title: The small RNA Teg41 Regulates Expression of the alpha Phenol Soluble Modulins and is Required for Virulence in Staphylococcus aureus

city: Athens

first: Ronan

middle: Kevin

last: Carroll

state: OHIO

address: 107 Irvine Hall

department: Biological Sciences

institute: Ohio University

summary: Small RNAs (sRNAs) remain an understudied class of regulatory molecules in bacteria.  Hundreds of sRNAs have been identified in the major human pathogen Staphylococcus aureus; however, only a few have been characterized in detail.  In this study we investigate the role of the sRNA Teg41 in S. aureus virulence.  We demonstrate that Teg41, an sRNA divergently transcribed from the locus that encodes the cytolytic alpha phenol soluble modulin (αPSM) peptides, plays a critical role in αPSM production.  Overproduction of Teg41 leads to an increase in αPSM levels and a corresponding increase in hemolytic activity from S. aureus cells and cell-free culture supernatants.  We demonstrate that the increase in αPSM production is post-transcriptional, as expression of the αPSM transcript is unaltered upon Teg41 overproduction. To identify regions of Teg41 important for its function we performed an in silico RNA:RNA interaction analysis which predicted an interaction between the 3’ end of Teg41 and the αPSM transcript.  Deleting a 24-nucleotide region from the S. aureus genome, corresponding to the 3’ end of Teg41, led to a 10-fold reduction in αPSM-dependent hemolytic activity and attenuation of virulence in a murine abscess model of infection.  Together these results demonstrate, for the first time, post-transcriptional regulation of the αPSM peptides by an sRNA in S. aureus.

overall_design: Six data sets in total.  Three biological replicates from wild type S. aureus cells and three biological replicates from the wild type overproducing the sRNA Teg41

last: Zapf

first: Richard

middle: E

last: Wiemels

first: Rebecca

last: Keogh

first: Emily

last: Trzeciak

first: Kayla

last: Howell

first: Kellie

last: King

first: Andrew

last: Caillet

first: Samantha

last: Selhorst

first: Donald

last: Holzschu

first: Jeffrey

last: Bose

middle: K


title: Gastric Lgr5+ stem cells secrete antimicrobial proteins to shield against infection

status: Public on Jan 01 2019

city: Berlin

first: Hans-Joachim

last: Mollenkopf

address: Charitéplatz 1

country: Germany

institute: Max-Planck-Institute for Infection Biology

summary: R-spondin (Rspo) signaling is crucial for stem cell renewal and tissue homeostasis in the gastrointestinal tract. In the stomach, Rspo is secreted from myofibroblasts and controls epithelial gland regeneration by inducing proliferation of Wnt-responsive Axin2+ cells. Infection with H. pylori results in increased expression of stromal Rspo, leading to an expansion of Axin2+ isthmus stem cells and gland hyperplasia. Lgr5+ stem cells are exposed to Rspo3 but the effects of this are not well understood. Here we demonstrate that in addition to its effect as a mitogen, endogenous Rspo3 regulates the gene expression of Lgr5+ cells in the gland base in both antrum and corpus. Rspo3 inhibits proliferation and induces differentiation within the Lgr5+ compartment towards a secretory phenotype. Strikingly, the Rspo3-Lgr5 axis turns out to be required for epithelial antimicrobial defense. Infection with H. pylori induces a strong antimicrobial response, with Lgr5+ cells expressing antimicrobial compounds that are secreted into the lumen in an Rspo3-dependent manner. Depletion of Lgr5+ cells or knockout of Rspo3 in myofibroblasts leads to dramatic hyper-colonization of gastric glands, including the stem cell compartment, whereas systemic application of recombinant Rspo is sufficient to clear H. pylori from the glands. We provide an intriguing, unexpected feature of Lgr5+ cells, exhibiting an indivisible connection between stem cell signaling and antimicrobial self-protection.

overall_design: Microarray experiments were performed as dual-color hybridizations on Agilent whole mouse catalog 4x44K (Agilent-014868) arrays. To compensate for dye-specific effects, a dye-reversal color-swap was applied.

first: Michael

last: Sigal

first: Stefanie

last: Müllerke

first: Hilmar

last: Berger

first: Manuel

last: Amieva

first: Thomas

last: Meyer


title: The methyltransferase HEN1 is required in Nematostella vectensis for microRNA and piRNA stability as well as larval metamorphosis

city: Plymouth, Devon

first: vengamanaidu

last: modepalli

address: The Laboratory,Citadel Hill

department: Cell and Molecular

country: United Kingdom

institute: Marine Biological Association of the UK

type: Non-coding RNA profiling by high throughput sequencing

summary: knockdown of HEN1 in Nematostella results in a developmental arrest. Small RNA sequencing revealed that the levels of both miRNAs and piRNAs drop dramatically in the morphant animals.

overall_design: Employ height throughput sequence of endogenous small RNAs

first: V

last: Modepalli

first: A

last: Fridrich

first: Y

last: Moran


title: Genomic resemblance of mouse models to human hepatocellular carcinoma matogenous metastasis of ovarian cancer: Re-thinking mode of spread

city: Houston

first: Sangbae

last: Kim

state: TX

address: 1 Baylor plaza

department: HGSC

country: USA

institute: Baylor Colleage of Medicine

summary: Two groupsHepatocellular carcinoma (HCC) is a heterogeneous malignant disease with molecularly and clinically distinct subtypes discovered in genomic studies. Mouse models are commonly used as preclinical model to study hepatocarcinogenesis, but how well these models recapitulate molecular subtypes of human HCC is unclear. Thus, we aimed to correlate nine mouse HCC models with clinical subtypes of human HCC by systematically comparing their genomic data. By integrating nine molecularly and clinically defined genomic signatures for human HCC with genomic data from nine mouse HCC models, we identified the mouse models that best resembled subtypes of human HCC and determined the clinical relevance of each model. Mst1/2 KO, Sav1 KO, and SV40 T antigen mouse model best recapitulated poor prognostic subtypes of human HCC, whereas the Myc transgenic model best resembled human HCCs with more favorable prognoses. The Myc model was also significantly associated with activation of β-catenin. E2f1, E2f1/Myc, E2f1/Tgfa, and diethylnitrosamine (DENA)-induced models were heterogeneous and were unequally split to poor and favorable prognoses. Most interestingly, Mst1/2 KO and Sav1 KO models best resembles human HCC with hepatic stem cell characteristics.  When we applied a genomic predictor for immunotherapy, the six-gene interferon-γ (IFNG6) score, Mst1/2 KO, Sav1 KO, SV40, and DEN models were predicted to be the least responsive to immunotherapy. Further analysis of immune checkpoint genes showed that high expression of immune inhibitory genes (Cd276 and Pvrl2) in Mst1/2 KO, Sav1 KO, SV40 and low expression of immune stimulatory genes (Cd86) in DENA model might be accountable for lack of predictive response to immunotherapy. Conclusion: Most of the mouse models effectively recapitulated molecular characteristics of human subtypes, including response to immunotherapy. of samples are included: 1.SKOV3-ip1 2.SKOV3-OM3. Gene expression profiles of SKOV3-OM3 cells were compared to that of parental SKOV3 ip1 cells.

overall_design: Nine genetically engineered or chemically induced mouse HCC models were used in this study. Total of 108 HCC tumors were collected for the study. Tumors from transgenic mice expressing myelocytomatosis oncogene (Myc) (n = 15), Myc/transforming growth factor alpha (Tgfa) (n = 15), E2F transcription factor 1 (E2f1) (n = 18), or Myc/E2f1 (n = 15) were carried out microarray experiment. The diethylnitrosamine (DEN)-induced model (n = 16), simian vacuolating virus 40 (SV40) T-antigen transgenic model (n = 10), Mst1/2 double KO (n = 4) and Sav1 KO (n = 11) mouse models were used for screening.

first: Elizabeth

middle: A

last: Conner

first: Valentina

middle: M

last: Factor

first: Snorri

middle: S

last: Thorgeirsson

first: Ju-Seog

last: Lee


title: Plasma miR-181a-5p down-regulation predicts response and improved survival after FOLFIRINOX in pancreatic ductal adenocarcinoma

city: Amsterdam

first: Elisa

last: Giovannetti

address: De Boelelaan 1117

department: Medical Oncology

country: Netherlands

institute: VUmc

summary:
Purpose: FOLFIRINOX has become standard therapy for patients with advanced stages pancreatic ductal adenocarcinoma (PDAC). However, only a subset of patients benefits from this therapy and biomarkers to guide clinical decisions are lacking. This study aimed to discover circulating microRNAs (miRNAs) as potential stratifying and monitoring biomarkers in patients with PDAC treated with FOLFIRINOX and to investigate their functional roles.
Methods: A microarray was used in plasma samples from a first cohort of 11 patients selected based on their long versus short progression-free survival (PFS) after FOLFIRINOX. Nine miRNAs were validated using RT-qPCR in an independent cohort (n=43). The best discriminative miRNA was evaluated in tumor tissue samples and associated with clinicopathological features by Cox regression analyses. In vitro studies explored its role on cell proliferation, key downstream targets, and interaction with 5-fluorouracil, irinotecan, and oxaliplatin.
Results: MiR-181a-5p was validated as significantly down-regulated in non-progressive compared to progressive patients after FOLFIRINOX. In multivariate analysis, this down-regulation correlated with improved PFS and overall survival, especially combined with CA19.9 decline (log-rank p<0.001, HR=0.153, 95% C.I. 0.067–0.347 and log-rank p=0.033, HR=0.201, 95% C.I. 0.070–0.576, respectively). Overexpression of miR-181a-5p increased proliferation of PDAC cells and inversely correlated with expression of ATM. Furthermore, inhibition of miR-181a-5p coupled with oxaliplatin exposure increased DNA damage and decreased cell viability.
Conclusion: Our findings endorse miR-181a-5p as a biomarker for monitoring response to FOLFIRINOX and prognostication. MiR-181a-5p inhibition can potentially enhance sensitivity to oxaliplatin by amplifying the DNA damage response and cell death.

overall_design: For the first discover cohort of this study, a microarray was performed on plasma samples of 11 patients. These samples included five patients with early disease progression and six patients with no progression during FOLFIRINOX chemotherapy. Of these patients, blood samples were collected both before FOLFIRINOX therapy and after 5-6 cycles of FOLFIRINOX. Of each sample, RNA was isolated with the Small RNA isolation kit (Exiqon). Technical duplicates were included in the subsequent analysis. The plasma microRNA expression before FOLFIRINOX therapy of progressive patients was compared to the microRNA expression of non-progressive patients. In addition, the miRNA expression after FOLFIRINOX was compared to miRNA expression before therapy to determine the change in miRNA expression during therapy.

first: Laura

middle: L

last: Meijer

first: Ingrid

last: Garajova

first: Chiara

last: Caparello

first: Tessa

middle: Y

last: Le Large

first: Adam

last: Frampton

first: Enrico

last: Vasile

first: Niccola

last: Funel

first: Geert

last: Kazemier


title: Mutational landscape of ocular marginal zone lymphoma identified frequent alterations of TNFAIP3 followed by TBL1XR1 and CREBBP mutation

city: Seoul

first: Sung-Yeon

last: Hwang

address: School of Biological Sciences, Seoul National University

country: South Korea

summary: Assessment of TBL1XR1 mutations  on transcriptome

overall_design: TBL1XR1 mutations (L282P and H348Q) were transfected into BJAB cell line.

first: Seung-Ho

first: Hae-Yong

last: Yoo


title: Microarray expression profile of long noncoding RNAs in germinal center-like diffuse large B-cell lymphoma cell lines.

