title: Application of the TGx-28.65 toxicogenomics biomarker to classify genotoxic and non-genotoxic chemicals in human TK6 cells in the presence of rat liver S9

status: Public on Aug 25 2016

city: Ottawa

first: Julie

last: Buick

state: Ontario

address: 50 Colombine Driveway

department: Mechanistic Studies Division

institute: Health Canada

summary: In vitro toxicogenomics signatures to predict mode of action can facilitate chemical screening. We recently demonstrated the use of the TGx-28.65 genomic biomarker (representing: toxicogenomics (TGx), developed using a 28 chemical training set, and comprising 65 genes) in classifying agents as genotoxic (DNA damaging) and non-genotoxic in human lymphoblastoid TK6 cells. Because TK6 cells do not possess cytochrome P450 activity, we confirmed accurate classification in cells co-exposed to 1% 5,6 benzoflavone/phenobarbital-induced rat liver S9 for metabolic activation. However, chemicals may require different types of S9 for activation. Here we conducted experiments in TK6 cells exposed to chemicals in the presence of 2% or 10% Aroclor-induced, or 5% ethanol-induced rat liver S9 to expand TGx-28.65 biomarker application. Gene expression profiles were produced 3-4 hr following a 4 hr co-exposure of TK cells to test chemicals (seven genotoxic and two non-genotoxic, three concentrations, and concurrent solvent controls) and S9. Relative survival and micronucleus frequency was assessed by flow cytometry in cells 20 hr after the exposure. We found that genotoxicity/non-genotoxicity could be accurately predicted for the test compounds using the different S9s. One technical replicate of cells co-treated with dexamethasone and 10% Aroclor-induced S9 was falsely predicted as genotoxic, suggesting caution in using high concentrations of S9. TGx-28.65 correctly classified low concentrations of genotoxic chemicals (those not causing cytotoxicity or micronuclei) as genotoxic, demonstrating that it is a sensitive biomarker of genotoxicity. Overall, the work confirms that different S9s can be used in TK6 cells without impairing predictivity using the TGx-28.65 biomarker.

overall_design: This experiment examined the whole genome transcriptional response of TK6 cells exposed to 9 test chemicals, including acetaminophen, 2-aminoanthracene, cyclophosphamide, dibenz[a,h]anthracene, dimethylnitrosamine, furan, 2-nitrofluorene, phenanthrene, sucrose, and for 4 hours followed by a recovery time of 3-4h in fresh media at 3 different concentrations, including a low, a medium, and a high concentration, in addition to vehicle controls (+S9).  Each concentration and time point had 3 biological replicates, which were pooled for gene expression analysis. There were a total  31 samples (9 arrays) included in the final analysis using a two-colour dye swap design.

first: Carole

middle: L

last: Yauk

middle: K

first: Andrew

last: Williams

first: Carol

last: Swartz

first: Leslie

last: Recio

first: Heng-Hong

last: Li

first: Albert

middle: J

last: Fornace

first: Errol

last: Thomson

first: Jiri

last: Aubrecht


title: Epigenetic Alterations in Dense Human Spermatozoa for Assisted Reproduction

status: Public on Aug 01 2016

city: Guangzhou

first: Zhaofeng

last: Huang

state: Guangdong

address: 74# zhongshan 2nd Road

department: Zhongshan School of Medicine

country: China

institute: Sun Yat-sen University

type: Methylation profiling by genome tiling array

summary:
Selected human sperms with ART technique demonstrate many changes in the genetic and epigenetic aspects. There are many evidances shown that DNA damange and histone retention ratio have significant improved after selection with different methods. These changes may relate with DNA epigenetic changes, however no evidance demonstate these relevance.
In this study, MeDIP-ChIP method has been employed to detect DNA methylation loci in human sperm genome processed with density selection. Results demonstrated that DNA methylation changed in specific gene location.

overall_design: comparison the DNA methylation site between 3 pair human sperm DNA samples before or after density selection

first: Z

first: B

last: Yu


title: Experimental identification of apoptosis-associated miR-21 target genes in Jurkat T-cells using a high-throughput experimental approach

status: Public on Aug 03 2016

city: Groningen

first: Joost

last: Kluiver

state: Groningen

address: Hanzeplein 1

department: Pathology and Medical Biology

country: Netherlands

institute: University Medical Center Groningen

summary: MiR-21 is an important suppressor of T-cell apoptosis that is also widely overexpressed in many types of cancers. The exact mechanisms related to the anti-apoptotic effect of miR-21 is not well understood. In this study, we applied AGO2 RNA Immunoprecipitation followed by gene expression profiling (RIP-Chip) in Jurkat cells to identify apoptosis-associated miR-21 target genes. We showed that expression of miR-21 rapidly increases upon αCD3/αCD28 activation of Jurkat cells. Inhibition of miR-21 resulted in reduced cell growth and induced apoptosis. Upon AGO2-RIP-Chip, we observed an overall increased enrichment of miR-21 target genes in the IP fraction of miR-21-overexpressing Jurkat cells as compared to the IP fraction of empty vector control cells. We noted a systematic decrease in transcript levels of predicted miR-21 target genes compared to EV control. We identified 72 genes that were 2-fold enriched in the AGO2-IP fraction of miR-21-overexpressing cells that contained a predicted miR-21 binding site. Of these, 71 were enriched 2-fold more in the miR-21-overexpressing cells as compared to EV Jurkat cells. The target gene for which the enrichment was most prominently increased upon miR-21 overexpression was the pro-apoptotic protein LATS1. Luciferase reporter assays confirmed direct targeting of the LATS1 3'UTR by miR-21. In line with the luciferase results, Western blot analysis revealed a decrease in LATS1 upon miR-21 inhibition. LATS1 qRT-PCR analysis in primary T-cells showed that LATS1 levels decrease upon T-cell stimulation while the miR-21 levels increase. Collectively, these data identify the miR-21 target LATS1 as a likely candidate whose inhibition contributes to the anti-apoptotic function of miR-21 in T-cells and perhaps also many types of cancers.

overall_design: Gene expression array on Jurkat cells overexpressing miR-21 and empty vector (EV).

first: Nato

last: Teteloshvili

first: Katarzyna

last: Smigielska-Czepiel

first: Ye

last: Yuan

first: Annika

last: Seitz

first: Debora

last: de Jong

first: Bea

last: Rutgers

first: Pytrick

last: Jellema

first: Roelof

last: van der Lei

first: Izabella

last: Slezak-Prochazka

first: Annemieke

middle: M

last: Boots

first: Bart

last: Kroesen

first: Anke

last: van den Berg


title: The effect of CSF1-Fc treatment in pigs on liver gene expression

city: Roslin

first: Kristin

last: Sauter

address: Easter Bush, Midlothian

country: United Kingdom

institute: Roslin Institute/The University of Edinburgh

summary: The expression was designed to determine whether exposure to CSF1-Fc has any effect on liver-specific gene expression in pigs.

overall_design: livers from pigs exposed to CSF1-Fc

middle: A

first: David

last: Hume


title: Microarray based metatranscriptomics in the human gut microbiome

city: Kongens Lyngby

first: Henrik

middle: Bjørn

last: Nielsen

address: Kemitorvet, b. 208

department: Systems Biology

country: Denmark

institute: Technical University of Denmark

summary: Hundreds of microbial species were found to be transcriptionally active in the human gut microbiome based on the expression profiling of ca. 680.000 microbial genes

overall_design: As a part of the MetaHIT cohort 233 human stool samples were transcriptionally profiled using a custom made microarray that included probes for most prevalent microbial genes in the cohort as established by whole-genome sequencing of the same samples

middle: B

first: Damian

middle: R

last: Plichta


title: Point mutations in exon 1B of APC reveal gastric adenocarcinoma and proximal polyposis of the stomach as a familial adenomatous polyposis variant

city: Brisbane

first: Katia

last: Nones

state: QLD

address: 300 Herston Road

country: Australia

institute: QIMR Berghofer MEdical Research Institute

summary: Gastric  adenocarcinoma and proximal polyposis of the stomach is an autosomal dominant cancer predisposition syndrome of fundic gland polyposis with a significant risk of gastric adenocarcinoma. We mapped the gene to 5q22 and found loss of heterozygosity (LOH) only on 5q in fundic gland polyps from affected individuals. Sanger sequencing revealed novel point mutations in APC promoter 1B that co-segregated with disease. All three mutations reduced binding of YY1, and all three mutations showed abrogated activity of the APC promoter 1B luciferase assays. Whole genome sequencing of fundic gland polyps without 5q LOH identified somatic truncating mutations in APC.

overall_design: Fourteen fundic gland polyps from six members of Family 1 were obtained during gastrectomies and snap frozen. ‘Book end’ sections stained with haematoxylin and eosin (H&E) were reviewed by a gastrointestinal pathologist (MB) to estimate the percentage of fundic gland polyps .

first: Jun

last: Li

first: Sue

last: Healey

first: Jonathan

last: Beesley

first: Susan

last: Woods

first: Xiaoqing

last: Chen

first: Jason

middle: S

last: Lee

first: Haran

last: Sivakumaran

first: Nicci

last: Wayte

first: Joshua

last: Waterfall

first: John

last: Pearson

first: Anne-Marie

last: Patch

first: Pardeep

last: Kaurah

first: Robertson

last: Mackenzie

first: Alireza

last: Heravi-Moussavi

first: Samantha

last: Hansford

first: Amanda

last: Spurdle

first: Peter

last: Simpson

first: Leonard

last: daSilva

first: Sunil

last: Lakhani

first: Andrew

last: Clouston

first: Mark

last: Bettington

first: Rita

last: Busuttil

first: Alex

last: Boussioutas

first: Geoffrey

last: Faulkner

first: Evangelos

last: Bellos

first: Lachlan

last: Coin

first: Kevin

last: Rioux

first: Oliver

middle: F

last: Bathe

first: Xiaogang

last: Wen

first: Hilary

middle: C

last: Martin

first: Deborah

middle: W

last: Neklason

first: Sean

last: Davis

first: Robert

last: Walker

first: Martin

last: Peneda

first: Udo

last: Rudloff

first: Kathleen

last: Calzone

first: Pavel

last: Pichurin

last: Hulick

first: Scott

last: Weissman

first: Anna


title: The protein phosphatase 2A regulatory subunit PR70 is a gonosomal melanoma tumor suppressor gene

city: VILLEJUIF

first: Bastien

last: Job

address: 39 rue Camille Desmoulins

country: France

institute: Institut Gustave Roussy

type: Genome variation profiling by genome tiling array

summary: Men with melanoma have a significantly worse prognosis than women, and the biological underpinnings of this difference are unknown. The current study demonstrates that loss of the inactivated X chromosome in melanomas arising in females is strongly associated with poor distant metastasis free survival. High expression of the gonosomal PPP2R3B gene, a gene that escapes inactivation, is independently correlated with survival. PPP2R3B downregulates melanoma growth by negatively interfering with DNA replication and cell cycle progression through its role in stabilizing CDC6/CDT1 interaction during the replication origins firing and as such behaves functionally as a tumor suppressor gene.

overall_design: Fourty-nine fresh frozen primary melanoma samples were profiled by CGH array using sex-matched commercial DNA as reference.

