title: Transcriptome-wide identification of novel UV-B- and light modulated flavonol pathway genes controlled by VviMYBF1

status: Public on Jul 24 2017

city: Tuebingen

first: Stefan

last: Czemmel

address: Auf der Morgenstelle 10

department: University of Tuebingen

country: Germany

institute: Quantitative Biology Center (QBiC)

summary: Flavonols constitute a group of flavonoids with important photoprotective roles in plants. In addition, flavonol content and composition greatly influences fruit quality. We previously demonstrated that the grapevine R2R3-MYB transcription factor VviMYBF1 promotes flavonol accumulation by inducing the expression of flavonol synthase (VviFLS1/VviFLS4), a key step of the initial flavonol pathway. Despite this, gene networks underlying flavonol modification in grapevine including both structural and regulatory genes remain poorly understood. In order to identify flavonol modifying genes and transcription factors acting downstream of VviMYBF1 a microarray-based transcriptome analysis was performed on grapevine hairy roots ectopically expressing VviMYBF1 or a Green Fluorescent Protein as control. VviFLS1 was induced in VviMYBF1 transgenic roots and flavonols, mainly quercetin 3-glucoside and quercetin 3-galactoside, accumulated significantly compared with control lines. Among the differentially expressed genes, potential flavonol-modifying enzymes with predicted rhamnosyltransferase (e.g. RhaT1) or glycosyltransferase (e.g. GT3) activities were identified. In addition, important transcription factors of the MYB and bZIP families such as the proanthocyanidin regulator VviMYBPA1 and the UV-B light responsive HY5 homologue VviHYH were significantly altered in their expression pattern by overexpression of VviMYBF1. In silico promoter sequence analysis confirmed that the significantly differentially expressed genes contained binding sites similar to known MYB recognition elements. Co-temporal expression analysis demonstrated positive correlation of VviMYBF1 and accumulation of glycosylated flavonols with VviGT3 and VviRhaT1 during berry development and in fruits ripened with different light and UV-B radiation conditions at field. These results show that VviMYBF1 overexpression led to the identification of novel genes of the flavonol pathway and that the flavonol modifying machinery can be influenced by agricultural practices to optimize flavonol composition in grapes.

overall_design: Transgenic hairy roots were generated by infiltration of Vitis vinifera cv. ‘Chardonnay’ leaves with Agrobacterium rhizogenes carrying either VviMYBF1 or GFP (control) cDNA. To analyze differential gene expression between VviMYBF1 and GFP control hairy roots, total RNA was extracted from stable transgenic lines and subsequent array hybridization and microarray analysis was performed using the custom Affymetrix GrapeGen chip.

first: Jochen

last: Bogs


title: Expression data in Arabidopsis rdr1/2/6 mutant under drought stress

status: Public on Jul 13 2017

city: Yokohama

first: Motoaki

last: Seki

address: 1-7-22, Suehiro-cho, Tsurumi

country: Japan

institute: RIKEN CSRS

type: Expression profiling by genome tiling array

summary: We applied the tiling arrays to study RNA-dependent RNA polymerase (RDR)-mediated expression under drought stress condition.

overall_design: The total RNA was prepared from 14-day-old Arabidopsis plants  grown on the agar plates and used for the microarray hybridization. Three replicative hybridization experiments for each strand array were carried out using the independent biological RNA samples of drought-treated condition and untreated condition.

first: Akihiro

last: Matsui

first: Maho

last: Tanaka

first: Taeko

last: Morosawa

first: Yoshiki

last: Mochizuki

first: Tetsuro

last: Toyoda


title: Transcriptional analysis of Escherichia coli O157:H7 delta yhaO in MEM-HEPES

city: Sydney

first: Jai

middle: Justin

last: Tree

state: NSW

address: Rm s110 Bldg F25, UNSW, Gate 11 Botany St

department: School of Biotechnology and Biomolecular Sciences

country: Australia

institute: University of New South Wales

summary: Deletion of yhaO was found to signifcantly decrease type three secretion in EHEC O157:H7. Transcriptional profiles of Escherichia coli O157: H7 and the isogenic yhaO mutant were generated and compared.

overall_design: RNA was extracted from biological tripicate flasks and labelled with Cy3 or Cy5. Reference RNAs (w.t. TUV93-0) were pooled and divided into 80pmol aliquots for hybridisation. 80pmol of test Cy3 labelled cDNA was mixed with 80 pmol of pooled reference Cy5 labelled cDNA and hybrised to a single micorarray. Triplicate microarrays were scanned and data analysed using Genespring GX 7.3

middle: J

first: David

middle: L

last: Gally

first: Andrew

last: Roe


title: Detection of miRNA signals in compromised RNA samples

status: Public on Jul 17 2017

city: Homburg

first: Nicole

last: Ludwig

address: Kirrberger Strasse

department: Human Genetics

institute: Saarland University

summary: The aim of these experiments was to clarify the origin of increased expression signals of certain miRNAs in degrading tissues, we found in a previous study.

overall_design: We generated the following RNA samples from liver tissue of three mice (biological replicates) to measure the influence of RNA degradation and DNA contamination on miRNA expression profiles using Agilent microarrays: i) undegraded total RNA including small RNAs without potential DNA contamination, ii) naturally degraded total RNA including small RNAs without potential DNA contamination, iii) undegraded total RNA including small RNAs with potential DNA contamination, iv) naturally degraded total RNA including small RNAs with potential DNA contamination v) undegraded total RNA depleted of small RNAs, vi) partially, in vitro degraded RNA from total RNA depleted of small RNAs, vii) fully degraded, in vitro degraded RNA from total RNA depleted of small RNAs.


title: Msi1 assists CPEB1-driven polyadenylation [Msi1 RIP]

city: Barcelona

first: Oscar

last: Reina Garcia

state: Barcelona

address: C/Baldiri Reixac 10

department: Biostatistics and Bioinformatics

country: Spain

institute: IRB Barcelona

summary: The translational reactivation of maternal mRNAs encoding the drivers of vertebrate meiosis is accomplished mainly by cytoplasmic polyadenylation. The Cytoplasmic Polyadenylation Elements (CPEs) present in the 3’ UTR of these transcripts, together with their cognate CPE-binding proteins (CPEBs), define a combinatorial code that determines the timing and extent of translational activation upon meiosis resumption. In addition, the RNA-binding protein Musashi1 (Msi1) regulates the polyadenylation of CPE-containing mRNAs by an as yet undefined CPEB-dependent or -independent mechanism. Here we show that Msi1 alone does not support cytoplasmic polyadenylation, but its binding triggers the remodeling of RNA structure, thereby exposing adjacent CPEs and stimulating polyadenylation. Thus, Msi1 directs the preferential use of specific CPEs, which in turn affects the timing and extent of polyadenylation during meiotic progression. Genome-wide analysis of CPEB1- and Msi-associated mRNAs identified 491 common targets, thus revealing a new layer of CPE-mediated translational control.

overall_design: To obtain a global perspective of the CPEB1- and Msi1-regulated transcripts, and their degree of overlap, we performed CPEB1 and Msi1 RNA immunoprecipitation (RIP) from immature oocytes, followed by microarray hybridization. Stage VI oocytes were lysed and immunoprecipitations were performed with the indicated antibody. Co-Immunoprecipitated RNAs were eluted in proteinase K buffer (200 mM Tris pH7.5, 100M NaCl, 10 mM EDTA, 1%SDS) with 100 µg of proteinase K (30 min at 37ºC).. For each IP, ¼ of the IP was kept to verify the efficiency of the IP by Western blot. GeneChip Xenopus laevis Genome 2.0 Array  on GeneChip Xenopus laevis Genome 2.0 Array were processed with Bioconductor 34, using RMA background correction, quantile normalization and RMA summarization 35. Significantly enriched target genes in CPEB1 vs. preserum and HA-MSI vs. HA samples were detected with the phenoTest package36, using a fold-change threshold of 1.5 times or more and a Benjamini-Hogberg adjusted p-value < 0.05

first: Laure

last: Weill

first: Eulalia

last: Belloc

first: Raul

last: Mendez


title: Cadmium (Cd) induced expression changes in the Arabidopsis thaliana accessions Col-0 and Bur-0

city: Loughborough

first: Sina

last: Fischer

state: Leicestershire

address: Sutton Bonington Campus

department: School of Biosciences

country: United Kingdom

institute: University of Nottingham

summary:
Metal tolerance is often a result of metal storage or distribution. Thus, with the goal of advancing the molecular understanding of such metal homeostatic mechanisms, natural variation of metal tolerance in Arabidopsis thaliana was investigated. Substantial variation exists in tolerance of excess copper (Cu), zinc (Zn) and cadmium (Cd). Two accessions, Col-0 and Bur-0, and a recombinant inbred line (RIL) population derived from these parents were chosen for further analysis of Cd and Zn tolerance variation, which is evident at different plant ages in various experimental systems and appears to be genetically linked. Three QTLs, explaining in total nearly 50 % of the variation in Cd tolerance, were mapped. The one obvious candidate gene in the mapped intervals, HMA3, is unlikely to contribute to the variation. In order to identify additional candidate genes the Cd responses of Col-0 and Bur-0 were compared at the transcriptome level. The sustained common Cd response of the two accessions was dominated by processes implicated in plant pathogen defense. Accession-specific differences suggested a more efficient activation of acclimative responses as underlying the higher Cd tolerance of Bur-0. The second hypothesis derived from the physiological characterization of the accessions is a reduced Cd accumulation in Bur-0.
The microarray analysis was used to identify candidate genes for Cd-tolerance and -accumulation differences between the accessions Bur-0 and Col-0 as well as to analyse the expressional response of A.thaliana to Cd-stress.

overall_design: Samples were generated in duplicates from root material of A.thaliana Col-0 and Bur-0 grown under control conditions and Cd-stress. 8 samples were analysed in total.

first: Thomas

last: Spielau

first: Stephan

last: Clemens


title: Myogenic precursor cells differentially participate in vascular remodeling in Juvenile Dermatomyositis and Duchenne Muscular Dystrophy

status: Public on Jul 27 2017

city: 91400 Orsay

first: Florent

last: Dumont

state: Ile de France

address: 17 avenue des sciences

country: France

institute: Université Paris-Saclay

summary: Skeletal muscle is highly vascularized. Beyond oxygen and nutriment supply, new functions for vessels have been recently identified, via the interactions that vessel cells establish with muscle progenitor cells. These latter cells closely interact with endothelial cells for their expansion and their differentiation, while periendothelial cells are involved in muscle cell self-renewal and return to quiescence. Thus, vessels play a central role in the tissue remodeling after an injury, while the mechanisms are poorly understood. We investigated myogenic/endothelial cell (MPCs/ECs) interactions in two paradigmatic contexts of regenerating muscle in the child: Juvenile Dermatomyositis (JDM), which is characterized by a transient loss of capillaries, and Duchenne Muscular Dystrophy (DMD), which is associated with an increase in vessel density. We showed in vitro specific interactions between myoblasts isolated from muscle of JDM and DMD patients and endothelial cells. In vitro myogenesis/angiogenesis studies demonstrated that MPCs exhibited various angiogenic properties depending on the pathological environment. In DMD, MPCs promoted the development of an anarchic, although strong, ECs stimulation, leading to the formation of weakly functional vessels. DMD cells presented an unbalanced homeostasis with nonspecific deregulation of several processes involved in muscle and vessel development. On the contrary, in JDM, MPCs enhanced the vessel reconstruction to efficiently restore the vessel function via the expression of a set of specific angiogenic effectors. MPCs exhibit a strong specific type I IFNs signature and ECs a dysregulation of their angiogenic capacities, suggesting a drastic reprogrammation of these cells in response to an inflammatory environment during JDM.

