title: Transcriptional profiling of whole-blood in Mycobacterium avium subsp. paratuberculosis-infected cattle

status: Public on Oct 31 2014

city: Seoul

first: Min-Kyoung

last: Shin

address: 1, Gwanak ro, Gwanak gu

institute: Seoul National University

summary: To provide novel insights into understanding the host-immune response during the different stages of progression of the disease, we performed gene expression profiling in Mycobacterium avium subsp. paratuberculosis infection in cattle.

overall_design: We analyzed the transcriptional profiles of whole-blood cells of cattle identified and grouped according to the presence of MAP-specific antibodies and the MAP shed by them. The grouping was based on the results obtained by ELISA and PCR analyses as follows: 1) Test1 group: MAP-negative results obtained by ELISA and positive results obtained by PCR; 2) Test2 group: MAP-positive results obtained by ELISA and negative results obtained by PCR; 3) Test3 group: MAP-positive results obtained by ELISA and positive results obtained by PCR; 4) uninfected control: MAP-negative results obtained both by ELISA and PCR analysis.

first: Han

last: Yoo


title: Characteristics of microRNA expression in mammary tissue of dairy and beef breed heifers

status: Public on Sep 15 2014

city: Warsaw

first: Zofia

last: Wicik

state: mazovia

address: Pawinskiego 5

department: Department of Human Epigenetics

country: Poland

institute: Mossakowski Medical Research Center

summary: MicroRNAs (miRNAs) are small noncoding RNAs that participate in regulation of gene expression. Their role during mammary gland development is still largely unknown. In the present study, we performed a microarray analysis to identify miRNAs associated with high mammogenic potential of bovine mammary gland. We identified 54 miRNAs differing significantly between mammary tissue of dairy (Holstein-Friesian, HF) and beef (Limousine, LM) post-pubertal heifers. Fifty two miRNAs had higher expression in the mammary tissue of LM heifers. Enrichment analyses for targeted genes revealed that the major differences between miRNA expression in the mammary gland of HF vs. LM were associated with regulation of signalling pathways crucial for mammary gland development, such as: TGF-beta, insulin, WNT and inflammatory pathways. Moreover, a number of genes potentially targeted by differentially expressed miRNAs was associated with mammary stem cells’ activity. These data indicate that in dairy cattle high developmental potential of the mammary gland, leading to high milk productivity, not only depends on central neuro-endocrine regulation but also on specific miRNA expression pattern.

overall_design: miRNA  profiling of Holstein Freisian (dairy breed) and Limousne heifers (beef breed) mammay glands. Two-condition experiment, LM (test) vs. HF (reference). Total RNA was isolated from quarters of 4 LM and 4 HFmammary glands.

first: Małgorzata

last: Gajewska

first: Alicja

last: Majewska

first: Ewa

last: Osińska

first: Tomasz

last: Motyl


title: Altered molecular expression of the TLR4/ NF-κB signaling pathway in mammary tissue of Chinese Holstein cattle with mastitis

status: Public on Oct 30 2014

city: nanjing

first: jie

last: wu

address: Nanjing Agricultural University Weigang 1, Nanjing, Jiangsu Province

country: China

institute: Nanjing Agricultural University

summary: In this study, the profile of mastitis-induced differential gene expression in the mammary tissue of Chinese Holstein cattle was investigated by Gene-Chip microarray and bioinformatics

overall_design: Our experiments included RNA samples was isolated from the mammary tissue of adult Chinese Holstein cows during late lactation with (n=3) and without (n=3) mastitis

first: Jie

last: Wu

first: Lian

last: Li

first: Yu

last: Sun

first: Shuai

last: Huang

first: Juan

last: Tang

first: Pan

last: Yu

first: Genlin

last: Wang


title: Intratumoral heterogeneity of colorectal cancers with distant metastases

status: Public on Jun 16 2014

first: Tae-Min

last: Kim

address: Seocho-Gu, Banpo-Dong

department: Dept of Medical Informatics

country: South Korea

institute: The Catholic University of Korea, College of Medicine

type: Genome variation profiling by genome tiling array

summary: Copy number analyses of regionally separated biopsies from primary and metastatic lesions of five colorectal cancers

overall_design: A total of 35 intratumoral biopsies were obtained from primary and metastatic lesions of five colorectal cancers. Board-certified pathologists reviewed the hematoxylin&eosin stained sections and identified tumor-rich regions (> 80% purity) to ensure minimal contamination of normal tissues.  We selected two to six different areas for biopsy that were at least 5mm apart in primary and distant metastatic lesions from a same patient.  Copy number profiling was performed using Agilent 180K platform according to the manufacturer's protocol. The genomic DNA obtained from the adjacent normal tissues were used as reference genomic DNA for the tumor DNA of the corresponding patients.

first: Yeun-Jun

last: Chung

first: Sug-Hyung

last: Lee


title: Microarray analysis indicates that vitamin A alters expression profiles of bovine intramuscular preadipocytes during adipogenesis

status: Public on Jul 08 2014

city: kawasaki

first: Daiki

last: Taniguchi

address: higashimita 1-1-1

country: Japan

institute: Meiji University

summary: Beef marbling is caused by intramuscular deposition, and it is an economically important trait in the beef industry. Vitamin A (VA) is an important feed supplement for cattle, but it can hinder marbling if provided in excess. In cattle, VA forms various derivatives such as all-trans retinoic acid (ATRA) and 9-cis retinoic acid (9cRA). Therefore, we investigated the genes involved in bovine intramuscular adipogenesis after VA treatment with ATRA and 9cRA. Differential gene expression levels were validated by microarray analysis in a clonal bovine intramuscular preadipocyte (BIP) cell line derived from the intramuscular adipose tissue of Japanese Black cattle. BIP cells were harvested six days after adipogenic stimulation with either 1 μM ATRA, 1 μM 9cRA, or nonretinoic acids control. The ATRA- and 9cRA-treated cells exhibited reduced transcription of genes involved in the circulatory system and muscle development compared with the no retinoic acid (RA) treatment. In addition, the ATRA- and 9cRA-treated cells exhibited increased transcription of genes involved in the immune system, protein kinase B signaling, and responses to various stimuli. These results demonstrate the lower expression of muscle development in ATRA- and 9cRA-treated BIP cells during adipogenesis.

overall_design: BIP cells were cultured according to previously reported methods (Aso et al. 1995, Mizoguchi et al. 2014). Confluent cultures were transferred to fresh Dulbecco’s modified Eagle’s medium, which contained 50 ng/mL insulin, 0.25 μM dexamethasone, 5 mM octanoate, 10 mM acetic acid, 10% fetal bovine serum, 100 U/mL penicillin, and 100 μg/mL streptomycin. The cells were cultured for up to 6 days and the medium was changed every 2 days. BIP cells were treated with ATRA (1 μM), 9cRA (1 μM), or they received no treatment (control).

first: Yasushi

last: Mizoguchi


title: The effects of arsenic on Silurana tropicalis embryos

status: Public on Jul 31 2014

city: Gainesville

first: Christopher

middle: Joseph

last: Martyniuk

state: FL

address: CEHT Mowry Road

department: Physiological Sciences

country: USA

institute: UF

summary: Arsenic is a carcinogenic metalloid element found naturally in the environment; however human activities such as mining and pesticide use have led to increased concentrations in some areas.  Silurana tropicalis eggs were exposed to sublethal concentrations  of sodium arsenate (0, 0.5 and 1 ppm) for 3 days during embryogenesis. Four pooled of 10 larvae were sampled per treatment and analyzed for gene expression changes using a microarray approach.

overall_design: Silurana tropicalis eggs were exposed to sublethal concentrations  of sodium arsenate (0, 0.5 and 1 ppm) for 3 days during embryogenesis. There were 5 controls, 5 low dose and 6 high dose microarrays perfomed.

first: Chris

first: Jennifer

last: Loughery

first: Valerie

last: Langlois


title: Transcriptome profiling of male gametophyte development in Nicotiana tabacum

status: Public on Oct 16 2014

city: Prague 6

first: David

last: Honys

state: CZ

address: Rozvojova 263

country: Czech Republic

institute: IEB ASCR

summary: Transcriptome profiling of three developmental stages of immature male gametophyte intobacco (Nicotiana tabacum)

overall_design: Total RNA isolated from tobacco microspores and early and late bicellular pollen was hybridised on Agilent Tobacco Gene Expression Microarray 4x44K in two biological replicates per sample

first: Pavel

last: Bokvaj


title: Gene expression-based, six individualized outcomes for cancer cells treated by TMEFF2 adenovirus and 2837 genes changes after treatment.

