title: Genome wide transcriptional alterations during post-infarct remodeling in type 2 diabetic mice.

city: Kuopio

first: Merja

last: Heinäniemi

address: Yliopistonranta 1

institute: university of eastern finland

summary: The cellular and molecular aspects of post-infarct left-ventricle remodeling in presence of type-2 diabetes is poorly understood. In this study we have addressed the cellular and molecular aspects underlying post-infarct left-ventricle remodeling in type 2 diabetic (T2DM) mice using genome-wide mRNA-sequencing. Myocardial infarction was induced by ligating left-anterior descending artery (LAD) in 12-14 month old T2DM and control mice. Cardiac MRI was performed at baseline, day 7 and 14 post-LAD ligation. Blood and tissue samples were collected for biochemical and immunohistochemical, molecular biology analysis after sacrification at day 7 and 14.  Genome-wide mRNA sequencing analysis was performed from left-ventricular tissues collected at day 7 post-LAD ligation. Mitochondrial dynamics, Leukocyte recruitment and Collagen I deposition were analyzed using electron microscopy, fluorescent assisted cell sorting (FACS) and fourier-transform infra-red (FTIR) spectroscopy from left ventricular tissues collected at day 7 and 14 post-LAD ligation. Cardiac ejection fraction (EF) and stroke volume (SV) were significantly reduced along with increased mortality in T2DM compared to controls. Ingenuity pathway analyses of differentially expressed genes were enriched for mitochondrial dysfunction, TCA cycle and fatty acid oxidation. Additionally, upstream transcription factor analysis showed inhibition of PGC1a, PGC1b, ESRRA, ESRRB and TFAM in infarcted myocardium of T2DM mice. Electron microscopy analysis showed an altered mitochondrial dynamics and cardiomyocyte death in ischemic myocardium of T2DM mice. Leukocytes exhibited an altered phenotype in ischemic myocardium of T2DM mice. Neovascularization was impaired and collagen deposition was increased in ischemic myocardium of T2DM mice. We conclude that an altered mitochondrial dynamics, cell death modalities, leukocyte phenotype, neovascularization responses and fibrosis may contribute to an increased mortality after myocardial infarction in T2DM. Modulation of mitochondrial dynamics and cardiomyocyte cell death modalities may offer a novel therapeutic target.

overall_design: Myocardial infarction was induced by ligating left anterior descending artery (LAD). Total RNA was isolated from remote, Infarct and border zones at day 7 after myocardial infarction. Poly (A)+RNA fraction was subjected to RNA sequencing using Illumina HiSeq.

first: Babu

last: Mohan

first: Devi

last: Durga

first: Minna

last: Kaikkonen

first: Seppo

last: Ylä-Herttuala


title: Next Generation Sequencing Facilitates Quantitative Analysis of pancreatic tissue transcriptomes from Wild Type and miR-21-/- mice treated with caerulein

