title: Expression data from DU145 prostate cancer cells treated with DHA or DMSO

status: Public on Nov 17 2018

city: Cape Town

first: Luiz

middle: F

last: Zerbini

address: Wernher and Beit Building (South), Anzio Road

country: South Africa

institute: ICGEB

summary: Axl expression is deregulated in several cancer types, predicts poor overall patient survival and is linked to increase in resistance to drug therapy. Here, we have evaluated a library of natural compounds for inhibitors of Axl. We identified dihydroartemisin (DHA), the active principle of the anti-malarial drug artemisinin, as a specific Axl inhibitor in prostate cancer (PCa). DHA blocks Axl expression leading to apoptosis induction, decrease in cell proliferation, migration and tumor development of PCa cells. Furthermore, DHA treatment synergizes with docetaxel, a standard of care in metastatic PCa, and increases the overall survival of mice with human PCa xenografts. We demonstrated that DHA-mediated control of miR-34a and miR-7 expression leads to inhibition of Axl expression. This process is dependent on regulation of the chromatin via methylation of histone H3 lysine 27 residues (H3K27) by Jumonji, AT-rich interaction domain containing 2 (JARID2) and the enhancer of zeste homolog 2 (EZH2), components of the Polycomb Complex Repressor 2 (PCR2). Our discovery of a previously unidentified miR-34a/miR-7/JARID2 pathway that controls DHA-mediated effects on Axl expression and inhibition of cancer cell proliferation, migration, invasion and tumor formation provides new molecular and mechanistic insights into DHA’s anti-cancer effect on PCa with potential therapeutic implications.

overall_design: Total RNA was isolated from DU145treated with 5μM DHA or vehicle control (DMSO) for 6 hours and hybridized to HT Human U133 gene .

first: Manoj

last: Bashin

first: Towia

last: Libermann

first: Xuesong

last: Gu


title: RNA sequencing of total RNA from the vagina of hormone treated C57Bl/6J mice

status: Public on Nov 16 2018

city: St. Louis

first: Maxim

last: Artyomov

state: Missouri

address: 425 S Euclid Ave

department: Pathology & Immunology

country: USA

institute: WASHINGTON UNIVERSITY IN ST LOUIS

type: Expression profiling by high throughput sequencing

summary:
Purpose: The goal of this study was to compare transcriptome profiles (RNA seq) from the vaginas of uninfected mice. The mice have had ovariectomy surgeries and hormone replacement (estradiol, progesterone, vehicle, or a combination of estradiol and progesterone).

Methods: 6 week old female C57Bl/6J mice had ovariectomy surgeries and a week later, started hormone replacement treatment as mentioned above. After a week of hormones, the vaginas of all mice were removed and total RNA was extracted. RNA samples were sent for RNA sequencing.

Results: Upon analysis, vehicle and progesterone treated mice had similar profiles. The progesterone treated group also had progesterone stimulated genes upregulated. Estradiol regulated genes were upregulated in the estradiol treated group and the estradiol and progesterone group had a mixture of both progesterone and estradiol stimulated genes upregulated.

Conclusion: This data provided a data to ensure that our hormone replacement treatments were working by the expression of certain genes based on treatment.

first: Elizabeth

middle: A

last: Caine

first: Michael

middle: S

last: Diamond

first: Konstantin

last: Zaitsev


title: Regulation of xylem fiber differentiation by gibberellins through DELLA-KNAT1 interaction

city: Valencia

first: David

last: Alabadi

state: Valencia

address: Av de los Naranjos s/n, Campus UPV, Edificio 8E

department: Biologia del Desarrollo

country: Spain

institute: Instituto de Biologia Molecular y Celular de Plantas (CSIC-UPV)

summary: Our analysis indicates that at least 37% of the transcriptome mobilized by KNAT1 is potentially dependent on this interaction, and includes genes involved in secondary cell wall  modifications and phenylpropanoid biosynthesis.

overall_design: Seven-day-old Arabidopsis wild-type (No-0) and 35S::KNAT1 seedlings growing in MS plates under continuous light were transferred to a liquid growing medium supplemented with 10 μM paclobutrazol (PAC) for 18 h. Seedlings were then incubated with 10 μM PAC+100 μM GA3 or maintained in 10 μM PAC for 5 h.

first: Amelia

last: Felipo-Benavent

last: Alabadí

first: Miguel

last: Blázquez


title: Next Generation Sequencing Facilitates Quantitative Analysis of Wild Type and 2.5ppm iAs Treated Mouse Gastrocnemius Muscle Transcriptomes

city: HOUSTON

first: Jidong

last: Liu

state: TX

address: One Baylor Plaza

institute: Baylor College of Medicine

summary: Inorganic arsenic (iAs) is a widespread environmental toxin. In addition to being a human carcinogen, its effect on systemic glucose metabolism has started to gain recognition recently. However, its in vivo effect on insulin sensitivity is not clear. Here we use mouse models to dissect the dose-dependent effects of iAs in glucose metabolism. We found that a low-dose exposure (0.25 ppm iAs in drinking water) caused glucose intolerance in adult male C57BL/6 mice, likely by disrupting glucose-induced insulin secretion without affecting peripheral insulin sensitivity. However, a higher-dose exposure (2.5 ppm iAs) has diminished effects on glucose tolerance despite disrupted pancreatic insulin secretion. We performed hyperinsulinemic euglycemic clamp, the gold standard analysis of systemic insulin sensitivity, and found that the 2.5 ppm iAs enhanced systemic insulin sensitivity by simultaneously enhancing insulin-stimulated glucose uptake in skeletal muscles and insulin-mediated suppression of endogenous glucose production. RNA-seq analysis of muscles revealed that 2.5 ppm iAs regulated expression of many genes involved in the metabolism of fatty acids, pyruvate, and amino acids. These findings suggest that iAs has distinct effects on distinct metabolic tissues at different dose thresholds, which could help reconcile some of the conflicting epidemiological results. The study shed light on the complex interactions between an environmental factor and the systemic glucose metabolism.

overall_design: Gastrocnemius Muscle mRNA profiles of 24-week 2.5 ppm iAs in drinking water treatment and control mice were generated by deep sequencing, in triplicate, using Illumina HiSeq 3000.

first: Yingyun

last: Gong

first: Ying-Wooi

last: Wan

first: Zheng

last: Sun


title: Transcripts identified by microarray analysis that were deregulated in E14.5 Tbx18cre/+;Tbx2fl/fl;Tbx3fl/fl (Tbx2/Tbx3cDKO) ureters

city: Hannover

first: Andreas

last: Kispert

address: Carl-Neuberg-Str. 1

department: Molekularbiologie

country: Germany

institute: Medizinische Hochschule Hannover

summary: Evaluation of the transcriptional changes in E14.5 ureters upon combined loss of Tbx2 and Tbx3 in the ureteric mesenchyme.

overall_design: Total RNA from dissected ureters of E14.5 Tbx2/Tbx3cDKO and control mice was analyzed by microarray analysis.


title: TBX2 and TBX3 act downstream of canonical WNT signaling in patterning and differentiation of the ureteric mesenchyme

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

overall_design: Refer to individual Series


title: Transcripts identified by microarray analysis that were deregulated in E18.5 Tbx18cre/+;Tbx2fl/fl;Tbx3fl/fl (Tbx2/Tbx3cDKO) ureters

summary: Evaluation of the transcriptional changes in E18.5 ureters upon combined loss of Tbx2 and Tbx3 in the ureteric mesenchyme.

overall_design: Total RNA from dissected ureters of E18.5 Tbx2/Tbx3cDKO and control mice was analyzed by microarray analysis.


title: Transcripts identified by microarray analysis that were deregulated in E13.5 Tbx18cre/+;HprtTbx2/Y (Tbx2-GOF) ureters

summary: Evaluation of the transcriptional changes in E13.5 ureters upon overexpression of Tbx2 in the ureteric mesenchyme.

overall_design: Total RNA from dissected ureters of E13.5 Tbx2-GOF and control mice was analyzed by microarray analysis.


title: T cell receptor-triggered nuclear actin network formation drives CD4 T cell effector functions

status: Public on Nov 15 2018

city: Heidelberg

first: Nikolaos

last: Tsopoulidis

address: Im Neuenheimer Feld 344

institute: Universitätsklinikum Heidelberg

summary:
T cell antigen receptor (TCR) signaling triggers selective cytokine expression to drive T cell proliferation and differentiation required for immune defense and surveillance. The nuclear signaling events responsible for specificity in cytokine gene expression upon T cell activation are largely unknown. Here, we uncover formation of a dynamic actin filament network in the nucleus that regulates cytokine expression for effector functions of CD4 T lymphocytes. TCR engagement triggers the rapid and transient formation of a nuclear actin filament network via nuclear Arp2/3 complex, induced by elevated nuclear Ca2+ levels and regulated via N-Wasp and NIK. Specific interference with TCR-induced formation of nuclear actin filaments impairs production of effector cytokines and prevents generation of antigen-specific antibodies, but does not interfere with immune synapse formation and cell proliferation. Ca2+-regulated actin polymerization in the nucleus allows CD4 T cells the rapid conversion of TCR signals into effector functions required for T cell help
Identification of nuclear F-actin sensitive genes upon TCR signaling

overall_design: 4 Donors control (DMSO) treatment (CK-869)

first: Oliver

last: Fackler


title: Multiple Environmental Stressors Induce Complex Transcriptomic Responses Indicative of Phenotypic Outcomes in Western Fence Lizard [Exposure 2: food limitation x malaria infection]

city: Vicksburg

first: Kurt

last: Gust

state: MS

address: 3909 Halls Ferry Rd.

department: Environmental Laboratory

institute: US Army ERDC

summary: The health and resilience of species in natural environments are increasingly challenged by complex anthropogenic stressor combinations including climate change, habitat encroachment, and chemical contamination. To better understand impacts of these stressors, we examined the individual- and combined-stressor impacts of malaria infection, food limitation, and 2,4,6-trinitrotoluene (TNT) exposures on gene expression in livers of Western fence lizard (WFL, Sceloporus occidentalis) using custom WFL transcriptome-based microarrays. Computational analysis including annotation enrichment and correlation analysis identified putative functional mechanisms between transcript expression and toxicological phenotype. TNT exposure increased transcript expression for genes involved in erythropoiesis, potentially in response to TNT-induced anemia and/or methemoglobinemia, and caused dose-specific effects on genes involved in lipid and overall energy metabolism consistent with a hormesis response of growth stimulation at low doses contrasted with adverse effects on lizard growth at high doses. Functional enrichment and inguinal fat body weights suggest inhibition of lipid mobilization and catabolism by TNT coupled with a decreased overall energy budget. Malaria infection elicited enrichment of the expression of multiple immune-related functions likely corresponding to increased white blood cell (WBC) counts. Food limitation alone enriched functions related to cellular energy production and decreased expression of immune response consistent with a decrease in WBC levels. Despite these findings, the lizards demonstrated immune resilience to malaria infection under food limitation with transcriptional results indicating a fully competent immune response to malaria, even under bioenergetic constraints. Interestingly, each TNT and malaria individually tended to increase transcriptional expression of immune-related genes and increase overall WBC concentrations in blood; responses that were retained in the TNT x malaria combined exposure. The results demonstrate complex and sometimes unexpected responses to multiple stressors where the lizards displayed remarkable resiliency to the stressor combinations investigated.

