title: RNASeq libraries of quorum-sensing induced and wild-type M. ciceri bv. biserrulae WSM1271

status: Public on Mar 01 2018

city: Perth

first: Timothy

last: Haskett

state: WA

address: 50 South Street Murdoch

department: Biological Sciences

country: Australia

institute: Murdoch University

summary: M. ciceri WSM1271 carries a novel integrative and conjugative element (ICE) termed a tripartite ICE (ICE3) that exists as thee separated DNA regions in the chromosome. Three site-specific recombinases acting on three distinct pairs of attachment sites catalyse recombination between the three ICE3 DNA regions leading to their excision from the chromosome to form a single plasmid-like entity for horizontal conjugative transfer. RNASeq was used to probe for differentially expressed ICE3-encoded genes in WSM1271 wild-type cells, and engineered WSM1271 cells carrying cloned copies of two quorum-sensing loci that induce ICE3 excision and transfer. Overall, 187 significantly differentially expressed genes (adjusted P-value < 0.05) were identified and although ICEMcSym1271 comprised only ~7.6% of the chromosome, 15.5% (29) of the differentially expressed genes were located on ICEMcSym1271. Genes likely involved in activation of excision and conjugation including rdfS, rlxS, msi172-msi171 and the type-IV conjugative pilus gene cluster msi031-trbBCDEJLFGI-msi021 were all significantly induced. The RNA-Seq libraries generated in this study have strongly aided the development of our model detailing the regulation of excision and transfer of ICE3s.

sample_organism: Mesorhizobium ciceri biovar biserrulae WSM1271

overall_design: rRNA depleted total RNA profiles of WSM1271 wild-type cells or those overexpressing two quorum-sensing loci traI1 (Mesci_2552) and traR1 (Mesci_2553) were generated using Ion Proton sequencing.

middle: L

first: Jason

last: Terpolilli

first: Vinoy

last: Ramachandran

first: Joshua

last: Ramsay


title: The differences of Bcr-abl+ tumor stromal cell gene expression between wild type B6 mice and Sipa1 knock out mice

status: Public on Mar 05 2018

city: Kyoto

first: Yan

last: Xu

address: 53 Shogoin Kawahara-cho

country: Japan

institute: Kyoto University

summary: To assess the activation status of mesenchymal stroma cells and CD8 T cells in tumor tissues, we sorted the GFP– CD45– CD31– Ter119– cell populations mostly representing mesenchymal cells and GFP- TCRb+CD8+ cell populations mostly representing CD8 T cells from Bcr-Abl+ tumors of Wt and Sipa1–/– mice and subjected them to comparative DNA microarray analysis.

overall_design: Tumor gene expression in mesenchymal stroma cells and CD8 T cells are measured in wide type B6 mice and Sipa1 knock out mice. 5 heads wide type mice and 5 heads of Sipa1 knock out mice were used for the experiment

first: Kentaro

last: Sumida

first: Satoshi

last: Ikeda


title: Short-term mastication after weaning upregulates GABAergic signalling and reduces dendritic spine in thalamus

status: Public on Mar 06 2018

city: Bunkyo-ku

first: Tomiko

last: Asakura

state: Tokyo

department: Graduate School of Agricultural and Life Sciences

institute: University of Tokyo

summary:
Mastication enhances brain function and even mental health, but little is known molecular basis underlying the effects of chewing on neural development in early childhood we conducted experiment with rats fed a with soft or hard chow diet immediately after weaning and investigated the expression of genes were investigated after another 8 days of breeding.
These results suggest that mastication in the early developing period upregulates GABAergic signaling genes, with a decrease of spine pruning in thalamus

overall_design: As a preparatory phase of the breeding process, the rats were provided with powdered feed and water for two days to get, ad libitum. After that, the rats were divided into two groups in a manner such that the average weight is approximately the same between the groups. One group was fed a powdered feed (powder, P), other group was fed a solid feed (chow, C) for eight days.

first: Keiko

last: Abe

first: Toshitada

last: Nagai

first: Mana

last: Ogawa

first: Hitonari

last: Miyaguchi

first: Yoshikazu

last: Saito

first: Kei

last: Kumakura


title: PPARg controls proinflammatory responses in alveolar macrophages

city: Heidelberg

first: Markus

last: Feuerer

address: Im Neuenheimer Feld 280

country: Germany

institute: DKFZ

summary:
Tissue resident macrophages are a heterogeneous population with unique functions. During steady state conditions most tissue macrophages are of embryonic origin and maintained locally. Despite their common fetal origin, tissue macrophages are able to fulfil tissue specific functions, suggesting that the local environment can modulate cell function. It has been reported that PPARg is critical for the development of macrophages in the lung.
Here, we show that PPARg functions as a transcriptional repressor in alveolar macrophages. Alveolar macrophages lacking Pparg responded more strongly to LPS stimulation by producing more cytokines and phagocytosed more particles in vitro. Certain prostaglandins can act as endogenous ligands for PPARg. We show that prostaglandins were expressed in an organ-specific fashion and modulated cytokine production by alveolar macrophages as well as bone marrow-derived macrophages and monocytic U937 cells. Pparg expression was further induced in macrophages by different cytokine combinations including IL-4, IL-3 and IL-13 suggesting a global role for PPARg which can be regulated by the local environment on two levels. Lastly, repression of inflammatory genes was mediated by PPARg interacting with NFkB and STAT signalling cascades rather than direct transrepression. Therefore PPARg is a modulator of macrophage functions, that changes the inflammatory state of macrophages by regulating classical immune signalling cascades.

overall_design: We isolated alveloar macrophages lacking the transcription factor Pparg from Pparg-/-.LysmCre mice. As control we isolated wild type alveolar macrophages from Pparg+/-.LysmCre and Pparg-/-.LysmCre mice. Cells were isolated based on cell surface expression of SiglecF and CD11b by FACS. RNA was extracted and gene expression measured.

first: Ulrike

last: Träger


title: Gene expression data of PFKFB3 KD in SMMC7721 cell line

city: Zhengzhou

first: Wen-Kai

last: Shi

state: Henan

address: Jianshedong Road No.1

department: Department of hepatopancreatobiliary surgery

country: China

institute: The first affiliated hospital of Zhengzhou university

summary: Overexpression of 6-phosphofructo-2-kinase/fructose-2,6-biphosphatase 3 (PFKFB3), a key molecule of glucose metabolism in cytoplasm, was found in various tumors. Emerging evidence suggested that PFKFB3 also located in nucleus and shown regulatory functions other than glycolysis. In this study, we found that PFKFB3 expression is associated with hepatocellular carcinoma (HCC) growth and mainly located in the nucleus of tumor cells. PFKFB3 overexpression was associated with large tumor size, and poor survival of patients with HCC. Knockdown of PFKFB3 inhibited HCC growth, not only by reducing glucose consuming but also damaging DNA repair function leading to G2/M phase arrest and apoptosis. Therefore, we performed a cDNA microarray in PFKFB3 knockdown SMMC7721 cells.

overall_design: Analysis of RNA isolated from SMMC7721-shVector and SMMC7721-shPFKFV3 cell lines.

first: Wenkai

first: Huichuan

last: Sun


title: Gene expression difference of small cell lung cancer cell after treatment with a kind of drug.

status: Public on Mar 03 2018

city: Wuhan

first: M.

last: Peng

address: Wujiadun 156

department: Oncology Center

institute: Wuhan Union Hospital

summary: Examine gene expression changes of NCI-H446 after treatment with a kind of chemotheraputic drug

overall_design: Treat three flasks of cells with DMSO and  three flasks with drug of the same concentration, then detect the whole  gene expression difference between them by Phalanx OneArrayTM .

first: Dan Dan

last: Yu

first: Miao


title: Different expression profiles of miRNAs in preeclampsia and normal placenta (miRNA)

city: Beijing

first: Zhenyu

last: Zhang

address: Gongtinanlu 8hao

institute: Beijing Chao-Yang Hospital,Capital Medical University

summary: Preeclampsia is usually considered as a placental basis of diseases, as there are many differently expressed proteins or pathogenic proteins expressed in the placenta. Owing to the important role of post-transcriptional gene regulation in phenotypes and functions of cells, non-coding ribonucleic acid (ncRNA) molecules contributed to the regulation. We collected 7 placental samples from 3 preeclampsia patients and 4 normal women, focused on the basal plate of placenta, as it is the direct connection of mother and fetal, and adopted SBC human ceRNA array V1.0（4×180K）and human miRNA microarray (8*60 K). The results revealed that expressions of 2840 lncRNAs, 1093 mRNAs, 4282 circRNAs and 4 miRNAs were different between preeclampsia and normal placentas. The functions of differentially expressed lncRNAs and co-expressed potential targeting genes were predicted by analyzing Gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) biological pathway analysis. Furthermore, we analyzed and find the co-expression and interaction patterns of different RNAs and possible ceRNA mechanism. The present study provided a systematic perspective on the potential function of non-coding RNAs (ncRNAs) in the pathogenesis of preeclampsia.

overall_design: 7 placental samples from 3 preeclampsia patients and 4 normal women were enrolled in. there were no replicates, control and/or reference Samples or dye-swaps.


title: The embryo affects day 14 uterine transcriptome depending on the nutritional status in sheep

city: Urbana

first: Mario

middle: Pietro Emilio

last: Vailati Riboni

state: IL

address: 1207 W Gregory Dr

department: Animal Science

country: USA

institute: University of Illinois at Urbana-Champaign

summary: Transcriptomics and functional bioinformatics were used to investigate the potential interactions of undernutrition and the presence of the conceptus at the time of maternal recognition of pregnancy on uterine indicators of metabolism and reproduction. Adult Rasa Aragonesa ewes were allocated to one of two planes of nutrition during 28 days: maintenance energy intake (control; 5 cyclic, 6 pregnant ewes) providing 7.8 MJ of metabolisable energy per ewe and 0.5 maintenance intake (undernourished; 6 cyclic, 7 pregnant ewes) providing 3.9 MJ of metabolisable energy per ewe. RNA from uterine tissue was harvested at slaughter on day 14 of estrus or pregnancy, and hybridized to the Agilent 15K Sheep Microarray chip. Functional bioinformatics analyses were performed using the Dynamic Impact Approach (DIA) and Ingenuity Pathway Analysis. Among metabolic pathways, citrate cycle, oxidative phosphorylation, pentose and glucuronate interconversions and biosynthesis of unsaturated fatty acids were upregulated in control pregnant compared with control cyclic ewes. However, these pathways were not altered in undernourished ewes. The presence of an embryo in undernourished ewes upregulated fatty acid and glycogenic amino acid metabolism. RIG-I and Toll like receptors and chemokine signaling pathways were upregulated by the presence of the embryo in both control and undernourished ewes, but in the latter group the impact was lower. Undernutrition alone upregulated carbohydrate metabolism, but different pathways were altered in cyclic versus pregnant ewes. Citrate cycle, glycolysis/gluconeogenesis, and pentose and glucuronate interconversions were upregulated in undernourished cyclic compared with control cyclic ewes. Glycolysis/gluconeogenesis, pyruvate and propanoate metabolism, beta-alanine and phenylalanine metabolism were upregulated in undernourished pregnant compared with control pregnant ewes, whereas biosynthesis of unsaturated fatty acids and replication and repair were downregulated. Undernutrition alone led to an overall weak activation of immune system pathways both in cyclic and pregnant ewes. However, undernourished cyclic compared with control cyclic ewes had a high activation of NOD-like and RIG-1 like receptor signaling pathways, whereas undernourished pregnant compared with control pregnant ewes only had a weak upregulation of T cell receptor signaling pathways. Overall, data revealed that metabolic and immune adaptations of the uterus to nutrient restriction are dependent on the presence of the conceptus.