status: Public on Nov 07 2017

city: Guangzhou

first: Xiaodong

last: Ma

state: Guangdong

address: Rm406,Building 29, South China Normal University

country: China

institute: South China Normal University

type: Expression profiling by high throughput sequencing

summary:
Purpose: Purpose: we used next generation sequencing to analyze gene expression profiles of pancreatic tissues from wild-type (WT) and miR-21-/- (miR-21 KO) mice treated with saline(control) or caerulein. The goals of this study are to compare the different gene expression profiles of pancreatic tissue between WT and miR-21 KO mice treated with caerulein.
Methods: Female WT and miR-21 KO mice were administered 8-hourly intraperitoneal injection of 50μg/kg caerulein. Mice were sacrificed at 24 hours after the first caerulein injection and total RNA was extracted. mRNArna profiles were generated by deep sequencing WT treated with saline in single, WT treated with caerulein in duplicate, miR-21KO treated with caerulein in duplicate, using High-seq 2000 Illumina sequencing platform. The sequence reads that passed quality filters were analyzed at the transcript isoform level with two methods: Burrows–Wheeler Aligner (BWA) followed by ANOVA (ANOVA) and TopHat followed by Cufflinks. qRT–PCR validation was performed using TaqMan and SYBR Green assays
Results: After quality filtering of raw sequencing data, we obtained 32,797,327 (69.9%) out of 46,941,672 tags from WT mice treated with saline, 42,587,312 (87.1%) out of 48,919,213 tags from WT mice treated with caerulein, and 57,139,408 (85.1%) out of 67,111,415 tags from miR-21 KO mice treated with caerulein. We then mapped these tags to the mouse genome. We identified 1457 differential expressed genes (DEGs) between WT mice treated with caerulein and with saline, and 152 genes between WT mice and miR-21 KO mice treated with caerulein with a fold change more than 2.0 (up-regulation) or less than 0.5 (down-regulation). Altered expression of 16 genes was confirmed with qRT-PCR.
Conclusions: Our study represents the first detailed analysis of pancreatic transcriptomes generated by RNA-seq technology. By using RNA-seq based transcriptome analysis, we identified 6 miR-21 target genes and 10 downregulated genes involved in pancreatic injury. Specifically, up-regulation of Pias3 and down-regulation of Hmgb1 when miR-21 was ablated coincided with reduced pancreatitis severity. We conclude that RNA-seq based transcriptome characterization would expedite genetic network analyses and permit the dissection of complex pancreatic functions.

overall_design: Pancreatic mRNA profiles of WT and miR-21 KO mice treated with caerulein were generated by deep sequencing, WT treated with saline in single, WT treated with caerulein in duplicate, miR-21KO treated with caerulein in duplicate, using High-seq 2000 Illumina sequencing platform.


title: Hippocampus CA1 pyramidal cells Transcriptomic profile in WT and Fmr1 KO mice, using Wfs1-CreERT2:RiboTag:Frm1 knockout and wildtype mice

status: Public on Nov 08 2017

city: Montpellier

first: Julie

last: Perroy

address: 141 rue de la Cardonille

country: France

institute: CNRS

summary: Comparing WT mice to a mouse model of mental retardation, this work identifies genes which display differences in ribosome-bound mRNAs, in hippocampus CA1 pyramidal cells. These genes products are potent functional components of neuronal plasticity and hippocampus-dependent memory.

overall_design: Using a triple transgenic mouse line, we immunoprecipitated the HA-Rpl22 protein to isolate and sequence ribosome-associated mRNA in CA1 pyramidal cells. Pairwise comparison of wild type and Fmr1 KO mice defined a specific gene expression profile.

first: Laura

last: Ceolin

first: Nathalie

last: Bouquier

first: Jihane

last: Vitre

first: Federica

last: Bertaso

first: Stéphanie

last: Rialle

first: Dany

last: Severac

first: Emmanuel

last: Valjent

first: Emma

last: Puighermanal


title: H9-hESC derived human neural stem cells with combinations of mutant IDH1-R132H overexpression, P53 shRNA knockdown and/or ATRX shRNA knockdown

status: Public on Nov 09 2017

city: New York

first: Aram

middle: S

last: Modrek

state: NY

address: 460 E 26th Street

department: Radiation Oncology

country: USA

institute: New York University School of Medicine

type: Methylation profiling by genome tiling array

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

overall_design: Refer to individual Series


title: SOX2 promoter 4C-seq of H9-hESC derived human neural stem cells with mutant IDH1-R132H overexpression, P53 shRNA knockdown and ATRX shRNA knockdown

summary: 4C-seq was performed to assess genomic contacts with the SOX2 protmoter, human neural stem cells with no oncogenic alterations were compared to those with concurrent IDH1-R132H overexpression, P53 shRNA knockdown and ATRX shRNA knockdown.

overall_design: 4C-seq was performed in duplicates, there are two conditions total. Vector NSCs are the control line and have an empty mCherry vector and a scramble shRNA vector. Three-hit NSCs express mutant-IDH1, P53 knockdown and ATRX knockdown.