overall_design: n=3/condition/cell type (endothelial cells from JDM, DMD, or normal condition; satellite cells from JDM, DMD, or normal condition).

first: Cyril

last: Gitiaux

first: Benedicte

last: Chazaud


title: Expression data from Burkholderia multivorans ATCC 17616 wild-type and Bmul_2557 (ldhR) gene deletion mutant

status: Public on Jul 28 2017

city: Lisboa

first: Leonilde

middle: Morais

last: Moreira

address: A. Rovisco Pais

department: Bioengineering

country: Portugal

institute: Instituto Superior Tecnico

summary: Within this work we identified and characterized gene Bmul_2557 (ldhR) of B. multivorans ATCC 17616, a bacterial species associated with chronic respiratory infections in cystic fibrosis patients. LdhR belongs to the LysR-type family of transcriptional regulators and its deletion from the B. multivorans genome affected considerably the formation of planktonic cellular aggregates and surface-attached biofilms.

platform_organism:
Burkholderia cenocepacia J2315
Burkholderia multivorans ATCC 17616

overall_design: For expression profiling, triplicates of the wild-type Burkholderia multivorans ATCC 17616 and the Bmul_2557 (delta ldhR) deletion mutant were grown in S liquid medium supplemented with 20 g/l of D-glucose for 22 hours at 37ºC and 200 rpm, followed by total RNA extraction. The wild-type strain was additionally grown in S liquid medium supplemented with 20 g/l of D-mannitol (SM medium) under the same incubation  and RNA extraction conditions.

first: Inês

middle: N

last: Silva

first: Jorg

middle: D

last: Becker

middle: M


title: Gene expression alterations in transporters with Pb (lead) exposure in mice tissues

status: Public on Jul 12 2017

city: Sapporo

first: Shouta

last: Nakayama

address: Kita18, Nishi9

institute: Hokkaido Univ

summary: To understand the entry mechanisms of Pb into the cells in mice, we have employed microarray analysis. We examined gene induction of the candidates suspected to be responsible for Pb entry into cells such as STIM1, Orai1, TRP, VGCC, divalent metal transporter 1, and anion exchanger in the liver, kidney, and brain by microarray. However, no significant induction was observed in the liver, kidney, and brain. As a confirmation, the induction of metallothionein, which is known to be induced with Pb exposure, was observed to be two and eight times greater in the liver and kidney, respectively, in the high dosage groups compared with the control group

overall_design: Two different concentrations of lead acetate (100 mg/L and 1,000 mg/L) were given to two of the groups (the low and high dosage groups, respectively) in the drinking water for three weeks. The control groups were provided with distilled water. Gene expression in the brain, kidney and liver of mice were examined.

first: Masao

last: Togao


title: Effect of RNA integrity on miRNA expression profiles by microarrays and Detection of miRNA signals in compromised RNA samples

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

overall_design: Refer to individual Series


title: Molecular biomarkers for weight control in obese individuals subjected to a multi-phase dietary intervention

status: Public on Jul 21 2017

city: Toulouse

first: Nathalie

last: Viguerie

address: Avenue Poulhes

institute: INSERM

summary:
Subcutaneous adipose tissue transcriptomes were compared between 21 obese individuals that either maintained weight loss (good controllers) or regained weight (poor controllers) during a 2-phase dietary Intervention.
Dietary intervention: Individuals underwent 8-weeks of calorie-restriction, then 6-months of ad libitum diet.

overall_design: Two groups,good- and poor-controllers; two conditions for each individual, baseline (before dietary intervention) and after dietary intervention.

first: Jennifer

last: Bolton

first: Dominique

last: Langin


title: SAMHD1 degrades nascent DNA at stalled Forks to promote replication restart

status: Public on Jul 29 2017

city: Paris

first: Jean-Charles

last: Cadoret

address: 15 rue hélène Brion

institute: CNRS/ Université de Paris

summary: SAMHD1 is a triphosphohydrolase and a 3'-5' exonuclease that restricts HIV-1 infection in non-cycling cells. It is also mutated in the Aicardi-Goutières Syndrome (AGS) and in different cancers, including chronic lymphotic leukemia. We report herre that SAMHD1 localizes to DNA replication foci during S phase suggesting that it is involved in DNA synthesis. Using microarray analysis, we examine the replication timing program an we show that SAMHD1 regulates the fork progression but also the replication timing program.

overall_design: Two experimen tal condition : shRNA LUC cells (control) versus shRNA SAMHD1 cells

first: Yeah-lih

last: Lin

first: Philippe

last: Pasero


title: Impact of dietary restriction (DR) on the transcriptome of the rodent malaria parasite Plasmodium berghei [microarray]

status: Public on Jul 14 2017

city: Almada

first: Ana

middle: Rita

last: Grosso

address: Campus de Caparica

department: Departamento Ciências da Vida

institute: Unidade de Ciências Biomoleculares Aplicadas (UCIBIO)/Faculdade de Ciências e Tecnologia - Universidade Nova de Lisboa

summary:
The aim was to understand the molecular basis of the parasite response to DR. Transcriptomic analysis of synchronized wildtype parasites, collected with 4h intervals, from mice under the two dietary conditions.
We found that WT parasites on DR and control diets have different transcriptomes, with a remarkable general repression of transcription in DR.

overall_design: Pairwaise comparison between the control and DR for each timepoint was performed. 3 biological replicates of each condition were used.

first: Liliana

last: Mancio-Silva

first: Katarzyna

middle: K

last: Modrzynska

middle: R


title: Effect of RNA integrity on miRNA expression profiles by microarrays

first: Nicole

last: Ludwig

summary: The aim of the study was to determine the influence of tissue degeneration due to prolonged storage of tissues on RNA integrity and the miRNA expression profile using microarrays. There is some dispute as to which RNA integrity level is still acceptable for miRNA expression profiling by microarrays. Some authors claim that miRNAs are stable even in degraded total RNA, others say the opposite. Therefore, we wanted to clarify if miRNA are stable in degraded tissues and which miRNAs are the most susceptible to RNA degradation.

overall_design: Time-course analysis of miRNA expression in degrading mouse liver, heart and brain tissues stored at different temperatures.


title: Transcriptome comparison of the Streptococcus pneumoniae D39∆tpxD treated with 1mM to 0mM H2O2

city: STOCKHOLM

first: Sulman

last: Shafeeq

address: nobel vag 16

department: MTC

country: Sweden

institute: Karolinska Institutet

summary: Transcriptome comparison of the Streptococcus pneumoniae D39∆tpxD grown in THY medium till OD620=0.25 and then treated with or without 1mM H2O2 for 40mins.

overall_design: Two conditions design comparison of one strain including a dye swap.

first: Barak

last: Hajaj

first: Nurith

last: Porat

first: Oscar

middle: P

last: Kuipers


title: Msi1 assists CPEB1-driven polyadenylation [CPEB1 & Msi1 RIP replicate]

last: Reina Garcia

first: Laure

last: Weill

first: Eulalia

last: Belloc

first: Raul

last: Mendez


title: Msi1 assists CPEB1-driven polyadenylation [CPEB1 RIP]


title: Transcriptome comparison of the Streptococcus pneumoniae D39 wild-type treated with 1mM to with 0mM H2O2

summary: Transcriptome comparison of the Streptococcus pneumoniae D39 wild-type grown in THY medium till OD620=0.25 and then treated with or without 1mM H2O2 for 40mins.


title: Expression data from human colorectal cancer cell line

city: Mannheim

first: Carsten

last: Sticht

address: Theodor-Kutzer-Ufer

department: ZMF

institute: University Heidelberg

summary:
Tumor suppressor candidate-3 (TUSC3/N33) is a subunit of oligosaccharyltransferase in the endoplasmatic reticulum and catalyzes N-glycosylation of membrane and secretory proteins. The aim of the study was to identify target genes for TUSC3 in human colorectal cancer cells.
We used microarrays to reveal the global programme of gene expression in TUSC3-mediated glycan and protein processing at the endoplasmatic reticulum and identified distinct up- and down-regulated target genes involved in cell survival and apoptosis.

overall_design: We transiently transfected SW480 cells in triplicates with empty vector (EV) or the putative tumor suppressor candidate-3 (TUSC3) and hybridized the cRNA to microarrays.

first: P

last: Hoede

first: E

last: Burgermeister


title: TpxD is a global sensor and transcriptional regulator for pneumococcal response to H2O2, and is regulated by CodY

summary:
Thiol peroxidase (TpxD) is one of the key enzymes used to cope with oxidative stress conditions in S. pneumoniae. Previously, we demonstrated that TpxD expression is modulated in response to H2O2 and is involved in the regulation of the psa operon. In the current study, we focus on TpxD function as a sensor and global regulator in the bacterial response to H2O2. By using microarray assays, we show that TpxD expression is necessary for the activation of bacterial global gene response to H2O2. The mechanism underlying TpxD regulatory function was further elucidated by replacing the catalytic cysteine (Cys58) with alanine (Ala58) in TpxD. This point mutation prevented tpxD up-regulation by H2O2, as well as the effect of H2O2 on additional genes that were affected by H2O2 in the WT but not in ∆tpxD, signifying that this cysteine is crucial for TpxD signaling activity. We then tried to identify a candidate transcription factor which regulates tpxD expression under H2O2 stress. Bioinformatics analysis identified a putative CodY 15 bp binding site in the proximal upstream region of tpxD coding sequence. Genetic engineering techniques and EMSA assays confirmed the presence of an active CodY box. Indeed, no up-regulation of TpxD was noticed in ∆codY challenged with H2O2. These data identify CodY as the transcription factor modulating tpxD expression under H2O2 stress. We propose a model of gene regulation under oxidative stress conditions which places TpxD as an intermediary between H2O2 and the global bacterial response to oxidative stress.