overall_design: 46 adult multiparous Rasa Aragonesa ewes were housed in individual pens and offered a diet (once daily) that provided 1 x live weight maintenance requirements for 1 month prior to the beginning of the experimental procedures [12]. The estrus cycles were synchronized using intravaginal sponges, which were inserted for 14 days. At the time of sponge insertion, ewes were allocated to one of two planes of nutrition: a control (n= 21; 7.8 MJ of metabolisable energy per ewe), which continued to receive the same diet for 28 days, and a low plane of nutrition (n = 25; 3.9 MJ of metabolisable energy per ewe), which was offered at 50% of estimated daily requirements (pellet and straw) until the end of the experiment. At the time of sponge withdrawal, ewes were injected with 300 IU, i.v., equine chorionic gonadotropin (Intervet, Salamanca, Spain), and the occurrence of estrus (Day 0) was monitored every 8 h. Thirteen control ewes and 18 ewes in the low plane of nutrition were mated to vasectomized or intact rams to establish a cyclic and pregnant group, respectively, within each plane of nutrition

first: Victoria

last: de Brun

first: Juan

middle: J

last: Loor

last: Vailati-Riboni

first: Omar

last: Bulgari

first: Khuram

last: Shahzad

first: José

middle: A

last: Abecia

first: Cecilia

last: Sosa

first: Ana

last: Meikle


title: root hair-expressed genes in rice

city: Yongin-si

first: Moon

last: Sunok

state: Gyeonggi-do

address: 1732, Deogyeong-daero

department: genetic engineering

country: South Korea

institute: kyung hee university

summary: To identifiy root hair-preferred genes in rice, we perform microarray using root hairs sample from don-gin and lon-gin cultivar

overall_design: After sterilizing, seeds of rice were placed on an MSO medium during 3 day. The seminal roots were detached and submerged in liquid nitrogen and then gently were rubbed to purify root hairs

first: Sunok

last: Moon

first: Ki-Hong

last: Jung


title: Arabidopsis degradome analysis from Tobacco rattle virus (TRV) infected plants

city: Madrid

first: Jose M.

last: Franco-Zorrilla

state: Madrid

address: Darwin, 3

department: Plant Molecular Genetics

country: Spain

institute: Centro Nacinal de Biotecnologia-CSIC

summary: We aimed to identify targets of miRNAs/small RNAs in Arabidopsis inflorescences after infection with Tobacco rattle virus (TRV).

overall_design: The experiment consists in 3 biological replicates of TRV-infected plants and Mock-inoculated plants. Each RNA sample was split into two and obtained both RNA-ligated and non-ligated labeled samples separately for hybridization of Affymetrix ATH1 microarrays.

first: César

last: Llave

first: Jose

middle: M


title: The miRNA expression characteristics in alopecia areata

city: Shanghai

first: Youyu

last: Sheng

address: 12 Middle Wulumuqi Road, Shanghai 200040, China.

institute: Huashan hospital

summary: To explore the regulatory effect between miRNAs and mRNAs and the possibility of miRNAs as specific blood-based biomarkers in the developmental process of severe alopecia areata (AA), human peripheral blood samples from AA patients and healthy donors were obtained for analysis. we identified 36 significantly differentially expressed miRNAs in severe active AA patients. MiRNA target gene prediction and functional annotation analysis showed a significant enrichment in several pathways including the ribosome, cancer, cell cycle, insulin signaling, TGF-β signaling and p53 signaling pathways. Analysis of the three kinds of network showed that miR-185-5p, miR-125b-5p, and miR-186-5p might play important and synergistic roles in the developmental process of AA. According to the receiver operating characteristic curve analysis, several miRNAs were selected for the quantitative real-time PCR validation and further applied as biomarkers to classify severe active AA patients and healthy individuals. Among the miRNAs, hsa-miR-210 and hsa-miR-1246 had high prediction with high accuracy.

overall_design: Ten blood samples were analyzed, including 5 severe active AA patients and 5 healthy controls.

first: Qinping

last: Yang


title: caveolin-1 induced gene expression change in retinae

city: GuangZhou

first: Zhongshu

last: Tang

state: Guangdong

address: 54 South Xianlie Road

institute: Sun Yat-sen University

summary: Caveolin-1 (Cav1) is the main structure protein of caveolae. Its main functional domain is the scaffolding domain that is the bind site of many interactors. A fused peptide called cavtratin is used to test Cav1 function which includes the scaffolding domain and a short internalizing peptide AP. Cav1 has been reported to be associated with glaucoma in the GWAS study. To explore its role in the retina, we explored the gene expression change after Cav1-shRNA or cavtratin was injected into the mouse eye vitreous.

overall_design: Cav1-shRNA or cavtratin was injected into the mouse eye vitrous and kept for 2 days or 2 hours, respectively. AP was used as the control at the same time as cavtratin. 5-6 Retinae were collected and pooled in one group for the array.

first: Wei

last: Chen

first: Minquan

first: Lijuan

last: Huang

first: Shasha

last: Wang

first: Xuri

last: Li


title: Anopheles coluzzii larval response to two purified Pseudomonas aeruginosa phenazine pigments 1-HP and Pyo.

city: Berlin

first: Philip

middle: Adrian

last: Huegli

state: Berlin

address: Charitéplatz 1

department: Vector Biology

institute: Max Planck Institute for Infection Biology

summary: Pseudomonas aeruginosa, the type species of the Pseudomonas genus, is an environmental Gram negative bacterium, well-known for its ability to produce toxins, resist antibiotics, and opportunistically colonize various niches, including invertebrate and vertebrate hosts. P. aeruginosa produces redox active secondary metabolites called phenazines involved in quorum sensing, biofilm formation, virulence, and iron acquisition. Moreover, these colorful pigmented virulence factors act as ligands for the highly conserved aryl hydrocarbon receptor (AhR) thereby regulating antibacterial defenses in vertebrates. Pseudomonas spp. are some of the most frequently identified bacteria in larval and adult stages of wild mosquito populations. Here we investigated global transcriptional changes induced in A. coluzzii third instar larvae incubated with a sublethal concentration (50 µM) of 1-hydroxyphenazine (1-HP) or pyocyanin (Pyo) at 4 h and 8 h of continuous incubation by whole-genome DNA microarrays.

overall_design: Two experimental replicates (containing 15 pooled third instar larvae each) of 1-hydroxyphenazine (1-HP, 50 µM), pyocyanin (Pyo, 50 µM) or DMSO (50 µM equivalent volume) control; two timepoints of 4 h and 8 h. Microarray experiments were performed as dual-color hybridizations with color-swap dye-reversal (=two technical replicates for each sample). 1-HP or Pyo treatment samples were hybridized with respective DMSO controls. Total samples: 3 treatments * 2 experimental replicates * 2 timepoints = 12 samples; Total hybridizations: 2 comparisons * 2 experimental replicates * 2 timepoints * 2 technical replicates = 16 hybridizations.

first: Elena

last: Levashina


title: Profiling of L3 to L4 molting genes of Brugia malayi

city: Bethesda

first: Sasisekhar

last: Bennuru

state: MD

address: 10 Center Dr, Bldg 10, Rm 11N208

department: LPD

institute: NIH/NIAID

summary: To understand the genes regulating the molting of L3 to L4 larvae upon induction with ascorbic acid over a 10-day period in a controlled in-vitro molting model of the filarial parasite B.malayi.

overall_design: Comparative gene expression of B. malayi L3 larval development during 8 time points of in vitro molting model. Total RNA extracted and processed for microarray analysis.

first: Sasisekhark

first: Thomas

middle: B

last: Nutman


title: Analysis of microRNAs in familial Mediterranean fever

status: Public on Mar 02 2018

city: Tel Aviv

first: Nir

last: Pillar

state: Israel

address: Faculty of Medicine (Room 303), Tel Aviv University

country: Israel

institute: Tel Aviv University

summary: microRNA analysis of PBMC from FMF patients vs healthy controls

overall_design: Case control study


title: Transcriptional adaptation of L. monocytogenes EGDe to acidified nitrite.

city: Freising

first: Stefanie

last: Müller-Herbst

address: Weihenstephaner Berg 3

department: ZIEL and Chair for Microbial Ecology

institute: Technical University Munich

summary: Camparison of the transcriptome of L. monocytogenes EGDe exposed for 1 h to pH 6.0 and 200 mg/l NaNO2 to that of L. monocytogenes EGDe exposed for 1 h to pH 6.0 (0 mg/l NaNO2).

overall_design: In total, 6 biological replicates of RNA sets were analyzed. each in technical duplicates. In cDNA synthesis reactions of three RNA sets, cDNA derived from L. monocytogenes EGDe cells incubated in BHI pH 6.0 (pH adjusted with concentrated lactic acid (90 %, Merck, Darmstadt, Germany) prior to autoclaving) at 24 °C with 200 mg/l NaNO2 was labeled with Cy3-dCTP and cDNA of cells incubated in BHI pH 6.0 at 24 °C without NaNO2 (0 mg/l) was labelled with Cy5-dCTP (GE Healthcare, Freiburg, Germany). Dye swap was performed for the three other RNA sets.

last: Wüstner

first: Claudia

last: Held

first: Armin

last: Ehrenreich


title: Expression data from susceptible rice cultivar innoculated with Magnaporthe oryzae isolate (Mo-ei-11)

status: Public on Feb 28 2018

city: New Delhi

first: T

middle: R

last: Sharma

state: Delhi

address: Pusa Campus New

country: India

institute: NRCPB

summary:
The molecular mechanisms underlying infection of rice host system with compatible M. oryzae isolates at 12, 24, 48 and 72 hours post innoculation (hpi) are investigated in the study. In addition, the identification of highly commonly upregulated genes by both isolates of M. oryzae may be useful candidates for M.oryzae inducible promoter characterization
We used microarrays to detail the global programme of gene expression underlying M. oryzae infection during compatible host-pathogen interaction

overall_design: 14-day-old healthy rice seedlings were inoculated with highly virulent M. oryzae isolate, Mo-ei-11. For pathogen inoculation, spores were dissolved in 0.2 % gelatin to a concentration of 105/ml. Healthy 14-day-old healthy old plants of the same cultivar sprayed with 0.2 % gelatin were taken as control. Leaf tissues were harvested at 24, 48 and 72 hpi in case of Mo-ei-11 isolate and 24 hpi with Mo-ni-25 isolate for RNA extraction and hybridization on Affymetrix microarrays from both pathogen inoculated and control plants.

first: Joshitha

last: Vijayan

first: Soham

last: Ray

first: Sourabh

last: Jain

first: B

middle: N

last: Devanna


title: Epigenetic analysis of the DMD locus

city: bologna

first: Samuele

last: Gherardi

state: Bologna

address: via selmi 3

country: Italy

institute: UNIBO

type: Genome binding/occupancy profiling by high throughput sequencing

summary: The Dystrophin gene (DMD) is the largest gene in the human genome, mapping on Xp21, spanning 2.2Mb and accounting for approximately 1% of the entire human genome. Mutations in this gene cause Duchenne and Becker muscular dystrophy, X-linked dilated cardiomyopathy, and other milder muscle phenotypes. Beside the remarkable number of reports describing dystrophin gene expression and the pathogenic consequences of the gene mutations in dystrophinopathies, the full scenario of the DMD transcription dynamics remains however, poorly understood. Considering that the full transcription of the DMD gene requires about 16 hours, we have investigated the activity of RNA Polymerase II along the entire DMD locus within the context of specific chromatin modifications using a variety of chromatin-based techniques.  Our results unveil a surprisingly powerful processivity of the RNA pol II along the entire 2.2 Mb of the DMD locus with just one site of pausing around intron 52. More importantly, epigenetic marks highlighted the existence of four novel cis-DNA elements, two of which, located within intron 34 and exon 45, appear to govern the architecture of the DMD chromatin with implications on the expression levels of the muscle dystrophin mRNA.   Overall, our findings provide a global view on how the entire DMD locus is dynamically transcribed by the RNA pol II and shed light on the mechanisms involved in dystrophin gene expression control, which can positively impact on the optimization of the novel ongoing therapeutic strategies for dystrophinopathies.