overall_design: Three separate microarray analyses were conducted within this study. The three experiments investigated 3 pairwise stressor combinations, including: Exposure 1 - TNT x food limitation, Exposure 2 - food limitation x malaria infection, and Exposure 3 - TNT x malaria infection. All exposure details can be found in the companion paper, McFarland et al. (2012 Ecotoxicol. 21:2372–2390 DOI 10.1007/s10646-012-0993-1). This GEO entry represents Exposure 2 (food limitation x malaria infection): Briefly, the experiment was conducted as 30-day bioassay utilizing male Western fence lizards. Experimental treatments were deployed in a factorial treatment arrangement within a completely randomized experimental design. The Western fence lizards were inoculated with lizard malaria or vehicle control (see McFarland et al. 2012 for methods) paired with either ad libitum feeding (10 crickets/day) or restricted feeding treatments of 5 or 2 crickets per day. All genomics investigations included at least 5 replicate liver samples collected from individual lizards per condition. At the completion of the exposures, animals were euthanized by CO2 asphyxia, dissected, and liver samples were fixed in RNA Later™ (Ambion, Austin, TX) following manufacturer's recommendations and stored at -80C until RNA extraction. Blood and various tissues were also collected for clinical endpoint analysis where individual and pair-wise stressor effects were tested for 29 toxicological endpoints (McFarland et al. 2012. Ecotoxicol. 21:2372–2390 DOI 10.1007/s10646-012-0993-1). All protocols were conducted consistent with Good Laboratory Practices and approved by the Institutional Animal Care and Use Committee at the U.S. Army Public Health Center.

first: Vijender

last: Chaitankar

first: Preetam

last: Ghosh

first: Mitchell

last: Wilbanks

first: Xianfeng

last: Chen

first: Natalie

middle: D

last: Barker

first: Don

last: Pham

first: Leona

last: Scanlan

first: Arun

last: Rawat

first: Larry

middle: G

last: Talent

middle: J

last: Quinn Jr

first: Christopher

last: Vulpe

first: Mohamed

middle: O

last: Elasri

first: Mark

last: Johnson

first: Edward

last: Perkins

first: Craig

last: McFarland


title: Multiple Environmental Stressors Induce Complex Transcriptomic Responses Indicative of Phenotypic Outcomes in Western Fence Lizard [Exposure 3: TNT x malaria infection]

overall_design: Three separate microarray analyses were conducted within this study. The three experiments investigated 3 pairwise stressor combinations, including: Exposure 1 - TNT x food limitation, Exposure 2 - food limitation x malaria infection, and Exposure 3 - TNT x malaria infection. All exposure details can be found in the companion paper, McFarland et al. (2012 Ecotoxicol. 21:2372–2390 DOI 10.1007/s10646-012-0993-1). This GEO entry represents Exposure 3 (TNT x malaria infection): Briefly, the experiment was conducted as 30-day bioassay utilizing male Western fence lizards. Experimental treatments were deployed in a factorial treatment arrangement within a completely randomized experimental design. The Western fence lizards were inoculated with lizard malaria or vehicle control (see McFarland et al. 2012 for methods) and then dosed by daily gavage to TNT at 0 (control), 5, 10 and 20 mg/kg/d. The lizards were fed ad libitum feeding (10 crickets/day) through the course of the experiment. All genomics investigations included at least 4 replicate liver samples collected from individual lizards per condition where most treatments included 6 replicates. At the completion of the exposures, animals were euthanized by CO2 asphyxia, dissected, and liver samples were fixed in RNA Later™ (Ambion, Austin, TX) following manufacturer's recommendations and stored at -80C until RNA extraction. Blood and various tissues were also collected for clinical endpoint analysis where individual and pair-wise stressor effects were tested for 29 toxicological endpoints (McFarland et al. 2012. Ecotoxicol. 21:2372–2390 DOI 10.1007/s10646-012-0993-1). All protocols were conducted consistent with Good Laboratory Practices and approved by the Institutional Animal Care and Use Committee at the U.S. Army Public Health Center.

first: Michael


title: Filtered reproductive long non-coding RNAs by genome-wide analyses of goat ovary at different estrus periods

city: Fuyang

first: Yong

last: Liu

address: Qinghe West Road

country: China

institute: Key Laboratory of Embryo Development and Reproductive Regulation of Anhui Province

summary:
Background: The goat is an important farm animal. Reproduction is an important process of goat farming. The ovary is the most important reproductive organ for goats. In recent years, an increasing number of long non-coding RNAs (lncRNAs) have been implicated in the regulation of mammal reproduction. However, there are few studies on the function of lncRNAs in reproduction, particularly lncRNAs in the ovary.

Results: The sequencing of goat ovaries generated 1,122,014,112 clean reads, and 4,926 lncRNAs and 1,454 TUCPs(transcripts of uncertain coding potential) were identified for further analysis by using the coding potential analysis software, CNCI, CPC and Pfam-sca. There were 115 /22 differential lncRNAs /TUCPs transcripts between the ovaries of the luteal phase and the follicular phase. We predicted the target genes of lncRNA /TUCP based on co-expression and co-localization methods. In total, 2584 /904 target genes were predicted by co-expression, and 326/73 target genes were predicted by co-localization. The functions of these target genes were further analyzed with GO and KEGG analysis. The results showed that lncRNAs /TUCPs, which are highly expressed in goat ovaries in the luteal phase, are mainly associated with the synthesis of progesterone, and we filtered the lncRNAs /TUCPs, such as XR_001918177.1 and TUCP_001362, which may regulate the synthesis of progesterone; lncRNAs /TUCPs, which are highly expressed in goat ovaries in the follicular phase, are mainly associated with oogenesis and the maturation of oocytes, and we filtered the lncRNAs /TUCPs that may regulate the oogenesis and maturation of oocyte, such as XR_001917388.1 and TUCP_000849.

Conclusion: The present study provided the genome expression profile of lncRNAs /TUCPs in goat ovaries at different estrus periods and filtered the lncRNAs /TUCPs associated with goat reproduction. These results are helpful to further study the molecular mechanisms of goat reproduction.

overall_design: ovary lncRNA profiles of follicular and luteal phases were generated by deep sequencing,five repetitions

first: Juan

last: Xie


title: MicroRNA and mRNA regulatory network in EGFR-mutated lung adenocarcinoma [mRNA]

status: Public on Nov 13 2018

city: Tokyo

first: Sophia

last: Subat

address: 3-8-31 Ariake, Koto-ward,

country: Japan

institute: Japanese Foundation for Cancer Research

summary:
We have examined the both miRNA and mRNA expression profiles in 155 lung adenocarcinoma samples with known EGFR mutation status (52 mutated and 103 wild-type cases).
An integrative analysis was performed to identify the unique miRNA-mRNA regulatory network in EGFR-mutated lung adenocarcinoma.

overall_design: 155 samples are analyzed.  52 cases with EGFR mutation,  103 cases with EGFR nagative status. No replicates or control samples included.

first: Kentato

last: Inamura

first: Hiroko

last: Nagano

first: Yuichi

last: Ishikawa


title: Transcriptome‐based analyses of phosphite‐mediated suppression of rust pathogens Puccinia emaculata and Phakopsora pachyrhizi

status: Public on Nov 14 2018

city: Ardmore

first: Kiran

last: Mysore

state: Oklahoma

address: 2510 Sam Noble Parkway

institute: Noble Research Institute

summary: We explored the use of Phi in controlling the fungal pathogens Puccinia emaculata and Phakopsora pachyrhizi, the causal agents of switchgrass rust and Asian soybean rust, respectively. RNA sequencing of both the pathogens with and without treatment with Phi was conducted. Differentially expressed genes were identified in both pathogens and comparison of differentially expressed genes was made to identify commonly regulated genes by Phi. Total RNA from Phi‐treated Pe and Pp was isolated using an RNeasy plant mini kit (Qiagen). Two biological replicates were used for each treatment (12 samples). Illumina TruSeq sequencing‐by‐synthesis chemistry was used on a HiSeq 2000 platform (Illumina, https://www.illumina.com/) to generate paired‐end reads (2 × 100 bp).

sample_organism:
Phakopsora pachyrhizi
Puccinia emaculata

overall_design: Urediniospores of Pe and Pp were dusted on 1× germination solution [500× stock: 0.0036% nonanol (v/v), 0.025% Tween 20 (v/v), 50% ethanol (v/v), in autoclaved distilled water] supplemented with 0, 10 or 100 mM Phi on a Petri plate. Urediniospores were allowed to germinate for 24 h in the dark. After 24 h, germinated urediniospores were collected by skimming them from the surface of the solution with the help of a cover slip.

first: Upinder

last: Gill

first: Liang

last: Sun

first: Sachin

last: Rustgi

first: Yuhong

last: Tang

first: Diter

last: von Wettstein

first: Kirankumar


title: miRNA Profiles of Camptothecin-Sensitive and Resistant Jurkat T-Cells

city: Izmir

first: ipek

last: erdogan

address: Gulbahce

country: Turkey

institute: Izmir Institute of Technology

summary: MicroRNAs which are non-coding RNAs 19-25 nt in length regulate gene expression at post-transcriptional and translational stages. Although it is known that they play a role in critical processes such as development and differentiation of T cells, a major component of the immune system, the function of miRNAs in T cell apoptosis is unknown. This study has aimed to identify miRNAs’ involvement in camptothecin-induced T cell apoptosis in the  Jurkat T cell leukemia cell line model. Following the enrichment of the apoptotic population by magnetic seperation, the negative and apoptotic fractions were profilled and compared according to the expression levels of microRNAs.

overall_design: Jurkat T Lymphocytes were treated with 8 µM camptothecin for 4 hours to keep the population in early apoptotic phase, confirmed by immunoflorescent labeling. Treated and untreated populations were subjected to magnetic cell sorting. Four subfractions were obtained as untreated antiapoptotic (JNN-Jurkat Negative Negative), untreated apoptotic-which are naturally apoptotic- (JNP-Jurkat Negative Positive), camptothecin-treated apoptotic (JAP-Jurkat Apoptotic Positive) and camptothecin-treated antiapoptotic (JAN-Jurkat Apoptotic Negative). JNP fraction was not used for further analysis because of insufficient number of cells. Total RNA was extracted from all of the samples samples having higher RNA Quality due to RIN were chosen for miRNA array analysis. 2 replicates of JNN, 3 replicates of JAP and JAN were subjected to array analysis. 3 replicates of JNN fraction were mixed in 2 replicates because array analysis was performed in 8 channels.

first: Bunyamin

last: Akgul

first: Ayten

last: Nalbant

first: Ipek

last: Erdogan

first: Ilyas

last: Cosacak


title: Transcriptomic comparison of Listeria monocytogenes EGDe and its ΔlftR mutant

status: Public on Nov 12 2018

city: Wernigerode

first: Samuel

last: Hauf

address: Burgstr. 37

department: Division of Enteropathogenic Bacteria and Legionella (FG11)

institute: Robert Koch-Institute

summary: Using RNA-Seq we showed that expression of the lieAB and lftRS genes is strongly induced in cells lacking the PadR-type transcriptional repressor LftR

overall_design: Comparison of wildtype and mutant cell transcriptomes. Harvest of cells in mid exponential phase (OD600 = 0.5). Three replicates were analyzed.

first: Sven

last: Halbedel


title: Lung response to Respiratory Syncytial Virus Infection in Adult and Old Mice

city: Bilthoven

first: Jeroen

last: Pennings

address: A. van Leeuwenhoeklaan 9

country: Netherlands

institute: Natl. Inst. Public Health & Environment

summary: We infected adult (6-8 weeks) and old (62-72 weeks) mice with RSV or mock control and determined transcriptional responses in their lungs.