status: Public on Oct 01 2014

city: Shanghai

first: jingyuan

last: fang

address: 145 Shandong Rd Middle

institute: Shanghai Institute of Digestive Disease

summary: The genes expression changes after the adenovirus treatment for 36 hours

overall_design: In this study, the three control groups and three treatment groups were used to acquire expression profiles


title: The effect of ZnO and CuO nanoparticles on gene expression patterns in Daphnia magna

status: Public on Mar 01 2014

city: Antwerp

first: Nathalie

last: Adam

address: Groenenborgerlaan 171

department: Biology

country: Belgium

institute: University of Antwerp

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

overall_design: Refer to individual Series


title: The effect of ZnO nanoparticles on gene expression patterns in Daphnia magna

summary: There is still a lot of contradiction on whether metal ions are solely responsible for the observed the toxicity of ZnO and CuO nanoparticles to aquatic species. While most tests have studied nanoparticle effects at organismal levels (e.g. mortality, reproduction), effects at suborganismal levels may clarify the role of metal ions, nanoparticles and nanoparticle aggregates. In this study, the effect of ZnO, CuO nanoparticles and zinc, copper salts was tested on the gene expression levels in Daphnia magna. D. magna was exposed during 96 hours to 10% immobilization concentrations of all chemicals, after which daphnids were sampled for a differential gene expression analysis using microarray. When comparing the nanoparticle exposed daphnids (ZnO or CuO) to the metal salt exposed daphnids (zinc or copper salt), the microarray results showed no significantly differentially expressed genes. These results indicate that the toxicity of the tested ZnO and CuO nanoparticles to D. magna caused is solely caused by toxic metal ions.

overall_design: 4 replicate exposures of ZnO nanoparticles, ZnCl2, Blank (for Zn); 4 replicate exposures of CuO nanoparticles, CuCl2.2H2O, Blank (for Cu); Individual reference design with swapped dyes for zinc (e.g. ZnO-REFZn; REFZn-bl) and copper exposure (e.g. CuO-REFCu; REFCu-bl); Zinc reference sample is a mixture of equal aliquots of ZnO nanoparticle, ZnCl2 and blank; Copper reference sample is a mixture of equal aliquots of CuO nanoparticle, CuCl2.2H2O and blank

first: Lucia

last: Vergauwen

first: Ronny

last: Blust

first: Dries

last: Knapen


title: The effect of CuO nanoparticles on gene expression patterns in Daphnia magna


title: Profiling of genes related to cross protection and competition for NbTOM1 by HLSV and TMV

status: Public on May 12 2014

city: Singapore

first: Sek Man

last: WONG

state: Singapore

address: 14 Science Drive 4

department: Biological sciences

country: Singapore

institute: National University of Singapore

summary: To investigate the mechanism under the cross protection between HLSV and TMV, microarray analysis was conducted to examine the transcriptional levels of global host genes during cross protection, using Tobacco Gene Expression Microarray, 4x44k slides. The transcriptional level of some host genes corresponded to accumulation level of TMV. Some host genes were up-regulated only by HLSV.

overall_design: The gene expression in Nicotiana benthamiana during cross protection was measured at 12 days post HLSV or mock buffer inoculated as well as TMV infected N. benthamiana which pre-inoculated HLSV or mock bufer at 3 dpi (which is equal to 15 dpi by HLSV).

first: Yi

last: WEN

first: Sek-Man


title: IgMhigh vs IgMlow B cells from bovine leukemia virus-infected cattle

status: Public on Apr 01 2014

city: Sapporo

first: Ryoyo

last: Ikebuchi

state: Hokkaido

address: Kitaku Kita18jou Nishi9tyoume

department: Disease Control

institute: Graduate School of Veterinary Medicine, Hokkaido University

summary: Transcriptional profiling of blood B cells from bovine leukemia virus-infected cattle comparing IgMhigh B cells with IgMlow B cells. Goal was to estimate the difference of cellular function in both subset.

overall_design: Two-condition experiment, IgMhigh B cells vs. IgMlow B cells from three bovine leukemia virus-infected cattle.


title: Expression profiling of SMMC-7721 cells: stably express lncRNA-ATB vs pcDNA3.1

status: Public on Feb 08 2014

city: shanghai

first: shu-han

last: sun

address: 800 Xiang-Yin Road

institute: Second Military Medical University

summary: lncRNA-ATB induced transcriptional changes in SMMC-7721

overall_design: Two-condition experiment, control (pcDNA3.1) vs lncRNA-ATB expression (pcDNA3.1-ATB). Each has 3 biological repeats.

first: Ji-hang

last: Yuan

first: Shu-han

last: Sun


title: Silver Nanowire Exposure Results in Internalization and Toxicity to Daphnia magna

status: Public on Dec 31 2013

city: Gaithersburg

first: Leona

middle: Dance

last: Scanlan

state: MD

address: 100 Bureau Dr

institute: NIST

summary: Nanowires (NWs), high-aspect-ratio nanomaterials, are increasingly used in technological materials and consumer products and may have toxicological characteristics distinct from nanoparticles. We carried out a comprehensive evaluation of the physicochemical stability of four silver nanowires (AgNWs) of two sizes and coatings and their toxicity to Daphnia magna. Inorganic aluminum-doped silica coatings were less effective than organic poly(vinyl pyrrolidone) coatings at preventing silver oxidation or Ag+ release and underwent a significant morphological transformation within 1 h following addition to low ionic strength Daphnia growth media. All AgNWs were highly toxic to D. magna but less toxic than ionic silver. Toxicity varied as a function of AgNW dimension, coating, and solution chemistry. Ag+ release in the media could not account for observed AgNW toxicity. Single-particle inductively coupled plasma mass spectrometry distinguished and quantified dissolved and nanoparticulate silver in microliter-scale volumes of Daphnia magna hemolymph with a limit of detection of approximately 10 ppb. The silver levels within the hemolymph of Daphnia exposed to both Ag+ and AgNW met or exceeded the initial concentration in the growth medium, indicating effective accumulation during filter feeding. Silver-rich particles were the predominant form of silver in hemolymph following exposure to both AgNWs and Ag+. Scanning electron microscopy imaging of dried hemolymph found both AgNWs and silver precipitates that were not present in the AgNW stock or the growth medium. Both organic and inorganic coatings on the AgNW were transformed during ingestion or absorption. Pathway, gene ontology, and clustering analyses of gene expression response indicated effects of AgNWs distinct from ionic silver on Daphnia magna.

overall_design: Four replicates each of five toxicant exposure groups of ~20 animals and four replicates of control, unexposed animals. Each control was compared to each exposed data set for a total of 16 comparisons per chemical condition.

middle: D

first: Robert

middle: B

last: Reed

first: Alexandre

middle: V

last: Loguinov

first: Philipp

last: Antczak

first: Abderrahmane

last: Tagmount

first: Shaul

last: Aloni

first: Daniel

middle: T

last: Nowinski

first: Pauline

last: Luong

first: Christine

last: Tran

first: Nadeeka

last: Karunaratne

first: Don

last: Pham

first: Xin Xin

last: Lin

first: Francesco

last: Falciani

first: Christopher

middle: P

last: Higgins

first: James

middle: F

last: Ranville

last: Vulpe

first: Benjamin

last: Gilbert


title: The transcriptomic profile of peripheral blood nuclear cells in bovine and cervine in peak lactation and dry period

status: Public on Feb 11 2014

first: Magdalena

last: Łój

address: Nowoursynowska 166

department: Department of Physiological Sciences

institute: Warsaw University of Life Sciences

summary: The aim of the study was to identify genes which are differentially expressed in the peripheral blood nuclear cells of two breeds of cattle (Holstein-Friesian and Polish Red) and cervine in different points in their physiological states (dry-off period, peak of lactation)

sample_organism:
Cervus elaphus
Bos taurus

overall_design: RNA from peripheral blood nuclear cells taken from cattle and cervine in peak lactation and dry period were hybridized to Agilent two color microarrays with a common reference. There were four Holstein-Friesian cattle, four Polish Red cattle and four deer investigated. The whole blood was drawn in two time point from each animal – during dry period and peak lactation. This means that there were six research groups (Holstein-Friesian cattle in dry period and Holstein-Friesian cattle in peak lactation; Polish Red cattle in dry period and Polish Red cattle in peak lactation; Deer in dry period and Deer in peak lactation). Using Gene Spring Software (one-way ANOVA and Tukey's HSD Post-hoc test) three lists of differentially expressed transcripts were obtained: a list of 576 transcripts which differ deer in dry period and in peak lactation, a list of 437 transcripts which differ Holstein-Friesian cattle in dry period and in peak lactation and a list of 158 transcripts which differ Polish Red cattle in dry period and in peak lactation.