overall_design: ChIP/chip on DMD locus in SJCRH30 and HeLa cell line using Anti-RNA Poyimerase II, Anti-RNA polymerase II CTD repeat YSPTSPS (phospho S2),Anti-RNA polymerase II CTD repeat YSPTSPS (phospho S2), Anti-H3ac and Anti-H3K4me2. Experimental duplicates were provided for both cell lines and for all antibodies with exception of Anti-RNA polymerase II CTD repeat YSPTSPS (phospho S5), Anti-H3ac and Anti-H3K4me2 in HeLa cells.

first: Matteo

last: Bovolenta

first: Chiara

last: Passarelli

first: Maria

middle: S

last: Falzarano

first: Daniela

last: Erriquez

last: Scotton

first: Francesca

last: Gualandi

first: Marina

last: Mora

first: Pia

last: Bernasconi

first: Lorenzo

last: Maggi

first: Lucia

last: Morand

first: Alessandra

last: Ferlini

first: Giovanni

last: Perini


title: Transcriptome Analysis of hub2-3 vs the wild-type Col

first: xi

last: chen

address: No.2 Yuanmingyuan West Road

institute: China Agricultural University

summary: HUB2 had been previously identified as a H2B monoubiquitinating E3 ligase. Loss of HUB2 leads to a pleiotropic phenotype, including reduced seed dormancy, smaller plant size and early flowering. Microarray expression profiling was used to identify differentially expressed genes between hub2-3 mutant and wild-type Col seedlings.

overall_design: The goal is to compare hub2-3 mutant to the wild-type Col. The experiment design comprised three biological replicates of each genotype.

first: X

last: Chen

first: T

last: Wang


title: Patterns of IgH rearrangement stratify prognosis of diffuse large B-cell lymphoma, which could be associated with CDC25A

status: Public on Feb 24 2018

city: Hiroshima

first: Tetsumi

last: Yoshida

address: Kasumi 1-2-3 Minami-ku

institute: Hiroshima University

summary: Over 80% of patients with diffuse large B-cell lymphoma (DLBCL) treated with R-CHOP achieve complete remission with variable 5-year overall survival (OS) rates of 60 to 70% depending on the preexisting risk factors. We herein attempted to stratify DLBCL by the patterns of immunoglobulin heavy chain gene rearrangement (IgH-R) by using a PCR-based clonality detection method to predict prognosis of the patients with DLBCL. We retrospectively analyzed 81 patients with DLBCL who were treated at our hospital from 2006 to 2013 and had data on IgH-R of lymphoma cells at diagnosis. IgH-R analyses identified a uniform pattern of IgH-R harboring all frame regions (FR)1-3 not completely involving DH1-7 in 15 out of 26 patients, who failed to obtain complete remission (CR). Moreover, CR rate was quite low ((7/22 (32%)) in these patients with this IgH-R pattern. We evaluated prognostic parameters of these patients with special reference to patterns of IgH-R by univariate and multivariate proportional-hazard model. Multivariate analysis revealed that IgH-R in all FR1-3 without entire DH1-7 was significantly associated with adverse overall survival. Then, gene expression profiling of mRNA elicited the candidate genes associated with poorer prognosis stratified by IgH-R patterns. Among them, CDC25A mRNA was significantly amplified by real-time PCR and then further analysis of its protein with immunostaining confirmed that CDC25A could be a responsible gene for prognosis of patients with DLBCL. These results may shed light on individualized therapeutic modalities by the stratification of patients in accordance with patterns of IgH-R.

overall_design: Statistical analyses suggested that IgH-R in all FR1-3 regions in conjunction with no IgH-R in DH1-7 is associated with significant adverse impact on prognosis of the patients with DLBCL. Next, we conducted gene expression profiling test of mRNA between consecutive IgH-R in FR1-3 and the other patterns to identify responsible genes associated with poor prognosis. 3 samples showing IgH-R in entire FR1-3 but not DH1-7 and 3 samples bearing no IgH-R in all FR1-3 were selected for gene expression profiling of mRNA.

first: Keichiro

last: Mihara

first: Megu

last: Ohtaki

first: Yoshinori

last: Ohno

first: Yoshihiro

last: Takihara

first: Noriyuki

last: Shiroma

first: Koji

last: Arihiro

first: Naomi

last: Sasaki

first: Tatsuo

last: Ichinohe


title: Reverse genomic analysis of ethylene signaling in apple fruit

city: Davis

first: Abhaya

last: Dandekar

state: CA

address: One Shields Ave

department: Plant Sciences

institute: University of California, Davis

summary: Gene expression associated with apple fruit ripening and postharvest treatments was studied to identify transcripts that are regulated by ethylene signaling.

overall_design: This study included two sets of samples, from cortex and peel tissues.

first: Sagayamary

last: Sagayaradj

first: Russell

last: Reagan

first: Ying

first: Ana

last: Ibáñez

first: Sandra

last: Uratsu


title: Microarray study of tumoral tissue transcriptome of breast cancer in mexican women who are overweight or obese

status: Public on Feb 23 2018

city: Mexico City

first: Esau

middle: Floriano

last: Sanchez

address: Cerrada de Palomas SN

department: Military School of Graduate of Health

country: Mexico

institute: SEDENA

summary: In this work, transcriptoma of invasive breast carcinoma was studied by means of microarray expression in Mexican women who are overweight or obese. The dysfunction of the adipokines signaling pathways has recently been linked to more aggressive features of breast cáncer. We hypothesized that there are changes related to the signaling of adipokines in the expression profile of invasive breast carcinoma of Mexican women with overweight or obesity. The objectives were as follows: 1) Determine the expression profile of tumour tissue of Mexican women who are overweight or obese by comparing tumoral tissue and non -tumoral tissue, both from the same patient, 2) Identification of over- or underexpressed genes involved in signalling pathways related to adipokines and the tumour process, 3) Identify the signalling pathways that presented genes with expression changes and were related to adipokines and the tumoural process.

overall_design: Six independent pools: three samples from obese patients, two samples from obese patients,  two samples from overweight patients,  two samples from overweight patients, three samples from overweight patients, two samples from overweight patients, comprised of total RNA isolated from tumor and adjacent tissue.

last: Floriano

first: Ivan

last: Ignacio

first: Noemi

last: Cardenas

first: Fernando

middle: G

last: Brindis

first: Maria

last: Cordova

first: David

last: Comoto

first: Angel

last: Heredia

last: Millan

first: Juan

last: Ortiz

first: Ithamar

last: Arroyo

first: Laura

middle: E

last: Estrada


title: Gene expression profiling of CD45+ leukocytes infiltrating the prostate of TRAMP and TRAMP-Jα18-/- (iNKT cell-deficient) mice

status: Public on Feb 21 2018

city: Padova

first: Silvio

last: Bicciato

address: via U. Bassi 59/b

department: Molecular Medicine

institute: University of Padova

summary: To investigate the impact of the iNKT cells on the tumor-infiltrating leukocytes in TRAMP mouse prostate cancer.

overall_design: Two experimental groups (TRAMP, TRAMP-Jα18-/-), with 3 biological replicates for each time point (8, 12, 16 weeks), for a total of 18 samples.

first: Filippo

last: Cortesi

first: Gloria

last: Delfanti

first: Arianna

last: Calcinotto

first: Francesca

last: Gorini

first: Ferdinando

last: Pucci

first: Michele

last: De Palma

first: Andrea

last: Grilli

first: Alessandra

last: Recchia

first: Matteo

last: Bellone

first: Giulia

last: Casorati

first: Paolo

last: Dellabona


title: Oxidative stress time-course in adipocytes

status: Public on Feb 14 2018

city: Camperdown, Sydney

first: Rima

last: Chaudhuri

state: NSW

address: D17 Johns Hopkins Drive

department: Charles Perkins Center

institute: University of Sydney

summary: 3T3-L1 adipocytes were treated inhibitors against the glutathione and thioredoxin cycling pools for several time-points (2-24 h).

overall_design: Drug (Aranufin, BCNU and both) treatment timecourse (2,4,8 and 24hr) transcriptomics

first: Fatemeh

last: Vafaee


title: Messenger RNA (mRNA) microarray analyses of MRC5 cells and primary lung fibroblasts that were transiently transfected with miR-210 mimic and control

status: Public on Feb 19 2018

city: chuo-ku

first: Yu

last: Fujita

address: 5-1-1 Tsukiji

department: Research of Molecular Functions and Targets

institute: National Cancer Center Research Institute

summary: To strategically identify direct miR-210 target genes, we first performed messenger RNA (mRNA) microarray analyses of MRC5 cells and primary lung fibroblasts that were transiently transfected with miR-210 mimic and the control

overall_design: To detect the mRNAs in MRC5 cells and lung fibroblasts treated with miR-210 mimic or pre-miR-NC , 100 ng of total RNA was labelled and hybridized using a SurePrint G3 Human GE v2 8x60K Microarray (Agilent Technologies) according to the manufacturer’s protocol.

first: Takahiro

last: Ochiya


title: lncRNA and mRNA expression responsive to p53 that induced by doxycycline

status: Public on Feb 06 2018

city: hefei

first: Wanglai

last: Hu

address: 81 Meishan road

institute: Anhui Medical University

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

summary: Take advantage of TP53-null H1299 human lung adenocarcinoma cells carrying an inducible wild-type p53 expression system to interrogate lncRNAs and mRNAs responsive to p53 by use of lncRNA microarray.

overall_design: lncRNA and mRNA expression in TP53-null H1299 cells carrying an inducible p53 expression system were measured at 24 hours with and without exposure to doxycycline. Three independent experiments were performed.


title: Air Liquid Interface Model of Gastric Mucosa and H.pylori Infection

status: Public on Feb 15 2018

first: Thomas

middle: F

last: Meyer

address: Chariteplatz 1

department: Molecular Biology

summary: The Air Liquid Interface Model of Gastric Mucosa allows to provide a fully polarized epithelium accessible to infection experiments with H.pylori. The influence of several factors on immune response has been studied.

overall_design: Primary cells were isolated from healthy tissue of surgery specimen taken from patients undergoing sleeve resections, seeded on collagen coated filters and cultured after 3d in air liquid interface. Total RNA was extracted from samples and hybridized on Agilent-8x60k Human custom arrays as single-color hybridizations.

first: Francesco

last: Boccellato

first: Hilmar

last: Berger


title: Riboflavin deficiency regulates inflammation-associated genes in rat esophageal intraepithelial neoplasia

city: Shantou

first: Feng

last: Pan

address: No.22, Xinling Road

institute: Medical College of Shantou University

summary:
Transcriptome analysis of RNA samples from riboflavin deficiency combined with NMBA-induced rat esophageal intraepithelial neoplasia tissues.
Epidemiological studies suggest that dietary riboflavin deficiency and environmental exposure to N-nitrosomethylbenzylamine (NMBA) are common in China's high incidence area of esophageal cancer. Riboflavin deficiency has been documented as an important risk factor for esophageal cancer. In this study, we established a F344 rat esophageal tumor model that combines dietary riboflavin deficiency with exposure to NMBA. The results showed that riboflavin deficiency combined with NMBA (R0N+) enhanced the incidence of esophageal intraepithelial neoplasia, including in situ carcinoma, whereas normal levels of riboflavin combined with NMBA (RcN+) mainly induced the occurrence of esophageal benign hyperplasia and small amount of esophageal intraepithelial neoplasia. Oxidative DNA damage (8-OHdG) and DNA double-strand breaks (p-γH2AX) in R0N+ rats were higher than that in RcN+ rats. The aim of the present study is to analyze the mechanism of riboflavin deficiency-induced tumorigenesis. So, we used Affymetrix Clariom D(also known as Rat Transcriptome Array 1.0) to identify genes that were differentially expressed upon R0N+ esophageal intraepithelial neoplasia tissues.

