title: Mycobacterium tuberculosis: yidC (Rv3921c) induced Vs Control cultures

status: Public on Nov 28 2018

city: Faridabad

first: Nisheeth

last: Agarwal

state: Haryana

address: 3rd Milestone, Faridabad-Gurugram Expressway

department: Infection and Immunity

country: India

institute: Translational Health Science and Technology Institute

summary: Transcriptional profiling of Mycobacterium tuberculosis H37Ra::pTetR-yidC (Test) compared with Mycobacterium tuberculosis H37Ra::pTetR (Control) bacteria after 4 days of treatment with 50ng/ml ATc with shaking at 200rpm at 37°C.

overall_design: Two-condition experiment, yidC-induced (Test) Vs yidC-uninduced cells (Control). Biological replicates: 3 test, 3 control. Three technical replicates per array.

first: Preeti

last: Thakur


title: Comprehensive transcriptome analysis regarding aging using normal human derived fibroblasts (NHDF)

status: Public on Nov 30 2018

city: Kamakura

first: Satoshi

last: Kondo

state: Kanagawa

address: Tebiro 6-10-1

department: New Projects Development Division

country: Japan

institute: Toray Industries,Inc.

summary: We determined the gene expression changes by the cDNA status using NHDF cells at early passage and at later passage

overall_design: Aging cells were produced by serial passages of NHDFs. To determine the gene expression changes dependent onaging, we used NHDF cells at p5 and p23 for the cDNA microarrya analyses.

first: Mari

last: Yamagami

first: Motoyuki

last: Otsuka

first: Kazuhiko

last: Koike


title: Transcriptional and interactome network analyses of Substantia Nigra in progressive stages of Parkinson’s disease

city: Sao Paulo

first: Carlos

middle: Alberto

last: Moreira-Filho

state: SP

address: Av. Dr. Eneas Carvalho de Aguiar 647

department: Departments of Pediatrics

country: Brazil

institute: Faculdade de Medicina da Universidade de Sao Paulo

summary: We analyzed the transcriptomic profile of post-mortem substantia nigra explants from controls, intermediate - Braak 3 (BK3) and 4 (BK4) - stages of Parkinson’s disease in order to investigate how gene-gene interaction patterns vary along disease development. The comparative transcriptional networks analyses indicate that the main hubs in CT network showed less gene-gene connections in BK3 and BK4 networks, probably reflecting changes in SN cell metabolism, population and density along PD stages.

overall_design: Substantia nigra transcriptomic profiles of controls and intermediate stages of Parkinson’s disease were compared using ANOVA in order to identify differentially expressed transcripts

first: Silvia

middle: Y

last: Bando

first: Priscila

last: Iamashita

first: Andre

last: Fujita

first: Edilaine

last: Tampellini

first: Jose

middle: M

last: Farfel

first: Lea

middle: T

last: Grinberg

middle: A


title: Cellular and genetic factors involved in the difference among rat strains to develop procainamide - induced Autoimmunity

city: Beijing

first: wang

last: liang

address: 7A North Yongchang Road BDA

country: China

institute: BioChainBJ

summary: To examine the influence cellular and genetics on the procainamide-induced autoimmune response in spleens we compared rats that are genetically Th2-predisposed (Brown Norway), Th1-predisposed (Lewis) or not genetically predisposed (Sprague Dawley). Rats were treated with procainamide three times per week. From the second week, blood samples were taken once a week for antinuclear antibody (ANA) detection. At 56d after treatment, rats were sacrificed and spleens samples were collected for microarray test and histopathology examination. Frequencies of T cell subsets and B cells in rat spleen were measured to assess the effects on splenocyte. Also, 12 serum cytokines/chemokines were determined to explored the Th1/Th2 cytokine pattern after treatment. We found that ANA were makedly elevated in BN and SD rats, while the elevated appeared earlier in BN rats, and the magnitude of its increase were much higher than that of SD rats. There was no marked change in serum ANA in Lewis rats. Histopathological analysis indicated that spleen weight increased significantly both in BN and SD rats after stimulated with procainamide. No significant changes in spleen weight and lesions were observed in Lewis rats. We also found the percentage of CD86 positive cells in spleen of BN rats was significantly increased, while the percentage of CD4+CD25+ cells was decreased in BN rats. In addition, percentage of CD11b/c positive cells were decreased, and the levels of Th-2 (IL-10), Th-1 type cytokine (IFN-γ) and chemokine (IL-1β) in serum were markedly elevated both in BN and SD rats after treatment. Th-2 type cytokine (IL-4, IL-6) in serum were markedly increased only in BN rats. Furthermore, similar immune mechanisms were found in BN and SD rat, and the altered genes were mainly associated in immune response, and inflammatory response. However, the number of differentially expressed genes (DEGs) in BN rats was higher than that in SD rats. Overall, we revealed significant differences in response to autoimmunity induced by procainamide among three strains rats, the BN rats was the most sensitive one, SD rats exhibited less sensitive while Lewis resistance to procainamide. Much more pronounced of Th2-type responses and more complex DEGs involved in immune regulation and response in BN rats might contribute to its susceptible to drug-induced lupus erythematosus. Moreover, similar immune mechanisms were found between BN and SD rat, which suggesting that these changes would served as the potential bridge biomarkers to predict drug-induced autoimmune reactions among species. The results may also provide a scientic basis for the high sensitivity of BN rats in prediction immunotoxicity in preclinical studies.

overall_design: In this study, different responses of BN, SD and LEW to procainamide were first analyzed in different levels of immune systems such as gene, protein, cell and organ levels to explore the relative contributions of cellular and genetic factors to the development of autoimmune disease induced by drug. This study is also benefit to further understand the immune mechanism of drug-induced autoimmune reactions.

first: Ying

last: Huang

first: Zhi

last: Lin

first: Yan

last: Huo

first: Xingchao

last: Geng

first: Ming

last: Li

first: Yanwei

last: Yang

first: Bo


title: Single cell RNA sequencing reveals a cardioprotective role for resident macrophages following myocardial infarction (microarray)

status: Public on Nov 29 2018

city: Toronto

first: Slava

last: Epelman

state: Ontario

address: 101 College St

department: Cardiology, University Health Network

country: Canada

institute: Toronto General Hospital Research Institute

summary:
Human left ventricular cardiac tissue was isolated from patients at the time of surgery. Tissue was digested into single cell suspension and labeled with CD45, CD14, HLA-DR and CCR2 antibodies.
Macrophages were sorted into three groups (CCR2+ Monocytes: CD14+ CCR2+ HLA-DRNeg; CCR2+ Macrophages: CD14+CCR2+HLA-DR+; MHC-II hi Macrophages: CD14+CCR2-HLA-DR+)

overall_design: RNA was extracted from each subset for Gene array analysis

first: Sara

last: Nejat


title: Aberrant expression of interleukin-23-regulated miRNAs in T cells from patients with ankylosing spondylitis

city: Chia-Yi

first: Hui

middle: Chun

last: Yu

address: No. 2, Min-Sheng Rd, Dalin Town

department: Medical research

country: Taiwan

institute: Dalin Tzu Chi Hospital, Buddhist Tzu Chi Medical Foundation

summary: Among the miRNAs regulated by IL-23, expression levels of 5 miRNAs were increased in T cells from patients with AS. The transfection of miR-29b-1-5p mimic could inhibit the IL-23-mediated STAT3 phosphorylation and might play a negative feedback control in the immunopathogenesis of AS.

overall_design: K562 cells, a human erythroleukemia line, purchased from the American Type Culture Collection (Manassas, USA) were cultured in medium with or without the presence of IL-23 (20 ng/mL) for 3 days. These cells were used for subsequent analysis.

first: Ning-Sheng

last: Lai

first: Hui-Chun

first: Chien-Hsueh

last: Tung

first: Kuang-Yung

first: Hsien-Bin

first: Ming-Chi

last: Lu


title: Expression data from mouse skin treated with a miR-29 mimic or a miR-29 inhibitor

status: Public on Nov 27 2018

city: Boulder

first: Aimee

last: Jackson

state: CO

address: 6200 Lookout Rd.

country: USA

institute: miRagen Therapeutics

summary: We performed a microarray analysis of mouse skin treated with a miR-29b mimic or a miR-29 inhibitor in order to identify pharmacodynamic (PD) biomarkers that were reciprocally regulated in vivo in the skin

overall_design: miR-29b mimic or vehicle was injected intradermally at the site of an incisional wound, and antimiR-29 or vehicle was injected intradermally into intact skin in C57BL/6 mice. (N=3 per cohort)

first: C

middle: L

last: Gallant-Behm

first: A


title: A stress-responsive bZIP transcription factor OsbZIP62 improves drought and oxidative resistance in rice

city: Shanghai

first: Kai

last: Xu

address: No.2901, Beidi Rd.

institute: Shanghai Agrobiological Gene Center

type: Expression profiling by high throughput sequencing

summary: Transcription factors play a crucial regulatory role in plant drought stress responses. In this study, a novel drought stress related bZIP transcription factor, OsbZIP62, was identified in rice. This gene was selected from transcriptome analysis of several typical rice varieties with different drought tolerance. The expression of OsbZIP62 was obviously induced by drought, hydrogen peroxide, and abscisic acid (ABA) treatment. Overexpression of OsbZIP62-VP64 (OsbZIP62V) enhanced the drought tolerance and oxidative stress tolerance of transgenic rice, while the osbzip62 mutants showed the opposite phenotype.  RNA-seq analysis showed that many stress-related genes (e.g. OsGL1, OsNAC10, and DSM2) were up-regulated in OsbZIP62V plants. OsbZIP62 could bind to the abscisic acid–responsive element (ABRE) and promoters of several putative target genes. Taken together, OsbZIP62 positively regulated rice drought tolerance through regulated the expression of genes associated with stress.

overall_design: To search the downstream genes of OsbZIP62, we performed transcriptome analysis of the OsbZIP62-VP64-overexpressor, osbzip62 mutant and wild-type plants under normal conditions using high-throughput sequencing.

first: Shiqin

first: Lijun

last: Luo


title: Studies in an early development window unveils a severe HSC defect in both murine and human Fanconi anemia [human]

city: Paris

first: Franck

last: Letourneur

address: 22 rue mechain

country: France

institute: INSERM

summary:
We performed a unique kinetics study of hematopoiesis in Fancg-/- mouse embryos, between E12.5 and E14.5 developmental window.
We also report for the first time that a deep HSC defect is also observed during human FA development, and that human FA FL HSCs present a transcriptome profile similar to that of mouse E12.5 Fancg-/- FL HSCs.