city: Shenyang

first: Wei

last: Yang

state: Liaoning

address: Huaxiang Road 39

department: Hematology

country: China

institute: Shengjing Hospital of China Medical University

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

summary: The contributions of long noncoding RNAs (lncRNAs) to the development of germinal center (GCB)-like diffuse large B-cell lymphoma (DLBCL) remain largely unknown. The aim of this study was to investigate the expression profile of lncRNAs in human GCB DLBCL cell lines (OCI-ly1 and OCI-ly19) and normal B lymphocytes by microarray. We demonstrated that 21,539 lncRNAs were expressed in all samples analyzed, of which 1,648 lncRNAs were upregulated and 2,671 lncRNAs were downregulated in GCB DLBCL cell lines (OCI-ly1 and OCI-ly19) (≥2.0-fold, P<0.05).

overall_design: Three groups of samples were used for microarray, and each group contains three replicates. Human GCB DLBCL cell lines (OCI-ly1 and OCI-ly19) were selected as tumor groups, and CD19-positive B cells were selected as control group. OCI-ly1 and OCI-ly19 cell lines were cultured in Dulbecco's Modified Eagle Medium (DMEM) of high glucose with 10% fetal bovine serum (FBS) at 37°C in a humidified incubator with 5% CO2. CD19-positive B cells were isolated from buffy coats of healthy donors’ blood obtained from the Regional Blood Donor Center using the human CD19 microbeads.

first: Hongyu

last: Gao

first: Bin

last: Wu

last: Yan

first: Zimu

last: Gong

first: Qi

last: Sun

first: Huihan

last: Wang


title: Neuropilin-1 is Required for the Suppressive Function of Human Regulatory T Cells

city: Oxford

first: Ruud

last: van Stiphout

address: Old Road Campus Research Building

institute: University of Oxford

summary: Regulatory T cells (Tregs), lymphocytes that suppress immunological reactions, are of great interest for our comprehension of homeostasis and regulation in the immune system and as a therapeutic target in the treatment of both immune-mediated pathologies and reactivation of the immune response in patients with cancer. Understanding the molecular mechanisms by which these cells are regulated in respone to their environment will help to inform clinical strategies targeting Tregs.  We hypothesised that Neuropilin-1, a transmembrane co-receptor for ligands of the semaphorin and growth factor families,  promotes the suppressive function of human Tregs.  Utilising in vitro lentivirus-mediated transduction with shRNA to knock down neuropilin-1 in primary human Tregs, we demonstrated that neuropilin-1 knockdown Tregs were severely impaired in their capacity to suppress cell proliferation in vitro and in their ability to prolong allograft survival in a humanised mouse model of transplantation. While neuropilin-1-KD Tregs exhibited no defects in survival, proliferation and activation upon stimulation in vitro, we hypothesised that loss of NRP1 expression would alter the global gene expression profile of human Tregs, revealing a NRP1-dependent Treg-associated transcriptional signature.

overall_design: All samples are human T CD4+ T lymphocytes (FACS-sorted from peripheral blood), transduced with lentivirus and expanded in vitro for 16days.   Either regulatory T cells (Tregs) (CD4+CD25+CD127lo FACS-sorted or effector T cells (CD4+CD25-)  Either experimental (transduced with shRNA to NRP1 (neuropilin-1 gene) to yield NRP1 knockdown) or control (transduced with scrambled control (pLKO1))  Either stimulated (with anti-CD3 anti-CD28-coated beads for 72hrs) or unstimulated (cultured for 72hrs without beads)  Groups:  A. human Tregs, unstimulated, control vector pLKO1 (N=5 donors) - control for (B)  B. human Tregs, unstimulated, NRP1-KD (N= 5 donors)  C. human Tregs, stimulated, control vector pLKO1 (N=4 donors) = control for (C)  D. human Tregs, stimulated, NRP1-KD (N= 4 donors)  E. human Teffs, unstimulated, control vector pLKO1 (N=3 donors) = control for (F)  F. human Teffs, unstimulated, NRP1-KD (N=3 donors)  Samples derived from the same blood donor are paired between groups A and B, C and D, and E and F

first: Kate

last: Milward

first: Joanna

last: Hester


title: Effects of TNF-alpha blocking in sorted Th1 cells from co-cultures of human CD4-positive and CD14-positive cells

city: Måløv

first: Klaus Stensgaard

last: Frederiksen

address: Novo Nordisk Park F9.1.07

department: Molecular Genetics

country: Denmark

institute: Novo Nordisk A/S

summary: Human CD4+ T cells and CD14+ monocytes from healthy donors were co-cultured with anti-CD3 for three days in the presence or absence of TNF-alpha mAb (Adalimumab). Classical Th1 cells or those generated in the presence of the inhibitor were then sorted and analyzed by full transcriptome microarray analysis.

overall_design: Sorted Th1-cells from co-cultures of CD4+ T-cells and CD14+ monocytes (+/- Adalimumab) were prepared from 8 healthy volunteers. Total RNA was isolated and profiled using Affy HG-U219  chips.

first: Klaus

first: Leonie

last: Taams


title: Gene expression analysis of RNAs isolated from TSA-untreated and TSA-treated human keratinocytes

status: Public on Dec 31 2018

city: Pohang

first: Bhin

last: Jin-hyuk

address: Ji-gok research center, hyoja-dong, Nam-gu

department: Department of Chemical engineering

institute: POSTECH

summary: In order to identify the TSA responsive genes, we performed a gene expression microarray analysis for the RNAs isolated from TSA-untreated and TSA-treated human keratinocytes

overall_design: Duplicate experiments were performed for TSA-untreated and TSA-treated human keratinocytes. Total RNA was isolated from tissues using Qiazol (QIAGEN) following the manufacturers’ protocols.

first: Bum-Ho

last: Bin

first: Jinhyuk

last: Bhin


title: benzene effects on brassica leaves-Study of benzene metabolism in higher plants

city: evry

first: Soubigou-Taconnat

last: Ludivine

address: 2 rue gaston crémieux

department: URGV

country: France

institute: INRA

summary: au11_04_benzene - benzene effects on brassica leaves - Improving the knowledge of the metabolic pathways of benzene in higher plants. - Cabbages (Brassica oleracea variety Prover), placed in a 300L exposure chamber, are directly subjected to a single dose of benzene (3ppm) for 24 hours.

overall_design: 1 dye-swap - treated vs untreated comparison

first: Ludivine

last: Taconnat

first: Sylvain

last: Dumez

first: Sandrine

last: Balzergue

first: Marie-Laure

last: Martin-Magniette


title: Impact of exosomal miR-92b in hepatocellular carcinoma: its role for cancer immunoediting and clinical value for prognosis

city: Kaohsiung

first: I-Hsuan

middle: Ann

last: Chen

address: 123 Ta-Pei Rd., Niao-Sung

country: Taiwan

institute: CGMH

summary: To further development of our gene expression approach to HCC development, we have employed whole genome microarray expression profiling as a discovery platform to identify genes with the potential to distinguish defferent grades of HCC development by real-time PCR, confirming variability betweenHCC grades as well as the predicted HCC biomarkers

overall_design: HCC exosomes induced gene expression in rat blood was measured on 0 and Day 35, Day 49 (moderate ) and Day 49 (severe) after injecting   one dose to baffolo rats.  Four independent experiments were performed at each time (0 to 49 days) using different rats for each experiment.

first: T

last: Nakano

first: I

middle: H


title: rotenone-Effect of the inhibition of the mitochondrial respiratory chain complex I (CI) on shoot initiation on protoplast-derived calli

city: Orsay

first: Stéphanie

last: Pateyron

address: Rue de Noetzlin _ Batiment 630

institute: IPS2_Institute of Plant Sciences Paris-Saclay

summary: ra16-03_rotenone - rotenone - How does inhibition of CI enhance organogenesis? - NA

overall_design: 18 dye-swap - time course,treated vs untreated comparison

first: Pierre

last: Hilson

first: Alberto

last: Macho


title: Deletion of Mediator (Med1) induces epidermal fate in dental epithelial stem cells

city: San Francisco

first: Yuko

last: Oda

state: CA

address: 111N-MB 360 1700 Owens St, Suite 360

department: Endocrine Research

institute: VA Medical Center UCSF

summary: Cell fates are defined by specific transcriptional program. We developed a mouse model, in which transcriptional program for ectoderm cell fate is altered in tooth and skin. Previously, we showed that genomic deletion of one subunit of Mediator complex, Mediator 1 (Med1) in vivo regenerate ectopic hair in incisors by disrupting Notch mediated enamel epithelial differentiation. However, precise process and molecular mechanism to induce epidermal fate are not clear. Med1 deficient dental epithelial stem cells exerts transcriptional program for skin epithelia reminiscent of the pattern in the skin. Epidermal transcripts were first induced prior to hair genes during dental epithelial differentiation, resemble to the pattern of embryonic developmental process of the skin. Hair genes was specifically induced at the anagen stage synchronized with hair cycling in the skin. Epidermal program was also induced in cultured adult stem cells called dental epithelial stem cell (DESC) that is derived from micro-dissected Med1 KO cervical loop tissues that are essential for continuous regeneration of mouse incisors. Gene expression profiles for the primary DESC with colony forming capability revealed that Med1 deletion suppressed Tgfb signaling by reducing the expression of ligands (Tgfb1, Inhibin ba), receptors and their extracellular targets such as Ctgf. Med1 deletion also induced Tgfb regulated reprogramming transcription factor, Klf4 that also known to drive transcription for epidermal genes. TGFb signaling was also suppressed in Med1 null epidermis in skin, in which epidermal fate was induced in hair follicle keratinocytes. Med1 silencing blocked expression of TGFb1 and suppressed both basal and recombinant TGFb induced Smad2/3 mediated transcription of TGFb target genes in vitro. These results demonstrate that Med1 deletion enhances epidermal transcriptional program in adult stem cells through regulation of TGFb signaling.

overall_design: n=3 CON and KO (each sample contain RNA extracted from cultured dental epithelial cells (DESC), which is isolated from cervical loop of Med1 KO and littermate control mice (3 mice each)

first: Thai

last: Nguyen

first: Daniel

middle: D

last: Bikle


title: Evolution of gene expression levels in Anopheles male reproductive organs

city: Nottingham

first: Richard

last: Emes

state: Nottinghamshire

department: School of Veterinary Medicine and Sciences.

