title: Mouse P10 cerebellum: Smarca5 conditional KO mice (cKO) versus wild type controls

city: Ottawa

first: Alan

last: Mears

address: 401 Smyth Rd

department: Research Institute

institute: Children's Hospital of Eastern Ontario

summary: Gene expression profiling of mouse cerebellum in which the experimental strain conditionally lack the Smarca5 gene that encodes for the catalytic subunit of multiple chromatin remodeling complexes. Deletion of Smarca5 was restricted to those cells expressing Cre-recombinase driven by the Nestin promoter.

overall_design: Comparison of gene expression in P10 cerebella of Smarca5 cKO mice versus wild type controls. Three samples of each strain were used in a total of 3 replicates.

first: Matías

last: Alvarez-Saavedra

first: Pamela

last: Lagali

first: Keqin

last: Yan

middle: J

first: Valerie

last: Wallace

first: Tomas

last: Stopka

first: Arthur

middle: I

last: Skoultchi

first: David

last: Picketts


title: Destabilization of Nucleophosmin mRNA by the HuR/KSRP complex is required for muscle fiber formation

status: Public on Apr 26 2014

city: Montreal

first: Imed

last: Gallouzi

state: QC

address: 3655 Promenade Sir William Osler

department: Biochemistry

country: Canada

institute: McGill University

summary: HuR promotes myogenesis by stabilizing MyoD, Myogenin and p21 mRNAs during the fusion step of muscle cells to form myotubes. Here we show that HuR, via a novel mRNA destabilizing activity, promotes the early steps of myogenesis by reducing the expression of the cell cycle promoter nucleophosmin (NPM). Depletion of HuR stabilizes the NPM mRNA, increases NPM protein levels and inhibits myogenesis, while its overexpression elicits the opposite effects. NPM mRNA destabilization involves the association of HuR with the decay factor KSRP as well as the ribonuclease PARN and the exosome complex. The C-terminus of HuR mediates the formation of the HuR-KSRP complex and is sufficient for maintaining a low level of the NPM mRNA as well as promoting the commitment of muscle cells to myogenesis. We therefore propose a model whereby the downregulation of the NPM mRNA, mediated by the HuR/KSRP complex and its associated ribonucleases, is required for proper myogenesis.

overall_design: RNA was extracted from C2C12 treated with siRNA against HuR and compared to control siRNA

first: Anne

last: Cammas

first: Brenda

last: Sanchez

first: Xian

last: Lian

first: Virginie

last: Dormoy-Raclet

first: Kate

last: van der Giessen

first: Isabel

last: Lopez de Silanes

first: Jennifer

middle: F

last: Ma

first: Carol

last: Wilusz

first: John

last: Richardson

first: Myriam

last: Gorospe

first: Stefania

last: Millevoi

first: Matteo

last: Giovarelli

first: Roberto

last: Gherzi

first: Sergio

last: Di Marco

first: Imed-Eddine


title: Mouse cerebellum: Smarca5 conditional KO mice (cKO) versus wild type controls

status: Public on Apr 30 2014

first: Alan

last: Mears

state: ON

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

overall_design: Refer to individual Series


title: Genome wide characterization reveals complex interplay between TP53 and TP63 in response to genotoxic stress [Affymetrix]

city: Belfast

first: Simon

middle: S

last: McDade

address: 97 Lisburn Road

department: CCRCB

country: United Kingdom

institute: Queen's University Belfast

summary:
In response to genotoxic stress the TP53 tumour suppressor activates target gene expression to induce cell cycle arrest or apoptosis depending on the extent of DNA damage.  These canonical activities can be repressed by TP63 in normal stratifying epithelia to maintain proliferative capacity or drive proliferation of squamous cell carcinomas, where TP63 is frequently overexpressed/amplified.  Here we use ChIP-sequencing, integrated with microarray analysis, to define the genome wide interplay between TP53 and TP63 in response to genotoxic stress in normal cells.  We reveal that TP53 and TP63 bind to overlapping, but distinct cistromes of sites through utilization of distinctive consensus motifs and that TP53 is constitutively bound to a number of sites.  We demonstrate that cisplatin and adriamycin elicit distinct effects on TP53 and TP63 binding events, through which TP53 can induce or repress transcription of an extensive network of genes by direct binding and/or modulation of TP63 activity.  Collectively, this results in a global TP53 dependent repression of cell cycle progression, mitosis and DNA damage repair concomitant with activation of anti-proliferative and pro-apoptotic canonical target genes. Further analyses reveals that in the absence of genotoxic stress TP63 plays an important role in maintaining expression of DNA repair genes, loss of which results in defective repair
Examination of gene expression levels of HFKS siRNA depleted for p53 or p63 in response to adriamycin or cisplatin treatment

overall_design: We analyzed RNA using the Affymetrix Human Exon 1.0 ST platform. Array data was processed using the AltAnalyze.

first: Dennis

last: McCancer


title: RNA-Direct Regulation of pri-miRNA Processing by a Long Noncoding RNA Transcribed from an Ultraconserved Region

status: Public on May 01 2014

city: L'Hospitalet de Llobregat

first: Manel

last: Esteller

state: Barcelona

address: Hospital Duran i Reynals Av. Gran Via s/n km, 2.7

department: PEBC

country: Spain

institute: IDIBELL

summary: We investigate the role of a long ncRNA transcribed from an ultraconserved region (T-UCR) in the control of post-transcriptional pri-miRNA processing. The regulation is based on complementarity between the lower stem region in pri-miR-195 transcript and the ultraconserved sequence in Uc.283+A, which prevents pri-miRNA cleavage by Drosha. Mutation of the site in either RNA molecule uncouples regulation in vivo and in vitro. We propose a model in which lower-stem strand invasion by Uc.283+A impairs microprocessor recognition and efficient pri-miRNA cropping.   In this work, we characterize a new role for Uc.283+A as a direct interactor and regulator of pri-miRNA-195 maturation at the level of Drosha processing. We combine cellular assays with in vitro biochemical analyses to reveal the first case of RNA-directed downregulation of miRNA biogenesis by a T-UCR

overall_design: In the study presented here, a colorrectal cancer cell line (HCT-116) was transiently transfected with Uc.283+A in order to identify putative miRNA targets for Uc.283+A. Variant 1 represents a SNP variant (8x(T) repeat in the sequence). Variant 2 represents a SNP variant (9x(T) repeat in the sequence).

first: Liz

last: Julia

first: Esteller

last: Manel

first: Calin

last: George


title: Life on the edge: Functional genomic response of Ignicoccus hospitalis to cellular takeover by Nanoarchaeum equitans

status: Public on Apr 24 2014

city: Knoxville

first: Louie

last: Wurch

state: TN

address: M313 Walters Life Sciences

country: USA

institute: University of Tennessee

summary:
Investigation of changes in global gene expression patterns as Ignicoccus hospitalis becomes increasingly populated by Nanoarchaeum equitans
These microarray data are complemented by shot gun proteomics (see manuscript)

overall_design: A total of 16 chips were used (each experimental sample was done in duplicate, totally 8 samples) to examine total RNA from I. hospiatalis over a time course grown in pure culture and in co-culture with N. equitans.

middle: L

first: Richard

last: Giannone

first: Thomas

last: Heimerl

first: Stanton

last: Martin

first: Zamin

last: Yang

first: Harold

last: Huber

first: Reinhard

last: Rachel

first: Robert

last: Hettich

first: Mircea

last: Podar


title: Mouse P0 cerebellum: Smarca5 conditional KO mice (cKO) versus wild type controls

overall_design: Comparison of gene expression in P0 cerebella of Smarca5 cKO mice versus wild type controls. Three samples of each strain were used in a total of 4 replicates.

first: Matías

last: Alvarez-Saavedra

first: Pamela

last: Lagali

first: Keqin

last: Yan

first: Valerie

last: Wallace

first: Tomas

last: Stopka

first: Arthur

last: Skoultchi

first: David

last: Picketts


title: Expression analysis of an enrofloxacin and a tetracline resistant Escherichia coli strain

city: Amsterdam

first: Nadine

last: Händel

address: Science Park 904

department: Swammerdam Institute for Life Sciences

country: Netherlands

institute: University of Amsterdam

summary:
Comparison of the whole genome gene expression level of an enrofloxacin and tetracycline resistant E. coli strain with the wildtype it was derived from.
The process of drug adaptation of E. coli MG1655 wildtype cells is further descibed in van der Horst, M, J.M. Schuurmans, M. C. Smid, B. B. Koenders, and B. H. ter Kuile (2011) in Microb. Drug Resist. 17:141-147. Resistance to amoxicillin was induced in E. coli by growth in the presence of stepwise increasing antibiotic concentrations. To investigate consequences of the aquisition of amoxicillin resistance the transcriptomic profile of sensitive and resistant cells was compared in the absence and presence of sub-inhibitory (0.25xMIC) amoxicillin concentrations was compared.

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

overall_design: Total RNA of 3 biological replicates of E. coli MG1655 wildtype cells and drug resistant cells cultured with (0.25xMIC) or without the drug was hybridized on a 12x135k custom designed microarraychip against one common reference.

first: N

first: B

middle: H

last: ter Kuile


title: Binding in wild type embryos: SoxN.

status: Public on Apr 23 2014

city: Cambridge

first: Enrico

last: Ferrero

address: Downing Street

department: Genetics

institute: University of Cambridge

type: Genome binding/occupancy profiling by genome tiling array

summary: Genome-wide binding of SoxN in wild type embryos: SoxNDam (DamID, stage 8-11), SoxND1 (ChIP, stage 8-11), SoxND2 (ChIP, stage 8-11), SoxNPA179 Early (ChIP, stage 7-10), and SoxNPA179 Late (ChIP, stage 11-13).

overall_design:
One DamID experiment, four ChIP experiments. Three biological replicates per experiment. Two conditions: Dam (control) vs SoxNDam (sample) for DamID, anti-βgal (control, 40-1a antibody from DSHB) vs anti-SoxN (sample, either SoxND1, SoxND2 or SoxNPA179 antibody) for ChIP.

The only commercially available antibody is the anti-BetaGal. All the anti-SoxN antibodies are home-made.
anti-BetaGal: Developmental Studies Hybridoma Bank (DSHB), 40-1a, mouse, monoclonal (http://dshb.biology.uiowa.edu/beta-galactosidase_2)
SoxND1: polyclonal antiserum raised in rabbit immunized with a protein fragment corresponding to amino acids 2-92 of SoxN. Produced by the modENCODE consortium (http://www.modencode.org/).
SoxND2: polyclonal antiserum raised in rabbit immunized with a protein fragment corresponding to amino acids 317-417 of SoxN. Produced by the modENCODE consortium (http://www.modencode.org/).
SoxNPA179: affinity purified polyclonal antibody raised in rabbit immunized with a small peptide corresponding to amino acids 506-521 of SoxN. Commisioned by our lab and produced by Eurogentec (http://www.eurogentec.com/eu-home.html).

first: Bettina

last: Fischer

first: Steven

last: Russell


title: Gene expression timecourse: SoxN homozygous mutant embryos vs SoxN heterozygous mutant embryos.

summary: Timecourse of gene expression changes in Drosophila SoxN homozygous mutant embryos compared with their heterozygous siblings, from stage 7 to 13 of embryonic development.

overall_design: Five time points: stage 7-8, stage 9, stage 10, stage 11 and stage 12-13. Four biological replicates per time point. Two conditions: SoxN homoxygous vs SoxN heterozygous mutant embryos.


title: A BRCA1 Deficient-Like Signature is Enriched in Breast Cancer Brain Metastases

city: Boston

first: Ben

middle: S.

last: Wittner

state: MA

address: 149 13th Street

department: Center for Cancer Research

institute: Massachusetts General Hospital

summary:
Purpose: There is an unmet clinical need for biomarkers to identify breast cancer patients who are at increased risk of developing brain metastases. The objective is to identify gene signatures and biological pathways associated with HER2+ brain metastasis.