overall_design: Sorted CD34+CD38-CD45+CD117hi HSC-enriched population from a unique 13 WG Fanconi FL (FANCB)(n=1) and from control FL from fetuses at the same stage of development (i.e. second trimester, 13 and 17.7 WG) (n=2)were sorted and RNA was purified using RNeasy Plus Micro Kit (Qiagen). RNA concentration and integrity  was evaluated with the Agilent Bioanalyzer 2100 and 2 ng of total RNA reverse transcribed  following the Ovation Pico System V2  (Nugen). cDNA is then hybridized to GeneChip® HumanGene2.0ST (Affymetrix)

first: Michèle

last: SOUYRI


title: Efferocytosis induces a novel SLC program to promote glucose uptake and lactate release

city: New York

first: Justin

middle: Shaun Arnold

last: Perry

state: New York

address: 408 East 69th Street, 408-15

department: Immunology Program

institute: Sloan Kettering Institute for Cancer Research

summary: On a daily basis, we turnover billions of apoptotic cells that are removed by professional and non-professional phagocytes1-10. While characterizing the transcriptional program of phagocytes, we discovered a novel solute carrier family (SLC) gene signature (33 SLC members) that is specifically modified during engulfment of apoptotic cells (efferocytosis) but not during antibody-mediated phagocytosis. When we assessed the functional relevance of these SLCs, we noted robust induction of an aerobic glycolysis program in engulfing phagocytes, initiated by SLC2A1-mediated glucose uptake, and suppression of oxidative phosphorylation program. Interestingly, the different steps of phagocytosis10,11, i.e. smell (‘find-me’ signals / sensing factors released by apoptotic cells), taste (phagocyte- apoptotic cell contact), and ingestion (corpse internalization), activated different molecules to promote this glycolytic process. Further, lactate, a natural by-product of aerobic glycolysis12,13, was released from engulfing phagocytes via SLC16A1, an SLC member activated after corpse uptake. While glycolysis within phagocytes contributed to actin polymerization and the continued uptake of corpses, the lactate released via SLC16A1 influenced the establishment of an anti-inflammatory environment. Collectively, these data reveal a novel SLC program activated during efferocytosis, identify a previously unknown reliance on aerobic glycolysis during apoptotic cell uptake, and that glycolytic byproducts of efferocytosis can also influence other cells in the microenvironment.

overall_design: The experiment consisted of two conditions: Phagocytes (LR73 cells) alone or co-cultured with apoptotic Jurkat lymphoma cells. Each condition consisted of four biological replicates.

first: Sho

last: Morioka

middle: S

first: Michael

middle: H

last: Raymond

first: Christopher

middle: B

last: Medina

first: Yunlu

last: Zhu

first: Liyang

last: Zhao

first: Vlad

last: Serbulea

first: Suna

last: Onengut-Gumuscu

first: Norbert

last: Leitinger

first: Sarah

last: Kucenas

first: Jeffrey

middle: C

last: Rathmell

first: Liza

last: Makowski

first: Kodi

last: Ravichandran


title: Studies in an early development window unveils a severe HSC defect in both murine and human Fanconi anemia

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

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: Refer to individual Series


title: Gene expression signatures associated with PI3Kα-induced senescence

first: Xue-Ling

last: Liu

address: 555 Zuchongzhi Road

department: Shanghai Institute of Materia Medica

institute: University of Chinese Academy of Sciences

summary: To investigate the mechanisms of PI3Kα-induced senescence, we performed a gene expression microarray analysis with MCF-10A/H and parental MCF-10A cells.

overall_design: MCF-10A/H and parental MCF-10A cells cultured in serum-depleted or nutrient-sufficient medium for 96 h were collected for microarray analysis.

first: Xue-ling


city: Taian

first: Ru Chang

last: Ren

address: Daizong

department: College of Life Sciences

institute: Shandong Agricultural University

summary:
We performed a molecular characterization of the maize defective kernel mutant that is a seed-lethal mutant with developmental deficiency phenotypes, transcriptomic analysis revealed numerous differentially expressed genes related to storage proteins and starch biosynthesis.
The developmental difference between the WT and mutant might be caused by differences in gene expression. To explain the developmental difference between them at the genomic level, RNA-Seq analysis was performed with total RNA isolated from WT and  mutant endosperms at 10 DAP

overall_design: Total RNAs were extracted from the endosperm of WT and mutant at 10 DAP used CTAB-based method. Two biological repeats (8-10 individuals/pool) of WT and mutant were isolated from two different segregating ears, and used for RNA sequencing

first: Ru

first: Xiang


title: A multi-tissue full lifespan epigenetic clock for mice [II]

city: Los Angeles

first: Steve

last: Horvath

state: CA

address: 695 Charles E. Young Drive South, Box 708822

department: Human Genetics

institute: University of California, Los Angeles

type: Methylation profiling by high throughput sequencing

summary: Human DNA-methylation data have been used to develop highly accurate biomarkers of aging ("epigenetic clocks"). Recent studies demonstrate that similar epigenetic clocks for mice (Mus Musculus) can be slowed by gold standard anti-aging interventions such as calorie restriction and growth hormone receptor knock-outs. Using DNA methylation data from previous publications with data collected in house for a total 1189 samples spanning 193,651 CpG sites, we developed 4 novel epigenetic clocks by choosing different regression models (elastic net- versus ridge regression) and by considering different sets of CpGs (all CpGs vs highly conserved CpGs). We demonstrate that accurate age estimators can be built on the basis of highly conserved CpGs.  However, the most accurate clock results from applying elastic net regression to all CpGs. While the anti-aging effect of calorie restriction could be detected with all types of epigenetic clocks, only ridge regression based clocks replicated the finding of slow epigenetic aging effects in dwarf mice. Overall, this study demonstrates that there are trade-offs when it comes to epigenetic clocks in mice. Highly accurate clocks might not be optimal for detecting the beneficial effects of anti-aging interventions.

overall_design: To complement our in-house data DNA-methylation data collection, we retrieved reduced-representation-bisulfite-sequencing (RRBS) and whole genome bisulfite-sequencing (WGBS) data from previous studies that were available on GEO  (GSE52268, GSE58129, GSE67507, GSE80672, GSE85251, GSE89275, GSE93957).  We re-processed these data using the BS_Seeker2 methylation calling pipeline for the sake of consistency in all the samples used in our study.

middle: J

last: Thompson


title: Gene expression profile of RAW264.7 monocytes treated with or without IL-33

first: Yunlong

last: Yang

address: Department of Cellular and Genetic Medicine, School of Basic Medical Sciences, Dong'an road 130

institute: Fudan University

summary: Molecular mechanisms underlying the cancer stroma in metastasis is largely unknown. Here we show that cancer-associated fibroblasts (CAFs) produce high levels of IL-33 that acted on tumor-associated macrophages (TAMs) to induce the M1 to M2 transition. Genome profiling of metastasis-related genes in the IL-33-stimulated TAMs showed a > 200-fold increase of metalloproteinase 9 (MMP9). Signaling analysis demonstrated the IL-33-ST2-NFkB-MMP9-laminin pathway that mediates cancer metastasis. In mouse and human fibroblast-rich pancreatic cancers, genetic deletion of IL-33, ST2 and MMP9 markedly blocked metastasis. Pharmacological inhibition of NFkB and MMP9 also blocked cancer metastasis. Deletion of IL-33, ST2 and MMP9 restored laminin, a key basement membrane component associated to tumor microvessels. Together, our data provide novel mechanistic insights on the IL-33-NFkB-MMP9-laminin axis that mediates the CAF-TAM-committed cancer metastasis. Thus, targeting the CAF-TAM-vessel interaction provides an outstanding therapeutic opportunity for cancer treatment.

overall_design: Raw 264.7 monocytes are treated with or without 50 ng/ml IL-33 (n=3 samples/group)

first: Patrik

last: Andersson

first: Yihai

last: Cao


title: Gene Expression in Hip Soft Tissues in a Natural Canine Model of Developmental Dysplasia of the Hip

city: Ithaca

first: Jennifer

middle: K

last: Grenier

state: NY

address: 526 Campus Rd

department: Biomedical Sciences

institute: Cornell University

summary: We provide data that compares global gene expression in dysplastic hip compared to control hip tissue in dogs.

overall_design: Descriptive for age at sample conparisons and Case/control

first: Rory

last: Todhunter


title: Expression analysis of circPan3+/+ and circPan3-/- ISCs

first: Pingping

last: Zhu

state: Beijing

address: Datun Road 15#

institute: Institute of Biophysics, Chinese Academy of Sciences

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

summary: Investigation of differentially expressed genes in circPan3 deficient ISCs

overall_design: RNA (including mRNA, miRNA and lncRNA) expression profiling of circPan3+/+ and circPan3-/- ISCs.  Intestinal crypts from Lgr5GFP-CreERT2 mice were isolated for ISCs enrichment by FACS. Total RNA from each samples was quantified using the NanoDrop ND-1000. The sample preparation and microarray were performed in accordance with the Affymetrix ClariomTM D mouse array analysis protocol (previously known as GeneChip™ Mouse Transcriptome Array 1.0)

first: JiaYi

last: Wu

first: Zusen

last: Fan


title: Studies in an early development window unveils a severe HSC defect in both murine and human Fanconi anemia [mouse]

first: Franck

last: Letourneur

overall_design: Fancg-/- and WT LSA cells were sorted from mouse FL at E12.5 and E14.5 in three independent experiments.RNA of sorted cells was purified using RNeasy Plus Micro Kit (Qiagen) and RNA concentration and integrity  evaluated with the Agilent Bioanalyzer 2100. 2 ng of total RNA is reverse transcribed  following the Ovation Pico System V2  (Nugen). cDNA is then hybridized to GeneChip® MTA1.0 (Affymetrix)

first: Michèle

last: SOUYRI


title: Genome-wide analysis of RNAs associated with Populus euphratica Oliv. heterophyll morphogenesis [miRNA-Seq]

city: Alar

first: Shaowei

last: Qin

state: Xinjiang

address: Hongqiao Road 705

institute: Tarim University

type: Non-coding RNA profiling by high throughput sequencing

summary: The desert plant Populus euphratica Oliv. has typical heterophylly; linear (Li), lanceolate (La), ovate (Ov) and broad-ovate (Bo) leaves grow in turn from young to adult trees. It is therefore a potential model organism for leaf development. To investigate the roles of RNAs (including mRNAs, miRNAs, lncRNAs and circRNAs) in the morphogenesis of P. euphratica heterophyll, the juvenile heterophyll were respectively sampled, and then their expression patterns were analyzed by small RNA sequencing and strand-specific RNA sequencing. We found that 1374 mRNAs, 19 miRNAs, 71 lncRNAs and 2 circRNAs were P. euphratica heterophyll morphogenesis associated (PHMA) RNAs, among them, 17 PHMA miRNAs could disturb the expression of 46 PHMA mRNAs, furthermore, 11 lncRNAs and 2 circRNAs interacted with 27 PHMA mRNAs by ceRNA hypothesis, respectively. According to GO and KEGG pathway analysis, PHMA RNAs were mainly involved in metabolic, response to stimulus and developmental processes. Our results indicated that both external environmental factors and genetic factors of P. euphratica co-regulated the expression of PHMA RNAs, caused the cell division was repressed, while cell growth was reinforced, and resulted in the morphogenesis of P. euphratica heterophyll, ultimately.

overall_design: Small RNA-seq of linear (Li), lanceolate (La), ovate (Ov) and broad-ovate (Bo) leaf groups of Populus euphratica, every group including three biology replicates, were named  Li1, Li2, Li3, La1, La2, La3, Ov1, Ov2, Ov3, Bo1, Bo2 and Bo3, respectively.And all the raw data of miRNA-seq have been submitted to Sqeuence Read Archive(SRA) of NCBI under accession number SRP162961.

first: L

middle: F

last: Zhao

first: S

middle: W

first: C

last: Li

first: Z

middle: Z

last: Guo

last: Bao


title: Transcriptome change in response to ochratoxin A (OTA) in Yarrowia lipolytica Y-2

city: Zhenjiang

first: Kaili

last: Wang

state: Jiangsu

address: Xuefu Road 301

department: School of food and biological engineering

institute: Jiangsu University

summary: The yeast Yarrowia lipolytica Y-2 shown the capability to degrade OTA by the intracellular enzymes. However, the enzymes which risponsible for the degradation process was unkonown. Transcriptome change in response to mycotoxin OTA was analyzed. The molecular mechanism of Yarrowia lipolytica Y-2 withstand OTA was revealed.