institute: University of Nottingham

type: Expression profiling by high throughput sequencing

summary: Gene expression was determined for Male accessory gland and testes in different members of the Anopheles gambiae complex, including An. gambiae (Savannah, MRA-762), An. coluzzii (Mopti) [2], An. arabiensis [3], An. merus [4] and An. quadriannalatus [5. All the mosquito stocks were obtained from the Malaria Research and Reference Reagent Resource Center (MR4) in Atlanta (https://www.beiresources.org/Catalog/BEIVectors/MRA-762.aspx).      References:  1. MR4 wild stocks information. Access Jenuary 2018. (Kisumu) https://www.beiresources.org/Catalog/BEIVectors/MRA-762.aspx  2. MR4 wild stocks information. Access Jenuary 2018. (Mopti)   https://www.beiresources.org/Catalog/BEIVectors/MRA-763.aspx  3. MR4 wild stocks information. Access Jenuary 2018. (arabiensis) https://www.beiresources.org/Catalog/BEIVectors/MRA-856.aspx  4. MR4 wild stocks information. Access Jenuary 2018. (merus) https://www.beiresources.org/Catalog/BEIVectors/MRA-1156.aspx  5. MR4 wild stocks information. Access Jenuary 2018. (quadriannulatus) https://www.beiresources.org/Catalog/BEIVectors/MRA-1155.aspx

sample_organism:
Anopheles gambiae
Anopheles arabiensis
Anopheles merus
Anopheles quadriannulatus
Anopheles coluzzii

overall_design: MAGs and Testes mRNA profiles of Anopheles species were generated by deep sequencing, in triplicate, using Illumina HiSeq 1500

first: Tania

last: Dottorini


title: Mesenchymal-Epithelial Transition Regulates Initiation of Pluripotency Exit before Gastrulation

city: Kyoto

first: Cantas

last: Alev

address: Medical Faculty Bldg. B, Yoshida-Konoe-cho, Sakyo-ku

department: Institute for the Advanced Study of Human Biology (ASHBi)

country: Japan

institute: Kyoto University

summary: The pluripotent epiblast gives rise to all tissues and organs in an adult body. Its differentiation starts at gastrulation when the epiblast generates mesoderm and endoderm germ layers through a process called epithelial-mesenchymal transition (EMT). Although gastrulation EMT coincides with loss of epiblast pluripotency, pluripotent cells in development and in culture can adopt either mesenchymal or epithelial morphology. The relationship between epiblast pluripotency and epiblast morphology is not well understood. In this work, using chicken epiblast and human induced pluripotent stem cell (hiPSC) models, we show that pluripotent cells undergo an obligatory mesenchymal-epithelial transition (MET) prior to EMT-associated pluripotency loss. Epiblast MET and the subsequent EMT are two distinct processes. The former, a partial MET, is associated with reversible pluripotency exit; whereas the latter, a full EMT, is associated with complete and irreversible pluripotency loss. We provide evidence that integrin-mediated cell-matrix interaction, but not E-cadherin-mediated cell-cell interaction, is a key player in pluripotency exit regulation. We propose that epiblast partial MET is an evolutionarily conserved process among all amniotic vertebrates and its developmental function is to mediate planar symmetry-breaking within an epithelialized epiblast, taking place after epiblast MET but before gastrulation EMT.

overall_design:
Using the chick embryonic model, we generated transcriptomic datasets of the avian epiblast and area pellucida during the first 14h of embryonic development, with a special focus on genes associated with epithelialization and pluripotent state of the epiblast.
Total RNA from 0.5h, 5h, 9h and 14h incubated area pelucida (AP) epiblast samples (two sets of independent samples) were isolated and used for gene expression profiling.

first: Takeya

last: Kasukawa

first: Guojun

last: Sheng


title: Effect of loss of ciliogenesis on myoblast quiescence

city: Hyderabad

first: Nisha

last: Venugopal

state: Telangana

address: Habsiguda, Uppal Road

country: India

institute: CCMB

summary: Quiescence is an actively maintained state of the cell cycle;aberrations in which can result in severe consequencces for development and tissue homeostasis. Primary cilia are signaling centres derived from the centrosome which are associated with quiescence.Using a mouse skeletal myoblast cell culture system that can be induced to exit the cell cycle reversibly into quiescence or irreversibly into differentiation, we studied the effect of loss of ciliogenesis on quiescence.

overall_design: We performed microarray analysisis to study changes in the global transcriptome of IFT88KD myoblasts in different cell cycle states. RNA was harvested from C2C12 myoblasts that underwent siRNA treatment using either IFT88 or negative control siRNA at four different cell cycle states- Proliferating (MB), Quiescent (G0), Reentry into cell cycle for 2 hours (R2), and 48 hours into terminal differentiation (D48). RNA was converted to cDNA, labelled and used to probe Affymetrix mouse 420A 2.0 arrays.

first: Hardik

middle: P

last: Gala

first: Jyotsna

last: Dhawan


title: Global expression profile of long non-coding RNAs in gastric cancer and adjacent tissues

city: NanJing

first: Zhengdong

last: Zhang

address: 101 Longmian Avenue

department: Department of Environmental Genomics, School of Public Health

institute: Nanjing Medical University

summary: We implemented lncRNA microarray analysis in 5 paired gastric cancer tissues to detect the lncRNA expression profile. Moreover, we set out to explore the biological function, clinical application and molecular basis of the aberrant lncRNA in GC

overall_design: The total RNA of 5 paired gastric cancer and adjacent tissues  was extracted, and detected the global expression profile of lncRNA and mRNA with Arraystar Human LncRNA Microarray v2.0

first: Gaoxiang

last: Ma


title: Gene expression in human activated memory CD4+ T cells

city: Darlinghurst

first: Stuart

last: Tangye

state: NSW

address: 384 Victoria St

department: Immunology

country: Australia

institute: Garvan Institute of Medical Research

summary: Effect of inactivating mutations in ZNF341 on the function of human CD4 T cells

overall_design: Memory CD4+ T cells from healthy donors and patients with ZNF341 mutations were cultured in vitro under Th0 or Th17 polarising conditions for 4 days; RNA was then harvested and gene expression determined


title: RNA expression in MDA-MB-231 cells with stable knockdown or overexpression of LSD2 (KDM1B).

city: Pittsburgh

first: Yi

last: Huang

state: Pennsylvania

address: 204 Craft Ave

department: Pharmacology & Chemical Biology

institute: University of Pittsburgh Cancer Institute

summary: Abnormal activities of histone lysine demethylases (KDMs) are associated with aberrant gene expression in breast cancer development. However, the precise molecular mechanisms in chromatin remodeling and regulation of gene transcription are still elusive. In this study, we performed Gene Expression Microarray (HG-U133A_2) using RNA from the aggressive breast cancer cell line MDA-MB-231 expressing stable knockdown or overexpression of LSD2. The goal of this study is to identify genes and pathways differentially expressed in triple negative breast cancer cells with genetically modified LSD2 expression.

overall_design: Twelve samples were subject to microarray analysis:  3 biological replicates from MDA-MB-231 cells stably transfected with 1) Scramble shRNA, 2) LSD2 shRNA, 3) eGFP/Flag vector, or 4) LSD2/eGFP/Flag vector.

first: Shauna

middle: N

last: Vasilatos

first: Lin

last: Chen

first: Tiffany

last: Katz


title: Study comprehensive changes in gene expression profile under different pH stresses in wheat roots

city: Xinxiang

first: Haiyan

last: Hu

state: Henan

address: East Hualan Road

department: School of Life Science and Technology

institute: Henan Institue of Science and Technology

summary: To study the transcriptional profiling of seedling roots under different solution pH stresses in winter wheat (Triticum aestivum L.). We identify genes that are differentially expressed in response to different solution pH (4.0 and 10.0) comparing with control pH 6.5 using microarray technology.

overall_design: Seeds of wheat Bainongaikang 58 (AK58) were synchronously germinated by pre-incubation and plants were grown in containers in deionized water (DIW, pH 6.5). At the one-leaf stage wheat seedlings were treated with pH 4.0 and 10.0 DIW, respectively.  The seedling roots of a 2 h time point under pH 4.0, 2 and 24 h under pH10.0 were chosen to capture genes with early responses and were compared with those at the 0 h time point as the control (CK). Three biological replicates were used in each treatment time point.

first: Zhengang

last: Ru


title: The effect of OsWOX4 knockdown on the expression profile in rice the leaf primordia and the SAM

city: Tokyo

first: Yukiko

last: Yasui

address: Hongo 7-3-1, Bunkyo-ku

department: Department of Biological Sciences

institute: The University of Tokyo

summary:
We used an inducible knockdown system, in which the OsWOX4 expression is silenced by the application of dexamethasone (DEX) using a pACT1-GVG>OsWOX4:RNAi construct.
To compare gene expression profiles between mock and DEX treated plants, we performed microarray analysis, using Rice (US) gene 1.0 ST array.

overall_design: After 3 or 12 h of  DEX treatment of 5-day-old plants, the shoot apices including the SAM and leaf primordia, which contained the whole part of P1 and P2, most part of P3, and the basal parts of P4 and P5, were harvested.

last: Sugisawa

first: Hiro-Yuki

last: Hirano


title: Gene expression of bursa fabricius of Thai indigenous chicken breeds

city: Dummerstorf

first: Klaus

last: Wimmers

address: Wilhelm-Stahl-Allee 2

department: Genome Biology

institute: FBN Dummerstorf

summary: Analysis of gene expression of Bursa of Fabricius samples of 3 male chickens of 6 breeds revealed differential expression of genes related to Ingenuity pathways immune cell trafficking, cell-mediated immune response, humoral immune response and infectious disease.

overall_design: We measure gene expression of bursal tissues in chicken by the GeneChip® Chicken Gene-1_0-st Array of Affymetrix.

first: Siriluck

last: Ponsuksili

first: Supamit

last: Mekchay

first: Worrarag

last: Norseeda

first: Nares

last: Trakooljul


title: Long-term neuroinflammation induced by influenza A virus infection and the impact on hippocampal neuron morphology and function

city: Braunschweig

first: Robert

last: Geffers

address: Inhoffenstr. 7

department: Dep. Molecular Bacteriology

institute: HCI - Helmholtz Centre for Infection Research

summary: Acute influenza infection can be associated with neurological symptoms. Especially after the major pandemics reports about neuropsychiatric complications accumulated. However, the long-term consequences for the CNS of an infection with neurotropic but also non-neurotropic influenza A virus (IAV) variants remain largely elusive. The results presented here show that synapse loss in the hippocampus upon an infection with neurotropic H7N7 (rSC35M) as well as non-neurotropic H3N2 (maHK68) persists well beyond the acute phase of the disease. While hippocampal synapse number was significantly reduced 30 days post infection with both H7N7 and H3N2, full recovery could be observed 120 days post infection. Notably, infection with H1N1 (PR8) which was shown previously to affect spine number and hippocampus-dependent learning during the acute phase had no significant long-term effects. Spine loss was associated with an increase in the number of activated microglia, reduced long-term potentiation and an impairment in spatial memory formation in the water maze indicating long-term inflammation induced functional and structural alterations in the hippocampus. Our data, therefore, provide evidence that while neuroinflammation induced by neurotropic H7N7 showed the strongest effect, also the systemic infection with a non-neurotropic influenza virus can result in long-term impairments in synapse number and function in the hippocampus. While young animals fully recover the outcome might be different in aged or otherwise compromised individuals, thereby directing future treatment strategies to pay attention to IAV induced processes of neuroinflammation.

overall_design: To follow IAV induced gene expression changes in the hippocampus, we performed transcriptome studies. Hippocampi of mice infected with two respective IAVs were prepared at 18 dpi and 30 dpi. RNA was isolated for whole genome microarray analysis.

first: K

last: Schughardt

first: E

last: Wilk

first: R

last: Geffer

first: M

last: Korte


title: Transcriptional profiling of Arabidopsis nuclear and cytoplasmic fractions from leaf tissue

city: Beaucouzé

first: Jean-Marc

last: Celton

address: 42 rue Georges Morel

institute: INRA-IRHS

summary: Transcriptional profiling of Arabidopsis nuclear and cytoplasmic fractions using probes complementary to both sense and anti-sense transcripts.

overall_design: 3 nuclear RNA samples and 3 cytoplasmic RNA samples from leaf tissue.

first: Etienne

last: Bucher

first: Emilja

last: Hristova

first: Sandra

last: Pelletier

first: Jean-Pierre

last: Renou

first: Sandrine

last: Balzergue


title: Transcriptional regulation of BNTX-mediated immunosuppression on B cells

city: Taipei city

first: Shiang-Jong

last: Tzeng

address: 11F, No.1, Sec.1, Ren-ai Rd

department: Department and Graduate Institute of Pharmacology, College of Medicine

institute: National Taiwan University

summary: BNTX, naloxone and naltrindole are known to be immunosuppressive. Other than independency of the DOR, the molecular basis is unclear. We performed transcriptome analysis to determine up-regulated and down-regulated genes to decipher the underlying mechanisms.

overall_design: Total RNAs isolated from BJAB B cells treated with 2 uM or 10 uM of BNTX, naloxone or naltrindole for 9 hours.

