title: Endocytic and signalling function of stabilin-1 in tumor associated macrophages

status: Public on Oct 30 2014

city: Mannheim

first: Carsten

last: Sticht

address: Theodor-Kutzer-Ufer

department: ZMF

country: Germany

institute: University Heidelberg

summary:
Stabilin-1 is a scavenger/sorting receptor expressed by sinusoidal endothelial cells, alternatively-activated and tumor-associated macrophages (TAM) in several types of human cancer and mouse tumor models. We have found abundant expression of stabilin-1 on TAM in mouse model of mammary adenocarcinoma (TS/A)
We performed microarrays with TAM isolated from wild type (wt) and stabilin-1 knock out (ko) mice in order to examine if stabilin-1 affects gene expression in TAM using mouse model of TS/A mammary adenocarcinoma

overall_design: Balb/c Wt and stabilin-1 ko female mice (8-12 weeks old) were inoculated s.c. with 5x10e6 TS/A cells. TAM were isolated from TS/A tumors 21 days after tumor challenge using CD11b MACS beads (Miltenyi Biotec), lysed for RNA and used for microarrays. Samples from 3 wt and 3 stabilin-1 ko mice were analyzed.

first: Vladimir

last: Riabov

first: Ilja

last: Ovsij

first: Kai

last: Schledzewski

first: Alexei

last: Gratchev

last: Wang

first: Christina

last: Schmuttermaier

first: Hiltrud

last: Schönhaber

first: Christel

last: Weiss

first: Alan

middle: P

last: Fields

first: Bernd

last: Arnold

first: Sergij

last: Goerdt

first: Julia

last: Kzhyshkowska


title: Transcription map of the Swine Leukocyte Antigen complex and comparative biology of MHCs among vertebrates

status: Public on Oct 31 2014

city: Jouy en Josas

first: Yu

last: GAO

address: INRA, BAT440

department: Animal Genetics

country: France

institute: GABI-GIS

type: Expression profiling by genome tiling array

summary: Tiling arrays have been reported as highly relevant tools to improve annotation and identify new transcripts in genome sequences. Our aim was to refine annotation of the Swine Leucocyte Antigen (SLA) complex, which is a gene dense region spanning 2.4 megabases on both sides of the centromere of chromosome 7 with many genes involved in immune response and inflammation. To date, one hundred and fifty-one SLA genes and pseudogenes have been characterized or predicted. A high-density tiling array was produced, which covered the entire Hp1a.0 haplotype sequence and partially the centromeric junction on the q-arm. The array contained 386,620 55-70-mer oligonucleotides designed on both strands and tiled on average every nine bases. It was used to compare the transcriptome of peripheral blood mononuclear cells (PBMCs) either mock-stimulated or stimulated with phorbol myristate acetate (PMA) and ionomycin for 24 hours. In both conditions, 19% of the probes were expressed among which 47% not previously annotated. In addition to the expected transcripts, segmentation analysis revealed new transcriptional architectures of previously annotated genes, a limited transcription activity in the centromeric junction and frequent transcription in antisense orientation. Differential expression of non-annotated transcripts was detected between non-stimulated and stimulated PBMCs, suggesting a regulatory role during immune cell activation. These results contribute to drawing an extensive transcription map of the SLA complex and to comparative functional mapping between mammals. This kind of approach can be applied to any candidate region of the pig genome in order to carry out a consistent functional annotation.

overall_design: Two-condition experiment, PMA ionomycine stimulated PBMCs vs. Control PBMCs. Biological replicates: 1 control, and 1 PMA ionomycine stimulated from 4 animals independently grown and harvested. One replicate per array. Total 8 slides.

last: Gao

first: Claire

last: Rogel-Gaillard


title: Human transcriptome expression analysis of cervical cancer

status: Public on Oct 27 2014

city: shanghai

first: chen

last: ye

address: Xiangyin road, no.800

country: China

institute: the second military medical university

summary:
Although many protein-coding genes have been identified to be aberrantly expressed in cervical cancer, the mechanisms of development and progression of cervical cancer remain unclear. In recent years, non-coding RNAs, especially including microRNAs and long non-coding RNAs, have been shown to play important regulatory roles in mammalian cell biology.
In our study, we investigated the whole genome gene expression level changes by human transcriptome array in tumor tissues and paired adjacent non-tumor tissue of patients with cervical cancer. The functions of different expression microRNAs, long non-coding RNAs and mRNAs were further analyzed in vitro and in vivo using loss-of-function and gain-of-function approaches.

overall_design: A ten chip study using total RNA recovered from five separate cervical cancer tissues and five paired adjacent non-tumor samples.

first: Chen

last: Ye

first: Ning-xia

last: Sun

first: Qian

last: Zhao

first: Qing

last: Zhang

last: Xu

first: Shao-bing

first: Fang

first: Wen

last: Li


title: Chromosome 20 Aberrations at the Diploid-Aneuploid Transition in Sporadic Colorectal Cancer

status: Public on Oct 20 2014

city: Amsterdam

first: Daoud

last: Sie

address: De Boelelaan 1117

department: Pathology

country: Netherlands

institute: Vrije Universiteit Medical Center

type: Genome variation profiling by genome tiling array

summary: DNA aneuploid sublines in sporadic colorectal cancers (CRCs) are quite frequent (about 85%) and likely the consequence of chromosomal instability and DNA copy number aberrations (CNAs). In order to gain insight into the mechanisms of the diploid-aneuploid transition in CRCs, we compared the CNA status in both diploid and aneuploid sublines. We used fresh/frozen material from 17 aneuploid CRCs, which was separated into 17 DNA diploid and 17 aneuploid sublines using enrichment of the epithelial component by multiparameter flow cytometry and sorting. CNA status of both sublines was obtained by array comparative genomic hybridization. The DNA diploid sublines from the aneuploid CRCs showed already CNAs, in particular, gains at 20p and 20q. The same aberrations were detected at increased frequencies in the corresponding DNA aneuploid sublines. Moreover, the very frequent gains/losses of chromosomes 4, 7, 8, 13, 15, and 18 in the DNA aneuploid sublines were absent or rare in the DNA diploid sublines from the same sporadic aneuploid CRCs. The comparison of the DNA diploid and aneuploid sublines from aneuploid CRCs suggests that 20p and 20q gains may play a role in the diploid-aneuploid transition. The 20q chromosomal arm appears of particular interest since it harbors several genes implicated in chromosomal instability.

overall_design: Fresh/frozen multiple superficial and intra-tumor tissue samples of 17 diploid and 17 matched aneuploid colorectal adenocarcinomas. Test samples are compared to an external pool of normal male/female reference DNA.

first: Massimo

last: Maffei

first: Sandra

last: Mongera

first: Libia

last: Terpstra

first: Alessandra

last: Donadini

first: Patrizio

last: Castagnola

first: Quirinus

middle: M

last: Voorham

first: Gerrit

middle: A

last: Meijer

first: Beatriz

last: Carvalho

first: Walter

last: Giaretti


title: Variability in white blood cell counts in swine: identification of putative positional and functional candidate genes by a transcriptome-based study

first: Yu

last: GAO

summary:
The counts of total white blood cells (WBCs) and WBC subsets are well-established diagnostic factors for various diseases. It has been shown that variations in WBC counts are significantly controlled by individuals’ genetics in swine. However, despite detection of quantitative trait loci (QTLs) for these phenotypes, little is known on the molecular basis underlying their variations. Our aim was to study gene profiling variations according to variations in WBC counts and to connect results with available QTL mapping. Whole blood transcriptome of animals contrasted for levels of WBC counts were compared. A pig generic microarray enriched in immunity-related genes was used. 378 probes representing 334 genes were found significantly differentially expressed between high- and low-count WBC groups. 65 genes were associated with hematological system development and function. 336 probes could be mapped on all autosomes and the X chromosome, and 59 transcripts fell within 28 QTLs reported to affect the counts of WBC and WBC subsets. By combining probe mapping results and biological functions, 6 genes (CDKN2A, TCIRG1, SIPA1, RGL2, FLT1 and CFLAR) were found as putative relevant positional candidate genes for the WBC traits. Genetic linkage experiments are warranted to validate these candidate genes, and further investigating a possible pleiotropic effect of these genes could contribute to elucidate molecular mechanisms involved in WBC development.
differentially expressed genes or transccripts between high- and low-count white blood cells groups

overall_design: The dual channel microarray experiments were carried out using a common reference hybridization design. In this study the reference RNA sample was prepared by pooling of total RNAs from different porcine tissues. The test samples were RNA samples isolated from total porcine blood. According to the total white blood cells count, 18 animals were selected from the edges of the distribution, named high-count group (HC, 9 animals) and low-count group (LC, 9 animals).

last: Gao

first: Claire

last: Rogel-Gaillard


title: Translation value of the bleomycin rat model for the treatment of patients with Idiopathic Pulmonary Fibrosis (IPF)

status: Public on Oct 28 2014

city: Allschwil

first: Axel

last: Klenk

address: Hegenheimermattweg 91

department: Research Informatics

country: Switzerland

institute: Idorsia Pharmaceuticals Ltd.

summary: Intratracheal application of bleomycin is known to induce inflammatory and fibrotic reactions in the lung within a short period of time and histological features include infiltration of inflammatory cells, collagen deposition and obliteration of alveolar spaces. Because some of these features are found in patients with idiopathic pulmonary fibrosis (IPF), the bleomycin-induced lung fibrosis animal model is commonly used. However, exploratory treatments that were successfully used in this animal model and progressed to clinical trials lacked significant efficacy in humans. Here, the bleomycin-induced rat lung fibrosis model was studied using whole genome expression data that was collected at various time points and the relevance to human disease was evaluated through comparison with whole genome expression data from IPF patient-derived lung biopsies. The highest gene expression correlation between both species was observed in animals 7 days after bleomycin instillation. These gene expression signatures helped to identify a set of twelve novel disease-relevant translational gene markers that were able to separate IPF patients from controls. Furthermore, three Wnt/-catenin pathway-related genes that belong to this translational gene marker set showed, together with clinical diffusing capacity of the lung for carbon monoxide (DLCO) measurements, the potential to stratify IPF patients according to disease severity.  Pirfenidone attenuated a subset of the translational gene markers in the bleomycin-induced fibrosis model, in particular those related to Wnt/-catenin-signaling. This novel translational gene marker panel offers improved possibilities to evaluate disease-modifying efficacy of novel therapeutic concepts in the bleomycin-induced rat lung fibrosis model and could be applied as a diagnostic and prognostic tool for IPF patient care.

overall_design: Comparison of bleomycin-treated and control rats after 3 days, 1 week, 2 weeks, 3 weeks, 4 weeks, 6 weeks and 8 weeks; 5 animals per group

first: Yasmina

last: Bauer

first: John

last: Tedrow

first: Simon

last: de Bernard

first: Kevin

middle: F

last: Gibson

first: Brenda

middle: J

last: Guardella

first: Patrick

last: Hess

first: Kathleen

middle: O

last: Lindell

first: Bérengère

last: Renault

first: Markus

last: Rey

first: Edgar

last: Weber

first: Oliver

last: Nayler

first: Naftali

last: Kaminski


title: Genomic profiling of primary and metastatic clear cell renal cell carcinoma by array-based comparative genomic hybridization.