Experimental Design: Gene expression of 19 HER2+ breast cancer brain metastases was compared with HER2+ nonmetastatic primary tumors. Gene Set Enrichment Analysis was used to identify a signature, which was evaluated for correlation with BRCA1 mutation status and clinical outcome using published microarray datasets and for correlation with pharmacological inhibition by a PARP inhibitor and temozolomide using published microarray datasets of breast cancer cell lines.

Results: A BRCA1 Deficient-Like (BD-L) gene signature is significantly correlated with HER2+ metastases in both our and an independent cohort. BD-L signature is enriched in BRCA1 mutation carrier primary tumors and HER2-/ER- sporadic tumors, but high values are found in a subset of ER+ and HER2+ tumors. Elevated BD-L signature in primary tumors is associated with increased risk of overall relapse, brain relapse, and decreased survival. The BD-L signature correlates with pharmacologic response to PARP inhibitor and temozolomide in two independent microarray datasets, and the signature outperformed four published gene signatures of BRCA1/2 deficiency.

Conclusions: The BD-L signature is enriched in breast cancer brain metastases and identifies a subset of primary tumors with increased propensity for brain metastasis. Furthermore, this signature may serve as a biomarker to identify sporadic breast cancer patients who could benefit from a therapeutic combination of PARP inhibitor and temozolomide.

overall_design: Gene expression of 19 HER2+ human breast cancer brain metastases was compared with gene expression of 19 HER2+ nonmetastatic primary human breast tumors.

first: Ryan

middle: P

last: McMullin

first: Chunwei

last: Yang

first: Raj

last: Singavarapu

first: Sharon

last: Moulis

first: Jeongeun

last: Lee

first: Kenneth

middle: D

last: Aldape

first: Patricia

last: Steeg

first: Sridhar

last: Ramaswamy

first: Dennis

middle: C

last: Sgroi


title: Binding in wild type, D and SoxN mutant embryos: SoxN vs D.

summary: Genome-wide binding of transcription factors SoxN and D in stage 12-17 wild type embryos (SoxNDam and DDam), of SoxN in D mutants (D-SoxNDam) and of D in SoxN mutants (SoxN-DDam).

overall_design: Four DamID experiments. Three biological replicates per experiment. Two conditions: Dam (control) vs SoxNDam or DDam or D-SoxNDam or SoxN-DDam (sample)


title: Analysis of SoxNeuro gene expression changes, genome-wide binding, and comparison of SoxNeuro and Dichaete binding profiles in wild type and mutant embryos


title: Alternative Splicing of MBD2 Supports Self-Renewal in Human Pluripotent Stem Cells [HJAY]

status: Public on Apr 20 2014

city: Rochester

first: Hu

last: Li

state: MN

address: 200 First Street, Gonda Building G19-408

department: Molecular Pharmacology & Experimental Therapeutics

institute: Mayo Clinic

summary: Alternative RNA splicing (AS) regulates proteome diversity, including isoform-specific expression of several pluripotency genes. Here, we integrated global gene expression and proteomic analyses and identified a molecular signature suggesting a central role for AS in maintaining human pluripotent stem cell (hPSC) self-renewal. We demonstrate the splicing factor SFRS2 is an OCT4 target gene required for pluripotency. SFRS2 regulates AS of the methyl-CpG-binding protein MBD2, whose isoforms play opposing roles in maintenance of, and reprogramming to, pluripotency. While both MDB2a and MBD2c are enriched at the OCT4 and NANOG promoters, MBD2a preferentially interacts with repressive NuRD chromatin remodeling factors and promotes hPSC differentiation, whereas overexpression of MBD2c enhances reprogramming of fibroblasts to pluripotency. The miR-301 and miR-302 families provide additional regulation by targeting SFRS2 and MDB2a. These data suggest that OCT4, SFRS2, and MBD2 participate in a positive feedback loop, regulating proteome diversity complexity in support of hPSC self-renewal and reprogramming.

overall_design: We isolated RNA from human fibroblasts and human embryonic stem cells for hybridization to the Affymetrix gene expression microarrays.

first: James

last: Collins


title: Regulation of the raffinose and melezitose utilization operons of B. breve UCC2003

city: Cork

first: Mary

last: O'Connell Motherway

address: Western Road

department: Department of Microbiology and Alimentary Pharmabiotic Centre

country: Ireland

institute: University College Cork

summary: Members of the genus Bifidobacterium are Gram-positive bacteria which are commonly found in the gastrointestinal tract (GIT) of mammals, including humans.  Growth of bifidobacteria has been shown to be selectively stimulated by various carbohydrates found in the human diet. To extend our understanding of the regulation of bifidobacterial carbohydrate utilization systems, we investigated the regulation of two carbohydrate utilisation clusters dedicated to the metabolism of  raffinose type sugars and melezitose. Transcriptomic and functional genomic approaches clearly identified that the raffinose utilisation system is positively regulated by the activator RafR, while the melezitose utilisation system is negatively regulated by lacI type transcriptional regulators. A B. breve UCC2003-rafR insertion mutant was incapable of utilising  raffinose containing sugars or melibiose as a sole carbohydrate source, while the UCC2003-lacI1 and  UCC2003-lacI2 insertion mutants retained their ability to utilise melezitose as a sole carbohydrate source. In silico analysis and DNA/protein interaction studies revealed a novel conserved 22 bp palindromic sequence as the RafR binding operator sequence in the rafB promoter region. Within the melezitose utilisation cluster a 20bp palindromic sequence for the melA promoter region and a 24bp palindromic sequence for the Bbr_1863 promoter region

overall_design: DNA-microarrays containing oligonucleotide primers representing each of the 1864 annotated genes on the genome of B. breve UCC2003  (O'Connell Motherway et al., 2011) were designed by and obtained from Agilent Technologies (Palo Alto, Ca., USA). Methods for cell disruption, RNA isolation, RNA quality control, complementary DNA synthesis and labeling were performed as described previously (Pokusaeva et al., 2009). Labeled cDNA was hybridized using the Agilent Gene Expression hybridization kit (part number 5188-5242) as described in the Agilent Two-Color Microarray-Based Gene Expression Analysis v4.0 manual (G4140-90050). Following hybridization, microarrays were washed in accordance with Agilent’s standard procedures and scanned using an Agilent DNA microarray scanner (model G2565A). Generated scans were converted to data files with Agilent's Feature Extraction software (Version 9.5). DNA-microarray data were processed as previously described (Garcia De La Nava et al., 2003). Differential expression tests were performed with the Cyber-T implementation of a variant of the t-test (Long et al., 2001). A gene was considered differentially expressed when p < 0.001 and an expression ratio of >3 or <0.33 relative to the control.

first: Kerry

last: O'Connell


title: Stroma provides an intestinal stem cell niche in the absence of epithelial Wnts

status: Public on Apr 19 2014

city: Singapore

first: David

middle: Marc

last: Virshup

address: 8 College Road

department: Program in Cancer and Stem Cell Biology

country: Singapore

institute: Duke-NUS Graduate Medical School

summary: Wnt/b-catenin signaling supports intestinal homeostasis by regulating proliferation in the crypt. Multiple Wnts are expressed in Paneth as well as other intestinal epithelial and stromal cells. Ex vivo, Wnts secreted by Paneth cells can support intestinal stem cells when Wnt signaling is enhanced with supplemental R-Spondin 1 (RSPO1). However, in vivo, the source of Wnts in the stem cell niche is less clear. Genetic ablation of Porcn, an endoplasmic reticulum resident O-acyltransferase that is essential for the secretion and activity of all vertebrate Wnts, confirmed the role of intestinal epithelial Wnts in ex vivo culture. Unexpectedly, mice lacking epithelial Wnt activity (PorcnDel/Villin-Cre mice) had normal intestinal proliferation and differentiation, as well as successful regeneration after radiation injury, indicating epithelial Wnts are dispensable for these processes. Consistent with a key role for stroma in the crypt niche, intestinal stromal cells endogenously expressing Wnts and Rspo3 support the growth of PorcnDel organoids ex vivo without RSPO1 supplementation. Conversely, increasing pharmacologic PORCN inhibition, affecting both stroma and epithelium, reduced Lgr5 intestinal stem cells, inhibited recovery from radiation injury, and at the highest dose fully blocked intestinal proliferation. We conclude that epithelial Wnts are dispensable, and that stromal production of Wnts can fully support normal murine intestinal homeostasis.

overall_design: Microarray was performed on samples enriched for stromal or epithelial cells from small intestine from Porcn(Del)/Villin-Cre and Porcn(WT)/Villin-Cre male C57Bl/6 mice.

middle: M


title: Expression profiles and initial confirmation of long non-coding RNAs in Chinese patients with pulmonary adenocarcinoma

status: Public on Apr 17 2014

city: Nanjing

first: Wen

last: Zhu

state: Jiangsu

address: 300 Guangzhou Road

department: Respiratory Medicine

country: China

institute: The First Affiliated Hospital, Nanjing Medical University

summary: There are significant differences in the lncRNA expression profiles in Chinese patients with pulmonary adenocarcinoma. LncRNAs such as AK124939 may be anti-cancer factors related to the progress of pulmonary adenocarcinoma.

overall_design: RNA extracted from three paired pulmonary adenocarcinoma tissue and adjacent normal lung tissue specimens was used to synthesize double-stranded complementary DNA (cDNA) after labeling and hybridization. The cDNA was labeled and hybridized to the lncRNA expression microarray, and array data were analyzed for hierarchical clustering. Gene coexpression networks were constructed to identify interactions among genes. To validate the microarray findings, we measured the relative expression levels of four random differentially expressed lncRNAs in the same tissue used for microarray using real-time quantitative polymerase chain reaction (qRT-PCR). The expression level of one lncRNA AK124939, in the paired pulmonary adenocarcinoma/adjacent normal lung tissue of another 30 patients was measured using qRT-PCR. The experimental data were further analyzed and compared with clinical features.

first: Xin

last: Zhao


title: miRNA expression in PTEN-deficient premalignant DP thymocytes

status: Public on Apr 12 2014

city: Berkeley

first: Megan

last: Burger

state: CA

address: UC Berkeley, 465 Life Sciences Addition

department: Molecular and Cell Biology

institute: University of California, Berkeley

summary:
T cell-specific deletion of PTEN induces premalignancy in CD4+ CD8+ (DP) immature T cells in the thymus, which progresses to the development of mature CD4+ T cell lymphomas in the lymph nodes and spleen.
As part of a screen to identify factors that inhibit progression to malignancy, we compared miRNA expression in premalignant PTEN-deficient DP thymocytes versus wild-type controls.

platform_organism:
Homo sapiens
Mus musculus
Rattus norvegicus

overall_design: DP thymocytes were collected by cell sorting from three 9-week-old, premalignant T cell-specific PTEN-deficient mice (tPTEN-/-) and three littermate controls. miRNA expression was assessed relative to a reference pool generated from an equal mixture of all samples.


title: Chip-chip from C-33 cells expressing FLAG-HPV1 E2 with FLAG-HPV1 E2

status: Public on Apr 14 2014

city: Bethesda

first: Kui

last: Shen

state: MD

address: Room 3B62, 31 Center Drive

institute: National Institute of Allergy and Infectious Diseases, NIH

summary: HPV1 E2 binds with Brd4 to host mitotic chromosomes. To identify the targets, chromatin was prepared from mitotic C-33 cells expressing HPV1 E2, and analyzed by ChIP-chip analysis for binding to a portion of the human genome. E2 and Brd4 bind to active promoters in interphase C-33 cells (Jang et al., 2009), however, in mitosis E2 was observed instead to bind to a few extremely broad peaks on several chromosomes. These peaks ranged in size from several hundred Kb to >1 Mb and, for the most part, overlapped coding regions.