overall_design: Each two samples were analyzed , the yeast Yarrowia lipolytica Y-2 amending with ochratoxin A and the control which was not amending with OTA

first: Xiaoyun

last: Zhang

first: Hongjuan


title: Escherichia coli Lrp regulates one-third of the genome via direct, cooperative, and indirect paths

city: Ann Arbor

first: Peter

last: Freddolino

state: MI

address: 1150 W. Medical Center Dr.

department: Biological Chemistry

institute: University of Michigan

type: Genome binding/occupancy profiling by high throughput sequencing

summary: The global regulator Lrp plays a crucial role in regulating metabolism, virulence and motility in response to environmental conditions.  Lrp has previously been shown to activate or repress approximately 10% of genes in Escherichia coli.  However, the full spectrum of targets, and how Lrp acts to regulate them, has stymied earlier study.  We have combined matched ChIP-seq and RNA sequencing under nine physiological conditions to map the binding and regulatory activity of Lrp as it directs responses to nutrient abundance. In addition to identifying hundreds of novel Lrp targets, we observe two new global trends: first, that Lrp will often bind to promoters in a poised position under conditions when it has no regulatory activity, and second, that nutrient levels induce a global shift in the equilibrium between non-specific and sequence-specific DNA binding.  The overall regulatory behavior of Lrp, which as we now show regulates 35% of E. coli genes directly or indirectly under at least one condition, thus arises from the interaction between changes in Lrp binding specificity and cooperative action with other regulators.

overall_design: Profiles of Lrp binding and global transcription levels determined under nine conditions with duplicates in WT and Lrp::kanR strains

first: Grace

last: Kroner

first: Michael

last: Wolfe


title: Aberrant DNA methylation of hypothalamic angiotensin receptor in prenatal-programmed hypertension

city: Meguro-ku

first: Fumiko

last: Mori

state: Tokyo

address: 4-6-1 Komaba

department: Research Center for Advanced Science and Technology

institute: University of Tokyo

summary: Malnutrition during pregnancy, which causes prenatal exposure to excessive glucocorticoid, induces adverse metabolic programming leading to hypertension in offspring. Pregnant rats receiving a low-protein diet exhibited moderate downregulation of 11-beta-dehydrogenase isozyme 2, which inactivates corticosterone, in the placenta, resulting in prenatal exposure to excessive corticosterone. In offspring of pregnant rats receiving a low-protein diet or dexamethasone, mRNA expression of angiotensin receptor type 1a (Agtr1a) in the paraventricular nucleus (PVN) of the hypothalamus was upregulated, concurrent with reduced expression of DNA methyltransferase 3a (Dnmt3a), reduced binding of DNMT3a to the Agtr1a promoter, and DNA demethylation, suggesting hypothalamic Agtr1a expression is epigenetically modulated by excess glucocorticoid. Dexamethasone treatment of PVN cells downregulated DNMT3a while upregulating Agtr1a, and decreased DNMT3a binding and DNA demethylation at the Agtr1a promoter. Consistent with Agtr1a upregulation in the hypothalamus, salt loading increased BP in both types of offspring. Even without dexamethasone treatment, hypothalamic neuron-specific DNMT3a-deficient mice, in which Agtr1a was upregulated, exhibited salt-induced BP elevation. By contrast, dexamethasone-treated Agtr1a-deficient mice failed to show salt-induced BP elevation, despite reduced expression of DNMT3a. Thus, epigenetic modulation of hypothalamic angiotensin signaling contributes to salt-sensitive hypertension induced by prenatal glucocorticoid excess in offspring of mothers that are malnourished during pregnancy.

overall_design: The samples were extracted from 12-week-old male offspring  whose  mothers were treated with vehicle or 200μg/kg dexamethasone at the third trimester.

first: Mitsuhiro

last: Nishimoto

first: Latapati

last: Reheman

first: Wakako

last: Kawakazaki

first: Nobuhiro

last: Ayuzawa

first: Kohei

last: Ueda

first: Daigoro

last: Hirohama

first: Daisuke

last: Kohno

first: Sigeyoshi

last: Oba

first: Tatsuo

last: Shimosawa

first: Takeshi

last: Marumo

first: Toshiro

last: Fujita


title: Transcriptome-wide analysis of wild Asari (=Manila) clams affected by the Brown Muscle Disease: etiology and impacts of the disease

city: Arcachon

first: Anthony

last: Bertucci

address: Place du Dr Peyneau

institute: University of Bordeaux

summary: Recently, we reported an emerging pathology named Brown Muscle Disease (BMD) affecting Asari clams inhabiting the most productive area for this species in France, the Arcachon Bay. The main macroscopic feature of the pathology relies on the atrophy of the posterior adductor muscle, affecting the ability of clams to burry. The research of the etiological agent of BMD privileged a viral infection. Contrary to healthy clams, infected animals are always found at the surface of the sediment and exhibit 30 nm virus-like particles in muscle, granulocytic and rectal cells. In order to get more insights on the etiology and impacts of the BMD on clams, we took advantage in the present study of next generation sequencing technologies. An RNA-Seq approach was used (i) to test whether viral RNA sequences can be specifically found in the transcriptome of diseased animals and (ii) to identify the genes that are differentially regulated between diseased and healthy clams. Contrary to healthy buried animals, in diseased clams one sequence showing extensive homologies with retroviridae-related genes was detected. Among the biological processes that were affected in diseased clams, the synaptic transmission process was the most represented. To deepen this result, a new sampling was carried out and the transcription level of genes involved in synaptic transmission was determined in healthy and diseased clams but also in clams with no visible sign of pathology but located at the surface of the sediment. Our findings suggest that muscle atrophy is a latter sign of the pathology and that nervous system could be instead a primary target of the BMD agent.

overall_design: Two pools of total RNA material were formed using a total of 5 clams : a pool of 3 animals exhibiting signs BMD (SURF+) and a pool of 2 animals with no sign of BMD (BUR-). Pools were done with equal amount of RNA from each samples and sequenced on one flow cell.

first: Fabien

last: Pierron

first: Patrice

last: Gonzalez

first: Cindy

last: Binias

first: Emilie

last: Mérour

first: Michel

last: Brémont

first: Xavier

last: De Montaudouin


title: Genome wide mapping of R-loops in the repriming deficient human cells using RNA DIP-Seq

status: Public on Nov 26 2018

city: Cambridge

first: Alastair

last: Crisp

address: Francis Crick Avenue

country: United Kingdom

institute: MRC Laboratory of Molecular Biology

summary: The goal of this study was to compare the qualitative and quantitative differences in the presence of DNA:RNA hybrids (R-loops) between human wild type and PrimPol knockout human iPS cell lines. Our initial genetic experiments on a reporter locus have showed a link between the formation of R-loop and non-B DNA motifs; we have therefore analysed the correlation between R-loop abundance and of sequences computationaly predicted to form triplex-DNA or G-quadruplex forming sequences, and whether this changes between the two cell lines.

sample_organism:
Gallus gallus
Homo sapiens

platform_organism:
Gallus gallus
Homo sapiens

overall_design: We examined abundance of R-loops in wild type and PrimPol deficient BOBSC iPS cell lines using an immunoprecipitation approach using DNA:RNA hybrid specific monoclonal antibody S9.6. To allow for quantitative comparisons between the cell lines, prior to extraction we have spiked-in each mutant cells with the same ratio of chicken DT40 cells to act as a calibrator.

first: Saša

last: Šviković

first: Suemei

last: Tan-Wong

first: Guillaume

last: Guilbaud


title: Repriming limits R-loop formation at DNA secondary structures during S phase

summary: The goal of this study was to compare the qualitative and quantitative differences in the presence of DNA:RNA hybrids (R-loops) between wild type and PrimPol knockout cell lines. Our initial genetic experiments on a reporter locus have showed a link between the formation of R-loop and non-B DNA motifs; we have therefore analysed the correlation between R-loop abundance and of sequences computationaly predicted to form triplex-DNA or G-quadruplex forming sequences, and whether this changes between the two cell lines.

sample_organism:
Drosophila melanogaster
Gallus gallus
Homo sapiens


title: In vivo haematopoietic cell production by bone marrow-derived hemogenic endothelium

status: Public on Nov 24 2018

first: Thierry

last: JAFFREDO

address: 9, Quai St Bernard

department: Developmental Biology

institute: CNRS

summary:
By tracing the VE-cadherin expression in the newborn bone marrow hematopoietic LSK (lineage minus/Sca-positive/Kit-positive) cells, we demonstrated that the late foetal/newborn BM hemogenic endothelial cells produce a small cohort of hematopoietic stem and progenitor cells (HSPCs) capable of circulating and colonizing the secondary haematopoietic organs. Phenotypic and functional analyses disclosed that BM endothelium-derived HSPCs are mainly Multipotent Progenitors (MPPs) and a few Hematopoietic Stem Cells.
We used microarrays to detail the global programme of gene expression underlying the endothelial origin of LSK cells in the newborn bone marrow.

overall_design: Six samples were analyzed including YFP positive cells (3 replicates) and YFP negative cells (3 replicates). We used the tamoxifen inducible Tg(Cdh5-Cre/ERT2) mice crossed to Rosa 26 YFP mice. Tamoxifen induction was performed at 1, 2 and 3 days after birth. At day 26 after day 1 induction, LSK cells were FACS-sorted and separated into YFP-positive and YFP-negative cells. YFP reports the expression of VE-Cadherin

last: Jaffredo

first: Laurence

last: Petit


title: Molecular signal communication in soil during arbuscular mycorrhizal formation changes the transcriptome profiles in wheat (Triticum aestivum L.) roots

city: Yangling

first: HUI

last: TIAN

institute: Northwest A&F University

summary: We aimed to test the hypothesis that the transcriptional profile of wheat roots can be changed by the AM symbiotic signals, even though there is no physical contact with AM fungi. A total of 2,360 differentially expressed genes (DEGs), including 1,888 up-regulated DEGs and 472 down-regulated DEGs were found. Among them, 59 were highly induced DEGs (gene expression fold changed > 500), and 121 genes only expressed in the NM treatment. The DGEs covered all the 21 chromosomes of wheat genome, and were dominantly distributed on the 2A, 2B, 2D, 3B, 5B and 5D chromosomes. Most of the DEGs located at membrane, and functioned in catalytic activity, transferase activity and binding. 63 orthologues of the previously reported genes wich play important roles during AM symbiosis in model plants were found.

overall_design: 6 samples for the two treatments, and three biological replicates for each treatment

first: Hui

last: Tian

first: Runze

last: Wang

first: Zakaria

last: Solaiman

first: Khalil

last: Kariman


title: Genome wide mapping of R-loops in the repriming deficient DT40 cells using DRIP-Seq

summary: The goal of this study was to compare the qualitative and quantitative differences in the presence of DNA:RNA hybrids (R-loops) between chicken DT40 wild type and PrimPol knockout cells. Our initial genetic experiments on a reporter locus have showed a link between the formation of R-loop and non-B DNA motifs; we have therefore analysed the correlation between R-loop abundance and of sequences computationaly predicted to form triplex-DNA or G-quadruplex forming sequences, and whether this changes between the two cell lines.