status: Public on Oct 16 2014

city: Yufu

first: Takahiro

last: Narimatsu

state: Oita

address: Hasamamachi Idaigaoka 1-1

department: Medicine

country: Japan

institute: Oita University

summary: In this study, we investigated CNAs of 20 primary clear cell renal cell caricinomas (ccRCCs), 20 corresponding metastases and another subsets of 30 primary ccRCCs by 44k oligonucleotide-based array comparative genomic hybridization (array CGH).

overall_design: 20 primary ccRCCs, 20 corresponding metastases and another subsets of 30 primary ccRCCs.

first: Tomoki

last: Kai

first: Chisato

last: Nakada

first: Yoshiyuki

last: Tsukamoto

first: Naoki

last: Hijiya

first: Toru

last: Inoue

first: Takeo

last: Nomura

first: Fuminori

last: Sato

first: Masao

last: Seto

first: Ichiro

last: Takeuchi

first: Hiromitsu

last: Mimata

first: Keiko

last: Matsuura

first: Masatsugu

last: Moriyama


title: Murine Adult Cortex: Gtf2i (+/Δex2 ) VS WT (+/+)

city: Barcelona

first: Victoria

last: Campuzano

address: Dr Aiguader, 88

department: CEXS

country: Spain

institute: Universitat Pompeu Fabra

summary: Transcriptional profiling of mouse cortex tissue comparing control animals with Gtf2i-mutated mouse (Gtf2i+/Δex2 ).  Goal was to determine the specific deregulated genes in the cortex of mutated animals.

overall_design:
Pools of total RNA derived from five-three mice of each genotype were subjected to microarray analysis. We compared pools instead of single individuals in order to minimize individual and technically-related variation.

The original raw data file (i.e. Agilent feature extraction files) are not available. The modified raw data files are provided along with the file contents description (raw_data_readme.txt available on Series records).

first: V

first: M

last: Segura


title: Transcriptional effects of lack of Reg1

city: Cerdanyola

first: Antonio

last: Casamayor

state: Barcelona

address: Edifici IBB, Campus UAB

institute: Universitat Autonoma de Barcelona

summary: Reg1 is a regulatory subunit of Glc7, the type 1 Ser/Thr protein phosphatase in the yeast Saccharomyces cerevisiae. The Reg1/Glc7 complex is responsible for the dephosphorylation and inactivation of the Snf1 protein kinase, thus controlling Snf1 functions (i.e. expression of glucose-repressed genes). Snf1 is also involved in the response to certain stresses, such as alkaline pH. Surprisingly, both snf1 and reg1 mutants are hypersensitive to high pH. We show here that this phenotype in the reg1 strain is unrelated to the role of Reg1 in regulating Snf1, but depends on the ability of Reg1 to interact with Glc7. Transcriptomic profiling of reg1 cells in the absence or the presence of high pH stress and biochemical analyses suggest that lack of Reg1 impedes the normal downregulation of Pma1 in response to high pH stress. Our results highlight a role of Reg1/Glc7 in the regulation of Pma1 function and hence in the overall cellular cation homeostatic mechanisms.

overall_design:
We identified the transcription pattern of reg1 cells (2 chips).

We also identified the changes in the expression profiles caused by alkalinization of the medium (pH8 vs. pH5.5 for 10 min) in the reg1 strain (2chips)

Total: 4 chips

Changes in the transcriptomic profile in WT cells cause by alkalinization of the medium are included in Series GSE25697 (GSM631186,
GSM631187, GSM631188 and GSM631189)

first: Raquel

last: Serrano

first: Lina

last: Barreto

first: Maria

last: Platara

first: Carlos

last: Casado

first: Jofre

last: Ferrer-Dalmau

first: Amparo

last: Ruiz

first: Joaquín

last: Ariño


title: Long noncoding RNA as putative biomarkers for protstate cancer detection [Set 1]

status: Public on Oct 17 2014

city: Durham

first: Jian-Liang

last: Li

state: NC

address: 111 TW Alexander Dr

country: USA

institute: NIEHS

summary: To identify which lncRNAs are differentially expressed in prostate cancer, total RNA from prostate cancer cell line, PC3, and normal epithelial prostatic cells were screened using NCode (Life Technologies) . The NCode microarray is designed to interrogate 12,784 lncRNAs and 25,409 mRNA target protein-coding genes.

overall_design: Gene expression in prostate epithelial cells and PC3 was measured. Three independent experiments (biological replicates) were performed.

first: Bongyong

last: Lee

first: Joseph

last: Mazar

first: Jian

middle: L

first: Subramaniam

last: Govindarajan

first: Ranjan

last: Perera


title: DNA methylation (5mC) and DNA 5-hydroxy methylation (5hmC) analysis in WT murine ES cells

status: Public on Oct 21 2014

city: Yokohama

first: Takaho

middle: A.

last: Endo

state: Kanagawa

address: 1-7-22 Suehiro, Tsurumi

department: IMS

institute: RIKEN

type: Methylation profiling by genome tiling array

summary: DNA methylation in murine WT ES cells was investigated by MBD domain mediated pull down of methylated DNA followed by chip analysis. For examination of 5hmC, hydroxymethylated DNA was enriched by Click-chemistry mediated pull down. Because of the lower amount of 5hmC, two different approached were adopted. The first approach was based on direct labeling of 5hmC DNA, and in the second method DNA was labeled after amplification with vitro transcription (IVT) .

overall_design: Microarray based hybridization (chip) analysis of epigenetic modifications, namely, 5mC and 5hmC for murine WT ES cells.

first: Shoji

last: Tajima


title: Transcriptional profiling of ATCC46645 strain and isogenic ΔpacC Aspergillus fumigatus mutant during murine infection

city: Manchester

first: Margherita

last: Bertuzzi

address: Core Technology Facility, 46 Grafton Street

department: Institute for Inflammation and Repair

country: United Kingdom

institute: University of Manchester

summary:
In lung diseases caused by the major mould pathogen Aspergillus fumigatus the pulmonary epithelium is destroyed by invasive growth of fungal hyphae, a process thought to require fungal proteases. Here we show that the A. fumigatus pH-responsive transcription factor PacC governs expression of secreted proteases during invasive lung infections and is required for epithelial invasion and pathogenicity. In addition, A. fumigatus ΔpacC mutants aberrantly remodel the fungal cell wall during infection. This study defines distinct PacC-mediated mechanisms of host damage during pulmonary aspergillosis.
ch1: treatment protocol

overall_design: Temporal transcriptional profiling of ATCC46645 strain and isogenic ΔpacC Aspergillus fumigatus mutant during murine infection

first: M

first: W

middle: C

last: Nierman

first: E

last: Bignell


title: Gene expression profile of rice leaf from selected cultivars

city: Sapporo

first: Kouji

last: Satoh

state: Hokkaido

address: Hitsujigaoka 1

institute: NARO/HARC

summary: The genome structrure of domesticated species is influenced by complexity of breeding practices exercised by humans. Hokkaido is the northern-most regio of Japan, and one of northern limit of rice cultivation of world. The climatic conditions of Hokkaido are considered to be unsuitable for rice cultivation. Rice breeding programs of Hokkaido have focused on adaptability to specific local environmental condiitons (such as short growth period, low temperature conditions). These specific selection pressures have generated the unique genetic structures of Hokkaido rice cultivars. The genotype of sixty-three Hokkaido rice varieties were already analyzed by SSR marker, and the results showed that Hokkaido rice varieties were classified into six groups (Shinada et al, 2014). The unique genomic structures of six groups may have related to specific gene expression. This study analyze the gene expression profiles of Hokkaido rice variety.

overall_design: Akage, Hayayuki, Sorachi, Yukara, Norin No15, Hoshinoyume and Kitaake are classified into group I, II, IIIa, IIIb, IV, V and V, respectively. Full-expanded third leaf blade was used for this study. Biological replicates; 2 (Yukara, Kitaake) , 3 (Akage, Hayayuki, Sorachi, Norin No.15, Hoshinoyume). 1 samples derived from 5 plants grown under same conditons

first: Kenji

last: Fujino


title: Expression in Aseel (an indigenous chicken breed) as compared to broiler chicken in 7th and 18th days of embryonic stage

city: Hyderabad

first: Tarun

middle: K

last: Bhattacharya

address: Rajendranagar

country: India

institute: Directorate of Poultry Research

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

overall_design: Refer to individual Series


title: Comparison of Holstein and Jersey day 6 embryos

status: Public on Oct 22 2014

city: Quebec

first: Eric

last: Fournier

state: Quebec

address: 2325 Rue de l'Universite

department: Departement des sciences animales

country: Canada

institute: Universite Laval

summary: Some embryos display better survival potential to cryopreservation than others. The cause of such phenotype is still unclear and might be due to cell damage during cryopreservation, resulting from over-accumulation and composition of lipids. In cattle embryos, in vitro culture conditions have been shown to impact the number of lipid droplets within blastomeres. So far, the impact of breed on embryonic lipid content has not yet been studied. In this study were compared the colour, lipid droplet abundance, lipid composition, mitochondrial activity, and gene expression of in vivo collected Jersey breed embryos which are known to display poor performance post-freezing and in vivo Holstein embryos which have good cryotolerance.

overall_design: Holstein in vivo day 6 embryos vs Jersey in vivo day 6 embryos: 4 replicates of each breed, with dye-swap.

first: Luis

last: Baldoceda

first: Isabelle

last: Gilbert

first: Dominic

last: Gagné

first: Christian

last: Vigneault

first: Patrick

last: Blondin

first: Christina

middle: R

last: Ferreira

first: Claude

last: Robert


title: Control of breast cancer cell migration by a p63-regulated signaling network (miRNA)

city: Dallas

first: Xiaoyu

last: Wang

state: Texas

address: ND3 200, 6001 Forest Park Rd

department: Cancer Center

institute: Ut Southwestern Medical Center

summary: Through analysis of a high-content screen we discovered that mir-203 can impair cell migration by suppressing p63 expression.  We further determined that p63 promotes motility by inducing the expression of multiple target genes.

overall_design: Total RNA  isolated from cell lines with different rated of motility was compared.

first: Gray

last: Pearson


title: Fold change of expression in Aseel (an indigenous chicken breed) as compared to broiler chicken in 7th day of embryonic stage

summary: The expression of genes were analysed in 7th day of embryonic stage between Aseel, an indigenous slow-growing chicken, and control broiler, a fast-growing broiler chicken line. The whole embryo was collected in TRIZOL and total RNA was isolated. The expression profile of gene was determined in 64k Agilent chicken microarray chip. The Cy3 dye was used for detection. The fold change of expression was analysed in Aseel as compared to broiler chicken line.

overall_design: Embryo of 7th day of Aseel and broiler birds in duplicate were analysed. The broiler sample was used as control sample and Aseel sample was used as treatment sample.