overall_design: A 28 array study with a common reference design

first: Teun

last: Guichelaar


title: Group 2 Sigma Factors Are Central Regulators of Oxidative Stress Acclimation in Cyanobacteria

city: Turku

first: Taina

last: Tyystjarvi

address: Pharmacity/Itäinen Pitkäkatu 4 C, 6th floor

department: Biochemistry

country: Finland

institute: University of Turku

summary: The model cyanobacterium Synechocystis sp. PCC encodes nine different σ factors. SigA is the essential primary σ factor that is mainly responsible for expression of housekeeping genes during normal growth. Group 2 σ factors are non-essential in standard conditions, and actually all single, double, triple and quadruple inactivation strains of group 2 factors grow well in standard growth conditions. The roles of group 2 σ factors in oxidative stress acclimation were studied using the ΔsigBCDE strain of Synechocystis sp. PCC 6803 which is devoid of all group 2 σ factors, and triple inactivation strains, each containing one group 2 σ factor. The ΔsigBCD strain contains only SigE, ΔsigBCE only SigD, ΔsigBDE only SigC and ΔsigCDE only SigB. The expression of genes encoding known players of oxidative stress tolerance in the triple and quadruple mutants were compared in standard growth conditions using DNA microarray analysis.

overall_design: Cells from cyanobacteria Synechocystis sp. PCC 6803 named as control strain (CS), the ΔsigBCDE strain, devoiding of all group 2 σ factors, and triple inactivation strains, each containing one group 2 σ factor (the ΔsigBCD strain contains only SigE, ΔsigBCE only SigD, ΔsigBDE only SigC and ΔsigCDE only SigB)  were harvested (A730=1, 40 mL) directly from standard growth conditions (continuous illumination at the PPFD of 40 µmol m-2s-1, 32°C, ambient CO2). From three to four independent experiments were performed at each conditions.

first: Tyystjarvi

last: Taina

first: Hakkila

last: Kaisa

first: Gunnelius

last: Liisa

first: Matthijs

last: Hans C.P.


title: MicroRNA and mRNA regulatory network in EGFR-mutated lung adenocarcinoma [miRNA]

first: Sophia

last: Subat

first: Kentato

last: Inamura

first: Hiroko

last: Nagano

first: Yuichi

last: Ishikawa


title: RNA-sequencing analysis of umbilical cord plasma microRNAs from healthy newborns

city: Dublin

first: Catherine

last: Mooney

address: Belfield

department: School of Computer Science

country: Ireland

institute: University College Dublin

type: Non-coding RNA profiling by high throughput sequencing

summary: MicroRNAs are a class of small non-coding RNA that regulate gene expression at a post-transcriptional level. MicroRNAs have been identified in various body fluids  under normal conditions and their stability as well as their dysregulation in disease has led to ongoing interest in their diagnostic and prognostic potential. Circulating microRNAs may be valuable predictors of early-life complications such as birth asphyxia or neonatal seizures but there are relatively few data on microRNA content in plasma from healthy babies. Here we performed small RNA-sequencing analysis of plasma processed from umbilical cord blood in a set of healthy newborns. MicroRNA levels in umbilical cord plasma of four male and four female healthy babies, from two different centres were profiled. A total of 1,004 individual microRNAs were identified, which ranged from 426 to 659 per sample, of which 269 microRNAs were common to all eight samples. Many of these microRNAs are highly expressed and consistent with previous studies using other high throughput platforms. While overall microRNA expression did not differ between male and female cord blood plasma, we did detect differentially edited microRNAs in female plasma compared to male. Of note, and consistent with other studies of this type, adenylation and uridylation were the two most prominent forms of editing. Six microRNAs, miR-128-3p, miR-29a-3p, miR-9-5p, miR-218-5p, 204-5p and miR-132-3p were consistently both uridylated and adenylated in female cord blood plasma. Although only a few microRNAs were differentially edited in females and expression levels were low, it is an interesting finding as the effects of sex on RNA editing is poorly understood and warrants further investigation. These results provide a benchmark for microRNA profiling and biomarker discovery using umbilical cord plasma  and can be used as comparative data for future biomarker profiles from complicated births or those with early-life developmental disorders.

first: Gary

middle: P

last: Brennan

first: Dimitrios

middle: M

last: Vitsios

first: Ann-Marie

last: Looney

first: Boubou

last: Hallberg

first: David

middle: C

last: Henshall

first: Geraldine

middle: B

last: Boylan

first: Deirdre

last: Murray


title: A single JAZ repressor controls the jasmonate pathway in Marchantia polymorpha

status: Public on Nov 10 2018

city: Madrid

first: Jose M.

last: Franco-Zorrilla

state: Madrid

address: Darwin, 3

department: Plant Molecular Genetics

institute: Centro Nacinal de Biotecnologia-CSIC

summary: JAZ genes are negative regulators of jasmonate responses with a dual function as repressors of transcription factors and co-receptors, together with COI1, of the hormone jasmonoyl-isoleucine (JA-Ile). This family has been mainly studied in angiosperms, where high gene redundancy hinders the characterization of a complete depletion of JAZ function. Moreover, the recent discovery that JA-Ile is not the sole COI1/JAZ ligand in land plants, as dn-OPDA is the bioactive ligand in Marchantia polymorpha, underscores the importance of studying JAZ co-receptors in bryophytes. Here we exploited the low gene redundancy of the liverwort Marchantia polymorpha to characterize the function of the single MpJAZ in this early-divergent plant lineage. We demonstrate that MpJAZ is the ortholog of AtJAZ and acts as a repressor of dinor-OPDA responses in Marchantia. Mpjaz mutants show a dwarf phenotype and severe developmental defects related to growth inhibition, consistent with a constitutive activation of the dinor-OPDA pathway and the overaccumulation of both dinor-OPDA and its precursor OPDA. The expression of AtJAZ3 in Mpjaz complements MpJAZ repressor function, indicating that JAZ function is conserved across land plants. However, AtJAZ3 is unable to form co-receptor complexes with MpCOI1 and dn-OPDA, which evidences that the Jas domain, and not only COI1, determines ligand specificity.

overall_design: Transcriptomic analysis of Mpjaz mutants: 4 replicates  Mpjaz-1 (Experiment)  vs Tak-1 (Control)

first: Isabel

last: Monte

first: José

last: Franco‑Zorrilla

first: Gloria

last: García-Casado

first: Angel

last: Zamarreño

last: García-Mina

first: Ryuichi

last: Nishihama

first: Takayuki

last: Kohchi

first: Roberto

last: Solano


title: Neutrophil gene expression in systemic juvenile idiopathic arthritis

city: CINCINNATI

first: Grant

last: Schulert

state: OH

address: 3333 Burnet Ave

institute: Cincinnati Children's Hospital Medical Center

summary: Systemic juvenile idiopathic arthritis (SJIA) is a chronic childhood arthropathy with features of autoinflammation. Early inflammatory SJIA is associated with expansion and activation of neutrophils with a sepsis-like phenotype, but neutrophil phenotypes present in longstanding and clinically inactive disease (CID) are unknown. The objective of this study was to examine activated neutrophil subsets, S100 alarmin release, and gene expression signatures in children with a spectrum of SJIA disease activity.  Methods: Highly-purified neutrophils were isolated using a two-step procedure of density-gradient centrifugation followed by magnetic-bead based negative selection prior to flow cytometry or cell culture to quantify S100 protein release. Whole transcriptome gene expression profiles were compared in neutrophils from children with both active SJIA and CID.  Results: Patients with SJIA and active systemic features demonstrated a higher number of CD16+CD62Llo neutrophil population compared to controls. This neutrophil subset was not seen in patients with CID or patients with active arthritis not exhibiting systemic features. Using imaging flow cytometry, CD16+CD62Llo neutrophils from patients with active SJIA and features of macrophage activation syndrome (MAS) had increased nuclear hypersegmentation compared to CD16+CD62L+ neutrophils. Serum levels of S100A8/A9 and S100A12 were strongly correlated with peripheral blood neutrophil counts. Neutrophils from active SJIA patients did not show enhanced resting S100 protein release; however, regardless of disease activity, neutrophils from SJIA patients did show enhanced S100A8/A9 release upon PMA stimulation compared to control neutrophils. Furthermore, whole transcriptome analysis of highly purified neutrophils from children with active SJIA identified 214 differentially expressed genes compared to neutrophils from healthy controls. The most significantly upregulated gene pathway was Immune System Process, including AIM2, IL18RAP, and NLRC4. Interestingly, this gene set showed intermediate levels of expression in neutrophils from patients with long-standing CID yet persistent serum IL-18 elevation. Indeed, all patient samples regardless of disease activity demonstrated elevated inflammatory gene expression, including inflammasome components and S100A8.  Conclusion: We identify features of neutrophil activation in SJIA patients with active disease and CID, including a proinflammatory gene expression signature, reflecting persistent innate immune activation. Taken together, these studies expand understanding of neutrophil function in chronic autoinflammatory disorders such as SJIA.

overall_design: Highly purified neutrophils isolated from patients with SJIA and healthy controls

first: Rachel

last: Brown

first: Maggie

last: Henderlight

first: Thuy

last: Do

first: Shima

last: Yasin

first: Alexei

last: Grom

first: Monica

last: DeLay

first: Sherry

last: Thornton


title: Gene expression in rat lumbar spinal cord tissues

status: Public on Nov 08 2018

city: Vienna

first: Isabella

last: Wimmer

address: Spitalgasse 4

department: Center for Brain Research

country: Austria

institute: Medical University of Vienna

summary: We assessed the transcriptome within lumbar spinal cord tissue of wild-type Lewis rats and attractin-mutant rats (LEWzizi; LEW.SD-Atrn zi/zi).

overall_design: The study bases on lumbar spinal cord tissue of 4-months-old rats. We included 5 samples derived from wild-type Lewis rats and 5 samples derived from LEWzizi (LEW.SD-Atrn zi/zi) rats. Rats have been intracardially perfused with PBS prior to tissue harvest.

first: I


title: Mouse polycomb group gene Cbx2 promotes osteoblastic but suppresses adipogenic differentiation in postnatal long bones

status: Public on Nov 09 2018

city: Fukuoka

first: Tetsuya

last: Sato

address: 3-1-1, Maidashi Higashi-ku

institute: Kyushu University

summary: A set of key developmental genes is essential for skeletal growth from multipotent progenitor cells at weaning. Polycomb group proteins, which regulate such genes contributes to the cell lineage commitment and subsequent differentiation via epigenetic chromatin modification and remodeling. However, it is unclear which cell lineage and gene sets are targeted by polycomb proteins during skeletal growth. We now report that mice deficient in a polycomb group gene Cbx2 (cterm/cterm) exhibited skeletal hypoplasia in the tibia, femur, and cranium. Long bone cavities in these mice contained fewer multipotent mesenchymal stromal cells. RNA-sequencing of bone marrow cells showed downregulation and upregulation of osteoblastic and adipogenic genes, respectively. Furthermore, the expression levels of genes specifically expressed in B-cell precursors were decreased. Forced expression of Cbx2 in Cbx2 (cterm/cterm) bone marrow stromal cell recovered fibroblastic colony formation and suppressed adipogenic differentiation. Collectively, our results suggest that Cbx2 controls the maintenance and adipogenic differentiation of mesenchymal stromal cells in the bone marrow.

overall_design: mRNA profiles of 3-week-old wild type (WT) and Cbx2-/- mice were generated by deep sequencing, in triplicate, using Illumina HiSeq 1000.

