary:
Expression data for Desulfovibrio alaskensis strain G20 and mutants in regulator proteins grown on lactate sulfate media and then pelleted and transferred to another media when they reached stationary phase. The Choline mutant was transferred to lacte/sulfate minimal media and choline/sulfate minimal media. The LysX mutant was transferred to minimal media with lysine and rich media. G20 was transferred to minimal media, choline/sulfate minimal media, lactate/choline/sulfate minimal media, minimal media with lysine, and rich media.
We aimed to confirm or expand the regulons of each of the transposon interupted regulator mutants and compare gene expression responses of the regulators in different growth conditions.

overall_design: 10 samples were collected: 2 regulator mutants (2 conditions each), Desulfovibrio alaskensis G20 (5 conditions), 2 replicates for G20 minimal media condition. Control sample -G20 rich media.


title: Adaption of Dinoroseobacter shibae to anaerobic conditions

status: Public on Aug 30 2013

city: Braunschweig

first: Sebastian

middle: Walter Friedrich

last: Laaß

address: Spielmannstraße 7

department: Inst. f. Mikrobiologie

country: Germany

institute: Technische Universität Braunschweig

summary: To unravel the adaptation strategies of D. shibae to anaerobic conditions in microaerobic to anaerobic parts of the ocean and to define the underlying regulatory network an anaerobic shift experiment in Salt-Water-Medium in a chemostate was established. Transcriptome analyses were used to investigate the physiological status of D. shibae under this conditions.

platform_organism: Dinoroseobacter shibae DFL 12 = DSM 16493

overall_design:
Dinoroseobacter shibae wild type strain DSM 16493T was grown in a chemostate in saltwater mininmal medium (SWM) mimicking the conditions in the marine habitat under anaerobic conditions. For growth under oxygen depletion the media were supplemented with 50 mM KNO3 to sustain anaerobic respiration. Therefore, D. shibae was grown aerobically in the chemostate until the culture reached the exponential phase, than countinuously cultivaion was started. The dilution rate was 0.1 h-1, establishing the approximate half-maximum growth rate of D. shibae in the exponential phase. The anaerobic shift was initialised after 20 hours by stopping the aeration. The samples were harvested before (as reference) and 30 minutes after stopping the airation. Three biological replica were analyzed.
Comparison:
Identification of genes induced or repressed under aerobic conditions in the Dinoroseobacter shibae wild type strain DSM 16493T. Here we compared the transcriptome profile of D. shibae wild type strain DSM 16493T grown aerobically in the chemostate in exponential phase with the transcriptome profile of the D. shibae wild type strain DSM 16493T which was  grown without aeration for 5, 10, 15, 20, 30, 60 and 120 min.

last: Laass

first: Johannes

last: Klein

first: Petra

last: Tielen

first: Dieter

last: Jahn


title: A Proneural to Mesenchymal Transition Mediated by NFkB Promotes Radiation Resistance in Glioblastoma (part 1)

first: Brian

last: Vaillant

overall_design: Gene expression data for 17 isolated Glioma Stem Cells

first: Krishna

last: Bhat

first: Veerakumar

last: Balasubramaniyan

first: Ravesanker

last: Ezhilarasan

first: Karlijn

last: Hummelink

first: Faith

last: Hollingsworth

first: Khalida

last: Wani

first: Lindsey

last: Heathcock

first: Johanna

last: James

last: Goodman

first: Siobhan

last: Conroy

first: Lihong

last: Long

first: Nina

last: Lelic

first: Suzhen

last: Wang

first: Joy

last: Gumin

first: Divya

last: Raj

first: Yoshinori

last: Kodama

first: Aditya

last: Raghunathan

first: Adriana

last: Olar

first: Kaushal

last: Joshi

first: Christopher

last: Pelloski

first: Amy

last: Heimberger

first: Se

middle: H

last: Kim

first: Daniel

middle: P

last: Cahill

first: Ganesh

last: Rao

first: Wilfred

last: denDunnen

first: Hendrikus

last: Boddeke

first: Heidi

last: Phillips

first: Ichiro

last: Nakano

first: Frederick

last: Lang

first: Howard

last: Colman

first: Erik

last: Sulman

first: Kenneth

last: Aldape


title: KB001-Gene expression profiling of histiocytic sarcomas in a canine model: the predisposed Flatcoated retriever dog