This SuperSeries is composed of the SubSeries listed below.


title: Transcriptome response to different nitrogen sources and aerobic/anaerobic conditions in Hydrogenobacter thermophilus

status: Public on Jul 23 2017

city: Tokyo

first: Masafumi

last: Kameya

state: No U.S. state/territory

address: 2-12-1, Ookayama, Meguro-ku

department: Earth-Life Science Institute

institute: Tokyo Institute of Technology

summary: Transcriptome profile of the Hydrogenobacter thermophilus TK-6 cells aerobically or anaerobically grown on ammonium, nitrate,  or mix of ammonium and nitrate was determined by NimbleGen Eukaryotic Expression array (4x72K).

overall_design: Hydrogenobacter thermophilus TK-6 was aerobically or anaerobically grown on ammonium or nitrate as nitrogen sources in sealed vials with shaking. Total RNA was extracted when optical density at 600 nm was 0.4-0.5. The experiment was performed in duplicate independent cultures.

first: Hiroyuki

last: Arai

first: Haruna

last: Kanbe


title: Transcriptional analysis of Escherichia coli O157:H7 delta yedL in MEM-HEPES

first: Jai

last: Tree

summary: Deletion of yedL was found to signifcantly decrease type three secretion in EHEC O157:H7. Transcriptional profiles of Escherichia coli O157: H7 and the isogenic yedL mutant were generated and compared.

first: David

last: Gally

first: Andrew

last: Roe


title: Msi1 assists CPEB1-driven polyadenylation


title: Microarray analysis of the impact of ParB excess on gene expression in Pseudomonas aeruginosa

status: Public on Jul 25 2017

city: Warszawa

first: Adam

last: Kawałek

address: Pawinskiego 5A

department: Department of Microbial Biochemistry

country: Poland

institute: Institute of Biochemistry and Biophysics, PAS

summary:
In Pseudomonas aeruginosa, partitioning protein ParB facilitates segregation of newly replicated chromosomes but is not essential for cell survival. Unlike in other bacteria, inactivation of parB leads to major changes of the transcriptome, suggesting that, directly or indirectly, ParB plays a role in regulation of gene expression in this organism.
To identify primary targets of ParB, we analysed the impact of a slight increase in ParB amount on the transcriptome using microarrays. A several-fold increased ParB level does not cause recognizable phenotypic changes but leads to significant changes in the expression of 211 loci, including transcriptional regulators of operons involved in SOS response, virulence and adaptation. Most notably, the mRNA level of genes adjacent to high affinity ParB binding sites parS1-4 close to oriC is reduced. Our data support the role of partitioning protein ParB as a transcriptional regulator in Pseudomonas aeruginosa.

overall_design:
Pseudomonas aeruginosa PAO1161 (leu, r-, RifR) [Bartosik et al. (2009), Microbiology 155(4), 1080-1092], a derivative of PAO1, was used in this study. Cells were grown in rich medium (L broth) at 37oC with shaking 200 rpm. Arabinose (Ara) was used to induce the expression from the araBAD promoter. RNA was isolated from PAO1161 planktonic cultures grown in L broth without Ara (WT control, 2 replicates), PAO1161 (pKGB8.0.2 araBADp) cultures grown under selection in L broth with 0.02% Ara (empty vector control, 3 replicates), PAO1161 (pKGB8.62.2 araBADp-parB) cultures grown under selection in L broth without Ara (mild ParB overproduction, 3 replicates) or with 0.02% Ara (higher ParB overproduction, 3 replicates).
In the final draft of the paper plasmid names have been shortened. pKGB8.0.2 is now called pKGB8 and pKGB8.62.2 is now called pKGB9.

last: Kawalek

first: Krzysztof

last: Glabski

first: Aneta

middle: A

last: Bartosik

first: Anna

last: Fogtman

first: Grazyna

last: Jagura-Burdzy


title: Human smooth muscle cells at 2 hr post-stimulation with IL-1beta

status: Public on Jul 22 2017

city: Philadelphia

first: Emanuela

last: Ricciotti

state: PA

address: 3400 Civic Center Blvd.

department: Department of Pharmacology/Institute for Translational Medicine and Therapeutics

country: USA

institute: University of Pennsylvania

summary: The aim of this data set is to measure the effect of IL-1beta stimulation on the transcription profile in an in vitro inflammation model. Transcription profiling was carried out using Affymetrix HG U-133A v2 microarrays.

overall_design: Human aortic smooth muscle cells (3F1243) were pre-treated with DMSO for two hours and subsequently exposed to IL-1beta (10 ng/ml). Transcription profiling was carried out at 0h and 2h points of IL-1beta exposure, with four samples at each time point 0hr and 2hr. 8 samples in total.

first: Tilo

last: Grosser

first: Max

last: Homilius

first: Garret

last: FitzGerald


title: Expression of sulfamethoxazole biotransformation pathways in a macaque model of HIV infection

status: Public on Jul 11 2017

city: Madison

first: Brian

last: Johnson

state: WI

address: 1400 University Ave

department: Oncology

institute: UW-Madison

summary: Potentiated sulfonamide antibiotics such as trimethoprim/sulfamethoxazole (cotrimoxazole or TMP/SMX) remain the drugs of choice for treatment and prevention of Pneumocystis jiroveci pneumonia, toxoplasma encephalitis, and Isospora infections in HIV infection (aidsinfo.nih.gov). However, HIV-infected patients show a markedly increased risk of delayed hypersensitivity (HS) reactions to TMP/SMX (20-57% incidence) when compared to the general population (3% incidence). The typical manifestation is maculopapular rash with or without fever, and TMP/SMX is the most common cause of cutaneous drug reactions in HIV-infected patients TMP/SMX can also lead to thrombocytopenia, hepatotoxicity, and bullous skin eruptions in more severely affected patients. The risk of sulfonamide HS increases with progression to AIDS, with higher risk seen at lower CD4+ counts.  This risk has been attributed, at least in part, to acquired alterations in SMX drug disposition in HIV infection.  We hypothesized that HIV infection leads to impaired hepatic SMX detoxification or enhanced SMX bioactivation pathways, which may contribute to the increased incidence of sulfonamide HS. We addressed this question using liver tissue from SIVmac239-infected macaques, a well accepted model of HIV infection. The aim of this study was to evaluate differences in the hepatic expression and activity of SMX biotransformation pathways from drug naïve SIV-infected macaques compared to sex- and age-matched uninfected controls.

overall_design: Male Rhesus macaques (Macaca mulatta) chronically infected with SIVmac239 (N=3), along with age and sex-matched uninfected controls (N=3), were obtained through the Wisconsin National Primate Research Center. Animals were studied during chronic infection, at least 10 weeks after inoculation. All macaques were screened prior to inclusion in the study with a physical exam, CBC, and serum biochemical panel. Infected animals also had a CD4+ count and viral load performed prior to sampling. All animals were fed a fixed formula global primate diet (Teklad, Harlan Laboratories, Madison WI), and no animals had a history of prior TMP/SMX exposure.

first: Yat

middle: Y

last: Wong

first: Lauren

last: Trepanier


title: Distinct Sets Of Genes Representing Overlapping Biological Functions Are Altered By Intrinsic Properties Of Carbon Nanomaterials In Vitro And In Vivo

status: Public on Jul 18 2017

city: Tampere

first: Dario

last: Greco

address: Arvo ylpön Katu 34

department: Faculty of Medicine and Health Technology

country: Finland

institute: Tampere University

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus


title: Autoantibodies as diagnostic biomarkers for the detection, subtyping, and progression of Multiple Sclerosis

status: Public on Jul 26 2017

city: Stratford

first: Robert

middle: G

last: Nagele

state: NJ

address: 2 Medical Center Drive

department: NJISA

institute: UMDNJ-SOM

summary: Human serum samples from Multiple Sclerosis (MS) subjects and healthy control subjects were probed onto human protein microarrays in order to identify differentially expressed autoantibody biomarkers that could be used as diagnostic indicators.  Other neurodegenerative and non-neurodegenerative diseases were also used to help measure the specificity of the selected biomarkers.

overall_design: In the study presented here, 51 mixed-MS serum samples and 31 control human serum samples were probed onto human protein microarrays in order to identify differentially expressed autoantibodies.  Microarray data was analyzed using several statistical significance algorithms, and autoantibodies that demonstrated significant differences in group prevelance were selected as potential biomarkers of disease.  Prediction classification analysis using Invitrogen's Prospector v5.2.1 and Random Forest tested the diagnostic efficacy of the identified biomarkers.  Differentiation of MS samples from other neurodegenerative and non-neurodegenerative controls (early-stage Parkinson's disease and breast cancer) assessed the specificity of the selected biomarkers. Ccomparison of relapsing-remitting MS serum samples with secondary progressive MS serum samples assessed their utility for use in subtype staging and disease progression.

first: Cassandra

last: DeMarshall

first: Eric

last: Goldwaser

first: Abhirup

last: Sarkar

first: George

last: Godsey

first: Umashanger

last: Thayasivam


title: Distinct Sets Of Genes Representing Overlapping Biological Functions Are Altered By Intrinsic Properties Of Carbon Nanomaterials In Vitro And In Vivo [mouse]

summary: Six different carbon nanomaterials (CNM) administered by oropharyngeal aspiration to C57BL/6 mice (on 4 consecutive days with 10ug of CNM per day in PBS, sacrificed on 5th day)  and to differentiated THP-1 cells in culture (6 hour and 24 hour, with 100ug of CNM /ml of medium)

overall_design: C57BL/6 mice were exposed to six different CNM by oropharyngeal aspiration (10 μg/day in 50μl of PBS) once per day for 4 consecutive days. Bronchoalveolar lavage and lung tissue samples were collected, histological sections analyzed and mRNA expression profiles were determined by Agilent microarray. Vehicle treated (PBS) was used as Controls. Two mRNA samples from same group were pooled as one sample.

first: Pia

last: Kinaret

first: Veer

last: Marwah

first: Vittorio

last: Fortino

first: Marit

last: Ilves

first: Henrik

last: Wolff

first: Lasse

last: Ruokolainen

first: Petri

last: Auvinen

first: Kai

last: Savolainen

first: Harri

last: Alenius


title: Gene and miRNA expression profiling of primary cell cultures of lung fibroblasts obtained from cancer or normal tissue of lung cancer patients

status: Public on Jul 10 2017

city: Milan

first: Luca

last: Roz

address: Via Venezian 1

department: Experimental Oncology and Molecular Medicine

country: Italy

institute: Fondazione IRCCS Istituto Nazionale dei Tumori

summary: There is increasing evidence for a crucial contribution of the tumor microenvironment to cancer development and progression since several stromal components, including fibroblasts, interact with cancer cells regulating their behavior and ultimately affecting tumor phenotype. To investigate the cross-talk between cancer cells and lung-derived fibroblasts we have prospectively collected surgical specimens of lung cancer and normal lung tissue and established primary fibroblast cultures from different areas of the lungs. We have generated cultures from cancer specimens (Cancer Associated Fibroblasts, CAF) and cultures from normal lung tissue either proximal (Adjacent Fibroblasts, AF) or distant from the neoplastic lesion (Normal fibroblasts, NF). Gene and miRNA expression profiles were obtained from 60 cultures to identify fibroblast properties related  to cancer progression.

overall_design: Primary cultures of patient-derived fibroblasts (CAF n=27, NF n=21, AF n=12) were comparatively analyzed for gene and miRNA expression profiles with the aim to define transcriptional pathways responsible for fibroblast activation.  This Series contains miRNA samples.

first: Francesca

last: Andriani


title: The Gene expression gradient through the intestine tract of European Sea Bass (Dicentrarchus labrax)

status: Public on Jul 08 2017

city: Castellón

first: Josep

last: Calduch-Giner

address: Ribera de Cabanes

institute: Institute of Aquaculture Torre de la Sal (CSIC)

summary: A custom high density oligo-microarray (8 x 15K) was designed and printed by means of the eArray web tool (Agilent) to analyze the transcriptome of the three intestinal sections  of Euroipan sea bass (Dicentrarchus labrax). Naïve stock juveniles sea bass, maintained under intensive rearing conditions in the indoor experimental facilities of IATS, were sampled after overnight fasting for anterior, middle and posterior sections of intestine. The array comprised 60-oligomer sequences for 14,147 different sea bass annotated sequences. Total RNA (150ng) from individual fish were labelled with cyanine 3-CTP and 1,000ng of each labelled cRNA were hybridized to microarray slides. Analysis of the scanned data, including principal component analysis and unpaired t-test with Benjamini-Hochberg multiple testing correction, was carried out with GeneSpring GX software (Agilent). Pathway analysis of differentially expressed sequences was performed using the Ingenuity Pathway Analysis (IPA) software.