sample_organism:
Drosophila melanogaster
Gallus gallus

platform_organism:
Drosophila melanogaster
Gallus gallus

overall_design: We examined abundance of R-loops in wild type and PrimPol deficient DT40 cell lines, in duplicate, using an immunoprecipitation approach using DNA:RNA hybrid specific monoclonal antibody S9.6. To allow for quantitative comparisons between the cell lines, prior to extraction we have spiked-in each mutant cells with the same ratio of Drosophila S2 cells to act as a calibrator.


title: Identification of molecular mechanisms related with fatness in pig at transcriptome and miRNAome level

status: Public on Nov 22 2018

city: Kraków

first: Artur

last: Gurgul

address: Rędzina 1C

department: Center for Experimental and Innovative Medicine

country: Poland

institute: University of Agriculture in Krakow

summary:
Purpose: The aim of present research was to identify miRNAs potentially related with fattness traits in pigs

Methods: miRNA-seq analysis was performed on subcutaneous fat samples collected from 22 pigs representing two sire-line breeds – Pietrain and Hampshire and one dam-line – Large White. Based on dissection data, pigs were selected from a larger population in terms of fatness traits to obtain the most extreme groups in each breed. The cDNA libraries were constructed form 300 ng of total RNA with the use NEBNext Multiplex Small RNA Library Prep Set for Illumina (New England Biolabs, Ipswich, MA, United States) according to the protocol. The quantification of obtained libraries was performed on Qubit 2.0 (Invitrogen, Life Technologies) and TapeStation 2200 (D1000 ScreenTape; Agilent). The RNA-seq was performed in 36 single-end cycles on HiScanSQ platform (Illumina) with the use of ruSeq SR Cluster Kit v3- CBOT-HS and TruSeq SBS Kit v 3 - HS (Illumina). Each library was sequences in 4 technical replications. The DEGs were detected using DESEq2 software and validation was performed by qPCR.

Results: RNA-seq approach allowed to identify miRNAs differentially expressed between pigs with various fatness traits in each analyzed breeds: 64 for Pietrain pigs; 41 for Hampshire and 46 for Large White pigs (pvalue <0.05; fold change≤1.5). The comparison of obtained miRNAs sets showed 13 miRNAs identified in all three breeds. The Gene Ontology analysis (mirPath v.3.0 DIANA Tools web with DIANA—TarBase v7.0 as a reference) confirmed that detected miRNAs were involved in fatty acid biosynthesis (pvalue <1e-325); fatty acid metabolism (pvalue 6.661338e-16); ECM-receptor interaction (pvalue <1e-325). The most important targeted genes regulated by identified miRNAs were: fatty acid synthase – FASN; Acetyl-CoA carboxylase 1 – ACACA; Malonyl CoA-acyl carrier protein transacylase – MCAT and  acetyl-CoA acyltransferase 1 and 2 (ACAA1 and ACAA2 genes).

Conclusions: Obtained results allow to propose the panel of miRNAs, which can be related with fatness in pig. Such analysis can be the basis of future research in terms of identification of molecular mechanisms related with adipogenesis and fatness traits in pigs.

overall_design: The fat (subcutaneous fat tissue) microRNA sequencing was performed for 22 samples collected form pigs representing three breeds – Large White, Pietrain and Hampshire, using Illumina HiScan SQ  in 36 single-end cycles.

first: Katarzyna

last: Ropka-Molik

first: Klaudia

last: Pawlina-Tyszko

last: Piórkowska


title: Transcriptional expressions of Nitrosomonas europae after CeO2 nanoparticle exposure and 12-h recovery

city: Nanjing

first: Junkang

last: Wu

address: 2 Sipailou Street

department: Energy and environment

institute: Southeast University

summary: To further explore the biotoxicity mechanisms of CeO2 nanoparticles (NPs) and the recovery strategies of the according impaired Nitrosomonas europaea (N. europaea, ATCC 19718) cells, a genome-sequenced model ammonia oxidizing bacterium (AOB) commonly detected in the activated sludge of biological wastewater treatment plants, the whole-genome microarray analysis was applied to retrieve the induced transcriptional responses, after their physiological and metabolic activities were evealed.

overall_design: The whole-genome expressions were measured after exposure to 50 ppm CeO2 NPs and 12-hr recovery incubation when the ammonia removal rate (ARA) declined by 10% in the chemostat bioreactor .Three biological replicates were included  for exposure and recovery experiment.

first: Ran

last: Yu


title: The BET Bromodomain inhibitor OTX015 (MK-8628) in mantle cell lymphoma: in vivo activity and identification of novel combinations to overcome adaptive resistance

status: Public on Nov 21 2018

city: Bellinzona

first: Francesco

last: Bertoni

state: Ticino

address: Via V. Vela 6

department: Lymphoma & Genomics Research Program

country: Switzerland

institute: IOR

summary: Activity of the BET Bromodomain inhibitor OTX015 (MK8628) in mantle cell lymphoma as single agent and in combination

overall_design: Gene Expression Profiling analysis of four mantle cell lymphoma cell lines exposed to treatment or to vehicle

first: Chiara

last: Tarantelli

first: Luciano

last: Cascione

first: Andrea

last: Rinaldi


title: The landscape of A-to-I RNA editome in mouse embryonic development

city: Beijing

first: Chenghui

last: Zhao

address: Haidian Taiping Road 27

institute: Beijing Institute of Radiation Medicine

type:
Other
Third-party reanalysis

summary: A-to-I editing, as a post-transcriptional modification process mediated by ADAR, plays a crucial role in many biological process in metazoans.The study of RNA editing in mouse early embryonic development can understand the dynamic changes of RNA editing during mouse early embryonic development, and further reveal the role of RNA editing in mouse early embryo development.We found that as embryonic developing, RNA editome in mice is getting more and more. Besides, RNA editome in mouse embryonic development is stage specified.

overall_design:
We collected 29 mouse embryonic samples RNA-seq from GSE71434 and GSE66582. Then we identified RNA editome by three identification method. We integrated these RNA editome to eight stages and record their position, reference, alter, strand and RNA editing level.
mRNA-seq reads were aligned to the mm10 genome assembly using STAR(version 2.5.2b) with default parameter.
Duplicated reads that mapped to the same location were removed using Picard(version 1.141)(https://broadinstitute.github.io/picard/) with default parameter.
Reads with a mapping quality <20 were removed using samtools(version 1.3.1) with parameter '-q 20'.
Variants were called using the GATK(version 3.5.0) HaplotypeCaller tool with options stand_call_conf of 20 and stand_emit_conf of 0.
Candidate RNA editing site were called using the following filtering steps: (1) all variants present in dbSNP (except SNPs of molecular type “cDNA”, database version 137, http://www.ncbi.nlm.nih.gov/SNP/); (2) variants located in the first 6 bp from either end of a sequence read were discarded; (3) in non-Alu regions, we removed sites in simple repeats according to RepeatMasker annotation, discarded intronic candidates if they were located within 4 bp of all known splicing junctions according to Ensembl gene annotations, and removed sites in homopolymer runs of ≥5 bp; (4) variant sites in regions of high similarity to other parts of the genome were discarded using the BLAST-like alignment tool (BLAT); (5) the editing type of each site was inferred based on the strand of overlapping annotated genes and only A-to-I base changing editing sites were retainned.
Tab-delimited text files include basic information of identified A-to-I editing sites for each sample;  basic information includes chromosome, position, strand, reference base, altered base, edting level of each A-to-I editing site.

first: Hebing

last: Chen

first: Hao

last: Li

first: Xiaochen

last: Bo


title: Pan-senescence transcriptome analysis identified RRAD as a marker and negative regulator of cellular senescence

status: Public on Nov 20 2018

city: TORONTO

first: Haiyang

last: Guo

address: 101 College Street, 11-601D, TMDT, 11-601D, TMDT

department: Princess Margaret Cancer Centre

institute: UNIV HEALTH NETWORK

summary: Cellular senescence, an irreversible proliferative arrest, functions in tissue remodeling during development and is implicated in multiple aging-associated diseases. While senescent cells often manifest an array of senescence-associated phenotypes, such as cell cycle arrest, altered heterochromatin architecture, reprogrammed metabolism and senescence-associated secretory phenotype(SASP), the identification of senescence cells has been hindered by lack of specific and universal biomarkers. To systematically identify universal biomarkers of cellular senescence, we integrated multiple transcriptome data sets of senescent cells obtained through different in vitro manipulation modes as well as age-related gene expression data of human tissues. Our analysis showed that RRAD (Ras-related associated with diabetes) expression is up-regulated in all the manipulation modes and increases with age in human skin and adipose tissues.

overall_design: Microarray experiments were performed to determine the lncRNA expression in corresponding   (normal human fibroblasts) NHFs. We used NHFs at passage 62 as replicative senescence model and NHFs at passage 11 as control. To obtain oxidative stress-induced senescent cells, we applied a single dose of 600μM H2O2 to NHFs at passage 11 for five days.

first: Zhao

last: Wei

first: Junchao

last: Qin

first: Qiao

last: Liu

first: Xiyu

last: Zhang

first: Yaoqin

last: Gong

first: Changshun

last: Shao


title: Melatonin mediates stress defense and improves development competence of bovine oocytes

first: Jianmin

last: Su

state: Shaanxi

address: Taicheng 3

summary: Oocyte quality, which is directly related to reprogramming competence, is a major important limiting factor in animal cloning efficiency. Compared with oocytes matured in vivo, in vitro matured (IVM) oocytes exhibit lower oocyte quality and reprogramming competence primarily because of their higher levels of reactive oxygen species (ROS). In this study, we investigate whether supplementing the oocyte maturation medium with melatonin, a free radical scavenger, could improve oocyte quality and reprogramming competence. We found that 10−9 M melatonin effectively alleviated oxidative stress, markedly decreased early apoptosis levels, recovered the integrity of mitochondria, ameliorated the spindle assembly and chromosome alignment in oocytes, and significantly promoted subsequent cloned embryo development in vitro. We also analyzed the effects of melatonin on epigenetic modifications in bovine oocytes. Melatonin increased the global H3K9 acetylation levels, reduced the H3K9 methylation levels, and minimally affected DNA methylation and hydroxymethylation. Genome-wide expression analysis of genes affected by melatonin during oocyte maturation was conducted by high-throughput scRNA sequencing. We found that several important genes altered by melatonin were involved in oocyte stress defense. These genes included GSTP1, mitochondrial DNA polymerase POLG, mitochondrial ATP synthase ATP5E, centriole-enriched gene CEP295, spindle assembly-related gene TCTP, cytoprotection, and anti-apoptosis-related gene HSP27. Our results indicated critical roles of melatonin during bovine oocyte maturation and development.

overall_design: Using RNA-seq, we sequenced six samples, namely, MII oocytes of control (n=3, C1, C2, C3) and 10−9 M melatonin treated (n=3, M1, M2, M3) groups.