status: Public on Aug 07 2013

city: Utrecht

first: Marian

last: Groot Koerkamp

state: Utrecht

address: Heidelberglaan 25

department: Research

institute: Princess Maxima Center for Pediatric Oncology

summary: Background: The determination of altered expression of genes in specific tumor types and their effect upon cellular processes may create insight in tumorigenesis and help to design better treatments. The Flatcoated retriever is a dog breed with an exceptionally high incidence of histiocytic sarcomas. The breed develops two distinct entities of histiocytic neoplasia, a soft tissue form and a visceral form. Gene expression studies of these tumors has value for comparable human diseases such as histiocytic/dendritic cell sarcoma for which knowledge is difficult to accrue due to their rare occurrence. In addition, such studies may help in the search for genetic aberrations underlying the genetic predisposition in this dog breed.  Methods: Microarray analysis and pathway analyses were performed on fresh-frozen tissues obtained from Flatcoated retrievers with localized, soft tissue histiocytic sarcomas (STHS) and disseminated, visceral histiocytic sarcomas (VHS) and on normal canine spleens from various breeds.  Expression differences of nine genes were validated with quantitative real-time PCR (qPCR) analyses.   Results: QPCR analyses identified the significantly altered expression of nine genes; PPBP, SpiC, VCAM1, ENPEP, ITGAD (down-regulated), and GTSF1,  Col3a1, CD90 and LUM  (up-regulated) in the comparison of both the soft tissue and the visceral form with healthy spleen. DAVID pathway analyses revealed 24 pathways that were significantly involved in the development of HS in general, most of which were involved in the DNA repair and  replication process.  Conclusions:  This study identified altered expression of nine genes not yet implicated in histiocytic sarcoma manifestations in the dog nor in comparable human histiocytic/dendritic sarcomas. Extraploration of this downside effect of canine inbreeding strategies for the study of similar sarcomas in humans might also lead to the identification of genes related to these rare malignancies in the human.

overall_design: Microarray expression dataset including STHS: Soft Tissue (localized) Histiocytic Sarcoma; VHS: Visceral (disseminated)Histiocytic Sarcoma; together with normal spleen (NS) samples. Comparisons were analysed in dyeswap on a 2-color platform against a common reference sample, consisting of a multitude of canine organs, including liver, spleen, kidney, lung, hart, intestine and bone.

first: Kim

last: M. Boerkamp

first: Marieke

last: van der Kooij

first: Frank

middle: G

last: van Steenbeek

first: Monique

last: van Wolferen

last: Koerkamp

first: Dik

last: van Leenen

first: Guy

last: Grinwis

first: Louis

last: Penning

last: Wiemer

first: Gerard

middle: R

last: Rutteman


title: Expression data from five primary human glioblastomas (frozen surgical resection) and one non-neoplastic adult brain (frozen autopsy tissue)

status: Public on Aug 13 2013

city: SAN FRANCISCO

first: RAMAN

middle: PAUL

last: NAGARAJAN

state: CA

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 expression data obtained for five GBMs and one normal brain. We identified loci with concurrent DNA hypomethylation and H3K4me3 in GBM, and analyzed expression of the nearest gene in the same sample using these data

overall_design: Six total samples were analyzed. Each GBM sample was compared to normal brain to obtain expression changes

first: Raman

last: Nagarajan

first: Joseph

last: Costello


title: Gene expression comparison of P. atrosepticum and it's derivative vasH mutant

status: Public on Jul 03 2013

city: Helsinki

first: Panu

last: Somervuo

address: Viikinkaari 4

institute: University of Helsinki

summary: Effect of mutagenesis of a sigma 54-dependent transcriptional regulator encoding gene vasH (ECA3425) to global gene expression in P. atrosepticum SCRI1043 in planta mimicking conditions.