overall_design: Signals of anti-FLAG E2 ChIP DNA from mitotic HPV1 E2 expressing C-33 cells

first: Alison

middle: A

last: McBride

first: M

last: Jang


title: microRNA signature in b-cell lymphomas and control human B cells from fresh tonsils

city: Madrid

first: Lorena

last: Di Lisio

address: C/ Melchor Fernández Almagro, 3

institute: CNIO

summary:
147 B-cell lymphomas were studies for miRNA expression
miRNA profiling of control human B cell populations
Comparison of miRNA expression profiles of naive B cells (CD19+ IgD+ CD27-) from 3 individuals and germinal center B cells (CD10+ CD19+) from 4 individuals

overall_design:
147 B-cell lymphomas were hybridized on a human miRNA one-color platform containing probes for 470 human miRNAs. Each lymphoma type was compared to all set of NHLs. Burkitt Lymphoma was also directly compared to DLBCL
miRNA expression signature is different in human naive B cells compared to Germinal Center B cells

last: DiLisio

first: Nerea

last: Martinez

first: Miguel

last: Piris


title: Comparison of genome-wide gene expression in wild-type and swd2.2delta fission yeast cells

city: Lyon

first: Vincent

last: Vanoosthuyse

address: 46 allée d'Italie

department: Laboratoire de Biologie Moléculaire de la Cellule

country: France

institute: CNRS

type: Expression profiling by genome tiling array

summary: Swd2.2 is associated with the Cleavage and Polyadenylation Factor (CPF) in fission yeast. The CPF is required for the 3'end processing of RNAs. To establish the contribution of Swd2.2 to gene expression, we used single-strand tiling array hybridization. The results show that 47 genes are significantly down-regulated (FC≤1,9, p<0,01) and 14 are up-regulated (FC≥1,9, p<0,01) when Swd2.2 is missing. To establish the contribution of Swd2.2 to transcription termination, we also used these data as follows: for every gene in the genome whose 3'UTR was annotated (4727 genes), the average RNA signal intensity observed in the 3'UTR of the gene was compared to the average signal intensity observed in the ORF of the gene. This ratio was named  "UTR ratio". This UTR ratio was calculated for every gene, in swd2.2+ or swd2.2delta cells. The UTR ratio observed in swd2.2delta cells was then compared to the UTR ratio observed in swd2.2+ cells. When this ratio is superior to 1.5,  it means that there was proportionnally a 50% increase of the RNA signal in the 3'UTR of this gene when Swd2.2 was missing. We interpreted this observation as a transcription termination defect. We detected 780 genes (out of 4727) for which this was the case. This list is highy enriched for convergent, overlapping genes.

overall_design: RNA extracted from swd2.2+ and swd2.2delta cells were retrotranscribed and labelled. These were then hybridized on an Affymetrix S. pombe Tiling 1.0FR Array (accession GPL7715). The data were established in triplicates.

first: Séverine

last: Croze

first: Nicoas

last: Nazaret


title: Differential expression of small RNAs from Burkholderia thailandensis in response to varying environmental and stress conditions

status: Public on Apr 05 2014

city: Los Alamos

first: Chris

last: Stubben

state: NM

address: MS M888

department: Bioscience Division

institute: Los Alamos National Lab

summary: Bacterial small RNAs (sRNAs) regulate gene expression by base-pairing with downstream target mRNAs to attenuate translation of mRNA into protein at the post-transcriptional level. In response to specific environmental changes, sRNAs can modulate the expression levels of target genes, thus enabling adaptation of cellular physiology. We profiled sRNA expression in the Gram-negative bacteria Burkholderia thailandensis cultured under 54 distinct growth conditions using a Burkholderia-specific microarray that contains probe sets to all intergenic regions (IGRs) greater than 90 bases. We identified 38 novel sRNAs and performed experimental validation on five sRNAs that play a role in adaptation of Burkholderia to cell stressors.

overall_design: A custom Affymetrix microarray was designed using Burkholderia thailandensis E264 gene annotations from Pathema and included 8711 probe sets targeting 5557 protein-coding genes and 2908 IGRs longer than 90 bases on the plus strand. Experiments were performed in four classes of media: nutrient broth, M9-minimal media, Luria broth, and various host conditions such as brain-heart infusion, calf serum, or tryptic soy broth. There were 101 samples in four time course arrays measuring temperature increase, pH drop, salt stress, and phosphate starvation (21 distinct conditions). Each condition was grown at 37° C, except the initial temperature experiment at 25°C, and replicated five times. In order to survey a diverse range of environmental and stress conditions, another 10 replicated and 23 unreplicated treatments were also tested.

first: Sofiya

middle: N

last: Micheva-Viteva

first: Yulin

last: Shou

first: Sarah

middle: K

last: Buddenborg

first: John

last: Dunbar

first: Elizabeth

last: Hong-Geller


title: Stress and adaptation of Listeria monocytogenes 08-5923 exposed to a sublethal dose of carnocyclin A

status: Public on Apr 08 2014

city: Edmonton

first: Lynn

last: McMullen

state: Alberta

address: 410 Ag/For

institute: University of Alberta

summary: This study investigated the alternative gene, protein expression and morphological changes of L. monocytogenes 08-5923 following 15min, 4h and 30h exposure to bacteriocin carnocyclin A (cclA). The microarray experiment studied the gene expression of untreated and treated Listeria cells following 4h exposure to cclA.

overall_design: A six chip study using total RNA recovered from six separate cultures of L. monocytogenes 08-5923; three grown in TSB (untreated) and three grown in TSB with cclA (treated); Each chip measures the expression level of 2,857 genes from L. monocytogenes 08-5923 with five 60-mer probe pairs (PM/MM) per gene, with 1-fold technical redundancy.

first: Xiaoji

last: Liu

first: Urmila

last: Basu

first: Petr

last: Miller


title: Expression data from human breast cancer cells MDA-MB-231-Luc knockdown for RRAS2 expression.

status: Public on Apr 09 2014

city: Montpellier Cedex 05

first: Romain

last: Larive

address: 1919, route de Mende

department: CRBM

institute: CNRS UMR5237

summary: We used microarrays to investigate gene expression changes induced by the inhibition of RRAS2 expression using shRNA techniques to stably knockdown the endogenous transcripts of this GTPase in human MDA-MB-231-Luc cells.

overall_design: MDA-MB-231-Luc shControl (MDA-Control) and RRAS2-deficient (KDRRAS2.p1) in exponential growth phase were selected for RNA extraction and and hybridization on Affymetrix microarrays.

first: Giulia

last: Moriggi

first: Mauricio

last: Menacho-Márquez

first: Marta

last: Cañamero

first: Enrique

last: de Álava

first: Balbino

last: Alarcón

first: Mercedes

last: Dosil

first: Xosé

middle: R

last: Bustelo


title: Analysis of gene expression changes in amyloid-beta (ADDL) and CAT-SKL antioxidant treated primary rat neuronal cells

status: Public on Apr 11 2014

city: Detroit

first: Aliccia

last: Bollig-Fischer

address: 4100 John R

department: Oncology

institute: Karmanos Cancer Institute & Wayne State University

summary: Amyloid-beta (Aβ)-induced neurotoxicity is a major contributor to the pathologies associated with Alzheimer’s disease (AD).  The formation of reactive oxygen species (ROS), and early response induced by the Aβ peptide, plays a significant role in effecting cellular pathogenesis.  Here we apply a particularly effective form of exogenous Aβ, i.e., amyloid beta-derived diffusible ligands (ADDLs), to cultured primary cortical/hippocampal neurons to elicit ROS and drive cellular dysfunction.  To prevent and even reverse such effects, we employed a cell-penetrating, peroxisome-targeted, protein biologic - called CAT-SKL.  We show the recombinant enzyme enters neurons, reverses Aβ-induced oxidative stress, and increases cell viability.  Dramatic restorative effects on damaged neuronal processes were also observed.  CAT-SKL, a targeted antioxidant, may represent a new therapeutic approach for treatment disorders, like Alzheimer’s disease, where oxidative stress is manifest.  Preclinical testing is warranted and ongoing

overall_design:
Primary Rat E18 coritical/hippocampal neurons (derived from Sprague Dawley E18 cortical/hippocampus tissue  obtained from BrainBits®, Springfield, IL) were treated with ADDLs in the presence or absence of the targeted antioxidant CAT-SKL to investigate genes that displayed altered expression in response to treatmetns
total RNA was isolated and analyzed in an Agilent two-color experiment. Two biological replicates of each condition were directly compared, ratios are treated relative to control (untreated)

first: Courtney

last: Giordano

first: Stanley

last: Terlecky


title: MicroRNA profiles discriminate among colon cancer metastasis

status: Public on Apr 01 2014

city: Columbus

first: Cecilia

last: Fernandez

address: 460 12th street

institute: OSU

summary: The aim of our study was to identify a microRNA signature for metastatic CRC that could predict and differentiate metastatic target organ localization.  Normal and cancer tissues of three different groups of CRC patients were analyzed. RNA microarray and TaqMan Array analysis were performed on 66 italian patients with or without lymph nodes and/or liver recurrences. Data obtained with the two assays, were analyzed separately and then intersected to identify a primary CRC metastatic signature. Five differentially expressed microRNAs (hsa-miR-21, -103, -93, -31 and -566) were validated by qRT-PCR on a second group of 16 american metastatic patients. In situ hybridization was performed on the 16 american patients as well as on three distinct commercial tissues microarray (TMA), containing normal adjacent colon, the primary adenocarcinoma, normal and metastatic lymph nodes and liver.  Hsa-microRNA-31,-21,-93, and-103 upregulation together with hsa-miR-566 downregulation defined the CRC metastatic signature, while in situ hybridization data identified a lymphonodal invasion profile.

overall_design: 33 patients had colon cancer with lymph nodes metastasis only (Any T, Any N, M0) and 15 were diagnosed with colon cancer, lymph nodes and liver metastases (Any T, Any N, M1). Separate tumor samples from the primary tumor, the metastatic lymph nodes and the liver metastasis were collected.

first: Alessandra

last: Drusco

first: Carlo

last: Croce


title: Transcriptome of phosphomimetic and phosphoablative kasB mutants of Mycobacterium tuberculosis

city: Saranac Lake

first: Brian

last: Weinrick

state: NY

address: 154 Algonquin Avenue

institute: Trudeau Institute

summary: Mechanisms governing Mycobacterium tuberculosis acid-fastness and its capacity to induce long-term infections remain unknown. Serine/Threonine phosphorylation represents an emerging theme allowing mycobacteria to adapt their cell envelope structure/composition in response to environmental changes. We addressed whether phosphorylation of KasB, a mycolic acid biosynthetic enzyme, modulates M. tuberculosis pathogenicity. Phosphorylation of KasB occurred at Thr334 and Thr336 in vitro and in mycobacteria. A mutant strain bearing an kasB_T334D/T336D allele, mimicking constitutive KasB phosphorylation, was generated by specialized linkage transduction. This resulted in shortened mycolic acids and the lack of trans-cyclopropanation. Structural/modeling analyses revealed Thr334 and Thr336 in the vicinity of the catalytic triad, implying that phosphorylation of these residues impaired KasB activity. Importantly, the phosphomimetic strain lost acid-fast staining and was more attenuated than a kasB deletion mutant in immunocompetent and immunodeficient mice. The absence of lung pathology and mortality infers this mutant to represent a valuable vaccine candidate. This work emphasizes the critical role of Ser/Thr kinase-dependent signaling in controlling mycolic acid elongation, acid-fastness, virulence and has important clinical implications for diagnosis of latent infections.