first: Alan

last: Spatz


title: Aedes aegypti (Aag2) Cells: Control (CTR) vs. Heme-incubated / Control vs. Paraquat-incubated

status: Public on Jul 29 2016

city: Campos dos Goytacazes

first: Thiago

middle: Motta

last: Venancio

state: RJ

address: Av Alberto Lamego 2000

country: Brazil

institute: UENF

summary: In order to study heme-induced global transcriptional changes, we performed a transcriptome-wide analysis of heme influence on the A. aegypti cell line Aag2. As heme-mediated effects on gene expression are thought to be related to oxidative stress, we compared the transcriptional profiles of Aag2 cells challenged with either 50 µM heme or 100 µM of the ROS inducer paraquat, using whole genome microarrays.

overall_design: Three-condition experiment, CTR vs. Heme- or Paraquat incubated cells. Biological replicates: 4 control and 4 experimental replicates.

first: Vanessa

last: Bottino-Rojas

first: Gabriela

middle: O

last: Paiva-Silva


title: Real-time quantitative PCR analysis of BV2 murine microglia cell line

status: Public on Jul 26 2016

city: London

first: Miguel

middle: Angel

last: Burguillos

address: 4 Newark Street

institute: Queen Mary University of London

summary:
Murine BV2 microglia cells were transfected either with siRNA negative control or siRNA against caspase-3 for 48h.  Later on some the of the BV2 transfected cells  were co-cultured with C6 glioma cells during 6h.  We used the SA Biosciences Mouse Wound Healing PCR Array (PAMM-121Z) to quantitate gene expression of  relevant genes related to the wound healing process
Glioma cells recruit and exploit microglia, resident immune cells of the brain, for their proliferation and invasion capability.  The underlying molecular mechanism used by glioma cells to transform microglia into a tumor-supporting phenotype remains elusive. Here, we report that glioma-induced microglia conversion is coupled to a reduction of basal microglial caspase-3 activity, increased S-nitrosylation of mitochondria-associated caspase-3 through inhibition of thioredoxin-2 activity, and demonstrate that caspase-3 inhibition regulates microglial tumor-supporting function. Further, we identified nitric oxide synthase-2 (NOS2) activity originating from the glioma cells as a driving stimulus in the control of microglial caspase-3 activity. Repression of glioma NOS2 expression in vivo led to reduction in both microglia recruitment and tumor expansion, whereas depletion of the microglial caspase-3 gene promoted tumor growth. This study provides evidence that the inhibition of Trx2-mediated denitrosylation of SNO-procaspase-3 is part of the microglial pro-tumoral activation pathway initiated by glioma cancer cells.

overall_design:
qPCR gene expression profiling.  Three independent experiments of siControl BV2 monoculture, siCaspase3 BV2 monoculture, siControl BV2 cocultured 6h with C6 glioma cells and siCaspase3 BV2 cocultured 6h with C6 glioma cells. Equal amount total RNA from each culture was used for the  gene expression analysis.
Please note that the raw data for three independent experiments (prior to averaging the data) is provided in the 'Raw_Data_File_with_the_Ct_values_for_3_indep_experiments.txt'.

first: Xianli

last: Shen


title: Gene expression analysis in floral tissues from thermogenic skunk cabbage

city: Miyazaki

first: Yasuko

last: Ito-Inaba

address: 1-1 Gakuenkibanadai-nishi

department: Organization for Promotion of Tenure Track

country: Japan

institute: University of Miyazaki

summary: We analyzed gene expression profiles in four different floral tissues, petals, pistils, stamens, and the pith, using Agilent custum array for Symplocarpus renifolius (4 x 44k).

overall_design: Gene expression in floral tissues dissected from one female-stage spadix was measured and compared.


title: Expression data from roots of Arabidopsis grown under sulfur, iron or potassium limitation

status: Public on Jul 21 2016

city: Mannheim

first: Carsten

last: Sticht

address: Theodor-Kutzer-Ufer

department: ZMF

country: Germany

institute: University Heidelberg

summary:
Deprivation of mineral nutrients causes significant retardation of plant growth. This slow growth is assumed to be associated with both nutrient specific transcriptional responses and additionally with common transcription patterns. In this study we adjusted the external supply of iron, potassium and sulfur to cause a similar retardation of growth. Global transcriptome analyses were performed to investigate whether the growth limitation by the different nutrient deficiencies triggered specific or similar transcriptional responses.
The global transcriptome responded specifically to sulfur, iron or potassium deprivation.

overall_design: Arabidopsis thaliana plants were grown hydroponically under short-day conditions (8h light / 16h dark cycles) under full nutrient supply or under the limitation of sulfur, iron or potassium. Arabidopsis root material was harvested when the plants reached the age of 7 weeks (from sowing) and used for RNA extraction and hybridization on Affymetrix microarrays. Four biological replicates from each condition were analyzed.

first: Ilaria

last: Forieri

first: Markus

last: Wirtz

first: Ruediger

last: Hell


title: Induction of cells expressing markers of GABAergic neurons by transcription factors (mRNA)

city: Baltimore

first: Minoru

last: Ko

state: MD

address: 251 Bayview Blvd, Suite 100, 10C

department: National Institute on Aging

country: USA

institute: NIH

summary: Specific neuronal types derived from embryonic stem cells (ESCs) can facilitate mechanistic studies and potentially aid in regenerative medicine. Existing induction methods, however, mostly rely on the effects of growth factors, which generally tend to result in  mixed populations of neurons. Here we report that over-expression of specific transcription factors (TFs) in ESCs can rather guide the differentiation of ESCs towards specific neuron types. Analysis of published data on gene expression changes early (two days) after induction of each of 185 induced TFs implicated candidate TFs for further ESC differentiation studies. After induction for 6 days four of them (Ascl1, Smad7, Nr2f1, and Ascl2) generated a high proportion (>35%) of cells with neural progenitor marker PSA-NCAM and clear neural morphology on day 14. The capacity of these TFs to induce neural differentiation is inferred to be most likely linked to early activation of the Notch signaling pathway. Among the neuron-like cells, GABA-positive cells were most abundant (32-97% for 4 top TFs), whereas Isl1-positive cells and TH-positive cells were less abundant (<12% and <5%, respectively). Enrichment of cells obtained with the induction of Ascl1, Smad7, and Nr2f1 using beads with anti-PSA-NCAM antibody resulted in essentially pure population of neuron-like cells with expression profiles similar to neural tissues and highly expressed markers of GABAergic neurons. A time-course experiment with induction of Ascl1 showed early upregulation of most neural-specific and GABAergic-specific mRNA and miRNAs. We identified mRNA and miRNAs, whose expression depended on the induction of Ascl1, and showed that they were enriched in Ascl1 target genes. In summary, this study indicates that induction of transcription factors is a promising approach to generate candidate specific neural cell types from ESCs.

overall_design: Individual transcription factors (TFs) (Ascl1, Smad7, and Nr2f1) were induced in mouse ESCs to facilitate neural differentiation. Expression of transgenic TFs was repressed by doxycycline (Dox); thus, TFs were induced in Dox- conditions, whereas Dox+ conditions represent control cells with no expression of a transgene. For neural differentiation, cells were cultured 3 days in alpha-MEM medium and then in NeuroCult neural differentiation medium. Cells marked as PSANCAM+ were enriched by magnetic microbeads with anty-PSA-NCAM antibody (Miltenyi Biotec) on day 6 of culturing, whereas remaining cells are marked as PSANCAM-. Both PSANCAM+ and PSANCAM- cells were then cultured for another 8 days (total 14 days in differentiation). A time course experiment with Ascl1 induction did not include cell enrichment procedure. RNA was extracted with either Trizol (invitrogen) or mirVana kit (Thermo Fisher Scientific).

first: Yusuke

last: Ota

first: Alexei

last: Sharov


title: Induction of cells expressing markers of GABAergic neurons by transcription factors (miRNA)

overall_design: Transcription factor Ascl1 was induced in mouse ESCs to facilitate neural differentiation. Expression of transgenic Ascl1 was repressed by doxycycline (Dox); thus, it were induced in Dox- conditions, whereas Dox+ conditions represent control cells with no expression of Ascl1 transgene. For neural differentiation, cells were cultured 3 days in alpha-MEM medium and then - in NeuroCult neural differentiation medium for 2-11 days (total up to 14 days). RNA was extracted with mirVana kit (Thermo Fisher Scientific).


title: Soleus Muscle of Aged PAPP-A-Deficient Mice

status: Public on Jul 15 2016

city: Rochester

first: Sean

last: Dowdy

state: Minnesota

address: 200 First St. SW

department: Obstetrics and Gynecology

institute: Mayo Clinic

summary: Mice deficient in pregnancy-associated plasma protein-A (PAPP-A) have extended lifespan associated with decreased incidence and severity of degenerative diseases of age, such as cardiomyopathy and nephropathy.  In this study, the effect of PAPP-A deficiency on aging skeletal muscle was investigated.

overall_design: Whole-genome expression profiling was performed on soleus muscles from 18-month-old wild-type and PAPP-A knock-out mice of the same sex and from the same litter ('womb-mates').

first: Cheryl

last: Conover

first: Diane

middle: E

last: Grill


title: Differentially expressed miRNAs profiling and identification of 2-month-old Irs-1smla/smla mice, Irs-1+/smla mice and Irs-1+/+ mice

status: Public on Jul 13 2016

city: Changsha

first: Hou-De

last: Zhou

state: Hunan

address: Renmin middle road 139

department: Department of Metabolism & Endocrinology

institute: The Second Xiangya Hospital, Central South University

summary: To investigate the role of insulin-receptor substrate-1 (Irs-1) in the regulation of bone metabolism, we generated Irs-1-deficient mice (Irs1smla/smla). Using the highly sensitive miRNA array, we screened the differentially expressed miRNAs of 2-month-old Irs-1smla/smla mice, Irs-1+/smla mice and Irs-1+/+ mice. Three prediction algorithms (TargetScanS, miRanda, and PicTar) were used to identify the target genes of differentially expressed miRNAs. Furthermore, the quantitative real-time polymerase chain reaction, immunohistochemistry and dual luciferase reporter assay results showed that miR-342-3p is a specific regulator of collagen type I alpha 2 (Col1a2), which will give new insights in disclosing the mechanism of diabetic osteopathy.

overall_design: In this study, one sample from each type (Irs-1smla/smla mice, Irs-1+/smla mice and Irs-1+/+ mice) were used to acquire the miRNA expression profiling and the function of the abundant miRNAs in the diabetic osteopathy were analyzed by bioinformatic methods, finally, miR-342-3p was experimentally validated to be a regulator of collagen type I alpha 2 (Col1a2), an important molecule in the diabetic osteopathy.