first: Yuko

last: Katoh-Fukui

first: Takashi

last: Baba

first: Hiroyuki

last: Otake

last: Nagakui-Noguchi

first: Miyuki

last: Shindo

first: Mikita

last: Suyama

first: Yasuyuki

last: Ohkawa

first: Hideki

last: Tsumura

first: Ken-ichirou

last: Morohashi

first: Maki

last: Fukami


title: RdDM is involved in epigenetic regulation of strawberry fruit ripening

city: shanghai

first: yijing

last: zhang

address: 2005 Songhu Road

institute: Fudan University

type: Methylation profiling by high throughput sequencing

summary: DNA methylation is a conserved epigenetic mark that influences diverse biological processes in many eukaryotes. Recently, DNA methylation was proposed to regulate fleshy fruit ripening. Fleshy fruits can be distinguished by their ripening process as climacteric fruits, such as tomatoes, or non-climacteric fruits, such as strawberries. Tomatoes undergo a global decrease in DNA methylation during ripening, due to increased expression of a DNA demethylase gene. The dynamics and biological relevance of DNA methylation during ripening of non-climacteric fruits, or other climacteric fruits, are unknown. Here, we generated and characterized single-base resolution maps of the DNA methylome in strawberry fruit, from immature to ripe stages. We observed an overall loss of DNA methylation during strawberry fruit ripening. Thus, ripening-induced DNA hypomethylation occurs not only in climacteric fruit, but also in non-climacteric fruit. However, we discovered that the mechanisms underlying DNA hypomethylation during ripening of tomato and strawberry are distinct. Unlike in tomatoes, DNA demethylase genes were not up-regulated during ripening of strawberries. Instead, genes involved in RNA-directed DNA methylation were down-regulated during strawberry ripening. Further, ripening-induced DNA hypomethylation was associated with decreased siRNA levels, consistent with reduced RdDM activity. Therefore, we propose that DNA hypomethylation during strawberry ripening is caused by diminished RdDM activity. Finally, hundreds of ripening-related genes displayed altered expression that was associated with, and thus potentially regulated by, DNA hypomethylation during ripening. Our findings provide new insight into the DNA methylation dynamics during the ripening of non-climateric fruit and reveal a novel function of RdDM in regulating an important process in plant development.

overall_design: Bisulfite-Seq: 4 samples examined, Fa1 (green stage, 2 replicates), Fa2 (intermediate red stage, 2 replicates), Fa3 (full red stage, 2 replicates), Leaf (1 replicate); RNA-Seq: 3 samples examined, Fa1 (green stage, 2 replicates), Fa2 (intermediate red stage, 2 replicates), Fa3 (full red stage, 2 replicates); small-RNA-Seq: 2 samples examined, Fa1 (green stage, 2 replicates), Fa3 (full red stage, 2 replicates).

first: Zhaobo

last: Lang

first: Yijing

last: Zhang


title: Multiple Environmental Stressors Induce Complex Transcriptomic Responses Indicative of Phenotypic Outcomes in Western Fence Lizard [Exposure 1: TNT x food limitation]

first: Kurt

last: Gust

overall_design: Three separate microarray analyses were conducted within this study. The three experiments investigated 3 pairwise stressor combinations, including: Exposure 1 - TNT x food limitation, Exposure 2 - food limitation x malaria infection, and Exposure 3 - TNT x malaria infection. All exposure details can be found in the companion paper, McFarland et al. (2012 Ecotoxicol. 21:2372–2390 DOI 10.1007/s10646-012-0993-1). This GEO entry represents Exposure 1 (TNT x food limitation): Briefly, the experiment was conducted as 30-day bioassay utilizing male Western fence lizards. Experimental treatments were deployed in a factorial treatment arrangement within a completely randomized experimental design. The Western fence lizards were dosed by daily gavage to TNT at 0 (control), 5, 10 and 20 mg/kg/d paired with either ad libitum feeding (10 crickets) or restricted feeding (2 crickets) treatments. All genomics investigations included at least 4 replicate liver samples collected from individual lizards per condition where most treatments included 6 replicates. At the completion of the exposures, animals were euthanized by CO2 asphyxia, dissected, and liver samples were fixed in RNA Later™ (Ambion, Austin, TX) following manufacturer's recommendations and stored at -80C until RNA extraction. Blood and various tissues were also collected for clinical endpoint analysis where individual and pair-wise stressor effects were tested for 29 toxicological endpoints (McFarland et al. 2012. Ecotoxicol. 21:2372–2390 DOI 10.1007/s10646-012-0993-1). All protocols were conducted consistent with Good Laboratory Practices and approved by the Institutional Animal Care and Use Committee at the U.S. Army Public Health Center.

first: Vijender

last: Chaitankar

first: Preetam

last: Ghosh

first: Mitchell

last: Wilbanks

first: Xianfeng

last: Chen

first: Natalie

last: Barker

first: Don

last: Pham

first: Leona

last: Scanlan

first: Arun

last: Rawat

first: Larry

last: Talent

first: Michael

last: Quinn Jr

first: Christopher

last: Vulpe

first: Mohamed

last: Elasri

first: Mark

last: Johnson

first: Edward

last: Perkins

first: Craig

last: McFarland


title: Genome-wide binding of STAT3 or CEBP beta in anaplastic large cell lymphoma

city: Boston

first: Roberto

last: Chiarle

state: Massachusetts

address: 300 Longwood Avenue

department: Department of Pathology

institute: Children’s Hospital Boston and Harvard Medical School

type: Genome binding/occupancy profiling by high throughput sequencing

summary: Examination of STAT3 or CEBP beta binding by ChIP-seq in Crizotinib treated Anaplastic large cell lymphoma.

overall_design: Genome-wide STAT3 or CEBP beta binding sites were measured in Anaplastic large cell lymphoma cell lines, JB6 and SUDHL-1 respectively treated with DMSO and Crizotinib. We sequenced anti-STAT3 and anti-CEBPb ChIP-seq as well as corresponding control (Input) libraries.

first: Taek-Chin

last: Cheong

first: Clayton

last: Collings

first: Seth

last: Cassel

first: Qi

last: Wang


title: Genome-wide maps of ParBVc1 binding on V .cholerae genome

city: Toulouse

first: Delphine

last: Labourdette

address: Hall Gilbert Durand - Bio5 - 135 Avenue de Rangueil

department: LISBP

country: France

institute: INSA

summary: We report the genome-wide analysis from chromatin immunoprecipitated DNA (ChIP-sequencing) at very high resolution of the DNA binding pattern of ParBVc1 on the chromosome of Vibrio cholerae.

overall_design: Differencial examination of ParBVc1 binding by comparing input and IP (affinity-purified anti-ParBVc1 antibody) samples

first: Roxanne

middle: E

last: Diaz

first: Jean-Yves

last: Bouet


title: Transcriptome analysis of mycorrhizal and non-mycorrhizal soybean root associated with F. virguliforme inoculation

city: Córdoba

first: Nathalie

last: Marquez

state: Córdoba

address: Camino 60 cuadras Km 5,5

country: Argentina

institute: INTA

summary: Many of the microorganisms that are normally present in the soil, actually inhabit the rhizosphere and interact with plants. Those plant–microorganisms interactions may be beneficial or harmful. Among the first are the arbuscular mycorrhizal fungi (AMF). These soil fungi have been reported to improve plant resistance/tolerance to pests and diseases. On the other hand, soilborne pathogens represent a threat to agriculture generating important yield losses, depending upon the pathogen and the crop. One example is the “Sudden Death Syndrome” (SDS), a severe disease in soybean (Glycine max (L.) Merr) caused by a complex of at least four species of Fusarium sp., among which Fusarium virguliforme and F. tuccumaniae are the most prevalent in Argentina. This study provides, under strict in vitro culture conditions, a global analysis of transcript modifications in mycorrhizal and non-mycorrhizal soybean root associated with F. virguliforme inoculation. Microarray results showed qualitative and quantitative changes in the expression of defense-related genes in mycorrhizal soybean, suggesting that AMF are good candidates for sustainable plant protection against F. virguliforme.

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

first: María

middle: L

last: Giachero

first: Adrien

last: Gallou

first: Stéphane

last: Declerck

first: Daniel

last: Ducasse


title: Merkel Cells Activate Sensory Neural Pathways through Adrenergic Synapses

city: New York

first: Benjamin

middle: U

last: Hoffman

state: NY

address: 1150 St. Nicholas Ave

institute: Columbia University

summary: Epithelial-neuronal signaling is essential for sensory encoding in touch, itch and nociception; however, little is known about the release mechanisms and neurotransmitter receptors through which skin cells govern neuronal excitability.  Merkel cells are mechanosensory epidermal cells that have long been proposed to activate neuronal afferents through chemical synaptic transmission.  We employed a set of classical criteria for chemical neurotransmission as framework to directly test this hypothesis. RNA sequencing of adult Merkel cells demonstrated that they express presynaptic molecules and biosynthetic machinery for adrenergic transmission. Moreover, live-cell imaging directly demonstrated that Merkel cells mediate activity- and VMAT-dependent release of fluorescent catecholamine neurotransmitter analogues.  Touch-evoked firing in Merkel-cell afferents was inhibited either by pre-synaptic silencing of SNARE-mediated vesicle release from Merkel cells or by neuronal deletion of b2-adrenergic receptors.  Together, these results identify both pre- and postsynaptic mechanisms through which Merkel cells excite mechanosensory afferents to encode gentle touch.

overall_design: RNA-seq of basal keratinocytes and Merkel cells purified with FACS

first: Yoshichika

last: Baba

first: Theanne

middle: N

last: Griffith

first: Eugene

middle: V

last: Mosharov

first: Seung-Hyun

last: Woo

last: Roybal

first: Gerard

last: Karsenty

first: Ardem

last: Patapoutian

first: David

last: Sulzer

first: Ellen

last: Lumpkin


title: Epigenetic mapping of the Arabidopsis metabolome reveals mediators of the epigenotype-phenotype map

city: Freising

first: Rashmi

middle: Rekha

last: Hazarika

address: Liesel Beckmann-Str-2

institute: Technical University of Munich

summary: Identifying the sources of natural variation underlying metabolic differences between plants will enable a better understanding of plant metabolism and provide insights into the regulatory networks that govern plant growth and morphology. So far, however, the contribution of epigenetic variation to metabolic diversity has been largely ignored. In the present study, we utilized a panel of Arabidopsis thaliana epigenetic recombinant inbred lines (epiRILs) to assess the impact of epigenetic variation on the metabolic composition. Thirty epigenetic QTL (QTL epi ) were detected, which partly overlap with QTL epi linked to growth and morphology. In an effort to identify causal candidate genes in the QTL epi regions or their putative trans -targets we performed in silico small RNA and qPCR analyses. Differentially expressed genes were further studied by phenotypic and metabolic analyses of knockout mutants. Three genes were detected that recapitulated the detected QTL epi effects, providing evidence for epigenetic regulation in cis and in trans . These results indicate that epigenetic mechanisms impact metabolic diversity, possibly via small RNAs, and thus aid in further disentangling the complex epigenotype-phenotype map.

overall_design: Previously published Bisulfite Sequencing data of epiRIL92, epiRIL150, epiRIL193, epiRIL232, Col_wt (series: GSE99404) were re-analyzed to confirm the stability of epiRILs

middle: R

first: Frank

last: Johannes


title: Role of CIZ1 in maintenance of epigenetic landscape in primary differentiated mouse embryonic fibroblasts

status: Public on Nov 07 2018

city: York

first: Dawn

last: Coverley

address: Wentworth Way

department: Department of Biology

country: United Kingdom

institute: University of York

summary: The inactive X chromosome (Xi) serves as a model for establishment and maintenance of repressed chromatin and the function of polycomb repressive complexes (PRC1/2). Here we show that Xi transiently relocates from the nuclear periphery towards the interior during its replication, in a process dependent on CIZ1. Compromised relocation of Xi in CIZ1-null primary mouse embryonic fibroblasts is accompanied by loss of PRC-mediated H2AK119Ub1 and H3K27me3, increased solubility of PRC2 catalytic subunit EZH2, and genome-wide deregulation of polycomb-regulated genes. Xi position in S phase is also corrupted in cells adapted to long-term culture (WT or CIZ1-null), and also accompanied by specific changes in EZH2 and its targets. The data are consistent with the idea that chromatin relocation during S phase contributes to maintenance of epigenetic landscape in primary cells, and that elevated soluble EZH2 is part of an error-prone mechanism by which modifying enzyme meets template when chromatin relocation is compromised.