overall_design: Three intestine sections (anterior-ANT-, middle-MED-, and posterior-POS-) were analyzed

first: Jaume

last: Pérez-Sánchez


title: Identification of interacting stromal properties in triple-negative breast cancer - Stromal Discovery Set

status: Public on Jul 06 2017

city: Montreal

first: Morag

last: Park

state: QC

address: The Cancer Research Building 1160 Pine Avenue, Room 602

country: Canada

institute: Mcgill University

summary: Triple-negative breast cancer is a molecularly heterogeneous cancer that is difficult to treat. TNBC microenvironmental (stromal) heterogeneity has not been well characterized despite the key role that it may play in tumor progression. To address this challenge we investigated the transcriptome of tumor-associated stroma isolated from TNBCs (n=57).

overall_design: 57 flash-frozen human primary breast cancer samples were subjected to laser capture microdissection to separately isolate tumor-associated and adjacent normal stromal components. RNA was isolated, subjected to 2 rounds of amplification, and hybridized on Agilent 8x60K microarrays along with a common reference two round-amplified commercially obtained Universal Human Reference RNA). For one sample each tumor-associated stroma and normal adjacent stroma, a second technical replicate was performed.

first: Sadiq

last: Saleh

first: Nicholas

last: Bertos

first: Michael

middle: T

last: Hallett


status: Public on Jul 02 2017

city: Ithaca

first: Siu

middle: Sylvia

last: Lee

state: NY

address: 526 Campus Road, 341 Biotech

department: MBG

institute: Cornell University

summary: Transcriptomic profile of the homeodomain protein CEH-23 under mitochondrial ETC stress in C. elegans by comparing gene expression profile between isp-1(qm150) vs. ceh-23(ms23);isp-1(qm150) mutants

overall_design: Two condition experiment, isp-1(qm150) and ceh-23(ms23);isp-1(qm150): 3 biological replicate and 1 technical dye-flip replicate. Synchronized mid-L4 staged worms grown at 20C on 10cm NGM plates with seeded OP50 E. coli were collected for the experiments

first: Hsin-Wen

last: Chang


title: Biological characterization of virulent therapeutic bacteriophage PAK_P4 infecting Pseudomonas aeruginosa

status: Public on Jul 07 2017

first: Monot

last: Marc

address: 25, rue du docteur roux

department: Genomes and Genetics

institute: Institut Pasteur

type: Expression profiling by high throughput sequencing

summary: We have isolated and characterized several bacteriophages infecting Pseudomonas aeruginosa distantly related to Felix O1 virus and proposed they form a new subfamily named Felixounavirinae. The infectious cycle of bacteriophages belonging to this subfamily has not been studied yet in terms of gene expression. The present study reports the RNA-Seq analysis of bacteriophage PAK_P4 infecting PAK strain of P. aeruginosa.

sample_organism:
Pseudomonas aeruginosa
Pseudomonas phage PAK_P4

overall_design: RNA profile of Host and Phage at 0min, 3.5min and 13 min after infection of Pseudomonas aeruginosa PAK strain with the Pseudomonas phage PAK P4. Three biological replicates for each time point.

first: Bob

last: Blasel

first: Marc

last: Monot

first: Anne

last: Chevallereau


title: Transcriptomic analysis of three Oenococcus oeni strains in the early response to stress

status: Public on Jul 03 2017

city: Tarragona

first: Cristina

last: Reguant

state: Tarragona

address: Marcel·lí Domingo 1

department: Biochemistry and Biotechnology

institute: University Rovira i Virgili

summary: In this work, three O.oeni strians were inoculated, two of them were of our own collection (3P2 and 2T2) and the other one is the type strain 217T (=ATCC 23279) in WLM-12 to develop MLF in these conditions (Bordas et al, 2015). Basic fermentation characteristics were monitored, such as growth rate and biomass yield, as well as the respective transcriptome. This approach allowed a better understanding of metabolic adaptation and its association with specific genes expression profiles, likewise we were able to identify some biological process directly involved in the fermentation conditions such as pH or ethanol content.

overall_design: Three Oenococcus oeni were used in this work (3P2, 2T2 and 217T) (Bordas et al. 2015), they were grown in rich medium, when they were in exponencial phase they were inoculated in wine like medium with 12 % v/v ethanol. Samples were taken 1 hour after inoculation and in the initial point of fermentation. Total RNA was analysed using a custom designed expression microarray.

first: Meritxell

last: Bordas

first: Albert

last: Bordons


title: Global transcriptional control by the alternative sigma factor SigB in Clostridium difficile

summary: Genes encoding the alternative sigma factor SigmaB, involved in the general stress response in firmicutes, as well as its regulators are present in the genome of the enteropathogen Clostridium difficile. We inactivated the sigB gene using the ClosTron technology in order to identify the role of this sigma factor in the physiology of this bacterium. Transcriptomic experiments showed that SigB positively and negatively controlls several genes involved in different cellular processes such as metabolism, sporulation and stress response.

overall_design: Two-conditions experiments, 630E strain vs SigB mutant grown in TY 10h, 4 biological replicates for each condition

first: Nicolas

last: Kint


title: EHEC O157 EDL933 & sdhA mutant comparison

status: Public on Jul 01 2017

city: Tainan

first: Jenn-Wei

last: Chen

address: No.1, University Road

country: Taiwan

institute: National Cheng Kung University

summary: The microarray study was used to compare the gene expression profile of EDL933 in LB, sdhA deletion mutant in LB, and sdhA deletion mutant in LB with 2.5 mM Fumaric acid.

overall_design: The total RNA samples from EDL933 in LB (two replicates), sdhA deletion in LB (three replicates) and sdhA deletion mutation in LB with 2.5 mM Fumaric acid (three replicates) were used in this microarray study.


title: Gene expression-based, molecular pathomechanism prediction for GNE myopathy III

first: Satoru

last: Noguchi

address: 4-1-1, Ogawahigashi, Kodaira

department: Neuromuscular Research

institute: National Institute of Neuroscience, NCNP

summary: Molecular impacts in the pathogenesis of GNE myopathy in model mouse muscles were well described through expression profiling of a total of 34000 genes

overall_design: In the study presented here, genetically defined GNE myopathy model mice were used to acquire expression profiles of a total of 34000 unique genes, for identification  of  pathomechanism of the disease and the theraputic pathways with N-acetylcysteine treatment.


title: RNAome Modulation in Lung During Metabolic Syndrome in a Rat Model

city: Cambridge

first: Madeline

last: Lancaster

state: Cambridgeshire

address: Cambridge Biomedical Campus, Francis Crick Avenue

department: Cell Biology Division

institute: MRC Laboratory of Molecular Biology

summary:
Metabolic syndrome (MetS) is the name of cluster of risk factors that increases the risk for heart disease and other health problems by which several organs are affected, but research is lacking for those not involved directly in metabolism. The cluster is integrated by central obesity, insulin resistance, dyslipidemia (elevated triglycerides and low density lipoprotein and decreased high density lipoprotein), and high blood pressure, according to the consensus released by the International Diabetes Federation [1]. This problem could be as the result of an unbalanced diets (high-fat and carbohydrates), and genetic background [2, 3].
There is evidence that suggests that MetS is a condition that increases the risk of different lung diseases. It have been reported in some MetS patients a diminished lung function, as assessed by spirometry, in addition, there is an association with insulin resistance, increase in body mass index; abdominal obesity and systemic inflammation (high levels of C reactive protein) [4-6]. In other cases, like asthma, some components of MetS such as abdominal obesity, hypertension and pro-inflammatory cytokines have been with related with this disease [7-9]. Also, a few clinical studies reported that abdominal obesity, hyperglycemia and elevated levels of systemic inflammatory markers, which are components of MetS, were significantly more prevalent in patients with chronic obstructive pulmonary disease [10-13]. In the present work we evaluated the  transcriptomic changes of lung tissue in an animal model of MetS induced by diet.

overall_design: 7 rats (3 with MetS and 4 control) were used for the microarray experiment for each group it has a one biological replicate

first: Sofia

last: Rodríguez-Peredo

first: Ashley

last: Castellanos-Jankiewicz

first: Ivan

last: Imaz-Rosshandler

first: Jose

last: Muñoz-Sánchez

first: Jorge

last: Meléndez-Zajgla

first: Elizabeth

last: Tejero

first: Roxana

last: Carbó-Zabala

first: Vilma

last: Maldonado

first: Laura

last: del Bosque-Plata


title: Gene expression-based, molecular pathomechanism prediction for GNE myopathy II

summary: Molecular impacts of 1% N-acetylcysteine treatment on GNE myopathy model mice were well described through expression profiling of a total of 34000 genes


title: Gene expression-based, molecular pathomechanism prediction for GNE myopathy

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

overall_design: Refer to individual Series


title: Influence of RNA modification on microRNAs

city: Kamakura

first: Satoshi

last: Kondo

state: Kanagawa

address: Tebiro 6-10-1

department: New Projects Development Division

institute: Toray Industries,Inc.

summary: Gene expression profiles of methylated or nonmethylated miRNA oligonucleotides transfected DICER exon 5-disrupted RKO cells.

overall_design: To investigate the effect of RNA modification on microRNAs, we transfected artificially synthesized nonmethylated or methylated oligonucleotides to a colorectal cancer cell line.

first: Hideshi

last: Ishii

first: Masaki

last: Mori


title: Copy number variation in an invasive fish of hybrid origin

city: Ploen

first: Stefan

last: Dennenmoser

address: August-Thienemann Str. 2

department: Evolutionary Genetics

institute: Max-Planck Institute for Evolutionary Biology

sample_organism:
Cottus
Cottus perifretum
Cottus rhenanus


title: Development of gene expression signature in Pseudomonas aeruginosa Strain UCBPP-PA14 without and with LAE treatment

status: Public on Jun 29 2017

city: Seoul

first: Taek-Seung

last: Kim

address: Anam-ro 145

department: school of civil, Environmental & Architectural Engineering

country: South Korea

institute: Korea University

summary: Pseudomonas aeruginosa is a ubiquitous gram-negative bacterium capable of forming biofilms on living and non-living surfaces, frequently leading to undesirable consequences. We found that lauroyl arginate ethyl (LAE), a synthetic non-oxidizing biocide, inhibited biofilm formation by P. aeruginosa at sub-growth inhibitory concentrations in both static and flow conditions. To identify the genes targeted by LAE, a global transcriptome analysis was conducted using a gene chip microarray.

overall_design: Samples for transcriptome analysis consist of non-LAE treated sample and LAE treated sample. Total RNA both samples was extracted from planktonic cells using TRIzol reagent following the manufacturer's instructions. And then, transcriptome analysis was conducted by Agilent's protocol provided by the manufacturer.

first: Hee-Deung

last: Park


title: Influence of RNA modification on microRNAs (ver 2)


title: Longitudinal transcriptomic and metabolomic data demonstrate altered lipid metabolism following the onset of hyperglycemia in spontaneously diabetic rats

status: Public on Jun 12 2017

city: Milwaukee

first: Martin

last: Hessner

address: 8701 Watertown Plank Road

department: Pediatrics

institute: Medical College of Wisconsin

summary:
Fat metabolism is also peturbed after the diagnosis of type 1 diabetes. Patients have less fat in the liver (4) and increased fasting lipid oxidation (5) compared to controls. Similarly, in a BioBreeding rat model of type 1 diabetes, the diabetes-prone animals develop a reduced respiratory quotient compared to non-diabetic rats before the onset of hyperglycemia, consistent with an increased use of fatty acids relative to carbohydrates as an energy substrate (6).
We hypothesized that a lack of insulin reaching the liver contributes to the metabolic shift towards lipid oxidation observed in humans with type 1 diabetes and rodent models of the disease. To test our hypothesis, we measured changes in the hepatic gene expression and serum metabolome of a BioBreeding rat model of type 1 diabetes before and after the onset of hyperglycemia.