first: Hou

middle: D


title: Plasticity of the berry ripening program in a white grape variety

city: Verona

first: Silvia

last: Dal Santo

address: Strada Le Grazie, 15

department: Department of Biotechnology

country: Italy

institute: University of Verona

summary: Grapevine (Vitis vinifera L) is considered one of the most environmentally sensitive crops and is characterized by broad phenotypic plasticity, offering important advantages such as the large range of different wines that can be produced from the same cultivar, and the adaptation of existing cultivars to diverse growing regions. The uniqueness of berry quality traits reflects complex interactions between the grapevine plant and the combination of natural factors and human cultural practices, defined as terroir, which leads to the expression of wine typicity. Despite the scientific and commercial importance of genotype interactions with growing conditions, few studies have characterized the genes and metabolites directly involved in this phenomenon. Here we used two large-scale analytical approaches to explore the metabolomic and transcriptomic basis of the broad phenotypic plasticity of Garganega, a white berry variety grown at four sites characterized by different pedoclimatic conditions (altitudes, soil texture and composition). These conditions determine berry ripening dynamics in terms of sugar accumulation and the abundance of phenolic compounds. Multivariate analysis unraveled a highly plastic metabolomic response to different environments, especially the accumulation of hydroxycinnamic and hydroxybenzoic acids and flavonols. Principal component analysis revealed that the four sites strongly affected the berry transcriptome allowing the identification of environmentally-modulated genes and the plasticity of commonly-modulated transcripts at different sites. Many genes that control transcription, translation, transport and carbohydrate metabolism showed different expression depending on the environmental conditions, indicating a key role in the observed transcriptomic plasticity of Garganega berries. Interestingly, genes representing the phenylpropanoid/flavonoid pathway showed plastic responses to the environment mirroring the accumulation of the corresponding metabolites. The comparison of Garganega and Corvina berries showed that the metabolism of phenolic compounds is more plastic in ripening Garganega berries under different pedoclimatic conditions.

overall_design: Grapevine (Vitis vinifera cv Garganega, clone 4) samples were collected from four vineyards of the Soave arean (Verona, Italy). Berries were collected at four ripening stages, starting from véraison, following a bi-weekly sampling schedule (August 22nd, September 4th, September 17th, September 30th; year 2013). Each stage comprised three biological replicates of about 30 berries each, sampled from clusters of different grapevine plants and located along different vineyard rows, and from different position within the same cluster. The above-described procedure was followed for each vineyard, thus the experiment entailed the collection and the analysis of 48 berry samples (4 vineyards X 4 stages X 3 replicates).

first: Marianna

last: Fasoli

first: Stefano

last: Negri

first: Erica

last: D'Incà

first: Nazareno

last: Vicenzi

first: Mario

last: Pezzotti

first: Flavia

last: Guzzo

first: Giovanni Battista

last: Tornielli

first: Sara

last: Zenoni


title: Effects of digested onion extracts on intestinal gene expression using rat intestine slices

status: Public on Jul 10 2016

city: Wageningen

first: Peter

last: Hendriksen

address: Akkermaalsbos 2

department: RIKILT

institute: Wageningen University & Research

summary: Rat small intestine precision cut slices were exposed for 6 hours to in vitro digested yellow (YOd) and white onion extracts (WOd) that was followed by transcriptomics analysis. The digestion was performed to mimic the digestion that in vivo takes place in the stomach and small intestine.  The transcriptomics response of the rat small intestine precision cut slices was compared to that of human Caco-2 cells and the pig in-situ small intestinal segment perfusion. The microarray data for the human Caco-2 cells (GSE83893) and the pig in-situ small intestinal segment perfusion (GSE83908) have been submitted separately from the current data on rat intestine. The goal was to  obtain more insight into to which extent mode of actions depend on the experimental model. A main outcome was that each of the three models pointed to the same mode of action: induction of oxidative stress and particularly the Keap1-Nrf2 pathway.

overall_design: The dataset contains results of 12 microarrays. 3 arrays for saline_digest that can be considered as the reference to which the response of the in vitro digested yellow (YOd) and white onion extracts (WOd) can be compared. 3 arrays were used for  in vitro digested yellow (YOd) and 3 arrays for in vitro digested yellow (YOd). In addition, 3 arrays (called DMSO) were included for an exposure without digestion enzymes. That is informative for the effect of the enzymes in the digestion mixture.

first: Nicole

last: de Wit

first: Marcel

last: Hulst

first: Coen

last: Govers

first: Jan

last: van der Meulen

first: Angeline

last: van Hoef

first: Geert

last: Stoopen

first: Astrid

last: Hamers

first: Arjan

last: Hoekman

first: Ric

last: de Vos

first: Toine

last: Bovee

first: Mari

last: Smits

first: Jurriaan

last: Mes


title: Molecular features of subtype-specific progression from ductal carcinoma in situ to invasive breast cancer [miRNA data]

status: Public on Jul 07 2016

city: St. Louis

first: Robert

last: Lesurf

state: MO

address: 4444 Forest Park Ave

department: McDonnell Genome Institute

institute: Washington University in St. Louis

summary: Breast cancer consists of at least five main molecular “intrinsic” subtypes, which are reflected in both pre-invasive and invasive disease. Although previous studies have suggested that many of the molecular features of invasive breast cancer are established early, it is unclear what mechanisms drive progression, and whether the mechanisms of progression are dependent or independent of subtype. We have generated mRNA, miRNA and DNA copy number profiles from a total of 59 in situ lesions and 85 invasive tumors, in order to comprehensively identify those genes, signaling pathways, processes, and cell types that are involved in breast cancer progression. Our work provides evidence that there are molecular features associated with disease progression that are unique to the intrinsic subtypes. We additionally establish subtype-specific signatures that are able to identify a small proportion of pre-invasive tumors with expression profiles that resemble invasive carcinoma, indicating a higher likelihood of future disease progression.

overall_design: One-color design, totaling 48 arrays and 41 unique tissues. Arrays consist of 4 normal controls (1 unique), 28 DCIS lesions (26 unique), and 16 small invasive breast cancers (14 unique).

first: Miriam

last: Aure

first: Hanne

middle: H

last: Mørk

first: Valeria

last: Vitelli

first: Steinar

last: Lundgren

first: Anne-Lise

last: Børresen-Dale

first: Vessela

last: Kristensen

first: Fredrik

last: Wärnberg

first: Michael

last: Hallett

first: Therese

last: Sørlie


title: Identification of differential signaling cues in insulin/IGF1 signaling pathways in breast cancer

city: Pittsburgh

first: Alison

last: Nagle

state: PENNSYLVANIA

address: 204 Craft Ave

department: Pharmacology and Chemical Biology

institute: University of Pittsburgh

summary: Temproral networks of (phospho)-proteins are constructed and analyzed to infer differential interactions under insulin and IGF1 stimulation.

overall_design: In total, 134 antibodies are tested in 21 breast cancer cell lines. The experiments are done in triplicate. Three serum-free-condition time points (5min, 24hr, 48hr) and six stimulation time points (5min, 10min, 30min, 6hr, 24hr, and 48hr) are obtained with either 10 nM IGF1 or 10 nM insulin stimulation.

first: Adrian

middle: V

last: Lee


title: Distinct and shared functions of ALS-associated TDP-43, FUS, and TAF15 revealed by comprehensive multi-system integrative analyses [array]

status: Public on Jul 05 2016

city: La Jolla

first: Gene

last: Yeo

state: CA

address: 2880 Torrey Pines Scenic Dr. Room 3805/Yeo Lab

institute: UCSD

summary: TDP-43, FUS, and TAF15 are implicated in amyotrophic lateral sclerosis (ALS) and frontotemporal dementia. We integrate CLIP-seq and RNA Bind-N-Seq technologies to discover that TAF15 binds to ~4,900 RNAs enriched for GGUA motifs. In the mouse brain, TAF15 and FUS, but not TDP-43, exhibit strikingly similar RNA binding profiles, yet they alter the expression of distinct mRNA populations upon their individual depletions. TAF15 has a minimal role in alternative splicing and instead affects RNA turnover, consistent with an enrichment of TAF15 binding sites in 3’ untranslated regions. In human stem cell-derived motor neurons, loss of both TAF15 and FUS affected mRNAs distinct from those altered by loss of either protein alone, revealing redundant roles for TAF15 and FUS in maintaining mRNA levels. Furthermore, concomitant rather than individual depletion of TAF15 and FUS more closely resembles RNA profiles of motor neurons derived from FUS R521G ALS patients or from late-stage, sporadic ALS patients. Our study reveals convergent and divergent mechanisms by which FUS, TAF15 and TDP-43 affects RNA metabolism in neurological disease.

overall_design:
RNA-seq, CLIP-seq and arrays in mouse and human against TAF15 knockdowns
This Series represents array sample(s).

first: Katannya

last: Kapeli

first: Gabriel

last: Pratt

first: Anthony

middle: Q

last: Vu

first: Kasey

last: Hutt

first: Fernando

middle: J

last: Martinez

first: Balaji

last: Sundararaman

first: Ranjan

last: Batra

first: Peter

last: Freese

first: Nicole

last: Lambert

first: Stephanie

last: Huelga

first: Seung

last: Chun

first: Tiffany

middle: Y

last: Liang

first: Jeremy

last: Chang

first: Shawn

last: Hoon

first: John

middle: P

last: Donohue

first: Lily

last: Shiue

first: Jiayu

last: Zhang

first: Haining

last: Zhu

first: Franca

last: Cambi

first: Edward

last: Kasarskis

first: Manuel

last: Ares Jr.

first: Christopher

last: Burge

last: Ravits

first: Frank

last: Rigo


title: Microarray-based annotation of the gut transcriptome of the migratory locust, Locusta migratoria

status: Public on Jul 02 2016

city: Leuven

first: Jozef

last: Vanden Broeck

address: Naamsestraat 59

department: Animal Physiology and Neurobiology

country: Belgium

institute: KU Leuven

summary: The migratory locust, Locusta migratoria, is a serious agricultural pest and important insect model to study insect digestion and feeding behavior. The gut is one of the primary interfaces between the insect and its environment. Nevertheless, knowledge on the gut transcriptome of L. migratoria is still very limited. With the development of two EST databases from L. migratoria (whole body and central nervous system (CNS)) and one EST database from Schistocerca gregaria (CNS), an abundance of transcript data was made available for locusts. In addition, the genome of Locusta was also recently published in an effort to create a better understanding of swarm formation and flight behavior (Wang et al., 2014). While the transcript composition of nervous tissue was relatively well studied after the development of the specific CNS-derived EST-databases from both L. migratoria and S. gregaria, little transcript profiling information is available for the digestive system at the moment. Locusts are, however, widely used as physiological model organisms regarding the regulation and control of feeding and digestion, and improved knowledge on the gut transcriptome could contribute significantly to a better understanding of their gut physiology. Therefore, we aimed to use the available sequence data to specifically identify gut-expressed transcripts in 5th larval locusts. By means of two independent self-self microarray hybridizations for two distinct tissues, the gut and the brain, a selection could be made of those ESTs that are present in the gut and/or the brain. Here, sequences that were found to be expressed in gut but not brain were further functionally annotated to shed new light on the complex physiology of the locust digestive system. Since the gut is the single most important organ in digestion, and both tissues are assumed to be involved in the regulation thereof, the resulting subset of sequences can also be valuable for further in-depth studies on the regulation of digestion. In addition, the method allowed us to rank the signal intensities, using them as a rough indicator to compare relative transcript abundance in the gut. Therefore, the data complement previously published transcript and genomic data, and provide a clear overview of the expressed portion of the genome in the gut. Taken together, the present data provide significant insight into locust larval gut physiology, and will be valuable for future studies on the insect gut.