overall_design: Transcriptome analysis of primary (before passage 5) and culture-adapted derivative cell lines of murine embryonic fibroblasts in female WT (6 replicates) and female CIZ1 null (6 replicates) by RNA-seq. Additional samples include 3 inducible CIZ1-null primary murine embryonic fibroblast, 2 of which were induced with doxycycline.

first: Emma

last: Stewart

first: Robert

last: Turner

first: Katherine

last: Newling

first: Rebeca

last: Ridings-Figueroa

first: Victoria

last: Scott

first: Peter

last: Ashton

first: Justin

middle: F

last: Ainscough


title: Intestinal toxicity in rats following administration of CDK4/6 inhibitors is independent of primary pharmacology

city: San Diego

first: Brad

last: Hirakawa

state: CA

address: 10646 Science Center Drive

department: Drug Safety R&D

institute: Pfizer

summary:
Male Sprague Dawley rats (CRL/CD SD, Charles River Laboratories, Hollister, CA) 6-8 weeks-old were utilized.
We used microarrays to analyze changes in gene expression in gastrointestinal tissue (musocal scrapings) after 4 days of dosing.  Total RNA was extracted from tissues of 3 rats per experimental group for analysis.

overall_design: Ten rats per group were administered vehicle (0.5% methyl cellulose), abemaciclib (36 or 120 mg/kg/day), palbociclib (30 or 100 mg/kg/day), or ribociclib (300 mg/kg/day) via oral gavage for 4 or 15 days. The vehicle for abemaciclib and ribociclib was 0.5% hydroxypropyl methylcellulose, 0.25% tween 80 in 10 mM citrate buffer, pH3; and the vehicle for palbociclib was 0.5% methylcellulose.

first: Wenyue

last: Hu


title: Comparative transcriptomics of Aspergillus niger when deleted or overexpressed for the putative transcription factors MjkA, MjkB and the histon deactelyase HdaX

city: Berlin

first: Paul

last: Schäpe

address: Gustav-Meyer-Allee 25

department: Applied and Molecular Microbiology

institute: TU-Berlin

summary:
Purpose: Expression profiling of two ORFs encoding putative transcription factors: An07g07370 (TF1/MjkA) and An12g07690 (TF2/MjkB), and a histone deacetylase (An09g06520, HdaX) under carbon-limited batch cultivations (biological duplicate runs) in Aspergillus niger.
Methods: Single deletion strains for TF1, TF2 and HD, respectively, (ii) a double deletion strain for TF1 and TF2, and (iii) individual conditional overexpression mutants for TF1, TF2 and HD using the Tet-on system were analysed. Samples were taken at exponential and post-exponential growth phase (technical duplicate) and analysed by RNA-Seq analysis (DOI).

overall_design: mRNA profiles of MjkA and MjkB transcription factors deletion and over expression strains  in A. niger in duplicates, Illumina HiSeq

first: Min

last: Kwon


title: Molecular perturbations of hepatocytes isolated from nonheart-beating donor rats

status: Public on Nov 06 2018

city: Bronx

first: Sanjeev

last: Gupta

address: 1300 Morris Park Ave.

department: Medicine

institute: Albert Einstein College of Medicine

summary: Organs from nonheart-beating donors are attractive for use in cell therapy. Understanding the nature of molecular perturbations following reperfusion/reoxygenation would be highly significant for nonheart-beating donor cells. Nonheart-beating donor rats hepatocytes were studied for global gene expression with Affymetrix microarraays.

overall_design: Groups of rats were used for isolating hepatocytes. The experimental conditions included controls (heart-beating donors) and nonheart-beating rats at various intervals after death as test groups. Each group included samples from three different donor animals.


title: The nucleosome remodeling and deacetylase complex protein CHD4 regulates neural differentiation of mouse embryonic stem cells by down-regulating p53

city: Kyoto

first: Eisuke

last: Nishida

address: Kitashirakawa, Sakyo-ku

department: Department of Cell and Developmental Biology

institute: Graduate School of Biostudies, Kyoto University

summary: Lineage specification of the three germ layers occurs during early embryogenesis and is critical for normal development. The nucleosome remodeling and deacetylase (NuRD) complex is a repressive chromatin modifier that plays a role in lineage commitment. However, the role of chromodomain helicase DNA-binding protein 4 (CHD4), one of the core subunits of the NuRD complex, in neural lineage commitment is poorly understood. Here, we report that the CHD4/NuRD complex plays a critical role in neural differentiation of mouse embryonic stem cells (ESCs). We found that RNAi-mediated Chd4 knockdown suppresses neural differentiation, as did knockdown of methyl-CpG binding domain protein Mbd3, another NuRD subunit. Chd4 and Mbd3 knockdowns similarly affected changes in global gene expression during neural differentiation and up-regulated several mesendodermal genes. However, inhibition of mesendodermal genes by knocking out the master regulators of mesendodemal lineages, Brachyury and Eomes, through a CRISPR/Cas9 approach could not restore the impaired neural differentiation caused by the Chd4 knockdown, suggesting that CHD4 controls neural differentiation not by repressing other lineage differentiation processes. Notably, Chd4 knockdown increased the acetylation levels of p53, resulted in increased protein levels of p53. Double knockdown of Chd4 and p53 restored the neural differentiation rate. Furthermore, overexpression of BCL2, a downstream factor of p53, partially rescued the impaired neural differentiation caused by the Chd4 knockdown. Our findings reveal that the CHD4/NuRD complex regulates neural differentiation of ESCs by down-regulating p53.

overall_design: Total RNA was isolated from control cells and knockdown cells using NucleoSpin RNA kit (TaKaRa). Biotinylated sense-strand DNA was synthesized using a GeneChip WT PLUS Reagent kit (Affymetrix; Santa Clara, CA), hybridized to the Mouse Gene 2.0 ST Array (Affymetrix) and was analyzed using the GeneChip Scanner 7G System (Affymetrix). The data were analyzed by the GeneSpringGX12.6.1 software (Agilent Technologies; Santa Clara, CA).

first: Akira

last: Hirota

first: May

last: Nakajima-Koyama

first: Yuhei

last: Ashida


title: Expression Data from Liver of Rats Dosed with Reference Hepatotoxicants (Microarray)

city: North Chicago

first: Rita

last: Ciurlionis

state: IL

address: 1 North Waukegan Road

institute: Abbvie

summary:
Male Sprague Dawley rats were treated orally for 5 days with reference hepatotoxicants, each at a single dose level
alpha-naphthylisothiocyanate 100mg/kg (vehicle 5ml/kg corn oil); carbon tetrachloride 1582mg/kg (vehicle 5ml/kg corn oil); methylenedianiline 100mg/kg (vehicle 35% ethanol); acetaminophen 1000mg/kg (vehicle 2ml/kg corn oil); diclofenac 10mg/kg (vehicle 10ml/kg water)

overall_design: 3 rats were treated with each hepatotoxicant, 3 rats were treated with corresponding vehicle for each hepatotoxicant, total RNA was isolated form left lateral lobe of liver of all rats, samples run individually on Affymetrix GeneChip Rat Genome 230_2.0 Arrays

first: Mohan

last: Rao


title: Characterization of wound healing in Atlantic salmon (Salmo salar) post-smolt, and the effect of stress on the healing process

city: Aas

first: Aleksei

last: Krasnov

address: Osloveien 1

department: Fish Health

country: Norway

institute: Nofima AS

summary: The aim of this study was to assess the effect induced by high fish density on cutaneous wound healing in post-smolt Atlantic salmon.  Our findings suggest that high fish density enhances inflammation and represses cell proliferation, tissue secretion and collagen synthesis in the healing wounds. These processes are further manifested in the different layers of the skin, such as delayed re-epithelialization, altered mucus response, reduced scale mineralization, enhanced wound pigmentation and delayed organization of dense connective tissue. Temporarily changes in wound healing mechanisms result in permanent differences in wound contraction. In conclusion, our results show that high fish density dispose the fish for an enhanced immune response and delayed tissue repair, which ultimately results in delayed wound healing.

platform_organism:
Oncorhynchus mykiss
Salmo salar

overall_design: Fish were wounded with a 5 mm skin punch biopsy needle and stocked at two different densities, high fish density (100 kg/m3) and control (20 kg/m3). Samples were collected before treatment and at seven time-points: 1, 3, 7, 14, 36, 43 and 57 days post wounding (dpw)

first: Krasnov

last: Aleksei

first: Sveen

last: Lene


title: Ubc9 overexpression and SUMO1 deficiency blunt inflammation after intestinal ischemia/reperfusion.

city: Bethesda

first: Kory

last: Johnson

state: MD

address: 10/3B01, 9000 Rockville Pike

department: DIR IT & Bioinformatics

institute: NINDS/NIH

summary: The intestinal epithelium constitutes a crucial defense to the potentially life-threatening effects of gut microbiota. However, due to a complex underlying vasculature, hypoperfusion and resultant tissue ischemia pose a particular risk to function and integrity of the epithelium. The small ubiquitin-like modifier (SUMO) conjugation pathway critically regulates adaptive responses to metabolic stress and is of particular significance in the gut, as inducible knockout of the SUMO-conjugating enzyme Ubc9 results in rapid intestinal epithelial disintegration. Here we analyzed the pattern of individual SUMO isoforms in intestinal epithelium and investigated their roles in intestinal ischemia/reperfusion (I/R) damage. Immunostaining revealed that epithelial SUMO2/3 expression was almost exclusively limited to crypt epithelial nuclei in unchallenged mice. However, intestinal I/R or overexpression of Ubc9 caused a remarkable enhancement of epithelial SUMO2/3 staining along the crypt-villus axis. Unexpectedly, a similar pattern was found in SUMO1 knockout mice. Ubc9 transgenic mice, but also SUMO1 knockout mice were protected from I/R injury as evidenced by better preserved barrier function and blunted inflammatory responses. PCR array analysis of microdissected villus-tip epithelia revealed a specific epithelial contribution to reduced inflammatory responses in Ubc9 transgenic mice, as key chemotactic signaling molecules such as IL17A were significantly downregulated. Together, our data indicate a critical role particularly of the SUMO2/3 isoforms in modulating responses to I/R and provide the first evidence that SUMO1 deletion activates a compensatory process that protects from ischemic damage.

overall_design: 24 Mouse samples representing six groups with four replicates each:  WT sham at 0hrs, Ubc9Tg sham at 0hrs, WT 45mins ischemia and 3hrs reperfusion, Ubc9Tg 45mins ischemia and 3hrs reperfusion, WT 45mins ischemia and 6hrs reperfusion, and Ubc9Tg 45mins ischemia and 6hrs reperfusion.

first: Jörn

last: Karhausen

first: Joshua

last: Bernstock

first: Huaxin

last: Sheng

first: Wei

last: Yang

first: John

last: Hallenbeck

first: Wulf

last: Paschen


title: The effect of soluble CD74 (sCD74) and recombinant macrophage migration inhibitory factor (MIF) treatment on the gene expression profile in cardiac myofibroblasts

city: Aachen

first: Bernd

last: Denecke

state: NRW

address: Pauwelsstrasse 30

department: IZKF Aachen

institute: RWTH Aachen University

summary: Co-treatment with soluble CD74 and MIF induced necroptosis in cardiac myofibroblasts. The underlying mechanism of sCD74/MIF-induced necroptosis are still unkown. We used a microarray to identify pathways regulated by co-treatment with sCD74 and MIF .