overall_design: There were 4 pairs of samples: 2 pairs of esophageal epithelial neoplasia VS adjacent normal tissues in RcN+ groups; 2 pairs of esophageal epithelial neoplasia VS adjacent normal tissues in R0N+ groups

first: Ye

last: Chen

first: En-Min

last: Li

first: Li-Yan

last: Xu


title: mRNA expression profile in Al2O3 nanoparticle treated A549 cells

status: Public on Feb 22 2018

city: Nanjing

first: Shizhi

last: Wang

state: Jiangsu

address: 87 Dingjiaqiao, Gulou District

department: Key Laboratory of Environmental Medicine Engineering, Ministry of Education

institute: Southeast University

summary: We evaluated the profile of mRNA expression in control and 100 μg/ml Al2O3 nanoparticle treated A549 cells using the  Arraystar Human LncRNA Array v3.0 array,7th generation.  Our findings implicates that dysregulation of cell death and cell cycle invovled mRNAs may play important role in cytotoxicity of Al2O3 nanoparticles.

overall_design: Examination of mRNA expression in wild type or Al2O3 nanoparticle treated A549 cells

first: Xiaobo

first: Rui


title: Oligodendrocyte progenitor cells and macrophages/microglia produce glioma stem cell niche at the tumor border

status: Public on Jan 26 2018

city: Kumamoto

first: Takuichiro

last: Hide

state: Kumamoto

address: 1-1-1 Honjo, Chuo-ku

department: Department of Neurosurgery

institute: Kumamoto University

summary: Characterization of the tumor border microenvironment is critical for improving prognosis in patients with GBM. Here, we compared microRNA (miRNA) expression in samples from the tumor, tumor border, and peripheral region far from tumor mass by miRNA microarray. The top three of miRNAs showing higher expression in the tumor border were related to oligodendrocyte differentiation, and pathologically oligodendrocyte lineage cells were increased in the border, where numbers of macrophages and microglia also colocalized. Medium cultured with oligodendrocyte progenitor cells (OPCs) and macrophages induced stemness and chemo-radioresistance in GBM cells. Thus, OPCs and macrophages/microglia may form a glioma stem cell niche at the tumor border, representing a novel promising target for prevention of recurrence.

overall_design: Tissues at three sites, tumor, border area, and peripheral area, were obtained from 12 GBM patients.   Upregulated miRNAs in the border region were defined as having more than two-fold higher expression than those in the tumor and periphery; downregulated miRNAs in the border region were defined as having less than half of the expression observed in the tumor and periphery.

first: Yoshihiro

last: Komohara


title: Gene expression data obtained from Oryza sativa adventitious roots (2-6 cm behind the root tip) grown in nutrient solution with (30 mgL-1) and without (3 mgL-1) Si

city: Seeland / OT Gatersleben

first: Martin

last: Becker

state: Lower Saxony

department: Plant Reproductive Biology

institute: Leibniz Institute of Plant Genetics and Crop Plant Research (IPK)

summary:
Si has a wide range of effects in plant growth. One of these effects is the Si mediated formation of Casparian bands (CB), and thereby a reduced radial oxygen loss (ROL). The GeneChip provided evidence for involved genes in plant Si reaction.
The given GeneChip-data revealed and influence of Si in the uptake of Fe. Additionally several genes involved in CB formation were found regulated through Si.

overall_design: Oryza sativa ssp. Japonica cv. Selenio roots were germinated for 14d and harvested 28 days after transfer in nutrient solution. The experimental design included two different Si conditions with 30 mgL-1 SiOH4 (Plus_Si) and, as a control, 3 mgL-1 Si (Minus_Si). Four biological replicates consisting of pools of adventitious roots of roots of five plants grown in the same pot were used for RNA extraction and hybridization on Affymetrix GeneChips. The Affymetrix GeneChip had two technical repetitions.

last: Hinrichs

first: Manfred

middle: K

last: Schenk

first: Oliver

last: Dittrich-Breiholz


title: Gene expression in mammary glands of lactating wild-type or Th-POK-deficient mice.

city: Shanghai

first: Gaoxiang

last: Ge

address: 320 Yue-Yang Rd

institute: Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences

summary:
The Th-inducing POK (Th-POK, also known as cKrox or ZBTB7B) transcription factor is a key regulator of lineage commitment of immature T cell precursors. It is yet unclear the physiological functions of Th-POK besides helper T cell differentiation. We found that Th-POK is restrictedly expressed in the luminal epithelial cells in the mammary glands. Th-POK is not required for mammary gland development in puberty and alveologenesis in pregnancy. Th-POK-deficient mice are defective in secretory activation upon parturition with large cellular lipid droplets retained within alveolar epithelial cells. We compared microarray gene expression in mammary glands of lactating wild-type or Th-POK-deficient mice.
We show that Th-POK directly regulates expression of insulin receptor substrate-1 (IRS-1) and insulin-induced Akt-mTOR-SREBP signaling. Th-POK deficiency compromises IRS-1 expression and Akt-mTOR-SREBP signaling in the mammary glands. Thus, Th-POK function as an important regulator of insulin signaling in mammary gland lactation.

overall_design: No. 4 mammary glands were harvested and snap frozen from quadruplicate wild-type or Th-POK-deficient dams at lactation day 1. Total RNA was extracted from the mammary glands for microarray analyses (Agilent Whole Mouse Genome Microarray 4x44K array, Design ID: 014868) at the Shanghai Biotech Corp., following the manufacturer's recommendation.

last: Zhang

first: Huimin

last: Ma


title: Prospective isolation of ISL1+ cardiac progenitors from human ESCs for myocardial infarction therapy

status: Public on Jan 19 2018

city: Pohang, Gyungbuk

first: Sehyun

last: Chae

address: San 31, Hyoja-Dong, Nam-Gu

department: Department of Interdisciplinary Bioscience and Bioengineering(I-BIO)

institute: POSTECH

summary: The LIM-homeodomain transcription factor ISL1 marks multipotent cardiac progenitors that give rise to cardiac muscle, endothelium, and smooth muscle cells. ISL1+ progenitors can be derived from human pluripotent stem cells, but the inability to efficiently isolate pure populations has limited their characterization. Using a genetic selection strategy, we were able to highly enrich ISL1+ cells derived from human embryonic stem cells. Comparative quantitative proteomic analysis of enriched ISL1+ cells identified ALCAM (CD166) as a surface marker that enabled the isolation of ISL1+ progenitor cells. ALCAM+/ISL1+ progenitors are multipotent and differentiate into cardiomyocytes, endothelial cells, and smooth muscle cells. Transplantation of ALCAM+ progenitors enhances tissue recovery, restores cardiac function and improves angiogenesis through activation of AKT-MAPK signaling in a rat model of myocardial infarction, based on cardiac MRI and histology. Our study establishes a new efficient method for scalable purification of human ISL1+ cardiac precursor cells for therapeutic applications.

overall_design: To investigate the effect of CD166+ cells, mRNA expression profiles of H9 hESCs, ALCAM-, ALCAM-/+, and ALCAM+ cells were generated using the Agilent-039494 Human 8x60k chip (Agilent, Santa Clara, CA, USA). In each condition, gene expression profiling was performed, according to the manufacturer's instructions, on two biological replicates obtained from independent cell cultures. Total RNA was extracted, and the integrity of the total RNA was analyzed using an Agilent 2100 Bioanalyzer. RIN numbers for all the samples were larger than 8. In vitro transcription was then performed to generate cRNA, which was hybridized onto each array. The array was scanned using a SureScan Microarray Scanner (Agilent).

first: Zaniar

last: Ghazizadeh

first: Faranak

last: Fattahi

first: Mehdi

last: Mirzaei

first: Delger

last: Bayersaikhan

first: Jaesuk

last: Lee

first: Kyunghee

last: Byun

last: Tabar

first: Sara

middle: T

last: Ahmad

first: Shahab

last: Mirshahvaladi

first: Parisa

last: Shabani

first: Hananeh

last: Fonoudi

first: Paul

last: Haynes

first: Hossein

last: Baharvand

first: Nasser

last: Aghdami

first: Todd

last: Evans

first: Bonghee

first: Ghasem

middle: H

last: Salekdeh


title: Acute treatment with chemical PPARGC1a1 activators in brown fat cells

status: Public on Feb 02 2018

city: Stockholm

first: Amanda

middle: Tove

last: Klein

address: von Eulers väg 8

department: Dept of Physiology and Pharmacology

country: Sweden

institute: Karolinska Institutet

summary:
The peroxisome proliferator-activated receptor-coactivator-1α1 (PGC-1α1) regulates genes involved in energy metabolism. Increasing adipose tissue energy expenditure through PGC-1α1 activation has been suggested to be beneficial for systemic metabolism. Pharmacological PGC-1α1 activators could be valuable tools in the fight against obesity and metabolic disease. Finding such compounds has been challenging partly because PGC-1α1 is a transcriptional coactivator with no known ligand-binding activities. Importantly, PGC-1α1 activation is regulated by several mechanisms but protein stabilization is a limiting step as the protein has a short half-life under unstimulated conditions.
We designed a cell-based high-throughput system to identify stabilizers of PGC-1α1 protein. Positive hits were tested for their ability to induce endogenous PGC-1α1 protein accumulation and activate target gene expression in brown adipocytes. Selected compounds were analyzed for their effects on global gene expression in brown adipocytes.

overall_design: Fully differentiated brown fat cells (previously described Uldry M et al 2006 Cell Metab.; PMID16679291) were treated for 8h with 10μM of compound (AM73 or AM80) or DMSO (control), in triplicate. RNA was extracted and used for global gene expression analyzes.

last: Pettersson-Klein

first: Jorge

middle: L

last: Ruas


title: Abnormal microglia and enhanced inflammation-related gene transcription in mice with conditional deletion of Ctcf in Camk2a-Cre-expressing neurons [RPL_HC_CTCF]

status: Public on Jan 05 2018

first: Ruteja

last: Barve

state: MO

address: 4515 McKinley Ave

department: Genetics

institute: Washington University

summary: CCCTC-binding factor (CTCF) is an 11 zinc finger DNA-binding domain protein that regulates gene expression by modifying 3D chromatin structure. Human mutations in CTCF cause intellectual disability and autistic features. Knocking out Ctcf in mouse embryonic neurons is lethal by neonatal age, but the effects of CTCF deficiency in postnatal neurons are less well studied. We knocked out Ctcf postnatally in glutamatergic forebrain neurons under the control of Camk2a-Cre. Ctcf loxP/loxP;Camk2a-Cre (Ctcf CKO) mice of both sexes were viable and exhibited profound deficits in spatial learning/memory, impaired motor coordination, and decreased sociability by 4 months of age. Ctcf CKO mice also had reduced dendritic spine density in the hippocampus and cerebral cortex. Microarray analysis of mRNA from Ctcf CKO mouse hippocampus identified increased transcription of inflammation-related genes linked to microglia. Separate microarray analysis of mRNA isolated specifically from Ctcf CKO mouse hippocampal neurons by ribosomal affinity purification identified upregulation of chemokine signaling genes, suggesting crosstalk between neurons and microglia in Ctcf CKO hippocampus. Finally, we found that microglia in Ctcf CKO mouse hippocampus had abnormal morphology by Sholl analysis and increased immunostaining for CD68, a marker of microglial activation. Our findings confirm that Ctcf KO in postnatal neurons causes a neurobehavioral phenotype in mice and provide novel evidence that CTCF depletion leads to overexpression of inflammation-related genes and microglial dysfunction.