first: Quanli

last: An


title: Comparative transcriptomics of tomato plants simultaneously infested with different species of herbivorous mites reveals distinct signatures of host defense suppression

city: Gent

first: Nicky

last: Wybouw

address: Coupure Links 653

department: Department of Crop Protection

country: Belgium

institute: University of Ghent

summary: Tomato plants are commonly attacked by herbivorous mites, including by generalist Tetranychus urticae and specialists Tetranychus evansi and Aculops lycopersici. Mite feeding induces plant defense responses that reduce mite performance. However, via poorly understood mechanisms, T. evansi and A. lycopersici suppress plant defenses and, consequently, maintain a high performance on tomato. Accordingly, on a shared host, non-adapted T. urticae can be facilitated by either of the specialist mites, likely via the suppression of plant defenses. To better understand defense suppression and indirect plant-mediated interactions between herbivorous mites, we used microarrays to analyze transcriptomic changes in tomato after attack by either a single mite species (T. urticae, T. evansi, A. lycopersici) or two species simultaneously (T. urticae plus T. evansi or T. urticae plus A. lycopersici). Additionally, we assessed mite-induced changes in defense-associated phytohormones using LC-MS/MS. Compared to non-infested controls, jasmonates (JAs) and salicylate (SA) accumulated to higher amounts upon all mite-infestation treatments, but lowest increases were detected after single infestations with defense-suppressors. Strikingly, whereas 8 to 10% of tomato genes was differentially expressed upon single infestations with T. urticae or A. lycopersici, only 0.1% was altered in T. evansi-infested plants. Transcriptome analysis of dual-infested leaves revealed that T. evansi dampened T. urticae-triggered host responses on a genome-wide scale, while A. lycopersici primarily suppressed T. urticae-induced JA defenses. Our results provide valuable new insights into the mechanisms underlying host defense suppression and the plant-mediated facilitation of competing herbivores.

overall_design:
Tomato plants underwent 5 infestation treatments and one non-infested control treatment, with 4 biological replicates each.
Specifically, tomato plants were infested for 7 days with: 1) T. urticae, 2) T. evansi, 3) A. lycopersici, 4) T.urticae and T. evansi, 5) T. urticae and A. lycopersici.
For spider mite (T. urticae or T. evansi) infestations, 15 adult female mites were individually transferred to each of three leaflets (belonging to three different compound leaves) per plant, so that in total each plant was infested with 45 spider mites. For russet mite (A. lycopersici) infestations, a small section (ca. 0,5 cm2) of a leaf containging approximately 250 mobile stages of mites (counted using a stereomicroscope) was transferred to each of three leaflets (belonging to three different compound leaves) per plant, so that in total each plant was infested with 750 russet mites. For dual infestations, each of three leaflets received either 15 T. urticae + 15 T. evansi (in total 90 spider mites per plant), or 15 T. urticae + ca. 250 A. lycopersici (in total 45 spider mites and 750 russet mites per plant). After 7 days, infested leaflets and corresponding leaflets from non-infested controls were harvested and stored at -80C until total RNA was isolated. The three leaflets obtained from the same plant were pooled to form one biological replicate. This experiment was replicated four times in consecutive weeks, each time using six plants per treatment, resulting in a total of 144 samples (6 treatments x 6 plants x 4 experimental replicates). However, for the microarray hybridizations, equal amounts of RNA, isolated from each of the six plants per treatment, were pooled, resulting in a total of 24 samples (6 treatments x 4 experimental replicates).

first: B

last: Schimmel

first: J

last: Alba

last: Glas

first: N

first: T

last: Meijer

first: R

last: Schuurink

first: M

middle: R

last: Kant


title: Expression data from A375 melanoma cells treated with Interferon-gamma and silvestrol

status: Public on Nov 23 2018

city: Villejuif

first: Caroline

last: Robert

state: ILE-DE-FRANCE

address: 114 rue Edouard Vaillant, Bâtiment de Médecine Moléculaire

institute: Institut Gustave Roussy

summary: Identify transcriptionnaly and translation regulated RNA by Interferon-gamma and silvestrol

overall_design: We have perform microarray analysis from total RNA and Polysomal associated RNA.

first: Michaël

last: Cerezo

first: Shensi

last: Shen

first: Stéphan

last: Vagner


title: Hormonal effects on grape berry ripening (HOM_06)

city: Glen Osmond

first: Mark

middle: Raymond

last: Thomas

state: SA

address: PO Box 350

department: Plant Industry

country: Australia

institute: CSIRO

summary:
This microarray experiment provides data which shows of the effects on gene expression from the artificial application of certain hormones on their own or in combination on ripening berries from the Adelaide Hills
Various hormones have been implicated as having an effect on the grape berry ripening process. Their application prior to ripening may change the gene expression profile at veraison. The identification of the genes which are expressed at different levels due to the various hormone treatments may give insight to key gene expression changes in the ripening process.
Keywords: Hormone treatment-Development

overall_design: Treatments were applied one to two weeks prior to ripening and the grape berries were sampled six hours after treatment. Three biological replicates were obtained for each treatment. Treatments were applied on their own or in combination. The hormone treatments were ethephon(ey), abscisic acid(ab), brassinosteroid(br), water and aminoethoxyvinylglycine(avg), ethanol(eh) and aminoethoxyvinylglycine, abscisic acid and aminoethoxyvinylglycine, brassinosteroid and aminoethoxyvinylglycine. Control treatments were water(wa) and ethanol. Biotin labeled probes were prepared from the extracted RNA from the pooled berry samples and hybridised to the Vitis vinifera GeneChip. The sample/GeneChip position on the Affymetrix hybridisation station was randomised using the AlgDesign package from R.

first: Christopher

last: Davies

first: Pat

last: Iocco


title: Analysis of gene expression in grape berries due to diurnal effects (DIU_05).

summary:
This is a 24 hour time course experiment to investigate changes in gene expression in deseeded berries sampled every three hours within a 24 hour period at 2 time points during development i.e. T5 (preveraison) & T17 (postveraison).
Changes in gene expression within the 24 hour period were analyzed to identify expression profiles that coincided with diurnal changes. The gene expression profiles were then to be compared between the two developmental time points T5 v T17).
Keywords: Diurnal time course

overall_design: Eight time points during the diurnal cycle were analyzed at preveraison and post veraison for gene expression changes using the Affymetrix one colour array platform. Two biological replicates were collected for each developmental stage. Biotin labeled probes were prepared from the extracted RNA from each of the pooled berry samples and hybridized to the Vitis vinifera GeneChip. The sample/GeneChip position on the Affymetrix hybridization station was randomized using the AlgDesign package from R.


title: Zebrafish preserve preserve germline epigenetic memory globally but demethylate and amplify sex-linked rDNA during feminisation

city: Dunedin

first: Oscar

middle: Javier

last: Ortega-Recalde

state: Otago

address: 60 Hanover Street

department: Anatomy

country: New Zealand

institute: University of Otago

summary: The germline is unique because it is the only cellular lineage capable of transferring genetic information from one generation to the next. Intergenerational transmission of epigenetic memory is also possible; however, in mammals this is largely prevented by extensive epigenetic erasure during germline definition from somatic precursors. We report that the ‘preformed’ germline of zebrafish, defined by inheritance of cellular components from the egg and not cellular reprogramming, shows consistently high levels of DNA methylation throughout development. This demonstrates epigenetic erasure is not a barrier to transgenerational epigenetic inheritance in zebrafish and likely other vertebrates with preformed germlines. Our analysis also uncovered female-specific germline amplification and demethylation of an 11.5-kb repeat region encoding 45S ribosomal RNA (fem-rDNA). The peak of fem-rDNA expansion coincided with the initial expansion of stage IB oocytes, the poly-nucleolar cell type responsible for zebrafish feminisation. Given that fem-rDNA overlaps with the only zebrafish locus identified thus far as sex-linked, we hypothesize fem-rDNA expansion is intrinsic to sex determination in this species.

overall_design: vasa:eGFP positive cells were isolated from zebrafish since day 1 post fertilisation (1 dpf) until sexual maturity (70 dpf) using fluorescence assisted cells sorting (FACS). Low coverage whole genome bisulfite sequencing  from eGFP positive and negative using a modified PBAT protocol was used to assess DNA methylation in the zebrafish germline.

first: Timothy

last: Hore


title: Timing of gene expression for inflorescence development and position of green latent buds on grapevine canes (BUD-06).

summary:
This is a time course experiment for inflorescence development in latent buds sampled from green canes at a single time point.
Keywords: Floral Development

overall_design: The 12 latent buds and the apical shoot meristem were sampled. The expression profile for each bud position was analyzed to determine gene expression patterns linked to the timing of gene expression for inflorescence development. Bud #1 (actually 2nd bud on a cane as the first one was not collected) is the oldest and will express genes involved in later developmental processes. Bud #12 is the youngest and will express genes that are responsible for the earlier processes in inflorescence development. The apical shoot meristem is a control as it does not develop an inflorescence. Biotin labeled probes were prepared from the extracted RNA from pooled green latent buds and apical shoot meristem and hybridized to the Vitis vinifera GeneChip. The sample/GeneChip position on the Affymetrix hybridization station was randomized using the AlgDesign package from R.


title: Three paralogous small proteins required for flagella-dependent motility in Salmonella

status: Public on Nov 16 2018

city: Chicago

first: Hyunwoo

last: Lee

state: IL

address: 900 S. Ashland Ave., MBRB #3020

department: Center for Biomolecular Sciences

institute: University of Illinois at Chicago

summary: Using RNA seq, gene expression profiles were compared between wild-type Salmonella enterica Typhimurium 14028s and its isogenic srfM2 mutant and genes differentially expressed in the srfM2 mutant were identified.

sample_organism: Salmonella enterica subsp. enterica serovar Typhimurium str. 14028S

overall_design: Three independent total RNAs of wild-type and srfM2 mutant cells were sequenced on the Illimina HiSeq 4000 in paired-end mode (2x75 bp).

first: Tamiko

last: Oguri

first: Jiyoung


title: Rational engineering of Corynebacterium glutamicum for the production of the dicarboxylic acid glutarate

city: Bielefeld

first: Fernando

last: Pérez-García

address: Universitaetsstr. 25

country: Germany

institute: University of Bielefeld

summary: The dicarboxylic acid glutarate is gaining attention in the chemical and pharmaceutical industry as promising building-block. Synthesis of glutarate via microbial fermentation is a desirable aim which will allow the production of biopolymers avoiding fossil raw materials. Here, by rational metabolic engineering of the biofactory microorganism Corynebacterium glutamicum the fermentative production of glutarate from glucose was established. Modifications focused on increase glucose consumption and reduce by-products formation together with the heterologous overexpression of the L-lysine decarboxylase, putrescine transaminase and putrescine dehydrogenase genes from E. coli in the L-lysine producer GRLys1 allowed production the glutarate precursor 5-aminovalerate. Additional heterologous overexpression of 5-aminovalerate amino transferase and glutarate-semialdehyde dehydrogenase genes from C. glutamicum and three Pseudomonas species enabled glutarate synthesis from glucose. By coupling glutarate production with the glutamate synthesis of C. glutamicum glutarate titer improved 10%. The final strain was tested in a glucose-based fed-batch fermentation

overall_design: Two condiotions tested, 200 mM NaCl Vs 200 mM glutarate supplemented in the culture medium, control experiments done with teh addition of 200mM of NaCl. Three technical replicates.

first: João

middle: P

last: Jorge

first: Annika

last: Dreyszas

first: Joe

middle: M

last: Risse

first: Volker

last: Wendisch


title: Analysis of gene expression changes involved in diurnal and circadian rhythms in grape berries. (DIU_05_circadian).