platform_organism:
Locusta migratoria
Schistocerca gregaria

overall_design: Self-self hybridisation of Cy5- and Cy3-labeled samples. One biological repeat per tissue type, i.e., brain and gut. Gut is a combination of foregut, midgut, gastric caeca and hindgut. Per tissue type, a pool was made from RNA from 3 pools of 5 locusts, and this for 3 different feeding conditions, resulting in samples derived from a total of 45 locust larvae. Feeding conditions were normally fed, fed with diet containing additional protease inhibitors (PIs), and starved locusts.

first: Jornt

last: Spit

first: Liesbeth

last: Badisco

last: Van den Broeck

first: Dries

last: Knapen

first: Lucia

last: Vergrauwen


title: Knock-down of the methyltransferase Kmt6 reliefs H3K27me3 and induces expression of cryptic otherwise silent secondary metabolite gene clusters in Fusarium fujikuroi [gene expression]

status: Public on Jul 04 2016

city: Freising

first: Ulrich

last: Guldener

state: Bavaria

address: Maximus-von-Imhof-Forum 3

department: Chair of genome-oriented bioinformatics

institute: Technische Universität München

summary: Filamentous fungi produce a vast array of secondary metabolites (SMs) and some of them are applied in agriculture or pharmacology. Recent sequencing of the rice pathogen Fusarium fujikuroi revealed the presence of far more SM-encoding genes than known products. SM production is energy-consuming and thus tightly regulated, leaving the majority of SM gene clusters silent under laboratory conditions. It is now well established that one important regulatory layer in SM biosynthesis involves histone modifications that render the genes either silent or poised for transcription. In this study, we show that the majority of the putative SM gene clusters in F. fujikuroi are located within facultative heterochromatin marked by H3K27me3. In this study, we performed comparative transcriptomics of a knock-down mutant of the responsible methyltransferase Kmt6 involved in H3K27 methylation grown on either solid complete medium or solid synthetic ICI medium. Overall four so far cryptic and otherwise silent putative SM gene clusters were significantly induced in the KMT6kd strain accompanied by reduced H3K27me3 levels at the respective gene loci and accumulation of novel metabolites. One of the four putative SM gene clusters, the STC5 gene cluster, was analysed in detail and heterologous expression of the key enzyme allowed for the identification of the first pathway-specific intermediate (1R,4R,5S)-guaia-6,10(14)-diene.

overall_design: 2 strains were analysed in overall two conditions, and each with 3 biological replicates

first: Lena

last: Studt

first: Sarah

middle: M

last: Rösler

first: Immo

last: Burkhardt

first: Birgit

last: Arndt

first: Michael

last: Freitag

first: Hans-Ulrich

last: Humpf

first: Jeroen

last: Dickschat

first: Bettina

last: Tudzynski


title: mRNA profiling of white  hMADS cells converted in brite adipocytes and transfected with mimic miR-125b-5p

status: Public on Jul 01 2016

city: Neuherberg

first: Maude

middle: Madeleine

last: Giroud

state: Bayern

address: Ingolstädter Landstr. 1

department: Helmholtz Diabetes Center

institute: Helmholtz center

summary: miR-125b-5p is a well known miRNA already describded in several forms of cancer. miR-125b-5p is expressed in adipose tissue, adipocytes as well as their precursor cells. We aim to invest the role of  miR-125b-5p in white adipocytes conversion into brite adipocytes.  To get an idea about putative targets of miR-125b-5p in adipocyte conversion, we transfected miR-125b-5p mimic in human Multipotent Adipose-Derived Stem (hMADS) cells,  differenciated in white adipocytes. Gene expression profiling is performed 48h after hMADSC transfection.

overall_design: Two-condition experiment, hMADS cells at day 16 after conversion of white adipocytes into brite adipocytes, comparison of cells transfected with a mimic miR-125b-5p to cells transfected with a negative controle. Biological replicates: 4, indepently grown and harvested. On each array, one biological replicate of mimic miR-125b-5p transfected cells was directly compared to one biological replicate of mimic negative control transfected cells (serving as reference sample). All hybridizations were repeated with reversed dye assignment (dye-swap) as technical replicates.

first: Ez-Zoubir

last: Amri

last: Karbiener

first: Marcel

last: Scheideler


title: LET-dependent change in rice gene expression profile after heavy-ion beam irradiation [time]

city: Wako

first: Kotaro

last: Ishii

state: Saitama

address: 2-1, Hirosawa

department: Nishina Center for Accelerator-Based Science

institute: RIKEN

summary: Linear energy transfer (LET) is an important factor affecting several aspects of the irradiation effect, e.g. cell survival and mutation frequency, making the heavy-ion beam an effective mutagen. To study the mechanisms behind LET-dependent effects, expression profiling was performed after heavy-ion beam irradiation of imbibed rice seeds. Array-based experiments at three time points (0.5, 1, 2 h after the irradiation) revealed that the number of up- or down-regulated genes was highest 2 h after irradiation. Array-based experiments with four different LETs at 2 h after irradiation identified LET-independent regulated genes that were up/down-regulated regardless of the value of LET; LET-dependently regulated genes, whose expression level increased with the rise of LET value, were also identified.

overall_design: Oryza sativa L. 'Nipponbare' seeds were imbibed for 3 days. The seeds were irradiated with 22.5 or 50 keV/μm C-ion at a dose of 15 Gy. Gene expressions of irradiated and unirradiated embryos were measured at 0.5, 1, and 2 hours after irradiation. Three independent experiments were performed at each time and LET.

first: Tomoko

last: Abe


title: Testicular toxicity induced by carbendazim, iprodione, alone or in combination

city: Bagnols sur Cèze

first: Odette

last: Prat

address: Site de Marcoule

department: Life Science

institute: CEA

summary: Using an ex-vivo testicular culture from rats, we carried out transcriptomic experiments to identify the pathway of toxicity ellicited by the fungicides carbendazim, iprodione alone or in combination. we used commercial Agilent Microarray GE 4x44K  Rat (V3) Gene Expression Microarray (G2514F) AMADID : 028282

overall_design: Cultures were performed with and without fungicides. When required, CBZ, IPR or mixture was added beginning from day 2, at 50 nM or 500 nM for CBZ and at 50 nM or 500 nM for IPR; 50 nM each or 500 nM each for the mixture. For microarray experiments, three different pools of seminiferous tubules were exposed to two concentrations of CBZ, IPR or their mixture (50 nM and 500 nM) or to complete medium with vehicle (control cells) for 7, 14, and 21 days. Each condition of exposure to fungicides was compared with control cells at the same time point.

first: Cedric

last: Pisani


title: LET-dependent change in rice gene expression profile after heavy-ion beam irradiation

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

overall_design: Refer to individual Series


title: Human HPV16 positive CaSki cells: Control vs. virus oncogene e6/e7 silenced

city: Guangzhou

first: Fei

last: LIU

address: North of Guangzhou avenue No,1838, Baiyun District

department: Department of Laboratory Medicine

institute: Nanfang Hospital, Southern Medical University

summary: The infection with high-risk human papillomavirus is aetiologically linked to cervical cancer, the role of miRNAs regulated by virus oncogene in cancer progression remain largely unknown. Here, we screened the differentially expressed miRNAs with miRNA array between virus oncogene e6/e7 silenced and not in HPV16-positive cervical cancer cell lines

overall_design: In the study, we screened the differentially expressed miRNAs with miRNA array (Exiqon, miRCURY LNA microRNA array, 7th gen [hsa, miRBase 18]) between virus oncogene e6/e7 silenced and not in HPV16-positive cervical cancer cell lines to found miRNAs regulated by virus oncogene e6/e7. Biological replicates: 3 control, 3 e6/e7 silenced, independently grown and harvested. four replicates per array.

last: Liu

first: Mengshi

last: Zhang


title: LET-dependent change in rice gene expression profile after heavy-ion beam irradiation [LET]

overall_design: Oryza sativa L. 'Nipponbare' seeds were imbibed for 3 days. The seeds were irradiated with 22.5 or 50 keV/μm C-ion or 63 or 80 keV/μm Ne-ion at a dose of 15 Gy. Gene expressions of irradiated and unirradiated embryos were measured at 2 hours after irradiation. Three independent experiments were performed at each time and LET.


title: Amaranth's transcription factors overexpression, AhERF and AhDOF, increase drought and salt tolerance in Arabidopsis thaliana

status: Public on Jun 30 2016

city: Irapuato

first: John P

last: Délano-Frier

state: Guanajuato

address: Km 9.6 del Libramiento Norte Carretera Irapuato-León SN

department: Biotechnology and Biochemistry

country: Mexico

institute: CINVESTAV Irapuato

summary: Transcriptional profiling of Arabidopsis rossette leaves comparing WT Col-0 with a transgenic line overexpressing AhERF or AhDOF genes from Amaranthus hypochondriacus under different conditions.

overall_design: Three-condition experiment of WT vs AhERF OE plant leaves. The analyzed conditions were: normal growth conditions, 5 days of water stress (no irrigation) and 24 hrs of recovery after watering water-stressed plants. Besides, a two-condition experiment where WT vs AhDOF OE plant leaves were compared. The experimental conditions were: normal growth conditions and plants watered with 40mL of 400mM NaCl solution for three straight days to produce salt stress.

first: Julio

last: Massange-Sánchez

first: John


title: Transcriptome Profiling of Black Poplar under Boron Toxicity Revealed Genetic Regulation of Boron Uptake, Transport and Detoxification

status: Public on Jun 28 2016

city: TOKAT

first: KUBILAY

last: YILDIRIM

address: TASLICIFTLIK

department: BIOENGINEERING

country: Turkey

institute: GAZIOSMANPASA UNIVERSITY

summary: Poplars are known to be highly tolerant species to boron toxicity and accumulation. However, genes and molecular networks responsible in boron toxicity tolerance have not been investigated yet. Therefore, we performed a pot experiment with 20 black poplar clones collected from the vicinity of boron mines and polluted areas to investigate its potential role in phytoremediation and to select the most boron toxicity tolerant genotype. Trees were treated with irrigation water containing seven elevated boron concentrations from 0 to 160 ppm. Then a microarray based comparative transcriptome profiling was conducted to identify boron toxicity regulated genes responsible in defence responses of black poplar. The results of the study indicated that black poplar is quite suitable for phytoremediation of boron pollution. It could resist 15 ppm soil B content and < 1600 mg/kg boron accumulation in leaves which are highly toxic concentrations for almost all agricultural plants.  Transcriptomics results of study revealed totally 1625 and 1419 altered probe sets under boron toxicity in leaf and root tissues, respectively. The highest induction were recorded for  the probes sets annotated to tyrosine aminotransferase, ATP binding cassette transporters, glutathione S transferases and metallochaperone proteins. Strong up regulation of these genes attributed to internal excretion of boron into the cell vacuole and existence of detoxification processes in black poplar. Many candidate genes functional in signalling, gene regulation, antioxidation, boron uptake, transport and detoxification processes were also identified in the current study.  This is the first transcriptomic study identifying boron toxicity regulated poplar genes and their potential role in boron toxicity tolerance.