overall_design:
To compare whole hippocampus gene expression in Ctcf loxP/loxP (control) and Ctcf loxP/loxP; Camk2a-Cre (Ctcf CKO) mice.
4 samples were prepared per genotype. We used the RiboTag isolation method to collect RNA from Camk2a-Cre expressing hippocampal neurons of adult (at least 3 months old) mice of both sexes (3 males and 1 females per genotype).

first: R

first: Bryan

last: McGill


title: Abnormal microglia and enhanced inflammation-related gene transcription in mice with conditional deletion of Ctcf in Camk2a-Cre-expressing neurons [Whole_HC_CTCF]

overall_design:
To compare whole hippocampus gene expression in Ctcf loxP/loxP (control) and Ctcf loxP/loxP; Camk2a-Cre (Ctcf CKO) mice.
3 pooled samples of each genotype were prepared by collecting total RNA from the hippocampal tissue of 3 adult (3-6 months old) mice of both sexes.


title: Sequence variation within similar cis-elements promotes context-specific functions of two Drosophila GA-binding transcription factors (protein binding microarray data set)

city: Boston

first: Michael

last: Tolstorukov

state: MA

address: 185 Cambridge Street

institute: Massachusetts General Hospital

type: Genome binding/occupancy profiling by array

summary: To more specifically define the sequence content that favors direct binding of GAF,  a genomic-context protein binding microarray (gcPBM) was used to detect GST-tagged GAF binding to double stranded DNA probes using a fluorescently conjugated anti-GST secondary antibody

overall_design: GPL22023 - PBM experiments were performed using a custom-designed oligonucleotide array in 4x180K format (Agilent Technologies, Inc., AMADID #037964), described in detail previously (Kuzu G, Kaye EG, Chery J, Siggers T et al. Expansion of GA Dinucleotide Repeats Increases the Density of CLAMP Binding Sites on the X-Chromosome to Promote Drosophila Dosage Compensation. PLoS Genet 2016 Jul;12(7):e1006120. PMID: 27414415). The array was converted to a double-stranded DNA array and used in PBM experiments essentially as described previously using PBS binding buffer with 50 μM zinc acetate (Berger et al., Nat Biotech, 2006 and Berger & Bulyk, Nat Protoc, 2009), except that here GST-GAF-DBD was applied to one fresh and one stripped array at a final concentration of 150 nM, and either 525 nM or 600 nM MBP, respectively. N-terminal GST-tagged protein samples were made for the protein GAF; samples were made by in vitro transcription translation (IVT). IVT reaction mixtures for the GAF construct were applied directly to the PBM microarray and incubated for 1hour. Microarray-bound protein was fluorescently labeled using Alexa488-conjugated antibodies targeting GST, and the microarray was scanned in using a standard microarray scanner. Median fluorescence intensity over eight replicate probes was reported for each unique DNA sequence on the microarray.

first: Emily

last: Kaye

first: Matthew

last: Booker


title: Sequential Design: time-course

status: Public on Mar 01 2018

city: Ikoma

first: Naotake

last: Ogasawara

state: Nara

institute: Nara Institute of Science and Technology

summary:
E.coli K-12 W3110 was grown in LB medium and harvested at each time point. And time-series microarray experiments were performed based on Sequential Design. In Sequential Design, the control sample is set to closest previous time point so that adjacent time points are compared directly. Combining with data from reference design, more accurate and reliable expression series could be collected.
Keywords: timecourse

overall_design:
The control sample is set to closest previous time point.
Adjacent time points are compared directly.

first: Ryosuke

last: Ito

first: Hiroki

last: Takahashi

first: Taku

last: Oshima

first: Shigehiko

last: Kanaya


title: Quality of reprogramming to induced pluripotency as a function of reprogramming method

status: Public on Dec 31 2017

city: Baltimore

first: Elias

middle: Thomas

last: Zambidis

address: 733 N. Broadway

department: Oncology

institute: Johns Hopkins School of Medicine

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

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

overall_design: Refer to individual Series


title: Abnormal microglia and enhanced inflammation-related gene transcription in mice with conditional deletion of Ctcf in Camk2a-Cre-expressing neurons

middle: A


title: Microarray global microRNA expression of donor cells, fibroblast-derived iPSC, and stromal-primed cord-blood iPSC

summary: Global microRNA analysis of (a) human embryonic stem cells, (b) low passage episomal stromal-primed myeloid iPSC, (c) intermediate passage fibroblast iPSC, and (d) samples of corresponding donor cells.

overall_design: Human miRNA Microarray Kit Version 3 kits (Agilent Technologies, Santa Clara, CA) were used for microarray assays to examine the global microRNA expression of human ES cells, iPS cells and target cell populations. The Human miRNA Microarray contains probes for 866 human microRNAs from the Sanger database v12.0. Total RNA was harvested from indicated donor cells, hESC, or iPSC, and prepared as described in the miRNeasy Mini Kit (Qiagen) with on-column DNase I digestion. A single sample of each cell line was used for this analysis.

first: Tea

last: Park

first: Jeffrey

last: Huo

first: C

middle: C

last: Talbot

first: Wayne

last: Yu

first: Karan

last: Verma

first: Ann

last: Peters

first: Renee

last: Reijo-Pera


title: Airway Exosomal miRNA predicts Bronchopulmonary Dysplasis in Extremely Preterm Infants

status: Public on Dec 29 2017

city: Birmingham

first: Charitharth

last: Lal

state: AL

address: 619 South 19th Street

institute: University of Alabama at Birmingham

summary: We conducted a prospective cohort study with independent Discovery and Validation cohorts, to formulate predictive biomarkers for Bronchopulmonary Dysplasia in extremely preterm infants. Tracheal aspirate samples were collected at birth from extremely preterm infants. Exosomes were extracted from tracheal aspirates and total RNA was extracted from these exosomes from individual samples. miRNA profiling for all ~ 800 miRNAs was conducted on each sample by nanostring platform. This study found that a distinct airway exosomal miRNA sigrature at birth (decreased miR 876-3p) predicts future development of severe Bronchopulmonary Dysplasia in extremely preterm infants.

overall_design: Prospective Cohort Study with independent discovery and validation cohorts when tracheal aspirates from extremely low birth weight infants at birth to formulate exosomal microRNA based predictive biomarkers for Bronchopulmonary Dysplasia.

middle: V


title: Engineered glycocalix regulates stem cell proliferation in murine crypt organoids

status: Public on Dec 27 2017

city: La Jolla

first: Aime

last: Lopez Aguilar

address: 10550 North Torrey Pines Road

institute: The Scripps Research Institute

summary: At the base of the intestinal crypt, long-lived Lgr5+ stem cells are intercalated by Paneth cells that provide essential niche signals for stem-cell maintenance. This unique epithelial anatomy makes the intestinal crypt one of the most accessible models for the study of adult stem cell biology. The glycosylation patterns of this compartment are poorly characterized and the impact of glycans on stem cell differentiation remains largely unexplored. We found that Paneth cells, but not Lgr5+ stem cells, express abundant terminal N-acetyllactosamine (LacNAc). Employing an enzymatic method to edit glycans in cultured crypt organoids, we assessed the functional role of LacNAc in the intestinal crypt. We show that blocking access to LacNAc on Paneth cells leads to hyperproliferation of the neighbouring Lgr5+ stem cells, which is accompanied by the down-regulation of genes that are known as negative regulators of proliferation

overall_design:
Lgr5+ mouse stem cells were sorted from dissociated organoids that had been treated with in situ fucosylation for 4 days or untreated control
RNA was isolated and analyzed, quality was determined using a spectrophotometer and was reverse transcribed using a cDNA conversion kit. The cDNA was used on the real-time RT2 Profiler PCR Array (QIAGEN, Cat. no. PAMM-405Z) in combination with RT2 SYBR® Green qPCR Mastermix (Cat. no. 330529). The average fold-change of gene expression in stem cells was analyzed for untreated vs. glycan modified organoids from six biological replicates for 84 genes. CT values were exported to an Excel file to create a table of CT values. This table was then uploaded on to the data analysis web portal at http://www.qiagen.com/geneglobe. Samples were assigned to controls and test groups. CT values were normalized based on a/an Manual Selection of reference genes.

first: Sara

last: Rouhanifard


title: Randomized PAM depeletion of NmeCas9

status: Public on Dec 21 2017

city: Raleigh

first: Chase

last: Beisel

state: NC

address: 840 Main Campus Drive

department: Chemical and Biomolecular Engineering

institute: North Carolina State University

summary: We report the PAMs of NmeCas9 using a cell-free TXTL-based cleavage assay. By adding randomized PAM library and NmeCas9-gRNA in vitro, functional PAM sequences were cleaved, while non-functional PAMs remained. By amplifying the non-cleaved DNA, we use next-generation sequencing to analyze the depletion of functional PAMs of NmeCas9.

overall_design: Pam determination assay for NmeCas9

first: Colin

last: Maxwell

first: Thomas

last: Jacobsen

first: Ryan

last: Marshall

first: Vincent

last: Noireaux


title: Expression data from mRNA in complex with EGFR from irradiated human A549 (ATCC CCL185) cells

city: Tuebingen

first: Stefan

last: Czemmel

address: Auf der Morgenstelle 10

department: University of Tuebingen

institute: Quantitative Biology Center (QBiC)

summary:
Immunoprecipitation of EGFR from irradiated A549 (ATCC CCL185) cells was performed in order to characterize bound mRNA species with the help of microarray analysis
As control experiment, immunoprecipitation was also performed with IgG

overall_design: A549 cells (ATCC CCL185) were treated with or without radiation and 24h after treatment EGFR or IgG was immunoprecipitated. To analyze gene expression changes related to irradiation in EGFR versus IgG samples, total RNA was extracted from biological triplicates (12 samples in total for the four groups) for subsequent array hybridization and microarray analysis using the Affymetrix Human Gene 2.1 ST Array chip.

first: Klaus

last: Dittmann


title: Combination therapy of NHS-IL12 and avelumab enhances antitumor efficacy in preclinical cancer models

status: Public on Dec 20 2017

city: Billerica

first: Chunxiao

last: Xu

address: 45A Middlesex Tpke

institute: EMD Serono Research and Development Institute

summary: Nanostring gene expression profiling of 24 BALB/c mice bearing EMT-6 tumors under avelumab and NHS-muIL12 mono and combination therapies.

overall_design: Six groups of four mice were profiled using samples collected on day 6.  G1 is isotype control.  Group 2 is 2ug NHS-muIL12.  Group 3 is 10ug NHS-muIL12.  Group 4 is avelumab 200ug.  Group 5 is avelumab 200ug plus 2ug NHS-muIL12.  Group 6 is avelumab 200ug plus 10ug NHS-muIL12.

first: Yanping

last: Zhang

first: P

last: Rolfe

first: Giorgio

last: Kradjian

first: Yan

last: Lan


title: Gpr97 exacerbates AKI via mediating Sema3A signaling

status: Public on Dec 19 2017

city: Jinan

first: Wei

last: Fang

address: Wenhua Xi Road 44#

institute: Shandong university

summary: We have employed whole genome microarray expression profiling as a discovery platform to identify genes with the potential to distinguish between the mice with renal IRI injury and sham-operated group.Expression of Gpr97 from this signature was quantified in the same kind of samples by real-time PCR, confirming the change pattern. By microarray analysis, we found that IR-induced Sema3A expression was significantly abolished by Gpr97 deficiency in mice

overall_design: The kidney from wild type mice and Gpr97 deficiency mice with or without renal IRI injury were analysed.