first: T

first: R

middle: N

last: Chatterjee


title: University of Manitoba/MGCB2 Pilot Study C. thermocellum Microarray Experiment

status: Public on Oct 26 2014

city: Winnipeg

first: Richard

last: Sparling

state: MB

address: 418 Buller Building

department: Microbiology

institute: University of Manitoba

summary: RNA expression observed in stationary relative to exponential phase cells of strain Clostridum thermocellum (ATCC 27405) grown on cellobiose. b) Comparative RNA expression of 3 Clostridium thermocellu strains (DSM 1237, 2650, and 4150) grown to mid exponential phase on cellobiose. There are 2 purposes for this experiment. 1) Purpose 1 was to verify whether observed differences in fermentation end-product ratios are reflected in differences in RNA expression profiles. Micro Array data will be compared with the same experiments performed with RNA seq and with proteomic experiments. Purpose 2 was to improve our general understanding of the genomes of these strains by doing the experiments on a chip that combined the current genome information for all three strains. It is expected that the Micro Array will confirm that these genomes as currently available are incomplete.

overall_design: Each test condition was provided as 6 biological replicates in order to test the sample to sample variability intrinsic to this type of sample. Statistical analysis will reveal the number of replacates needed to ensure stable results

first: David

middle: B

last: Levin

first: Thomas

last: Rydzak

first: Brian

middle: W

last: Fristensky

first: Xiangli

last: Zhang

first: Graham

middle: G

last: Alvare

first: Natalie

last: Björklund


title: Fold change of expression in Aseel (an indigenous chicken breed) as compared to broiler chicken in muscle of 18th day of embryonic stage

first: Tarun

last: Bhattacharya

summary: The expression of genes were analysed in muscle of 18th day of embryonic stage between Aseel, an indigenous slow-growing chicken, and control broiler, a fast-growing broiler chicken line. The whole embryo was collected in TRIZOL and total RNA was isolated. The expression profile of gene was determined in 64k Agilent chicken microarray chip. The Cy3 dye was used for detection. The fold change of expression was analysed in Aseel as compared to broiler chicken line.

overall_design: Muscle in embryo of 18th day of Aseel and broiler birds in duplicate were analysed. The broiler sample was used as control sample and Aseel sample was used as treatment sample.


title: microRNAs profiling of CD4+ T and CD8+ T lymphacytes from liver and mesentetic lymph nodes in NAFLD and normal mice

status: Public on Oct 23 2014

city: Beijing

first: yujun

last: zhang

address: No 11 xizhimen Nan street

institute: Peking University People's hospital

summary:
Emerging evidence suggests that microRNAs (miRNAs) are crucially involved in pathogenesis of NAFLD. The integrated analysis of expression profiles of miRNAs and mRNAs can be used to identify functional miRNA-target relationships with high precision. The purpose of this study was to provide insights into the immunopathogenesis of  NAFLD using this integrated analysis method.Differentially expressed miRNAs and mRNAs of  CD4+ T lymphocytes from liver and mesenteric lymph nodes(MLN) of NAFLD and normal mice  were analyzed by microarrays and RNA sequencing respectively. Subsequently, the target genes of the differentially expressed miRNAs were predicted and overlapped with the differentially expressed mRNAs. Then, GO and pathway analyses were performed for the intersecting key genes.
The microarray analysis indicated that 170 miRNAs and 2,791 mRNAs were significantly dysregulated in CD4+ T lymphocytes from liver between the two groups. Among the 2,791 mRNAs, 911 overlapped with putative miRNA target genes. A pathway analysis showed that the MAPK pathway was consistently enriched in the liver of NAFLD mice. miR-149-3p, miR-663a, miR-1908, miR-2861 and miR-3185 likely play important roles in the regulation of MAPK pathways. Furthermore, the Notch signaling pathway  This study provides an integrated dataset of the miRNA and mRNA profiles in NAFLD, and the results demonstrate that not only the MAPK pathway and its related miRNAs but also the Notch pathway may be involved in NAFLD immunological development.

overall_design: we pooled RNA of CD4+T cells and CD8+T cells form six individual mice equally into one pool, since the number of cells from one mouse is limited

first: Yujun


title: Expression analysis of genes in Rattus norvegicus lungs at postnatal day 4, 10 and 21 after intrauterine growth restriction induced by low protein diet

status: Public on Oct 29 2014

city: Paris

first: Elodie

last: Zana-Taïeb

address: 53 avenue de l'Observatoire

institute: PremUp

summary: We performed RNA microarray in a low protein diet (LPD) model of IUGR at three key time points of alveolarization process.  IUGR and control rat pups had been studied for each time point considered: on postnatal day 4 (P4) before beginning of the alveolarization process, on P10, peak of alveolarization process and on P21 at the end of it.

overall_design: A twelve chip study using total RNA extracted from 14 whole lungs intrauterine growth restricted rat pups compared to 15 controls. RNA was extracted at three key time points of alveolarization in postnatal life. RNA was pooled by groups of 2 ou 3 before analysis.

first: E

last: Zana-Taieb

first: D

last: Vaiman


title: Identification of a subtelomeric gene family expressed during the asexual-sexual stage transition in Plasmodium falciparum

city: Fuchu

first: Tetsuya

last: Furuya

state: Tokyo

address: 3-5-8 Saiwai-cho

department: Veterinary Medicine

institute: Tokyo University of Agriculture and Technology

summary: For malaria transmission, the parasite must undergo sexual differentiation into mature gametocytes. However, the molecular basis for this critical transition in the parasites life cycle is unknown. Six previously uncharacterized genes, Pfg14.744, Pfg14.745, Pfg14.748, Pfg14.763, Pfg14.752 and Pfg6.6 that are members of a 36 gene Plasmodium falciparum-specific subtelomeric superfamily were found to be expressed in parasites that are committed to sexual development as suggested by co-expression of Pfs16 and Pfg27. Northern blots demonstrated that Pfg14.744 and Pfg14.748 were first expressed before the parasites differentiated into morphologically distinct gametocytes, transcription continued to increase until stage II gametocytes were formed and then rapidly decreased. Immunofluorescence assays indicated that both proteins were only produced in the subpopulation of ring stage parasites that are committed to gametocytogenesis and both localized to the parasitophorous vacuole (PV)b of the early ring stage parasites. As the parasites continued to develop Pfg14.748 remained within the parasitophorous vacuole, while Pfg14.744 was detected in the erythrocyte. The 5' flanking region of either gene alone was sufficient to drive early gametocyte specific expression of green fluorescent protein (GFP). In parasites transfected with a plasmid containing the Pfg14.748 5' flanking region immediately upstream of GFP, fluorescence was observed in a small number of schizonts the cycle before stage I gametocytes were observed. This expression pattern is consistent with commitment to sexual differentiation prior to merozoite release and erythrocyte invasion. Further investigation into the role of these genes in the transition from asexual to sexual differentiation could provide new strategies to block malaria transmission.

overall_design: Microarray analysis was used to compare two clones derived from Plasmodium falciparum strain 3D7 parasites that differ in their ability to undergo gametocytogenesis. Clone G+ produces gametocytes and clone G- produces very few if any gametocytes. RNA was harvested from the cultures when the asexual parasitemia was 0.9-1.48% (day 4) (n=4) after setting up the gametocyte cultures and 5.2-5.58% (day 6) (n=4) prior to the appearance of morphologically distinct gametocytes and used to generate cDNA that was labeled with Cy3 or Cy5 and hybridized to the Plasmodium falciparum 70 mer oligonucleotide microarray developed by DeRisi and co-workers.


title: Ketogulonicigenium vulgare cells: Acid-stressed vs. Control

city: Wuxi

first: Haoru

last: Yang

address: 1800 Lihu Road

institute: Jiangnan University

summary: Transcriptional profiling of K. vulgare cells, co-cultured with Bacillus megaterium, comparing control untreated cells with cells treated with pH 4.0 for 2 h. Differentially expressed genes in acid-stressed cells were analyzed. The aim was to investigate the mechanisms of K. vulgare in response to acid stress on global gene expression.

overall_design: Two-condition experiment, acid-stressed (pH 4.0) cells vs. control cells. Biological replicates: 3 control replicates, 3 acid-stressed replicates.

first: Liming

last: Liu

first: Jian

last: Chen


title: Gene expression data in the brain of tadpoles [Rana pirica] exposed by larvae salamander.

city: Fujisawa

first: Tsukasa

last: Mori

address: Kameino 1866

department: Bioresource Sciences

institute: Nihon University

summary:
Tadpoles of the anuran species Rana pirica can undergo predator-specific morphological responses. Exposure to a predation threat by larvae of the salamander Hynobius retardatus results in formation of a bulgy body (bulgy morph) with a higher tail.
The objective of the present study was to use Affymetrix Xenopus Genechip to profile gene expression in the tail tissue by different predation threat.

overall_design: Tadpoles of Rana pirica treated with larvae salamander for 8days (brainS1, brainS2, brainS3) were analyzed with triplicate.  Controls were cultured for 8days without larvae salamander (brainC1,brainC2,brainC3,brainC4,brainC5,brainC6).  Brains from tadpoles after 8days of each treatment were dissected for RNA extraction and gene expression analysis using Affymetrix Xenopus Genechip arrays.


title: Discovery and validation of a novel expression signature for recurrence in high-risk bladder cancer post-cystectomy

city: vancouver

first: Mohammed

last: Alshalalfa

state: bc

address: water st

institute: GenomeDx

summary: Purpose: Selecting muscle-invasive bladder cancer patients for adjuvant therapy is currently based on clinical variables with limited power. We hypothesized that genomic-based signatures can outperform clinical models to identify patients at higher risk. Method:Transcriptome-wide expression profiles were generated using 1.4 million feature-arrays on archival tumors from 225 patients who underwent radical cystectomy and had muscle-invasive and/or node-positive bladder cancer. A 15-feature GC was developed on the discovery set with area under curve (AUC) of 0.77 in the validation set.

overall_design: A cohort comprised of 225 patients with organ-confined, muscle-invasive (pT2N0M0),extravesical (pT3-4aN0M0), and node-positive (pTanyN1-3M0) UCB who underwent radicalcystectomy at the University of Southern California between 1998 and 2004 was used. Each patient had aminimum two-year follow-up post-cystectomy unless they recurred prior to that date. Patients receiving neoadjuvant chemotherapy, and those with clinical evidence of lymphadenopathy or distant metastasis at diagnosis were excluded.