overall_design: Primary isolated cardiac fibroblasts (1-7 days old) differentiated into myofibroblasts were treated with carrier, sCD74, MIF or sCD74/MIF for 8 hours. 12 samples were analysed: n=3 per group.

first: Josefin

last: Soppert

first: Sandra

last: Kraemer

first: Christian

last: Beckers

first: Luisa

last: Averdunk

first: Julia

last: Möllmann

first: Andreas

last: Goetzenich

first: Gernot

last: Marx

first: Jürgen

last: Bernhagen

last: Stoppe


title: A systems biology approach identifies ANP32E and other biomarkers of glucocorticoid refractoriness in ulcerative colitis [miRNA-Seq]

city: Derio

first: Ana

middle: Maria

last: Aransay

state: BIZKAIA

address: Parque tecnologico de Bizkaia, Building 801-A

department: Genome Analysis Platform

institute: CIC bioGUNE

summary: BACKGROUND: Glucocorticoid (GC) refractoriness is a common and unpredictable phenomenon in ulcerative colitis (UC). Although it has been demonstrated that NFkB is involved in its mechanism of action (MoA), there are no conclusive studies on the molecular functions involved. The current study describes in depth the MoA related to GC failure, by integrating transcriptomic data from UC patients, and updated molecular data on UC and GC. METHODS: miRNA and mRNA expression from rectal biopsies of active UC patients, obtained before and on the 3rd day of GC treatment, were evaluated by sequencing and microarrays, respectively. The differential results obtained were integrated into the mathematical models generated by Systems Biology. RESULTS: This computational approach identified 64 proteins, among which 18 stand out, either by being associated to the MoA or by providing a major capacity to classify the patients according to GC response. The biological functions of these proteins have been linked with inflammation, machinery GC-induced transcription and angiogenesis. All the selected proteins but one —Acidic leucine-rich Nuclear Phosphoprotein 32 family member E (ANP32E) — had previously been related to UC and/or GC-induced biological actions. ANP32E has been linked to the exchange of H2A to H2A.z histone, which promotes CG receptor complex-activated transcription. Western blot and immunofluorescence assays confirmed the predictive results obtained by Systems Biology. CONCLUSIONS: A comprehensive MoA of GC refractoriness has been described, highlighting the key role of GC-induced transcription in this phenomenon. Several proteins have been identified as putative predictors of GC refractoriness.

overall_design: Intestinal tissue from individuals with or without active ulcerative colitis (AUC) was collected and, those with AUC were characterized for their capacity to response to glucocorticoids treatment. microRNAs and mRNAs profiles were studied for each sample by microRNAseq and gene expression microarray, respectively.

first: Violeta

last: Lorén

first: Arce

last: Garcia-Jaraquemada

first: Juan

last: Naves

first: Xavier

last: Carmona

first: Míriam

last: Mañosa

first: José

last: Lavin

first: Ivelisse

last: Sánchez

first: Eduard

last: Cabré

first: Josep

last: Manyé

first: Eugeni

last: Domènech


title: A systems biology approach identifies ANP32E and other biomarkers of glucocorticoid refractoriness in ulcerative colitis [microarray]


title: A systems biology approach identifies ANP32E and other biomarkers of glucocorticoid refractoriness in ulcerative colitis

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

overall_design: Refer to individual Series


title: 10x Genonics single-cell RNA-seq of immature (P6) ID4-EGFP mouse spermatogonia & testis cells

city: San Antonio

first: Brian

middle: P.

last: Hermann

address: 1 UTSA Circle

institute: University of Texas at San Antonio

summary: To reveal distinct transcriptomes associated with spermatogonial stem cell renewal vs. initiation of differentiation, single-cell transcriptomes from P6 ID4-EGFP+ spermatogonia (sorted for brightest or dimmest) or unselected testis cells were used for Drop-Seq analysis. The GFP-bright and dim phenotypes exhibit distinct fates when assayed by transplantation, with ID4-EGFPbright cells highly enriched for SSCs, and ID4-EGFPdim cells enriched for progenitors. We used the 10x Genomics Chromium (a commercial Drop-Seq variant) to perform single-cell RNA-seq

overall_design: Unselected or sorted P6 ID4-EGFP+ spermatogonia (sorted separately as EGFP-bright or EGFP-dim) were used for this study. Data are from a total of 13,094 cells.

first: Keren

last: Cheng

first: Anukriti

last: Singh

first: Lorena

last: Roa-de-la-Cruz

first: Kazadi

last: Mutoji

first: Heidi

last: Gildersleeve

first: I-Chung

last: Chen

first: Max

last: Mayo

first: Birgit

last: Westernströer

first: Nate

last: Law

first: Melissa

last: Oatley

first: Ellen

middle: K

last: Velte

first: Bryan

middle: A

last: Niedenberger

first: Danielle

last: Fritze

first: Sherman

last: Silber

first: Christopher

last: Geyer

first: Jon

first: John

last: McCarrey


title: Striated-for-smooth muscle replacement in the developing mouse esophagus

status: Public on Nov 01 2018

city: Halifax

first: Boris

last: Kablar

state: Nova Scotia

address: 5850 College Street

department: Medical Neuroscience

country: Canada

institute: Dalhousie University

summary: The esophagus is a muscular tube which transports swallowed content from the oral cavity and the pharynx to the stomach. Early in mouse development, an entire layer of the esophagus, the muscularis externa, consists of differentiated smooth muscle cells. Starting shortly after mid-gestation till about two weeks after birth, the muscularis externa almost entirely consists of striated muscle. This proximal-to-distal replacement of smooth muscle by the striated muscle depends on a number of factors. To identify the nature of the hypothetical “proximal” (mainly striated muscle originating) and “distal” (mainly smooth muscle originating) signals that govern the striated-for-smooth muscle replacement, we compared the esophagus of Myf5:MyoD null fetuses completely lacking striated muscle to the normal control using cDNA microarray analysis, followed by a comprehensive databases search. Here we provide an insight into the nature of “proximal” and “distal” signals that govern the striated-for-smooth muscle replacement in the esophagus.

overall_design: Mouse embryos were obtained at E18.5 for RNA extraction and hybridization on Affymetrix microarrays.

first: Mark

last: Baguma-Nibasheka

first: Anna

last: Fracassi

first: Willard

middle: J

last: Costain

first: Sandra

last: Moreno


title: Rel2-mediated transcriptional repression regulates vegetative and reproductive architecture in maize

status: Public on Nov 02 2018

city: Piscataway

first: Andrea

last: Gallavotti

state: New Jersey

address: 190 Frelinghuysen Rd

department: Waksman Institute

institute: Rutgers University

summary: RNA-seq was performed on 2-3mm WT and rel2-ref mutant maize tassels

first: Mary

last: Galli


title: Identifying regulatory network governed by Candida albicans SREBP transcription regulators

status: Public on Nov 05 2018

city: Würzburg

first: Valentina

last: del Olmo Toledo

state: Bayern

address: Josef-Schneider-Str. 2/D15

institute: Institute of Molecular Infection Biology

summary: Goal: We employed RNA-seq to identify targets of regulation of the Candida albicans SREBP transcription regulators Cph2 and Hms1.

overall_design: Comparison of the transcriptome of Candida albicans wild-type reference strain vs. two transcription regulator deletion mutants. One growth condition, two biological replicates per sample. RNA-seq data generated with Illumina HiSeq2500.

first: J

last: Pérez


title: Tobacco transcriptomic changes induced by C. sph. MVOC

city: Kearneysville

first: Chris

last: Dardick

state: WV

address: 2217 Wiltshire Road

department: Appalachian Fruit Research Station

institute: USDA-ARS

summary: Transciptomic changes in tobacco (Nicotiana tabacum cv. Samsun) following exposure to microbial volatile organic compounds (MVOCs) emitted by Cladosporium sphaerospermum isolate TC09 (NRRL 67603) were investigated. Germinated seedling plants were cultured in Magenta GA7 vessels containing Murashige and Skoog (MS) medium supplemented with 30 g/L sucrose with and without fungal cultures that were included in the vessel but placed in a separated container. Ten days after the onset of MVOC exposure, tissue samples including the apical meristem and terminal leaves were collected and subject to RNA sequencing and transcriptome analysis using available tomato genome as reference. Our study revealed massive number of differentially expressed genes (DEGs) associated with diverse biological processes including cell expansion and cell cycle, photosynthesis, phytohormone homeostasis and defense responses as a consequence of short-term exposure to potent MVOCs.

overall_design: Two exposure treatments (control without exposure and MVOC exposed), 4 biological replicates per treatment, 3 seedling plants er replicate

first: Zhijian

middle: T

last: Li

first: Wojciech

last: Janisiewicz

first: Zongrang

last: Liu

first: Ann

last: Callahan

first: Breyn

last: Evans

first: Wayne

last: Jurick

middle: D


title: DNA binding preferences of fungal SREBP transcription regulators

summary: Goal: We employed ChIP-seq to identify direct targets of regulation of the Candida albicans SREBP transcription regulator Cph2.

overall_design: Full genome chromatin immunoprecipitation of Candida albicans wild-type reference strain vs. a myc-tagged version of a transcription regulator. One growth condition, three biological replicates of the mutant and one untagged control. ChIP-seq data generated with Illumina HiSeq2500.

middle: C


title: RNA Seq to study gene expression changes mediated by phase-variable DNA methyltransferases in non-typeable Haemophilus influenzae

city: Gold Coast

first: John

middle: Michael

last: Atack

state: QLD

address: Gold Coast Campus

department: Institute for Glycomics

country: Australia

institute: Griffith University


title: Haemophilus influenzae strain 1209 RNA SEQ NTHi modA9

summary: comparison of RNA expression profiles from NTHi strain 1209 strains expressing methyltransferase ModA9 (ON) or not (OFF)

overall_design: RNA isolated from triplicate cultures of each strain (modA9 ON and modA9 OFF) grown in sBHI to mid-log; comparison of gene expression profiles by comparing modA9ON vs modA9 OFF to determine differential gene expression influenced by ModA2 methylation differences

middle: M

first: Michael

middle: P

last: Jennings


title: Haemophilus influenzae strain C486 RNA SEQ NTHi modA4

summary: comparison of RNA expression profiles from NTHi strain C486 strains expressing methyltransferase ModA4 (ON) or not (OFF)

overall_design: RNA isolated from triplicate cultures of each strain (modA4 ON and modA4 OFF) grown in sBHI to mid-log; comparison of gene expression profiles by comparing modA4ON vs modA4 OFF to determine differential gene expression influenced by ModA2 methylation differences


title: Haemophilus influenzae strain 477 RNA SEQ NTHi modA5

summary: comparison of RNA expression profiles from NTHi strain 477 strains expressing methyltransferase ModA5 (ON) or not (OFF)

overall_design: RNA isolated from triplicate cultures of each strain (modA5 ON and modA5 OFF) grown in sBHI to mid-log; comparison of gene expression profiles by comparing modA5ON vs modA5 OFF to determine differential gene expression influenced by ModA2 methylation differences


title: RNA-seq Analysis of U87: Ctrl, U87:EGFR, U87:EGFRvIII, U87:EGFR+EGFRvIII and U87:EGFR+EGFRvIII KRAS KO

city: San Francisco

first: Zhenyi

last: An

department: Neurology

institute: UCSF

summary: We found that U87 cells expressing EGFR and EGFRvIII upregulated a large group of cytokines. The upregulation of many of these cytokines was dependent on KRAS.