first: Fan

last: Yi


title: Transcriptional changes in mycorrhizal and non-mycorrhizal soybean roots in presence of the fungal pathogen Macrophomina phaseolina

city: Córdoba

first: Nathalie

last: Marquez

state: Córdoba

address: Camino 60 cuadras Km 5,5

country: Argentina

institute: INTA

summary: Macrophomina phaseolina, a soil borne pathogen with a wide host range, causes the charcoal rot in soybean (Glycine max (L.) Merr). In Argentina, soybean is the most important crop as far as sowing surface cultivation concerns, and for this reason it is important to assess integrated disease management strategies in order to minimize the incidence of this disease and the consequent loss of performance culture. Previous studies have demonstrated the protective effect that arbuscular mycorrhizal can promote on their hosts against various pathogens invasion, especially against soil borne fungi. Therefore, the goal of this study was to analyze the phenomenon of mycorrhizae mediated protection by characterizing transcriptional changes using cDNA microarrays as a tool. The objective of the present study was to investigate, under strict in vitro culture conditions, the global transcriptional change in the roots of pre-mycorrhized soybean plantlets challenged by M. phaseolina as compared to non-mycorrhizal soybean plantlets. The MapMan software was used to distinguish transcriptional change under these conditions, with special emphasis on plant defence response.

overall_design: Four-condition experiment.  Biological replicates: 3 replicates per condition. Roots of two plantlets were randomly selected and pooled for analysis (i.e. three biological replicates)

first: María

last: Giachero

first: Adrien

last: Gallou

first: Sylvie

last: Cranenbrouck

first: Julio

last: Di Rienzo

middle: J

last: Pozo

first: Daniel

last: Ducasse

first: Stéphane

last: Declerck


title: Gene expression dataset for nursery-reared Staghorn coral (Acropora cervicornis) under thermal stress

city: University Park

first: John

middle: Everett

last: Parkinson

state: PA

address: 208 Mueller Lab

department: Biology

institute: Penn State University

type: Expression profiling by high throughput sequencing

summary: Publication Abstract: As climate changes, sea surface temperature anomalies that negatively impact coral reef organisms continue to increase in frequency and intensity. Yet, despite widespread coral mortality, genetic diversity remains high even in those coral species listed as threatened. While this is good news in many ways it presents a challenge for the development of biomarkers that can identify resilient or vulnerable genotypes. Taking advantage of three coral restoration nurseries in Florida that serve as long-term common garden experiments, we exposed over thirty genetically distinct Acropora cervicornis colonies to hot and cold temperature shocks seasonally and measured pooled gene expression responses using RNAseq. Targeting a subset of twenty genes, we designed a high-throughput qPCR array to quantify expression in all individuals separately under each treatment with the goal of identifying predictive and/or diagnostic thermal stress biomarkers. We observed extensive transcriptional variation in the population, suggesting abundant raw material is available for adaptation via natural selection. However, this high variation made it difficult to correlate gene expression changes with colony performance metrics such as growth, mortality, and bleaching susceptibility. Nevertheless, we identified several promising diagnostic biomarkers for acute thermal stress that may improve coral restoration and climate change mitigation efforts in the future.

overall_design: This project studied the effects of thermal stress on gene expression in the Staghorn coral (Acropora cervicornis).  At four seasonal time points, tissue from at least ten colonies at three nurseries were exposed to three temperature treatments for one hour then preserved in RNALater.  RNA was extracted with TRI Reagent then cleaned with a Qiagen RNEasy kit.  A subset of samples were chosen and pooled for RNA-Seq.  The subset included genotypes from 2 of the 3 nurseries (Miami and Lower Keys), 2 of the 4 seasonal collections (Summer 1 and Winter 1), and all 3 temperature treatments (ambient, hot, and cold), resulting in 12 libraries.  For each library, RNA from 7 of the 10+ genotypes at each nursery were pooled (84 samples total). Following the manufacturer’s protocol, 150 bp single reads were generated from oligo(dT)-selected total RNA using the Illumina TruSeq Stranded mRNA HT Kit. mRNA sequencing libraries were individually barcoded, multiplexed in equal quantities, and run on three lanes of the Illumina HiSeq 2000 platform.  The data were demultiplexed into 12 individual library files.

first: Iliana

middle: B

last: Baums


title: microRNA expression profile in whole lung of rat pups at P10 or P21 day of life after a intrauterine growth restriction due to a low protein diet during gestation

city: Paris

first: Céline

last: Méhats

address: 24 rue du Faubourg St jacques

country: France

institute: Inserm

summary:
The aim of this study was to evaluate whether microRNA profiles during alveolarization are affected by an intrauterine growth restriction after a low protein diet during gestation.
MicroRNA expression were assessed in the lungs of five animals per group at P10 and P21 after birth in a rat model of low protein diet-induced IUGR.

overall_design: Total RNA was extracted using the Rneasy kit (Qiagen, Courtaboeuf, France), according to the manufacturer’s instructions. The 20 samples were individually hybridized on a miRNA-4_0 chips. Microarray hybridization on miRNA 4.0 chips (Affymetrix) was conducted at the genomic platform of the Institut Cochin, Paris.

first: Elodie

last: Zana-Taïeb

first: Sébastien

last: Jacques


title: MicroRNA differencial expression data between scrambled siRNA-treated mice and HN1L siRNA-treated mice tumor samples

city: Houston

first: Jenny

last: Chang

state: TX

address: 6670 Bertner Ave.

department: Houston Methodist Cancer Center

institute: Houston Methodist Hospital

summary:
(HN1L) is a targetable breast cancer stem cell (BCSC) gene that is altered in 25% of whole breast cancer and significantly correlated with shorter overall or relapse-free survival in triple negative breast cancer (TNBC) patients. HN1L silencing reduced the population of BCSCs, inhibited tumor initiation, re-sensitized chemo-resistant tumors to docetaxel, and hindered cancer progression in multiple TNBC cell line derived xenografts.
We used miRNA array to compare miRNA expression profiles from PDX BCM2665 xenograft tumors with or without HN1L knockdown, to identify role of HN1L in regulating miRNA.

overall_design: miRNA arrays were performed on 10 snap-frozen tumor samples from scrambled siRNA-treated and HN1L siRNA-treated BCM2665 xenografts (5 samples from each treatment group). Differencial expression was performed to identifiy significantly differencially expressed miRNA and corresponding pathways.

first: Olivier

last: Elemento

first: Akanksha

last: Verma

first: Yi

last: Liu

first: Dong

middle: S

last: Choi

first: Helen

last: Wong


title: MicroRNA microarray of Drosophila melanogaster extracted from cephalic complexes of lgl-hypomorph 3rd instar larvae

status: Public on Dec 18 2017

city: Tucson

first: Daniela

last: Zarnescu

state: AZ

address: 1007 E Lowell St LSS 514

department: Molecular and Cellular Biology

institute: University of Arizona

summary:
Single channel custom oligonucleotide array of 147 microRNAs to detect changes in expression of a lgl-hypomorph mutant versus wild-type
0, 3, and 5 day old 3rd instar lgl-hypomorph larvae were compared to 0 day 3rd instar wild-type larvae to test for differences in microRNA expression

overall_design: 3 biological replicates were sourced for each sample type and arrays were spotted with 3 technical replicates per probe

first: Scott

last: Daniel

first: Atlantis

middle: D

last: Russ


title: miRNA profiling of primary breast cancers from patients treated with radiotherapy

status: Public on Dec 07 2017

city: Darlinghurst

first: Tim

last: Molloy

address: Level 8, 405 Liverpool St

department: Haematology

institute: St Vincent's Centre for Applied Medical Research

summary: Radiotherapy is essential to the treatment of most solid tumors  and acquired or innate resistance to this therapeutic modality is a major clinical problem. This study aimed to identify miRNAs associated with local relapse following radiotherapy.

overall_design: Formalin-fixed paraffin embedded tumor material was used from 20 patients, consisting of two groups of 10 patients matched for all clinico-pathologic variables and differing only in local relapse status. Radiotherapy consisted of 45 Gy in 25 fractions plus a tumor bed boost of 16 Gy in 8 fractions.

first: T


title: Integrative analysis of the late maturation programme and desiccation tolerance mechanisms in intermediate coffee seeds

status: Public on Dec 13 2017

city: Montpellier

first: Thierry

last: JOET

address: 911 Avenue Agropolis

department: DIADE

institute: IRD (Institut de Recherche pour le Développement)

summary: The intermediate seed category was defined in the early 1990s using coffee (Coffea arabica) as a model. In contrast to orthodox seeds, intermediate seeds cannot survive complete drying, which is a major constraint for seed storage, for both biodiversity conservation and agricultural purposes. However, intermediate seeds are considerably more tolerant to drying than recalcitrant seeds, which are highly sensitive to desiccation. To gain insight into the mechanisms governing such differences, changes in desiccation tolerance (DT), hormone content and the transcriptome were analysed in developing coffee seeds. Acquisition of DT coincided with a dramatic transcriptional switch characterised by the repression of primary metabolism, photosynthesis and respiration, and the upregulation of genes coding for late embryogenesis abundant (LEA) proteins, heat shock proteins (HSP) and antioxidant enzymes. Analysis of heat-stable proteome in the mature coffee seed confirmed the accumulation of LEA proteins identified at the transcript level. Transcriptome analysis also suggests a major role for ABA and for the transcription factors CaHSFA9, CaDREB2G, CaANAC029, CaPLATZ and CaDOG-like in DT acquisition. The ability of CaHSFA9 and CaDREB2G to trigger HSP gene transcription was validated by Agrobacterium-mediated transformation of coffee somatic embryos.

overall_design: Three biological replicates were made for each seed developing stage analyzed. Each stage was compared to a unique reference (an equimolar pool of each stage). The following comparisons were made: ST1-reference, ST2-reference, ST3-reference, ST4-reference, ST5-reference, ST6-reference, ST7-reference. In all, we performed microarray analyses on 42 slides [3 (replicates) x 2 (dyes) x 7 (stages)].

first: Stéphane

last: Dussert

last: Joët


title: The role of a single non-coding nucleotide in the evolution of an epidemic African clade of Salmonella

status: Public on Dec 15 2017

city: Liverpool

first: Jay

last: Hinton

address: Crown Street

department: Institute of Integrative Biology

country: United Kingdom

institute: University of Liverpool

summary:
Salmonella enterica serovar Typhimurium ST313 is a relatively newly emerged sequence type that is causing a devastating epidemic of bloodstream infections across sub-Saharan Africa. Analysis of hundreds of Salmonella genomes has revealed that ST313 is closely-related to the ST19 group of S. Typhimurium that cause gastroenteritis across the world. The core genomes of ST313 and ST19 vary by just 1000 single-nucleotide polymorphisms (SNPs). We hypothesised that the phenotypic differences that distinguish African Salmonella from ST19 are caused by certain SNPs that directly modulate the transcription of virulence genes.
Here we identified 3,597 transcriptional start sites (TSS) of the ST313 strain D23580, and searched for a gene expression signature linked to pathogenesis of Salmonella. We identified a SNP in the promoter of the pgtE gene that caused high expression of the PgtE virulence factor in African S. Typhimurium, increased the degradation of the factor B component of human complement, contributed to serum resistance and modulated virulence in the chicken infection model. We propose that high levels of expression PgtE of by African S. Typhimurium ST313 promotes bacterial survival and bacterial dissemination during human infection.
Our finding of a functional role for an extra-genic SNP shows that approaches used to deduce the evolution of virulence in bacterial pathogens should include a focus on non-coding regions of the genome.