first: Shiang

middle: J

first: Liang

middle: C

last: Lai


title: Gene expression analysis of human permanent periodontal ligament tissue

city: Seoul

first: Seong-Oh

last: Kim

address: 250 Seongsanno, Seodaemun-gu

department: Pediatric dentistry

institute: Yonsei University College of Dentistry

summary: Gne expression analysis data of human permanent periodontal ligament tissues

overall_design: PDL samples were obtained from healthy permanent premolars (n=38; from 4 males and 10 females, aged 10-19 years) extracted for orthodontic reasons. Gene expression profiles were conducted using cDNA microarray analysis.


title: To investigate expression profile of Bacillus subtilis w.r.t. different inductions

city: Bangalore

first: Genotypic

last: technology

state: Karnataka

address: 259, Apoorva 4th cross,80 feet Road,RMV 2ND STAGE

institute: Genotypic Technology

summary: In this study, we have tried to comprehensively understand the differential expression of genes in B. subtilis when the cells are grown in media with combination of 'C' and 'N' sources compared to a control (in the presence of glucose).

platform_organism: Bacillus subtilis subsp. subtilis str. 168

overall_design: Organism: Bacillus subtilis str 168, Agilent B.subtilis Gene Expression 8x15k Array AMADID: 020941 designed by Genotypic Technology Private Limited.

first: Deepika

last: Pandey

first: Ashok

last: Dubey


title: Transcriptome effects mediated by forced repression of LncRNA BACE1-AS in HAOEC cells

city: Milan

first: Fabio

last: Martelli

address: via morandi 30

country: Italy

institute: IRCCS-Policlinico San Donato

summary: Recently, high-throughput studies identified tens of thousands of sites transcribed to produce transcripts with little protein-coding potential. The function of these transcripts remains largely obscure and their relevance to cardiovascular disease is mostly undefined. Many non-protein-coding transcripts belong to the group of Long non coding RNAs (LncRNAs), which are arbitrarily classified according to their length >200 nt. They control protein targeting to genomic loci, epigenetic silencing and serve as scaffolds for multiple proteins. We measured the expression of 83 diseases-related LncRNAs in biopsies from heart failure patients and in controls. We found 15 lncRNAs modulated in HF samples. To explore the functional relevance of BACE1-AS, we investigated the effects of its forced repression on transcriptome.

overall_design: BACE1-AS were blocked by LNA-GAPmers (Exiqon) in human aorta endothelial cells (HAOEC). We measured, by lllumina HumanHT-12 v4 BeadChip platform, the transcriptome changes induced by the forced repression of LncRNAs expression compared to a negative control (scrambled sequences).

first: Simona

last: Greco

first: Christine

last: Voellenkle

first: Jose

last: Garcia-Manteiga


title: Persistent microRNA-gene networks in primary human hepatocytes upon withdrawal of aflatoxin B1 exposure are related to hepatocellular carcinoma [mRNA]

city: Maastricht

first: Linda

last: Rieswijk

address: Universiteitssingel 50

department: Toxicogenomics

institute: Maastricht University

summary: Hepatocellular carcinoma (HCC), one of the most common cancer types, is a multi-factorial disease. One strongly associated factor is oral exposure to the food-contaminant aflatoxin B1 (AFB1). A clear link between AFB1-induced p53 mutations and HCC exists, however less is known about the association with microRNA expression changes. In particular, irreversible adverse effects that may occur at the transcriptomic level following repetitive exposure have not been investigated yet. Therefore, in this study, we aimed to dissect persistent changes in expression of microRNA-directed regulatory networks from transient transcriptome modifications contributing to AFB1-induced HCC. Primary human hepatocytes were exposed to 1 µM of AFB1 for 5 days followed by a 3 day wash-out period. Whole genome transcriptomic analysis and microRNA expressions were analyzed applying microarray technologies. By evaluating genes which remain significantly expressed into the same direction after the 3-day  wash-out period persistent AFB1-induced and HCC-related biological processes could be identified. Persistent genes could be linked with "Drug and energy metabolism" and "Pre-, post- and transcriptional regulation of gene expression" related processes. Especially, two HCC-related microRNAs, hsa-miR-34b-5p and hsa-miR-222-3p, which are persistently expressed, seem to regulate genes involved in these very characteristic AFB1-induced processes referring to cancer-associated metabolism changes and regulation of gene expression. Moreover, hsa-miR-34a-5p, hsa-miR-96-5p and hsa-miR-30a-3p which become differentially expressed only upon terminating AFB1 exposure, seem to regulate persistently expressed genes. The findings within this study therefore contribute to a better understanding of the AFB1-induced onset of HCC by causing persistent effects on microRNA and gene expression.

overall_design: The study investigated differential gene expression and microRNA expression changes in a pool of primary human hepatocyte RNA after 3 days of wash out following 5 days of repetative exposure to 1uM of aflatoxin B1 or DMSO. Three biological replicates per compound/solvent. In total 6 arrays.

first: L


title: Persistent microRNA-gene networks in primary human hepatocytes upon withdrawal of aflatoxin B1 exposure are related to hepatocellular carcinoma [miRNA]


title: Gene Expressoin Profile in the Hypothalamus and Liver of Male Fmod_KO Mice at 13 Weeks Old

city: Los Angeles

first: Xia

last: Yang

address: 610 Charles E. Young Dr. East

institute: UCLA

summary: To investigate the effects of gene Fmod on affecting brain dysfunction and metabolic disorders by profiling the transcripome in the hypothalamus and liver of male Fmod_KO mice at 13 weeks old.

overall_design: All mice (male Fmod_KO (n=4)) were maintained in a temperature-controlled room with a 12-hour light and 12-hour dark cycle. Wild Type (WT) control mice are the same as the mice used for BGN_KO analysis, thus data are not repeatedly uploaded here. Diet (Pico Lab 5053 rodent diet) and water were provided ad libitum. At 13 weeks old, mice were sacrificed. Hypothalamus and liver were dissected out, flash frozen, and stored at -80°C for later usage. All experiments were performed in accordance with the United States National Institutes of Health Guide for the Care and Use of Laboratory Animals and were approved by the University of California at Los Angeles Chancellor’s Animal Research Committee.

first: Qingying

last: Meng

first: Fernando

last: Gomez-Pinilla


title: Genome-wide association of Sus1 with RNAPII and tRNA genes depends on the distinctive SAGA subunits Spt8 and Spt7

city: VALENCIA

first: VARINIA

last: GARCIA-MOLINERO

address: EDUARDO PRIMO YÚFERA, 3

country: Spain

institute: CENTRO DE INVESTIGACIÓN PRÍNCIPE FELIPE

type: Expression profiling by genome tiling array

summary: We have analyzed the global effect of the conserved transcription-mRNA export factor Sus1 on transcription and its association with chromatin. We used genomic run-on experiments to show that Sus has a broad impact on the stability of most RNA polymerase II-transcribed genes. Genome association of Sus1 by the chromatin immunoprecipitation technique showed that Sus1 was widely distributed throughout coding regions, tending to accumulate towards the 3’ ends of highly transcribed transcription factor IID (TFIID) and Spt-Ada-Gcn5 acetyltransferase (SAGA) dependent genes. This accumulation depends on growth conditions, the transcriptional rate and whether the genes are TFIID- or SAGA-regulated. Validation of Sus1 occupancy data also revealed that Sus1 appears at tRNAs. Concomitantly, deletion of SUS1 leads to tRNA overexpression. In addition, we discovered that distinctive SAGA subunits Spt8 and Spt7 play a key role in Sus1 enrichment at the 3’ ends of SAGA-regulated genes upon temperature shift and at tRNAs. Thus, our study identifies the molecular mechanisms by which a SAGA factor is recruited genome-wide, and provides evidence of a more general role for this conserved coactivator in eukaryotic transcription.

overall_design: 12 samples, 4 strains (WT, spt8Δ, spt7-1180, spt8Δspt7-1180), 3 replicates per strain

first: Varinia

last: García-Molinero

first: Pedro

last: Furió-Tarí

first: Oreto

last: Antúnez

first: Kang

last: Han

first: Vinesh

last: Vinayachandran

first: Rohit

last: Reja

first: Frank

last: Pugh

first: José

last: Pérez-Ortín

first: Ana

last: Conesa

first: Susana

last: Rodríguez-Navarro


title: Persistent microRNA-gene networks in primary human hepatocytes upon withdrawal of aflatoxin B1 exposure are related to hepatocellular carcinoma

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

overall_design: Refer to individual Series


title: Expression profiling of MAPK inhibition in WM266-4 BRAF V600D mutant melanoma cell line

city: Emeryville

first: Guoying

middle: Karen

last: Yu

address: 4560 Horton St, MS 4.1

department: bioinformatics

institute: Novartis - NIBR

summary:
Extracellular signal regulated kinases, ERK1 and ERK2 are often considered as redundant due to their high homology, large number of overlapping substrates, and ability to substitute for each other in genetically engineered mouse models. We have investigated the individual contribution of ERK1 and ERK2 to the survival of human melanoma cell lines driven by oncogenic BRAF. ERK2, but not ERK1 activity, was crucial to drive survival and maintain transcriptional output of the MAPK pathway. Furthermore, we found that ERK2 DEF-domain interactions were crucial for transcriptional regulation and survival in some cells, but not in others, whereas ERK2-substrate interactions at the D-docking motif were largely dispensable.
We used microarrays to examine the global impact of gene expression by imhibiting different nodes of MAPK pathway.

overall_design: WM266-4 BRAF V600D mutant melanoma cell line was treated with inhibitors to BRAF (LGX818),  MEK1/2 (trametinib, MEK162), ERK1/2-inhibitor, or dox-inducible shRNAs targeting ERK1 or ERK2 at 2 different time points.

first: Michel

last: Faure

first: Tatiana

last: Zavorotinskaya

first: Darrin

last: Stuart


title: Gene Expressoin Profile in the Hypothalamus of Male Bgn_KO and Bgn_KO Mice fed with DHA at 13 Weeks Old

first: Xia

last: Yang

summary: To investigate the effects of DHA (omega-3) treatment on affecting brain dysfunction and metabolic disorders by profiling the transcripome in the hypothalamus of male Bgn_KO mice (with and without DHA) at 13 weeks old.

overall_design: All mice (Bgn_KO (n=3) and Bgn_KO_DHA (n=5)) were maintained in a temperature-controlled room with a 12-hour light and 12-hour dark cycle. Diet (Pico Lab 5053 rodent diet) and water were provided ad libitum, with DHA diet contained 0.5% of flaxseed oil and 1.2% of DHA capsule oil, and supplied to Bgn_KO_DHA mice for about 6 weeks. At 13 weeks old, mice were sacrificed. Hypothalamus and liver were dissected out, flash frozen, and stored at -80°C for later usage. Please note that one of the Bgn_KO samples was excluded as an outlier.  All experiments were performed in accordance with the United States National Institutes of Health Guide for the Care and Use of Laboratory Animals and were approved by the University of California at Los Angeles Chancellor’s Animal Research Committee.

first: Qingying

last: Meng


title: Gene expression in mouse whole proliferative phase wounds in response to alterations in β-Catenin levels [induced post-injury].