overall_design: Examination of transcriptome in 5 different cell lines

first: William

last: Weiss


title: Maternal exposure to high temperature in fish induces intergenerational emotional and cognitive disorders, associated with dysregulation of neurodevelopment genes in eggs and progeny

city: Rennes

first: Aurelie

last: LE CAM

address: Campus de Beaulieu

department: PHASE

institute: INRA

summary: Female fish are known to be sensitive to temperature during reproduction, but the long-term consequences on offspring adaptive behaviour and their underlying intergenerational mechanisms remain unknown. We studied the intergenerational consequences of female rainbow trout (Oncorhynchus mykiss) exposure to high (17°C) or normal temperature (12°C) on offspring behavioural phenotypes. We also analysed genome-wide gene expression in eggs and embryos to elucidate the mechanisms by which thermal maternal exposure impacts offspring behaviour. Here we show that a thermal maternal stress induces emotional and cognitive disorders in offspring. Fear responses to a novel environment were inhibited in 17°C offspring indicating global emotional blunting. Thermal stress in mothers also decreased spatial learning abilities in progeny. Behavioural phenotypes were associated with the dysregulation of several genes known to play major roles in neurodevelopment. This is especially true for auts2, a key gene for neurodevelopment in fish and mammals, more specifically neuronal migration and neurite extension, and critical for the acquisition of neurocognitive function in fish and mammals. In addition to auts2, our analysis revealed the dysregulation of another neurodevelopment gene (dpysl5) as well as genes associated with human cognitive disorders (arv1, plp2). Our study also revealed major differences in maternal mRNA abundance in the eggs following maternal exposure to high temperature indicating that some of the observed intergenerational effects are mediated by maternally-inherited mRNAs accumulated in the egg. Together, our observations shed new light on the intergenerational determinism of fish behaviour and associated underlying mechanisms. They also stress the importance of maternal history on fish adaptive capacities in a context of global climate changes.

overall_design: Two-year old females rainbow trout were exposed to either 12°C (12°C group, standard reproduction conditions) or 17°C (17°C group, high suboptimal temperature) for six weeks before ovulation. The temperature of 17°C was selected because it is known to induce a dramatic decrease in embryonic survival {Aegerter, 2004 #2630}. For each group, 30 marked (external tag placed on the dorsal fin) females were kept in 2.5 m3 tanks (2 x 2 x 0.62 m, length × width × water height). In the 17°C group, females initially reared at 12°C were acclimated for five days to an increase of 1°C/day until 17°C. For three weeks preceding ovulation, females were checked every two-three days to detect ovulation. In both experimental group, eggs originating from four simultaneously ovulating females of each group were collected and fertilized using a pool of sperm collected from four males held at 12°C. Fertilization was performed immediately in both groups in order to avoid any bias on subsequent behavioural phenotypes that would have been induced by differences during embryo development. For each of the eight females, fertilizations of 800 eggs were performed at 10°C using the medium ActiFish (IMV, L'Aigle, France; 100 ml ActiFish + 400 ml water) and fertilized eggs were distributed within a tray (20 x 50 cm) in two incubators (10 x 10 cm) (approximately 400 eggs/incubator and two incubators/tray) supplied with 10°C flow-though recycled water. Each tray was covered with a lid to avoid exposure to light.

first: Violaine

last: Colson

first: Morgane

last: Cousture

first: Danielle

last: Zanerato-Damasceno

first: Claudiane

last: Valotaire

first: Thaovi

last: Nguyen

first: Aurélie

last: Le Cam

first: Julien

last: Bobe


title: Study of microRNA associated with anti-tumor effect of galectin-9 in esophageal squamous cell carcinoma cell line

city: Kamakura

first: Satoshi

last: Kondo

state: Kanagawa

address: Tebiro 6-10-1

department: New Projects Development Division

institute: Toray Industries,Inc.

summary: The miRNAs expression was markedly altered with the treatment of galectin-9 in vitro and various miRNAs induced by galectin-9 also may contribute to tumor growth in vitro.

overall_design: Using a custom microarray platform, we analyzed the expression levels of 2555 human miRNA probes in KYSE150 cell line in vitro that was treated with and without galectin-9.

first: T

last: Chiyo

last: Masaki


title: Candida albicans SREBP transcription regulators

first: Valentina

last: del Olmo Toledo


title: JAK2V617F but not CALR mutations confer increased molecular responses to interferon-alpha via JAK1/STAT1 activation

status: Public on Oct 29 2018

first: Bernd

last: Denecke

summary: Pegylated interferon-alpha (peg-IFNa) treatment induces molecular remissions (MR) in patients with myeloproliferative neoplasms (MPN), including partial MR (PMR) in 30-40% of patients. Here, we compared the efficacy of IFNa treatment in JAK2V617F vs. CALR-mutated cells and investigated the mechanisms of differential response. Retrospective analysis of MPN patients treated with peg-IFNa demonstrated that patients harboring the JAK2V617F mutation were more likely to achieve PMR than those with mutated CALR (p=0.004), while there was no significant difference in hematological response. In vitro experiments confirmed an upregulation of interferon-stimulated genes in JAK2V617F-positive 32D cells compared to their CALR-mutated counterparts, and higher IFNa doses were needed to achieve the same IFNa response in CALR- as in JAK2V617F mutant 32D cells.

overall_design: 4 Total samples were analyzed.

first: Julia

last: Czech

first: Julian

last: Baumeister

first: Tiago

last: Maié

first: Ivan

middle: G

last: Costa

first: Claudia

last: Schubert

first: Deniz

last: Gezer

first: Nicolas

last: Chatain

first: Steffen

last: Koschmieder


title: Loss or oncogenic mutation of DROSHA impairs kidney development and function, but is not sufficient for Wilms tumor formation

status: Public on Oct 30 2018

city: Wuerzburg

first: Philip

last: Kruber

address: Am Hubland

department: Physiological Chemistry

institute: University of Wuerzburg

summary: To characterize the in vivo role of DROSHA mutations during kidney development and their oncogenic potential, we analyzed mouse lines with either a targeted deletion of Drosha or an inducible expression of human DROSHA carrying a tumor-specific E1147K mutation that acts in a dominant negative manner.

overall_design: Examination of miRNA expression of whole E16.5 kidneys in two different mouse lines

first: Manfred

last: Gessler


title: Long noncoding RNA and mRNA expression profiling following igf3 knockdown in common carp (Cyprinus carpio)

status: Public on Oct 27 2018

city: Wuxi

first: Lanmei

last: Wang

address: East Shanshui Road 9

institute: Freshwater Fisheries Research Centre of Chinese Academy of Fishery Sciences

summary: Growth and reproduction are two major physiological processes that are closely related in vertebrates, and IGFs are key factors that regulate the growth and reproduction axis. As a novel IGF system member, igf3 plays an important role in gonadal development of teleost fish. Although studies have reported the abnormal expression of igf3 in fish gonad, whether the igf3 regulates the expression of long noncoding RNAs (lncRNAs) in gonad remains unknown. In this study, a igf3 knockdown common carp (Cyprinus carpio) model was established by RNA interference. Than RNA sequencing of transcriptome in C. carpio after igf3 knockdown was performed. A total of 327,169,410 and 306,305,018 clean reads were identified from control and igf3-dsRNA group, respectively. After a stringent filtering, RNA-seq yielded 14199 lncRNA and 106932 mRNA transcripts with 124 and 353 differentially expressed lncRNAs and mRNAs. Gene Ontology analysis revealed that the target genes of differentially expressed lncRNAs and mRNAs mainly regulated male genitalia development, female gonad development, cellular response to gonadotropin-releasing hormone, insulin-like growth factor-activated receptor activity and insulin-like growth factor binding. Kyoto Encyclopedia of Genes and Genomes analysis showed that the target genes of differentially expressed lncRNAs and mRNAs mainly involved in pathways associated with insulin signaling pathway, GnRH signaling pathway, Wnt signaling pathway, PI3K-Akt signaling pathway and TGF-beta signaling pathway. The lncRNA-mRNA co-expression network highlight the inter-regulation of the differentially expressed lncRNAs and mRNAs in gonad. Our results provide essential data regarding differentially expressed lncRNAs and mRNAs after igf3 knockdown, which may be useful to elucidate the role of igf3 in the gonadal development of C. carpio.

overall_design: lncRNAs and mRNAs after igf3 knockdown in common carp were detected by deep sequencing using Illumina HiSeq X (BioProject Accession: PRJNA493964).

first: Feibiao

last: Song

first: Wenbin

last: Zhu

first: Zaijie

last: Dong

first: Zhenzhen

last: Yu

first: Jianjun

last: Fu

first: Mingkun

last: Luo


title: Application of Chromatrap® Solid-State Chromatin Immunoprecipitation (ChIP) for epigenetic profiling of insects

city: Swansea

first: Tomas

middle: Nicholas

last: Generalovic

state: West Glamorgan

address: Swansea University, Singleton Campus

department: Bioscience

institute: Swansea University

summary: We report the application of Chromatraps® Solid-State Chromatin Immunoprecipitation technology for epigenetic profiling of histone modifications in insects. Here, we present the optimised protocol and conditions of Chromatrap® kits for successful ChIP and high-throughput sequencing of established model species, Drosophila melanogaster and the emerging model for behavioural plasticity Nicrophorus vespilloides. We highlight successful ChIP-seq of Drosophila melanogaster (Oregon-R) of comparable quality to modENCODE data and present successful enrichment of histone marks for Nicrophorus vespilloides. The addition of this insect-based ChIP-seq protocol provides a set of optimal guidelines to aid streamline end-users epigenetic research focus and reduce experimental time.

sample_organism:
Drosophila melanogaster
Nicrophorus vespilloides

overall_design: Optimization of ChIP-seq protocol for insect tissue of two species; Drosophila melanogaster (strain: Oregon-R) and Nicrophorus vespilloides at two different life stages; 3rd instar larvae and adult whole brains respectively. Four replicates per insect investigated using one antibody; H3K4me3 including input controls for each ChIP assay.

middle: N

first: Christopher

middle: B

last: Cunningham

first: Amy

last: Johnson


title: Quantitative RNAseq analysis of Ugandan KS tumors reveals KSHV gene expression dominated by transcription from the LTd downstream latency promoter

city: Seattle

first: Timothy

last: Rose

state: WA

address: 1900 Ninth Ave., 8th floor

institute: Seattle Children’s Research Institute

summary:
Purpose: We used RNA deep sequencing to characterize KSHV expression in a large collection of KS biopsies (n=41) from HIV-infected Ugandans.  Using a novel approach to quantitate expression in complex genomes like KSHV, we found that RNA from a single KSHV promoter within the latency region constituted the majority of KSHV transcripts in the KS tumors.  Alternate RNA processing produced different spliced and un-spliced transcripts with different coding potentials.  Differential expression of other KSHV genes was detected which segregated the tumors into three different types depending on their expression of lytic or latency genes.  Quantitative analysis of KSHV expression in KS tumors provides an important basis for future studies on the role of KSHV in the development of KS

Methods: Total nucleic acids were extracted using RLT buffer (Qiagen) and then RNA was isolated using the RNeasy mini kit with DNAse treatment step.  Total RNA integrity was checked using an Agilent 2200 TapeStation (Agilent Technologies, Inc., Santa Clara, CA) and quantified using a Trinean DropSense96 spectrophotometer (Caliper Life Sciences, Hopkinton, MA).  Unstranded RNA-seq libraries were prepared from 300 ng of total RNA using the TruSeq RNA Sample Prep Kit v2 (Illumina, Inc., San Diego, CA, USA).  Four KS tumors libraries were prepared using the TruSeq Stranded mRNA Library Kit (Illumina) from 100 ng of total RNA.  Library size distributions were validated using an Agilent 2200 TapeStation (Agilent Technologies, Santa Clara, CA, USA).  Additional library QC, pooling of indexed libraries, and cluster optimization was performed using Life Technologies’ Invitrogen Qubit® 2.0 Fluorometer (Life Technologies-Invitrogen, Carlsbad, CA, USA).  The unstranded RNA-seq libraries were pooled (5-plex) and the stranded libraries were pooled (4-plex) and each pool was clustered onto a flow cell lane.  Sequencing was performed using an Illumina HiSeq 2500 in “High Output” mode with a paired-end, 50 base reads (PE50) sequencing strategy for the unstranded libraries and non-paired end for the stranded libraries.  Image analysis and base calling was performed using Illumina's Real Time Analysis v1.18 software, followed by 'demultiplexing' of indexed reads and generation of FASTQ files, using Illumina's bcl2fastq Conversion Software v1.8.2.