overall_design: In this study, we investigate liver gene expression in BBDR.+/+, BBDR.lyp/lyp rat at day50 (+/-5 days) which are before hyperglycemic, and day55 (+/-5 days) which is short after hyperglycemic. Liver transcriptomes of 50 day old BBDR.lyp/lyp and 55 day old BBDR.+/+ rats were compared to 55 day old BBDR.lyp/lyp rats.

first: SIMON

last: REGNÉLL

first: Mary

last: Kaldunski

first: Shuang

last: Jia

first: Marty

first: Åke

last: Lernmark


title: miRNA expression data in Huh-7 cell line transfected with HBeAg-expression vector

city: New Delhi

first: Perumal

last: Vivekanandan

state: Delhi

address: Kusuma School of Biological Sciences, IIT Delhi, Hauz Khas, New Delhi-110016

department: Kusuma School of biological Sciences, IIT Delhi

country: India

institute: Indian Institute of technology Delhi

summary:
The HBeAg is a well-documented risk factor for HCC in epidemiological studies. The biological role of HBeAg in HBV-related HCC remains poorly understood. The HBeAg-mediated differential expression of host miRNAs
We used miRNA microarray chips to assess the host cellular miRNA expression profile in response to HBeAg expression in Huh7 cells

overall_design: The total RNA from Huh-7 cells transfected with control and HBeAg-expression vector was harvested 48 hours post transfection and miRNA profiling was done miRNA-2_0 arrays

first: Jasmine

last: Samal

first: Manish

last: Kandpal

last: Vivekanadan


title: Gene expression-based, molecular pathomechanism prediction for GNE myopathy I

city: Tokyo

first: Satoru

last: Noguchi

summary: Molecular impacts of 0.1% N-acetylcysteine treatment on GNE myopathy model mice were well described through expression profiling of a total of 34000 genes


title: Copy number variation of genes (exons) in invasive Cottus compared to the parental species, Cottus rhenanus and Cottus perifretum.

summary: Hybridization between Cottus rhenanus and C. perifretum has resulted in an evolutionary young hybrid lineage of invasive Cottus that has colonized a new habitat where the parental species are not found (Nolte et al. 2005; Proc. R. Soc. B 272: 2379–2387). This CGH array was designed to screen for copy number variation among Cottus species and to find gene duplicates that are unique to the hybrid lineage (see also Dennenmoser et al. 2017; Copy number increases of transposable elements and protein coding genes in an invasive fish of hybrid origin).

overall_design: SurePrint G3 custom CGH 8x60k microarray with five technical replicates per probe and a 15 bp linker added to each probe as recommended by Agilent. The experimental design was a two-color experiment (Cottus individual vs. common reference) with 24 biological replicates (3 species x 8 individuals). Each Cottus individual was co-hybridized with the same Cottus perifretum individual as a common reference. The normalization procedure included a calibration step to account for probe-specific binding behavior, which was assessed using a custom designed calibration array  (see also Dennenmoser et al. 2017; Copy number increases of transposable elements and protein coding genes in an invasive fish of hybrid origin).

first: Arne

middle: W

last: Nolte


title: Root and shoot performance of Arabidopsis thaliana exposed to elevated CO2: a physiologic, metabolic and transcriptomic response

city: pamplona

first: Ivan

last: Jáuregui Mosquera

state: Navarra

address: Campus de Arrosadia, s/n,  Dpto. Ciencias del Medio Natural

institute: Universidad Pública de Navarra

summary:
In this study we explain the physiological, biochemical and gene expression mechanisms adopted by ammonium nitrate-fed Arabidopsis thaliana plants growing under elevated [CO2], highlighting the importance of root-to-shoot interactions in these responses
A transcriptomic analysis enabled the identification of photoassimilate allocation and remobilization as fundamental process used by the plants to maintain the outstanding photosynthetic performance. Moreover, based on the relationship between plant carbon status and hormone functioning, the transcriptomic analyses provided an explanation of why phenology accelerates in elevated [CO2] conditions.

overall_design: Arabidopsis thaliana, Columbia 0 ecotype (col 0) and NR mutant (NR double mutant G′4-3, nia1- 1/nia2-5) plants grown under hydroponic conditions. The nitrogen (N) source was NH4NO3 at 1 mM concentration. 4 weeks exposure to CO2 treatments, previous to first flower were buds visible (see Supplemental Figure 1 for the image of the plants), in 3.7 growth stage ontology from the scale described by Boyes (2001).

first: Iván

last: Jáuregui

first: Pedro

last: Aparicio-Tejo

first: Concepción

last: Avila

first: Iker

last: Aranjuelo


title: A phylogenetic framework to study the evolution of transcriptional regulatory networks [Agilent microarray]

city: Madison

first: Sushmita

last: Roy

address: 330 N. Orchard St.

institute: Wisconsin Institute for Discovery

sample_organism:
Schizosaccharomyces pombe
Saccharomyces cerevisiae
Candida albicans
Nakaseomyces glabratus
Naumovozyma castellii
Kluyveromyces lactis

overall_design: Comparative time-series expression analysis of growth curves through osmotic stress in the ascomycete yeasts

first: Christopher

last: Koch

first: Jay

last: Konieczka

first: Toni

last: Delorey

first: Ana

last: Lyons

first: Amanda

last: Socha

first: Kathleen

last: Davis

first: Sara

last: Knaack

first: Dawn

last: Thompson

first: Erin

last: O'Shea

first: Aviv

last: Regev


title: Response of rat liver to GW7647

city: Research Triangle Park

first: Patrick

last: McMullen

state: North Carolina

address: 6 Davis Drive, P.O. Box 12137

institute: The Hamner Institutes for Health Sciences

summary: Activation of PPARα pathways by some environmental chemicals causes hepatocyte proliferation and cancer in rodents.  While these responses do not seem to occur in humans, the biological basis of these species differences remains uncertain. We systematically evaluated multiple readouts in rat and human hepatocytes and gene expression in intact rat livers using a PPARα-selective agonist, GW7467. In vitro rat hepatocytes had more genes significantly altered by GW7647 than did human (2320 versus 192).  There were common pathways of fatty acid metabolism, amino acid metabolism and lipid transport, mostly represented by upregulated genes, shared between species.  In rat hepatocytes, there were many downregulated genes enriched for processes including apoptosis, inflammation, response to hormones and chemical stimuli.  In vivo, gene expression signatures for proliferation were present at high doses. In both species, a third of the genes with altered expression had direct binding of PPARα to a nearby peroxisome proliferator response element (PPRE).  While the PPRE associated with upregulated genes in both species, was similar, the downregulated genes in the rat had altered flanking region conservation of nucleotides. Among the down regulated genes with direct PPARα binding in the rat were two key transcription factors – Hnf6 (onecut1) and Ets.  Our results support a qualitative difference in biology of PPARα activation between human and rats.  The secondary downregulated pathways, in the rat, appear to be reversion to an earlier lineage more responsive to proliferative signals that likely arise from interactions between the PPARα activated hepatocytes and other cell types in the intact liver.

overall_design: Male rats were administered vehicle or GW7647 at 0.1, 1 or 10 mg/kg (n=10/dose) by oral gavage daily for 4 days. Whole livers were excised after exsanguination and used for transcriptomics.


title: Response of primary hepatocytes to GW7647

overall_design: We used microarray-based transcriptome profiling experiments to query the effect of GW7647 treatments on gene expression.  mRNA from primary rat hepatocytes isolated from four independent rats was collected at five time points (2, 6, 12, 24, and 72 h) from cells treated with five concentrations of GW7647 (0.001, 0.01, 0.1, 1.0 and 10μM).


title: Global tanscriptome analysis in Oryza sativa identifies genes regulated by copper in the medium

status: Public on Jun 20 2017

city: Cologne

first: Fernando

last: Andres

address: Carl von Linne 10

department: Plant Developmental Biology

institute: Max Planck Institute for Plant Breeding Research

summary: Higher plants have developed sophisticated mechanisms to efficiently acquire and use micronutrients such as copper and iron. In the present work, we studied effects produced by the presence of a wide copper range in growth media and altered copper transport on iron homeostasis in Oryza sativa plants. The global analysis of gene expression in the rice seedlings grown under copper deficiency versus excess in the medium showed an increased expression of the genes involved in iron homeostasis. Different iron-related genes are expressed under either copper deficiency and excess, such as those that encode ferredoxin and transcriptional regulator IRON-RELATED TRANSCRIPTION FACTOR 2 (OsIRO2), respectively. As expected, the expression of OsCOPT1, which encodes a high affinity copper transport protein, was up-regulated under copper deficiency, and the expression of OsIRO2 targets were increased under copper excess. Arabidopsis COPT1 overexpression (C1OE) in rice causes root shortening under copper excess, modifies the expression of the putative Fe-sensing factor HEMERYTHRIN MOTIF-CONTAINING REALLY INTERESTING NEW GENE- AND ZINC-FINGER (OsHRZ1) and enhances the expression of OsIRO2 and its targets, which suggests a role of copper in iron signaling. Our studies conducted under simultaneous copper and iron deficiencies indicate that C1OE plants are more sensitive than the wild-type controls to root growth inhibition. The C1OE rice plants grown on soil contained higher endogenous iron concentration in grains than the wild-type plants (both brown and white grains). The results obtained herein showed the interaction between homeostatic networks of iron and copper, and suggest that strategies to obtain crops with optimized nutrient concentrations in edible parts should take into account this interaction.

overall_design: 8-day-old O. sativa seedlings were used to perform a global gene expression analysis by DNA microarrays. Two different Cu concentration conditions were compared, slight Cu deficiency (0 µM CuSO4) and Cu excess (75 µM CuSO4). Four independent biological replicates of each condition (½MS and ½MS + 75 µM CuSO4) were employed. Each biological replicate was labeled with Cy3 and Cy5 to produce four pairs of replicate dye-swaps, which were used for microarray hybridization.

first: A

last: Andrés-Bordería

first: F

last: Andrés

last: Garcia-Molina

last: Perea-Garcia

first: C

last: Domingo

first: S

last: Puig

first: L

last: Peñarrubia


title: Response of primary hepatocytes and liver to GW7647


title: Transcriptome analysis of Paracoccus denitrificans during aerobic and anaerobic respiration (denitrification)

status: Public on Jun 30 2017

city: Richmond

first: Georgios

last: Giannopoulos

state: Virginia

address: 1000 W Cary st

department: Biology

institute: Virginia Commonwealth University

summary: Transcriptional profiling of Paracoccus denitrificans PD1222 wild type incubated in continuous culture (continuous culture (CSTR)) in minimal media with aerobic or anaerobic conditions. The goal was to define the core respiratory genes.

overall_design: Two growth conditions, three biological replicates of each condition. Each sample hybridised in a two-channel hybridization against Paracoccus denitrificans genomic DNA as the comparator/reference, which also acted as a control for spot quality.

first: Matthew

last: Sullivan

first: David

last: Richardson


title: Transcriptional Changes in Escherichia coli Upon Treatment with (-)-Roemerine

status: Public on Jun 21 2017

city: Udine

first: Dilara

last: Ayyıldız

address: p.le kolbe, 4

institute: University of Udine

summary: Transcriptional profiling of Escherichia coli TB1 cells under (-)-Roemerine treatment. The genome reprograming in the bacterial cells at transcription level was analyzed through treatment of the bacteria with plant-derived alkaloid, (-)-Roemerine, to elucidate the response of bacteria to the antibacterial drug.