summary:
This is a microarray experiment to investigate changes in gene expression in deseeded berries from field grown vines to identify genes involved in diurnal and circadian effects.
Changes in gene expression at two time points within a 24 hour cycle were analyzed to identify expression profiles that coincided with diurnal and circadian effects. The gene expression profiles were then to be compared between the two developmental time points T5 v T17).
Keywords: Diurnal v Circadian

overall_design: Two time points during the diurnal cycle were analyzed at preveraison and post veraison for gene expression changes caused by diurnal or circadian rhythms using the Affymetrix one colour array platform. Two biological replicates were collected for each developmental stage. Biotin labeled probes were prepared from the extracted RNA from each of the pooled berry samples and hybridized to the Vitis vinifera GeneChip. The sample/GeneChip position on the Affymetrix hybridization station was randomized using the AlgDesign package from R.


title: Gene expression analysis in grape berries at veraison (SIB_06)

summary:
A bunch of grapes at veraison is comprised of berries at different stages of development ranging from hard green to soft red. Veraison represents an important transition stage in the ripening process where key genes may be switched on or off.
Single berries at various stages of development from hard green to soft red were collected at a single time point from a single bunch of grapes going through veraison. Gene expression patterns were obtained from single berries representing different developmental stages.
Keywords: Developmental series

overall_design: Six different developmental stages were analysed for gene expression changes using the Affymetrix one colour array platform. The developmental stages were defined based on berry softness and colour. They were hard green, soft green, blush, soft red. Hard green berries were divided further into two categories based on their softness. Four biological replicates were collected for the firmer hard green berries and two biological replicates were collected for the less firm hard green berries. Two biological replicates were collected for each of the other developmental stages. Biotin labeled probes were prepared from the extracted RNA from each deseeded berry and hybridised to the Vitis vinifera GeneChip. The sample/GeneChip position on the Affymetrix hybridisation station was randomised using the AlgDesign package from R.


title: LncRNA expression profiling in advanced resected gastric adenocarcinoma tissues

status: Public on Nov 15 2018

city: Fuzhou

first: Yuan

last: Dang

address: Xi‘erhuanbei Road NO156

institute: Fuzhou General  Hospital

summary: We studied the lncRNA and mRNA expression in 6 advanced resected GA (ARGA) tissues using a lncRNA microarray chip.  Among 22,870 lncRNAs expressed in ARGA and paired non-neoplastic tissues (non-GA), 1,769 and 1,710 were up- or down- regulated, respectively in all 6 ARGA tissues (≥2.0-fold, p<0.05).

first: Dang

last: Yuan


title: Genome wide transcriptome analysis reveals complex regulatory mechanisms underlying phosphate homeostasis in soybean nodules

city: zhanjiang

first: ying

middle: bin

last: xue

state: Guangdong

address: Haida Road #1, Mazhang District

department: College of Chemistry and Environment

institute: Guangdong Ocean University

summary: Phosphorus (P) deficiency is a major limitation for legume crop production. Although overall adaptations of plant roots to P deficiency have been extensively studied, fragmentary information is available in regards to root nodule responses to P deficiency. In this study, genome wide transcriptome analysis was conducted using RNA-seq analysis to investigate molecular mechanisms underlying soybean (Glycine max) nodule adaptation to phosphate (Pi) starvation. Phosphorus deficiency significantly decreased soybean nodule growth and nitrogenase activity. Nodule Pi concentrations declined by 49% in response to P deficiency, but this was well below the 87% and 88% decreases observed in shoots and roots, respectively. Nodule transcript profiling revealed that a total of 2,055 genes exhibited differential expression patterns between Pi sufficient and deficient conditions. A set of DEGs appeared to be involved in maintaining Pi homeostasis in soybean nodules, including 8 Pi transporters (PTs), 8 proteins containing the SYG1/PHO81/XPR1 domain (SPXs), and 16 purple acid phosphatases (PAPs). The results suggest that a complex transcriptional regulatory network participates in soybean nodule adaption to Pi starvation, most notable a Pi signaling pathway specifically involved in maintaining Pi homeostasis in nodules.

overall_design: Soybean seedlings were inoculated with rhizobium, then transferred into nutrient solution containing 500 mM KH2PO4 (HP) or 25 mM KH2PO4 (LP). After 25 days, nodules with the size more than 3 mm were collected for mRNA library construction and sequencing. Nodules from two plants were pooled together as one replicate, and three replicates from each P treatment were used for RNA-seq analysis.

first: Yingbin

last: Xue

first: Qingli

last: Zhuang

first: Shengnan

last: Zhu

first: Bixian

last: Xiao

first: Cuiyue

last: Liang

first: Jiang

last: Tian

first: Hong

last: Liao


title: Gene expression analysis in grape berries at veraison (SIB-05)

first: Mark

last: Thomas

summary:
A bunch of grapes at veraison is comprised of berries at different stages of development ranging from hard green to soft ripe red. Veraison represents an important transition stage in the ripening process where key genes may be switched on or off.
Single berries at various stages of development from hard green to ripe red were collected at a single time point from a single bunch of grapes going through veraison. Gene expression patterns were obtained from single berries representing different developmental stages.
Keywords: Developmental series

overall_design: Five different developmental stages were analysed for gene expression changes using the Affymetrix one colour array platform. The developmental stages were defined based on berry softness and colour. They were hard green, soft green, blush, red and ripe red. Two biological replicates were collected for each developmental stage. Biotin labeled probes were prepared from the extracted RNA from each deseeded berry and hybridised to the Vitis vinifera GeneChip. The sample/GeneChip position on the Affymetrix hybridisation station was randomised using the AlgDesign package from R.

first: Christopher

last: Davies

first: Pat

last: Iocco


title: Analysis of gene expression in grape berries due to diurnal effects (DIU_06).

summary:
This is a 24 hour time course experiment to investigate changes in gene expression in deseeded berries sampled every three hours within a 24 hour period at 2 time points during development i.e. T4 (preveraison) & T15 (postveraison).
Changes in gene expression within the 24 hour period were analyzed to identify expression profiles that coincided with diurnal changes. The gene expression profiles were then to be compared between the two developmental time points T4 v T15).
Keywords: Diurnal time course

overall_design: Nine time points during the diurnal cycle were analyzed at preveraison and post veraison for gene expression changes using the Affymetrix one colour array platform. Two biological replicates were collected for each developmental stage. Biotin labeled probes were prepared from the extracted RNA from each of the pooled berry samples and hybridized to the Vitis vinifera GeneChip. The sample/GeneChip position on the Affymetrix hybridization station was randomized using the AlgDesign package from R.


title: Transcriptome Profiling of Japanese Encephalitis Virus (JEV) Infected Human Neuroepithelioma Cells (SK-N-MC)

city: kuala lumpur

first: Shu Pin

last: Yu

state: kuala lumpur

address: Kuala Lumpur

department: Pathology

country: Malaysia

institute: University Malaya

summary: Japanese Encephalitis (JE) is an important causal of viral encephalitis in Eastern and Southeast Asia. Neuronal injury and varying degrees of neuroinflammation are often pathological hallmarks of JE, which result in high morbility and mortality rates. However, a clear understanding on neuron cells' responses to JEV infection remains elusive. This study, therefore, utilized the Affymetrix Human PrimeView array for a robust profiling of JEV infected SK-N-MC cells during the active phase of infection in order to investigate the molecular details of the host cell responses.

overall_design: SK-N-MC cells were mock and  JEV infected at Multiplicity of Infection (MOI) 10. Mock infections were achieved by subtitution of the viruses with equal amount of medium. Total RNA of mock and JEV infected cells were extracted at 48 and 60 hour post infection. Total RNA to be hybridized to Affymetrix Human PrimeView arrays were processed using the Affymetrix GeneChip 3' IVT Plus kits. Three biological replicates were used for both time points post infection.

first: Shu


title: Breast cancer metastasis to gynecological organs – a clinico-pathological and molecular profiling study.

status: Public on Nov 19 2018

city: Herston

first: Jamie

last: Kutasovic

state: QLD

address: UQCCR, Building 71/918

department: Faculty of Medicine

institute: The University of Queensland

type: Genome variation profiling by genome tiling array

summary: Breast cancer metastasis to gynecological organs is an understudied pattern of tumor spread. We explored clinico-pathologic and molecular features of these metastases to better understand this unique pattern of dissemination.

overall_design: Copy number profiles were compared between primary breast cancers and the ovarian metastases to understand clonal evolution during progression to these sites.

first: Amy

middle: E

last: McCart Reed

first: Renique

last: Males

first: Sarah

last: Sim

first: Jodi

last: Saunus

first: Andrew

last: Dalley

last: McEvoy

first: Liana

last: Dedina

first: Gregory

last: Miller

first: Stephen

last: Peyton

first: Lynne

last: Reid

first: Samir

last: Lal

first: Colleen

last: Niland

first: Kaltin

last: Ferguson

last: Fellowes

first: Fares

last: Al-Ejeh

first: Sunil

last: Lakhani

first: Margaret

last: Cummings

first: Peter

middle: T

last: Simpson


title: OnPLS-based multi-block data integration: a multivariate approach to interrogating biological interactions in asthma

city: London

first: Akul

last: Singhania

address: 1 Midland Road

institute: The Francis Crick Institute

summary:
Integration of multi-omics data remains a key challenge in fulfilling the potential of comprehensive systems biology.
This study aimed to explore the potential for the multi-block projection method (OnPLS) and multi-block variable influence on the projection (MB-VIOP) to interrogate an example systems medicine study, using a subset of 22 individuals from an asthma cohort.

overall_design: Joint data structure in six data blocks was assessed: transcriptomics; metabolomics; targeted assays for sphingolipids, oxylipins, and fatty acids; and a clinical block including lung function, immune cell differentials, and cytokines.

first: Stacey

middle: N

last: Reinke

first: Craig

last: Wheelock

first: Timothy

middle: S

last: Hinks


title: Gene expression shifts in yellow-bellied marmots prior to natal dispersal

city: Los Angeles

first: Tiffany

last: Armenta

address: 610 Charles E. Young Dr. East

department: Ecology & Evolutionary Biology

institute: UCLA

summary: We evaluated genome wide expression patterns in  wild yellow-bellied marmots (Marmota flaviventris) prior to either dispersing from or remaining philopatric to their natal colony site. We identified differential expression of genes involved in lipid metabolism and muscle generation. Further, we found a network of genes involved in extra-cellular immune function and MHC class II pathways that increased in dispersers. Our results provide novel insights into the fundamental molecular changes required for natal dispersal in vertebrates.

overall_design: Blood samples from 16 yearling marmots that subsequently dispersed and 27 samples from resident marmots.

first: Daniel

last: Blumstein

first: Robert

last: Wayne

first: Steve

last: Cole

first: Dan

last: Geschwind


title: The effects of heat shock treatment on gene expression of grapevine berries (HSP_06)

first: Mark

last: Thomas

summary:
Pinot Meunier L1 dwarf grapevines were grown in a growth cabinet and both unripe (preveraison) and ripe (postveraison) berries were collected after various time points post heat shock treatment.
The gene expression profiles of treated berries were compared to controls to identify gene expression changes associated with the heat shock response.
Keywords: Heat shock treatment effect

overall_design: The effect of heat shock treatment on gene expression for preveraison and postveraison grape berries at seven time points was analyzed using the Affymetrix one colour array platform. Microarray data was obtained for berries on L1 mutant plants grown in a growth chamber at an ambient temperature of 16 degrees. They were heat shocked for 7 hours and then returned to ambient temperature. Berry samples were taken at 0, 1, 4, 7, 9, 14 and 24 hours after heatshock treatment. Two biological replicates were collected for each treatment. Biotin labeled probes were prepared from the extracted RNA from each deseeded berry sample and hybridized to the Vitis vinifera GeneChip. The sample/GeneChip position on the Affymetrix hybridization station was randomized using the AlgDesign package from R.