first: Anirban

last: Mitra

first: Lucia

last: Lam

first: Mercedeh

last: Ghadessi

first: Nicholas

last: Erho

first: Ismael

last: Vergara

first: Christine

last: Buerki

first: Zaid

last: Haddad

last: Sierocinski

first: Timothy

last: Triche

first: Eila

last: Skinner

first: Elai

last: Davicioni

first: Siamak

last: Daneshmand

first: Peter

last: Black


title: Local crosstalk between the lipid deposition and skeletal muscle growth inhibition from Bama minipig obesity model by high-fat high-sucrose diet

status: Public on Oct 15 2014

first: Jinxue

last: Ruan

state: Beijing

address: No.2 Yuanmingyuan West Road

department: Institute of Animal Sciences

institute: Chinese Academy of Agricultural Sciences

summary: The underlying mechanism of how the atopic lipids in skeletal muscle affect muscle growth remains elusive. Here we chose miniature Bama swine as our model to mimick human obesity and co-associated metabolic disorders by long time diet induction and study how the atopic fat accumulation in skeletal muscle influence muscle function. After 23 months high-fat high-sucrose diet (HFHSD) fed, the model minipig model of obesity accompanied with metabolic disorders like human, and they had increased body weight and extensive lipids deposition in adipose tissues (AT) and non-AT, especially in skeletal muscle. Further more, the mass of skeletal reduced greatly and the small area (0-2000μm2) muscle reduced after diet induced. The average fiber area of Gastroc reduced 25.2%, but no significant changes appeared in the other skeletal muscles. Antioxidant capacity of skeletal muscle also reduced. Microarray profiles showed genes related to fat deposition promotion (Peroxisome proliferator activated receptor γ, CCAAT/enhancer-binding protein α and apolipoprotein E), muscle growth inhibition (myostatin and p21) up regulated, and some other muscle cell differentiation related genes (myoD) down regulated. Meanwhile, adipokines like adiponectin and 11b-hydroxysteroid dehydrogenase type 1 (11βHSD1) which partake in the crosstalk between AT and skeletal muscles rose up. We draw a clear potential crosstalk pathway that, increased 11βHSD1 secreted by excess AT will promote the expression of the major inhibitor MSTN by activating corticosterone to cortisol, leading to the growth inhibition of skeletal muscle. Overall, this research announces how obesity affects skeletal muscle growth in a crosstalk sight.

overall_design: Male and female Bama minipigs, aged 6 months at the start of the study, were divided into the following two groups for 23 months of treatment. Bama minipigon control (CD group, N=3) were fed standard pig chow. The experimental group (N=6) were fed high-fat high-sucrose diet (53% basal diet, 37% sucrose, 10% lard, HFHSD).

first: Yuanyuan

last: Zhang

first: Jing

last: Yuan

first: Leilei

last: Xin

first: Jihan

last: Xia

last: Liu

first: Yulian

last: Mu

first: Yaoxing

first: Shulin

last: Yang

first: Kui

last: Li


title: Cell-cycle and cancer-associated gene networks activated by Dsg2: evidence of cystatin A deregulation and a potential role in cell

city: Philadelphia

first: My

last: Mahoney

state: PA

address: 233 South 10th Street, Suite 428  BLSB

department: Dermatology & Cutaneous Biology

institute: Thomas Jefferson University

summary: Our recently generated transgenic mouse model in which Dsg2 is overexpressed in the epidermis observed notable epidermal hyperplasia. We described how Dsg2 altered a number of genes important in epithelial cell growth including the cysteine protease inhibitor cystatin A. We offer a novel pathway of cystatin A regulation involving Dsg2 and a potential crosstalk between Dsg2 and CSTA that modulates cell adhesion.

overall_design: In this study, we used microarray and gene network analysis to compare full-thickness skin of Inv-Dsg2 transgenic mice overexpressing Dsg2 in the superficial layer of the skin compared to wild-type mouse skin expressing Dsg2 in the basal layer of the epidermis. We found 492 genes were altered by more than two-fold in response to Dsg2 that were important in epithelial dysplasia. We focused on the upregulation of Cystatin A, a cysteine protease inhibitor, that is deregulated and mutated in several skin cancers and skin fragility disorders. By knockdown of either Dsg2 or CSTA and by dual knockdown of Dsg2 and CSTA we show that there is increased susceptibility of cell-cell disadhesion and cytoplasmic localization of Dsg2 in response to mechanical stress.

first: Abhilasha

last: Gupta

first: Daniela

last: Nitou

first: Donna

last: Brennan-Crispi

first: Sankar

last: Addya

first: Natalia

last: Riobo

first: David

last: Kelsell

last: GMahoney


title: Chitosan-affected gene expression profiles in brain and stomach

city: Taichung

first: Chien-Yun

last: Hsiang

address: 91 Hsueh-Shih Road

country: Taiwan

institute: China Medical University

summary: Chitosan has been widely used in food industry as a weight-loss aid and a cholesterol-lowering agent. Previous studies have shown that chitosan affects metabolic responses and contributes to anti-diabetic, hypocholestermic, and blood glucose-lowering effects; however, the in vivo targeting sites and mechanisms of chitosan remain to be clarified. In this study, we constructed transgenic mice which carried the luciferase genes driven by peroxisome proliferator-activated receptor (PPAR), a key regulator of fatty acid and glucose metabolism. Bioluminescent imaging of PPAR transgenic mice was applied to report the organs that chitosan acted on, and gene expression profiles of chitosan-targeted organs were further analyzed to elucidate the mechanisms of chitosan. Bioluminescent imaging showed that constitutive PPAR activities were detected in brain and gastrointestinal tract. Administration of chitosan significantly activated the PPAR activities in brain and stomach. Microarray analysis of brain and stomach showed that several pathways involved in lipid and glucose metabolism were regulated by chitosan. Moreover, the expression levels of metabolism-associated genes like apolipoprotein B (apoB) and ghrelin genes were down-regulated by chitosan. In conclusion, these findings suggested the feasibility of PPAR bioluminescent imaging-guided transcriptomic analysis on the evaluation of chitosan-affected metabolic responses in vivo. Moreover, we newly identified that downregulated expression of apoB and ghrelin genes were novel mechanisms for chitosan-affected metabolic responses in vivo .

overall_design: Mice (6 to 8 weeks old) were subcutaneously injected saline or 0.2 g/kg chitosan. Chitosan oligosaccharide lactate (MW=4000-6000, >90% deacetylation) was purchased from Sigma-Aldrich (St. Louis, MO, USA) and dissolved in DDW. For rosiglitazone treatment, mice were orally administered 50 mg/kg rosiglitazone. Mice were then imaged for the luciferase activity or sacrificed for microarray analysis at indicated periods.

first: Tin-Yun

last: Ho


title: Application of CGH-array for the detection of genomic rearrangements responsible for sindromic mental retardation of unknown cause

city: Valencia

first: Francisco

last: Martinez

state: Valencia

address: Avenida Campanar 21

department: Unidad de Genetica

institute: Hospital Universitari i Politecnic La Fe

summary: Developmental delay/intellectual disability (DD/ID)affects 2% of our population. However, most patients are often left without aspecific diagnosis,with the corresponding consequences for the patients and their families.  The application of microarray technology in the study of patients with DD/ID allows whole-genome analysis with a high resolutionand performance. Here we present the results of  four cases included in a series of 246 patients with DD/ID, as part of the screening of the genetic causes responsible for their phenotype.

overall_design: Whole genome array-CGH was performed on Agilent oligo-chip 44K as recommended (human genome CGH microarray G4426B or custom design focused on ID/TEA with the Design ID 035925 from Agilent Technologies, Palo Alto, CA). The patients’ DNA samples were tested against a pool of sex-matched normal DNA samples, all of them (patients and normal controls) from our geographical area. Scanned images were quantified using Agilent Feature Extraction Software (v9.0). The results were analyzed using Agilent Genomic Workbench software. Annotations have been obtained from UCSC (http://genome.ucsc.edu) based on human genome build GRCh37/hg19.

first: Carmen

last: Orellana

last: Martínez

first: Mónica

last: Rosello

first: Silvestre

last: Oltra

first: Sandra

last: Monfort

first: Sonia

last: Mayo


title: Transforming growth factor beta-like stimulated clone 22 D4 promotes diabetic hyperglycemia and insulin resistance [abdominal fat]

city: Mannheim

first: Carsten

last: Sticht

address: Theodor-Kutzer-Ufer

institute: University Heidelberg

summary: Obesity-related insulin resistance represents the core component of the so-called Metabolic Syndrome, ultimately promoting glucose intolerance, pancreatic beta cell failure, and overt type 2 diabetes 1 2. Based on substantial side effects of existing pharmacological approaches, efficient and safe insulin sensitization and glucose control remain critical therapeutic aims to prevent diabetic late complications 3. Here, we identify Transforming Growth Factor beta-like Stimulated Clone (TSC) 22 D4 as a critical molecular determinant of insulin signaling and glucose handling. Hepatocyte-specific inactivation of TSC22D4 enhanced insulin signaling in liver and skeletal muscle, while hepatic TSC22D4 overexpression blunted insulin tissue responses. Consequently, hepatic TSC22D4 inhibition both prevented and reversed hyperglycemia, glucose intolerance, and insulin resistance in various diabetes mouse models, respectively. TSC22D4 was found to exert its effects on systemic glucose homeostasis - in large parts - through the transcriptional regulation of the small secretory protein lipocalin (LCN) 13 as demonstrated by chromatin recruitment and genetic rescue experiments in vivo. As hepatic TSC22D4 levels were found to be elevated in human diabetic patients, correlating with decreased insulin sensitivity and hyperglycemia, our results establish the inhibition of TSC22D4 as an attractive insulin sensitizing option in diabetes therapy.

overall_design: 28 BKS.Cg-Dock7m +/+ Leprdb/J (000642) mice (12 week old ) were divided to 4 forms of treatment (n=7 per treatment group) consisting of 4 different shRNA adenoviruses (reference sample: control shRNA), LCN13 (LCN13 shRNA), TSC22D4 (TSC22D4 shRNA), TSC22D4 plus LCN13 (TSC22D4+LCN13 shRNA). 1 week after shRNA injection animals were sacrificed, liver, abdominal fat tissue, gastrocnemius tissue was immediately snap frozen. 3 representative animals of each treatment group were selected for microarray analysis (abdominal fat tissue).

first: Kilian

last: Friedrich

first: Allan

last: Jones

first: Oksana

last: Seibert

first: Tjeerd

last: Sijmonsma

first: Xiaoyue

last: Wang

first: Norbert

last: Gretz

first: Thomas

last: Fleming

first: Peter

last: Nawroth

first: Wolfgang

last: Stremmel

first: Adam

last: Rose

first: Mauricio

last: Diaz

first: Matthias

last: Blüher

first: Stephan

last: Herzig


title: Comparison of murine whole gene expression on ligand immobilized surfaces

city: Clayton

first: Eun-ju

last: Lee

state: Victoria

address: Bayview Avenue

country: Australia

institute: Commonwealth Science and Industrial Research Organisation

summary: For the studies of cell migration in various micro-environments, self-assembled monolayer surfaces presenting adhesive ligand, RGD peptide, were used for the assay. Presentation of RGD ligands was based on the immobilization reaction with alkanethiols on a gold surface. There were differences in cell morphology and migration according to the ligand affinity (linear vs. cyclic RGD) and manner of ligand presentation (dynamic vs. non-dynamic). In dynamic surface experiment, cells initially grown on the fibronectin-coated patterns were exposed to either linear or cyclic RGD while in non-dynamic surface experiment cells interacted with the immobilized RGD from the beginning. Goal was to compare how the affinity and spatio-temporal exposure of ligand affect the overall transcriptional profiling.

overall_design: Five conditioned surfaces were prepared by chemical treatment for cell culture:  Fibronectin, Dynamic linear RGD, Dynamic cyclic RGD, Non-dynamic linear RGD, and Non-dynamic cyclic RGD surfaces. Reference:  cells cultured in standard tissue culture flasks. Biological replicates:  triplicates for each experiment (each surface was 1.25 cm x 1.25 cm and three surfaces were used for each condition). When reached 70-80% of confluency, cells from the triplicates were pooled and harvested for RNA extraction. Hybridization replicates:  4 replicates for each condition.