overall_design:
Transcriptome of kasB null, phosphoablative, and phosphomimetic mutants compared to parental.
Triplicate 10ml cultures of M. tuberculosis CDC1551 and kasB null, phosphoablative, and phosphomimetic mutants were grown to OD 1.0 and harvested for transcriptional profiling.

first: Catherine

last: Vilcheze


title: MicroRNA and mRNA biomarkers for short-term in vivo genotoxic and non-genotoxic carcinogen classification

city: Maastricht

first: Kasper

last: Derks

state: Limburg

address: P. Debyelaan 25

department: Clinical Genetics

institute: Maastricht University Medical Center

summary:
Many innovative techniques and scientific improvements are available to tackle societal concerns, like public health safety and confining the risk of cancerous exposure to chemicals, but have not been thoroughly tested and implicated yet. We investigated if microRNA and mRNA transcription profiles can be implemented in a short-term carcinogen classifier assay.  Our study is additionally focusing on the drawbacks of present-day carcinogen screening strategies and also aims to contribute to a more ethical approach towards animal use and welfare within risk assessment.
Since current in vitro and in silico assays are still not able to mimic the in vivo situation accurately we set out to develop an alternative short-term in vivo assay. Five genotoxic, seven non-genotoxic and five non-carcinogen exposure studies were used to investigate if murine hepatic microRNA and mRNA profiles after 7-day exposure are suitable tools to classify carcinogens. Classification analyses showed that a small transcript set, consisting of both microRNA and mRNA, is able to classify the genotoxic, non-genotoxic and non-carcinogens tested with 100% accuracy. The results indicate that microRNAs have the potential to be used as transcriptional classifiers and that a short-term transcriptional classifier assay in mice can be a powerful tool in carcinogenicity risk assessment.

overall_design: [microRNA profling] 68 hepatic samples in total, 3 control untreated samples, replicates per treated group n=3-4

first: Joost

last: Melis

middle: W

first: Paul

last: Wackers

first: Tessa

last: Pronk

first: Mirjam

last: Schaap

first: Edwin

last: Zwart

first: Jeroen

last: Pennings

first: Martijs

last: Jonker

first: Timo

last: Breit

first: Wilfred

last: van Ijcken

first: Joris

last: Pothof

first: Harry

last: van Steeg

last: Luijten


title: Shoot and root of barley seeds: Salt treatment

city: Tsukuba

first: Shingo

last: Nakamura

state: Ibaraki

address: Kannondai 2-1-18

country: Japan

institute: National Institute of Crop Science

summary: Transcriptional profiling  of barley shoot and root with 0.2M NaCl

overall_design: Time course experiments

first: Takashi

last: Matsumoto


title: Shoot and root of barley seeds

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

overall_design: Refer to individual Series


title: Shoot and root of barley seeds: Non-treatment (control)

summary: Transcriptional profiling  of barley shoot and root with no-treatment


title: Gene networks and putative toxicity pathways induced by acute exposure to low dose cadmium in largemouth bass (Micropterus salmoides)

status: Public on Apr 02 2014

city: Costa Mesa

first: Alvine

last: Mehinto

address: 3535 Harbor Blvd, Suite 110

institute: Southern California Coastal Water Research Project

summary: Cadmium is a natural element that can accumulate to toxic levels in the environment leading to detrimental effects in animals and humans including kidney, liver and lung injuries. Using a transcriptomics approach, genes and cellular pathways affected by a low dose of cadmium were investigated.  Adult largemouth bass were intraperitoneally injected with 20 µg/kg of cadmium chloride and microarray analyses were conducted in the liver and testis 48 hours after injection.  Transcriptomics profiles identified in response to cadmium treatment were tissue-specific with the most differential expression changes found in the liver tissues, which also contained much higher levels of cadmium than the testes.  Acute exposure to a low dose of cadmium induced oxidative stress response and oxidative damage pathways in the liver.  The mRNA levels of antioxidants such as catalase increased and numerous transcripts related to DNA damage and DNA repair were significantly altered.  Hepatic mRNA levels of metallothionein, a proposed marker of cadmium exposure, showed a small insignificant increase after 48 hours exposure.  Carbohydrate metabolic pathways were also disrupted in cadmium-exposed fish with hepatic transcripts such as UDP-glucose pyrophosphorylase 2 and sorbitol dehydrogenase highly induced.  Both tissues exhibited a disruption of steroid signalling pathways.  In the testis, estrogen receptor beta and transcripts linked to cholesterol metabolism were suppressed.  On the contrary, genes involved in cholesterol metabolism were highly increased in the liver including genes encoding for the rate limiting steroidogenic acute regulatory protein and the catalytic enzyme 7-dehydrocholesterol reductase.  Integration of the transcriptomics data using functional enrichment analyses revealed a number of enriched gene networks associated with previously reported adverse outcomes of cadmium exposure such as liver toxicity and impaired reproduction.

overall_design: Adult largemouth bass (n=4 per treatment) were ip injected with a single dose of cadmium chloride (20 ug/kg) or a saline solution. After 48 hours, liver and testis were excised and differential gene expression profiles were examined.

first: Melinda

last: Prucha

first: Reyna

last: Colli-Dula

first: Kevin

middle: J

last: Kroll

first: Candice

last: Lavelle

first: David

last: Barber

first: Christopher

last: Vulpe

first: Nancy

last: Denslow


title: Shoot and root of barley seeds: Drying  treatment

summary: Transcriptional profiling  of barley shoot and root with drying


title: Expression analysis of Vibrio cholerae O395N1 delta-nqrA-F mutant

city: Corvallis

first: Claudia

last: Hase

address: 105 Magruder Hall

institute: Oregon State University

summary: Investigation of whole genome gene expression level changes in a Vibrio cholerae O395N1 delta-nqrA-F mutant, compared to the wild-type strain.

platform_organism: Vibrio cholerae O1 biovar El Tor str. N16961

overall_design: Total RNA recovered from wild-type cultures of VIbrio cholerae O395N1 and its nqrA-F mutant strain. Each chip measures the expression level of  3,835 genes from Vibrio cholerae O1 biovar eltor str. N16961  with twenty average probes/gene, with five-fold technical redundancy.

first: Caprice

last: Rosato

first: Yusuke

last: Minato


title: The effect of genotype and in utero environment on inter-individual variation in neonate DNA methylomes (genotypes)

first: Dennis

last: Wang

address: 30 Medical Drive

institute: Singapore Institute for Clinical Sciences

summary:
We surveyed the genotypes and DNA methylomes of 237 neonates and found 1423 punctate regions of the methylome that were highly variable across individuals, termed variably methylated regions (VMRs), against a backdrop of homogeneity. Although methQTLs were readily detected in neonatal methylomes, genotype alone did not explain the majority of the VMRs.
We found that the best explanation for 75% of VMRs was the interaction of genotype with different in utero environments, including maternal smoking, maternal depression, maternal BMI, infant birth weight, gestational age and birth order.

first: Joanna

last: Holbrook


title: Regional commonalities and specificities of age-related changes in hippocampal transcriptome.

city: Hershey

first: Penn State

last: COM

state: PA

address: 500 University Drive

department: Genome Sciences Facility

institute: Penn State College of Medicine

summary: The project examined age-related change in hippocampal gene expression in Fisher 344 x Brown Norway F1 rats from the NIA aging colony (Adult = 12M, Aged = 24M).  CA1, CA3, and DG specific dissections were examined from one cohort of animals and from a second cohort whole hippocampus was used.

overall_design: Hippocampal gene expression with aging in a rat model was examined between Adult (12M) and Aged animals (24M)

first: Dustin

last: Masser

first: Georgina

middle: V

last: Bixler

first: Robert

last: Brucklacher

first: Heather

last: Starkey

first: Han

last: Yan

first: Jonathan

last: Wren

first: William

middle: E

last: Sonntag

first: Willard

last: Freeman


title: Shoot and root of barley seeds: Abscisic acid (ABA) treatment

first: Shingo

last: Nakamura

summary: Transcriptional profiling  of barley shoot and root with ABA

first: Takashi

last: Matsumoto


title: Genomic alterations of 332 malignant lymphoma using BAC array CGH analysis

city: Nagoya

first: Miyuki

middle: Suguro

last: Katayama

state: Aichi

address: 1-1 Kanokoden, Chikusa-ku

department: Division of Molecular Medicine

institute: Aichi Cancer Center Research Institute

type: Genome variation profiling by genome tiling array

summary: Clonal heterogeneity in lymphoid malignancies has been recently reported in adult T-Cell lymphoma/leukemia, peripheral T-cell lymphoma, not otherwise specified, and mantle cell lymphoma (MCL).   Our analysis was extended to other types of lymphoma including marginal zone lymphoma, follicular lymphoma, and diffuse large B-cell lymphoma (DLBCL). We examined the results of array comparative genomic hybridization analysis for 332 cases to determine if clonal heterogeneity existed in each case. Results showed that frequencies of clonal heterogeneity varied from 25% to 69% among different types of lymphoma. Multivariate analysis indicated that MCL and DLBCL with clonal heterogeneity showed a significantly poorer prognosis. Interestingly, 9p21.3 (CDKN2A/ 2B) loss and 17p13 (TP53, ATP1B2, SAT2, SHBG) loss were common regions among various types of lymphoma with clonal heterogeneity, suggesting at least in part that loss of these genes may play a role in clonal heterogeneity.

overall_design: We analyzed previously untreated 332 cases of lymphoma (comprising 29 cases of mantle cell lymphoma, 117 cases of diffuse large B-cell lymphoma (DLBCL), 79 cases of Follicular lymphoma, 24 cases of Burkitt lymphoma, 31 cases of mucosa-associated lymphoid tissue (MALT) lymphoma, and 51 peripheral T-cell lymphoma, not otherwise specified (PTCL-NOS)).

last: Suguro

first: Hiroyuki

last: Tagawa

first: Masao

last: Nakagawa

first: Noriko

last: Fukuhara

first: Sivasundaram

last: Karnan

first: Ichiro

last: Takeuchi

last: Seto


title: Evolution of microRNA expression at the onset of drosophila metamorphosis by mRNA

status: Public on Mar 01 2014

city: Wuhan

first: Xiao-Qin

last: Xia

state: Hubei

address: No. 7 Donghu South Road, Wuchang District

department: Center for Molelcular and Cellular Biology of Aquatic Organisms

institute: Institute of Hydrobiology, the Chinese Academy of Sciences

summary: We found two lines of evidence suggesting that miRNA abundance has been shaped by different evolutionary regimes at the two developmental stages attributed to functional constraints, which points to mechanisms more subtle and diverse than previously thought.

overall_design: 4 genotypes and 2 developmental states were investigated in this study, each with 3 biological replicates, so a total of 24 (4x2x3) hybridizations were conducted. Differential analysis between genotypes or sexes were analyzed.

first: Shu-Dan

last: Yeh

first: Marcin

last: von Grotthuss

first: Kania

last: Gandasetiawan

first: Suvini

last: Jayasekera

first: Vivek

last: Jayaswal

first: José

last: Ranz


title: Expression data from HeLa cells after hnRNP L knockdown (versus luciferase control), including cycloheximide treatment

status: Public on Feb 13 2014

city: Giessen

first: Lee-Hsueh

last: Hung

state: Hessen

address: Heinrich-Buff-Ring 58

department: Biochemistry

country: Germany

institute: University of Giessen

summary:
Transient siRNA-mediated knockdown of hnRNP L, followed by cycloheximide treatment to eliminate NMD.