city: Toronto

first: Benjamin

last: Alman

state: Ontario

address: TMDT, 101 College Street

department: Developmental and Stem Cell Biology

country: Canada

institute: Hospital for Sick Children

summary: β-Catenin is a regulator of cutaneous wound repair.  The expression of genes that are modulated in response to changes in β-Catenin levels (stabilization and downregulation) in cutaneous mouse wounds, post injury, during the proliferative phase of repair, was investigated.  We are particularly interested in genes that are modulated (in opposite directions) in response to both the induction (stabilization) versus downregulation of β-Catenin.  To investigate this, conditional β-Catenin stabilized (Harada, N., et al. EMBO J. 1999 Nov 1;18(21):5931-42) mice were injected with either a Cre-expressing adenovirus, or a GFP-expressing control virus, three days following injury, and wounds were harvested eight days post injury.  For conditional knockdown of β-Catenin, mice generated from a cross between conditional  β-Catenin knockdown mice (Brault, V. et al., Development. 2001 Apr;128(8):1253-64), and mice that express a tamoxifen-inducible form of Cre (Hayashi, S., and McMahon, A.P., Dev Biol. 2002 Apr 15;244(2):305-18), were treated with Tamoxifen for five days, beginning at the third day after injury.  Wounds were harvested eight days after wounding.  This provides insight into the identities of genes modulated in response to changes in β-Catenin levels during the proliferative stage of cutaneous wound repair.

overall_design: Total RNA obtained from mouse whole wounds, harvested eight days post injury, in which β-Catenin levels were induced or downregulated (compared to controls) after injury.

first: Kirsten

last: Bielefeld


title: Gene expression in mouse whole proliferative phase wounds in response to alterations in β-Catenin levels


title: Gene expression in mouse proliferative phase wounds in response to alterations in β-Catenin levels [initiated prior to injury].

summary: β-Catenin is a regulator of cutaneous wound repair.  The expression of genes that are modulated in response to changes in β-Catenin levels initiated prior to injury was investigated during the proliferative phase of repair.  We are particularly interested in genes that are modulated (in opposite directions) in response to both the induction ('stabilization') versus downregulation of β-Catenin.  To investigate this, conditional β-Catenin stabilized mice (Harada, N., et al. EMBO J. 1999 Nov 1;18(21):5931-42) were injected with either a Cre-expressing adenovirus, or a GFP-expressing control virus, four days prior to injury, and wounds were harvested eight days following injury.  For conditional knockdown of β-Catenin, mice generated from a cross between conditional  β-Catenin knockdown mice (Brault, V. et al., Development. 2001 Apr;128(8):1253-64), and mice that express a tamoxifen-inducible form of Cre (Hayashi, S., and McMahon, A.P., Dev Biol. 2002 Apr 15;244(2):305-18), were treated with Tamoxifen for five days prior to injury.  Wounds were harvested eight days after wounding.  This provides insight into gene expression changes that occur during the proliferative stage of cutaneous wound repair in response to changes in β-Catenin levels initiated before/at the time of injury.

overall_design: Total RNA obtained from mouse whole wounds, harvested eight days after injury, in which β-Catenin levels were induced or ablated (compared to controls) prior to injury.


title: Gene expression analysis of sensor kinase MSMEG_1918 (PdtaS) knockout compared to Wildtype M. smegmatis

status: Public on Dec 30 2018

first: Genotypic

last: technology

summary: Microarray analyses were performed on Wildtype Mycobacterium smegmatis and MSMEG_1918 gene knockout (ΔpdtaS) grown in two different carbon sources, glucose and glycerol.

overall_design: Organism : M. smegmatis, Agilent's M.smeg Gene Expression  8x15k Array (AMADID: 020791) designed by Genotypic Technology private Limited.

first: Vignesh

last: Hariharan

first: Deepak

last: Saini


title: The Histone Deacetylases HDA6 and HDA9 coordinately regulate valve cell elongation through depressing auxin signaling in Arabidopsis

city: guangzhou

first: Liang

middle: Bing

last: Yuan

state: Guangdong

address: No. 135, Xingang Xi Road, Guangzhou, 510275, P. R. China

department: Life of Science

institute: Sun Yat-Sen University

summary: Both of Histone Deacetylases HDA6 and HDA9 belong to RPD3/HDA1 class I subfamily, and they have similar protein structure. Loss of function of HDA9 display a blunt silique. Although there is not protein-protein interaction between HDA6 and HDA9, they simultaneously loss function led to “nock-shape” silique that more seriously silique phenotype than hda9. The silique valve cell of hda9 and hda6 hda9 were longer than wild type and hda6. The transcripts level of auxin signaling related genes were mis-regulated in hda9 and hda6 hda9 silique, and GFP signaling derived by auxin response promoter DR5 were weaker in hda9 and hda6 hda9 than wild type and hda6. Thus, our findings reveal that HDA6 and HDA9 coordinately control silique valve cell elongation through affecting auxin signaling related genes expression in silique.

overall_design: 4 samples from wild-type, hda6, hda9 and hda6 hda9 4 DAP silique

first: Liangbing

first: Shangzhi

last: Huang


title: MicroRNA-8073: Tumor suppressor and potential therapeutic treatment

city: Kamakura

first: Atsuko

last: Mizoguchi

state: Kanagawa

department: New Frontiers Research Laboratories

institute: Toray Industries, Inc.


title: MicroRNA-8073: Tumor suppressor and potential therapeutic treatment [miRNA]

summary: The introduction of miR-8073 into tumors could inhibit tumor growth, indicating its great potential as a therapeutic target for cancer.

overall_design: The cell content, the cultured supernatant and exosome of colorectal cancer cell and normal cell were individually assayed for microRNA expression profiling.

first: Aiko

last: Takayama

first: Taiga

last: Arai

first: Junpei

last: Kawauchi

first: Hiroko

last: Sudo


title: Gene expression signature of TATA DNA binding mutant- spt15_A101T mutant (MVA pathway flux increasing mutant)

summary: we applied the gene expression approach to identify the genes which are responsible for increasing the flux in MEV pathway in Saccharomyces cerevisiae by spt15_A101T

overall_design: Organism : Yeast, Agilent's Yeat Gene Expression  8x15k Array (AMADID: 016333)

first: Manisha

last: Wadhwa

first: Anand

last: Bachhawat


title: A methylated-DNA-binding complex required for plant development mediates transcriptional activation of promoter methylated genes [ChIP-seq]

status: Public on Dec 27 2018

city: Beijing

first: xinjian

last: He

address: No. 7, zhongguancun life science park road, changping district

institute: National Institute of Biological Sciences

type: Genome binding/occupancy profiling by high throughput sequencing

summary: We found SUVH-SDJ complex occupies promoter methylated genes and promotes the expression of these genes.

overall_design: Examination of SUVH1 enrichment in Arabidopsis.

first: Qiang-Qiang

last: Zhao

first: Xin-Jian


title: Systematic evaluation of C. elegans lincRNAs with CRISPR knockout mutants [ChIP-Seq]

city: Hefei

first: Ge

last: Shan

state: Anhui

address: 443 Huangshan Road

department: School of Life Sciences

institute: University of Science and Technology of China

summary:
Background: LincRNAs play critical roles in eukaryotic cells, but systematic analyses of lincRNAs of an animal for phenotypes have been missing. We have generated CRISPR knockout strains for C. elegans lincRNAs and have evaluated their phenotypes
Results: C. elegans lincRNAs demonstrate global features such as shorter length and fewer exons than mRNAs. For the systematic evaluation of C. elegans lincRNAs, CRISPR knockout strains for 155 out of all the 170 C. elegans lincRNAs were produced. Mutants of 23 lincRNAs have shown phenotypes in 6 traits analyzed. We have investigated these phenotypic lincRNAs for their gene expression patterns and their potential functional mechanisms. Some C. elegans lincRNAs play cis roles to modulate the expression of their neighboring genes, and some other lincRNAs play trans roles as ceRNAs against microRNAs. LincRNAs are extensively regulated by transcription factors, and we dissect the pathway that two transcription factors UNC-30 and UNC-55 control the expression of linc-73 together. Furthermore, linc-73 plays a cis role to modulate the expression of its neighboring gene unc-104, and thus regulates the formation of presynapses.
Conclusions: By using CRISPR/cas9 technology, we have generated knockout strains of 155 C. elegans lincRNAs as valuable resources for studies in noncoding RNAs, and we provide biological insights for 23 phenotypic lincRNAs identified from 6 traits examined.

overall_design: Examination of 2 different Histone markers in L4 stage

first: Shuai

last: Wei

first: Emmanuel

last: Dzakah


title: Polycomb Group protein EZH2-mediated transcriptional repression of microRNA-338/-421 drives SPINK1-positive prostate cancer

first: Genotypic

last: technology

summary: SPINK1 overexpression defines the second largest subtype of prostate cancer (PCa), however molecular mechanisms underlying its upregulation remains poorly understood. Here, we identified the role of miR-338-5p and miR-421 in post-transcriptional regulation of SPINK1. We established that miR-338-5p/miR-421 mediates several cellular responses against SPINK1-positive cancer by targeting oncogenic long non-coding RNA (lncRNA) MALAT1, inducing cell-cycle arrest, inhibiting epithelial-to-mesenchymal transition (EMT), cancer-stemness and drug resistance. Moreover, ectopic expression of miR-338-5p/miR-421 abrogates SPINK1-mediated oncogenesis, tumor growth and distant metastases in murine model. Importantly, RNA-sequencing expression analysis revealed an inverse correlation between miRNAs and SPINK1 or MALAT1 in PCa patients’ specimens. Further, we demonstrate Polycomb group protein EZH2-mediated epigenetic silencing of miR-338-5p/miR-421 in SPINK1-positive subtype. Thus, restoring miR-338-5p/miR-421 expression using epigenetic drugs or synthetic mimics could abrogate SPINK1-mediated oncogenesis by targeting multiple oncogenic pathways and eliciting anti-cancer pleiotropic effects. Taken together, the present study unravels the molecular mechanism underlying SPINK1 overexpression and suggests miR-338-5p and miR-421 replacement therapy for the treatment of SPINK1-positive malignancies.

overall_design: Global expression profile of microRNA-338-5p and miR-421 overexpressing SPINK1 positive 22RV1 prostate cancer cells were compared to control. Two color Experiment,Organism: Homo sapiens, Agilent's Human Whole Genome 8x60k GE Microarray (AMADID-72363)

first: Vipul

last: Bhatia

first: Anjali

last: Yadav

first: Ritika

last: Tiwari

first: Shivansh

last: Nigam

first: Apul

last: Goel

first: Bushra

last: Ateeq


title: Systematic evaluation of C. elegans lincRNAs with CRISPR knockout mutants


title: Expression of OsTPX Gene Improves Cellular Redox Homeostasis and Photosynthesis Efficiency in Synechococcus elongatus PCC 7942

status: Public on Dec 26 2018

city: Deagu

first: Young-Saeng

last: Kim

address: 80, Daehak-ro

institute: Kyungpook National University

summary: The goals of this study are to compare hydrogen peroxide (H2O2) stress tolerance through gene expression of wild type (WT) and OsTPX-expressing Synechoccous elongatus PCC 7942 (OT) under the normal and stress condition.

sample_organism: Synechococcus elongatus PCC 7942 = FACHB-805

overall_design: Cyanobacterial mRNA profiles of normal and stressed samples that WT and OT were performed as paired-end sequencing, in triplicate, using HiSeq 2500 (Illumina).

first: Jin-Ju

first: Il-Sup

first: James

middle: W

last: Golden

first: Ho-Sung

last: Yoon

first: Seong-Im

last: Park

first: Spencer

last: Diamond

first: Joseph

last: Boyd

first: Arnuaud

last: Taton


title: Systematic evaluation of C. elegans lincRNAs with CRISPR knockout mutants [lncRNA-seq]

first: Ge

last: Shan

overall_design: C. elegans mRNA profiles of 9 different stages (N2_embryo, N2_L1, N2_L2, N2_L3, N2_L4, N2_Young_Adult, N2_dauer, N2_starved_mixture, him-5) were generated by deep sequencing, using Illumina HiSeq 2500 and BGISEQ-500.

first: Shuai

first: Jingxin

last: Li


title: Human hookworm infection enhances mycobacterial growth inhibition and associates with reduced risk of tuberculosis infection.