last: Hulanicka

first: Wlodzimierz

last: Klucinski

first: Joanna

last: Kolodziejska

first: Michal

last: Jank


title: Discovery of genes involved in facial midline specification

status: Public on Feb 28 2014

city: Vancouver

first: Joy

last: Richman

state: BC

address: 2350 Health Sciences Mall

department: Oral Health Sciences

country: Canada

institute: University of British Columbia

summary: The patterning of the facial midline involves early specification of neural crest cells to form skeletal tissues that support the upper jaw . In order to understand the molecular mechanisms involved  we have taken advantage of a beak duplication model developed in the chicken embryo. Here we can induce the transformation of the side of the beak into a second midline that is easily identifiable by the formation of a supernumerary egg tooth. The phenotype is induced by implanting two microscopic beads, one soaked in retinoic acid and the other soaked in Noggin into the side of the head of the chicken embryo.  Here we use microarrays to profile expression of maxillary mesenchyme 16h after placing the beads.  A subset of genes were validated using in situ hybridization and QPCR. The aims of the study are to test the function of these genes using retroviral transgenesis, knockdown with morpholinos or expression of secreted proteins and their application to the embryo.

overall_design: Embryos were incubated at 38 degrees C until they reached Hamburger Hamilton Stage 15 or 25 somites. Four different treatments were carried out consisting of two beads simultaneously implanted into the side of the head between the eye and mandibular arch. The beads were either Noggin+retinoic acid, Tris+retinoic acid, Noggin+DMSO or the control, Tris+DMSO. Embryos were reincubated for another 16h until they reached stage 18.  Embryos were dissected on ice in Hanks Buffered Salt Solution and batches of 12-15 maxillary pieces were snap frozen in liquid Nitrogen. These pooled facial prominences comprised one biological replicate. A total of three biological replicates were generated for each treatment.

middle: M

first: Marcela

last: Buchtová

first: Suresh

last: Nimmagadda


title: Expression profiling of SMMC-7721 cells: stably expressing lncRNA-hPVT1 vs LV-Control

status: Public on May 20 2014

first: shu-han

last: sun

summary: In our present study, we found that lncRNA-hPVT1 could promote HCC cell proliferation. We want to know what were the target genes of   lncRNA-hPVT1. So we constructed the hPVT1-overexpressed SMMC-771 cells and observed the mRNA profile in hPVT1-overexpressed and control SMMC-771 cells.

overall_design:
lncRNA-hPVT1 induced transcriptional changes in SMMC-7721.
Two-condition experiment, control (LV-Control) vs lncRNA-hPVT1 expression (LV-hPVT1 Clone2 ). Each has 3 biological repeats.

first: Fang

last: Wang

first: Shu-han

last: Sun


title: Comparison of stem/progenitor cell number and transcriptomic profile in mammary tissue of dairy and beef breed heifers

status: Public on Jun 16 2013

first: Zofia

last: Wicik

summary:
Bovine mammary stem cells (MaSC) are a source of ductal and lobulo-alveolar tissue during development of mammary gland and its remodeling in repeating lactation cycles. We hypothesize that the number of MaSC, their molecular properties and interactions with their niche may be essential to determine the mammogenic potential in heifers. To verify this hypothesis we compared the number of MaSC and transcriptomic profile in mammary tissue of 2-year-old, non-pregnant dairy (Holstein-Friesian) and beef (Limousin) heifers. For identification and quantification of putative stem/progenitor cells in mammary tissue sections scanning cytometry was used with a new combination of MaSC molecular markers: stem cell antigen-1 (Sca-1) and fibronectin type III domain containing 3B (FNDC3B) protein. Double labeled cells were located mainly in the basal layers of mammary epithelium. Cytometric analysis of Sca-1pos FNDC3Bpos cells revealed significantly higher number in HF (2.94±0.35%) than in LM (1.72±0.20%) heifers. More advanced development of mammary tissue in HF heifers was accompanied by higher expression of intramammary hormones, growth factors, cytokines, chemokines and transcription regulators. The model of transcriptomic niche favorable for MaSC was associated with regulation of genes involved in MaSC maintanence, self renewal, proliferation, migration, differentiation, mammary tissue remodeling, angiogenesis, regulation of adipocyte differentiation, lipid metabolism and steroid and insulin signaling. In conclusion the high mammogenic potential in postpubertal dairy heifers is facilitated by a higher number of MaSC and up-regulation of mammary auto-, paracrine factors representing MaSC niche.
Keywords: stem/progenitor cells, transcriptomics, mammary gland, dairy and beef heifers

overall_design: Two-condition experiment, HF vs. LIM. Pulled quarters of mammary glands form 10 LIM heifers (reference) and 10 HF heifers (test). Sample 3 and 4 are dye swaps.

first: Ewa

last: Osińska

first: Michał

last: Godlewski

first: Karol

last: Pawłowski

first: Alicja

last: Majewska

first: Tomasz

last: Motyl


title: Quantitative transcriptional changes associated with chlorosis severity in mosaic leaves of tobacco plants infected with the Cucumber mosaic virus

status: Public on Sep 15 2013

city: Sakai

first: Tomofumi

last: MOCHIZUKI

state: Osaka

address: 1-1, Gakuen-cho, Naka-ku

department: Graduate School of Life and Environmental Sciences

institute: Osaka Prefecture University

summary: In this study, we compared transcriptomes in chlorotic tissues infected with wild type CMV or two CP mutants (129A and 129Q) with diverse chlorosis severity. Differentially expressed genes analysis showed that the CMV inoculation appeared to have similar effects on transcriptional expression profiles of the symptomatic chlorotic tissues and only the magnitude of expression differed among CMVs. Gene ontology analysis with biological process and cellular component terms revealed that many nuclear genes related to abiotic stress responses, including cadmium, heat, cold, and salt, were up-regulated while chloroplast- and photosynthesis-related genes (CPRGs) were down-regulated in the chlorotic tissues. Interestingly, down-regulation level of CPRGs was correlated with the chlorosis severity.

overall_design: The expression difference genes (DEGs) between mock-inoculated healthy tissues and CMV-inoculated chlorotic tissues in mosaic leaves of tobacco plants were examined by the comparison on one-colour microarray data. Three biological replicates per each treatment were used in this experiment.

last: Mochizuki

first: Satoshi

last: Ohki


title: Drosophila CNS mitochondrial DNA dysfunction microarray

status: Public on Dec 20 2013

city: London

first: Ariana

middle: Pia

last: Gatt

address: London

country: United Kingdom

institute: King's College London

summary: Mitochondrial DNA (mtDNA) encodes essential components of the respiratory chain and loss of mtDNA leads to mitochondrial dysfunction and neurodegeneration. Mitochondrial transcription factor A (TFAM) is an essential component of mtDNA replication and a regulator of mitochondrial copy number in cells. Studies have shown that TFAM knockdown leads to mitochondrial dysfunction and respiratory chain deficiencies.  ATP synthase is Complex V of the mitochondrial respiratory chain. It is driven by a proton gradient between the intermembrane space and the mitochondrial matrix and generates the majority of cellular ATP. The knockdown of coupling factor 6 (Cf6), one of the components of the proton channel F0, causes dysfunction in the complex, leading to mitochondrial dysfunction and respiratory chain deficiencies. Using gene expression analysis, we aimed to investigate the effects of mtDNA dysfunction in the CNS at the molecular level.