Supplementary files GSE37561_activated_exon.txt and GSE37561_repressed_exon.txt list exons predicted to be activated and repressed by hnRNPL, respectively.

overall_design: 3 biological replicates of hnRNP L (luciferase) knockdown samples

first: Albrecht

last: Bindereif


title: Array-based comparative genomics of Campylobacter jejuni sheep abortion isolates (Part 2)

status: Public on Feb 11 2014

city: Ames

first: Zuo-Wei

last: Wu

state: IA

address: 1113 Veterinary Medicine Bldg

institute: Iowa state university

summary: Campylobacter jejuni has become the predominant cause of sheep abortions in the U.S. However, little is know about the genetic diversity among the isolates collected from different time periods. In this study, the genetic diversity of sheep aborion isolates of C. jejuni was investigated by Array-based CGH

overall_design: Each isolate was compared to IA3902, a dye-swap replicate was applied for each isolate

first: Zuowei

first: Rachel

last: Sippy

first: Orhan

last: Sahin

first: Qijing

last: Zhang


title: Array-based comparative genomics of Campylobacter jejuni sheep abortion isolates (Part 1)

summary: Campylobacter jejuni has become the predominant cause of sheep abortions in the U.S. However, little is know about the genetic diversity among the isolates collected from different time periods. In this study, the genetic diversity of sheep abortion isolates of C. jejuni was investigated by Array-based CGH


title: Transcriptional Profiling of Class IV da Neurons

city: Fairfax

first: Daniel

last: Cox

state: VA

address: 4400 University Drive, MSN 2A1

department: School of Systems Biology, Krasnow Institute

institute: George Mason University

summary: Elucidating the molecular mechanisms controlling dendrite development is key to understanding the pivotal role these structures play in influencing synaptic integration and neural function.  Despite significant advances in this field, genetic pleiotropy remains a significant impediment to investigating such complex developmental processes.  To circumvent this problem, we have applied class specific neuron transcriptional expression profiling coupled to an in vivo RNAi functional validation screen in order to dissect the molecular bases of Drosophila class IV dendritic arborization (da) neuron dendritogenesis.  Microarray analyses reveal transcriptional regulation as one highly enriched biological and functional category with 420 transcription factors significantly expressed in class IV neurons.   Among these, we identify roles for 268 genes in mediating a broad spectrum of functions including dendritic field coverage, branching, routing, and tiling.  Collectively, our analyses provide a more comprehensive framework of the role complex transcriptional networks play in directing distinct aspects of class specific dendrite morphogenesis.

overall_design: Gene expression profiling of class IV da neurons performed at the third instar larval stage of development from two independent cell isolations from 40-50 age-matched third instar larvae expressing mCD8::GFP under the control of the GAL4ppk.1.9 driver

first: Eswar

last: Ramachandran Iyer

first: Srividya

last: Chandramouli Iyer

first: Ramakrishna

last: Meduri

first: Dennis

last: Wang


title: A rat toxicogenomics study with Calcium Sensitizer EMD 82571 reveals a pleiotropic cause in teratogenicity

status: Public on Jan 16 2014

city: Hannover

first: Juergen

last: Borlak

state: Lower Saxony

address: Feodor-Lynen-Str. 35

department: Centre for Pharmacology and Toxicology

institute: Hannover Medical School

summary: The aim of reprotoxicity testing is to reveal adverse effects of chemicals and drugs on reproduction and on pre and postnatal fetal development. There is very limited data available on gene expression profiling for elucidation of the teratogenic effects of nongenotoxic teratogens. Therefore, research was undertaken to obtain knowledge on the molecular effects of MSC1096199 (previously known as EMD 82571), a calcium sensitizer that was abandoned in the preclinical development phase due to its teratogenic effects in some foetuses. Pregnant wistar rats were dose daily with either MSC1096199 (50 or 150 mg/kg) or Retinoic acid (10 mg/kg) on gestational days 6-17. Microarray experiment were performed using four different tissues (maternal liver, embryo liver (GD20), embryo bone (GD20), and whole embryo (GD12)) under four different conditions (vehicle, low dose and high dose of MSC1096199 and Retinoic acid) to determine the drug regulated genes. In the high dose treatment group, approximately 58% of the fetuses showed malformations i.e. exencephaly and agnathia, and toxicogenomics evidenced that the genes critically involved in osteogenesis, odontogenesis and extra cellular matrix components to be significantly regulated by MSC1096199, therefore providing a molecular rational for the observed teratogenic effects.

overall_design:
Two-condition experiment, RA vs EMD 82571. Biological replicates:5 control, 5 treated.
RNA from control  and treatment groups were labeled with Cy3 and Cy5 fluorochromes, respectively.
Cy3-channel pictures and correspondig raw data files are marked as 1b.
Cy5-channel pictures and correspondig raw data files are marked as 2b.

first: Jurgen

first: Prafull

last: Singh

first: Arun

last: Kumar


title: Shoot and root of barley seeds: Cold  treatment

first: Shingo

last: Nakamura

summary: Transcriptional profiling  of barley shoot and root with incubating at 4˚C

first: Takashi

last: Matsumoto


title: A Single Amino-Acid Substitution of RNA Polymerase ß subunit Confers A Novel Class of VISA phenotype on hVISA Strain Mu3

status: Public on Mar 31 2014

city: Bunkyo-Ku

first: tomomi

last: hishinuma

state: Tokyo

institute: juntendo university

summary: hVISA clinical strain Mu3 spontaneously generates VISA at an extremely high frequency (1x10-6 or greater) within its cell population. The VISA-converted mutant strains generally grow slower than their parent hVISA strain, but they usually form colonies on vancomycin-containing agar plates after 48 hours of incubation on population analysis. However, we noticed a curious group of VISA mutants whose colony formation is much more delayed and observed as discrete colonies only after 96 hours incubation. They have extremely prolonged lag-phase and doubling-times, but recorded vancomycin MICs of 8 to 24 mg/L when determined after 48 to 96 hours of incubation.  We established strain Mu3-6RS having vancomycin MIC of 12 mg/L (at 72h) as a representative of the ‘slow VISA’ (sVISA) strains.  Its cell wall was thickened, and autolytic activity was decreased as compared with those of the parent strain Mu3. Whole genome sequencing of Mu3-6RS revealed only one mutation, which substituted the 512th amino-acid sequence of RNA polymerase ß-subunit from Arg of Mu3 to Proline. Its VISA phenotype was unstable, and the strain frequently reverted to hVISA with concomitant loss of small colony morphology, cell-wall thickness and reduced autolytic activity. Sequencing of rpoB genes of the reverted strains revealed mutations affecting the 512th codon replacing the Proline of Mu3-6RS to Leucine, Serine, or Histidine.  This study proposes sVISA as a discrete class of VISA phenotype, which can serve as a temporary shelter for S. aureus to survive relatively high concentrations of vancomycin. The sVISA spontaneously returns to hVISA when the threat of vancomycin passes by.  The rpoB(R512P) mutation may be regarded as a ‘regulatory mutation’ switching on and off the reversible sVISA phenotype.

overall_design: 5 sample analysis using 60mer-oligo microarray, 3 rpoB mutant(R512P,R512L,R512S),  2 wild-type strain(Mu3, ΔIP)

first: Michie

last: Saito

first: Yuki

last: Katayama

first: Tomomi

last: Hishinuma

first: Yoshifumi

last: Aiba

first: Longzhu

last: Cui

first: Nanae

last: Aritaka

first: Keiichi

last: Hiramatsu


title: Illumina HT-12 expression array data for Diffuse Intrinsic Pontine Glioma

city: Toronto

first: Pawel

last: Buczkowicz

state: Ontario

address: 686 Bay Street

department: Paediatric Laboratory Medicine

institute: Hospital for Sick Children

summary: Diffuse Intrinsic Pontine Glioma (DIPG) is a fatal brain cancer that arises in the brainstem of children with no effective treatment and near 100% fatality. The failure of most therapies can be attributed to the delicate location of these tumors and choosing therapies based on assumptions that DIPGs are molecularly similar to adult disease. Recent studies have unraveled the unique genetic make-up of this brain cancer with nearly 80% harboring a K27M-H3.3 or K27M-H3.1 mutation. However, DIPGs are still thought of as one disease with limited understanding of the genetic drivers of these tumors. To understand what drives DIPGs we integrated whole-genome-sequencing with methylation, expression and copy-number profiling, discovering that DIPGs are three molecularly distinct subgroups (H3-K27M, Silent, MYCN) and uncovering a novel recurrent activating mutation in the activin receptor ACVR1, in 20% of DIPGs. Mutations in ACVR1 were constitutively activating, leading to SMAD phosphorylation and increased expression of downstream activin signaling targets ID1 and ID2. Our results highlight distinct molecular subgroups and novel therapeutic targets for this incurable pediatric cancer.

overall_design:
Illumina HT-12 arrays were performed according to the manufacturer's directions on RNA extracted from FFPE biopsy and autopsy brain tissue from DIPG patients.
Gene expression profiling on Illumina HT-12 arrays was performed for 35 paediatric DIPG samples and 10 normal brain samples

first: Christine

last: Hoeman

first: Patricia

last: Rakopoulos

first: Sanja

last: Pajovic

first: Louis

last: Letourneau

first: Misko

last: Dzamba

first: Andrew

last: Morrison

first: Peter

last: Lewis

first: Eric

last: Bouffet

first: Ute

last: Bartels

first: Jennifer

last: Zuccaro

first: Sameer

last: Agnihotri

first: Scott

last: Ryall

first: Mark

last: Barszczyk

first: Yevgen

last: Chornenkyy

first: Mathieu

last: Bourgey

first: Guillaume

last: Bourque

first: Alexandre

last: Montpetit

first: Francisco

last: Cordero

first: Pedro

last: Castelo-Branco

first: Joshua

last: Mangerel

first: Uri

last: Tabori

first: Polly

last: Ho

first: Annie

last: Huang

first: Kathryn

last: Taylor

first: Alan

last: Mackay

first: Anne

last: Bendel

first: Javad

last: Nazarian

first: Jason

last: Fangusaro

first: Matthias

last: Karajannis

first: David

last: Zagzag

first: Nicholas

last: Foreman

last: Donson

first: Julia

last: Hegert

first: Amy

last: Smith

last: Chan

first: Lucy

last: Lafay-Cousin

first: Sandra

last: Dunn

first: Juliette

last: Hukin

first: Chris

last: Dunham

first: Katrin

last: Scheinemann

first: Jean

last: Michaud

first: Shayna

last: Zelcer


title: Mammary development during pregnancy (controlateral control vs. cleared fat pad) to define transdifferentiation factors

city: Graz

first: Andreas

last: Prokesch

state: Styria

address: Harrachgasse 21/7

department: Institute of Cell Biology, Histology, and Embryology

country: Austria

institute: Medical University Graz

summary:
Tissue from cleared mammary fat pad and sham-operated controlateral control was removed before and at 10, 15,17, and 19 days of pregnancy.
Cleared vs. controlateral tissue was hybridized in dye-swap design to in-house cDNA microarry platform.
This design aims to identify factors signaling from the epithelial part of the mammary gland to the surrounding fat pad to initiate adipo-epithelial transdifferentiation.