city: Oxford

first: Julius

last: Muller

state: Oxfordshire

address: ORCRB, Roosevelt Drive

department: Nuffield Department of Medicine

institute: The Jenner Institute, University of Oxford

summary: Soil-transmitted helminths and Mycobacterium tuberculosis frequently coincide geographically and it is hypothesized that gastrointestinal helminth infection may exacerbate tuberculosis (TB) disease by suppression of Th1 and Th17 responses. However, few studies have focused on latent TB (LTBI) infection, which predominates globally. We performed a large observational study of healthy adults migrating from Nepal to the UK (n=645). Individuals were screened for LTBI and gastrointestinal parasite (GIP) infections. A significant negative association between hookworm (HW) and LTBI-positivity was seen (OR=0.221; p=0.039). HW treatment did not effect LTBI conversions. Blood from individuals with HW had a significantly greater ability to control virulent mycobacterial growth in vitro than from those without, which was lost following HW treatment. There was a significant negative relationship between mycobacterial growth and eosinophil counts. We also analysed differential gene expression among individuals with and without HW infection, pre- and post- anti-helminth treatment. Eosinophil-associated differential gene expression characterised the whole blood transcriptome of hookworm infection and correlated with improved mycobacterial control. These data provide a potential alternative explanation for the reduced prevalence of LTBI among individuals with HW infection, and possibly an anti-mycobacterial role for helminth-induced eosinophils.

overall_design: Transcriptomics was performed on unstimulated whole blood samples from uninfected controls (n=9) and individuals with hookworm infection (matched pre- and post-treatment, n=11). Peripheral blood was collected in PAXgene© tubes and stored at -80oC until required for whole blood transcriptomic studies. Samples were subsequently thawed at room temperature for two hours, total intracellular RNA was extracted using the Blood RNA Kit (Qiagen) and the purity and quantity of RNA was assessed prior to storage at -20°C. Globin mRNA was depleted using the GLOBINclear Kit (Ambion), amplified and biotin-labelled using the TotalPrep RNA Amplification Kit (Illumina). RNA was purified and the quality assessed using an Agilent bioanalyser. Biotinylated cRNA was hybridised to Illumina HumanHT-12 (v4.0) expression beadchips according to the manufacturer’s instructions. Beadchips were scanned with an Illumina iScan bead array reader confocal scanner and data extracted using GenomeStudio software.

first: Matthew

last: O'Shea

first: Thomas

middle: E

last: Fletcher

first: Rachel

last: Tanner

first: Magali

last: Matsumiya

first: Wendi

last: Bailey

first: Jayne

last: Jones

first: Steven

last: Smith

first: Gavin

last: Koh

first: William

middle: G

last: Horsnell

first: Nicholas

last: Beeching

last: Dunbar

first: Duncan

last: Wilson

first: Adam

middle: F

last: Cunningham

first: Helen

last: McShane


title: Systematic evaluation of C. elegans lincRNAs with CRISPR knockout mutants [miRNA-seq]

first: Ge

last: Shan

last: Wei


title: MicroRNA expression profile of HCT-8 in the early phase of Cryptosporidium parvum infection

status: Public on Dec 23 2018

city: Zhengzhou

first: Chenrong

last: Wang

address: 95 Wenhua Road

department: College of Animal Science and Veterinary Medicine

institute: Henan Agricultural University

summary: Cryptosporidium parvum is an important zoonotic parasitic disease worldwide, but the molecular mechanisms of the host–parasite interaction are not fully understood. Noncoding microRNAs (miRNAs) are considered key regulators of parasitic diseases. Therefore, we used microarray, qPCR, and bioinformatic analyses to investigate the intestinal epithelial miRNA expression profile after Cryptosporidium parvum infection.Twenty miRNAs were differentially expressed after infection (four upregulated and 16 downregulated). Further analysis of the differentially expressed miRNAs revealed that many important cellular responses were triggered by Cryptosporidium parvum infection, including cell apoptosis and the inflammatory and immune responses.This study demonstrates for the first time that the miRNA expression profile of human intestinal epithelium cells is altered by C. parvum infection. This dysregulation of miRNA expression may contribute to the regulation of host biological processes in response to C. parvum infection, including cell apoptosis and the immune responses. These results provide new insight into the regulatory mechanisms of host miRNAs during cryptosporidiosis, which may offer potential targets for future C. parvum control strategies.

overall_design: In the study presented here,the miRNAs expression profiles of HCT-8 cells at 4 and 12 h post-Cryptosporidium parvum infection were analyzed via microarray, qPCR, and bioinformatic analyses.  Infected and uninfected HCT-8 cells were collected at 4h and at 12h. All HCT-8 cells were washed three times with PBS, and 1 ml TRIZOL reagent (Invitrogen, Carlsbad, CA, USA) was added to each well. Total RNA was isolated according to the manufacturer’s protocols.All assays were performed in triplicate.

first: Limin

last: Liu

first: Huili

last: Zhu


title: Tumorspheres from transformed fibroblasts highlight the great plasticity of differentiated tumorigenic cells

status: Public on Dec 25 2018

city: Biella

first: Paola

last: Ostano

address: via Malta 3

institute: Fondazione Edo ed Elvo Tempia

summary: Tumors are heterogeneous tissues. A subpopulation of cells with stemness features (cancer stem cells: CSCs) has been implicated in tumor maintenance and progression. There is evidence that CSCs can originate from tumor cell dedifferentiation. Here we used in vitro transformed human fibroblasts (cen3tel cells) and the tumorsphere assay to search for and possibly characterize CSCs from differentiated transformed cells.   To obtain tumorspheres, cen3tel cells were grown in the absence of serum and in the presence of growth factors. Sphere cells were analysed for the expression of specific genes and their genome wide gene expression profiles relative to cells grown in adhesion were determined by microarray analysis.  Cen3tel cells formed spheres showing self-renewal capacity and Sox2 overexpression, suggesting that they contained a subset of cells with CSC-like features. Sphere cells displayed the deregulation of a c-MYC-miR-34a circuitry, likely associated with cell protection from apoptosis. Gene expression profiles of sphere cells revealed an extensive transcriptional reprogramming. Genes upregulated in tumorspheres identified processes related to tumorigenesis and stemness, such as chromatin organization, cholesterol biosynthetic pathway, apoptosis suppression, immunity and defense, interferon mediated immunity and cytokine and chemokine mediated signalling pathway. However, sphere cells were only slightly more tumorigenic in vivo than adherent cells.  Our results indicate that tumorigenic cells obtained from differentiated human fibroblasts are highly plastic and can acquire cancer stem cells properties. However, tumorsphere cells are not the main tumorigenic population, highlighting a further level of complexity in tumor heterogeneity.

overall_design: Gene expression profiling of sphere and adherent cells

first: Bartolo

last: Bono

first: Martina

last: Peritore

first: Ilaria

last: Gregnanin

first: Cristina

last: Belgiovine

first: Giovanna

last: Chiorino

last: Chiodi

first: Chiara

last: Mondello


title: WhiB6 is required for the secretion-dependent regulation of ESX-1 substrates in pathogenic mycobacteria

city: Jeddah

first: Qingtian

last: Guan

address: Thuwal

country: Saudi Arabia

institute: King Abdallah University of Science and Technology

summary: These data show that WhiB6 is required for the secretion-dependent regulation of ESX-1 substrates and ESX-1 substrates are regulated independently from the structural components, both during infection and as a result of active secretion.

sample_organism:
Mycobacterium tuberculosis H37Rv
Mycobacterium marinum M
Mycobacterium marinum E11

overall_design: RNA expression profiles of Mycobacterium tuberculosis Wild-type and ESX1 mutant, Mycobacterium marinum Wild Type and ESX1 mutant was generated and compared. WhiB6 was then further selected as the target gene which has been knocked out and the transcriptome data was also generated in this study.

first: Abdallah

middle: M

last: Abdallah

first: E

last: Weerdenburg

first: R

last: Ummels

first: S

last: Borggreve

middle: A

last: Adroub

first: Tareq

middle: B

last: Malas

first: Raeece

last: Naeem

first: Huoming

last: Zhang

first: T

last: Otto

first: W

last: Bitter

first: A

last: Pain


title: A methylated-DNA-binding complex required for plant development mediates transcriptional activation of promoter methylated genes

first: xinjian

last: He

type: Methylation profiling by high throughput sequencing

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

overall_design: Refer to individual Series


title: The embryonic transcriptome of Arabidopsis thaliana

status: Public on Dec 21 2018

city: Wageningen

first: Michael

last: Nodine

state: Gelderland

address: Radix West

department: Plant Sciences

institute: Wageningen University & Research

summary: Cellular differentiation is associated with changes in transcript populations. Accurate quantification of transcriptomes during development can thus provide global insights into differentiation processes including the fundamental specification and differentiation events operating during plant embryogenesis. However, multiple technical challenges have limited the ability to obtain high quality early embryonic transcriptomes, namely the low amount of RNA obtainable and contamination from surrounding endosperm and seed-coat tissues. We compared the performance of three low-input mRNA sequencing (mRNA-seq) library preparation kits on 0.1 to 5 nanograms (ng) of total RNA isolated from Arabidopsis thaliana (Arabidopsis) embryos and identified a low-cost method with superior performance. This mRNA-seq method was then used to profile the transcriptomes of Arabidopsis embryos across eight developmental stages. By comprehensively comparing embryonic and post-embryonic transcriptomes, we found that embryonic transcriptomes do not resemble any other plant tissue we analyzed. Moreover, transcriptome clustering analyses revealed the presence of four distinct phases of embryogenesis which are enriched in specific biological processes. We also compared zygotic embryo transcriptomes with publicly available somatic embryo transcriptomes. Strikingly, we found little resemblance between zygotic embryos and somatic embryos derived from late-staged zygotic embryos suggesting that somatic and zygotic embryo transcriptomes are distinct from each other. In addition to the biological insights gained from our systematic characterization of the Arabidopsis embryonic transcriptome, we provide a data-rich resource for the community to explore.

overall_design: mRNA-seq libraries were generated from three biological replicates of 50 Col-0 (wild type) embryos at eight different developmental stages (i.e. 8-cell/16-cell to mature green). Additionally, mRNA-seq libraries were prepared from total RNA isolated from 50 bent-cotyledon staged embryos and then diluted to 5, 1, 0.5 or 0.1 nanograms prior to library construction with three different library preparation methods.

first: Falko

last: Hofmann

last: Schon


title: Gene expression profiling of metastasising and non-metastasising canine primary cutaneous mast cell tumours

status: Public on Dec 20 2018

city: Newmarket

first: Mike

last: Starkey

address: Lanwades Park

institute: Animal Health Trust

summary: In this study the global expression profiles of primary cutaneous mast cell tumours that metastasised were compared with those of primary tumours that did not metastasise. The objective was to identify genes involved in mast cell tumour metastatic progression that may represent targets for therapeutic intervention and biomarkers for prediction of tumour metastasis.

overall_design: Canine Gene 1.1 ST Arrays were employed for gene expression analysis of formalin-fixed, paraffin-embedded biopsies of mast cell tumours borne by 18 dogs that died due to confirmed mast cell tumour metastasis and 16 dogs that were still alive more than 1000 days post-surgery.


title: Integrated mRNA and miRNA profiles expression of liver between Jinhua and Landrace pigs

city: Hangzhou

first: Minjie

last: Huang

address: NO.388 Yuhangtang Rd

institute: Zhejiang University

summary: To explore the molecular mechanisms of fat metabolism and deposition in pigs, an experiment was conducted to identify hepatic mRNAs and miRNAs expression and determine the potential interaction of them in two phenotypically extreme pig breeds.

overall_design: mRNA and miRNA profiles of Jinhua pigs and  Landrace pigs were generated by deep sequencing, in triplicate, using Illumina Hiseq2500.