first: Yan

last: Shi


title: The global regulator FfSge1 is required for expression of secondary metabolite gene clusters but not for pathogenicity in Fusarium fujikuroi

status: Public on Oct 08 2014

city: Neuherberg, Germany

first: Christian

last: Sieber

address: Ingolstädter Landstraße 1

department: Institute of Bioinformatics and Systems Biology

institute: Helmholtz Zentrum München

summary:
The phytopathogenic fungus Fusarium fujikuroi is the causal agent of bakanae disease on rice due to its ability to produce gibberellins. Besides these phytohormones, F. fujikuroi is able to produce a wide range of other secondary metabolites (SMs), such as mycotoxins and pigments. Although much progress has been made in the field of secondary metabolism over the last years, the transcriptional regulation of SM biosynthetic genes is complex and far from being fully understood. Environmental conditions (e.g. nitrogen availability and pH), global and pathway-specific regulators as well as chromatin remodeling were shown to play major roles in this regulation. Here, the role of FfSge1, a homolog of the morphological switch regulators Wor1 and Ryp1 in Candida albicans and Histoplasma capsulatum, respectively, is explored with emphasis on secondary metabolism. FfSge1 is not required for conidia formation and pathogenicity, but is involved in vegetative growth. Genome-wide transcriptome analysis of the Δffsge1 deletion mutant compared to the wild type revealed that FfSge1 is a global regulator of secondary metabolism in F. fujikuroi that activates the expression of several SMs. In addition, FfSge1 is also required for expression of a yet uncharacterized SM gene cluster containing a noncanonical non-ribosomal peptide synthetase.
Investigation of whole genome gene expression of the Fusarium fujikuroi wild type IMI58289, Δffsge1 mutant under nitrogen starvation and nitrogen sufficient conditions.

overall_design:
In this study we hybridized in total 8 microarrays using total RNA recovered from a wild-type culture of F. fujikuroi IMI58289 and Δffsge1 mutant culture. All cultures were grown on a 6 mM Gln (10%) and a 60 mM Gln medium (100%). For each combination of culture and medium a biological replicate was created. Each chip measures the expression level of 14,397 genes from F. fujikuroi IMI58289 with eight 60-mer probes.

Please note that the wild type samples have been published as part of the GEO accession GSE43745, but re-analyzed with the Δffsge1 mutant samples in the current study.

first: Caroline

last: Michielse

first: Lena

last: Studt

first: Slavica

last: Janevska

first: Philipp

last: Wiemann

first: Ulrich

last: Güldener

first: Bettina

last: Tudzynski


title: Exploring the response of Kluyveromyces lactis to arsenite and peroxide stress and the role of the transcription factor KlYap8 and KlYap1

status: Public on Oct 06 2014

city: Thiverval - Grignon

first: Djamila

last: Onesime

address: CBAI

department: MICA

institute: INRA

summary:
The transcriptional response of  K. lactis yeast was investigated following exposure to sodium arsenite (As(III)) and tert-butyl hydroperoxide (t-BOOH).
We compared the genome-wide expression profile of Klyap8∆ mutant cells to that of the wild type.

overall_design: 3 conditions experiment  :  untreated (UT) , or  exposure to sodium arsenite (As (III))  or   to ter-butyl peroxide (t-BOOH) ; Four biological experiments with a dye switch for  Wild type cells Klwt (reference) and the yap8 mutant cells Klyap8D (test)

first: Jenny

last: Veide-Vilg

first: Nallani

last: Vijay Kumar

first: Ewa

last: Maciaszczyk-Dziubinska

last: Sloma

last: Onésime

first: Julie

last: Aubert

first: Magdalena

last: Migocka

first: Robert

last: Wysocki

first: Markus

last: Tamás


title: Genome-wide identification and analysis of gene expression in BV-2, a murine microglial cell line, infected with rabies virus CVS-11 (Challenge virus standard)

status: Public on Oct 10 2014

city: Changchun

first: Pingsen

last: Zhao

state: Jilin

address: No. 666 Liuying Xilu

department: The research centre for canine diseases

institute: Institute of Military Veterinary Academy of Military Medical Sciences

summary: The hypothesis tested in the present study was that rabies virus (RABV) infection affects the gene expression in microglial cells. Results provide important information that RABV infection led to alteration of gene expression in microglia.

overall_design: A twelve-chip study was performed using total RNA isolated from RABV- or mock-infected BV-2 at 12, 24, or 48 hpi.

first: Lili

first: Songtao

last: Yang

first: Xianzhu

last: Xia


title: Genome-wide identification and analysis of microRNA expression in mouse neuroblastoma cells (NA) and BV-2, a murine microglial cell line, infected with rabies virus CVS-11 (Challenge virus standard)

summary: Rabies virus (RABV) infection led to alteration of microRNA expression in NA and microglia.

overall_design: A sixteen-chip study was performed using total RNA isolated from NA and microglia infected with rabies virus CVS-11 (Challenge virus standard) or mock infected as a control. RNA was isolated from microglia at 12, 24, or 48 hpi and from NA at 24 hpi.


title: Transforming growth factor beta-like stimulated clone 22 D4 promotes diabetic hyperglycemia and insulin resistance [skeletal muscle]

first: Carsten

last: Sticht

department: ZMF

summary: Obesity-related insulin resistance represents the core component of the so-called Metabolic Syndrome, ultimately promoting glucose intolerance, pancreatic beta cell failure, and overt type 2 diabetes 1 2. Based on substantial side effects of existing pharmacological approaches, efficient and safe insulin sensitization and glucose control remain critical therapeutic aims to prevent diabetic late complications. Here, we identify Transforming Growth Factor beta-like Stimulated Clone (TSC) 22 D4 as a critical molecular determinant of insulin signaling and glucose handling. Hepatocyte-specific inactivation of TSC22D4 enhanced insulin signaling in liver and skeletal muscle, while hepatic TSC22D4 overexpression blunted insulin tissue responses. Consequently, hepatic TSC22D4 inhibition both prevented and reversed hyperglycemia, glucose intolerance, and insulin resistance in various diabetes mouse models, respectively. TSC22D4 was found to exert its effects on systemic glucose homeostasis –in large parts- through the transcriptional regulation of the small secretory protein lipocalin (LCN) 13 as demonstrated by chromatin recruitment and genetic rescue experiments in vivo. As hepatic TSC22D4 levels were found to be elevated in human diabetic patients, correlating with decreased insulin sensitivity and hyperglycemia, our results establish the inhibition of TSC22D4 as an attractive insulin sensitizing option in diabetes therapy.

overall_design: 28 BKS.Cg-Dock7m +/+ Leprdb/J (000642) mice (12 week old ) were divided to 4 forms of treatment (n=7 per treatment group) consisting of 4 different shRNA adenoviruses (reference sample: control shRNA), LCN13 (LCN13 shRNA), TSC22D4 (TSC22D4 shRNA), TSC22D4 plus LCN13 (TSC22D4+LCN13 shRNA). 1 week after shRNA injection animals were sacrificed, liver, abdominal fat tissue, gastrocnemius tissue was immediately snap frozen. 3 representative animals of each treatment group were selected for microarray analysis (gastrocnemius tissue).

first: Kilian

last: Friedrich

first: Allan

last: Jones

first: Oksana

last: Seibert

first: Tjeerd

last: Sijmonsma

first: Xiaoyue

last: Wang

first: Norbert

last: Gretz

first: Thomas

last: Fleming

first: Peter

last: Nawroth

first: Wolfgang

last: Stremmel

first: Adam

last: Rose

first: Mauricio

last: Diaz

first: Matthias

last: Blüher

first: Stephan

last: Herzig


title: Genome-wide identification and analysis of gene and microRNA expression in BV-2, a murine microglial cell line, infected with rabies virus CVS-11

first: Pingsen

last: Zhao

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

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

overall_design: Refer to individual Series


title: Transcriptome profiling of sugarcane root in response to low-K stress

status: Public on Oct 02 2014

city: Guangzhou

first: Qiaoying

last: Zeng

address: Chi Gang

institute: Guangzhou Sugarcane Industry Research Institute

summary: To explore the molecular mechanism of low-K tolerance in sugarcane, we have employed whole genome microarray expression profiling to identify sugarcane genes in response to low-K stress. seeldings were transplanted to low-K hydroponic (containing 0.1 mmol.L-1 K+) and the roots were collected at 0 (CK), 8, 24 and 72 h after exposure to low-K condition. The expressions of genes in sugarcane roots were detected by microarray analysis. Totally 1545 genes at 8 h, 1053 genes at 24 h and 3155 at 72 h differentially expressed under low-K stress, when the 2-fold change was adopted as the threshold for determining differentially expressed genes. Among these genes, a certain amount of transcription factors, transporters, kinases, oxidative stress-related genes and genes in Ca+ and ethylene signaling pathway were detected to differentially express.

overall_design: Seeldings were treated with low-K hydroponic (containing 0.1 mmol.L-1 K+) and after 0 (CK), 8, 24 and 72 h exposure to low -K stress, the roots of sugarcane were collected. Four independent experiments were performed using roots collected at different time points

first: Yongwen

last: Qi

first: Qiwei

last: Li


title: Correlating citric acid formation and manganese limitation in Aspergillus niger using transcriptome and proteome analysis

status: Public on Oct 03 2014

city: Kgs. Lyngby

first: Lars

last: Poulsen

address: Soltofts Plads 1

department: Department of Systems Biology

country: Denmark

institute: Technical University of Denmark

summary: Aspergillus niger is well known for its capability to produce citrate in high amounts but the detailed metabolic response causing citrate production has not been fully elucidated. Manganese is known to have an important effect as its limitation is a requirement to obtain high-level citrate formation. To identify the translational regulation causing citric acid overflow metabolism, transcriptome and proteome data from cultivations in manganese limitation and manganese excess conditions were analyzed. In addition to four already described main responses, two novel events were identified. The first metabolic response was down regulation of phosphoenolpyruvate carboxykinase (PEPCK) during manganese limited conditions, which was confirmed by in vivo experiments. Down regulation of the first step in the gluconeogenesis, while maintaining a high activity through glycolysis, promoted secretion of citrate into the medium as an alternative regulatory mechanism for adjusting the intracellular concentrations of TCA intermediates. The other novel observation was down regulation of two cation transporters at manganese limited conditions. It was hypothesized that lowered cation transport across the mitochondrial membrane reduced the ability of the cell to maintain homeostasis thereby favoring citric acid secretion. Finally, upregulation of an ABC transporter was measured, which was assumed to be a citrate permease.

platform_organism:
Aspergillus niger
Aspergillus oryzae
Aspergillus nidulans

overall_design: 9 samples in total. Three conditions in triplicates


title: Anaerobic Degradation of Butyrate By the Hyperthermophilic Archaeon, Ferroglobus placidus

status: Public on Oct 01 2014

city: Amherst

first: Dawn

middle: E

last: Holmes

state: Massachusetts

address: 639 N Pleasant St Morrill IVN 422C

institute: University of Massachusetts Amherst

summary: Comparison of acetate- to butyrate-grown F. placidus cells to identify genes that are potentially involved in fatty acid degradation by this unique hypertherophilic archaeon.