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

overall_design: Two-condition experiment, DMSO vs. DMSO+Roemerine treated cells, at two different time points, 0 vs. 60 min. after treatment. Biological replicates: 7 control replicates (3 samples for 0 min., 4 samples for 60 min.), 6 Roemerine treated replicates (3 samples for 0 min., 3 samples for 60 min)

first: Berna

last: Sariyar Akbulut

last: Ayyildiz

first: Kazim Yalcin

last: Arga


title: Calibration array

first: Stefan

last: Dennenmoser

summary: Calibration array used to assess probe specific binding behaviour across eight different amounts of DNA starting material. This calibration step was performed to select one best out of three probes per gene based on probe responsiveness on increasing DNA staring material. It was further used to calibrate a subsequent microarray experiment to account for probe specific binding behaviour as part of the normalization process (see also Dennenmoser et al. 2017 Copy number increases of transposable elements and protein coding genes in an invasive fish of hybrid origin).

sample_organism:
Cottus perifretum
Cottus rhenanus

overall_design:
SurePrint G3 custom CGH microarray (8x60k) with two replicates per probe and the addition of a 15 bp linker as recommended by Agilent. The calibration experiment folloed a two-color design (Cottus rhenanus vs. C.perifretum) with 8 replicates representing different starting (genomic) DNA amounts of 25, 50, 100, 200, 400, 800, 1200, and 1600 ng, respectively. For each color, linear regressions were performed to evaluate how signal intensities change with increasing amount of hybridized genomic DNA. This information was used to optimize probe selection for the design of a subsequent experimental microarray, and to include probe responsiveness as part of the normalization procedure of the experimental array (see also Dennenmoser et al. 2017 Copy number increases of transposable elements and protein coding genes in an invasive fish of hybrid origin). Reported are average signal intensities (of two technical replicates) for all probes for each red and green channels separately.
Please note that the very high signal values (in the calibration array) are due to raw (not normalized) signal intensities on arrays overloaded with genomic DNA (up to 1600ng starting DNA opposed to the recommended 400ng).

first: Arne

last: Nolte


title: Pumilio regulates mRNA decay during the late maternal-to-zygotic transition in Drosophila melanogaster

city: Toronto

first: Howard

last: Lipshitz

state: ON

address: 1 King's College Circle

department: Molecular Genetics

institute: University of Toronto

summary: Pumilio (PUM) is a Drosophila member of a conserved family of sequence-specific RNA-binding proteins that have been shown to regulate mRNA stability and/or translation in a variety of organisms.  PUM has been shown to repress the translation of several mRNAs in the Drosophila early embryo; failure to repress these targets leads to lethal developmental defects.  Here we use a combination of microarray-based gene expression profiling and next-generation sequencing to identify more than 200 mRNAs that are associated with full-length PUM protein in early embryos and to define a global role for PUM in mRNA decay.  Surprisingly, despite the fact that PUM is maternally supplied and thus is present from the beginning of embryogenesis, the vast majority of PUM-directed decay occurs only after zygotic genome activation.  We show that the smaug mRNA, which itself encodes an RNA-binding protein that directs transcript decay, is a direct target of PUM via binding sites in the smg 3'UTR.  Whereas the endogenous smaug mRNA and the transgenic reporter mRNA that carries the smaug 3'UTR undergo decay after zygotic genome activation, a reporter with an array of PUM-binding sites decays before zygotic genome activation.  These data support a model in which additional cis-elements in the smg 3'UTR delay decay until after zygotic genome activation.

overall_design: Comparison of mRNA expression levels between cold-sensitive pum13/pumMsc embryos and corresponding wild-type controls at 18°C; and between  pumET7/pumMsc embryos and corresponding wild-type controls at 25°C.  The comparison of pum13/pumMsc embryos with their corresponding wild-type controls was done in two replicates: one was a direct comparison between pum13/pumMsc and wild-type samples at corresponding time points; the replicate was a comparison of pum13/pumMsc and corresponding wild-type time points through a common reference, wild-type stage 14 oocytes.  The comparison of pumET7/pumMsc and corresponding wild-type samples was done with two replicates, each of which used a common reference (wild-type stage 14 oocytes).

first: Tim

last: Hughes


title: Genome-wide transcriptome analysis of the wild type and the Nsd1 deletion mutant of Fusarium fujikuroi under 3 different culture conditions

status: Public on May 10 2017

city: Freising

first: Ulrich

last: Guldener

state: Bavaria

address: Maximus-von-Imhof-Forum 3

department: Chair of genome-oriented bioinformatics

institute: Technische Universität München

summary:
We performed genome-wide transcriptome analyses of the Fusarium fujikuroi wild type compared to the ∆nsd1 mutant
Nsd1 is a GATA type transcription factor which has a major impact on growth, conidiation and secondary metabolism in F. fujikuroi

overall_design: The 2 strains were grown, each with 2 biological replicates, under 3 different conditions: synthetic medium with 1) 6 mM glutamine; 2) 60 mM glutamine; and 3) 6 mM NaNO3

last: Güldener

first: Martin

last: Münsterkötter

first: Bettina

last: Tudzynski


title: Inhalation and oropharyngeal aspiration exposure to rod-like carbon nanotubes induces highly similar airway inflammation and biological pathways in mouse lungs

status: Public on May 01 2017

city: Tampere

first: Dario

last: Greco

address: Arvo ylpön Katu 34

department: Faculty of Medicine and Health Technology

institute: Tampere University

summary: Inhalation and low-dose aspiration elicit highly similar pulmonary inflammation which was confirmed by activation of essentially similar biological pathways and even the same genes. Present results provide evidence that oropharyngeal aspiration is valid approach for hazard assessment of nanomaterials and proper alternative method for inhalation exposure.

overall_design: To compare two alternative airway exposure methods, C57BL/6 mice were exposed to rCNT by inhalation method (aerosol mass concentrations of 6.2-8.2 mg/m3; 4h/day for 4 days), or by oropharyngeal aspiration. Low-dose (10 ug/day in 50 ul of PBS ) or high-dose (40 ug/day in 50ul of PBS) aspiration exposure of rCNT was used for four days. Bronchoalveolar lavage and lung tissue samples were collected, histological sections analyzed and mRNA expression profiles were determined by Agilent microarray. Untreated mice were used as Controls for inhalation, and vehichle treated (PBS) as Controls for aspiration.

first: Pia

last: Kinaret

first: Marit

last: Ilves

first: Vittorio

last: Fortino

first: Elina

last: Rydman

first: Karisola

last: Piia

first: Henrik

last: Wolff

first: Kai

last: Savolainen

first: Harri

last: Alenius


title: cowpea: short-podded pools vs. long-podded pools

status: Public on Apr 30 2017

city: Hangzhou

first: Pei

last: Xu

address: 198 Shiqiao Rd

department: Vegetable Institute

country: China

institute: Zhejiang Academy of Agricultural Sciences

summary: Microarray hybridizations of a long-pod and a short-pod pool, each consisting of RNA from seven independent genotypes, were performed to reveal the gene regulatory basis underlying the genotypic pod length difference.

overall_design: Sample groups: 4; Technical replicates each: 3


title: Gene expression signature of WT siblings and hif1α mutants in normoxia and after hypoxia chamber incubation

city: Bad Nauheim

first: Claudia

last: Gerri

address: Ludwigstraße 43

department: Developmental Genetics

country: Germany

institute: Max Planck Institute for Heart and Lung Research

summary:
We have employed whole genome microarray expression profiling as a discovery platform to identify genes with differential expression in WT and hif1α mutants and consequent different response to normoxia or hypoxia conditions.
Two different conditions were considered: 50 hpf mutants and WT in normoxia, 50 hpf mutants and WT after hypoxia chamber treatment (2 hours after 3% O2)

overall_design: Embryos at 50 hpf

first: C

first: D

last: Stainier


title: Genome-wide profiling of H3K27me3 in Drosophila primary spermatocytes.

status: Public on May 02 2017

city: Cambridge

first: Rob

last: White

address: Downing Street

department: Physiology, Development and Neuroscience

institute: University of Cambridge

type: Genome binding/occupancy profiling by genome tiling array

summary: YFP-tagged primary spermatocytes were sorted by FACS, then ChIP together with microarray analysis was used to generate a genome-wide map for the H3K27me3 histone mark.

overall_design: We performed two biological replicates with a Cy3/Cy5 dye swap. Input chromatin was used as the reference control to assay ChIP enrichment.

first: Sherif

last: El-Sharnouby

last: Fischer

first: Robert


title: Comprehensive functional screening of miRNAs involved in human fat cell insulin sensitivity

city: Stockholm

first: Ingrid

last: Dahlman

address: Karolinska Huddinge

institute: Karolinska

summary:
The aim of this study was to detect and functionally investigate miRNAs linked to insulin sensitivity in human subcutaneous white adipose tissue (scWAT). Subjects were selected based on the insulin-stimulated lipogenesis response of subcutaneous adipocytes.
Eleven miRNAs displayed differential expression between OIR and OIS states. Overexpression of miR-143-3p and miR-652-3p increased insulin-stimulated lipogenesis in human in vitro-differentiated adipocytes. MicroRNAs-143-3p and -652-3p are linked to scWAT insulin resistance independently of obesity.

overall_design: Global miRNA profiling by array was performed in abdominal scWAT of obese insulin resistance (OIR), obese insulin sensitive (OIS) and lean women. Signicance analysis of microarrays (SAM) was use to compare the difference in gene expression between groups.MicroRNAs demonstrating differential expression between OIR and OIS women were overexpressed in human in vitro-differentiated adipocytes followed by assessment of lipogenesis and identification of miRNA targets by measuring mRNA/protein expression and 3’UTR analysis.


title: Expression data in Arabidopsis hda6 mutant axe1-5 and its parental line DR5 under drought and control conditions

status: Public on Apr 29 2017

city: Yokohama

first: Motoaki

last: Seki

address: 1-7-22, Suehiro-cho, Tsurumi

country: Japan

institute: RIKEN CSRS

summary: To understand the role of Arabidopsis histone deacetylase HDA6 in drought tolerance, we have employed transcriptional profiling of the hda6 mutant and its parental line under drought and control conditions to identify genes differentially expressed in the hda6 mutant under drought and control conditions. Aligent's Whole Arabidopsis Gene Expression Microarray (Agilent-015059, G2519F, V3, 4x44K) was used.

overall_design: Arabidopsis hda6 mutant axe1-5 and its parental line DR5 were grown in soil for 3 weeks (16 hours light / 8 hours dark). For drought-treated sample, the plants were subjected to drought by withhelding water supply for indicated days. Then total RNA was prepared from the above-ground tissue and used for the microarray hybridization. Three replicative hybridization experiments for each array were carried out using the independent biological samples.

first: Jong

last: Kim

first: Taiko

last: To

first: Akihiro

last: Matsui

first: Junko

last: Ishida

first: Taeko

last: Morosawa

first: Maho

last: Tanaka


title: Expression data in Arabidopsis Col-0 with acetic acid treatment and subsequent drought treatment

summary: To understand the role of acetic acids in drought tolerance, we have employed transcriptional profiling of plants treated with (or without) acetic acid and subsequent drought treatments. Agilent-021169 Arabidopsis 4 Oligo Microarray (V4) were used.