first: Lixing

last: Chen

first: Yifei

last: Shen

first: Jiucheng

first: Xiaoling

last: Guo

first: Ningying

last: Xu


title: A methylated-DNA-binding complex required for plant development mediates transcriptional activation of promoter methylated genes [RNA-seq]

overall_design: Examination of the mRNA expression in Arabidopsis

first: Qiang-Qiang

last: Zhao

first: Xin-Jian


title: Comparison of Porphyromonas gingivalis W83 gene expression when grown with or without galactose

city: Gainesville

first: Zachary

middle: Daniel

last: Moye

state: Florida

address: 1395 Center Drive

institute: University of Florida

summary: Porphyromonas gingivalis (P. gingivalis) W83 cultures in early exponential phase were supplemented with 0.1% galactose or vehicle control. The cultures were then permitted to grow anaerobically at 37°C for 3 hours, which corresponds to approximately one doubling of P. gingivalis. At this point, RNA extraction was performed using the cultures, and these samples were processed and submitted for RNA sequencing using an Illumina platform. Modest changes in gene expression were observed between cultures grown with or without galactose, and the majority of changes were associated with processes occurring at the cell membrane.

overall_design: Cultures of P. gingivalis W83 were grown in Trypticase Soy Broth without glucose supplemented with hemin and menadione (TSBHK). Once cultures reached mid-exponential phase, the bacterial cultures were supplemented with 0.1% galactose or water (as a control). Both sets of cultures were grown in triplicate.

first: Courtney

last: Gormley

first: Mary

last: Davey


title: The RNA helicases Has1, Mak5 and Spb4 mediate diverse functions at distinct regions of pre-ribosomal complexes

status: Public on Dec 19 2018

city: Goettingen

first: Markus

middle: T.

last: Bohnsack

address: Humboldtallee 23

department: Institute for Molecular Biology

institute: Goettingen University

summary: Assembly of eukaryotic ribosomal subunits is a highly dynamic and energy-consuming process involving numerous structural and compositional changes. Here, we identify the pre-ribosomal binding sites of three ATP-dependent RNA helicases Has1, Mak5 and Spb4 and by elucidating the precise targets of these enzymes, we uncover direct roles of Has1 in mediating release of the U14 snoRNA and dissociation of a cluster of early pre-60S biogenesis factors. We further discover pre-rRNA remodelling by Mak5 enables recruitment of the ribosomal protein Rpl10 in the cytoplasm and show that binding of Spb4 to a molecular hinge at the base of ES27 facilitates binding of the export adaptor Arx1 to pre-60S complexes. Our data highlight RNA helicases as key regulators of critical events during ribosome biogenesis and provide novel insights into the structural remodelling events that take place during assembly of the ribosomal subunits.

overall_design: Wild-type BY4741 yeast cells or cells expressing genomically His-Tev-ProtA-tagged Has1, Mak5 or Spb4 were grown in the presence of 4-thiouracil, crosslinked using light at 365 nm and analysed by CRAC.

first: Lukas

last: Brüning

first: Philipp

last: Hackert

first: Roman

last: Martin

first: Katherine

last: Sloan

middle: T


title: Variation in DNA methylation of human blood over a 1-year period using the Illumina MethylationEPIC array

status: Public on Dec 18 2018

city: Kansas City

first: Devin

middle: Charles

last: Koestler

state: KS

address: 3901 Rainbow Boulevard

department: Biostatistics

institute: The University of Kansas Cancer Center

summary: Assessing DNA methylation profiles in human blood has become a major focus of epidemiologic inquiry. Understanding variability in CpG-specific DNA methylation over moderate periods of time is a critical first step in identifying CpG sites that are candidates for DNA methylation-based etiologic, diagnostic and prognostic predictors of pathogenesis. Using the Illumina MethylationEPIC [850K] BeadArray, DNA methylation was profiled in paired whole blood samples collected approximately 1 year apart from 35 healthy women enrolled in the Nurses Study II cohort. The median intraclass correlation coefficient (ICC) across all CpG loci was 0.19 [Interquartile Range (IQR) 0.00–0.50]; 74.8% of ICCs were in the low range (0–0.5), 16.9% in the mid-range of ICCs (0.5–0.8), and 8.3% in the high-range of ICCs (0.8–1). ICCs were similar for CpG probes on the 450K Illumina array (median 0.17) and the new probes added to the 850K array (median 0.21). ICCs for CpG loci on the sex chromosomes and known metastable epialleles were high (median 0.71, 0.97, respectively), and ICCs among methylation quantitative trait loci (mQTL) CpGs were significantly higher as compared to non-mQTL CpGs (median 0.73, 0.16, respectively, P < 2 × 10–16). We observed wide variation in DNA methylation stability over a 1-year period. Probes considered non-stable, due to substantial variation over a moderate period of time and with minimal variability across individuals could be removed in large epidemiological studies. Moreover, adjusting for technical variation that arises from using high-dimensional arrays is critical.

overall_design: Peripheral blood samples collected from 35 healthy women enrolled in the Nurses Study II cohort at two time-points, spaced approximately 1 year from one another, were profiled for DNA methylation using the Illumina Infinium HumanMethylationEPIC Beadchip.  One of the study samples was excluded due to poor quality DNA methylation data, leaving 69 total samples with 34 individuals having DNA methylation measurements at both time-points.

first: Ina

last: Zaimi

first: Dong

last: Pei

first: Carmen

last: Marsit

first: Immaculata

last: De Vivo

first: Shelley

middle: S

last: Tworoger

first: Alexandra

last: Shields

first: Karl

last: Kelsey

first: Dominique

last: Michaud


title: Curcumin and novel synthetic analogs in Alzheimer’s disease prevention

city: Pavia

first: Stella

last: Gagliardi

state: Pavia

address: Via Mondino, 2

department: GPG center

institute: IRCCS Mondino Foundation

summary: Alzheimer's disease (AD) is a chronic neurodegenerative disorder that is associated with the most common type of dementia and is characterized by the presence of deposits of the protein fragment beta‐amyloid (Aβ) in the brain. The natural product mixture of curcuminoids that improves certain defects in innate immune cells of AD patients may selectively enhance Aβ phagocytosis by alteration of gene transcription. In this work, we evaluated the protective effects of curcuminoids in cells from AD patients by investigating the effect of a panel of curcuminoids on NF-kB and BACE1 signaling pathways by gene expression profiling on the clearance of Beta Amyloid (Aβ). Bisdemethoxycurcumin (BDC) showed the most potent protective action to reduce levels of NF‐kB and BACE1, decrease the inflammatory cascade and diminish Aβ aggregates in cells from AD patients. Moreover, mannosylglycoprotein 4-beta-N-acetylglucosaminyltransferase (MGAT3) and vitamin D receptor (VDR) gene mRNAs were up-regulated in peripheral blood mononuclear cells from AD patients treated with BDC. BDC treatment impacts both gene expression, such as Mannosyl (Beta‐1,4‐)‐Glycoprotein Beta‐1,4‐N‐Acetylglucosaminyltransferase, Vitamin D and Toll like receptors and Aβ phagocytosis. Down-regulation of BACE1 and NF-kB following administration suggests a method to treat asymptomatic AD patients with selective curcumins as a dietary supplement.

overall_design: XX AD paients (codes)  were treated with different compounds (YY) and compared to healthy controls with identical treatment.

first: Valentina

last: Franco

first: Stefano

last: Sorrentino

first: Susanna

last: Zucca

first: Cecilia

last: Pandini

first: Paola

last: Rota

last: Bernuzzi

first: Alfredo

last: Costa

first: Elena

last: Sinforiani

first: Orietta

last: Pansarasa

first: John

last: Cashman

first: Cristina

last: Cereda


title: The G-rich repeats in FMR1 and C9orf72 loci are hotspots for R-loop retention and for local unpairing of DNA

city: jerusalem

first: Manar

last: Abu Diab

address: Shmu'el Bait St 12, Jerusalem, 9103102

department: Genetics

country: Israel

institute: Shaare Zedek Medical Center

summary: We finely mapped single strand DNA displacements in FMR1 and C9orf72 and RPLA13A, a non-repetitive control locus.

overall_design: Single strand DNA displacements were mapped by locus-specific DNA deep-sequencing following bisulfite treatment under non-denatured conditions in wild type alleles of FMR1, C9orf72 and RPLA13A

first: Eiges

last: Rachel


title: Conserved Transcriptomic Profiles Underpin Monogamy across Vertebrates

city: Austin

first: Rebecca

middle: L

last: Young

state: TX

address: 2415 Speedway

department: Integrative Biology

institute: University of Texas at Austin

summary: We compare fore- and mid-brain transcriptomes of reproductive males in monogamous and non-monogamous species pairs of Peromyscus mice, Microtus voles, parid songbirds, dendrobatid frogs, and Xenotilapia species of cichlid fishes. Our study provides evidence of a universal transcriptomic mechanism underlying the evolution of monogamy in vertebrates.

sample_organism:
Peromyscus maniculatus
Microtus pennsylvanicus
Peromyscus californicus
Anthus spinoletta
Oophaga pumilio
Microtus ochrogaster
Ranitomeya imitator
Xenotilapia ornatipinnis
Prunella modularis
Xenotilapia spiloptera

overall_design: Fore- and mid-brain mRNA of  reproductive males samples (n=3) were pooled and sequenced using an Illuma HiSeq platform.

first: Michael

middle: H

last: Ferkin

first: Nina

last: Ockendon

first: Veronica

middle: N

last: Orr

first: Steven

last: Phelps

first: Ákos

last: Pogány

first: Corinne

last: Richards-Zawacki

first: Kyle

last: Summers

first: Tamás

last: Székely

first: Brian

last: Trainor

first: Araxi

middle: O

last: Urrutia

first: Gergely

last: Zachar

first: Lauren

last: O'Connell

first: Hans

last: Hofmann


title: A-to-I RNA editing affects lncRNAs expression after heat shock

status: Public on Dec 12 2018

city: Haifa

first: Ayelet

last: Lamm

address: Technion st

department: Biology

institute: Technion

summary: Adenosine to inosine (A-to-I) RNA editing is a highly conserved regulatory process carried out by adenosine deaminases (ADARs) on dsRNAs. Although a significant fraction of the transcriptome is edited, the function of most editing sites is unknown. Previous studies indicated changes in A-to-I RNA editing frequencies following exposure to several stress types. However, the overall effect of stress on the expression of ADAR targets is not fully understood. Here we performed high-throughput RNA sequencing of wildtype and ADAR mutant C. elegans worms after heat shock, to analyze the effect of heat shock stress on the expression pattern of genes. We found that ADAR regulation following heat shock does not involve directly heat shock related genes. Our analysis also revealed that, lncRNAs and pseudogenes, which have a tendency for secondary RNA structures, are enriched among upregulated genes upon heat shock in ADAR mutant worms, while they are downregulated in ADAR mutant worms under permissive conditions. Therefore, temperature increases may destabilize dsRNA structures and protect them from RNAi degradation, despite the lack of ADAR function. These findings shade a new light on the dynamics of gene expression under heat shock in relation to ADAR function.

overall_design: Wildtype (N2) and ADAR mutant worms (BB21 and BB4) were subjected to heat shock treatment. In parallel, the same strains were suspended under standard conditions, as a control. Total RNA was extracted and poly(A) enriched libraries were generated from each sample. High-throughput mRNA-sequencing was carried out. DESeq2 package (1) in R was used to identify differentially expressed genes under heat shock.