overall_design: A four chip study using total RNA recovered from three separate cultures of Ferroglobus placidus DSM 10642 grown with 1 mM butyrate (experimental condition) and three separate cultures of Ferroglobus placidus DSM 10642 grown on 10 mM acetate (control condition).  Each chip measures the expression level of 2613 genes from Ferroglobus placidus DSM 10642 with nine 45-60-mer probe pairs (PM/MM) per gene, with three-fold technical redundancy.

first: Carla

last: Risso

first: Jessica

last: Smith

first: Derek

last: Lovley


title: Expression Data from E. faecalis VE14089 and luxS mutant with and without DPD

city: Oeiras

first: Neuza

last: Teixeira

address: Av. da República, Estação Agronómica Nacional

country: Portugal

institute: ITQB

summary: Genes differentially regulated by the LuxS/AI-2 system in E. feacalis VE14089

overall_design: E. faecalis VE14082ΔluxS cells were collected after 15 minutes challenge with and without 10µM DPD , for RNA extraction and hybridization onNimbleGen microarrays. As a control VE14089 cells were collected for the same purpose without DPD. For each condition replicates were made.

first: Frederic

last: Gaspar

first: Maria de Fátima Silva

last: Lopes


title: eQTL Mapping of the Yeast Ethanol Response

city: Fayetteville

first: Jeffrey

last: Lewis

state: AR

address: 850 W. Dickson St.

department: Biological Sciences

institute: University of Arkansas

summary: In a previous study, we identified extensive natural variation in the response to acute ethanol treatment in three yeast strains: a lab strain derived from the commonly used S288c (DBY8268), vineyard isolate M22, and oak soil strain YPS163. Many expression differences persisted across several modules of co-regulated genes, implicating trans-acting systemic differences in ethanol sensing and/or response. To understand the genetic basis for these expression differences, we performed eQTL mapping analysis of the response to acute ethanol stress in ~100 F2 strains from two crosses: DBY8268x M22 and DBY8268 x YPS163.

overall_design: We measured the gene expression response to acute ethanol stress (5% for 30 min) in 6 replicates for the parental strains, and in biological duplicate for the eQTL mapping population. Dye swaps were performed in the replicates to control for dye-specific effects.

first: Aimee

middle: T

last: Broman

last: Will

first: Audrey

last: Gasch


title: CSF2 x gender interactions on the transcriptome of Day 15 bovine extra-embryonic membrane

city: Gainesville

first: Kyle

last: Dobbs

state: Florida

address: 2250 SW Shealy Drive

department: Animal Sciences

institute: University of Florida

summary:
We aimed to study the effects of CSF2 treatment on the transcriptome of the Day 15 female and male embryo.
Within the raw files, channel 1= Cy3 and channel 2= Cy5

overall_design: Transcriptional profiling of bovine extra-embryonic membrane at Day 15 post-insemination produced by IVF.  Oocytes were matured and fertilized in vitro using a single Holstein bull. After 5 days in vitro culture, the embryos were either treated with 10 ng/ml bovine recombinant CSF2 or the Control (DPBS/BSA) until Day 7.  At Day 7, the embryos were transferred into recipients.  At day 15 following insemination, embryos were flushed and collected for total RNA and gDNA extraction.  The gender of the embryos were determined by PCR prior to microarray analysis.    CSF2 males were compared to Control males while CSF2 females were compared to Control females. Control females were also compared to control males.

first: Isabelle

last: Dufort

first: Peter

last: Hansen

first: Marc-Andre

last: Sirard

first: Claude

last: Robert

first: Eric

last: Fournier


title: Interferon gamma down-regulates miR-3473b to promote macrophage activation

city: Shanghai

first: PIN

last: WANG

address: Xiangyin Road 800

institute: SMMU

summary: Macrophages are major effector cells and antigen presenting cells of the innate immune system and classical activation of macrophage function requires interferon–γ (IFN-γ) pretreatment (priming) and TLR stimuli, which promotes inflammatory responses though high levels of pro-inflammatory cytokines and lower level of the anti-inflammatory cytokines, resulting in microbicidal and tumoricidal effect. However, the underlying molecular mechanism of IFN-γ priming remains elusive. In this study, we explored the effect of IFN-γ on macrophages at miRNA level and discovered that miR-3473b, which was down-regulated after IFN-γ priming, could attenuate the priming effect of IFN-γ. Molecular study revealed that miR-3473b promoted Akt/GSK3 signaling and IL-10 production through directly targeting PTEN to suppress inflammatory response and tumor-suppressing capability of macrophages. In summary, our data demonstrate that IFN-γ beef up macrophage inflammatory response and tumor suppressing capacity by limiting miR-3473b-mediated PTEN suppression. Our work identified an IFN-γ/miR-3473b/Akt axis in the regulation of macrophage function and activation.

overall_design: the assay was performed with 5 μg total RNA samples from both normal BMM (labeled by Cy3) and BMM primed by IFN-γ (100U/ml) for 4 h(labeled by Cy5), normal BMM serves as control.

first: Pin

last: Wang

first: Yiquan

last: Xue

first: Cong

last: Wu

first: Junfang

last: Xu

first: Li

last: Lin

first: Qiuyan

last: Liu

last: Li

first: Xuetao

last: Cao


title: Gene expression analysis of diabetic kidney cortices obtained from ICAM-1 deficient mice and wild type mice.

city: Okayama

first: Satoshi

last: Miyamoto

address: 2-5-1 Shikata-cho

institute: Okayama University Graduate School of Medicine, Dentistry and Pharmaceutical sciences

summary:
In the present study, we aimed to determine the genes involved in inflammatory process of diabetic nephropathy.
ICAM-1+/+ and ICAM-1-/- mice aged 8 weeks were divided into four groups: 1) nondiabetic ICAM-1+/+ mice (ND-WT), 2) nondiabetic ICAM-1-/- mice (ND-KO), 3) streptozotocin (STZ)-induced diabetic ICAM-1+/+ mice (DM-WT), and 4) STZ-induced diabetic ICAM-1-/- mice (DM-KO). Three months after the induction of diabetes, total RNA was extracted from each specimen of renal cortex. We examined gene expression profiles of four groups.
We identified 193 genes; the ratio of expression level of DM-WT was >2 or <0.5 of that of DM-KO. Of 193 genes, hierarchical clustering identified 33 genes that were significantly upregulated only in DM-WT but not remarkable in ND-WT and ND-KO. Functional annotation of these 33 genes revealed that the significant functions of them were related to the immune or inflammatory process: immune response, response to stimulus, defense response, immune effector process and antigen processing and presentation. These genes contained several inflammatory related genes, such as chemokine (C-X-C motif) ligand 10, chemokine (c-c motif) ligand 12, and chemokine (c-c motif) ligand 8. In this cluster, we focused on cholecystokinin (CCK) because CCK is one of the most up-regulated genes. Real-time RT-PCR revealed that CCK mRNA expression was significantly up-regulated in DM-WT compared with DM-KO.
These results suggest that CCK may play a critical role in the progression of diabetic nephropathy by controlling inflammation in diabetic kidney.

overall_design:
 Male ICAM-1-/- mice (C57BL/6J background) were purchased from The Jackson Laboratory (Bar Harbor, ME). Male C57BL/6J mice (ICAM-1+/+) mice were used as controls. ICAM-1+/+ and ICAM-1-/- mice aged 8 weeks were divided into four groups (n = 5 each): 1) nondiabetic ICAM-1+/+ mice (ND-WT), 2) nondiabetic ICAM-1-/- mice (ND-KO), 3) streptozotocin (STZ)-induced diabetic ICAM-1+/+ mice (DM-WT), and 4) STZ-induced diabetic ICAM-1-/- mice (DM-KO). Mice in the diabetic groups received an intraperitoneal injection of STZ (Sigma Chemical, St.Louis, MO) at 200 mg/kg in citrate buffer (pH 4.5). Blood glucose levels were determined 7 days after STZ injection and only mice with blood glucose concentrations >16 mmol/L were used in the study. Nondiabetic ICAM-1+/+ and ICAM-1-/- mice received citrate buffer injections only. All mice had free access to standard diet and tap water. All animal procedures were performed according to the Guidelines for Animal Experiments at Okayama University Medical School, Japanese Government Animal Protection and Management Law (no. 105), and Japanese Government Notification on Feeding and Safekeeping of Animals (no. 6). Three months after the induction of diabetes, all mice were killed, and the kidneys were harvested. Total RNA was extracted from each specimen of renal cortex using standard protocol from RNeasy midi kit (Qiagen, Valencia, CA) at 3 months.
 The concentration and the quality of the total RNA sample were assessed by Agilent Bioanalyzer. Biotin-labeled target cRNA was prepared using First and Second strand cDNA Synthesis Kit (Amersham Biosciences, No. 320000) and In Vitro Transcription Kit (Amersham Biosciences, No.320001). Incubate total RNA (5 μg), diluted bacterial mRNA spike controls and T7 oligo (dT) primer for 10 min at 70 C. Add first-strand reaction components and incubate 1 hour at 42C. Add the first-strand cDNA product to the second-strand reaction components and incubate for 2 hours at 16 C. Double-strand cDNA was purified using QIAquick purification kit (Qiagen), eluted twice, each time with 30μl of nuclease-free water then dried in a SpeedVac concentrator. Prepare IVT mix of biotinylated UTP, ribonucleotides, and the 10x T7 enzyme mix and add to the resuspended cDNA. Incubate at 37C for 14 hours. Purify cRNA using RNeasy Mini Kit (Qiagen) and elute the cRNA twice, each time with 50 μl nuclease-free water. Measure the absorbance at 260 nm and 280 nm to determine the ratio (A260:A280=2).
 In 25 μl total volume, add 10 μg of cRNA to 5 μl of 5x fragmentation buffer and incubate at 94 C for 20 min. Bring 10 μg of fragmented cRNA, 78 μl of hybridization buffer component A, and 130 μl of hybridization buffer component B to a final volume of 260 μl with water. Incubate at 90C for 5 min and immediately chill on ice for 5 min. Slowly inject 250 μl of hybridization reaction mixture into array input port and seal ports with sealing strips. Set the shaker speed to 300 rpm and incubate slides for 18 hours at 37C in an Innove 4080 shaker. Remove the Flex Chamber using the hybridization removal tool. Then, place the bioarrays into the bioarray rack while it sits inside the medium reagent reservoir containing 0.75xTNT. Transfer the bioarray rack to the large reagent reservoir containing preheated 0.75xTNT, and incubate at 46 C for exactly 1 hour. Fill each slot of the small reagent reservoir with 3.4 ml of Cy5-Streptavidin working solution. Transfer the bioarray rack from the large reagent reservoir in to the small reagent reservoir and incubate bioarrays at RT for 30 min. Wash the bioarrays four times with 1xTNT at RT for 5 min. Rinse the bioarrays in 0.1xSSC/0.05%Tween by moving rack up and down 5 times in 5 seconds. Immediately follow the rinse with centrifugation to dry bioarrays, and store dried bioarrays in the dark.
 We scanned bioarrays with Axon GenePix 4000B and analyzed with CodeLink Expression Analysis software version 2.3.2.
 The 10,000 spot intensities on the scanned microarray image were normalized to a median value of 1 and data were exported for analysis with CodeLink Expression Analysis software version 2.3.2

first: Kenichi

last: Shikata

first: Kyoko

last: Miyasaka

first: Shinichi

last: Okada

first: Motofumi

last: Sasaki

first: Hirofumi

last: Makino


title: Zebrafish presenillin1 mutant transcriptome

city: Dresden

first: Judith

last: Paridaen

address: Pfotenhauerstr 108

institute: MPI-CBG

summary: Gene expression profile comparing 17-month old wild-type with psen1hu2547 zebrafish.