overall_design: RNA was purified from the late third instar larval CNS from control larvae, or larvae over-expressing mitochondrial transcription factor A (TFAM) in post-mitotic neurons using the neuron specific driver nsyb-Gal4. Three replicates are included for each condition. RNA was purified from the late third instar larval CNS from control larvae, or larvae expressing ATP Cf6 RNAi in post-mitotic neurons using the neuron specific driver nsyb-Gal4.  Three replicates are included for each condition.

first: Joseph

last: Bateman


title: Compendium of deletion mutant gene expression profiles, 784 non-responsive mutants [hs1990]

status: Public on Apr 24 2014

city: Utrecht

first: Patrick

last: Kemmeren

state: Utrecht

address: Universiteitsweg 100

department: Department of Molecular Cancer Research

country: Netherlands

institute: UMC Utrecht

summary: This dataset consists of 784 non-responsive mutants (three or less significant mRNA expression changes as a result of the deletion) from a gene expression profile compendium of 1,484 deletion mutants that have a role or are implicated in mRNA transcription regulation, mRNA turnover, signaling or are located in the nucleus.

overall_design: Two channel microarrays were used. RNA isolated from a large amount of wt yeast from a single culture was used as a common reference. This common reference was used in one of the channels for each hybridization and used in the statistical analysis to obtain an average expression-profile for each deletion mutant relative to the wt. Two independent cultures were hybridized on two separate microarrays. For the first hybridization the Cy5 (red) labeled cRNA from the deletion mutant is hybridized together with the Cy3 (green) labeled cRNA from the common reference. For the replicate hybridization, the labels are swapped. Each gene is represented twice on the microarray, resulting in four measurements per mutant. Using the Erlenmeyer growth protocol up to five deletion strains were grown on a single day. In the tecan platereader, up to eleven deletion strains could be grown on a single day. Wt cultures were grown parallel to the deletion mutants to assess day-to-day variance.

first: Katrin

last: Sameith

first: Loes

last: van de Pasch

first: Frank

last: Holstege


title: Compendium of deletion mutant gene expression profiles, 700 responsive mutants [hs1991]

summary: This dataset consists of 700 responsive mutants (four or more significant mRNA expression changes as a result of the deletion) from a gene expression profile compendium of 1,484 deletion mutants that have a role or are implicated in mRNA transcription regulation, mRNA turnover, signaling or are located in the nucleus.


title: The genome expression profile of human umbilical vein endothelial cells (HUVECs) overexpressing miR-146a

status: Public on Apr 13 2013

first: Kai

last: Zhu

address: 136 Yi Xue Yuan Road

institute: liver cancer institute, Fudan University

summary: Endothelial cells are critical for angiogenesis, and microRNAs plays important roles in this process. We investigated the regulatory role of microRNAs in endothelial cells of hepatocellular carcinoma (HCC) by examining the microRNA expression profile of human umbilical vein endothelial cells (HUVECs) in the absence or presence of human HCC cells, and identified miR-146a as the most highly up-regulated microRNA. Furthermore, we revealed that miR-146a promoted the expression of platelet-derived growth factor receptor (PDGFRA) in HUVECs, and this process was mediated by BRCA1. Overexpression of PDGFRA in the ECs of HCC tissues was associated with microvascular invasion, and predicted a poorer prognosis. These results suggest that MiR-146a plays a key role in regulating the angiogenic activity of ECs in HCC through miR-146a-BRCA1-PDGFRA pathway. MiR-146a may emerge as a potential anti-angiogenic target on ECs for HCC therapy.

overall_design: We have employed whole genome OneArray to examine the genome expression changes of HUVECs overexpressing miR-146a.

first: Jian

last: Zhou


title: Gene regulation and priming by Topoisomerase IIα in embryonic stem cells [ChIP-chip]

status: Public on Oct 10 2013

city: Cambridge

first: Sudhir

last: Thakurela

address: 7 Divinity Avenue

institute: HSCRB

type: Genome binding/occupancy profiling by genome tiling array

summary: Topoisomerases are essential for resolving topological problems in the genome, while their function in gene regulation, especially during cellular differentiation, remains elusive/unknown. We reveal that the expression of two Topo II isoforms, Top2α and Top2β, is characteristic of dividing and postmitotic tissues, respectively. In embryonic stem cells, Top2α preferentially binds to promoters embedded in an active chromatin environment. Inhibition of Top2α activity results in misregulation of target gene expression that accompanies accumulation of double-strand breaks. Common targets of Top2α and Top2β are housekeeping genes while their unique targets are involved in proliferation/pluripotency and neurogenesis (Can we say this as this might be because we are driving neurons from ES cells), respectively. Moreover, a small subset of Top2α targets exhibit bivalent chromatin state that is resolved upon differentiation concomitant with their activation and occupancy by Top2β, a feature further observed for large lengthlong genes. These findings suggest that Top2α not only contributes to stem cell transcriptome regulation but may also prime developmental genes for subsequent activation by Top2β.

overall_design: Chromatin IP was performed with Top2α antibodies in WT ES cells and hybridized to custom designed tiling array.

first: Angela

last: Garding

first: Johannes

last: Jung

first: Lukas

last: Burger

first: Vijay

last: Tiwari


title: Compendium of deletion mutant gene expression profiles


title: The Lin28b-let-7-Hmga2 axis determines the higher self-renewal potential of fetal haematopoietic stem cells

status: Public on Jun 27 2013

first: Connie

last: Eaves

address: 675 West 10th Avenue

department: Terry Fox Laboratory

institute: BC Cancer Agency

summary: Mouse haematopoietic stem cells (HSCs) undergo a post-natal transition in several properties, including a marked reduction in their self-renewal activity. We now show that the developmentally timed change in this key function of HSCs is associated with their decreased expression of Lin28b and an accompanying increase in their let-7 microRNA levels. Lentivirus(LV)-mediated overexpression of Lin28 in adult HSCs elevates their self-renewal activity in transplanted irradiated hosts, as does overexpression of Hmga2, a well-established let-7 target that is upregulated in fetal HSCs. Conversely, HSCs from fetal Hmga2-/- mice do not display the heightened self-renewal activity that is characteristic of wild-type fetal HSCs. Interestingly, overexpression of Hmga2 in adult HSCs does not mimic the ability of elevated Lin28 to activate a fetal lymphoid differentiation program. Thus Lin28b may act as a master regulator of developmentally timed changes in HSC programs with Hmga2 serving as its specific downstream modulator of HSC self-renewal potential.

overall_design: Lin-Sca1+cKit+ cells were isolated from E14.5 fetal livers (of wild-type of Hmga2-/- embryos) or the bone marrow of 8-12 week old mice by fluorescence activated cell sorting. The RNA was extracted and hybridized on Affymetrix mpuse gene 1.0 ST microarrays.

first: Michael

middle: R

last: Copley

first: Sonja

last: Babovic

first: Claudia

last: Benz

first: David

middle: J

last: Knapp

first: Philip

middle: A

last: Beer

middle: G

last: Kent

first: Stefan

last: Wohrer

middle: Q

last: Treloar

first: Christopiher

last: Day

first: Keegan

last: Rowe

first: Heidi

last: Mader

first: Florian

last: Kuchenbauer

first: R

middle: K

last: Humphries


title: Analysis of  transcriptional response to mutated Potyvirus Potato virus A that induces necrotic symptoms.

status: Public on Mar 23 2013

city: Helsinki

first: Tuuli

last: Haikonen

address: Latokartanonkaari 7

department: Department of Agricultural Sciences

country: Finland

institute: University of Helsinki

summary: Mutations introduced to a highly variable region in HCpro reduced HCpro-HIP2 interactions and virulence of PVA, and induced novel types of necrotic symptoms in the systemically infected leaves of Nicotiana species. Microarray-based analysis of gene expression revealed induction of large numbers of defence-related genes including jasmonic acid and ethylene inducible pathways in the leaves systemically infected by the mutated PVA.

overall_design: Three treaments: infection with wild type PVA (WT), infection with mutated PVA (MUT), and mock-inoculation (Mock). Six plants were treated for each treatment. Experiment was repeated three times. WT and MUT samples from all three experiments were hybridised on microarray. Mock samples from experiments 1 and 2 were hybridised as healthy controls.