first: Dimitris

middle: G

last: Placantonakis


title: Brain-specific deletion of histone variant H2A.z results in cortical neurogenesis defects and neurodevelopmental disorder

city: Beijing

first: Jianwei

last: Jiao

state: Beijing

address: 1 Beichen West Road

department: State Key Laboratory of Reproductive Biology

institute: Institute of Zoology, Chinese Academy of Sciences

type: Genome binding/occupancy profiling by high throughput sequencing

summary: ChIP experiment was performed with antibody against H3K36me3 (active motif; 61101). we generated genome-wide characterization of H3K36me3 occupancy in E13 H2A.Z cKO forebrain. We found H3K36me3 is decreased throughout the whole genome in E13 H2A.Z cKO forebrain.

overall_design: Genomic characterization of H3K36me3 binding in E13 WT and brain-specific deficit H2A.z forebrain.

first: Tianjin

last: Shen


title: RNA-seq of H9-hESC derived human neural stem cells with combinations of mutant IDH1-R132H overexpression, P53 shRNA knockdown and/or ATRX shRNA knockdown

summary: RNA-seq was performed to assess gene expression alterations by the addition of serial oncogenic hits (mutant-IDH1, P53 knockdown and ATRX knockdown) in human neural stem cells.

overall_design: All RNA-seq was performed in duplicates, there are four conditions total. Vector NSCs are the control line and have an empty mCherry vector and a scramble shRNA vector. One hit NSCs express mutant-IDH1 and have a scamble shRNA vector. Two-hit NSCs express mutant IDH1 and have p53 knockdown. Three-hit NSCs express mutant-IDH1, P53 knockdown and ATRX knockdown.


title: A Tripartite Amplification Loop Involving WRKY75, Salicylic Acid and ROS Accelerates Leaf Senescence in Arabidopsis

city: Shenzhen

first: Bosheng

last: Li

address: SUStech Huiyuan #1 406

department: MCDB

institute: SUSTC (current, may different with previous institution )

summary: Leaf senescence is a highly coordinated and complicated process with the integration of numerous internal and environmental signals. Salicylic acid (SA) and reactive oxygen species (ROS) are two well-defined inducers of leaf senescence, whose contents progressively and inter-dependently increase during leaf senescence via a yet unknown mechanism. Here, we have characterized a newly identified positive regulator of leaf senescence, WRKY75, and demonstrated that knock-down or knock-out of WRKY75 delays, while over-expression of WRKY75 accelerates age-dependent leaf senescence. The WRKY75 transcription is induced by age, SA, H2O2, as well as multiple plant hormones. Meanwhile, WRKY75 is able to promote SA production by inducing the transcription of SA INDUCTION-DEFICIENT 2 (SID2), and suppress H2O2 scavenging partly by repressing the transcription of CATALASE 2 (CAT2). Genetic analysis reveals that the SID2 mutation or an increase of catalase activity rescues the precocious leaf senescence phenotype evoked by WRKY75 over-expression. Based on these results, we propose a “tripartite amplification loop” model in which WRKY75, SA and ROS undergo a gradual but self-sustained rise driven by three interlinked positive feedback regulations. This tripartite amplification loop provides a molecular framework connecting the upstream signals, such as age, ethylene, JA and ABA, to the downstream regulatory network executed by those SA-responsive and H2O2-responsive transcription factors during leaf senescence.

overall_design: We performed transcriptome profiles analysis of 28-day-old Col-0 and WRKY75RNAi leaves by RNA-seq. The third and fourth leaves of Col-0 and WRKY75RNAi plants were collected and ground into powder in liquid nitrogen. Total RNA was extracted using the RNeasy Plant Mini kit (QIAGEN). RNA-sequencing and differential gene expression analysis was performed by the BIOPIC institution at Peking University.

first: Pengru

last: Guo

first: Zhonghai

first: Peixin

last: Huang

first: Fang

last: Shuang

first: Jinfang

last: Chu

first: Hongwei


title: Genome-wide RNA-seq transcriptional analysis of splenocyte responses to Dengue virus infection in WT, Irf3(-/-)×Irf7(-/-) (DKO), Irf3-/-xIrf5-/-xIrf7-/- (TKO), and Ifnar1-/- (AB6) mice.