Analysis: Low-quality reads were removed prior to alignment to the KSHV (aka HHV-8) reference sequence (accession number NC_009333 for the KSHV GK18 strain) using TopHat2 (version 2.0.14) in a local instance of Galaxy. For quantitation purposes, the reads from paired-end libraries (non-stranded) were analyzed as unpaired (single-end data) to allow each read of the pair to map unambiguously to a single gene feature.  The reads from both strands of the stranded libraries (non-paired end) were either concatenated and analyzed together (librarytype=unstranded) for comparison to the non-stranded paired end libraries or were analyzed separately (librarytype=FR) to show strand specificity.  TopHat2 was used to detect splicing events ab initio.  The default presets were used except that the maximum intron length was decreased to 10,000 and the maximum number of alignments allowed was decreased from 20 to 1, to avoid overcounting reads to repetitive regions.  HTSeq (version 0.6) was used to quantitate the reads mapping to the unique set of UCDS gene features within the novel revised gene feature file "KSHV NC_009333 UCDS ver 121715.gff".  The “intersection (non-empty)” setting in HTSeq was used to count all reads mapping completely or partially to a UCDS feature to maximize read count (featuretype=UCDS; IDattribute=gene). No reads were eliminated by ambiguity since the UCDS features were 50 bp apart, the length of a read.  The read count was expressed as transcripts per million (TPM) by first normalizing the read count to reads per kilobase (RPK) by dividing the read counts by the length of the UCDS gene feature, in kilobases.  The “per million” scaling factor was determined by summing all of the RPK values in a sample and dividing by 1,000,000.  Each RPK value was then divided by the “per million” scaling factor to give TPM of mapped KSHV reads.  Hierarchical clustering of TPM normalized expression levels was performed using the algorithm implemented in CIMminer.  Hierarchical clustering of the gene correlation matrix was performed by calculating the Pearson correlation between the normalized transcript levels (TPM) associated with each pair of UCDS gene features, using a script in R to create and output the correlation matrix.  Shiny web applications were developed for R-based principal component analysis (available at https://efg-ds.shinyapps.io/pcaApp/) and boxplot analysis of gene expression levels (available at https://efg-ds.shinyapps.io/boxplotApp/).

Conclusions: We have used RNAseq to analyze and quantitate KSHV gene expression in a large collection of 41 KS tumor biopsies from HIV-infected individuals in Uganda that were naïve to ART.  The RNAseq libraries were sequenced to an average depth of 100 million reads yielding up to 159,000 KSHV-mapped reads, and RNA reads mapping to non-overlapping UCDS features were quantitated using the new UCDS gene feature file.  Phylogenetic analysis of the complete ORF75 sequence revealed the presence of at least six different KSHV strains in these tumor samples.  We identified a set of transcripts from the latency region at the right end of the genome that was highly and consistently expressed in all the KS tumors.  Variable expression of genes involved with transcription regulation and immune modulation was observed, with minimal expression of genes involved with viral replication, virion structure, or assembly.  No correlation was observed between the KSHV transcript patterns detected in macular, nodular or fungating KS lesions.  In contrast, the transcript patterns of different tumor lesions from the same individual showed the most similarity regardless of the tumor morphotype.

overall_design: Examine KSHV (HHV-8) viral transcriptome in 41 Kaposi's sarcoma skin biopsies with different morphotypes

first: A

last: Bruce

first: Serge

last: Barcy

first: Matt

last: Fitzgibbon

first: Minako

last: Ikoma

first: Corey

last: Casper

first: Jackson

last: Orem

first: Warren

last: Phipps


title: Expression data from the kidney of Sprague-Dawley rats given colistin methanesulfonate sodium

status: Public on Oct 26 2018

city: Daejeon

first: Jung-Hwa

last: Oh

address: 141 Gajeong-ro, Yuseong

country: South Korea

institute: Korea Institue of Toxicology

summary:
To investigate the mechanism of nephrotoxicity, colistin methanesulfonate sodium (CMS; 25 or 50 mg/kg) was administered via intraperitoneal injection to Sprague–Dawley rats daily over 7 d.
Affymetrix GeneChip microarrays indicated 894 differentially expressed genes in groups treated with CMS (ANOVA, FDR < 0.05, fold change ≥ 1.3).

overall_design: The Affymetrix GeneChip Rat 230 2.0 (Affymetrix, Santa Clara, CA, USA) was used for microarray analysis. We randomly selected three rats from each CMS-treated group (0, 25, and 50 mg/kg). Microarray analysis was conducted according to the GeneChip® 3' Expression Arrays User Guide (Affymetrix). cDNA synthesis, cRNA synthesis, biotin labeling, cRNA purification, and fragmentation were performed according to the manufacturer’s instructions (Affymetrix). The microarrays were hybridized at 45°C at 60 rpm for 16 h. The microarrays were stained and washed using a Fluidics Station 450 system (Affymetrix). A GeneChip® Scanner 3000 (Affymetrix) was used to scan the microarrays. The reproducibility of the microarray experiments was confirmed using well-defined quality control criteria according to the manufacturer’s instructions.

first: Seokjoo

last: Yoon


title: Expression data of T, DC, and TDC sorted from spleens of naive C57BL/6 mice

city: Milan

first: Mirela

last: Kuka

address: Via Olgettina, 58

country: Italy

institute: Vita-Salute San Raffaele University

summary: TDC are an hematopoietic cell subset identified and characterized by Mirela Kuka, Ivana Munitic and Jonathan D. Ashwell (Kuka et al., 2012, Nat Commun). TDC combine dendritic cell (DC) and conventional ab T cell markers and functional properties. Such duality might render TDC particularly responsive to infectious organisms, because they can bridge innate and adaptive traits. This novel cell subset substantially differs from other known innate T cells in many ways: they undergo an antigen-specific selection process indistinguishable from classical ab cells, they can proliferate in response to cognate antigens, and they lack markers of NKT or gd T cells. The expression data found in this dataset confirm that TDC have a genetic signature distinct from that of classical DC or of conventional T cells. This distinct genetic profile identifies them as a separate cell type and raises the possibility that TDC may have functions other than those of T and DC.

overall_design: Three cell subsets (T, DC, and TDC) were sorted from spleens pooled from 12 naive C57BL/6 mice. Total RNA was isolated with the RNeasy Micro kit (Qiagen). Microarray gene expression was performed by the Laboratory of Molecular Technology (NCI), with Affymetrix 430 2.0 GeneChip technology after RNA was amplified with a NuGEN WT-Ovation kit (Nugen).

first: Ivana

last: Munitic

first: Jonathan

last: Ashwell


title: RNA Sequencing Facilitates Quantitative Analysis of differentially expressed genes during  human erythroipoiesis

city: TianJin

first: Hua

middle: Jin

last: Liu

address: 288 Nanjing Road

department: State Key Laboratory of Experimental Hematology

institute: Chinese Academy of Medical Sciences & Peking Union Medical College

summary:
Purpose: The goals of this study are to determine the differentially expreseed non-coding RNAs during human erythropoiesis
Methods:gene expression profiling with cells on days 4,8,11,14 during erythroid differentiation, with two replicated using Illumina Genome Analyzer IIx. qRT–PCR validation was performed using TaqMan and SYBR Green assays.
Conclusions: ncRNAs were differentially expressed during erythroid differentiation

overall_design: mRNA profiles of day4,8,11,14 erythroid cells were generated by deep sequencing, in duplicate.

first: Lihong

last: Shi


title: UV-protection timer controls a trade-off between skin protection systems

city: Tel Aviv

first: Carmit

last: Levy

address: Ramat Aviv

department: Human Genetics and Biochemistry

country: Israel

institute: Tel Aviv University

summary: Tanning is a skin protection mechanism against UV radiation. Pigment production initiates hours after exposure, and the mechanism controlling this delay was unknown. Here we reveal a skin UV-protection timer, governed by damped oscillatory dynamics of the melanocyte master regulator, MITF, which after UV exposure, synchronizes regulatory programs, first cell survival and later pigmentation. Remarkably, the same amount of UV dosage resulted in higher pigmentation of human skin when given every-other day compared to daily exposure. Daily UV exposure appears to perturb MITF dynamics, thus re-ordering the survival and pigmentation programs. This demonstrates that the skin is more sensitive to frequency than quantity of UV exposure. Mathematical modeling identified a double negative regulatory loop involving HIF1a and microRNA-148a that regulates MITF dynamics. Our study suggests evolutionary leverage of the UV-protection timer, as it evolved to induce maximum protection with minimum damage for the reduction of skin cancer risk.

overall_design: We analyzed 10 RNA samlpes from MNT-1 melanoma line upon treatment with cAMP (which mimic the sun exposure signaling) using Affymetrix Clarioum S Human Array platform. No techinical replicates were performed.

first: Hagar

last: Malcov

first: Ayelet

last: Alpert


title: Expression data from retinal pigment epithelium in pigmented and albino mouse embryos

status: Public on Oct 25 2018

city: New York

first: Lena

last: Iwai-Takekoshi

address: 3227 Broadway, Room L3-043, Quad 3C

department: Pathology and Cell Biology

country: USA

institute: Columbia University

summary:
In mammalian albinism, disrupted melanogenesis in the retinal pigment epithelium (RPE) is associated with fewer retinal ganglion cells (RGCs) projecting ipsilaterally to the brain, resulting in numerous abnormalities in the retina and visual pathway, especially binocular vision.
To further understand the molecular link between disrupted RPE and a reduced ipsilateral RGC projection in albinism, we compared gene expression in the embryonic albino and pigmented mouse RPE.

overall_design: Embryonic day (E) 13.5 mouse RPE was detached from the eyes.  Three biological replicates were analyzed. For each biological replicate (pigmented and albino), RPE tissues of three - four littermate embryos were pooled.

first: Carol

last: Mason


title: Genome-wide analysis of circular RNAs in Goat skin fibroblast cells (GSF cells) in response to Orf virus infection

city: Haikou

first: Feng

last: Pang

address: Renmin Road 58

country: China

institute: Hainan University

summary: To find out differently expressed  circRNAs during Orf virus infection of GSF cells and their potential roles in response to ORFV infection

overall_design: Three mock GSF samples and three ORFV-infected GSF samples (OV samples)

first: Fengyang

last: Wang


title: Mapping replication domains using the Ion Torrent semiconductor sequencing platform [BrdU-IP]

status: Public on Oct 19 2018

city: Tsu

first: Shin-ichiro

last: Takebayashi

state: Mie

address: 2-174, Edobashi

department: Graduate School of Medicine

country: Japan

institute: Mie University

summary: We show that semiconductor-based sequencing technology can be used to map mammalian replication domains, chromosomal units with similar DNA replication timing. Replicating DNA purified from mammalian cells was successfully sequenced by the Ion Torrent platform. The resultant replication domain map of mouse embryonic cells is comparable to those obtained by the conventional microarray-based method.

overall_design: Analysis of early and late replicating chromosomal regions in mouse embryonic stem cells