first: Minna-Liisa

last: Rajamaki

first: Yan-Ping

last: Tian

first: Jari

last: Valkonen


title: Medicago truncatula wild-type and mutant roots treated with symbiotic lipochitooligosaccharides

status: Public on May 31 2012

city: Hannover

first: Helge

last: Küster

address: Herrenhäuser Str. 2

department: Institut für Pflanzengenetik

country: Germany

institute: Leibniz Universität Hannover

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

platform_organism:
Sinorhizobium meliloti
Medicago sativa
Medicago truncatula

overall_design: Refer to individual Series

first: Natalija

last: Hohnjec

first: Lisa

last: Czaja

last: Hogekamp

first: Fabienne

last: Maillet

first: Jörg

last: Becker

first: Jean

last: Dénarié


title: Responses of Monocytes derived macrophages from TB-infected and TB-free cattles to in vitro M.bovis challenge

status: Public on Dec 31 2012

city: Beijing

first: Xiangmei

last: Zhou

address: No.2 Yuanmingyuan Xilu, Haidian District

department: College of Veterinary Medicine

institute: China Agricultural University

summary: Macrophages from cattles with different infectious status of bovine tuberculosis have different responses to in vitro Mycobacterium bovis challenge. This is confirmed in our previous study exploring several immune-related genes using qPCR. Microarrays can help us better understand the differences by screening thousands of genes.

overall_design: Monocytes Derived Macrophages from 3 TB-infected cattles and 3 TB-free cattles were challenged with Mycobacterium bovis at a MOI of 10 at 6 hours, and the control group were the same unchallenged macrophages at 6 hours.

first: Jingjun

last: Lin


title: Gene expression profiling for placentas from pre-eclamptic and normal pregnancies

status: Public on Feb 01 2013

first: qian

middle: Yu

last: Xiang

state: 上海市

address: Yixuanyuan road NO.138

institute: Fudan University

summary:
Investigation of whole genome gene expression level changes between placentas from pregnancies with PE and placentas from normal pregnancies to search for the candiadate genes for further DNA methylation analysis
The differentially expressed genes LEP and SH3PXD2A were further analyzed by DNA methylation.

overall_design: 5 placentas from pregnancies with PE and 7 from normal subjects were included in the gene expression microarray analysis.

first: Yuqian

first: Xinzhi

last: Zhao


title: Deletion mutant analysis of established glucose signaling and metabolic pathway members in Saccharomyces cerevisiae

status: Public on Jun 18 2012

first: Patrick

last: Kemmeren

summary: To understand the organisation of the glucose regulatory system, we analysed 91 deletion mutants of established glucose signalling and metabolic pathway members in Saccharomyces cerevisiae by DNA microarrays. These deletion mutants do not induce pathway-specific transcriptional responses reflecting the tight interconnection between pathways of the glucose regulatory system. Instead, one main transcriptional response is discerned, which varies in direction to mimic either a high or a low glucose response. The study reveals both known and unknown relationships within and between individual pathways and their members. Metabolic components of the glucose regulatory system are most frequently affected at the transcriptional level. A new network approach is applied that exposes the hierarchical organisation of the glucose regulatory system. Tps2 and Tsl1, two enzymes involved in trehalose biosynthesis, are predicted to be the most downstream transcriptional components. This prediction is further validated by epistasis analysis of Tps2 double mutants. Taken together, this suggests that changes in perceived glucose levels ultimately lead to a shift in trehalose biosynthesis.

overall_design: RNA isolated from a large amount of wt yeast from a single culture was used as a common reference. This common reference was used for each separate hybridization and used in the statistical analysis to obtain an average expression-profile for each deletion mutant relative to the wt. Two independent cultures were hybridized on two separate microarrays. For the first hybridization the Cy5 (red) labeled cRNA from the deletion mutant is hybridized together with the Cy3 (green) labeled cRNA from the common reference. For the replicate hybridization, the labels are swapped. Each gene is represented twice on the microarray, resulting in four measurements per mutant. Up to five deletion strains were grown on a single day. Wt cultures were grown parallel to the deletion mutants to assess day-to-day variance.

first: Eva

last: Apweiler

first: Katrin

last: Sameith

first: Thanasis

last: Margaritis

first: Nathalie

last: Brabers

first: Loes

last: van de Pasch

first: Linda

last: Bakker

first: Dik

last: van Leenen

first: Frank

last: Holstege


title: Glucose signaling


title: Gene expression response in roots of Medicago truncatula mutants treated with Myc LCOs

first: Helge

last: Küster

summary:
Legumes interact with soil fungi, leading to the development of arbuscular mycorrhizal (AM) roots. Diffusible AM fungal signals were identified as sulphated and non-sulphated LCOs (sMyc-LCOs and nsMyc-LCOs).
Applying Myc-LCOs on roots of symbiotic mutants, we used GeneChips to detail the global programme of gene expression in these mutants in response to the external application of Myc-LCOs.

overall_design: To harvest tissues for transcriptome profiling, three biological replicates consisting of 10 plantlets per treatment were selected. After 6 h of incubation in the climate chamber, 10 plantlets per batch were removed from the treatment (Myc-LCOs) or control solutions and harvested. During harvest, one mm of the root tip of each plantlet was removed and discarded. The remaining 2 to 2.5 cm of the distal root region were cut off and directly frozen in liquid nitrogen.

first: Natalija

last: Hohnjec

first: Lisa

last: Czaja

first: Claudia

last: Hogekamp

first: Fabienne


title: Transcriptome of tobacco leaves in different environmental conditions

status: Public on Feb 23 2012

city: Beibei

first: Kun

last: Lu

state: Chongqing

address: 2 Tiansheng Road

department: College of Agronomy and Biotechnology

institute: Southwest University

summary:
Comparative analysis of tobacco leaves transcriptomes unveils carotenoid pathway potentially determined the characteristics of aroma compounds in different environmental regions. Tobacco (Nicotiana tabacum) is a sensitive crop to environmental changes, and a tobacco with unique volatile aroma fractions always formed in specific ecological conditions.
In order to investigate the differential expressed genes caused by environmental changes and reveal the formation mechanism of characteristics of tobacco in three different aroma tobacco regions of Guizhou Province, Agilent tobacco microarray was adapted for transcriptome comparison of tobacco leaves in medium aroma tobacco region Kaiyang and light aroma tobacco regions Weining and Tianzhu.
Results showed that there was big difference among the gene expression profiles of tobacco leaves in different environmental conditions. A total of 517 differential expressed genes (DEGs) between Weining and Tianzhu were identified, while 733 and 1,005 genes differentially expressed between Longgang and another two tobacco regions Weining and Tianzhu, respectively. Compared with Longgang, up-regulated genes in Weining and Tianzhu were likely involved in secondary metabolism pathways, especially carotenoid pathway, including PHYTOENE SYNTHASE, PHYTOENE DEHYDROGENASE, LYCOPENE ε-CYCLASE, CAROTENOID β-HYDROXYLASE and CAROTENOID CLEAVAGE DIOXYGENASE 1 genes, while most down-regulated genes played important roles in response to temperature and light radiation, such as heat shock proteins. Gene Ontology and MapMan analyses demonstrated that the DEGs among different environmental regions were significantly enriched in light reaction of photosystem II, response of stimulus and secondary metabolism, suggesting they played crucial roles in environmental adaptation and accumulation of aroma compounds in tobacco plants.
Through comprehensive transcriptome comparison, we not only identified several stress response genes in tobacco leaves from different environmental regions but also highlighted the importance of carotenoid pathway genes for characteristics of aroma compounds in specific growing regions. Our study primarily laid the foundation for further understanding the molecular mechanism of environmental adaptation of tobacco plants and molecular regulation of aroma substances in tobacco leaves.

first: Fu-Zhang

last: Ding

first: Wei

last: Ren

first: Yi

last: Chen

first: Zhu

first: Hui-Na

first: Xiao-Rong

last: Liu

first: Wen-Jie

last: Pan

first: Hong-Xun

last: Li

first: Bo

last: Lei


title: Gene expression response of Medicago truncatula roots treated with symbiotic lipochitooligosaccharides (LCOs)

summary:
Legumes interact with soil microbes, leading to the development of nitrogen-fixing root nodules and arbuscular mycorrhizal (AM) roots. While nodule initiation by diffusible lipochitooligosaccharide (LCO) Nod-factors of bacterial origin (Nod-LCOs) is well characterized, diffusible AM fungal signals were only recently identified as sulphated and non-sulphated LCOs (sMyc-LCOs and nsMyc-LCOs).
Applying Myc-LCOs in parallel to Nod-LCOs, we used GeneChips to detail the global programme of gene expression in response to the external application of symbiotic LCOs.