city: La Jolla

first: Aaron

middle: F

last: Carlin

state: California

address: 9500 Gilman Drive GPL Rm 118

department: Pathology and Medicine

institute: University of California, San Diego

summary: Interferon-regulatory factors (IRFs) are a family of transcription factors (TFs) that play critical roles in translating viral recognition into antiviral responses, including type I IFN production. Dengue virus (DENV) and other clinically important flaviviruses are controlled by functional type I interferon (IFN) responses. Using an experimental model of DENV infection that recapitulates key aspects of the human disease in mice, we demonstrate that while mice lacking the type I IFN receptor (Ifnar1-/-) succumb to DENV infection, mice that are deficient in IRF-3, IRF-5, and IRF-7 – the three transcription factors thought to regulate type I IFN production – survive DENV challenge. Genome-wide RNA-seq analysis of WT, Irf3(-/-)×Irf7(-/-) (DKO), Irf3-/-xIrf5-/-xIrf7-/- (TKO), and Ifnar1-/- (AB6) splenocytes identified minimal type I IFN production but a robust type II IFN (IFN-γ) response in DKO and TKO mice later shown to be dependent on IRF-1. These results reveal a key role for IRF-1 in antiviral defense by activating both type I and II IFN responses during DENV infection.

overall_design: RNA-seq of total splenocytes from WT, Irf3(-/-)×Irf7(-/-) (DKO), Irf3-/-xIrf5-/-xIrf7-/- (TKO), and Ifnar1-/- (AB6) mice either mock infected or infected with Dengue virus for 6 or 24 hours.

first: Sujan

last: Shresta


title: Genome-wide chromatin-immunoprecipitation studies of sympathetic neurons  reveals critical direct targets of ISL1 and suggests potential co-factor families for ISL1 action in sympathetic neurons

city: Shanghai

first: Youqiong

last: Ye

address: 280 Chongqing south road

institute: Shanghai Jiao Tong University School of Medicine

summary: Understanding factors that drive development  of the sympathetic neuron is crucial to development of potential therapies for neuroblastoma. Here, we identify a key cell autonomous role for the LIM homeodomain transcription factor ISL1 for survival, proliferation and differentiation of sympathetic neurons throughout development. Chromatin immunoprecipitation assays performed utilizing antibody to ISL1 in chromatin extracts from sympathetic neurons demonstrated that ISL1 directly binds genomic regions within several genes critical for sympathetic neuron development and function, including subunits of the Insm1, Lmo1,Tlx3 and Prox1.  Our studies represent in vivo ChIP-seq studies for sympathetic neurons which provide a basis for further exploration of factors critical to sympathetic neurons development and function .

overall_design: ISL1 ChIP-seq profiling was performed in sympathetic neurons from E12.5-14.5 Embryos .

first: Qingquan

last: Zhang

first: Jun

last: Lu

first: Ru

first: Xiaodong

last: Zhao

first: Cizhong

last: Jiang

first: Xingqun

last: Liang

first: Yunfu

last: Sun


title: Small RNA analysis of ASR5 knockdown rice plants (ssp. Japonica cv. Nipponbare) under Al stress conditions

city: Porto Alegre

first: Guilherme

last: Cordenonsi da Fonseca

state: RS

address: Av. Bento Gonçalves, 9500

department: Centro de Biotecnologia

country: Brazil

institute: UFRGS

type: Non-coding RNA profiling by high throughput sequencing

summary: Aluminum (Al) toxicity in plants is one of the primary constraints in crop production. Al³⁺, the most toxic form of Al, is released into soil under acidic conditions and causes extensive damage to plants, especially in the roots. In rice, Al tolerance requires the ASR5 gene, but the molecular function of ASR5 has remained unknown. This data establish a comparative study of miRNAome profiles in ASR5 knockdown rice plants (ssp. Japonica cv. Nipponbare) under Al stress conditions.

overall_design: microRNA profiles in 4 different shoot libraries of Oryza sativa  (ssp. Japonica cv. Nipponbare)  by deep sequencing (Illumina HiSeq2000).