overall_design: We surgically removed the epithelial part of the 4th mammary gland (including the nipple and the rudimentary ductal tree) in three weeks old CD1 mice where the ductal anlage is confined to the proximal part of the mammary fat pad close to the nipple. The controlateral gland was sham-operated as control. This leaves a cleared mammary fat pad in its endogenous environment. The dissected tissues were subjected to whole mount analysis to judge if the removal of epithelial tissue was complete. At the age of 10 to 15 weeks the tissues were harvested before and 10, 15, 17, and 19 days after the start of pregnancy. RNA from cleared fat pads were compared to sham-operated contralateral controls by competitive hybridization on two-channel microarrays. If enough material was available three different pools of RNA (= three biological replicates) were used for hybridization (from d19 material only two replicates were obtained) in a dye-swap configuraiton (one biological replicate of d17 and d19 samples did not provide sufficient amount for a dyw-swap pair).

first: Arianna

last: Smorlesi

first: Jessica

last: Perugini

first: Monia

last: Manieri

first: Pina

last: Ciarmela

first: Zlatko

last: Trajanoski

first: Karsten

last: Kristiansen

first: Juliane

middle: G

last: Bogner-Strauss

first: Saverio

last: Cinti


title: Parental binge alcohol abuse alters F1 generation hypothalamic gene expression in the absence of direct fetal alcohol exposure

status: Public on Mar 19 2014

city: Maywood

first: Toni

last: Pak

state: IL

address: 2160 S. First Ave

department: Cell and Molecular Physiology

institute: Loyola University Stritch School of Medicine

summary: Adolescent binge alcohol exposure has been previously shown to have long-lasting effects on the expression of hypothalamic genes that regulate the stress response, even in the absence of subsequent adult alcohol exposure. Those data suggested that alcohol can induce permanent gene expression changes, potentially through epigenetic modifications. Importantly, epigenetic modifications can be transmitted to future generations therefore, in these studies we investigated the effects of adolescent binge alcohol exposure on hypothalamic gene expression patterns in the F1 generation offspring. It has been well documented that maternal alcohol exposure during fetal development can have devastating neurological consequences. However, less is known about the consequences of maternal and/or paternal alcohol exposure outside of the gestational time frame. Here, we exposed adolescent male and female rats to a repeated binge EtOH exposure paradigm and then mated them in adulthood. Hypothalamic samples were taken from the offspring of these animals at postnatal day (PND) 7 and subjected to a genome-wide microarray analysis followed by qRT-PCR for selected genes. Importantly, the parents were not intoxicated at the time of mating and were not exposed to EtOH at any time during gestation therefore, the offspring were never directly exposed to EtOH. Our results showed that the offspring of alcohol-exposed parents had significant differences in the expression of hypothalamic genes that mediate neurogenesis and synaptic plasticity during neurodevelopment, genes important for directing chromatin remodeling, posttranslational modifications or transcription regulation, as well as genes involved in regulation of obesity and reproductive function. These data demonstrate that repeated binge alcohol exposure during pubertal development can potentially have detrimental effects on future offspring even in the absence of direct fetal alcohol exposure.

overall_design: Male and female Wistar rats were purchased from Charles River Laboratories (Wilmington, MA) at weaning (postnatal day (PND) 23) and allowed to acclimate for 7 days after arrival. Animals were handled for 5 min./once/day beginning at PND 30. Pubertal EtOH exposure began on PND 37, which is defined as peri-puberty.  Animals were undisturbed following the first exposure of our binge EtOH exposure paradigm until PND 68 (late puberty/early adult) at which time they received a second exposure to the same treatment paradigm. During the duration of the experiment, males and females were separately housed in pairs on a 12:12 light/dark cycle with lights on at 0700 h with food and water available ad libitum.     Binge Exposure Paradigm and Treatment Design. Rats were handled 5min./once/day for 7 d prior to treatment to control for nonspecific stress responses. At 37 d, animals were given 3 g/kg EtOH (20% v/v in tap water; N = 3/sex), or tap water alone (N = 3/sex), once/day via oral gavage at 10:00 AM to avoid disrupting normal feeding patterns. This process was repeated according to the following schedule for a total duration of 8 consecutive days: 3 d EtOH, 2 d tap water, 3 d EtOH. Control animals were given tap water alone once/day for 8 consecutive days. Our previous studies showed that this repeated binge-pattern EtOH paradigm does not affect body weight/growth curves and consistently results in blood alcohol concentrations (BAC) of 150-180 mg/dl in males and 210-240 mg/dl in females. We and others have previously used this paradigm as a model for the pattern of binge alcohol consumption observed in adolescents and BAC achieved are similar to those observed in humans following a binge drinking episode . After peri-pubertal treatments, animals were left undisturbed in their home cage until PND 68 when each group was again exposed to their respective treatment (i.e. control or binge EtOH. We waited 24 hours after the last dose of EtOH to ensure that blood alcohol concentrations in the parents were undetectable at the time of mating (data not shown). Animals were grouped into mating pairs: binge male + binge female (N = 3 pairs); water male + water female (N = 3 pairs). All of the females gave birth to 12-16 pups approximately 28 d after being housed with a male, indicating that conception took place approximately 6 d after pairing; therefore, the pups were never directly exposed to alcohol at any time. At PND 7 pups were deeply anesthetized on ice and sacrificed. Brains were rapidly removed, the hypothalamus microdissected on ice, and then stored in -80ºC until further processing for a genome-wide analysis on hypothalamic total RNA samples using a chip-based microarray (Southern California Genotyping Consortium, SCGC, Illumina Rat Ref-12). The PND 7 time point was chosen because the extent of rat neurodevelopment at PND 7 is roughly equivalent to that of a human infant at birth

first: Magdalena

last: Przybycien-Szymanska

first: Yathindar

middle: S

last: Rao

first: Sarah

last: Prins


title: Illumina Infinium 450K array data for Diffuse Intrinsic Pontine Glioma

first: Pawel

last: Buczkowicz

overall_design:
Illumina Infinium 450K arrays were performed according to the manufacturer's directions on bisulfite converted gDNA extracted from fresh frozen biopsy and autopsy brain tissue from DIPG patients.
CpG methylation profiling on Illumina Infinium 450K arrays was performed for 28 paediatric DIPG samples.

first: Christine

last: Hoeman

first: Patricia

last: Rakopoulos

first: Sanja

last: Pajovic

first: Louis

last: Letourneau

first: Misko

last: Dzamba

first: Andrew

last: Morrison

first: Peter

last: Lewis

first: Eric

last: Bouffet

first: Ute

last: Bartels

first: Jennifer

last: Zuccaro

first: Sameer

last: Agnihotri

first: Scott

last: Ryall

first: Mark

last: Barszczyk

first: Yevgen

last: Chornenkyy

first: Mathieu

last: Bourgey

first: Guillaume

last: Bourque

first: Alexandre

last: Montpetit

first: Francisco

last: Cordero

first: Pedro

last: Castelo-Branco

first: Joshua

last: Mangerel

first: Uri

last: Tabori

first: Polly

last: Ho

first: Annie

last: Huang

first: Kathryn

last: Taylor

first: Alan

last: Mackay

first: Anne

last: Bendel

first: Javad

last: Nazarian

first: Jason

last: Fangusaro

first: Matthias

last: Karajannis

first: David

last: Zagzag

first: Nicholas

last: Foreman

last: Donson

first: Julia

last: Hegert

first: Amy

last: Smith

last: Chan

first: Lucy

last: Lafay-Cousin

first: Sandra

last: Dunn

first: Juliette

last: Hukin

first: Chris

last: Dunham


title: ChIP-chip Monocyte H3K9Ac from DCCT/EDIC patients

status: Public on Dec 31 2013

city: Duarte

first: Nancy

last: Chen

state: CA

address: 1500 Duarte Road

department: Diabetes

institute: City of Hope

summary: Chromatin immunoprecipitation linked to tiling arrays (ChIP-chip) were performed to profile histone H3K9Ac at 22K gene promoters in peripheral blood monocytes obtained in 2009-10 from 60 selected DCCT participants being followed in the long-term observational EDIC study.

overall_design: Comparison of histone H3K9Ac at 22K gene promoters in 60 peripheral blood monocytes samples obtained from the conventional and intensive therapy DCCT groups

first: Rama

last: Natarajan

first: Feng

last: Miao

first: Zhuo


title: A genome-wide transcriptome analysis reveals diverse roles of two-component system DraR-K in physiological and morphological differentiation of Streptomyces coelicolor

status: Public on Mar 10 2014

city: Shanghai

first: Yinhua

last: Lu

address: 300 Fenglin Road

department: Institute of Plant physiology and ecology

institute: Shanghai Institutes for Biological Sciences

summary: A novel two-component system (TCS) DraR-K was identified previously to play a differential role in antibiotic biosynthesis (ACT, RED and yCPK) of Streptomyces coelicolor M145 on defined minimal medium (MM) conditions. In order to assess whether DraR-K has more global roles, a genome-wide transcriptomic analysis of the wild-type strain M145 and ∆draR-K under the condition of 75 mM glutamine-based MM was performed using DNA microarray. The analysis demonstrated that deletion of draR-K led to the differential expression not only of the biosynthetic gene clusters of ACT, RED and yCPK, but also of other six secondary metabolite biosynthetic clusters, revealing the widely differenital regulation of DraR-K on secondary metabolism of S. coelicolor. Besides, a number of primary metabolism-related genes in the ∆draR-K mutant, such as ureA/B/C/D/G/F, pstSCAB operon and chb gene also exhibited altered expression, which might enable the rebalance of C/N/P ratio under the condition of high concentration of Gln. We also observed that expression of many developmental genes (chpA/B/D/E, ramR/S and rdlA/B) was affected as well after draR-K deletion. Furthermore, the direct role of DraR-K on the transcription of several genes, including cdaR (the pathway-specific activator gene for CDA biosynthesis), chb, and pepA/pepA2 (SCO7336/7337, possibly involved in aerial mycelium development) were validated by electrophoresis mobility shift assays (EMSAs). In summary, our transcriptome analyses revealed the global regulation of DraR-K on physiological and morphological differentiation, especially its differential roles on secondary metabolism of S. coelicolor.

overall_design: The global transcription profiles of M145 and the ∆draR-K mutant was compared using DNA microarray. RNA samples were isolated from these two strains grown on MM supplemented with 75 mM glutamine as the sole nitrogen source at three time points, 36, 48 and 60 h.

first: Zhenyu

last: Yu

first: Guosong

last: Zheng

first: Hong

last: Zhu

first: Weihong

last: Jiang

first: Panpan

last: Liu


title: Global gene regulation in permanent focal ischemia in an in vivo rat model

city: Hobart

first: Minghui Jessica

state: Tasmania

address: Menzies Research Institute, University of Tasmania, Private Bag 24

department: Neuroscience group

country: Australia

institute: Menzies Research Institute

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

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

overall_design: Refer to individual Series


title: ChIP-chip Lymphocyte H3K9Me2 from DCCT/EDIC patients

summary: Chromatin immunoprecipitation linked to tiling arrays (ChIP-chip) were performed to profile histone H3K9Me2 at 22K gene promoters in peripheral blood lymphocytes obtained in 2009-10 from 60 selected DCCT participants being followed in the long-term observational EDIC study.

overall_design: Comparison of histone H3K9Me2 at 22K gene promoters in 60 peripheral blood lymphocytes samples obtained from the conventional and intensive therapy DCCT groups


title: ChIP-chip Lymphocyte H3K9Ac from DCCT/EDIC patients

summary: Chromatin immunoprecipitation linked to tiling arrays (ChIP-chip) were performed to profile histone H3K9Ac at 22K gene promoters in peripheral blood lymphocytes obtained in 2009-10 from 60 selected DCCT participants being followed in the long-term observational EDIC study.