sample_organism: Salmonella enterica subsp. enterica serovar Typhimurium str. D23580

overall_design: Examination of global gene expression of Salmonella enterica subsp. enterica serovar Typhimurium strain D23580 in 3 different growth conditions, using RNA samples with and without Terminator 5′-phosphate-dependent exonuclease (TEX) treatment in order to identify

first: Disa

last: Hammarlöf

first: Carsten

last: Kröger

first: Siân

last: Owen

first: Rocío

last: Canals

first: Lizeth

last: Lora

first: Nicolas

last: Wenner

first: Anna

last: Schager

first: Timothy

last: Wells

first: Ian

middle: R

last: Henderson

first: Paul

last: Wigley

first: Karsten

last: Hokamp

first: Nicholas

last: Feasey

first: Melita

last: Gordon


title: lncRNA changes in the livers of db/db mice than that of C57 mice

status: Public on Dec 14 2017

city: Beijing

first: Jian

last: Li

address: Dahua Road

institute: Beijing Hospital

summary: To identify putative lncRNA changes in the livers of db/db mice and C57 mice, we isolated the liver tissues and carried out a microarray analysis. Here, we found significant changes of lncRNAs in the livers of db/db mice. Among them, abnormal expression of ultraconserved elements was noticed.

overall_design: RNA was isolated from the mixed samples of liver tissues from 6 male db/db mice and 6 age-matched male wild-type (WT) mice. Total RNA was reverse-transcribed with biotin end-labeled random oligonucleotide primers. Then, the cDNA was hybridized to the Agilent mouse lncRNA+mRNA Array V1.0, including sense and antisense probes to all 481 human ultraconserved sequences, each spotted in duplicate.

first: Jun

last: Guo

first: Weiwei

last: Fang


title: Uterine Influences on Conceptus Development in Fertility-Classified Animals

status: Public on Dec 12 2017

city: Columbia

first: Thomas

last: Spencer

address: 920 East Campus Drive

department: Animal Sciences

institute: University of Missouri

summary: This study relates to pregnancy outcome after assisted reproduction of fertility-classified cattle.  The aim is to investigate how the uterine environment impacts and programs conceptus survival and development. The study found that ripple effects of dysregulated conceptus-endometrial interactions elicit post-elongation pregnancy loss in subfertile animals during the implantation period.

overall_design: Heifer cows classified as high fertile (HF), subfertile (SF), or infertile (IF) were investigated.  The RNA-seq analysis was performed for  endometrium samples at day 17 of pregnancy. For comparison, non-pregnant cows were  included in the analysis. RNA from conceptus of HF and SF pregnant animals (day 17) were also included in the RNA-seq analysis. A total of 25 endometrium samples (5 non-pregnant of each fertilty group, 5 pregnant HF, and 5 pregnant SF) and 27 conceptus samples (10 SF and 17 HF) were used in the RNA-seq analysis.

first: Joao

middle: G

last: Moraes

first: Susanta

last: Behura

middle: W

last: Geary

first: Peter

last: Hansen

first: Holly

last: Neibergs

middle: E


title: lncRNA changes in the livers of NAFLD patients compared with that of healthy control

summary: RNA was isolated from the mixed samples of liver tissues from 5 liver tissues from  NAFLD patients and 5 healthy controls. Total RNA was reverse-transcribed with biotin end-labeled random oligonucleotide primers.

overall_design: RNA was isolated from the mixed samples of liver tissues from liver tissues of 5 NAFLD patients and 5 healthy controls. Total RNA was reverse-transcribed with biotin end-labeled random oligonucleotide primers. Then, the cDNA was hybridized to the Agilent human lncRNA+mRNA Array V4.0, including sense and antisense probes to all 481 human ultraconserved sequences, each spotted in duplicate.


title: Interferon-alpha dendritic cells in active tuberculosis, latent and healthy donors

city: Rome

first: Luciano

last: Castiello

address: Viale Regina Elena 291

institute: Istituto Pasteur Italia - Fondazione Cenci Bolognetti

summary: Individuals exposed to  Mycobacterium tuberculosis (Mtb) may become infected and are classified as  with latent tuberculosis infection (LTBI) and remain whole time life in this condition or develop active tuberculosis (TB). Among the multiple factors governing the outcome of the infection, dendritic cells (DC) play a major role in dictating protective immunity. However, current knowledge on the role of the diverse components of human DC in shaping specific T cell response during Mtb infection is limited. In this study, we performed a comparative evaluation of  peripheral blood circulating DC subsets along with the functional capability of monocyte-derived IFN-α DC to induce Mtb antigen-specific T cell response in patients with active TB, subjects with LTBI and healthy donors (HD). The percentage of BDCA3+ mDC2 and CD123+ pDC declined significantly in active TB patients with respect HD whereas the same subsets displayed a remarkable activation in LTBI. Simultaneously, IFN-α-driven differentiation of DC resulted profoundly impaired from monocytes of active TB patients as compared to LTBI and HD individuals. Importantly, the specific altered developmental trait of IFN-α DC from active TB patients was associated with a marked change of molecular signalings conveying antigen presentation as well as full inability to induce antigen-specific T cell response. Thus, these data unravel an unavoidable role of IFN-α in determining the induction of Mtb-specific protective immunity which is essential to control Mtb infection.

overall_design: Three group of samples: IFNa-DC from Active TB patients, Latent TB patients, and healthy donors. 5 samples per group

first: Stefania

last: Parlato

first: Teresa

last: Chiacchio

first: Debora

last: Salerno

first: Linda

last: Petrone

first: Irene

last: Canini

first: Giulia

last: Romagnoli

first: Delia

last: Goletti

first: Lucia

last: Gabriele


title: Fasting induced changes in gene expression profiles of 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: Many species undergo sexual reproduction to distribute the parental genomes and increase the genomic diversity of the progeny. Among such species, sexual dimorphism is often displayed through morphology, size, behavior, and life-span, depending on the survival and reproduction strategies of the species. The nematode Caenorhabditis elegans has two sexes, hermaphrodite and male, and only the hermaphrodites, which produce both oocytes and sperm, are essential for the perpetuation of the species. In this study, we found that dietary restriction, which is the most reproducible way to retard aging in many species, extends the life-span of C. elegans hermaphrodites but not that of males. Our analysis revealed that fasting induces male-enriched genes in hermaphrodites and that the sex determination pathway affects life-span regulation, even after the completion of development, and is regulated by food availability. Furthermore, fasting activates the entire X-chromosome only in hermaphrodites. Our tiling array analysis identified a fasting-inducible, X-linked non-coding RNA for which expression positively correlated with the activation level of the X-chromosome and longevity. These links between the sex determination mechanism and dietary restriction at multiple levels may give priority to the survival of hermaphrodites during food shortages in C. elegans.

overall_design: In a experiment, 4 samples (hermaphrodite-fed, hermaphrodite-fasting, male-fed, and male-fasting) were analyzed. Three independent experiments were performed.

first: Sakiko

last: Honjoh

first: Takuya

last: Yamamoto


title: Induction of changes in primary human hepatocytes by valproic acid

city: Maastricht

first: Simone

last: van Breda

state: Limburg

address: Universiteitssingel 50

department: Toxicogenomics

country: Netherlands

institute: Maastricht University

type: Methylation profiling by genome tiling array

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

overall_design: Refer to individual Series


title: mRNA profiling of MCF7 cells transfected with a miR-139-5p mimic

status: Public on Dec 08 2017

first: Tim

last: Molloy

summary: Gene expression profiling of MCF7 cells transfected with a miR-139-5p or negative control mimic

overall_design: MCF7 cells were transfected with a miR-139-5p or negative control mimic. Total RNA was extracted 24 hours later and analyzed by Agilent gene expression microarray

first: T


title: Expression data from mouse adrenals during recovery after dexamethasone treatment

status: Public on Dec 06 2017

city: Ann Arbor

first: Antonio

middle: Marcondes

last: Lerario

state: MI

address: 109 Zina Pitcher Place, 1528 BSRB

department: MEND

institute: University of Michigan

summary:
Long-term pharmacological glucocorticoid therapy causes atrophy and hypofunction of the adrenal cortex. Following glucocorticoids withdrawal, a functional and anatomic regeneration take place, whose  cellular and molecular mechanisms  are poorly understood
We used microarrays to detail the  gene expression changes occurring during adrenal regeneration following administration of dexamethasone

overall_design: Six weeks old wild type C57BL/6J male mice were administered dexamethasone in drinking water for 14 consecutive days. Adrenal glands were collected at the time of dexamethasone withdrawal, and 3 and 7 days after withdrawal to study the regenerative process. Adrenals harvested from mice before dexamethasone treatment were considered as controls.

first: Isabella

last: Finco

first: Gary

last: Hammer


title: Expression data from PU.1low URE-/- AML cell line after treatment with small molecule acting as PU.1 inhibitor

city: Bronx

first: Ileana

last: Antony-debre

address: 1300 Moris park Avenue

department: cell biology

institute: albert einstein college of medicine

summary:
Downregulation of the hematopoietic transcription factor PU.1 in PU.1 low acute myeloid leukemia cells (AML) by novel heterocyclic diamidines or PU.1 inhibitors leads to decrease cell proliferation and apoptosis, representing a new therapeutic strategy for AML treatment. These inhibitors induces decreased PU.1 binding on its target sites, as well as deregulation in PU.1 canonical target genes
We used microarray to identify the pathways deregulated after drug treatment.

overall_design: We treated PU.1low URE-/- AML cell line, derived from an URE-/- mouse at leukemic stage, with Vehicle (H2O) or PU.1 inhibitor (DB2313) during 24h. After cell collection and RNA extraction, samples were hybridized on Affymetrix microarrays.

last: Antony-Debre

first: Ulrich

last: Steidl


title: The FibroChip, a functional DNA microarray to monitor cellulolysis and hemicellulolysis activities of rumen microbiota

status: Public on Dec 01 2017

city: Saint-Genès-Champanelle

first: Sophie

last: Comtet-Marre

address: Centre Auvergne-Rhône-Alpes

institute: Université Clermont Auvergne, INRA

type:
Expression profiling by array
Other

summary:
Ruminants are the most efficient herbivorous animals to transform plant biomass into edible products, principally thanks to the rumen microbiota that produces a large array of enzymes responsible for the hydrolysis of plant cell wall polysaccharides. Several biotic and abiotic factors influence the efficiency of fiber degradation, which can ultimately impact the animal productivity and health. To provide more insight on mechanisms involved in the modulation of fibrolytic activity, a functional DNA microarray targeting genes coding for key enzymes involved in cellulose and hemicellulose degradation by rumen microbiota was designed. The DNA microarray, designated FibroChip, was validated using targets of increasing complexity. This new tool demonstrated sensitivity and specificity as well as explorative and semi-quantitative potential.
The FibroChip was designed with the objective to propose a high throughput tool that enables to get a rapid picture of the capacity of rumen microorganisms to degrade cellulose and hemicellulose based on a targeted metatranscriptomics approach. We chose to focus on a few number of genes by targeting main ruminal fibrolytic microorganisms and selected CAZyme families that may have a pivotal role in cellulose and hemicellulose degradation. The microarray targets the coding sequence of catalytic domains from 8 CAZyme families involved in cellulose and hemicellulose degradation (i.e. glycoside hydrolases GH5, GH9, GH10, GH11, GH43 and GH48, and carbohydrate esterases CE1 and CE6). Taken together, these families present complementary activities needed for the complete degradation of cellulose and hemicellulose. In total, 392 nucleic sequences encoding 363 GH and 29 CE were kept for the microarray design. These sequences originated from 41 bacterial species, 4 protozoal species and 10 fungal species. The microarray is composed of 1631 25-mer probes. GoArrays strategy consisting by associating 2 25-mer probes targeting the same gene (Rimour et al., 2005) was also emplyed to determine 2618 composite probes of 54-mers. Triplicate of probes of 25 and 54-mers were synthetized in situ on an Agilent 8x15K DNA microarray. The microarray contained also 382 Agilent internal control probes including positive controls, negative controls and quality control probes. Probes were randomly placed on the array to avoid position bias.