overall_design: Total RNA used in microarray experiment was isolated from the leaves and roots of black poplar clone; N.92.237 which accumulated the highest amount of boron its tissues. Total RNA used in the microarray experiment was isolated from leaves and roots of three black poplar saplings grown in ~ 2 ppm (control) and ~ 15 ppm (toxic) soil B contents. RNA isolation was made according to Lithium chloride precipitation method described in Chang et al. (1993). These three isolated RNAs (biological replicates) for each tissue loaded onto three Affymetrix poplar Gene Chips (technical replicates). Totally, 12 GeneChips (2 tissues × 2 different B treatment × 3 biological replicates) were used for transcriptional analysis.

first: Kubilay

first: Senem

last: Uylaş


title: Transcriptional profiles of Haloferax mediterranei based on nitrogen availability

city: San Vicente del Raspeig

first: Julia

last: Esclapez

state: Alicante

address: Crta San Vicente del Raspeig s/n

department: Biochemistry

country: Spain

institute: University of Alicante

summary: Transcriptional profiling of Haloferax mediterranei in three culture media with different nitrogen sources: a) cells were grown stationary and exponentially on ammonium, b) cells were grown exponentially on nitrate, and c) cells were shifted to nitrogen starvation conditions.  The main differences in the transcriptional profiles have been identified between the cultures with ammonium as nitrogen source and the cultures with nitrate or nitrogen starvation, supporting previous results which indicate the absence of ammonium as the factor causing the expression of genes involved in nitrate assimilation pathway.

overall_design: Four-conditions experiment with four biological replicates, combined in a loop design.

first: J

first: C

last: Pire

first: M

last: Camacho

first: V

last: Bautista

first: R

last: Martinez-Espinosa

first: B

last: Zafrilla

first: A

last: Vegara

first: L

middle: A

last: Alcaraz

last: Bonete


title: Gene regulation by EZH2 inhibitors

status: Public on Jun 23 2016

city: Taipei

first: Pei-Ming

last: Yang

address: 250 Wu-Hsing St

department: Graduate Institute of Cancer Biology and Drug Discovery

country: Taiwan

institute: Taipei Medical University

summary: Our previous study has found that UNC1999 and GSK343 are potent autophagy inducers. To further investigate the underlying mechanisms, microarray analysis was performed.

overall_design: EZH2 inhibitor-induced gene expression in HCT116 was measured at 4 hours after exposure to 5 uM UNC1999 or 10 uM GSK343.


title: Gene expression in Arabidopsis leaves after P. brassicae egg deposition, chilling, and/or herbivory by P. brassicae larvae

city: Berlin

first: Reinhard

last: Kunze

state: Berlin

address: Albrecht-Thaer-Weg 6

department: Institute of Biology

institute: Freie Universität Berlin

summary: Plant defence against insects is well known to be affected by previous exposure to cues warning of herbivory. Using Arabidopsis thaliana and the herbivore Pieris brassicae, we addressed the question whether the maintenance of the effects of the warning cue depends on its reliability. We determined the transcriptomes of Arabidopsis leaves that were treated by P. brassicae egg deposition (i) five days after oviposition, (ii) one day after removal of the eggs following the egg treatment, (iii) three days after removal of the eggs, (iv) after two days of herbivory that started one day after removal of the eggs; or that were treated by chilling (v) five days after transfer to 4°C, (vi) one day after transfering the plants to 20°C following the chilling treatment, (vii) three days after transfering the plants to 20°C, (viii) after two days of herbivory that started one day after transfering the plants to 20°C.

overall_design: Arabidopsis thaliana Col-0 wild type plants were grown under short day conditions (10 h/14 h light/dark) at 20°C for 7 weeks. Subsequently (i) the plants were transferred to 4°C for 5 days, or (ii) Pieris brassicae deposited ca. 40 eggs on leaf 17 where they remained for five days, or (iii) as controls plants grew untreated for five days. Next, the plants were transferred back to 20°C and the eggs were removed, respectively. Next, all plants rested for 1 day at 20°C. Next, P. brassicae larvae were allowed to feed for 2 days on leaf 17 adjacent to the former egg deposit site or at a respective leaf region of chilling-treated or untreated plants. Control plants were not exposed to larvae. From all treated and untreated plants material from a leaf region proximal to the egg deposition and/or feeding site was harvested for transcriptome analysis.

first: Vivien

last: Firtzlaff

first: Jana

last: Oberländer

first: Sven

last: Geiselhardt

first: Monika

last: Hilker


title: Hypocotyl and cotyledon transcriptome in Arabidopsis thaliana treated with 1 ppm ethylene and shade (low PAR, low blue and low R:FR)

status: Public on Jun 10 2016

city: Utrecht

first: Rashmi

last: Sasidharan

address: Hugo R. Kruytgebouw, Padualaan 8

department: Plant Ecophysiology

institute: Utrecht University

summary: Plants have evolved shoot elongation mechanisms to escape from diverse environmental stresses such as flooding and vegetative shade. The apparent similarity in growth responses suggests possible convergence of the signalling pathways. Shoot elongation is mediated by passive ethylene accumulating in flooded plant organs and by changes in light quality and quantity under vegetation shade. Here we study hypocotyl elongation as a proxy for shoot elongation and delineated Arabidopsis hypocotyl length kinetics in response to ethylene and shade. Based on these kinetics, we further investigated ethylene and shade-induced genome-wide gene expression changes in hypocotyls and cotyledons separately. Both treatments induced a more extensive transcriptome reconfiguration in the hypocotyls compared to the cotyledons. Bioinformatics analyses suggested contrasting regulation of growth promotion- and photosynthesis-related genes. These analyses also suggested an induction of auxin, brassinosteroid and gibberellin signatures and the involvement of several candidate regulators in the elongating hypocotyls. Pharmacological and mutant analyses confirmed the functional involvement of several of these candidate genes and physiological control points in regulating stress-escape responses to different environmental stimuli.  We discuss how these signaling networks might be integrated and conclude that plants, when facing different stresses, utilise a conserved set of transcriptionally regulated genes to modulate and fine tune growth.

overall_design: 1 day old Arabidopsis seedlings were subjected to control, ethylene and shade conditions. Hypocotyl and cotyledon tissues were harvested at 1.5 h, 13.5 h and 25.5 h of treatment time respectively. Microarray hybridization was carried out with 3 biological replicates (collected over 3 independent experiments) of each sample using the Affymetrix Arabidopsis Gene 1.1 ST platform.

first: Debatosh

last: Das

first: Kate

first: Ronald

last: Pierik

last: Voesenek


title: Mating and sperm free seminal plasma changes gene expression in the oviductal sperm reservoirs of sows

city: Linköping

first: Mohammad

last: Atikuzzaman

address: Linköping

department: Clinical and Experimental Medicine

country: Sweden

institute: Linköping University

summary: Sperms being foreign to the female are to be promptly eliminated by the female local immune defense. However, avoiding the local immune defense sperm can be stored for lenthy period in the oviductal sperm reservoir. It is currently unknown whether oviductal sperm reservoirs changes their gene expression to tolerate the spermatozoa after mating or sperm free seminal plasma infusion. Therefore this was tested using Swedish Landrace pigs in this study using cDNA microarray.

overall_design: We used 12 sows seperated into three groups- either oestrus sows were inseminated with 50 ml BTS (control, n=4) or mated with boars (treatment 1, n=4) or inseminated with sperm-free seminal plasma (treatment 2, n=4). The utero-tubal junction was retrieved within 24 h of treatment by operation.

first: Heriberto

last: Rodriguez-Martinez


title: Gene expression differences between pterygium and conjunctiva tissues

city: Singapore

first: Wanwen

last: Lan

address: 9 Hospital Drive SON Blk C #02-03

country: Singapore

institute: Singapore Eye Research Institute

summary: Comparison of endogenous gene expression differences between pterygium and conjunctiva tissues

overall_design: RNA from donor-matched pterygium and conjunctiva tissues obtained from four patients were evaluated for differences in gene expression

first: Louis

last: Tong


title: Comparison between GT and hoxH mutant strains of cyanobacteria

status: Public on Jun 01 2016

city: Kawasaki

first: Takashi

last: Osanai

state: Kanagawa

address: 1-1-1, Higashimita, Tamaku

department: School of Agriculture

institute: Meiji University

summary: HoxH is a subunit of hydrogenase in a unicelluar cyanobacterium Synechocystis sp. PCC6803. We constructed hoxH mutant strain, which the mRNA levels of hoxH reduced to 50% of the wild-type.

overall_design:
Total RNAs from three independent wilde-type (GT) and three independent hoxH mutant were labeled by Cy3 followed by hybridyzation on a microarry chip generated by Agilent Technologies (Design ID 036279).
Microarray is designed by Prof. Tomohisa Hasunuma, Kobe University.
CITATION: Metabolomics-based analysis revealing the alteration of primary carbon metabolism by the genetic manipulation of a hydrogenase HoxH in Synechocystis sp. PCC 6803 Iijima H, Shirai T, Okamoto M, Pinto F, Tamagnini P, Hasunuma T, Kondo A, Hirai MY, *Osanai T (2016) Algal Res. 18: 305-313, doi.org/10.1016/j.algal.2016.06.026


title: Identification of Drosophila Mid regulated genes in embryos

city: Taian

first: Chong

middle: lei

last: Fu

state: Shandong

address: No. 61 Daizong Street

country: China

institute: Shandong Agricultural University

summary:
Drosophila midline(mid), encodes a T-box transcription factor that is required for cell fate specification and tissue morphogenesis during a series of developmental processes. However, little is known about the target of Mid.
To identify the Mid regulated genes, we compared expression profiles of mRNA purified from wild-type and mid mutant embryos. Summary file is yw-mid.CHP.

overall_design: yw and mid mutant embryos were selected at later stage of development for RNA extraction and hybridization on Affymetrix microarrays. We identified mid mutant embryos using CyOact-GFP balancer chromosome.

first: Q

middle: X

last: Liu

first: C

middle: L

first: S

last: Hirose


title: Transcriptional profiling of setb morphants

city: Ioannina

first: Katerina

middle: Periklis

last: Soupsana

address: Dourouti

department: Medical School

country: Greece

institute: University of Ioannina

summary: We have characterised the zebrafish ortholog, setb, and investigated its role in embryogenesis. Phylogenetic analysis showed that zebrafish Setb has an amino acid sequence identity of approximately 96% with the mammalian orthologs. Whole mount immunofluorescence analysis revealed that Setb is expressed mainly in the eye, the lateral line neuromasts and the olfactory pit. Knockdown of setb using antisense morpholino oligonucleotides resulted in increased apoptosis, reduced cell proliferation and severe morphological defects. The morphant phenotypes were partially rescued when setb MO1 was co-injected with human set mRNA. In vivo labelling of hair cells in the lateral line of setb morphants with the vital fluorescent dye FM1-43 showed a significant decreased number of functional neuromasts. Gene expression analysis of setb morphants, employing DNA microarrays revealed a role of Setb in neurogenesis and the mechanosensory lateral line system.