overall_design: Arabidopsis Col-0 were grown in soil for 2 weeks (16 hours light / 8 hours dark). 10mM acetic acid was supplied for 9 days. For drought-treated samples, the plants were subjected to drought by withholding water supply for indicated days. Then total RNA was prepared from the aboveground tissue and used for the microarray hybridization. Three replicative hybridization experiments for each array were carried out using the independent biological samples.


title: Cholesterol regulates DAF-16 nuclear localization and fasting-induced longevity in C. elegans

city: Kyoto

first: Eisuke

last: Nishida

address: Kitashirakawa, Sakyo-ku

department: Department of Cell and Developmental Biology

institute: Graduate School of Biostudies, Kyoto University

summary: Cholesterol has attracted significant attention as a possible lifespan regulator. It has been reported that serum cholesterol levels have an impact on mortality due to age-related disorders such as cardiovascular disease. Diet is also known to be an important lifespan regulator. Dietary restriction retards the onset of age-related diseases and extends lifespan in various organisms. Although cholesterol and dietary restriction are known to be lifespan regulators, it remains to be established whether cholesterol is involved in dietary restriction-induced longevity. Here, we show that cholesterol deprivation suppresses longevity induced by intermittent fasting, which is one of the dietary restriction regimens that effectively extend lifespan. We also found that cholesterol is required for the fasting-induced upregulation of transcriptional target genes such as the insulin/IGF-1 pathway effector DAF-16 and that cholesterol deprivation suppresses the long lifespan of the insulin/IGF-1 receptor daf-2 mutant. Remarkably, we found that cholesterol plays an important role in the fasting-induced nuclear accumulation of DAF-16. Moreover, knockdown of the cholesterol-binding protein NSBP-1, which has been shown to bind to DAF-16 in a cholesterol-dependent manner and to regulate DAF-16 activity, suppresses both fasting-induced longevity and DAF-16 nuclear accumulation. Furthermore, this suppression was not additive to the cholesterol deprivation-induced suppression, which suggests that NSBP-1 mediates, at least in part, the action of cholesterol to promote fasting-induced longevity and DAF-16 nuclear accumulation. These findings identify a novel role for cholesterol in the regulation of lifespan.

overall_design: Two independent replicates were performed. Total RNA was extracted with TRIzol (Invitrogen). The extracted RNA was purified with PureLink RNA Micro Kit (Invitrogen) and analyzed with Agilent 2100 Bioanalyzer to assess the RNA integrity. The microarray procedures were performed according to Affymetrix protocols. Hybridized arrays were scanned using an Affymetrix GeneChip Scanner.

first: Akiko

last: Ihara

first: Masaharu

last: Uno

first: Koichi

last: Miyatake

first: Sakiko

last: Honjoh


title: Systematic identification of changes in the yeast protein interaction network in response to environmental, chemical, and genetic perturbation [interactome data]

city: Palo Alto

first: Ulrich

last: Schlecht

address: 3165 Porter Drive

department: Biochemistry

institute: Stanford University

summary: To understand the principles underlying protein-protein interaction (PPI) complex changes in response to external perturbations, we created a highly multiplexed version of the murine dihydrofolate reductase protein complementation assay (mDHFR PCA) in Saccharomyces cerevisiae, allowing quantitative PPI complex profiling in vivo. We investigated the effects of 14 different conditions (including small molecules, abiotic stress factors, and nutrient composition) on a total of 1383 PPIs. More than half of PPIs (758) were found to be variable, and their Gene Ontology (GO) annotations were found to be informative of both the nature of the perturbation within each condition, as well as the overall variability of the interactions across conditions. Many perturbations triggered network changes characterized by large connected modules centered around highly connected proteins ('hubs'), suggesting that cellular control of a few proteins (e.g., by mRNA levels) can induce widespread PPI remodeling. Under a diauxic shift from glucose to ethanol as the main carbon source, we found a striking relationship between PPI changes measured by our assay and those predicted by mRNA expression under a simple law of mass action based model.

overall_design: In the murine Dihydrofolate Reductase-based Protein-fragment Complementation Assay (mDHFR PCA), the interaction of two proteins of interest allows a yeast strain to grow in the presence of the DHFR inhibitor methotrexate (MTX). We have created a pool of mDHFR-PCA strains each containing unique 20-bp barcode sequences flanked by common priming sites, allowing the relative abundance of individual strains to be quantitatively monitored within a pool of competitively-grown strains. To identify protein-protein interactions that change in response to environmental perturbation, we measured the fitness of 1383 mDHFR-PCA strains in parallel in minimal media (i.e., yeast nitrogen base and ammonium sulfate) in the presence or absence of methotrexate and in the presence of an environmental perturbation. Each condition was tested in duplicate. To test the impact of single protein deletion on the network, we implemented a Tet-inducible CRISPRi system to repress the transcription of a target gene in a controlled manner. In this system, the expression of a guide RNA is activated by addition of anhydrotetracycline (ATC) into the media, which then recruits a Cas9-repressor fusion protein to a locus of interest. We targeted the RBD2 gene in this manner.

first: Albi

last: Celaj

first: Justin

last: Smith

first: Sundari

last: Suresh

first: Molly

last: Miranda

first: Ronald

last: Davis

first: Fritz

last: Roth

last: St. Onge


title: Systematic identification of changes in the yeast protein interaction network in response to environmental, chemical, and genetic perturbation [transcriptome data]

platform_organism:
Schizosaccharomyces pombe
Saccharomyces cerevisiae

overall_design: We chose to investigate the relationship between interactome and transcriptome changes in the shift from glucose to ethanol as the sole carbon source. To obtain relative mRNA expression data in our pool, cells were grown in selective media supplemented with dextrose as a pre-culture and then shifted to selective media containing ethanol as the sole carbon source, with samples taken at 0, 0.5, 1, 4, and 12 hours after the transfer.

first: Robert


title: An essential role of FBXL5-mediated cellular iron homeostasis in the maintenance of hematopoietic stem cells

city: St. Louis

first: Yoshiharu

last: Muto

state: MO

address: 660. S Euclid Ave., CB 8118

department: Medicine / Nephrology

institute: Washington University in St. Louis

summary: Hematopoietic stem cells (HSCs) are maintained in the hypoxic niche so as to limit oxidative stress. Although iron is a major factor to evoke oxidative stress, the importance of cellular iron homeostasis in HSCs has been unrecognized. We now demonstrate that iron regulation mediated by FBXL5 is required for the self-renewal capability of HSCs. Conditional ablation of Fbxl5 gene in mouse HSCs resulted in cellular iron overload, leading to the reduction in the number of HSCs. Bone-marrow transplantation experiments revealed that FBXL5-deficient HSCs were unable to reconstitute the hematopoietic system as a result of stem cell exhaustion. Transcriptomic analysis showed abnormal activation of oxidative stress response as well as cell cycle in HSCs. Suppression of IRP2 activity in FBXL5-deficient HSCs restored the stem cell function, suggesting that IRP2 is potentially a novel therapeutic target of stem cell diseases such as myelodysplastic syndrome, which is associated with FBXL5 downregulation in humans.

overall_design: 3000 HSCs were purified as c-Kit+Sca-1+Lin–CD150+CD48– bone marrow cells from 3 control mice and 3 mice with conditional FBXL5 knockout on C57Bl/6 background.

first: Keiich

last: Nakayama


title: Root transcriptional profile of maize seedlings treated with protein hydolysate, free amino acids and inorganic nitrogen.

status: Public on Apr 26 2017

city: Verona

first: Anita

last: Zamboni

address: Strada Le Grazie, 15

department: Biotechnology

institute: University of Verona

summary: Different forms of N can affect plant metabolism. Differences can be observed at physiological and transcriptional levels comparing maize 4-day-old maize seedlings tretaed for three days with three different N forms: protein hydrolysates (SICIT2000 Spa), inorganic nitrogen (NH4H2PO4) or a mixture of free amino acids.

overall_design: Transcriptional profiles were obtained using roots of 4-day-old maize seedlings grown for three additional days in a diluted nutrient solution (Pinton et al. 1999) supplemented with either protein hydrolysates (SICIT2000 Spa) or inorganic nitrogen (NH4H2PO4) or a mixture of amino acids mimicking the amino acids content of the protein hydrolysates. Three different biological replicates were used for each treatment repeating the grown and treatement experiment three times.

first: Chiara

last: Santi

first: Zeno

last: Varanini

first: Tiziana

last: Pandolfini


title: Expression data from Tip110 transgenic mouse blastocyst-derived outgrowths

city: Fort Worth

first: Johnny

last: He

state: TX

address: 3500 Camp Bowie Blvd

department: Cell Biology, Immunology & Microbiology

institute: University of North Texas Health Science Center at Fort Worth

summary:
LONG SUMMARY: In this study, we aimed to characterize the function of Tip110 in embryonic development and in mESC survival and self-renewal using a Tip110+/- mouse model. Mating these mice produces wild-type, Tip110+/-, and Tip110-/- offspring. Tip110-/- offspring die early in mouse postimplantation development and mESCs cannot be derived from Tip110-/- blastocysts. Array analysis was performed to gain a better understanding of the underlying molecular mechanisms at play and to appreciate the biological role of Tip110 in embryo and ESC development.
SHORT SUMMARY: We used microarray analysis to detail the global program of gene expression in Tip110-/- outgrowths compared to their wild-type counterparts to gain a better understanding of the biological role of the Tip110 protein in embryonic development and mESC survival and self-renewal.

overall_design: Mouse blastocysts were flushed from the uterine horns of pregnant females at 3.5 dpc after successful Tip110+/- intercrosses. Blastocysts were cultured in knockout serum replacement embryonic stem cell media for 4-6 days before isolating RNA. RNA was extracted using the RNeasy Micro Kit (Qiagen) for hybridization on Affymetrix microarrays (WTA 1.0, Mouse). We collected many embryos from both natural matings and superovulations and generated cDNA from 1-2 ul of RNA to confirm whether each was wild-type, Tip110+/-, or Tip110-/-.  The Veriquest One-Step qR-PCR Quantification Assay from Affymetrix was used to quantify the RNA from wild-type and Tip110-/- outgrowths. 100 pg of RNA was used per sample.

first: Amanda

last: Whitmill


title: Comparison of Solanum dulcamara transcriptome after real and simulated herbivory

status: Public on Apr 24 2017

city: Berlin

first: Tobias

last: Lortzing

state: Berlin

address: Haderslebener Str. 9

institute: Freie Universität Berlin

summary: Plants are attacked by diverse herbivores and respond with manifold defense responses. To study transcriptional and other early regulation events of these plant responses, herbivory is often mimicked to standardize the temporal and spatial dynamics that vary tremendously for natural herbivory. Yet to what extent such mimics of herbivory are able to elicit the same plant response as real herbivory remains largely undetermined. We examined the transcriptional response of a new model plant to herbivory by a lepidopteran larva and to a commonly used herbivory mimic by applying the larvae’s oral secretions to standardized wounds. We designed a microarray for Solanum dulcamara and showed that the transcriptional response to real and to simulated herbivory by Spodoptera exigua overlapped moderately by about 40%. Interestingly, certain responses were mimicked better than others; 60% of the genes up-regulated but not even a quarter of the genes down-regulated by herbivory were similarly affected by application of oral secretions to wounds. While the regulation of genes involved in signaling, defense and water stress were mirrored well by the herbivory mimic, most of the genes related to photosynthesis, carbohydrate- and lipid metabolism were exclusively regulated by real herbivory. Thus, wounding and elicitor application decently mimics herbivory-induced defense responses but likely not the re-allocation of primary metabolites induced by real herbivory.