first: Rafael

middle: A

last: Arenhart

first: Lauro

middle: B

last: Neto

first: Luiz

last: de Oliveira

first: Nureyev

last: Rodrigues

middle: C

last: da Fonseca

first: Rogerio

last: Margis

first: Marcia

middle: P


title: Identification of two types of GGAA microsatellites and their roles in EWS/FLI binding and gene regulation in Ewing sarcoma

city: Columbus

first: Cenny

last: Taslim

address: 700 Children's Drive

institute: Nationwide Children's Hospital

summary: Ewing sarcoma is a bone malignancy of children and young adults, frequently harboring the EWS/FLI t(11;22)(q24;q12) chromosomal translocation. The resulting fusion protein is an aberrant transcription factor that uses highly repetitive GGAA-containing elements (microsatellites) to activate and repress thousands of target genes mediating oncogenesis. However, the mechanisms of EWS/FLI interaction with microsatellites and regulation of target genes expression is not clearly understood. Here, we profile genome-wide protein binding and gene expression. Using a combination of unbiased genome-wide computational and experimental analysis, we define GGAA-microsatellites in a Ewing sarcoma context. Our study identifies two distinct classes of GGAA-microsatellites and demonstrates that EWS/FLI responsiveness is dependent on microsatellite length. At close range (within 5 kb) “promoter-like” microsatellites, EWS/FLI binding and subsequent target genes activation is highly dependent on the number of GGAA-motifs. “Enhancer-like” microsatellites demonstrate a positive correlation with length-dependent EWS/FLI binding, but minimal correlation for activated and none for repressed target genes. Our data suggest that EWS/FLI binds to “promoter-like” and “enhancer-like” microsatellites to mediate activation and repression of target genes through different regulatory mechanisms. Such characterization contributes valuable insight to EWS/FLI transcription factor biology and clarifies the role of GGAA-microsatellites on a global genomic scale. This may provide a unique perspective on the role of non-coding DNA in cancer susceptibility and therapeutic development.

overall_design: Examination of EWS/FLI binding in A673 cells.

first: Kirsten

middle: M

last: Johnson

first: Ranajeet

last: Saund

first: Stephen

middle: L

last: Lessnick


title: Simultaneous detection of chromatin accessibility and DNA methylation in cell cycle

first: Huaibing

last: Luo

address: 130# Dongan Rd

department: Institute of Biomedical Science

institute: Fudan University

type: Methylation profiling by high throughput sequencing

summary: The goal of this study is to comprehensively assess chromatin accessibility and DNA methylation dynamic in different cell cycle phases, we found DNA methylation is stable in different phases wherase chromatin accessibility underwent enormous changes, but local structure at NDR and NSR are well preserved to maintain cellular identity.

overall_design: Examine DNA methylation and chromatin accessibility by high throughput sequencing

first: Wenqiang

last: Yu

first: Yanping

last: Xi


title: RNA Sequencing Analysis of Wild Type and Ezh2 knock out CD8 T cell Transcriptomes

city: Camden

first: Jozef

last: Madzo

state: NJ

address: 403 Haddon Avenue

department: Bioinformatics

institute: Coriell Institute

summary: Our data represents the first analysis of histone methyltransferase Ezh2 regulated transcriptomes in mouse CD8 T cells.

overall_design: Naïve and in vitro TCR stimulated CD8 T cell mRNA profiles of Pmel-1 wild type (WT) and Ezh2-/- mice were generated by deep sequencing, in triplicate, using Illumina.

first: Shan

last: He

first: Yi

last: Zhang


title: RNA sequencing and ATAC sequencing of developing cone photoreceptors

city: Basel

first: Botond

last: Roska

address: Maulbeerstrasse 66

country: Switzerland

institute: FMI


title: RNA sequencing of developing cone photoreceptors

summary: We determined the transcriptomes of postmitotic cone photoreceptors in the central region of the mouse retina every day between birth (P0) and eye opening (P12). At each postnatal day we isolated GFP-labeled cells from three different Chrnb4-GFP mice (biological triplicates) using fluorescence-activated cell sorting. We then acquired the transcriptomes of the sorted cones using next generation RNA sequencing. Our data set contained 39 transcriptomes.