overall_design: 48hpf control morpholino- and setb MO1-injected embryos in triplicates

first: Illiana

last: Serifi

first: Eleni

last: Tzima

first: Zoe

last: Karetsou

first: Dimitris

last: Beis

first: Thomais

last: Papamarcaki


title: An improved method for the isolation of endometrial epithelial and stromal cells from the total hysterectomy specimen

status: Public on Jun 14 2016

city: Setagaya

first: Kazuhiko

last: Nakabayashi

state: Tokyo

department: Department of Maternal-Fetal Biology

institute: National Research Institute for Child Health and Development

summary: We aimed to improve the efficiency of isolating endometrial epithelial and stromal cells (EMECs and EMSCs) from hysterectomy specimens. We revealed by immunohistochemical staining that the large tissue fragments remaining after collagenase treatment, which are usually discarded after the first filtration in the conventional protocol, consisted of glandular epithelial and stromal cells. Therefore, we established protease-treatment and cell suspension conditions to dissociate single cells from the tissue fragments, and isolated epithelial (EPCAM-positive) and stromal (CD13-positive) cells by fluorescence-activated cell sorting. Four independent experiments showed that, on average, 1.2 x 10^6 of EMECs and 2.8 x 10^6 EMSCs were isolated from one hysterectomy specimen. We confirmed that the isolated cells presented transcriptomic features highly similar to those of epithelial and stromal cells obtained by the conventional method. Our improved protocol facilitates future studies to better understand the epigenetic regulation underlying the dynamic changes of the endometrium during the menstrual cycle.

overall_design: Although protocols for the isolation of endometrial stromal and epithelial cells (EMSCs and EMECs) have been well established, the number of EMECs obtainable by the current protocols is relatively small. To improve the efficiency of isolating EMECs as well as EMSCs from endometrial tissues, we established protease-treatment and cell suspension conditions to efficiently dissociate single cells from endometrial tissue fragments, and isolated epithelial (EPCAM-positive) and stromal (CD13-positive) cells by fluorescence-activated cell sorting. By conducting a microarray-based transcriptome analysis, we confirmed that the cells isolated by the modified protocol developed in this study maintain the transcriptomic properties of endometrial epithelial and stromal cells.

first: Ayako

last: Masuda

first: Kenichiro

last: Hata

first: Junko

last: Tomikawa


title: Genome-wide transcriptional analysis of Drosophila ring gland

status: Public on Jun 20 2016

city: Edmonton

first: Kirst

last: King-Jones

state: Alberta

address: 11455 saskatchewan driver

department: Biological Sciences

country: Canada

institute: University of Alberta

summary:
Samples 1-24: Tissue-specific gene expression microarrays (Nimblegen) using dissected ring glands isolated from FOUR different time points of control (w1118, otherwise wild type) third instar larvae. Time points are 4, 8, 24 and 36 hours after the molt from second to third instar larvae.
Samples 25-42: Tissue-specific gene expression microarrays (Nimblegen) using dissected ring glands isolated from TWO different time points of third instar larvae. Genotypes were phantom22-GAL4/RasV12 and phantom22/Torso-RNAi. Goal was to identify PTTH-dependent gene sets in the ring gland. Time points were 18 hours and 8 hours prior to puparium formation.

overall_design: This study comprises two parts: first, a microarray timecourse on Drosophila wildtype ring gland versus whole body. Two NimbleGen 12X135K chips were used for total RNA isolated from dissected ring glands and whole larvae at four different time points during the third instar (the last larval stage of Drosophila development). The second part reflect gene expression changes in ring glands where we altered PTTH signaling by genetic means. Two 12X135K chips were used for total RNA isolated from ring glands of controls, ring gland-specific Torso-RNAi (phm>torso-RNAi), and RasV12 (phm>RasV12) larvae at two different time points during the larval third instar (18 and 8 hours before puparium formation). Each condition was measured by using three biological samples.

first: Qiuxiang

last: Ou

first: Jie

last: Zeng


title: Large scale transcript analysis of PI compensatory effects in the midgut and caeca of Locusta migratoria

status: Public on Apr 07 2016

city: Leuven

first: Jozef

last: Vanden Broeck

address: Naamsestraat 59

department: Animal Physiology and Neurobiology

institute: KU Leuven

summary: Protease inhibitors (PIs) are among the most ubiquitous plant defences against herbivorous insects. These inhibitors arrest proteolytic digestion by binding to the proteases in the gut. However, many pest insects have coevolved mechanisms to counteract these effects. While the nature of these counter-defensive strategies has been well described for several insect pests, our understanding of how these responses are triggered and regulated remains limited. In this study we investigated the initiation of this adaptive response in the economically damaging migratory locust (Locusta migratoria), via microarray analysis of gut tissues following the dietary uptake of PIs. For this purpose, the total number of ESTs available for locusts was narrowed down to transcripts that were found expressed in gut and/or brain tissue. The remaining subset was used for the construction of an optimized microarray platform.

overall_design: Two condition experiment: locusts fed on control diet vs locusts fed on protease inhibitor-supplied diet (midgut samples), 3 biological repeats per condition. The overall experimental design consisted of an n+2 A-optimal design (n=6: 3 pooled midgut samples derived from control locusts - 3 pooled midgut samples derived from protease inhibitor-fed locusts)

first: Jornt

last: Spit

first: Liesbeth

last: Badisco

last: Vanden Broek

first: Dries

last: Knapen

first: Lucia

last: Vergrauwen


title: Transcriptome changes in response to accumulation of cyclic di-AMP in Bacillus subtilis.

status: Public on May 25 2016

city: Greifswald

first: Ulrike

last: Mäder

address: F.-L.-Jahn-Str. 15A

department: Functional Genomics

institute: University Medicine Greifswald

summary: Cyclic di-AMP is an essential second messenger in many Gram-positive bacteria, including the model organism Bacillus subtilis. Here, we analyzed the transcriptome of a strain accumulating c-di-AMP in vivo. Our results demonstrate that accumulation of c-di-AMP affects the expression of several hundred genes, among them many mother-cell specific sporulation genes. Additionally, the two major biofilm operons, epsA-O and tapA-sipW-tasA, are affected. High levels of c-di-AMP abolish transcription of genes responsible for biofilm formation which in turn leads to a defect in complex colony formation in B. subtilis.

platform_organism: Bacillus subtilis subsp. subtilis str. 168

overall_design:
Cells were grown under vigorous agitation at 37 °C in Spizizen minimal medium supplemented with glutamate. Samples were taken at OD600 of 0.5.
Microarray hybridizations were performed with RNA from three biological replicates. The individual samples were labeled with Cy5; a reference pool containing equal amounts of RNA from all samples was labeled with Cy3.

first: Hermann

last: Rath

first: Jan

last: Gundlach

first: Christina

last: Herzberg

first: Jörg

last: Stülke


title: Angiopoietin-like 4 enhances the ability of tendon fibroblasts to undergo proliferation and migration

status: Public on Apr 17 2016

city: Vancouver

first: Shawn

last: Anderson

state: BC

address: 2660 Oak Street

institute: Vancouver Prostate Centre

summary: This microarray study provides novel insights into the role of Angiopoietin-like 4 in tendon biology with implications for injury repair and exercise physiology.

overall_design: To gain an insight into Angiopoietin-like 4 -induced modifications in tendon fibroblasts by global transcriptional analysis

first: Sarwat

last: Jamil

first: Rouhollah

last: Mousavizadeh

first: Mani

last: Roshan-Moniri

first: Scott

last: Tebbutt

first: Robert

middle: G

last: McCormack

first: Vincent

last: Duronio

first: Alex

last: Scott


title: Identification and characterization of a glycosulfatase-encoding gene cluster in Bifidobacterium breve UCC2003

status: Public on May 10 2016

city: Cork

first: Muireann

last: Egan

address: Western Road

country: Ireland

institute: University College Cork

summary:
A bacterial nursling stool isolate, Bifidobacterium breve UCC2003, encodes two putative sulfatases. The sulfated monosaccharide N-acetylglucosamine-6-sulfate (GlcNAc-6-S) was shown to support growth of B. breve UCC2003, while three other tested sulfated monosaccharides, N-acetylglucosamine-3-sulfate, N-acetylgalactosamine-3-sulfate and N-acetylgalactosamine-6-sulfate, did not. Using a combination of transcriptomic and functional genomic approaches, a gene cluster, designated ats2, was shown to be specifically required for GlcNAc-6-S metabolism. Transcription of the ats2 cluster is shown to be regulated by a ROK-family transcriptional repressor.
Expression profiling by array

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.


title: Reconstruction of microRNA/genes transcriptional regulatory networks of multiple myeloma through in silico integrative genomics analysis [MM, gene]

status: Public on Mar 23 2016

city: MILAN

first: Luca

last: Agnelli

address: Venezian 1

department: Department of Advanced Diagnostics

institute: IRCCS Istituto Nazionale dei Tumori

summary: The identification of deregulated miRNA in multiple myeloma (MM) has progressively added a further level of complexity to MM biology. In the present study, we take virtue of in silico integrative genomics analysis to generate an unprecedented global view of the transcriptional regulatory networks modulated in MM to define microRNAs impacting in regulatory circuits with potential functional and clinical relevance. miRNA and gene expression profiles in two large representative MM datasets, available from retrospective and prospective clinical trials and encompassing a total of 249 patients at diagnosis, were analyzed by means of two robust computational procedure to identify (i) relevant miRNA/transcription factors/target gene circuits in the disease and (ii) highly modulated miRNA-gene networks in those pathways enriched with miRNA-target gene interactions in specific MM subgroups. The analysis reinforced the pivotal role the miRNA cluster miR-99b/let-7e/miR-125a, specifically deregulated in MM patients with t(4;14) translocation, and disentangled its major relationships with transcriptional relevance. Integrated pathway analyses performed on the expression data of the MM patients stratified according to t(4;14) further allowed to define the pathway composed by the interactions that mainly characterize this MM subset and unravel connected pathways with putative role in the tumor biology.

overall_design:
miRNA and transcripts expression data were analyzed using MAGIA2, to identify mixed circuits (triplets) involving miRNA/gene/transcription factor (TF; http://gencomp.bio.unipd.it/magia2/), as previously described [Bisognin A et al, 2012, Nucl Acid Res]. Specifically, Targetscan was used as target prediction algorithm, and Pearson coefficient was used to measure relationships between microRNA and target mRNA expression profiles. Only the most variable 75% genes according to the coefficient of variation were considered. Lower threshold for absolute correlation coefficients within circuits was set to 0.2; 0.4 was used for miRNA/target binary relationships. Micrographite pipeline allows integrating pathway topologies with predicted and validated miRNA–target interactions, to perform integrated analyses of miRNA and gene expression profiles, for the identification of modulated regulatory circuits involved in the disease in terms of both expression variations and differential strength of inferred interactions [Calura E et al, 2014, Nucl Acid Res]. Micrographite has two steps: i) the extension of pathway annotation using miRNA-target interaction and ii) recursive topological pathway analysis on these networks. We considered network topologies derived from KEGG database by Graphite package [Sales G et al, 2012, BMC Bioinformatics] and miRNA-target gene interactions identified by the above-described MAGIA2 analysis. Specifically, a miRNA was added to a pathway-derived network only if one (or more) of its validated or predicted target genes is a pathway component. Then, a modified recursive version of CliPPER topological pathway analysis [Martini P et al, 2013; Nucl Acid Res] was applied to the composite network, as previously described [Calura E et al, 2014, Nucl Acid Res] in order to identify the most important and non-redundant circuit modulated across groups. Briefly, (i) in the first step, the most significant pathways were selected using P<0.1 as cut-off value for significance; (ii) for each dataset, the upper-scored 10th percentile of the portion of these previously selected pathways (i.e. “paths”, calculated over a 10,000-permutation step) mostly associated with phenotype were selected; and (iii) for each dataset a meta-pathway was assembled using the paths extracted from previous step and finally re-analyzed.