first: Christopher

last: Davies

first: Pat

last: Iocco


title: Paternal chronic folate supplementation induced transgenerational inheritance of acquired developmental and metabolic changes in chickens

city: Yangling

first: Shengru

last: Wu

address: 22 St.XiNong

department: College of Animal Science and Technology

institute: Northwest A&F University

summary: Increasing evidence indicates that the paternal diet can result in offspring metabolic changes. A proposed mechanism for paternal transmission of environmental information is via the sperm noncoding RNAs, but the definite mechanism remains unclear in birds.

overall_design: We hypothesized that the dietary supplement of folate will alter noncoding RNAs expression profiles in sperm and further transgenerational regulate the metabolic process of offspring. Here, we fed breeder roosters with five different levels (0, 0.25, 1.25, 2.50, and 5.00 mg/kg) of folate throughout life, obtained the samples from breeder roosters and their offspring broilers, and further measured the development and metabolic indexes of breeder roosters and their offspring broilers. As results, different levels of paternal folate supplement were associated with the development changes in the offspring, which include the birth weight, postnatal feed conversion ratio, and the development of livers, bursa of fabricius, and small intestine. And mostly, the lipid and glucose metabolism process of offspring broilers could also be affected by the paternal dietary folate supplement, which has the similar effect with the metabolic changes in breeder roosters. Meanwhile, we employed global analyses of the hepatic mRNAs, lncRNAs, and miRNAs to test the effect of folate on the metabolic changes of breeder roosters and transgenerational effects of folate on offspring broilers. We found that some key genes involved in the glycolysis or gluconeogenesis and PPAR signaling pathway, such as PEPCK, ANGPTL4, and THRSP, could be regulated by the differentially expressed miRNAs and lncRNAs in the livers of breeder roosters and offspring broilers, which were induced by the dietary folate supplement of breeder roosters. Furthermore, global analyses of the breeder roosters’ sperm miRNAs and lncRNAs identified differentially expressed non-coding RNAs also implicated in the glycolysis or gluconeogenesis, PPAR signaling pathway, FOXO pathway, and several other lipid and glucose metabolism pathways as well. Overall, this model suggests dietary folate supplement could transgenerational regulate the lipid and glucose metabolism of offspring broilers and epigenetic transmission may involve the changes of miRNAs and lncRNAs expression profiles in sperm.

first: Xiaojun

last: Yang


title: The in vitro influence of adiponectin on the porcine myometrium on days 15 to 16 of gestation.

status: Public on Nov 17 2018

city: Olsztyn

first: Kamil

last: Dobrzyn

state: Warminsko-Mazurskie

address: Oczapowskiego, 1A

department: Department of Animal Anatomy and Physiology

institute: University of Warmia and Mazury

summary: Adiponectin is secreted by the white adipose tissue and is one of the most important hormones that regulate metabolic homeostasis. The expression of adiponectin and adiponectin receptor genes and proteins in reproductive organs, such as the testes, ovaries and uterus, suggests that adiponectin is also involved in the regulation of reproductive functions. The aim of this study was to explore the influence of adiponectin on global gene expression in the porcine endometrium during early gestation, on days 15 to 16 of pregnancy (implantation period).

overall_design: We analized samples obtained from 4 indyviduals (n=4). Obtained from the uterine horns tissue explants were divided for two groups: controls [without treatment] and adiponectin treated grous. The concentration of adiponectin in the culture medium was 10 µg/ml. In vitro tissue cultures were cultivated with treatments for 24 hours.

first: Nina

last: Smolinska

first: Karol

last: Szeszko

first: Marta

last: Kiezun

first: Edyta

last: Rytelewska

first: Katarzyna

last: Kisielewska

first: Marlena

last: Gudelska

first: Tadeusz

last: Kaminski


title: Integrated analysis of miRNA and mRNA expression profiles in 2-, 6-, and 12-month-old Small Tail Han Sheep ovaries reveals that oar-miR-432 downregulates RPS6KA1 expression

city: Changchun

first: Bo

last: Gu

state: China

address: Jilin Agricultural University

institute: Jilin Agricultural University

summary: In this study, we selected differentially expressed miRNAs through construcing and analyzing the miRNA expression profile during 2-, 6-, and 12- month-old Small Tail Han Sheep ovaries, which provided a theoretical basis for the study of miRNAs regulating the reproduction of Small Tail Han Sheep. RNASeq techniques were used to perform profile analysis for these ovaries. The results showed that 11, 13 and 19 DE miRNAs were identified in 2- vs 6-, 6- vs 12-, and 2- vs 12-month-old ovaries, respectively. In total, 54, 37, and 198 predicted target genes of DE miRNAs were obtained from these three groups, respectively. GO and KEGG analyses showed that, in 2- vs 6-month-olds, the target genes of DE known sheep miRNAs were involved in 102 GO terms and 7 signaling pathways; in 6- vs 12-month-olds, the target genes of DE known sheep miRNAs were involved in 52 GO terms and 3 signaling pathways; and in 2- vs 12-month-olds, the target genes of DE known sheep miRNAs were involved in 88 GO terms and 6 signaling pathways. Three miR–target regulatory networks were constructed based on these DE miRNA–targets. 9 miRNAs were selected to validate the accuracy of miRNA sequencing data by qRT-PCR. The binding sites of oar-miR-432 with RPS6KA1 was validated by a dual luciferase reporter gene detection system.  This is the first integrative analysis of miRNA and mRNA expression profiles in Small Tail Han Sheep ovarian development. These data help elucidate the molecular regulatory mechanisms in sheep ovarian development and identify the biomarkers that influence reproductive performance of Small Tail Han Sheep ewe.

overall_design: Integrated analysis of miRNA and mRNA expression profiles in 2-, 6-, and 12-month-old Small Tail Han Sheep ovaries by RNAseq techniques which reveals that oar-miR-432 downregulates RPS6KA1 expression

first: Hang

last: Liu

first: Yue

last: Han

first: Yang

last: Chen

first: Huaizhi

last: Jiang


title: Avermectin treatment for Lepeophtheirus salmonis: Impacts on host (Salmo salar) and parasite immunophysiology

city: Victoria

first: Ben

last: Koop

state: BC

address: PO Box 3020 STN CSC

department: Biology

institute: The University of Victoria

summary: This study investigates the transcriptomic responses of salmon lice (L. salmonis) infecting salmon treated with emamectin benzoate (either 1x or 3x), ivermectin, or commercial feed controls

overall_design: Copepodid-staged larvae of L. salmonis were used to infect Atlantic salmon fed 1x or 3x emamectin benzoate, ivermectin, or commercial feed controls. Pre-adult I lice were collected from each group, pooled by treatment group and sex (pools of 6 lice) and stored at -80C for RNA extraction and microarray analyses. A total of 48 pools were used (n = 6 per condition except n = 5 for male controls and n = 7 for male 3xEMB)

first: Shona

last: Whyte

first: Jordan

middle: D

last: Poley

first: Anita

last: Mueller

first: Carter

last: VanIderstine

first: Kaitlin

last: Fitzpatrick

first: Sara

middle: L

last: Purcell

first: Stewart

last: Johnson

first: Simon

last: Wadsworth

first: Mark

last: Fast


title: Dnmt1 has an essential function despite the absence of CpG DNA methylation in the red flour beetle Tribolium castaneum

status: Public on Nov 14 2018

city: Heidelberg

first: Guenter

last: Raddatz

address: Im Neuenheimer Feld 580

institute: German Center for Cancer Research

summary: Epigenetic mechanisms, such as CpG DNA methylation enable phenotypic plasticity and rapid adaptation to changing environments. CpG DNA methylation is established by DNA methyltransferases (DNMTs), which are well conserved across vertebrates and invertebrates. There are insects with functional DNA methylation despite lacking a complete set of Dnmts. But at least one of the enzymes, DNMT1, appears to be required to maintain an active DNA methylation system. The red flour beetle, Tribolium castaneum, lacks Dnmt3 but possesses Dnmt1 and it has been controversial whether it has a functional DNA methylation system. Using whole genome bisulfite sequencing, we did not find any defined patterns of CpG DNA methylation in embryos. Nevertheless, we found Dnmt1 expressed throughout the entire life cycle of the beetle, with mRNA transcripts significantly more abundant in eggs and ovaries. A maternal knockdown of Dnmt1 caused a developmental arrest in offspring embryos. We show that Dnmt1 plays an essential role in T. castaneum embryos and that its downregulation leads to an early developmental arrest. This function appears to be unrelated to DNA methylation, since we did not find any evidence for this modification. This strongly suggests an alternative role of this protein.

overall_design: One sample has been analyzed, consisting of two replicates.

first: Joachim

last: Kurtz

first: Frank

last: Lyko


title: Tissue-based mapping of the fathead minnow (Pimephales promelas) transcriptome and proteome

city: GAINESVILLE

first: FAHONG

last: YU

state: FL

address: 2033 Mowry Rd

department: ICBR

institute: UNIVERSITY OF FLORIDA

summary: Omics approaches are broadly used to explore endocrine and toxicity-related pathways and functions. Nevertheless, there is still a significant gap in knowledge in terms of understanding the endocrine system and its numerous connections and intricate feedback loops, especially in non-model organisms. The main purpose of this analysis was to generate tissue-specific omics data in order to support future aquatic ecotoxicogenomic and endocrine-related studies as well as to improve our understanding of the fathead minnow as an ecological model.

overall_design: All fish husbandry was conducted under the supervision of the University of Florida Institutional Animal Care and Use Committee.  Adult fathead minnows (Pimephales promelas) were obtained from an in-house culture at the Aquatic Toxicology Core Laboratory at the University. The main objective of this study was to increase the value of the FHM as a model by creating comprehensive transcriptomic and proteomic databases. This study also aims to survey tissue-specific baseline transcriptomic and proteomic expression profiles in adult male FHM to support aquatic ecotoxicogenomic studies.

first: C

last: Lavelle

first: L

middle: C

last: Smith

first: J

middle: H

last: Bisesi

first: F

last: Yu

last: Silva-Sanchez

first: D

last: Moraga-Amador

first: K

middle: J

last: Kroll

first: N

middle: G

last: Reyero

first: T

last: Sabo-Attwood

last: Denslow


title: The in vitro influence of orexin B on the porcine myometrium on days 15 to 16 of gestation.

first: Kamil

last: Dobrzyn

summary: Orexin A (OXA) and orexin B (OXB) are hypothalamic-derived peptides that participate in the regulation of energy metabolism, food intake and reproductive function by influencing the hypothalamic-pituitary-ovarian axis. Orexins are also produced in the endometrium, myometrium and placenta, which suggests that they could act as a link between energy metabolism and the reproductive system. The aim of this study was to explore the influence of orexin B on global gene expression in the porcine myometrium during early gestation, on days 15 to 16 of pregnancy (implantation period).

overall_design: We analized samples obtained from 4 indyviduals (n=4). Obtained from the uterine horns tissue explants were divided for two groups: controls [without treatment] and orexin B treated groups. The concentration of orexin B in the culture medium was 10 nM. In vitro tissue cultures were cultivated with treatments for 24 hours.

first: Ewa

last: Zaobidna

first: Karol

last: Szeszko

first: Marta

last: Kiezun

first: Edyta

last: Rytelewska

first: Katarzyna

last: Kisielewska

first: Marlena

last: Gudelska

first: Tadeusz

last: Kaminski

first: Nina

last: Smolinska


title: The in vitro influence of orexin B on the porcine endometrium on days 15 to 16 of gestation.