overall_design: Four treatment groups were analyzed in S. dulcamara clones from different locations (Siethen, Erkner, Grunewald, and Mehrow, all in the vicinity of Berlin, Germany). Leaves were either undamaged controls (control), fed upon by S. exigua (spodo) caterpillars for 24 h or damaged with a pattern wheel and treated with S. exigua oral secretions (w+os) and harvested either after 1 h or 24 h.

first: Vivien

last: Firtzlaff

first: Duy

last: Nguyen

first: Ivo

last: Rieu

first: Sandra

last: Stelzer

first: Martina

last: Schad

first: Jim

last: Kallarackal

first: Anke

last: Steppuhn


title: Systematic identification of changes in the yeast protein interaction network in response to environmental, chemical, and genetic perturbation

first: Ulrich

last: Schlecht

type:
Other
Expression profiling by array

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

overall_design: Refer to individual Series


title: Toxicogenomic module associations with pathogenesis: A network based approach to understanding drug toxicity

status: Public on Apr 12 2017

city: Indianapolis

first: Keith

last: Goldstein

state: IN

address: Lilly Corporate Center

department: Investigative Toxicology

institute: Eli Lilly & Co.

summary: Despite investment in toxicogenomics, nonclinical safety studies are still used to predict clinical liabilities for new drug candidates. Network-based approaches for genomic analysis help overcome challenges with whole-genome transcriptional profiling using limited numbers of treatments for phenotypes of interest. Herein, we apply co-expression network analysis to safety assessment using rat liver gene expression data to define 415 modules, exhibiting unique transcriptional control, organized in a visual representation of the transcriptome (the ‘TXG-MAP’). Accounting for the overall transcriptional activity resulting from treatment, we explain mechanisms of toxicity and predict distinct toxicity phenotypes using module associations. We demonstrate that early network responses compliment traditional histology-based assessment in predicting outcomes for longer studies and identify a novel mechanism of hepatotoxicity involving endoplasmic reticulum stress and Nrf2 activation. Module-based molecular subtypes of cholestatic injury derived using rat translate to human. Moreover, compared to gene-level analysis alone, combining module and gene-level analysis performed in sequence identifies significantly more phenotype-gene associations, including established and novel biomarkers of liver injury.

overall_design: Male CD/IGS (Sprague-Dawley) rats were assigned to 16 experimental groups consisting of three (3) animals/group and fed ad libitum.  Half of the experimental groups (8) consisted of sham-operated animals, and the other half (8) of the experimental groups had their common bile duct surgically ligated. Three (3) sham and three (3) ligated animals were necropsied at 3, 6, 12, and 24 hours, and 3, 5, 10 and 14 days after surgery.  (51 total samples).

first: Jeffrey

last: Sutherland

first: Yue

last: Webster

last: Willy

first: George

middle: H

last: Searfoss

first: Armando

last: Irizarry

first: David

last: Hall

first: James

last: Stevens


title: Transcriptional impairments in mouse model of mucopolysaccharidosis IIIA and responses to systemic gene delivery using adeno-associated virus serotype rh74 vector (AAVrh74)

status: Public on Apr 14 2017

city: Columbus

first: Haiyan

last: Fu

state: Ohio

address: 700 Children's Dive

department: Center for Gene Therapy

institute: Research Institute at Nationwide Childrens Hospital

summary: Mucopolysaccharidosis (MPS) IIIA is a neuropathic lysosomal storage disease caused by deficiency in SGSH. Genome-wide gene expression microarrays in MPS IIIA mice detected broad molecular abnormalities (≥2 fold, FDR≤10) in numerous transcripts (314) in the brain and blood (397). Importantly, 22 dysregulated blood transcripts are known to be enriched in the brain and linked to broad neuronal functions. To target the root cause, we used a self-complementary (sc) AAVrh74 vector to deliver the human SGSH gene into 4-6-wk-old MPS IIIA mice by an intravenous injection. The treatment resulted in global CNS and widespread somatic restoration of SGSH activity, clearance of CNS and somatic GAG storage, improved behavior performance, and significantly extended survival. The scAAVrh74-hSGSH treatment also led to the correction of the majority of the transcriptional abnormalities in the brain (95.9%) and blood (97.7%), of which 182 and 290 transcripts were normalized in the brain and blood, respectively. These results demonstrate that a single systemic scAAVrh74-hSGSH delivery mediated efficient restoration of SGSH activity and resulted in a near complete correction of MPS IIIA molecular pathology. This study also demonstrates that blood transcriptional profiles reflect the biopathological status of MPS IIIA, and also respond well to effective treatments.

overall_design: To assess the therapeutic impacts of scAAVrh74 gene delivery, we treated 4-6-wk-old MPS IIIA mice with an IV injection of scAAVrh74-U1a-hSGSH (5x1012vg/kg, n=13), using wt and non-treated MPS IIIA littermates (n=15) as controls. The animals were tested for behavioral performance in a hidden task in Morris water maze (n=13) and observed for longevity (n=9). At 7 mo post injection (pi), blood and tissue were collected from groups of male mice (n=4/per group) for analyses to assess therapeutic impact. We focused on males to minimize individual variation in the gene array analysis.  Total RNA was isolated from the brain and peripheral blood of individual wt, non-treated MPS IIIA and scAAVrh74-treated mice (all male, n=4/group) and then analyzed separately (n=4/group) using genome-wide gene expression microarrays of >60,000 transcripts, to assess the potential blood-brain molecular association in MPS IIIA and their response to the vector treatment.

first: F

middle: J

last: Duncan

first: Bartholomew

last: Naughton

first: Kimberly

last: Zaraspe

first: Darren

last: Murrey

first: Aaron

middle: S

last: Meadows

first: K

last: Clark

middle: E

last: Newsome

first: Peter

last: White

first: Douglas

last: McCarty


title: BRG1 Chromatin Remodeling ATPase Balances Germ Layer Patterning by Amplifying the Transcriptional Burst at Midblastula Transition [MBT]

status: Public on Apr 20 2017

city: Martinsried

first: Tobias

last: Straub

address: Großhadener Str. 9

department: Biomedical Center, Bioinformatics

institute: LMU Munich

summary: Zygotic gene expression programs control cell differentiation in vertebrate development. In Xenopus, these programs are initiated by local induction of regulatory genes through maternal signaling activities in the wake of zygotic genome activation (ZGA) at the midblastula transition (MBT). These programs lay down the vertebrate body plan through gastrulation and neurulation, and are accompanied by massive changes in chromatin structure, which increasingly constrain cellular plasticity. Here we report on developmental functions for Brahma related gene 1 (BRG1), a key component of embryonic SWI/SNF chromatin remodeling complexes. Carefully controlled, global BRG1 protein depletion in X. tropicalis and X. laevis leads to embryonic lethality from gastrulation on, similar to BRG1-/- mice. Transcriptome analysis at late blastula, before development becomes arrested, indicates predominantly a role for BRG1 in transcriptional activation of a limited set of genes involved in pattern specification processes and nervous system development. Mosaic analysis by targeted microinjection defines BRG1 as an essential amplifier of gene expression in dorsal (BCNE and Nieuwkoop centers) and ventral (BMP/Vent) signaling centers. By tissue transplantation, we define BRG1-dependent activation of chordin (chrd) transcription in the prospective neural plate (BCNE region) as an essential step in head formation. BRG1-sensitive genes are typically characterized by a robust burst of transcription at MBT. These results define a systemic function for BRG1-containing SWI/SNF chromatin remodelers as a transcriptional amplifier of the gene network that initiates embryonic patterning.

overall_design: RNA isolated from X. tropicalis embryos before and after midblastula transition. 3 replicate experiments with cells from 10 embryos pooled.

first: Gabriele

last: Wagner

first: Nishant

last: Singhal

first: Dario

last: Nicetto

first: Elisabeth

last: Kremmer

first: Ralph

last: Rupp


title: BRG1 Chromatin Remodeling ATPase Balances Germ Layer Patterning by Amplifying the Transcriptional Burst at Midblastula Transition [BRG1]

overall_design: RNA isolated from X. tropicalis embryos injected radially at the 2-4 cell stage with Brg1 or control morpholinos and cultivated until late blastula stage. 4 replicate experiments with cells from 10 embryos pooled.


title: BRG1 Chromatin Remodeling ATPase Balances Germ Layer Patterning by Amplifying the Transcriptional Burst at Midblastula Transition


title: Expression profiling of microRNAs in Bovine ovarian follicular development; comparative analyses between LHF and CL groups

city: Midlothian

first: Xavier

last: Donadeu

address: Easter Bush

institute: Roslin Institute, University of Edinburgh

summary: The study aimed to identify miRNAs expression profiles associated with growth and regression of dominant-size follicles in bovine. Follicles were collected from abattoir ovaries and their status (healthy/atretic) was assessed by measuring steroid levels and aromatase expression. Corpora lutea (CL) were collected from ovarian pairs correponding to days 1 to 4 of the oestrus cycle. Total RNA was isolated from whole follicles at different developmental stages and from CL. An heterologous microarray (Exiqon, Denmark) approach followed by RT-qPCR validation (Qiagen, UK) was used to identify and compare miRNA profiles between large healthy follicles (diameter, 13–16 mm, n=6) and each of small (4–8 mm, n=6 pools of follicles), large atretic folllicles (13-16 mm, n=6)  and CL (n=6). RNA from the above groups was hybridized to the miRCURY LNA™ microRNA Hi-Power Labeling Kit,Hy3™/Hy5™ (Exiqon) and hybridized on the miRCURY LNA™ microRNA Array (6th gen).  A total of 17 and 57 microRNAs were differentially expressed (> 2 fold, adj. P-value < 0.05) between Large Healthy and each of Small and Large Atretic follicles, respectively, a fraction of which corresponded to registered bovine miRNA sequences.  A subset of 5 bovine miRNAs (miR-144, miR-202,vmiR-451, miR-652, miR-873) were confirmed by qPCR to be upregulated in Large Healthy follicles, were enriched in mural granulosa cells and their predicted targets mapped to genes involved in follicular cell proliferation and differentiation, suggesting an involvemet of this subset of microRNAs in ovarian follicle development.  In addition, the miR-183-96-183 cluster was identified as upregulated in CL and was shown to be involved in luteal survival and progesterone production.

platform_organism:
Homo sapiens
Mus musculus
Rattus norvegicus
Human alphaherpesvirus 1
Human alphaherpesvirus 2
Human betaherpesvirus 5
Murid betaherpesvirus 1
human gammaherpesvirus 4
JC polyomavirus
Human immunodeficiency virus 1
Murid gammaherpesvirus 4
Human gammaherpesvirus 8
Merkel cell polyomavirus
Mus musculus cytomegalovirus 2
Betapolyomavirus hominis
Betapolyomavirus macacae

overall_design: Six biological replicates per developmental stage (total of 24 samples) were used in a double dye microRNA microarray experiment. Samples were distributed among slides so that each experimental group was represented at least once in each slide. For each gene, mean normalized intensities (n= 6 biological replicates/group) were compared between follicle stages (SF vs LHF, LHF vs LAF and LHF vs CL).

middle: X

first: S

last: Sontakke