overall_design: To harvest tissues for transcriptome profiling, three biological replicates consisting of 20 plantlets per treatment were selected. After 6 h of incubation in the climate chamber, 10 plantlets per batch were removed from the treatment (Myc-LCOs or Nod-LCOs) or control solutions and harvested, while the other 10 remained in the respective solutions for a total of 24 h. During harvest, one mm of the root tip of each plantlet was removed and discarded. The remaining 2 to 2.5 cm of the distal root region were cut off and directly frozen in liquid nitrogen.

last: Maillet

first: Jörg

last: Becker

first: Jean

last: Dénarié


title: BW001: E2F7 represses a network of oscillating cell cycle genes to control S-phase progression

status: Public on May 01 2012

first: Marian

last: Groot Koerkamp

address: Heidelberglaan 25

department: Research

institute: Princess Maxima Center for Pediatric Oncology

summary: E2F transcription factors are known to be important for timely activation of G1/S and G2/M genes required for cell cycle progression, but transcriptional mechanisms for deactivation of cell cycle-regulated genes are unknown. Here, we show that E2F7 is highly expressed during mid to late S-phase, occupies promoters of G1/S-regulated genes and represses their transcription. ChIP-seq analysis revealed that E2F7 binds preferentially to genomic sites containing the TTCCCGCC motif, which closely resemble the E2F consensus site. We identified 89 target genes that carry E2F7 binding sites close to the transcriptional start site and that are directly repressed by short term induction of E2F7. Most of these target genes are known to be activated by E2Fs and are involved in DNA replication, metabolism and DNA repair. Importantly, induction of E2F7 during G0-G1/S resulted in S-phase arrest and DNA damage, whereas expression of E2F7 during G2/M failed to disturb cell cycle progression. These findings provide strong evidence that E2F7 directly controls the downswing of oscillating G1/S genes during S-phase progression.

overall_design: Overexpression of E2F7 was studied in a doxycyclin-inducable system. Four cellcultures were treated with and without doxycyclin and RNA was isolated to run direct comparisons on a 2-channel human expression microarray.

first: Bart

last: Westendorp

first: Michal

last: Mokry

first: Frank

first: Edwin

last: Cuppen

first: Alain

last: de Bruin


title: Top2β ChIP-chip

status: Public on May 02 2012

city: Basel

first: Dirk

last: Schuebeler

address: Fabrikstrasse 24

country: Switzerland

institute: Friedrich Miescher Institute for Biomedical Research

summary: Chromatin IP was performed with Top2β antibodies in WT neurons and hybridized to custom designed tiling array.

overall_design: HD 2.1 (custom- made)

first: Vijay

last: Tiwari

first: Lukas

last: Burger


title: Transcriptomic response of the Pacific oyster Crassostrea gigas to hypoxia

status: Public on Sep 01 2010

city: Nantes

first: Rossana

last: Sussarellu

address: Rue de l'Ile d'Yeu

department: Ressources Biologiques et Environnement

country: France

institute: Ifremer

summary: Marine intertidal organisms commonly face hypoxic stress during low tide emersion; moreover, eutrophic conditions and sediment nearness could lead to hypoxic phenomena; it is indeed important to understand the molecular processes involved in the response to hypoxia. In this study the molecular response of the Pacific oyster Crassostrea gigas to prolonged hypoxia (2 mg O2 L-1 for 20 d) was investigated under experimental conditions. A transcriptomic approach was employed using a cDNA microarray of 9058 C. gigas clones to highlight the genetic expression patterns of the Pacific oyster under hypoxic conditions. Lines of oysters resistant (R) and susceptible (S) to summer mortality were used in this study. This is the first study employing microarrays to characterize the genetic markers and metabolic pathways responding to hypoxic stress in C. gigas.

overall_design: For the microarray analysis oysters were sampled at days 0, 2, 10, and 20 after the beginning of hypoxia. On each date, the digestive gland from 6 oysters was dissected, pooled, and stored at -80°C in Extract-All Reagent (Eurobio) at a concentration of 1 mL/50 mg tissue until total RNA was extracted. For each condition (hypoxia and normoxia) and oyster line (R and S), 4 pools were sampled (biological replicates) for a total of 56 pools during the 4 days of sampling. Furthermore, the entire tissue from 10 wild oysters was collected, pooled, and homogenized in Extract-all Reagent (Eurobio) to constitute a single total RNA sample to use as a reference in all slide hybridizations and Real-Time PCR analyses. Five μg of total RNA were directly labeled by reverse transcription using the Direct ChipShot Direct Labeling and Clean-Up Kit (Promega). The samples were labeled with Cyanine-5 (Cy5). The reference samples were labeled with Cyanine-3 (Cy3) in separate tubes following the same protocol. The Cy3-labeled cDNAs were pooled and re-divided to obtain a homogeneous reference sample. cDNA samples and references were evaporated in a SpeedVac and mixed into a single pool in equimolar amounts with the Chip Hybe hybridization buffer (Ventana Discovery). Hybridization was performed using a Ventana automatic hybridization station (Ventana Discovery).

first: Caroline

last: Fabioux

first: Gilles

last: Le Moullac

first: Elodie

last: Fleury

first: Dario

last: Moraga


title: Gene deletion expression profiles of yeast chromatin modifiers

status: Public on May 23 2011

first: Patrick

last: Kemmeren

summary: Packaging of DNA into chromatin has a profound impact on gene expression. To understand how changes in chromatin influence transcription, we analyzed 165 mutants of chromatin machinery components in Saccharomyces cerevisiae. mRNA expression patterns change in 80% of mutants, always with specific effects, even for loss of widespread histone marks. This results in the first network of chromatin interaction pathways. The network is function-based, has a branched, interconnected topology and lacks strict one-to-one relationships between complexes. Chromatin pathways are not separate entities for different gene sets, but share many components. The study evaluates which interactions are rate-limiting for which genes and predicts new interactions, for example between Paf1C and Set3C, as well as a role for Mediator in subtelomeric silencing. The results indicate the presence of gene-dependent effects that go beyond context-dependent binding of chromatin factors and provide a framework for understanding how specificity is achieved through regulating chromatin.

first: Tineke

last: Lenstra

first: Joris

last: Benschop

first: TaeSoo

last: Kim

first: Julia

last: Schulze

first: Nathalie

last: Brabers

first: Thanasis

last: Margaritis

first: Loes

last: van der Pasch

first: Sebasitaan

last: van Heesch

first: Cheuk

last: Ko

first: Dik

last: van Leenen

first: katrin

last: Sameith

first: Sander

last: van Hooff

first: Philip

last: Lijnzaad

first: Thomas

last: Hentrich

first: Michael

last: Kobor

first: Stephen

last: Buratowski

last: Holstege


title: Microarray Analysis of Differentially Expressed Genes in Placental Tissue of Severe Preeclampsia

status: Public on Apr 25 2006

city: Toyoake

first: Haruki

last: Nishizawa

state: Aichi

address: 1-98 Dengakugakubo Kutsukake-cho

department: Gynecology & Obstetrics

institute: Fujita Health University

summary:
Pre-eclampsia is one of the most serious pregnancy-associated disorders, and is defined by hypertension (systolic blood pressure higher than 140mmHg or diastolic blood pressure higher than 90mmHg) with proteinuria (more than 0.3g/day). It is not a simple complication of pregnancy, but is rather a syndrome of multiple organ failure involving the liver, kidney, and lung, as well as coagulatory and neural systems. There is now an emerging consensus that pre-eclampsia is a complex polygenetic trait in which maternal and fetal genes, as well as environmental factors, are involved, although the precise mechanism of the disorder has remained elusive. In this study, we have performed gene expression profiling to further elucidate the mechanisms underlying the development of the pre-eclamptic condition. We thus compared the expression profiles in placentas from women who underwent a normal pregnancy and from women suffering from severe pre-eclampsia. In addition, we compared the expression data between the early and late onset forms of pre-eclampsia and obtained a number of potential new prognostic biomarkers for this disease.
Keywords: disease state analysis