summary: Orexins, namely orexin A (OXA) and orexin B (OXB) belongs to the family of neuropeptides produced mainly by specific neurons of the lateral region of the hypothalamus. Primarily orexins were recognized as hormones involved exclusively in the regulation of food intake and energy homeostasis. However, a growing body of evidences indicate their involvement in the regulation of an increasing number of biological processes, inter alia, in the regulation of the reproductive functions. The aim of this study was to explore the influence of orexin B on global gene expression in the porcine endometrium during early gestation, on days 15 to 16 of pregnancy (implantation period).

overall_design: We analized samples obtained from 4 indyviduals (n=4). Obtained from the uterine horns tissue explants were divided for two groups: controls [without treatment] and orexin B treated grous. The concentration of orexin B in the culture medium was 10 nM. In vitro tissue cultures were cultivated with treatments for 24 hours.


title: Microarray expression data from the dissected MNTBs of FVB wild-type mice at P0, P1, P2, P3, P4, P6 and P14

city: Morgantown

first: George

last: Spirou

state: WV

address: One Medical Center Drive

department: Otolaryngology

institute: West Virginia University

summary:
The medial nucleus of the trapezoid body (MNTB) contains a nearly homogeneous population of neurons, which are innervated by large glutamatergic nerve terminals called calyces of Held (CH). Key steps in maturation of CHs and MNTB neurons, including CH growth and competition, occur very quickly for most cells between postnatal days (P)2 and P6. Therefore, we characterized genome-wide changes in this system, with dense temporal sampling during the first postnatal week.
We identified 541 genes whose expression changed significantly between P0-6 and clustered them into eight groups based on temporal expression profiles. Candidate genes from each of the eight profile groups were validated in separate samples by qPCR.

overall_design: 33 total samples were analyzed with 4-5 replicates of each age at P0, P1, P2, P3, P4, P6, and P14.

first: Douglas

last: Kolson

first: Jun

last: Wan

first: Peter

last: Mathers

middle: A


title: RNA sequencing analysis of transcriptomics to study the growth of Lactobacillus salivarius Ren in raffinose

city: BeiJing

first: Xiong

last: Yao

address: No. 17, Tsinghua East Road, Haidian District

institute: China Agriculture University

summary:
Purpose: To understand the metabolic mechanism of  Lactobacillus salivarius Ren in raffinose
Methods: Samples of Lactobacillus salivarius Ren grown in glucose and raffinose were sequenced on the Illumina Hiseq platform. Three independent biological replicates were generated, including a total of six samples.
Results:  Raw data were firstly processed through in-house perl scripts to generate clean data, and then clean date were mapped to the reference genome, getting about 8-10 million total mapped reads per sample.

overall_design: Lactobacillus salivarius Ren is cultured in MRS medium with carbon source as glucose and raffinose

first: Hu

last: Huizhong


title: Transcriptome analysis of an incompatible Persea americana-Phytophthora cinnamomi interaction reveals the involvement of SA- and JA-pathways in a successful defense response

city: Pretoria

first: Dave

middle: Kenneth

last: Berger

state: Gauteng

address: Lynnwood Road

department: Plant and Soil Science

country: South Africa

institute: University of Pretoria

summary: Phytophthora cinnamomi Rands (Pc) is a hemibiotrophic oomycete and the causal agent of Phytophthora root rot (PRR) of the commercially important fruit crop avocado (Persea americana Mill.). Plant defense against pathogens is modulated by phytohormone signaling pathways such as salicylic acid (SA), jasmonic acid (JA), ethylene (ET), auxin and abscisic acid. The role of specific signaling pathways induced and regulated during hemibiotroph-plant interactions has been widely debated. Some studies report SA mediated defense while others hypothesize that JA responses restrict the spread of pathogens. This study aimed to identify the role of SA- and JA- associated genes in the defense strategy of a resistant avocado rootstock, Dusa® in response to Pc infection. Transcripts associated with SA-mediated defense pathways and lignin biosynthesis were upregulated at 6 hours post-inoculation (hpi). Results suggest that auxin, reactive oxygen species (ROS) and Ca2+ signaling was also important during this early time point, while JA signaling was absent. Both SA and JA defense responses were shown to play a role during defense at 18 hpi. Induction of genes associated with ROS detoxification and cell wall digestion (β-1-3-glucanase) was also observed. Most genes induced at 24 hpi were linked to JA responses. Other processes at play in avocado at 24 hpi include cell wall strengthening, the formation of phenolics and induction of arabinogalactan, a gene linked to Pc zoospore immobility. This study represents the first transcriptome wide analysis of a resistant avocado rootstock treated with SA and JA compared to Pc infection. The results provide evidence of a biphasic defense response against the hemibiotroph, which initially involves SA-mediated gene expression followed by the enrichment of JA-mediated defense from 18 to 24 hpi. Genes and molecular pathways linked to Pc resistance are highlighted and may serve as future targets for manipulation in the development of PRR resistant avocado rootstocks.

overall_design: Reference design, infected and treated samples at different time points, relative to pooled reference sample

first: N

last: van den Berg

first: W

last: Mohamed

last: Olivier

first: V

last: Swart

first: B

last: Crampton


title: Multiple Environmental Stressors Induce Complex Transcriptomic Responses Indicative of Phenotypic Outcomes in Western Fence Lizard

city: Vicksburg

first: Kurt

last: Gust

state: MS

address: 3909 Halls Ferry Rd.

department: Environmental Laboratory

institute: US Army ERDC

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

overall_design: Refer to individual Series


title: The effect of aging on the transcriptome of murine dermal fibroblasts isolated from male mice

city: Sabadell

first: Antoni

last: Berenguer-LLergo

state: Barcelona

address: Parc del Taulí, 1

department: A8G2 Group - Rheumatology Service

country: Spain

institute: Parc Taulí Research and Innovation Institute (I3PT)

summary: During aging, stromal functions are thought to be impaired, yet little is known whether this stems from molecular and cellular changes of fibroblasts, a major component of stroma. Using population- and single-cell whole transcriptomics, and long-term lineage tracing, we studied alterations in murine dermal fibroblasts during physiological aging under different dietary regimes known to affect longevity. We show that the identity of aged fibroblasts becomes undefined, with the distinct fibroblast states present in young skin no longer clearly demarcated. In addition, old fibroblasts not only reduce the expression of genes involved in the formation of the extracellular matrix, but intriguingly, also gain adipogenic traits, paradoxically becoming similar to neonatal pro-adipogenic fibroblasts. These age-related alterations are sensitive to systemic changes in metabolism: long-term caloric restriction prevents them in old fibroblasts in a reversible manner, whereas a high-fat diet potentiates them in young fibroblasts. Finally, inhibition of the master regulator of adipogenesis, PPARgamma, attenuates fibroblast aging in vivo, providing potential anti-aging therapeutic alternatives to caloric restriction.

overall_design: Dermal fibroblasts were isolated from four young (2-months-old) and four old (18-months-old) male C57/Bl6 mice. For sample collection two young and two old mice were sacrificed per day. N=4

first: Marion

last: Salzer

first: Salvador

last: Aznar-Benitah


title: Azithromycin treatment modifies airway and blood gene expression networks in neutrophilic COPD

city: Newcastle

first: Thomas

middle: K

last: Wright

state: NSW

address: Callaghan

department: Faculty of Health and Medicine

institute: The University of Newcastle

summary:
Long-term, low dose azithromycin reduces exacerbation frequency in COPD yet the mechanism remains unclear. This study characterises changes to gene expression in  patients with neutrophilic COPD in response to long term low dose azithromycin therapy.
Patients with neutrophilic COPD (>61% or >162x10^4/mL sputum neutrophils) were randomised to 12 weeks of either azithromycin or placebo treatment. RNA was extracted from sputum and blood collected before (pre) and after (post) treatment.

overall_design: Microarray analysis was performed on blood (n=11 azithromycin; n=11 placebo group) and sputum (n=11 azithromycin group; n=13 placebo group) in a subset of patients who had paired samples from pre and post treatment visits.

first: Katherine

last: Baines

last: Gibson

first: Heather

last: Powell

first: Phillip

last: Hansbro

first: Jodie

last: Simpson


title: Phosphate deficiency negatively affects early steps of the symbiosis between common bean and rhizobia

city: Tlalnepantla

first: Oswaldo

last: Valdés-López

state: Mexico

address: Av. De los Barrios 1. Los Reyes Iztacala

country: Mexico

institute: FES Iztacala, UNAM

summary: We report how phosphate deficiency early rhizobia-induced genes in Phaseolus vulgaris (common bean)

overall_design: We evaluate the gene expression by mRNA-seq in common bean seedlings growing under optimal and deficient phosphate conditions and inoculated during 24 hours with Rhizobium tropici CIAT899. Samples were harvested 24 hours after mock (control) or R. tropici (rhizobia). For each condition three biological replicates, each one continaing rhizobia responsive zone from four roots of different seedlings, were included.


title: Whole-genome bisulfite sequencing of wild-type and thick aleurone 2-1 (ta2-1) mutant in rice

city: Beijing

first: Jinxin

last: Liu

address: No.20 Nanxincun, Xiangshan

institute: Institute of Botany, CAS

summary: Using whole genome bisulfite sequencing to provide single-base resolution of DNA methylation status in the endosperm of wild-type (ZH11) and ta2-1 rice plants, and identify hypermethylated regions in ta2-1.

overall_design: Examination of Wild-type and ta2-1 mutant's methylome. 3 samples (ZH11 9-DAP embryo and endosperm, ta2-1 9-DAP endosperms).


title: Transcriptome analysis of mRNAs, lncRNAs, and circRNAs during the differentiation of porcine subcutaneous preadipocytes

city: Nanjing

first: Xin

state: Jiangsu

institute: Nanjing Agricultural University

summary: Subcutaneous preadipocyte differentiation play a critical role in fat deposition of pigs. However, the action of different RNAs in subcutaneous preadipocyte differentiation, such as messenger RNAs (mRNAs), long noncoding RNAs (lncRNAs), and circular RNAs (circRNAs), are still largely unclear. In the present study, a transcriptome analysis including mRNAs, lncRNAs, and circRNAs was performed in different stages of D0, D2, D4, and D8 using RNA-seq technology. Our results identified 1,554, 470, 1,344, 1,777, and 676 differentially expressed (DE) mRNAs, 112, 58, 95, 136, and 93 DE lncRNAs, and 902, 787, 710, 932, and 850 DE circRNAs between D2 and D0, between D4 and D2, between D8 and D4, between D4 and D0, and between D8 and D0, respectively. Moreover, functional enrichment analysis showed that the common DE mRNAs during entire differentiation were mainly involved in lipid metabolic and cell differentiation processes. Additionally, co-expression network analysis identified the potential lncRNAs related to adipogenesis, e.g., MSTRG.42239 and MSTRG.146410. Taken together, this study provides a genome-wide landscape of RNA expression profiles during subcutaneous preadipocyte differentiation, thus improving our understanding of molecular mechanism in regulating subcutaneous adipogenesis of pigs.

overall_design: mRNA, lncRNA, and circRNA profiles during the differentiation of porcine subcutaneous preadipocytes were generated by RNA-Seq using Illumina HiSeq X Ten.

first: Lifan

last: Zhang