sample_organism: Fibrobacter succinogenes subsp. succinogenes S85

platform_organism:
Bacteroides fragilis
Bacteroides thetaiotaomicron
Butyrivibrio fibrisolvens
Fibrobacter succinogenes
Xylanibacter ruminicola
Selenomonas ruminantium
Ruminococcus albus
Ruminococcus flavefaciens
Enterococcus faecium
Lactococcus lactis
Clostridium acetobutylicum
Clostridium cellulovorans
Clostridioides difficile
Acetivibrio thermocellus
Clostridium beijerinckii
Ruminiclostridium cellulolyticum
Levilactobacillus brevis
Limosilactobacillus fermentum
Bifidobacterium adolescentis
Cellulomonas fimi
Cellulomonas flavigena
Neocallimastix frontalis
Neocallimastix patriciarum
Piromyces communis
Bifidobacterium animalis
Bacteroides ovatus
Fibrobacter intestinalis
[Eubacterium] cellulosolvens
Bacteroides sp.
Pseudobacteroides cellulosolvens
Lachnospira eligens
Agathobacter rectalis
Ruminococcus sp.
Enterobacter sp.
Piromyces sp.
Epidinium caudatum
Eudiplodinium maggii
Polyplastron multivesiculatum
Orpinomyces joyonii
Piromyces rhizinflatus
Segatella bryantii
Piromyces sp. 'equi'
Roseburia intestinalis
Pseudobutyrivibrio xylanivorans
Butyrivibrio hungatei
Bifidobacterium longum
Acetivibrio clariflavus
Epidinium ecaudatum
Roseburia hominis
uncultured Neocallimastigales
Bacteroides xylanisolvens
Cellulosilyticum ruminicola
Ruminococcus champanellensis
Orpinomyces sp.

overall_design: The objective of this work was to validate the FibroChip design and evaluate its sensitivity and specificity. For this, targets of increasing complexity were tested: PCR products, then bacterial genomic DNA, RNA from one bacteria, and finally RNA from a cow rumen content (complex microbial community). (1) PCR products were amplified from 7 genes selected to represent the diversity of targeted CAZyme families and microorganisms. Genes were cloned beforehand to ensure that a unique sequence was hybridized. (2)  Genomic DNA from the strain Escherichia coli K12 was used to assess the specificity of probes as no gene from this bacterium was targeted on the FibroChip whearas the gDNA from 3 targeted bacteria strains (Fibrobacter succinogenes S85, Ruminococcus albus 20 and Bacteroides xylanisolvens XB1A) were used to assess the sensitivity of the DNA microarray. (3) To test the ability of the FibroChip to detect the differential expression of genes, the microarray was used to analyze the transcriptome of the rumen bacterium Fibrobacter succinogenes S85, cultivated in two media differing by their carbon source, i.e. the simple sugar cellobiose (C) or the complex substrate wheat straw (WS). (4) The FibroChip was then used to analyze the metatranscriptome of a cow rumen content. The rumen sample was from a dairy cow fed a mixed diet and was previously analyzed for fibrolytic activity using a RNAseq metatranscriptomics approach (Comtet-Marre et al., 2017).

first: Frédérique

last: Chaucheyras-Durand

first: Ourdia

last: Bouzid

first: Pascale

last: Mosoni

first: Ali

last: Bayat

first: Kevin

last: Shingfield

first: Pierre

last: Peyret

first: Evelyne

last: Forano


title: Ex vivo P. falciparum from High vs Low transmission areas in east Africa

first: Margaret

middle: Jane

last: Mackinnon

summary: The aim of this study was to compare the transcriptomes of Plasmodium falciparum parasites sourced from high vs. low malaria transmission settings in east Africa in order to test the hypothesis that malaria parasites are locally adapted to their environment.  In three separate experiments, parasites from ‘High’ vs. ‘Low’ transmission populations were taken from non-immune children and measured for gene expression levels by microarray against a reference genome. Two of these population comparisons were geographic in nature while the third was temporal, i.e., before and after a marked decline in malaria. This study is described in Rono MK, Nyonda MA, Simam JJ, Ngoi, JM et al. Nat Ecol Evol. PMID: .

overall_design: 515 samples were analysed.  These derived from 96 parasite isolates obtained from children below 13 years of age with three or fewer previous clinical episodes of malaria who were diagnosed with uncomplicated P. falciparum malaria at hospitals and dispensaries in western Kenya (2008, Kisumu), coastal Kenya (Kilifi, in 1994-1996 and in 2010-2012) and eastern Sudan (2007) which have long-term high, medium and low malaria transmission intensities, respectively.   Each isolate was placed into in vitro culture and sampled every 10h for up to 9 times: this yielded parasites at all stages of maturity during the 48h intraerythrocytic development cycle.  Five of the 96 isolates were replicates but were processed separately.

first: Martin

middle: K

last: Rono


title: Expression profiling in cortical GABAergic neurons at neonate

city: Wako

first: Kota

last: Tamada

state: Saitama

address: Hirosawa 2-1

department: BSI

institute: RIKEN

summary: During embryonic development, GABAergic interneurons, a main inhibitory component in the cerebral cortex, migrate tangentially from the ganglionic eminence (GE) to cerebral cortex. After reaching the cerebral cortex, they start to extend their neurites for constructing local neuronal circuits around the neonatal stage. Aberrations in migration or neurite outgrowth are implicated in neurological and psychiatric disorders such as epilepsy, schizophrenia and autism. Previous studies revealed that in the early phase of cortical development the neural population migrates tangentially from the GE in the telencephalon and several genes have been characterized as regulators of migration and specification of GABAergic interneurons. However, much less is known about the molecular mechanisms of GABAergic interneurons-specific maturation at later stages of development. Here, we performed genome-wide screening to identify genes related to the later stage by flow cytometry based-microarray (FACS-array) and identified 247 genes expressed in cortical GABAergic interneurons. Among them, Dgkg, a member of diacylglycerol kinase family, was further analyzed. Correlational analysis revealed that Dgkg is dominantly expressed in somatostatin (SST)-expressing GABAergic interneurons. The functional study of Dgkg using GE neurons indicated alteration in neurite outgrowth of GABAergic neurons. This study shows a new functional role for Dgkg in GABAergic interneurons as well as the identification of other candidate genes for their maturation.

overall_design: GAD67-EGFP+/- mice (P0) were used for FACS-array analysis. Single cell suspension derived from cerebral cortice were prepared and sorted by fluorescent signal (GFP+ and GFP-). Four biological replicate were used for the comparison of GFP- v.s. GFP+.

first: Keita

last: Fukumoto

first: Tsuyoshi

last: Toya

first: Tasuku

last: Nishino

first: Yuchio

last: Yanagawa

first: Toru

last: Takumi


title: Gorlin syndrome-derived induced pluripotent stem cells are hypersensitive to Hedgehog-mediated osteogenic induction

city: chiyodaku misakichou

first: Shoko

last: Onodera

state: Tokyo

department: biochemistry

institute: Tokyo Dental collage

summary: Gorlin syndrome is an autosomal dominant inherited syndrome that predisposes a patient to the formation of basal cell carcinomas, odontogenic keratocysts, and skeletal anomalies. Patched-1 (PTCH1) is a Hedgehog (Hh) receptor that acts as a negative regulator of constitutive Hh signaling by preventing the G protein-coupled receptor Smoothened from entering the cilium in the absence of Hh protein binding. We generated iPSCs from four unrelated Gorlin syndrome patients with loss-of-function mutations in PTCH1 using the Sendai virus vector (SeVdp(KOSM)302).  The patient-derived iPSCs exhibited basic iPSC features, including stem cell marker expression, totipotency, and the ability to form teratomas. To check the Patient-derived iPSCs mimic patinet phenotype, We performted osteoblast differentiation and checked mRNA expression by hedgehog PCR array systems.

overall_design: qPCR gene expression profiling.  2 control hiPSC (KD iPS and 201B7) and 4 disease specific hiPSC (G1-1,G1-6,G2-5,G2-8) were used and treated separately as indicated in the summary. Two disease specific iPSc (G1-1,G1-6) were established by same patient fibroblasts. Two disease specific iPSc (G2-5,G2-8) were established by other patient fibroblasts. There were two experimental group named iPS and OBM. iPS group cultured EB and then collect samples. OBM group cultured EB, performed osteoblast differentiation until day 10 and then collect samples. Equal amount total RNA from each donor was pooled prior to gene expression analysis.

first: Daigo

last: Hasegawa

first: Toshifumi

last: Azuma


title: Differential Expression of LncRNAs and mRNAs in normal and inflamed human pulp

city: Guangzhou

first: Xin

last: Huang

address: No.9 Jinsui Road

institute: Guangzhou Women and Children’s Medical Center

summary: Dental pulp inflammation provides an excellent model for the interaction between tissue inflammation and regenerative processes. It is worthwhile to better understand molecular signaling of repair and regeneration in inflammatory processes. Emerging evidence suggests that lncRNAs participate in immune/inflammatory processes. We aimed to investigate the expression of lncRNAs in pulpitis and predict lncRNAs that possibly involved in inflammation and odontogenesis.

overall_design: For microarray analysis, seven cases of inflamed pulp tissue samples and five cases of normal pulp tissue samples were obtained.Normal pulps were picked from healthy third molars or teeth extracted for orthodontic purpose.Inflamed pulp tissues were extracted from teeth diagnosed with irreversible pulpitis  in accordance with the endodontics diagnoses system from the American Association of Endodontists. Any teeth that suffered from periodontitis were excluded. Patients who had a compromised immune system or those who were taking medications known to influence the immune response were excluded from the study.

first: Jin

last: Hou


title: miRNA expression from gp130F/F mice antrum at 4 weeks of age

city: Chapel Hill

first: Di

last: Wu

state: North Carolina

address: 385 S. Columbia Street, CB#7455

institute: University of North Carolina

summary:
The molecular events promoting the initiation of gastric cancer (GC), the third most lethal cancer worldwide, are ill-defined. Here, we demonstrate that upregulation of miR-200 family members is associated with tumor initiation in the gp130F/F mouse model of early GC.
The onset of gastric inflammation-associated adenomatous hyperplasia in gp130F/F mice occurs at ~6 weeks of age, with established intestinal-type tumors (3 months of age) progressively growing until a maximum size is reached at 6 months of age, with some evidence of carcinoma in situ. Since this phenotype histologically mimics early stage human GC, we therefore utilized gp130F/F mice as a model to identify miRNAs involved in the initiating molecular events leading to early stage GC. For this purpose, we performed miRNA microarrays on mouse gastric antrum tissue from gp130F/F and sex-matched littermate wild-type (gp130+/+) control mice aged 4 weeks; this age was chosen since antrum tissue from 4 week old (wo) gp130F/F mice is devoid of any histological signs of inflammation or hyperplasia, and is thus comparable to wild-type gastric antrum tissue

overall_design: Total RNA from 4 week old mouse antrum samples was subjected to an Affymetrix miRNA 2.0 array which included 722 mouse mature miRNAs and 690 mouse pre-miRNAs (Affymetrix).

first: Anna

last: Tsykin

first: Liang

last: Yu

first: Hugh

last: Gao

first: Brendan

last: Jenkins