overall_design: Placental biopsies were obtained during Caesarean section from both normotensive patients and from those with pre-eclampsia (n = 14) (early onset type; earlier than 31 weeks gestation, n = 6 and late onset type; 31 weeks gestation or later, n = 8). Pre-eclampsia was defined as a blood pressure of higher than 160/110 mmHg, with proteinuria of more than 2g in a 24 hour collection. The expression profiles of approximately 47,669 genes were analyzed using a Whole Human Genome Oligo Microarray Kit (Agilent Technologies). A total of 10 placentas from women with pre-eclampsia and four from normal subjects were used in the hybridizations. Reverse transcription labeling and hybridization was performed using the protocol recommended by the manufacturer. The microarray experiments were then carried out using competitive hybridization experiments with Cy3 and Cy5-labeled targets; one with test placental RNAs from patients or normal control subjects, and another using pooled normal placental RNA as a template control for normalization. The glass slides were scanned using an Agilent G2565BA microarray scanner. Scanned images were then analyzed using Feature Extraction software. The average signal intensities were corrected for median background intensity and transferred with GenBank descriptors to a Microsoft Excel data spreadsheet (Microsoft, Redmond, WA). Data analysis was performed using Genespring software version 6.1 (Silicon Genetics, Redwood City, CA). After intensity dependent normalization (Lowess), the expression levels relative to the control were calculated as a ratio, and the expression profiles were then compared between each pre-eclamptic or normal sample.


title: Evaluation of auto-antibody serum biomarkers for breast cancer screening

status: Public on Dec 21 2011

city: Vienna

first: Parvez

last: Syed

address: Muthgasse 11

country: Austria

institute: Austrian Institution of Technology

summary: Using protein microarrays, derived from 642 His-tag proteins, we could distinguish sera from breast-nodule positive patients and healthy control individuals.

overall_design: Each Protein microarray was divided in to 4 sub-arrays. Each protein was spotted in duplicates in each sub-array. For evaluation 24 malignant, 16 benign breast cancer serum samples and 20 healthy control serum samples were used.

first: Andreas

last: Weinhäusel


title: Gene expression profiles following GR24, smoke water and KAR1 treatments in Nicotiana benthamiana seedlings

status: Public on Feb 25 2010

city: Stellenbosch

first: Paul

last: Hills

state: Western Cape

address: Natural Sciences Building, Merriman Avenue

department: Genetics

country: South Africa

institute: Stelllenbosch University

summary: GR24, a synthetic strigolactone, and KAR1, the main bioactive compound in smoke water, both share a common α,β unsaturated furanone moiety which promotes biomass accumulation in three week old N. benthamiana seedlings. In order to investigate whether this D ring is responsible for the biomass accumulation, gene expression profiles were evaluated for co-expression on the Agilent 44k N. tabacum microarray. GR24, smoke and KAR1 induced different transcripts, and suggests that they trigger independent growth responses.

overall_design: Control (untreated), GR24 (10-7M), smoke water (1:1000 dilution) and butenolide (10-7M) gene expression profiles were evaluated on three week old seedlings, in two independent experimental trials.

first: Liske

last: Kotze

first: Margaretha

last: Van Der Merwe

first: Stephanus

last: Ferreira

first: Letitia

middle: E

last: Steenkamp

first: Marnie

last: Light

first: Johannes

last: Van Staden

first: Uwe

last: Sonnewald

middle: N

first: Jens

last: Kossmann


title: Transcriptome analysis of Aspergillus fumigatus delta crzA mutant upon 10 and 30 minutes treatment with CaCl2 (200 mM)

status: Public on Apr 02 2009

city: Ribeirao Preto

first: Gustavo

middle: Henrique

last: Goldman

state: Sao Paulo

address: Avenida do Café, s/n

department: Departament of Pharmaceutical Sciences

country: Brazil

institute: Faculty of Pharmaceutical Sciences of Ribeirao Preto

summary:
CRZ is a C2H2 zinc finger transcription factor activated by calcineurin, a protein phosphatase activated by calcium-calmodulin, in different stress conditions related with calcium cell accumulation. CRZ binds to a specific element on the promoter region of genes called CDRE (calcineurin-dependent response element) shown to be sufficient for calcium- and calcineurin-dependent gene expression. In order to investigate which pathways are involved under calcium stress conditions, we determined the transcriptional profile of A. fumigatus delta crzA mutant strain upon a time course 200 mM calcium chloride treatment. Conidia from the mutant and wild type strains were incubated at 37°C in complete medium for 16 hours and were challenged with 200 mM calcium chloride for 10 and 30 minutes. At each time point, the mycelia were harvested by centrifugation and used for competitive microarray hybridizations. We were able to observe a decreased mRNA expression of genes encoding inorganic ion transport proteins and lipid transport. In contrast, increased mRNA expression was observed for several genes involved in transcription, energy production and conversion, cell cycle control, cell division, chromosome partitioning, amino acid, lipid and carbohydrate transport and metabolism, nucleotide transport, cell wall and membrane biogenesis, posttranslation modifications, protein turnover, chaperones, inorganic ion transport, signal transduction mechanisms, intracellular trafficking, secretion and vesicular transport.
Keywords: gene expression array-based (log2 ratio)

overall_design:
For the time course microarray experiments, 5.0 x 108 conidia of A. fumigatus wild type [CEA17 delta akuB(KU80)] and delta crzA strains were inoculated in 300 ml of pre-warmed liquid cultures (YG) in 500-mL erlenmeyer flasks and allowed to grow for 16 hours in a reciprocal shaker (250 rpm) at 37°C. After this time, the cultures were added by calcium chloride (200 mM) and incubated for 10 and 30 more minutes before mycelia recovery and RNA extraction. Hybridization experiments were competitive using probes derived from calcium chloride shock cultures using the wild type strain exposed to calcium (10 or 30 minutes)  as the reference RNA for every hybridizantion. Normalized signal intensities were used to generate relative hybridization ratios (query/reference).

Following normalization, the values for each gene's in-slide replicates were averaged (median variance <0.01), and corresponding flip-dye replicates were averaged to compensate for dye-specific effects. These final, processed data are linked below as supplementary files.

first: Frederico

last: Soriani

first: Iran

last: Malavazi

middle: H


title: Consequences of conceptus exposure to colony stimulating factor 2 on survival, elongation, interferon-{tau} secretion and gene expression

status: Public on Dec 15 2011

city: Gainesville

first: Peter

last: Hansen

state: Florida

address: L.E. "Red" Larson Professor  Dept. of Animal Sciences  University of Florida

department: Animal Sciences

institute: University of Florida

summary: Exposure of bovine conceptuses to colony stimulating factor 2 (CSF2) from Day 5 to 7 of development can increase the percent of transferred conceptuses that develop to term. The purpose of this experiment was to understand the mechanism by which CSF2 increases embryonic and fetal survival. Conceptuses were produced in vitro in the presence or absence of 10 ng/ml CSF2 from Day 5 to 7 after insemination, transferred into cows, and flushed from the uterus at Day 15 of pregnancy. There was a tendency (P=0.07) for the proportion of cows with a recovered conceptus to be greater for those receiving a CSF2 treated conceptus (35% for control vs. 66% for CSF2).  Antiviral activity in uterine flushings, a measure of the amount of interferon-{tau} (IFNT2) secreted by the conceptus, tended to be greater for cows receiving CSF2-treated conceptuses than for cows receiving control conceptuses. This difference approached significance when only cows with detectable antiviral activity were considered (P=0.07).  In addition, CSF2 increased mRNA for IFNT2 (P=0.06) and keratin 18 (P<0.05) in extraembryonic membranes.  Among a subset of filamentous conceptuses that were analyzed by microarray hybridization, there was no effect of CSF2 on gene expression in the embryonic disc or extraembryonic membranes.  Results suggest that the increase in calving rate caused by CSF2 treatment involves, in part, more extensive development of extraembryonic membranes and capacity of the conceptus to secrete IFNT2 at Day 15 of pregnancy.

overall_design: Experimental conditions: CSF2 treated vs. CSF2 nontreated bovine in vitro produced preimplantation embryos were tranfered to a receptor cow and recovered at Day 15 of embryo development. The embryonic disc (ED) and the trophectoderm (Tr) were used for the expression analysis separately.  Biological replicates: CSF2 treated vs. nontreated bovine preimplantation embryos were used in a dye switch two-color microarray experimental design.