overall_design: Total RNA from 3-4 brains of 17-month old adult psen1hu2547 or WT fish was extracted using RNeasy mini columns (Qiagen) and quality-checked using NanoDrop 1000 (Thermo Scientific) and formaldehyde gel electrophoresis. cDNA was generated and labeled with Cy3 or Cy5-CTP using the low RNA input linear amplification kit (Perkin-Elmer). Upon purification and fragmentation, labeled cRNA was hybridized to the zebrafish 22K 60-mer oligonucleotide microarray (G2518A-001, Agilent Technologies, Santa Clara, CA, USA) at 65ºC for 17 hours. Three independent biological repeats were performed.

last: Lam


title: Expression analysis of Cellvibrio japonicus grown in either glucose or cellulose

status: Public on Oct 07 2014

city: Baltimore

first: Jeffrey

middle: G.

last: Gardner

state: MD

address: 1000 Hilltop Circle

department: Department of Biological Sciences

institute: University of Maryland - Baltimore County

summary: Investigation of whole genome gene expression level changes in Cellvibrio japonicus wild-type, comparing glucose vs cellulose. Study was purposed with determining changes in polysaccharide degradation pathways during utilization of insoluble cellulose.

overall_design: A NimbleGen microarray study using total RNA recovered from two separate wild-type cultures of Cellvibrio japonicus (per growth condition) with 3710 24-mer probes with three-fold technical redundancy.


title: Transcriptomic analysis reveals differential response in the teleost spleens and head kidneys towards vaccination and pathogen challenge

city: Singapore

first: Junhui

last: Jiang

address: 1 Research Link National University of Singapore

country: Singapore

institute: Temasek Life Sciences Laboratory

summary: In this study we attempt to elucidate some of the pathways involved in the immune response to vaccination and subsequent disease challenge using a transcriptomic approach.  We exposed, via intra-peritoneal injection, three months old Asian seabass (Lates calcarifer) to a Streptococcus iniae vaccine. A control group was also set up where no vaccine was injected. Spleen and head kidney samples were collected at one and seven days post vaccination for transcriptomic analysis. At this point, there are four groups per organ: Day 1 vaccinated, Day 1 control, Day 7 vaccinated and Day 7 control.  Subsequently, a pathogen challenge was carried out three weeks later and spleen and head kidneys were sampled at 25-29 hours post challenge for transcriptomic analysis. For control, mock challenged was carried out. At this point, there are four groups per organ: unvaccinated challenged, unvaccinated mock challenged, vaccinated challenged and vaccinated mock challenged.

overall_design: Total 57 samples.     Spleen samples:  At Day 1 and Day 7 post vaccination, 4 spleens were analyzed for each of the D1 control and D1 vaccinated groups and 3 spleens were analyzed for each of the D7 control and D7 vaccinated groups  (total = 14 samples). At post pathogen challenge, 4 spleens were analyzed for each of these three groups - unvaccinated mock challenged, vaccinated challenged and vaccinated mock challenged and 3 spleens for the unvaccinated challenged group (total = 15 samples).    Head Kidney samples: At Day 1 and Day 7 post vaccination, 3 head kidneys were analyzed for the control and vaccinated groups for both time points (total = 12 samples). At post pathogen challenge, 4 head kidneys were analyzed for each of the groups:  unvaccinated challenged, unvaccinated mock challenged, vaccinated challenged and vaccinated mock challenged (total = 16 samples).

first: Laszlo

last: Orban


title: Comparison between type-I vascular endothelial cells (VECs) and type-II VECs

status: Public on Sep 30 2014

city: Shinjuku-ku

first: Kumiko

last: Saeki

address: 1-21-1 Toyama

department: Department of disease control

institute: National Center for Global Health and Medicine

summary: Human VECs are categorized into two groups regarding their effects on the proliferation of vascular smooth muscle cells (VSMCs):type-I, pro-proliferative VECs and type-II anti-proliferative VECs. The effects of VECs on VSMC proliferation were quantitatively assessed according to the following method: human aortic smooth muscle cells, which were stained by PKH-26 in advance, were cultured on the layer of CFSE-stained VECs, and VSMC proliferation were evaluated after four days by flow cytometry analyses using ModFit LT™ software (Verity Software House Inc., Topsham, ME). Commercially available primary human VECs including HUVEC, HAEC and HMVEC as well as the majority of endothelial progenitor cell (EPC)-derived VECs (EPCdECs), whether EPCs were obtained from adult or fetal tissues, enhanced VSMC proliferation, showing type-I phenotype. EPCdECs of minor donors including EPC1dEC suppressed VSMC proliferation, showing type-II phenotype. However, type-II VECs turned into type-I VECs after a few rounds of subcultures. Comparative analyses on gene expression profiles between type-I VECs and type-II VECs revealed that regulator of G-protein signaling 5 (RGS5) was the only gene that showed the discriminative expression pattern: high expressions in type-I VECs and low expressions in type-II VECs.

overall_design: Totally six samples of type-I VECs (HUVEC, HAEC, HMVEC, EPC1dEC[P12], UCEPC1dEC, EPC2dEC[P7]) and two samples of type-II VECs (EPC1dEC[P7] and EPC1dEC[P7] purchased at a different time point) were subjected to the analyses.

first: Miwako

last: Nishio

first: Chikako

last: Sato

first: Akira

last: You


title: Bovine Day 15 Extra-embryonic membrane (EEM): Male and Female Control vs. Male and Female CSF2 Methylation

first: Kyle

last: Dobbs

summary: We aimed to study the effects of CSF2 treatment on the methylome of the Day 15 female and male embryo.

overall_design: Methylomic profiling of bovine extra-embryonic membrane at Day 15 post-insemination produced by IVF. Oocytes were matured and fertilized in vitro using a single Holstein bull. After 5 days in vitro culture, the embryos were either treated with 10 ng/ml bovine recombinant CSF2 or the Control (DPBS/BSA) until Day 7. At Day 7, the embryos were transferred into recipients. At day 15 following insemination, embryos were flushed and collected for total RNA and gDNA extraction. The gender of the embryos were determined by PCR prior to microarray analysis. CSF2 males were compared to Control males while CSF2 females were compared to Control females

first: K

first: D

last: Gagne

first: E

last: Fournier

first: M

last: Sirard

first: C

last: Robert

first: P

last: Hansen


title: Vitamin D Prevents Cognitive Decline and Enhances Hippocampal Synaptic Function in Aging Rats

status: Public on Sep 23 2014

city: Lexington

first: Eric

middle: M

last: Blalock

state: KY

address: 800 Rose St.

department: Molecular and Biomedical Pharmacology

institute: University of Kentucky

summary: Vitamin D is an important calcium-regulating hormone with diverse functions in numerous tissues including the brain.  Increasing evidence suggests that vitamin D may play a role in maintaining cognitive function and that vitamin D deficiency may accelerate age-related cognitive decline.  Using aging rodents, we attempted to model the range of human serum vitamin D levels, from deficient to sufficient, to test whether vitamin D could preserve or improve cognitive function with aging.  For 5-6 months, middle-aged F344 rats were fed diets containing low, medium (typical amount) or high vitamin D3 (100, 1000 or 10,000 IU/kg diet, respectively) and then hippocampal-dependent learning and memory were tested in the Morris water maze.  Rats on high vitamin D achieved the highest blood levels (in the sufficient range) and significantly outperformed low and medium groups on maze reversal, a particularly challenging task that detects more subtle changes in memory.  In addition to calcium-related processes, hippocampal gene expression microarrays identified pathways pertaining to synaptic transmission, cell communication and G-protein function as being up-regulated with high vitamin D.  Basal synaptic transmission also was enhanced corroborating observed effects on gene expression and learning and memory.  Our studies demonstrate a causal relationship between vitamin D status and cognitive function and suggest that vitamin D-mediated changes in hippocampal gene expression may improve the likelihood of successful brain aging.

overall_design:
Sixty, middle-aged male F344 rats were divided into three groups, each receiving for 5-6 months a different dietary amount of cholecalciferol (vitamin D3; VitD3). Purified AIN-93G (Harlan-Teklad) diet was modified to contain low, medium or high VitD3 (IU/kg diet):  High = 10,000, Standard (Control) = 1000; Low = 100. Animal weight and amount of food consumed was recorded 2-3 times/week.  Serum levels of 25-hydroxy vitamin D were determined using liquid chromatography/tandem mass spectrometry (ZRT Laboratory). Hippocampal RNA was isolated, quantified and checked for RNA integrity. One low VitD3 sample failed RNA quality control. Remaining RNA samples were applied to Affymetrix Rat Gene 1.0 ST arrays (one array/subject). Pre-statistical filtering removed poorly annotated probe sets, low intensity signals, and outlier values (>2SD of the group mean). Filtered data were analyzed by 1-way ANOVA to identify significant differences and the False Discovery Rate (FDR) procedure was used to estimate the error of multiple testing. FDR was compared at 0.31 and 0.17. Significant genes were assigned to one of four idealized expression patterns using Pearson’s test and separated by the sign of their correlation; relative gene expression values are provided on the log-2 scale. Functional categorization for significant genes was determined using DAVID bioinformatic tools.