first: Roni

last: Haas


title: Global identification of Arabidopsis lncRNAs reveals the regulation of MAF4 by a natural antisense RNA

status: Public on Dec 11 2018

city: Beiing

first: Yijun

last: Qi

address: NO.1 Qinghuayuan

institute: Tsinghua University

summary: Long non-coding RNAs (lncRNAs) have emerged as important regulators of gene expression and plant development. Here, we identified 6,510 lncRNAs in Arabidopsis under normal or stress conditions. We found that the expression of natural antisense transcripts (NATs) that are transcribed in the opposite directionof protein-coding genes often positively correlates with and is required for theexpression of their cognate sense genes. We further characterized MAS, a NAT-lncRNA produced from the MADS AFFECTING FLOWERING4 (MAF4) locus.MAS is induced by cold and indispensable for the activation of MAF4 transcriptionand suppression of precocious flowering. MAS activates MAF4 by interacting with WDR5a, one core component of the COMPASS-like complexes, and recruiting WDR5a to MAF4 to enhance histone 3 lysine 4 trimethylation (H3K4me3). Our study greatly extends the repertoire of lncRNAs in Arabidopsis and reveals a role for NAT-lncRNAs in regulating gene expression in vernalization response and likely in other biological processes

overall_design: To globally identify lncRNAs in Arabidopsis, we reconstructed an Arabidopsis transcriptome using high depth strand-specific RNA sequencing (ssRNA-seq). We generated cDNA libraries for rRNA-depleted total, polyadenylated [poly(A)+] and non-polyadenylated [poly(A)-] RNAs in whole cell extract, nuclear and cytosolic fractions that were prepared from Arabidopsis grown under normal or stress conditions

first: Xinyue

last: Zhao

first: Jingrui

last: Li

first: Bi

last: Lian

first: Hanqing

last: Gu

first: Yan


title: Compared gene expression during seed germination (12 hai) in the nac25 (KO2) and nac1L (KO1) null mutants and wild-type (Columbia-0) controls using deep sequencing of RNA populations (RNA-seq).

city: Pozuelo de Alarcón

first: Luis

last: Oñate-Sánchez

state: Madrid

address: Campus de Montegancedo, Autopista M-40 (Km 38)

institute: Centro de Biotecnología y Genómica de plantas (Universidad Politécnica de Madrid)

summary: A key component of seed germination is the interplay of mechanical forces governing embryo growth and the surrounding restraining endosperm tissue. Endosperm cell separation is therefore thought to play a critical role in the control of this developmental transition. Here we demonstrate that in Arabidopsis thaliana seeds, endosperm cell expansion is a key component of germination. Endosperm cells expand to accommodate embryo growth prior to germination. We show that this is an actively regulated process supported by spatiotemporal control of the cell expansion gene EXPANSIN 2 (EXPA2). The NAC transcription factors NAC25 and NAC1L were identified as upstream regulatory effectors of EXPA2 expression, GA-mediated endosperm expansion and seed germination. The DELLA protein RGL2 repressed activation of EXPA2 promoter by NAC. Our findings demonstrate a key role of this gene network in regulating endosperm cell-expansion to control the seed to seedling transition.

overall_design: Three genotypes were analyzed: WT (Arabidopsis thaliana Col-0), nac25 (KO2; loss-of-function mutant) and nac1L (KO1; loss-of-function mutant). Seeds from each genotype (20mg) were imbibed in agarose (0,6%) plates and collected for RNA extraction after 12h. Three biological replicates per genotype were used.

first: Rocío

last: Sánchez-Montesino


title: Gene expression profiling of T cells of CLL patients, stimulated with antiCD3 antibody in presence or not of idelalisib

city: Modena

first: silvia

last: martinelli

address: via del pozzo 71

institute: University of Modena and Reggio Emilia

summary: The aim of the study is to identify genes modulated by idelalisib in T cells of CLL patients, that could suggest an impairment of T cell-mediated immunity caused by the drug. We found 61 genes downregulated by idelalisib in stimulated T cells with Anova p≤0.01 and [FC]≥2 and the most represented categories were chemokines involved in T cell migration (as CXCL9-10-11), inflammatory and T helper cytokines (as IL-2, TNFα, IFNg, IL-13, IL-21), mitogenic signal transducers (as IRF4, STAT1, EGR1-2-3-4) and receptors (as CD69, CD25) commonly induced during activation of T cells.

overall_design: T cells were purified from peripheral blood (Pan T cell Isolation kit, Miltenyi Biotech) of n=4 CLL patients and cultured with the three following conditions: i) ctrl (no treatment/no stimulation), ii) antiCD3 (stimulation with antiCD3 antibody), iii) antiCD3 + ide (pre-treatment with idelalisib followed by antiCD3 stimulation). After 4 hours, total RNAs were extracted from T cells and gene expression profiles were measured by hybridization on 4X44K Whole Human Genome Microarray (Agilent Technologies). We first identified differentially expressed genes between the three conditions with Anova p≤0.01. Among these, we focused on genes with [FC]≥2 between antiCD3 and antiCD3+ide conditions.

first: Silvia

last: Martinelli

first: Roberto

last: Marasca


title: Epigenome analysis of pheochromocytoma/paraganglioma samples

city: Brussels

first: Laura

last: Saucedo

address: Laarbeeklaan 103

country: Belgium

institute: Follicle Biology Lab - VUB

summary: Genome wide DNA methylation profiling of pheochromocytoma/paraganglioma samples carrying different mutations. The Illumina Infinium EPIC Human DNA methylation Beadchip was used to obtain DNA methylation profiles.

overall_design: Bisulphite converted DNA from the 31 samples were hybridised to the Illumina Infinium EPIC Human Methylation Beadchip

first: Remacha

last: Laura

first: Robledo

last: Mercedes

first: Cascon

last: Alberto


title: Cardiomyocyte mRNA  Content

city: Nashville

first: Dhivya

last: Sudhan

state: TN

address: 777 Preston Research Building

department: Hematology/Oncology Division

institute: Vanderbilt University

summary: Determine mRNA expression levels in cultured cardiomyocytes derived from human iPS cells

overall_design: 1 sample

first: Aidan

last: Fenix

first: Dylan

last: Burnette


title: anac019-1 (SALK_096295) flower transcritome under severe drought stress

status: Public on Dec 10 2018

city: University Park

first: Zhao

last: SU

state: PA

address: 354 N. Frear

institute: The Penn State University

summary: We performed microarray to determine transcriptomic changes upon anac019-1 under drought, identifying hundreds of genes that potentially function downstream of ANAC019 and mediate drought responses in the flower, including genes encoding transcription factors that likely play crucial regulatory roles.

overall_design: ANAC019 mutant (SALK_096295) were well-watered until after just bolting (after 24 days growth with the main stem about 1 cm high) when drought treatment was started by withholding water (defined as day 0 for drought treatment). The relative soil moisture content decreased sharply and, after about 80 hours (defined as day 3 for drought treatment), the relative soil moisture content was near 35% of the soil water-holding capacity. The soil water condition was maintained by daily watering until almost all the fruits were mature and ready to harvest. Unopened flower samples were collected from drought treated plants, at day 3, 4, 5.

last: Su

first: Noor Liyana

last: Sukiran

first: Hong

last: Ma


title: Oxygen-dependent proteolysis regulates the stability of angiosperm Polycomb Repressive Complex 2 subunit VERNALIZATION2

status: Public on Dec 07 2018

city: Birmingham

first: Daniel

middle: James

last: Gibbs

state: West Midlands

address: Edgbaston

department: School of Biosicences

country: United Kingdom

institute: The University of Birmingham

summary: The polycomb repressive complex 2 (PRC2) regulates epigenetic gene repression in eukaryotes.  Mechanisms controlling its developmental specificity and signal-responsiveness are poorly understood.  Here, we identify an oxygen-sensitive N-terminal (N-) degron in the plant PRC2 subunit VERNALIZATION(VRN)2, a homolog of animal Su(z)12, that promotes its degradation via the N-end rule pathway.  We provide evidence that this N-degron arose early during angiosperm evolution via gene duplication and N-terminal truncation, facilitating expansion of PRC2 function in flowering plants.  We show that proteolysis via the N-end rule pathway prevents ectopic VRN2 accumulation, and that hypoxia and long-term cold exposure lead to increased VRN2 abundance, which we propose may be due to inhibition of VRN2 turnover via its N-degron.  Furthermore, we identify an overlap in the transcriptional responses to hypoxia and prolonged cold, and show that VRN2 promotes tolerance to hypoxia. Our work reveals a mechanism for post-translational regulation of VRN2 stability that could potentially link environmental inputs to the epigenetic control of plant development.

overall_design: RNA was extracted from non-vernalized (0v; C) or 4 week vernalized (4v; V) seedlings.  Three biological replicates for each treatment were used for subsequent RNA sequencing

middle: J


title: Expression data in ischemic brain tissue and brain Tregs

status: Public on Dec 01 2018

city: Fukuoka

first: Minako

last: Ito

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

institute: Kyushu University

summary: Foxp3+ regulatory T cells (Tregs) are critical components of immune tolerance. In addition, Tregs residing in non-immune tissues perform specialized functions in tissue homeostasis and remodeling. The characteristics and functions of brain Tregs, however, are not well understood, in part because the number of Tregs in the brain under normal conditions is very low. However, during the chronic phase two weeks after a stroke caused by ischemic brain injury, a massive accumulation of Tregs occurs in the brain. We found that brain Tregs differ from Tregs in other tissues such as adipose tissue (VAT) and muscle Tregs.

overall_design: Total RNA was isolated using a TRIzolTM LS reagent (Invitrogen). Microarray analysis was performed using　 one-color and hybridized to SurePrint G3 Mouse Gene Expression 60K × 8 v2 (Agilent), all according to the respective manufacturer's instructions.

first: Setsuko

last: Mise

first: Mana

last: Iizuka-Koga

first: Kyoko

last: Komai

first: Taisuke

last: Kondo

first: Hiroko

last: Nakatsukasa

first: Makoto

last: Ando

first: Takashi

last: Shichita

first: Akihiko

last: Yoshimura


title: Editing of measles virus genomic RNA by ADAR1

status: Public on Dec 04 2018

city: Rochester

first: Christian

middle: Karl

last: Pfaller

state: MN

address: 200 First Street SW

department: Molecular Medicine

country: USA

institute: Mayo Clinic

summary: RNAseq analysis of purified measles virus RNA grown in standard HeLa cells, p150KO or ADAR1KO cells

overall_design: Six samples: MeV-vac2(GFP) RNA from HeLa, p150KO and ADAR1KO cells; MeV-CKO(GFP) RNA from HeLa, p150KO and ADAR1KO cells

middle: K

first: Roberto

last: Cattaneo


title: EnD-Seq and AppEnD: Sequencing 3' ends to identify non-templated tails and degradation intermediates

status: Public on Nov 30 2018

city: Chapel Hill

first: Christopher

last: Holmquist

state: NC

address: 208 Fordham Hall

institute: UNC Chapel Hill

summary: Existing methods for detecting RNA intermediates resulting from exonuclease degradation are low-throughput and laborious. In addition, mapping the 3’ ends of RNA molecules to the genome after high-throughput sequencing is challenging, particularly if the 3’ ends contain posttranscriptional modifications. To address these problems, we developed EnD-Seq, a high-throughput sequencing protocol that preserves the 3’ end of RNA molecules, and AppEnD, a computational method for analyzing high-throughput sequencing data. Together these allow determination of the 3’ ends of RNA molecules, including nontemplated additions. Applying EnD-Seq and AppEnD to histone mRNAs revealed that a significant fraction of cytoplasmic histone mRNAs end in one or two uridines, which have replaced the 1-2 nts at the 3’ end of mature histone mRNA maintaining the length of the histone transcripts.

overall_design: Libraries were prepared essentially as described in Welch, Slevin et al. (RNA. 2015 Jul; 21(7): 1375–1389.)

first: William

middle: F

last: Marzluff

first: Chistopher

middle: E