first: Barbara

last: Loureiro


title: Pseudomonas aeruginosa gene expression in artificial sputum medium using a broad capture array designated the PANarray

status: Public on Jul 16 2011

city: Sydney

first: Jim

last: Manos

state: NSW

address: Camperdown

country: Australia

institute: University of Sydney

summary: The PANarray design (GPL13324) contains the genes of eight P. aeruginosa genomes in non-redundant format, thus allowing identification of expression of non-PAO1 and other P. aeruginosa genes.

platform_organism:
Pseudomonas aeruginosa UCBPP-PA14
Pseudomonas aeruginosa PAO1
Pseudomonas aeruginosa 2192
Pseudomonas aeruginosa C3719
Pseudomonas paraeruginosa PA7
Pseudomonas aeruginosa PACS2
Pseudomonas aeruginosa LESB58
Pseudomonas aeruginosa AES-1R

overall_design: For the series GSE28152, isogenic isolates were sequentially collected from two cystic fibrosis (CF) patients several years apart. The isolates had not been eradicated in the meantime and represent persister strains. One was an Australian Epidemic Strain-1 isolate and the other a non-epidemic strain. Strains were cultured in an artificial sputum medium (ASMDM) closely resembling CF sputum.

first: Torsten

last: Seemann

first: Cynthia

last: Whitchurch

first: Dane

last: Parker

first: Sharna

last: Naughton

first: Lynne

last: Turnbull

last: Rose


title: Autoantibody Epitope Spreading in the Pre-Clinical Phase Predicts Progression to Rheumatoid Arthritis [ANALYTE: ANTIGEN]

status: Public on Sep 10 2011

city: Stanford

first: William

last: Robinson

state: CA

address: 269 Campus Dr

institute: Stanford University

summary: Rheumatoid arthritis is a prototypical autoimmune arthritis affecting nearly 1% of the world population and is a significant cause of worldwide disability. Though prior studies have demonstrated the appearance of RA-related autoantibodies years before the onset of clinical RA, the pattern of immunologic events preceding the development of RA remains unclear. To characterize the evolution of the autoantibody response in the preclinical phase of RA, we used a novel multiplex autoantigen array to evaluate development of the anti-citrullinated protein antibodies (ACPA) and to determine if epitope spread correlates with rise in serum cytokines and imminent onset of clinical RA. To do so, we utilized a cohort of 81 patients with clinical RA for whom stored serum was available from 1-12 years prior to disease onset. We evaluated the accumulation of ACPA subtypes over time and correlated this accumulation with elevations in serum cytokines. We then used logistic regression to identify a profile of biomarkers which predicts the imminent onset of clinical RA (defined as within 2 years of testing). We observed a time-dependent expansion of ACPA specificity with the number of ACPA subtypes. At the earliest timepoints, we found autoantibodies targeting several innate immune ligands including citrullinated histones, fibrinogen, and biglycan, thus providing insights into the earliest autoantigen targets and potential mechanisms underlying the onset and development of autoimmunity in RA. Additionally, expansion of the ACPA response strongly predicted elevations in many inflammatory cytokines including TNF-α, IL-6, IL-12p70, and IFN-γ. Thus, we observe that the preclinical phase of RA is characterized by an accumulation of multiple autoantibody specificities reflecting the process of epitope spread. Epitope expansion is closely correlated with the appearance of preclinical inflammation, and we identify a biomarker profile including autoantibodies and cytokines which predicts the imminent onset of clinical arthritis.

overall_design: A total of 559 human sera were profiled using a custom made panel of putative rheumatoid arthritis associated autoantigens. The cohort was comprised of 79 patients with clinical RA for whom stored serum was available from 1-10 years prior to disease onset and 80 control subjects without RA that were matched to cases based on age, gender, race, region of assignment, and time of serum sampling.

first: Jeremy

last: Sokolove

first: Reuven

last: Bromberg

first: Ryan

last: Tibshirani

first: Kevin

middle: D

last: Deane

first: Lauren

last: Lahey

first: Lezlie

last: Derber

first: Piyanka

last: Chandra

first: Jess

last: Edison

last: Gilliland

first: Robert

first: Jill

last: Norris

first: V

last: Holers


title: Comparative transcriptomic responses to compatible and incompatible plant-virus interactions that lead to cell death

status: Public on Feb 02 2012

city: Madrid

first: Francisco

last: Tenllado

state: Madrid

address: Ramiro de Maeztu, 9

department: Plant Biology

country: Spain

institute: Centro de Investigaciones Biológicas, CSIC

summary: Hypersensitive response-related programmed cell death (PCD) has been extensively analyzed in various plant–virus interactions. However, little is known about changes in gene expression associated with cell death caused by compatible viruses. The synergistic interaction of Potato virus X (PVX) with Plum pox virus (PPV) results in increased symptoms that lead to systemic necrosis (SN) in Nicotiana benthamiana. Here, we performed three transcriptome comparisons in response to i) a PVX recombinant virus expressing the helper component-proteinase (HC-Pro) gene from PPV that leads to SN, ii) a systemic incompatible interaction conferred by the Tobacco mosaic virus (TMV)-resistance gene N (SHR), and iii) the depletion of the PBE subunit of the proteasome that leads to PCD by virus induced gene silencing (VIGS Prot), at early and late stages of infection. Our analysis indicated that the SN response was clustered with SHR by the similarity of their overall gene expression profiles. However, the expression profiles of defence-related and hormone-responsive genes in response to SN were more closely related to the response to VIGS Prot than to that elicited by SHR. This suggests the potential contribution of proteasome dysfunction to the increase in pathogenicity observed in PVX-potyvirus infections

overall_design: We compare the gene expression profiles of Nicotiana benthamiana plants infected with either necrosis-inducing viruses or non-necrosis-inducing viruses, as follow: PVX/HCWT-infected plants versus plants infected with a PVX recombinant virus expressing a PPV HC-Pro mutant (PVX/HCLH) that was unable to induce the SN response (SN comparison), at 7 and 11 days postinoculation (dpi), (ii) TRV:NbPBE-silenced plants versus plants infected with the TRV empty vector (VIGS Prot comparison), at 4 and 8 days after infiltration (dpa), and (iii) TMV-GFP-infected, N-transgenic plants versus wild-type plants infected with TMV-GFP (SHR comparison), at 24 and 72 hours after temperature shift (hts). Per time and treatment, three independent biological replicates were used to monitor differences in gene expression between treatments

first: Remedios

last: Pacheco

first: Alberto

last: García-Marcos

first: Aranzazu

last: Manzano

first: Mario

last: García de Lacoba

first: Gemma

last: Camañes

first: Pilar

last: García-Agustín

first: José

last: Ramón Díaz-Ruíz


title: Transcriptional Profiling of Human Placentas from Pregnancies Complicated by Preeclampsia Reveals Disregulation of Sialic Acid Acetylesterase and Immune Signaling Pathways

status: Public on Dec 10 2010

city: Raleigh

first: Shengdar

last: Tsai

state: NC

address: 4700 Hillsborough St.

institute: North Carolina State University

summary: The placenta plays an important role as a regulator of fetal nutrition and growth throughout development and placental factors contribute to gestational abnormalities such as preeclampsia. This study describes the genome-wide gene expression profiles of a large (n=60) set of human placentas in order to uncover gene expression patterns associated with preeclampsia.  In addition to confirming changes in expression of soluble factors associated with preeclampsia such as sFLT1 (soluble fms-like tyrosine kinase-1), sENG (soluble endoglin), and INHA (inhibin alpha), we also find changes in immune-associated signaling pathways, offering a potential upstream explanation for the shallow trophoblast invasion and inadequate uterine remodeling typically observed in pathogenesis of preeclampsia.  Notably, we also find evidence of preeclampsia-associated placental upregulation of sialic acid acetylesterase (SIAE), a gene functionally associated with autoimmune diseases.

overall_design: 23 preeclamptic, and 37 control placentas included in this study were collected during the years of 2004-2008 and hybridized in two batches to microarrays.  Samples were randomized across arrays to control for array and batch variability.

first: Nicholas

last: Hardison

first: Andra

last: James

first: Alison

last: Motsinger-Reif

first: Steve

last: Bischoff

first: Betty

last: Thames

first: Jorge

last: Piedrahita