Please note that 'Marked' and 'Unmarked' (in the sample titles) refers to whether the rat had a mark on its tail. The rats were pair-housed and this is how two rats in one cage were distinguished.

first: Caitlin

middle: S

last: Latimer

first: Lawrence

middle: D

last: Brewer

first: James

last: Searcy

first: Kuey-Chu

last: Chen

first: Jelena

last: Popović

first: Susan

last: Kraner

first: Olivier

last: Thibault

first: Philip

last: Landfield

first: Nada

last: Porter


title: cardiomyocyte  induced from fibroblast

city: Beijing

first: yuan

middle: Yuan

last: Du

address: Yihe Yuan Road 5

institute: Department of Cell Biology and Genetics, College of Life Sciences, Peking University

summary: the fibroblast from the skin of the mouse dorsum become the cardiomyocyte

overall_design: do a lot of experiment and gradually find out the best combination of the induction

first: Du

last: yuanyuan

first: Deng

last: hongkui


title: Human K562 cells transfected with control or ETO2 siRNA

city: Kamakura

first: Satoshi

last: Kondo

state: Kanagawa

address: Tebiro 6-10-1

department: New Projects Development Division

institute: Toray Industries,Inc.

summary: microRNA profiling of  comparing control or  ETO2 siRNA-treated human K562 cells

overall_design: Two-condition experiment, K562-control siRNA vs. K562-ETO2 siRNA, Biological replicates: 1, 1 control siRNA, 1 ETO2 siRNA, independently.

first: Tohru

last: Fujiwara

first: Hideo

last: Harigae


title: Identification of CNA associated with bone metastatic breast cancer cells

city: Barcelona

first: Evarist

middle: Planet

last: Letschert

state: Spain

address: C/ Baldiri Reixac 10

department: Biostatistics

institute: IRB Barcelona

summary: We used comparative genomic hybridization (CGH) analysis between Bone metastatic derivatives isolated in vivo and parental cells and focused on genomic changes affecting the expression of potential bone metastasis.

overall_design: Total RNA from biological and technical replicates of parental MCF7 and BoM2 bone metastasis derivatives grown for 48 hours in regular media (see growth protocol). High-molecular DNA was isolated from in vitro cultured MCF7 and BoM2 cells using GeneElute™ Mammalian Genomic DNA Miniprep Kit (Sigma-Aldrich) following manufacture’s instructions.

first: Roger

last: Gomis


title: Microarray profiling of total testicular microRNAs in mouse

city: Trivandrum

first: Pradeep

last: Kumar

state: Kerala

address: Thycaud, Poojappura

department: Molecular Reproduction

institute: Rajiv Gandhi Centre for Biotechnology

summary: Gene expression in mammalian testis undergoing spermatogenesis is under strict post transcriptional regulation and microRNAs are known to play a role in this regulation. Considering the time window of first wave of spermatogenesis, we did a microarray profiling of total testicular microRNAs in mouse and found several significant patterns of variable expression of these molecules during the different stages analyzed here.

overall_design: Mouse testis tissue were taken at three stages, 8 days, 16 days and 24 days, during first wave of spermatogenesis for RNA extraction and hybridization on Locked Nucleic Acid(LNA) technology based Exiqon microarray platform. We included two biological replicates per age group and comparisons were done between the samples with respect to their hybridization to the 'reference' sample which had all the six samples pooled together.

first: Sreesha

last: Sree


title: Genomic Localization of TgSMC1 in Toxoplasma gondii parasites

status: Public on Sep 27 2014

city: Tampa

first: Kami

last: Kim

state: FL

address: 3720 Spectrum Blvd, Suite 304

department: Internal Medicine Medicine

institute: University of South Florida

type: Genome binding/occupancy profiling by genome tiling array

summary: Apicomplexa are intracellular parasites that cause human and animal disease. They proliferate by a unique mechanism that combines closed mitosis with daughter cell budding. In past work we demonstrated that the Toxoplasma gondii centromeres are sequestered to the nuclear periphery proximal to the centrosome throughout the cell cycle. Here we show that interphase centromere clustering is not mediated by the mitotic spindle. Instead we propose a chromatin model of centromere clustering and define structural maintenance of chromosomes protein 1 (SMC1) as a persisting centromeric protein. We biochemically identify proteins that physically interact with SMC1, and CenH3 (a centromeric histone); prominent among those are predicted peripheral soluble components of the  nuclear pore complex including TgExportin1. Treatment of parasites with the highly specific exportin1 inhibitor leptomycin B causes the dispersal of centromeres. Our results suggest that the nuclear envelope, and in particular peripheral components of the nuclear transport machinery orchestrate centromere positioning and parasite nuclear architecture.

overall_design: Chromatin immunoprecipitation (ChIP) of TgSMC1, three replicates applied to two microarrays each representing half of the Toxoplasma genome

first: Maria

last: Francia

first: Sheila

last: Bhavsar

first: Li-Min

last: Ting

first: Matthew

last: Croken

first: Jean-Francois

last: Dubremetz

first: Boris

last: Striepen


title: miRNA expression may account for chronic but not for acute regulation of mRNA expression in human  thyroid tumor models

city: brussels

first: aline

last: hébrant

address: 808 route de Lennik

department: iribhm

country: Belgium

institute: ulb

summary:
Background: For thyroid tumorigenesis, two main human in vitro models are available: primary cultures of human thyrocytes treated with TSH or EGF/serum as models for autonomous adenomas (AA) or papillary thyroid carcinomas (PTC) respectively, and human thyroid tumor derived cell lines. Previous works of our group have assessed properties of those models, with a special emphasis on mRNA regulations. It is often assumed that miRNA may be one of the primary events inducing these mRNA regulations.

Methods: The purpose of this study was to investigate the representativity of those models to study microRNA regulations and their relation with mRNA expression. To achieve this aim, the miRNA expressions profiles of primary cultures treated with TSH or EGF/serum and of 6 thyroid cancer cell lines were compared to the expression profiles of 35 tumor tissues obtained by microarrays.

Results: Our data on primary cultures have shown that the TSH or EGF/serum treatment did not greatly modify the microRNA expression profiles, which is contrary to what is observed for mRNA expression profiles, although they still evolved differently according to the treatment. The analysis of miRNA and mRNA expressions profiles in the cell lines has shown that they have evolved into a common, dedifferentiated phenotype, closer to ATC than to the tumors they are derived from.

Conclusions: Long-terms TSH or EGF/serum treatments do not mimic AA or PTC respectively in terms of miRNA expression as they do for mRNA, suggesting that the regulations of mRNA expression induced by these physiological agents occur independently of miRNA. The general patterns of miRNA expression in the cell lines suggest that they represent a useful model for undifferentiated thyroid cancer. Mirna probably do not mediate the rapid changes in gene expression in rapid cell biology regulation.

overall_design:
miRNA expressions profiles of primary cultures treated with TSH or EGF/serum and of 6 thyroid cancer cell lines were compared to the expression profiles of 35 tumor tissues obtained by microarrays.

Please note that there are two raw data files per sample (indicated in the description field) and sample data table contains  data combined across arrays (described in the sample data processing field). The raw data file 1 is labelled as 'tumor-Hy5+normal tissue-Hy3' and the raw data file 2 is labelled as tumor-Hy3+normal tissue-Hy5 as dye-swap experiments.

first: Sébastien

middle: L

last: Floor

first: Aline

last: Hebrant

first: Jaime

last: Pita

first: Manuel

last: Saiselet

first: Christophe

last: Trésallet

first: Frederick

last: Libert

first: G

last: Andry

first: JE

last: Dumont

first: Wilma

last: van Staveren

first: Carine

last: Maenhaut


title: Insights into acetate toxicity in Zymomonas mobilis 8b using different substrates

status: Public on Sep 08 2014

city: Golden

first: Shihui

last: YANG

state: CO

address: 1617 Cole Blvd

department: National Bioenergy Center

institute: National Renewable Energy Lab

summary:
Background
Lignocellulosic biomass is a promising renewable feedstock for biofuel production. Acetate is one of the major inhibitors liberated from hemicelluloses during hydrolysis. An understanding of the toxic effects of acetate on the fermentation microorganism and the efficient utilization of mixed sugars of glucose and xylose in the presence of hydrolysate inhibitors is crucial for economic biofuel production.

Results
A new microarray was designed including both coding sequences and intergenic regions to investigate the acetate stress responses of Zymomonas mobilis 8b when using single carbon sources of glucose or xylose, or mixed sugars of both glucose and xylose. With the supplementation of exogenous acetate, 8b can utilize all the glucose with a similar ethanol yield, although the growth, final biomass, and ethanol production rate were reduced. However, xylose utilization was inhibited in both media containing xylose or a mixed sugar of glucose and xylose, although the performance of 8b was better in mixed sugar than xylose-only media. The presence of acetate caused genes related to biosynthesis, the flagellar system, and glycolysis to be downregulated, and genes related to stress responses and energy metabolism to be upregulated. Unexpectedly, xylose seems to pose more stress on 8b, recruiting more genes for xylose utilization, than does acetate. Several gene candidates based on transcriptome results were selected for genetic manipulation, and a TonB-dependent receptor knockout mutant was confirmed to have a slight advantage regarding acetate tolerance.

Conclusions
Our results indicate Z. mobilis utilized a different mechanism for xylose utilization, with an even more severe impact on Z. mobilis than that caused by acetate treatment. Our study also suggests redox imbalance caused by stressful conditions may trigger a metabolic reaction leading to the accumulation of toxic intermediates such as xylitol, but Z. mobilis manages its carbon and energy metabolism through the control of individual reactions to mitigate the stressful conditions. We have thus provided extensive transcriptomic datasets and gained insights into the molecular responses of Z. mobilis to the inhibitor acetate when grown in different sugar sources, which will facilitate future metabolic modeling studies and strain improvement efforts for better xylose utilization and acetate tolerance.

overall_design: Two series of microarray studies using total RNA extracted from Zymomonas mobilis subsp mobilis 8b (an xylose-utilizing recombinant) were carried out to investigate the effect of carbon source and acetate on Z. mobilis. One study compared the acetate effect in either glucose or xylose at exponential phase and another study investigated the acetate effect in mixed sugar of glucose and xylose at three growth phases of exponential, transition, and stationary.  Tthree biological replicates were used for each condition.

last: Yang

first: Mary

last: Franden

first: Steven

last: Brown

first: Yat-Chen

last: Chou

first: Philip

last: Pienkos

first: Min

last: Zhang


title: Gene expression landscape of CS cerebellum

status: Public on Sep 22 2014

city: London

first: Yuming

last: Wang

address: South Mimms

department: Mechanisms of Transcription Laboratory

institute: Cancer Research UK

summary: The intricate features of human brain development and function are reflected on the precise regulation of transcriptional architecture. This study characterizes the gene expression perturbations of Cockayne Syndrome brain tissue samples underlying the complex neurological abnormalities.

overall_design: The Nimblegen human 12 x 135K gene expression array was used to define gene expression profiles of CS cerebellum tissues and age-matched controls.

first: Probir

last: Chakravarty

first: Jesper

last: Svejstrup


title: Beta-cell maturation is associated with miRNA expression changes

status: Public on Sep 04 2014

city: Indianapolis

first: Scot

middle: J

last: Matkovich

state: IN

address: Lilly Corporate Center

institute: Eli Lilly and Company

summary: We found that in rodents, postnatal beta-cell maturation is associated with changes in the expression of several islet microRNAs and discovered that these modifications are driven by changes in the nutrient supply. Mimicking the microRNA changes observed during β-cell maturation in newborn rat islet cells was sufficient to promote glucose-induced insulin release and to achieve a mature β-cell secretory phenotype. Moreover, the modifications in the level of some of these microRNAs reduced the proliferation of newborn β-cells, suggesting that they contribute to the limited proliferative capacity of adult β-cells. These findings demonstrated that miRNAs contribute to postnatal beta-cell maturation and development. Their role is likely to promote beta-cell adaptation to fuel supply and to maintain glucose homeostasis by regulating insulin release and proliferation.

overall_design: Islets from 10-day-old rats (P10) (n=4) or 3-month-old male rat (n=4) were taken. Total RNA was extracted and microRNA profiling was performed with miRNA Agilent arrays.

first: Cecile

last: Jacovetti

first: Romano

last: Regazzi