GSE70254 and GSE70319 Samples with the same patient number represent the same sample, profiled using two different Platforms.

first: Enrica

last: Calura

first: Andrea

last: Bisognin

first: Martina

last: Manzoni

first: Katia

last: Todoerti

first: Gabriele

last: Sales

first: Gareth

last: Morgan

first: Antonino

last: Neri

first: Chiara

last: Romualdi

first: Stefania

last: Bortoluzzi

first: Elisa

last: Taiana

first: Nicola

last: Amodio

first: Pierfrancesco

last: Tassone

first: Giovanni

last: Tonon


status: Public on Mar 03 2016

city: Tokyo

first: Tomoki

last: Muramatsu

address: 1-5-45 Yushima Bunkyo-ku

department: Medical research institute

institute: Tokyo Medical and Dental University

summary:
To explore metastasis-related genes in high-metastatic cells (HOC313-LM), we performed gene expression array analysis with HOC313-LM and HOC313-Parent (HOC313-P). Moreover, to identify metastasis-related signaling pathway, gene expression profiles of each of transplanted tumor tissues in the primary site or in the metastatic site were analyzed by systems biology analysis and Ingenuity Pathway Analysis (IPA; Ingenuity Systems, Inc., Redwood City, CA).  As a result, RhoA signaling pathway emerged as the critical molecular pathway in the metastatic tumor compared to the primary tumor.
Identification of metastasis-related genes and metastasis-related pathway in squamous cell carcinoma

overall_design: Extraction of difference of gene expression level between high-metastatic subline (HOC313-LM) and low-metastatic subline (HOC313-P)

first: Ken-ichi

last: Kozaki

first: Seiya

last: Imoto

first: Rui

last: Yamaguchi

first: Satoru

last: Miyano

first: Johji

last: Inazawa


title: Expression data from HHG affected and unaffected Vulpes vulpes gingival samples

status: Public on Apr 03 2016

city: St. John's

first: Jo-Anna

middle: Barbara Joyce

last: Clark

state: Newfoundland

address: Elizabeth Avenue

department: Biology

institute: Memorial University

summary: Hereditary hyperplastic gingivitis (HHG) is a progressive growth of gingival tissues in foxes resulting in dental encapsulation. It is an autosomal recessive condition displaying a sex-biased penetrance, with an association with superior fur quality.  The goal of this study was to explore potential molecular or cellular mechanisms underlying HHG by analysis of global gene expression patterns from Affymetrix Canine 2.0 microarrays cross-referenced.

overall_design: HHG affected and unaffected Vulpes vulpes gingival samples were collected either during pelting season or in the late spring after whelping season. Diagnosis of HHG was made based on early markers of the disease where red, raised, granular gingival tissue was present at the dental margins on the crowns of the teeth. RNA was extracted and hybridization on Affymetrix Canine 2 microarray.

first: H

last: Marshall


title: BIRC6-targeting as potential therapy for advanced, enzalutamide-resistant prostate cancer

status: Public on Feb 04 2016

first: Shawn

last: Anderson

summary: New transplantable patient-derived xenograft (PDX) CRPC model with intrinsic ENZ-Resistance were used to access therapeutic efficacy of BIRC6 targeting antisense oligonucleotide (ASO-6w2). Molecular pathways associated with the inhibitory effect of ASO-6w2 vs control Scrb ASO were examined by gene expression profiling.

overall_design: Patient-derived xenograft tumors from the LTL313BR xenograft lineage (PMID: 24356420) after treatment with BIRC6 targeting ASO or control ASO for 3 weeks (5 day on, 2 day off)

first: Iris

middle: S

last: Luk

first: Yuzhuo

last: Wang


title: Identifying Bit1-regulated genes in the EC9706 cells

city: Zhengzhou

first: chen

last: jing

state: Henan

address: 100 KeXue Avenue

institute: Zhengzhou University

summary: To further verify the underlying functions of Bit1 in ESCC, therefore, in the present study, we examined Bit1 expression in a panel of ESCC cell lines, and investigated the effects of Bit1 knockdown on tumor growth, migration and invasion as well as cell apoptosis in ESCC, and further preliminarily elucidated the possible molecular mechanisms. All data presented herein suggest Bit1 may be a promising molecular target for the therapy of ESCC, and thus intervention of Bit1 may lead to better therapeutic outcomes for the patients with ESCC.  To further verify the underlying functions of Bit1 in ESCC, therefore, in the present study, we examined Bit1 expression in a panel of ESCC cell lines, and investigated the effects of Bit1 knockdown on tumor growth, migration and invasion as well as cell apoptosis in ESCC, and further preliminarily elucidated the possible molecular mechanisms. All data presented herein suggest Bit1 may be a promising molecular target for the therapy of ESCC, and thus intervention of Bit1 may lead to better therapeutic outcomes for the patients with ESCC.

overall_design: EC9706 cells were harvested 72 h after transfection with pSilencer3.1-H1 -neo-Bit1-shRNA or pSilencer3.1-H1-neo-negative-shRNA. Approximate 1 × 106 cells from each sample were subjected to gene microarray assay. Total RNA was extracted  was extracted for analysis.


title: Expression Profiles of MicroRNA, its genes and proteins targets and Stromal Genes in Aggressive Behavior Tumors from Young Patients with Breast Cancer.

status: Public on Jan 29 2016

city: São Paulo

first: Renato

middle: David

last: Puga

state: São Paulo

address: Dr Ovidio Pires de Campos,785

department: Instituto de Psiquiatria

institute: Universidade de São Paulo

summary: Breast cancer (BC) in young adult patients (YA), has a more aggressive biological behavior and is associated with a worse prognosis than BC arising in middle aged patients (MA) partly explained by distinct biological features. Deregulated microRNAs (miRs) may had been implicate in modulating genes associated to YA-BC. Objective: Using miRs, their targets mRNA, proteins and stromal genes expression profiles, our aim was to identify differentially expression profiles between tumors from YA and MA. Methodology and results: Samples of ER+ invasive ductal breast carcinomas, divided into 2 groups: YA-BC (35 years or less, n=25) or MA-BC (50-65 years, n=25) were evaluated. All patients indicated low risk of carrying BRCA1/2 mutation. Aggressive characteristics such as large tumor size and advanced histological grade were more evident in YA-BC tumors versus MA-BC. Performing qPCR, we identified 8 miRs differentially expressed (miR-9, 18b, 33b, 106a, 106b, 210, 518a-3p and miR-372) between YA-BC and MA-BC tumors with high confidence statement, which were associated with worse clinico pathological biomarkers. Combined results from in silico prediction with mRNA expression profiles by microarray, identified 602 genes pointing to enriched biological functions related to proliferation, cell cycle and development. Performing RPPA, 24 targets proteins expression differed between both groups. Combination of eight mRNA targets (ESR1, RPS6KA1, YWHAZ, BCL7, PARP12, DUSP2, DUSP8 and PIGS) or the combination of eight target proteins (RAF1, BCL2L1, EIF4E, STAT5A, PARP1, ESR1, RPS6KA1 and YWHAZ) defined an indicator able to classify individual samples into YA-BC or MA-BC groups. A network was belted to protein-protein interaction including regulatory complexity by miRs reveling important biological processes such as proliferation, development and metabolism in YA-BC. Fibroblast-enriched stroma expression profile resulted in 308 stromal genes differentially expressed between YA-BC and MA-BC related to proliferation, differentiation, maturation and metabolism pathways. Conclusion: The differentially expressed miRNAs, their target genes, proteins and stromal genes distinguished early onset from late onset breast cancer and suggested that biological characteristics in YA-BC may be involved with tumor aggressiveness.

overall_design: 16 breast tumor from YA group, 13 breast tumors from MA group, 8 stromal breast tumor from YA group and 5 stromal breast tumor from MA group.

first: Bastos

last: Elen Pereira

first: Brentani

last: Helena

first: Pereira

last: Carlos Alberto de Bragança

first: Pasini

last: Fatima Solange

first: Roela

last: Rosimeire A.

first: Osorio

last: Cynthia A.B.T.

first: Achatz

last: Maria Isabel W.

first: Polpo

last: Adriano

first: Lima

last: Leandro

first: Puga

last: Renato D.

first: Trape

last: Adriana Priscila

first: Gonzales-Ângulo

last: AM

last: M. Mitzi


title: MicroRNA-124 and -137 cooperativity controls caspase-3 activity through BCL2L13 in hippocampal neural stem cells. [miRNA expression]

status: Public on Mar 12 2016

city: Amsterdam

first: Marijn

last: Schouten

address: Science Park 904

department: Swammerdam Institute for Life Sciences

country: Netherlands

institute: University of Amsterdam

summary:
Temporal lobe epilepsy (TLE) can develop from alterations in hippocampal structure and circuit characteristics, and can be modeled in mice by administration of kainic acid (KA). Adult neurogenesis in the dentate gyrus (DG) contributes to hippocampal functions and has been reported to contribute to the development of TLE. Some of the phenotypical changes include neural stem and precursor cells (NPSC) apoptosis, shortly after their birth, before they produce hippocampal neurons.
Here we explored these early phenotypical changes in the DG 3 days after systemic KA administration to mice. Our specific aim was to understand the molecular mechanisms underlying altered apoptosis levels in NSPC following KA-induced status epilepticus (KA-SE). Accordingly, we chose a multi-omics experimental setup and analyzed DG tissue samples using proteomics, transcriptomics and microRNA profiling techniques. We here present a description of how these date were obtained and provide them to others for further analysis and validation. This may help to further identify and characterize molecular mechanisms involved in the alterations induced shortly after KA-SE in the mouse DG.

overall_design: Total RNA obtained from dentate gyrus 72h after mice were subjected to repeated low dose kainic acid induced status epilepticus or saline i.p. injections

first: Pascal

last: Bielefeld

first: Silvina

last: Fratantoni

first: Chantal

last: Hubens

first: Sander

middle: R

last: Piersma

first: Than

last: Pham

first: Rob

last: Voskuyl

first: Paul

last: Lucassen

first: Connie

last: Jimenez

first: Carlos

last: Fitzsimons


title: Determination of transcriptional rates and mRNA levels during osmotic stress  in S. cerevisiae wild type and cbc1/sto1 mutant cells using Genomic Run On (GRO)

status: Public on Jan 25 2016

city: Burjassot

first: Jose

middle: E.

last: Perez-Ortin

state: Valencia

address: Dr. Moliner 50

department: Bioquimica y Biologia Molecular

institute: Universitat de Valencia

type:
Expression profiling by array
Other

summary: We analyzed the effect of the elimination of the cap-binding protein Cbc1 on transcription rate and mRNA amount during the response to osmotic stress using the Genomic Run-on assay

overall_design: This study focus on the transcriptional activity of RNA pol II in yeast genes during stress response. S. cerevisiae cells grown in YPD to exponential phase were subjected to osmotic stress and then processed for Genomic Run-On. Home-made microarrays containing entire ORFs were used. Three replicates of each time point were done. Each replicate has been hybridized on a different macroarray. A single DNA genomic hybridization was done on the same microarrays for normalization. Data were normalized by Median Absolute Deviation (MAD) using the ArrayStat software.