overall_design: Comparison of histone H3K9Ac at 22K gene promoters in 60 peripheral blood lymphocytes samples obtained from the conventional and intensive therapy DCCT groups


title: Epigenomic Approaches to explaining Metabolic Memory in the Epidemiology of Diabetes Intervention and Complications (EDIC) Study


title: Evolution of microrna expression at the onset of drosophila metamorphosis by miRNA

status: Public on Mar 06 2014

first: Xiao-Qin

last: Xia

summary: We found two lines of evidence suggesting that miRNA abundance  has been shaped by different evolutionary regimes at the two developmental stages. Attributed to functional constraints, which points to mechanisms more subtle and diverse than previously thought.

sample_organism:
Drosophila melanogaster
Drosophila simulans
Drosophila yakuba

overall_design: 6 genotypes, sex and 2 developmental states were investigated in this study, each with 4 biological replicates, a total of 72 hybridizations were conducted. Differential analysis between genotypes or sexes were analyzed.

first: Shu-Dan

last: Yeh

first: Marcin

last: von Grotthuss

first: Kania

last: Gandasetiawan

first: Suvini

last: Jayasekera

first: Vivek

last: Jayaswal

first: José

last: Ranz


title: Array-based comparative genomics of Campylobacter jejuni sheep abortion isolates

first: Zuo-Wei

last: Wu


title: Gene expression profile of liver tissue in low-dose, repeated diethylnitrosamine (DEN)-treated rat treated with erlotinib

status: Public on Feb 28 2014

city: Dallas

first: Yujin

last: Hoshida

state: TX

address: 5323 Harry Hines Blvd

institute: University of Texas Southwestern Medical Center

summary:
Gene-expression profiles of rat liver cirrhosis induced by diethylnitrosamine and the effect of erlotinib on liver fibrogenesis and liver cancer development

Hepatocellular carcinoma (HCC) is the sixth most common solid tumor worldwide and the third leading cause of cancer-related death. Given the lack of successful treatment options, chemoprevention in high-risk patients has been proposed as an alternative strategy. Mounting evidence supports a role for epidermal growth factor (EGF) during chronic liver disease and hepatocellular transformation. We address the hypothesis that blocking the EGF-EGF receptor (EGFR) pathway may be an effective strategy for inhibiting fibrogenesis and hepatocarcinogenesis. A rat model of diethylnitrosamine (DEN)-induced cirrhosis was used to examine the effects of erlotinib on underlying chronic liver disease and HCC formation. The DEN-induced rat model closely resembles disease progression in humans both pathologically and molecularly. Erlotinib significantly prevented the development of HCC tumor nodules in a dose-dependent fashion. Further, erlotinib inhibited the activation of hepatic stellate cells and prevented fibrogenesis. Erlotinib also reduced hepatotoxicity and improved liver function. Finally, a gene expression signature predictive of poor survival in human cirrhosis patients was reversed in response to erlotinib. Our data demonstrate for the first time that EGFR inhibition prevents liver fibrogenesis. Further, our results suggest that erlotinib is a potentially effective HCC chemoprevention strategy through inhibition of cirrhosis progression which can be monitored at the molecular level.

Keywords: Cirrhotic liver, Expression array, Illumina, Signatures, Outcome prediction

overall_design: Animals received humane care according to the criteria outlined in the “Guide for the Care and Use of Laboratory Animals” of the National Academy of Sciences. All animals were maintained in accordance with the institutional guidelines of the Massachusetts General Hospital Subcommittee on Research Animal Care. Male Wistar rats received weekly IP injections of diethylnitrosamine (DEN) at 50 mg/kg, 100mg/kg, or vehicle control (PBS) for 18 weeks. A subset of rats received either daily (5X a week) IP injections of 2 mg/kg erlotinib or vehicle control during weeks 13 - 18. In a separate study, the erlotinib dose was lowered to 0.5 mg/kg. The vehicle groups from the two studies were not significantly different so they were combined together for analysis. Rats were weighed at the end of each week. Animals were sacrificed at 9, 13 and 19 weeks after a one-week washout period to eliminate acute effects of DEN. At the time of sacrifice, the non-tumor liver tissues were collected in RNase-free tubes and snap-frozen in liquid nitrogen. Frozen tissues were stored at -80°C until RNA extraction.

first: Bryan

last: Fuchs

first: Tsutomu

last: Fujii

first: Gregory

middle: Y

last: Lauwers

first: Christopher

last: McGinn

first: Suguru

last: Yamada

first: Toshihiko

last: Kuroda

first: Michael

last: Lanuti

first: Todd

last: Golub

first: Kenneth

last: Tanabe


title: Gene expression profile of hepatocellular carcinoma in low-dose, repeated diethylnitrosamine (DEN)-treated rat treated with erlotinib

summary:
Gene-expression profiles of rat hepatocellular carcinoma induced by diethylnitrosamine (DEN) and the effect of erlotinib
Hepatocellular carcinoma (HCC) is the sixth most common solid tumor worldwide and the third leading cause of cancer-related death. Given the lack of successful treatment options, chemoprevention in high-risk patients has been proposed as an alternative strategy. Mounting evidence supports a role for epidermal growth factor (EGF) during chronic liver disease and hepatocellular transformation. We address the hypothesis that blocking the EGF-EGF receptor (EGFR) pathway may be an effective strategy for inhibiting fibrogenesis and hepatocarcinogenesis. A rat model of diethylnitrosamine (DEN)-induced cirrhosis was used to examine the effects of erlotinib on underlying chronic liver disease and HCC formation. The DEN-induced rat model closely resembles disease progression in humans both pathologically and molecularly. Erlotinib significantly prevented the development of HCC tumor nodules in a dose-dependent fashion. Further, erlotinib inhibited the activation of hepatic stellate cells and prevented fibrogenesis. Erlotinib also reduced hepatotoxicity and improved liver function. Finally, a gene expression signature predictive of poor survival in human cirrhosis patients was reversed in response to erlotinib. Our data demonstrate for the first time that EGFR inhibition prevents liver fibrogenesis. Further, our results suggest that erlotinib is a potentially effective HCC chemoprevention strategy through inhibition of cirrhosis progression which can be monitored at the molecular level.

first: Lan

last: Wei

first: Supriya

last: Gupta

first: Andrew

last: Crenshaw

first: Robert

last: Onofrio

first: Bradley

last: Taylor

first: Wendy

last: Winckler


title: Transcriptome analysis of Bovine granulosa cells of preovulatory follicles at 30, 60, 90 and 120 days postpartum

city: Québec City

first: Marc-André

last: Sirard

state: Quebec

address: Offfice 2732, 2440 Hochelaga Blvd.

department: Sciences Animales

institute: Université Laval

summary: Cows in Negative Energy Balance (NEB) may preferentially divert nutrients away from reproduction, thereby experiencing a period of anovulatory anestrus, delayed ovulation of large follicles and a condition of impaired fertility. To better understand the changes occurring in these large follicles as a function of time post-partum granulosa cells  of preovulatory follicles have been collected at different times: 30, 60, 90 and 120 days after calving . An analysis of the transcriptome was performed using a global bovine oligo-array microarray to map the differences in genes expression and cellular functions that occur in the follicular microenvironment during the progressive recovery from NEB condition in dairy cow

overall_design: Four time points experiment: 30, 60, 90 and 120 days. Granulosa cells from the 30, 60 and 90 days compare to the 120 days (reference). Biological replicates: 3 from each time point. One replicate per array.

first: Vittorio

last: Golini

first: Giuseppe

last: Stradaioli

first: Marc-Andre


title: cpsf30 mips1 transcriptome-Cell death control by CPSF30

status: Public on Feb 01 2014

city: evry

first: Soubigou-Taconnat

last: Ludivine

address: 2 rue gaston crémieux

department: URGV

institute: INRA

summary: au12-06_cpsf30 - cpsf30 mips1 transcriptome - How a mutation in the CPSF30 is able to suppress the cell death phenotype observed in the mips1-1 Arabidopsis mutant? - All the plants were cultivated in the same hanging conditions 10days in "short Days" then in long Days. The takings were later made 4days in "long Days" what corresponds to the appearance of the symptoms of cellular death at the mutant mips1-1. On the other hand, the gene CPSF30 codes for two transcribed. We have a double mutant mips1 cpsf30 complemented with the transcribed young.

overall_design: 6 dye-swap - genotype comparaison

first: Sandrine

last: Balzergue

first: Ludivine

last: Taconnat

first: Marianne

last: Delarue

first: Marie-Laure

last: Martin-Magniette


title: Genome-wide analysis of dorsal root ganglion (DRG) gene expression after morphine or oxycodone treatment

status: Public on Jan 09 2014

city: Paris

first: Karine

last: Thibault

address: 10 rue Vauquelin

institute: ESPCI

summary:
Analyse of gene expression modification after chronic analgesic treatment. The hypothesis tested in the present study was that oxycodone and morphine induced gene expression modification.
Results provide important information to understand the analgesic effects of oxycodone as compared to morphine in a neuropathic pain model

overall_design: Total RNA obtained from DRG of neuropathic or control animals after oxycodone or morphine treatment

first: Bernard

last: Calvino

first: Isabelle

last: Rivals

first: Fabien

last: Marchand

first: Sophie

last: Dubacq

first: Stephen

last: McMahon

last: Pezet


title: ChIP-chip Monocyte H3K4Me3 from DCCT/EDIC patients

first: Nancy

last: Chen

summary: Chromatin immunoprecipitation linked to tiling arrays (ChIP-chip) were performed to profile histone H3K4Me3 at 22K gene promoters in peripheral blood monocytes obtained in 2009-10 from 60 selected DCCT participants being followed in the long-term observational EDIC study.

overall_design: Comparison of histone H3K4Me3 at 22K gene promoters in 60 peripheral blood monocytes samples obtained from the conventional and intensive therapy DCCT groups

first: Rama

last: Natarajan

first: Feng

last: Miao

first: Zhuo


title: microRNAs involved in regulating embolic stroke recovery following spontaneous reperfusion [mRNA]

status: Public on Dec 09 2013

city: Singapore

first: Kandiah

last: Jeyaseelan

address: 8 Medical Drive

institute: National University of Singapore

summary: To date, miRNA and mRNA expression studies on cerebral ischemia in both human and animal models have focused mainly on acute phase of ischemic stroke. In this study, we present the roles played by microRNAs in the spontaneous recovery phases in cerebral ischemia using rodent stroke models.

overall_design: In this study presented here, Middle Cerebral Artery Occlusion stroke model was established by using embolus and the brain samples of stroke model were harvestd at 0hrs, 3hrs, 6hrs, 12hrs, 24hrs, 48hrs, 72hrs, 120hrs and 168hrs. RNAs were extracted from these samples and microRNA array and mRNA array were performed.

first: Fu

last: Liu

first: Kai

last: Lim

first: Prameet

last: Kaur

first: Sugunavathi

last: Sepramaniam

first: Arunmozhiarasi

last: Armugam

first: Peter

middle: T

last: Wong


title: Analysis of the global gene expression in the rat hearts transduced with adeno-associated viral vectors coding VEGF-B

status: Public on Nov 30 2013

city: Helsinki

first: Riikka

last: Kivelä

address: Haartmaninkatu 8

country: Finland

institute: University of Helsinki and Wihuri Research Institute

summary: We show that an excess of VEGF-B protects the heart via adaptive cardiac hypertrophy and increased coronary arterial reserve, and by inducing a shift from lipid to glucose metabolism.

overall_design: Six hearts transduced with AAV-VEGF-B  were compared to six AAV-HSA (human serum albumin) controls

last: Kivela

first: Kari

last: Alitalo


title: High resolution microRNA signatures in human whole saliva

status: Public on Apr 12 2014

city: Bethesda

first: Hyun Min

last: Jung

state: MD

address: 6 Center Drive

department: Division of Developmental Biology

institute: National Institutes of Health

summary: Recent studies have reported both mRNA and microRNA (miRNA) in saliva, but little information has been documented on the quality and yield of RNA collected. Therefore, the aim of the present study was to develop an improved RNA isolation method from saliva and to identify major miRNA species in human whole saliva.