overall_design: RNA-seq of isolated cone photoreceptors at 13 timepoints

first: Janine

last: Daum

first: Özkan

last: Keles

first: Hubertus

last: Kohler

first: Michael

last: Stadler


title: RNA sequencing of Aedes mosquitoes infected with Zika virus (ZIKV) or Dengue virus (DENV)

city: Baltimore

first: George

last: Dimopoulos

state: Maryland

address: 615 N Wolfe St.

department: Molecular Microbiology and Immunology

institute: Johns Hopkins School of Public Health

summary: Zika virus (ZIKV), a pathogen of global health concern, is transmitted to humans by Aedes mosquitoes. However, the molecular interactions between the vector and the virus remain largely unexplored. We demonstrated that ZIKV and dengue virus (DENV) have similar tropism and infection kinetics in two mosquito strains with different degrees of susceptibility to infection. Comparison of Aedes aegypti’s molecular responses to ZIKV and DENV infection indicated that around 40% of the mosquito’s infection-responsive transcriptome is virus-specific. Regulated genes also included key factors of the mosquito’s anti-viral immunity, pointing to the possible involvement of the Toll innate immune pathway. Comparison of ZIKV and DENV infection-responsive transcriptome data to those for yellow fever virus and West Nile virus identified 26 genes likely to play key roles in virus infection of Aedes mosquitoes. Through reverse genetic analyses, we showed that the Toll and the Jak/Stat innate immune pathways mediate increased resistance to ZIKV infection, and the virus use vATPase and inosine-5’-monophosphate dehydrogenase as mosquito’s host factors.

overall_design: Mosquito's midguts were collected 7 days post-infection with ZIKV or DENV, mosquitoes fed on a naïve blood meal were used as the control group.  Each group had three replicates.

first: Yesseinia

middle: I

last: Angleró-Rodríguez


title: Genome-wide mRNA expression analyses revealed dysregulation of genes important for sympathetic neuron development in isl1 cko and hypomorphic mutant embryos.

first: Youqiong

last: Ye

summary: Understanding factors that drive development and function of the sympathetic neuron  is crucial to development of potential therapies for neuroblastoma. Here, we identify a key cell autonomous role for the LIM homeodomain transcription factor ISL1 for survival, proliferation and differentiation of sympathetic neurons throughout development. Analysis of several Isl1 mutant mouse lines, including one in which Isl1 was specifically ablated in sympathetic neuron (Wnt1-cre;Isl1 f/f) revealed an early requirement for Isl1 within sympathetic neurons for  proliferation and surrvial. RNA-seq analyses on sympathetic neurons revealed dysregulation of a number of genes critical for sympathetic neuron development .Our studies demonstrated that ISL1 regulated the peoliferation, surrvial and differentiation.

overall_design: Expression profiling of sympathetic ganglion dissected from E11.5 or E14.5 wild-type and isl1 mutant embryos.

first: Qingquan

first: Jun

last: Lu

first: Ru

last: Huang

first: Xiaoxia

last: Guo

first: Fugui

last: Zhu

first: Jie

last: Yan

first: Lina

first: Peng

last: Geng

first: Yuefeng

last: Shen

first: Xiaohui

last: Gong

first: Qitong

first: Su

last: Pu

first: Xiaodong

last: Zhao

first: Cizhong

last: Jiang

first: Xingqun

last: Liang

first: Yunfu

last: Sun


title: Gene expression profiling of s-SHIP positive mammary epithelial cells

city: Houston

first: Chad

last: Creighton

state: TX

address: One Baylor Plaza, Mail Stop: BCM305

department: Biostatistics, Ducan Cancer Center

institute: Baylor College of Medicine

summary: We performed RNAseq on subpopulations of mammary epithelial cells.  We carried out sorting of a gradient of s-SHIP positive cells in the mammary gland (neg, low, and hi for s-SHIP eGFP).  High sSHIP-eGFP populations denote a postulated stem cell population, while low and negative represent more differentiated cell types.  s-SHIP eGFP hi to negative potentially represents a gradient from stem to more differentiated progeny, respectively, within the basal epithelial compartment.  We FACS sorted 3 replicates for each cell type to represent s-SHIP-neg, s-SHIP-low, and s-SHIP-high.