overall_design: Three biological replicates of the wild-type strain SCRI1043 and the mutant strain ΔvasH were grown in hrp inducing minimal media supplemented with 10% v/v tuber extract untill the culture reached late exponential phase. Differences in the gene expression in SCRI1043 and ΔvasH were analyzed by microarray.

first: Laura

last: Mattinen

first: Johanna

last: Nykyri

first: Minna

last: Pirhonen


title: Nanotoxicogenomic study of ZnO and TiO2 responses (Affymetrix)

status: Public on Jul 25 2013

city: Turku

first: Soile

last: Tuomela

address: P.O. Box 123

department: Turku Centre for Biotechnology

institute: University of Turku

summary:
A comprehensive in vitro assessment of two commercial metal oxide nanoparticles, TiO2 and ZnO, was performed using human monocyte-derived macrophages (HMDM), monocyte-derived dendritic cells (MDDC), and T cell leukemia-derived cell line (Jurkat). TiO2 nanoparticles were found to be non-toxic whereas ZnO nanoparticles caused dose-dependent cell death. Subsequently, global gene expression profiling was performed to identify signaling pathways underlying the cytotoxicity caused by ZnO nanoparticles. Analysis was done with doses, 1ug/ml and 10ug/ml after 6 and 24 hours of exposure. Interestingly, 2703 genes were significantly differentially expressed in HMDM upon exposure to 10ug/ml ZnO nanoparticles, while in MDDCs only 12 genes were affected. In Jurkat cells, 980 genes were differentially expressed. It is noteworthy that the gene expression of metallothioneins was upregulated in all the three cell types. In addition to the common ZnO-inducible changes, a notable proportion of the genes were regulated in a cell type-specific manner. Using a panel of ZnO nanoparticles, we obtained an additional support that the cellular response to ZnO nanoparticles is caused by particle dissolution. Gene ontology analysis revealed that the top biological processes disturbed in HMDM and Jurkat cells were regulating cell death and growth. In addition, genes controlling immune system development were affected. Bioinformatics assessment showed that the top human disease category associated with ZnO-responsive genes in both HMDM and Jurkat cells was cancer. Overall, the study revealed novel genes and pathways for mediating ZnO nanoparticle-induced toxicity and demonstrated the value of assessing nanoparticle responses through combined transcriptomics and bioinformatics approach.
Nanoparticles used in the study: ZnO-1 commercial (IBU-tec advanced materials AG), ZnO-2 (mandelic acid coated ZnO-1), ZnO-3 (mercaptopropyl-trimethoxysilane coated ZnO-1), ZnO-4 (methoxyl coated ZnO), ZnO-5 (diethylene glycol modified ZnO) and ZnO-9 (folic acid modified ZnO). Detailed particle production and characterization data can be found from the articles: Buerki-Thurnherr et al. 2012 Nanotoxicology and Tuomela et al.

overall_design: Altogether 71 samples were analyzed: 3 biological replicates of HMDM samples (untreated control, 10ug/ml of ZnO-1, 6 and 24 hours), 3 biological replicates of MDDC samples (untreated control, 6 and 24 hours), 7 biological replicates of MDDC samples (10ug/ml of ZnO-1, 24 hours), 3 replicates of Jurkat cells (untreated control, 10ug/ml of ZnO-1, 6 and 24 hours), 3 replicates of Jurkat cells (untreated control, 10ug/ml of ZnO-2, ZnO-3, ZnO-5 or ZnO-9, or 10, 25, 50 or 100ug/ml of ZnO-4, 24 hours).

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