overall_design: RNA samples were isolated from normal human saliva using a combined protocol based on the Oragene RNA collection kit and the mirVana miRNA isolation kit in tandem. RNA samples were analyzed for quality and subjected to miRNA array analysis. Twelve representing 6 males and 6 females, were selected for miRNA profiling using the TaqMan® Low Density Array Card (TLDA) Human miRNA Panel v2.0 (Applied Biosystems). The analysis of expression of the >700 miRNAs was performed by the DNA Core at the Interdisciplinary Center for Biotechnology Research Center at the University of Florida, according to the manufacturer’s protocol except the pre-amplification step was omitted. The NormFinder algorithm was used to identify the optimal normalization of miRNA among the 25 most abundantly expressed miRNAs detected.

first: Rushi

last: Patel

first: Edward

last: Chan


title: VEGF-B in rat hearts


title: ChIP-chip Lymphocyte H3K4Me3 from DCCT/EDIC patients

summary: Chromatin immunoprecipitation linked to tiling arrays (ChIP-chip) were performed to profile histone H3K4Me3 at 22K gene promoters in peripheral blood lymphocytes obtained in 2009-10 from 60 selected DCCT participants being followed in the long-term observational EDIC study.

overall_design: Comparison of histone H3K4Me3 at 22K gene promoters in 60 peripheral blood lymphocytes samples obtained from the conventional and intensive therapy DCCT groups


title: Characterization of gene expression in trigeminal nerves of BDIX, BDIV, BDIX.BDIV-Mss4a and BDIX.BDIV-Mss4d rats of both sexes.

status: Public on Dec 18 2013

city: Essen

first: Andrea

last: Kindler-Röhrborn

address: Hufelandstr. 55

institute: Department of Pathology

summary: Identification of genes being differentially expressed between a) female and male rats within each strain and b) tumor susceptible and tumor resistant strains using Microarray analyses.

overall_design: Isolation of total RNA from pooled untreated trigeminal nerves of 85 day old rats and gene expression analyses using RatRef-12-v1 and GenomeStudio 2010.

first: Linda

last: van den Berg

first: Bernd

middle: U

last: Koelsch


title: Global transcriptomic profiling of permanent focal ischemia in an in vivo rat model

first: Minghui Jessica

last: Chen

summary: Focal ischemia is triggered by the sudden significant reduction of blood supply to the brain, as a result of either the rupture or occlusion by thrombus/embolism of a blood vessel in the brain. Permanent focal ischemia occurred when blood supply to a specific part of the brain is impeded without reperfusion. Despite major steps achieved in the elucidation of the patho-physiology of cerebral ischemia, the available therapeutic avenues for acute ischemic stroke remain scarce. Cell cycle re-activation has been revealed as a novel signaling pathway during permanent focal ischemia. As such, non-specific aurora kinase inhibitor ZM447439, has been injected intracranial-ventricularly30min post-ischemia induction to determine its efficacy in reduction of neuronal damage in terms of infarct volume.

overall_design: Microarray analysis was performed on Illumina Rat Ref12V1 beadchips. Right cortex RNA samples were collected at two time-points (8h and 24h ) respectively for all three experimental conditions: Sham (n=4), vehicle (i.e. ischemic injury with i.c.v. injection 80% DMSO; n=4) and treatment (injury plusi.c.v.injection of 30mM ZM447439 in 80% DMSO; n=4).

first: Nam

last: Cheung

first: Minghui

first: Jayapal

last: Manikandan


title: Analysis of conditioned media cytokine levels of breast cancer cell lines

status: Public on Nov 01 2013

city: Guangzhou

first: Shicheng

last: Su

address: 107 Yanjiang West Road

institute: Sun-Yat-Sen Memorial Hospital

summary: To identify the cytokines secreted by mesenchymal-like cancer cells that activate macrophages, the cytokine profiles of conditioned media from MCF7, MCF7 induced to undergo EMT by treatment of TGF-β, TNF-α and prolonged mammosphere culture, and MDA-MB-231 cells were analyzed by RayBio® Human Cytokine Antibody Array V.

overall_design: 5 samples. There are 5 groups: MCF7, MCF7 induced to undergo EMT by treatment of TGF-β (TGF-β-MCF7), TNF-α (TNF-α-MCF7), prolonged mammosphere culture (MCF7M), and MDA-MB-231 cells


title: Gene expression data for liver, adipose, and skeletal muscle tissues of MKR and Healthy mice.

status: Public on Oct 30 2013

first: Amit

last: Kumar

address: 14A Service Rd West., Room 176

department: NIDDK

summary:
MKR mice is a Type 2 Diabetic mice, which was created by expressing mutation in IGF1 receptor in the skeletal muscle, and is widely used in diabetes research. Gene expression differences between MKR mice and Healthy (Wild type) mice are poorly understood.
We used microarrays to detail the differences between gene expression in liver, fat, and skeletal muscle of MKR and Healthy mice.

overall_design: Male 10-weeks old FVB/N – MKR and wild type mice were used for the microarray studies. 3 biological replicates for each tissue type  and for both MKR and WT mice were used in the studies.

first: Chithra

last: Keembiyehetty

first: Joseph

last: Shiloach

first: Michael

last: Betenbaugh

first: Emily

last: Gallagher

first: Derek

last: LeRoith


title: Brd2 regulates gene expression and alternative splicing.

status: Public on Dec 03 2013

city: Prague

first: David

last: Stanek

address: Videnska 1083

country: Czech Republic

institute: Institute of Molecular Genetics

summary: We analyzed a role of Brd2 protein in transcription and alternative splicing. 289 genes change alternative splicing after Brd2 knockdown and 1459 genes alter gene expression compared to cells treated with negative control siRNA.

overall_design: 6 samples (3 independent samples of cells treated with Brd2 siRNA, 3 samples of cells treated with negative control siRNA)

first: J

last: Hnilicova

last: Jarrells

first: D


title: Analysis of the global gene expression in VEGF-B transgenic rat hearts

first: Riikka

last: Kivelä

overall_design: Six VEGF-B overexpressing transgenic hearts were compared to six littermate wildtype controls

last: Kivela

first: Kari

last: Alitalo


title: Expression data from fine-needle aspiration biopsies of breast cancer metastases from different anatomical sites

status: Public on Dec 02 2013

city: Lund

first: Siker

last: Kimbung

address: Scheelevägen 2

department: Department of Oncology and Pathology, Clinical Sciences, Lund

country: Sweden

institute: Lund University

summary:
Breast cancer molecular subtypes preferentially metastasize to specific organs and the anatomical location of the metastasis is associated with the length of survival post-recurrence.
We used microarrays to provide a detailed characterization of breast cancer site-specific metastases  with particular focus on identifying genes predictive of breast cancer liver metastatic proprnsity

overall_design: We performed global gene expression profiling on fine-needle aspirates of metastatic lesions from different anatomical sites obtained  from breast cancer patients treated within the Swedish randomized trial (TEX) of first-line chemotherapy for locally advanced or metastatic breast cancer. Samples were collected before commencement of treatment.

first: Ingrid

last: Hedenfalk

first: Thomas

last: Hatschek


title: Expression data in KSHV-infected primary rat mesenchymal precursor (MM) cells

status: Public on Aug 28 2013

city: San Antonio

first: Xiaodong

last: Cui

state: Texas

address: 126 Arrow Oaks

department: Electrical engineering

institute: Univ of Texas SA

summary: Kaposi's sarcoma-associated herpesvirus (KSHV) can efficiently infect and transform primary rat mesenchymal precursor (MM) cells. Regulation of cell cycle progression and apoptosis by KSHV-encoded microRNAs is required for KSHV-induced cellular transformation and tumorigenesis.

overall_design: To determine the roles of KSHV miRs in growth deregulation, we infected MM cells with the KSHV miR cluster deletion mutant and monitored infection by examining green fluorescence protein expression from a cassette inserted in the KSHV genome.

first: Rosalie

last: Moody

first: Ying

last: Zhu

first: Shou

last: Gao


title: miRNAs involved in regulating embolic stroke recovery following spontaneous reperfusion

first: Kandiah

last: Jeyaseelan

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

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

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

overall_design: Refer to individual Series

first: Fu

last: Liu

first: Kai

last: Lim

first: Prameet

last: Kaur

first: Sugunavathi

last: Sepramaniam

first: Arunmozhiarasi

last: Armugam

first: Peter

last: Wong


title: Effects of PMA on exon usage of HL60, THP-1, and U937 cells

status: Public on Sep 25 2013

city: Ebetsu

first: Hiroshi

last: Kitamura

address: 582 Midorimachi, Bunkyodai

department: School of Veterinary Medicine

institute: Rakuno Gakuen University

summary:
Myeloid leukemia cell lines HL60, THP-1, and U937 undergo macrophage-like differentiation after treatment with phorbol ester.
To explore genes whose exon usage was altered during macrophage differentiation, we compared exome of PMA-treated (differentated) and vehicle-treated (undifferentiated) myeloid cell lines.

overall_design: HL60, THP-1, and U937 cells were treated with either phorbol 12-myristate 13-acetate (PMA,30nM) or its vehicle (DMSO) for 3 days, and subjected to exome analysis using Affymetrix human exon 1.0ST arrays.

first: Tomoko

last: Yuasa

last: Hasegawa

first: Chisato

last: Kikuguchi

first: Osamu

last: Ohara


title: Diversity of antibody responses to Borrelia burgdorferi in experimentally-infected beagle dogs

status: Public on Aug 22 2013

city: Irvine

first: Elisabeth

last: Baum

address: Med Surge II

institute: University of California Irvine

summary: Lyme borreliosis (LB) is a common infection of domestic dogs in areas where there is enzootic transmission of the agent Borrelia burgdorferi.  Immunodiagnostic assays for canine antibodies to B. burgdorferi are usually based on whole-cell preparations as substrate and, consequently, interpretation of results is confounded by antibody cross-reactivity between borrelial antigens and those of other bacterial species.  To more broadly characterize the antibody responses to B. burgdorferi infection and to assess the diversity in those responses between individual dogs, we examined sera from 32 adult, colony-bred beagle dogs that were experimentally infected with B. burgdorferi through tick bites and compared those on a protein microarray with sera from uninfected dogs in their antibody reactivities to various recombinant chromosome- and plasmid-encoded B. burgdorferi proteins, including 24 of the serotype-defining OspC proteins of North America.  The profiles of immunogenic proteins for the dogs were largely similar to those for humans and natural reservoir rodents.  These included the decorin-binding protein DbpB, BBA36, BBA57, BBA64, fibronectin-binding protein BBK32, VlsE, FlaB and other flagellar structural proteins, Erp proteins, Bdr proteins, and all of the OspC proteins.  In addition, the canine sera bound to the presumptive lipoproteins BBB14 and BB0844, which infrequently elicited antibodies in humans or rodents.  Although the beagle, like most other domestic dog breeds, has a small effective population size and features extensive linkage disequilibrium, the group of animals here demonstrated diversity in antibody responses by measures of antibody levels and specificities for conserved proteins, like DbpB, and polymorphic ones, like OspC.

overall_design: Antibody profiling was performed on sera from dogs experimentally-infected with B. burgdorferi and unexposed controls against antigens of B. burgdorferi. Thirty-two serum samples from experimental infections, and 4 unexposed controls were probed on a protein microarray displaying 72 unique proteins of B. burgdorferi .

first: Deborah

last: Grosenbaugh

first: Alan

last: Barbour