first: Paula

last: Alepuz

first: Nikki

last: De Clerk

first: Daniel

last: Medina

first: José

middle: E

last: Pérez-Ortín

first: Elena

last: Garre


title: Effect of Dietary Lysine on the Gene Expression Profile of Skeletal Muscle in Finishing Pigs

status: Public on Feb 09 2016

city: Mississipi State

first: Shengfa

last: Liao

state: MS

address: 4021 Wise Center, 240 Wise Center Drive

department: Animal & Dairy Sciences

institute: Mississippi State University

summary:
The main goal of swine production is to convert feedstuffs into edible meat whose major component is skeletal muscle. The overall objective of this project is to study the effect of dietary lysine on the gene expression profile of skeletal muscle in late stage finishing pigs.
The hypothesis for this is that adequate or excess level of dietary lysine will change the expression levels of numerous genes, and these changes are in favor of muscle protein accretion and are associated with various blood metabolites and growth performance parameters.

overall_design: Three experimental (lysine-deficient, lysine-adequate, lysine-excess) diets were respectively fed to 3 groups of pigs (initial body weight, ~95 kg/pig; 3 pigs/group) for a total of 5 weeks.

first: Taiji

last: Wang


title: Gene expression changes reflect clinical response in a placebo-controlled randomized trial of abatacept in patients with diffuse cutaneous systemic sclerosis

status: Public on Feb 01 2016

city: Lebanon

first: Tammara

last: Wood

state: NH

address: WTRB 674

department: Biomedical Data Science

institute: Dartmouth Medical School

summary: Systemic sclerosis (SSc) is an autoimmune disease characterized by inflammation and fibrosis of the skin and internal organs. We sought to assess the clinical and molecular effects associated with response to intravenous abatacept in patients with diffuse cutaneous systemic sclerosis (dcSSc).

overall_design: Adult dcSSc patients were randomized in a 2:1 double-blinded fashion to receive abatacept or placebo over 24 weeks. Primary outcomes were safety and the change in modified Rodnan Skin Score (mRSS) at week 24 compared with baseline. Improvers were defined as patients with a decrease in mRSS of ≥30% post-treatment compared to baseline. Skin biopsies were obtained for differential gene expression and pathway enrichment analyses and intrinsic gene expression subset assignment.

first: Eliza

middle: F

last: Chakravarty

first: David

middle: J

last: Haddon

first: Michael

last: Whitfield

first: Viktor

last: Martyanov

first: Justin

last: Jarrell

first: Lorinda

last: Chung

last: Fiorentino

last: Utz


title: Human Toxome Project, E2 and PPT induction of MCF-7 cells (NC series)

status: Public on Jan 27 2016

city: Santa Clara

first: Rick

last: Fasani

state: CA

address: 5301 Stevens Creek Blvd

institute: Agilent Technologies

summary: The central goal of the project is to define, experimentally verify, and systematically annotate pathways of endocrine disruption, as a proof of concept of mapping pathways of toxicity by systems toxicology. Microarray gene expression profiling is one of several -omics approaches used.

overall_design: Gene expression was measured in MCF-7 cells after exposure to doses of 0.01 nM, 0.1 nM or 1nM estradiol (E2), 5 nM propyl pyrazole triol (PPT) or vehicle control for 4 or 8 hours. The experiment was repeated at two different institutions, Johns Hopkins University (JHU) and Brown University (BU), where three biological replicates were produced for each condition.

first: Carolina

middle: B

last: Livi

first: Dipanwita

last: Choudhury

first: Andre

last: Kleensang

first: Mounir

last: Bouhifd

first: Salil

middle: N

last: Pendse

first: Patrick

middle: D

last: McMullen

first: Melvin

last: Andersen

first: Thomas

last: Hartung

last: Rosenberg

first: Marguerite

last: Vantangoli

first: Shelly

last: Odwin-DaCosta

first: Kim

last: Boekelheide

first: Albert

last: Fornace

first: Heng-Hong

last: Li

first: Samantha

last: Madnick

first: Alexandra

last: Maertens

first: James

last: Yager

first: Liang

last: Zhaog


title: Development of gene expression profiles for tumour derived endothelium vs. matched healthy tissues (in renal cell carcinoma, colorectal cancer and colorectal metastasis to the liver)

status: Public on Jan 26 2016

city: Birmingham

first: Joseph

middle: William

last: Wragg

state: West Midlands

address: Edgbaston

department: Institute of Biomedical Research

country: United Kingdom

institute: University of Birmingham

summary:
In order to establish a profile of tumour vascular expression which could potentially be targeted therapeutically, we performed agilient microarray analysis on 4 samples each or renal cell carcinoma, colorectal cancer, colorectal metastasis to the liver and matched healthy tissues. The tumours had recieved no treatement prior to resection. The expression profiles were compared by one colour microarray analysis between matched healthy and tumour tissue. Genes expressed in all/or most of the comparisons were taken forward for further analysis. See acompanying publication: Wragg JW, Finnity JP, Anderson JA, Ferguson HJM, Bhatt RI, Murray PG, Heath VL, Bicknell R. MCAM is a vascular target in renal cancer. Cancer Research. 2016.
The endothelum was isolated using collagenase V digestion, and dynabead magnetic bead isolation conjugated to lectin from Ulex Europaeus (Ulex Europaeus Agglutinin I (UEA I)), which binds human endothelial cells.

overall_design: Endothelium was isolated from fresh, matched, healthy and tumour tissue, total RNA was extracted using the Qiagen miRNAeasy kit, processed into cRNA using the Agilient low input, one colour labelling kit, hybridised onto the 8 x 66k whole human genome expression microarrays. Data was normalised in R64 and comparison matrices between matched Tumour and Healthy endothelum were constructed. Genes upregualated in all the comparisons were taken forward for further analysis.


title: microRNA expression in facet cartilage degeneration

status: Public on Mar 15 2016

city: Toronto

first: Akihiro

last: Nakamura

address: 60 Leonard Avenue

department: Genetics and Development

institute: University Health Network

summary: Osteoarthritis (OA) of spine (facet joints; FJ) is one of the major causes of severe low back pain and disability worldwide. The degeneration of facet cartilage is a hallmark of FJ OA. However, endogenous mechanisms that initiate degeneration of facet cartilage are unknown and there are no disease-modifying therapies to stop FJ OA. In this study we performed microRNA array analysis to identify differentially expressed microRNAs in facet cartilage from patients with FJ OA compared to  facet cartilage from patients with lumbar disc herniation (LDH).

platform_organism:
Homo sapiens
Human alphaherpesvirus 1
Human alphaherpesvirus 2
Macacine alphaherpesvirus 1
Human betaherpesvirus 5
human gammaherpesvirus 4
Herpesvirus saimiri (strain 11)
JC polyomavirus
Human immunodeficiency virus 1
Human betaherpesvirus 6B
Human gammaherpesvirus 8
Merkel cell polyomavirus
Betapolyomavirus hominis
Betapolyomavirus macacae

overall_design: 4 samples analyzed, 2 cartilage samples from patients with LDH (control). In FJ OA group two samples were analyzed. Each sample comprised of pooled cartilage samples from n=3 FJ OA patients.

first: Y

last: Rampersaud

first: Anirudh

last: Sharma

first: Stephen

last: Lewis

first: Brian

last: Wu

first: Poulami

last: Datta

first: Kala

last: Sundrarajan

first: Evgeny

last: Rossomacha

first: Igor

last: Jurisica

first: Mohti

last: Kapoor


title: Identification of mir-342-3p functionally associated with transcriptional activity of MYC in lung cancer [patients]

status: Public on Jan 06 2016

city: Nagoya

first: Takashi

last: Takahashi

state: Aichi

address: 1-1 Kanokoden, Chikusa-ku

country: Japan

institute: Aichi Cancer Center

summary: Accumulating evidence indicates that altered miRNA expression is crucially involved in lung cancer development, but only little has been elucidated about how MYC, an archetypical oncogene, is regulated by miRNAs, especially through a mechanism involving the MYC cofactor(s). In this study, we aimed at identifying miRNAs involved in the regulation of MYC transcriptional activity in lung cancers. To this end, we have taken an integrative approach with combinatorial usage of miRNA and mRNA expression profile datasets of patients’ tumor tissues as well as those of MYC-inducible cell lines in vitro. We report here that in addition to miRNAs previously reported to be directly regulating or regulated by MYC including let-7 and miR-17-92, our strategy allowed us to identify miR-342-3p as the one capable of indirectly regulating MYC activity through direct repression of a MYC-cooperating molecule, E2F1. Furthermore, the miR-342-3p module activity, which we defined as a gene set reflecting experimentally substantiated influence of miR-342-3p on mRNA expression, was found to be inversely correlated with MYC activity reflected in the MYC module activity in three independent datasets of lung adenocarcinoma patients obtained by the Director’s Challenge Consortium of the United States (P=1.94x10-73), the National Cancer Center of Japan (P=9.05x10-34) and our own in this study (P=3.37x10-6). Our integrative approach thus appears to be useful to elucidate inter-regulatory relationships between miRNAs and a protein coding-gene of interest, even those present in tumor tissues in patients, which still remains a challenge to better understand the pathogenesis of this devastating disease.

overall_design: Microarray analysis using a SurePrint G3 Human GE 8 x 60K Microarray G4851A (Agilent) was conducted.

first: Tai

last: MeiChee

first: Taisuke

last: Kajino

first: Masahiro

last: Nakatochi

first: Yukako

last: Shimada

first: Chinatsu

last: Arima

first: Shohei

last: Ito

first: Hiroyuki

last: Miyoshi

first: Tomoya

last: Yamaguchi

first: Kiyoshi

last: Yanagisawa

first: Motochi

last: Suzuki


title: Gene expression analysis of untreated and NT-shRNA transduced kidney proximal tubular epithelial cells (PTECs) at day 6 and day 16 after transduction,  as well as SETD2-shRNA transduced PTECs at day 25 after transduction

status: Public on Jan 09 2016

city: GRONINGEN

first: Jun

last: Li

state: Netherlands

address: Esdoornlaan

department: Genetics

institute: University Medical Center Groningen

summary: Primary kidney PTECs gradually became senescent after a few passages, but SETD2 depletion prevented PTECs from senescence and maintained their proliferation beyond their limited dividing capacity. Transcriptional profiling of human PTECs, with comparing of  SETD2 wild-type non-senescent PTECs at day 6 (WT-PTECs-day 6), SETD2 wild-type senescent PTECs at day 16 (WT-PTECs-day16), and SETD2 knockdown PTECs at day 25 (KD-PTECs-day 25).

overall_design: Three PTECs of different origins were transduced with shRNA constructs against SETD2 (sh1 or sh2), or with a non-targeting sequence. Untreated and NT-shRNA transduced samples were harvest at day 6 and day 16 respectively, SETD2-KD shRNA transduced PTECs were harvest at day 25.

first: Klaas

last: Kok

first: Anke

last: van den Berg

first: Rolf

middle: H

last: Sijmons

first: Helga

last: Westers

first: Joost

last: Kluiver

first: Jan

last: Osinga

first: Maaike

last: van Werkhoven

first: Marc

middle: A

last: Seelen

first: Debora

last: de Jong

first: Martijn

last: Terpstra