overall_design: We FACS sorted 3 replicates for each cell type to represent s-SHIP-neg, s-SHIP-low, and s-SHIP-high, profiling each of these groups using RNA sequencing.

first: Fengju

last: Chen

first: Jeffrey

last: Rosen


title: Next Generation Sequencing Facilitates Quantitative Analysis of Wild Type and AXL-/- astrocytes Transcriptomes

status: Public on Nov 06 2017

first: Jian

address: 2901 Caolang Road, Jin Shan District

institute: Shanghai Public clinical center

summary: Next-generation sequencing (NGS) has revolutionized systems-based analysis of cellular pathways. The goals of this study are to compare Wild Type astrocytes transcriptome profiling (RNA-seq) to AXL-/- astrocytes transcriptome profiling and to explore the mechanism by which AXL interferes with type I IFN signaling in WT astrocytes. We performed an RNA-Seq analysis of WT and AXL-/- U-251MG cells in the absence of ZIKV. Surprisingly, the intrinsic level of type I IFN signaling was lower in AXL-/- cells than in WT cells. This result was further confirmed by RT-qPCR

overall_design: U251 mRNA profiles of wild type (WT) and AXL-/- cells were generated by deep sequencing, in triplicate, usingIllumina Hiseq, PE150.

first: Jia

last: Liu


title: mRNA Sequencing of Human PromoCells Using 3'-directed Digital Gene Expression (3'-DGE) Technique

first: Ravi

last: Iyengar

address: 1425 Madison Avenue, Room 12-70C

department: Pharmacological Sciences

institute: Icahn School of Medicine at Mount Sinai

summary: The differential gene expression of human cardiomyocytes induced by kinase inhibitors sorafenib and sunitinib is measured by a high-throughput mRNA-sequencing approach called 3'-DGE, that is based on a 3' end-focused reference sequence library and a transcript molecule counting method with unique molecular identifiers (UMI) for correcting PCR bias.

overall_design: Cells were treated with sunitinib, sorafenib, or vehicle control for 48 hours, and gene expression levels of all samples were measured by 3'-DGE and conventional random-primed mRNA-sequencing methods using paired-end reading to obtain the genome-wide expression profiles for each sample.

first: Yuguang

last: Xiong

first: Magali

last: Soumillon

last: Wu

first: Jens

last: Hansen

first: Bin

last: Hu

first: Johan

last: G.C. van Hasselt

first: Gomathi

last: Jayaraman

first: Ryan

last: Lim

first: Mehdi

last: Bouhaddou

first: Loren

last: Ornelas

first: Jim

last: Bochicchio

first: Lindsay

last: Lenaeus

first: Jennifer

last: Stocksdale

first: Jaehee

last: Shim

first: Emilda

last: Gomez

first: Dhruv

last: Sareen

first: Clive

last: Svendsen

first: Leslie

last: M. Thompson

first: Milind

last: Mahajan

first: Eric

last: A. Sobie

first: Evren

last: U. Azeloglu

first: Marc

last: R. Birtwistle


title: Analysis of gene expression from CD45neg cells of lung tumors upon neutrophil depletion or not

city: Lausanne

first: Nadine

last: Fournier

state: Vaud

address: Agora Cancer Research Center, Bugon 25A

institute: Agora Cancer Research Center & Swiss Institute of Bioinformatics

summary: Interrogating the tumor immune compartment generates new prognostic and treatment modalities. We used the poorly immunogenic oncogenic Kras driven mouse model of lung cancer, to challenge the predictive value of an immune signature, using a new algorithm called MegaClust. It highlighted a predominant negative impact of neutrophil infiltration on multiple immune populations. Human samples and depletion experiments in mice revealed that neutrophils promote tumor growth by altering angiogenesis, associated to increased PI3K/Akt/mTOR signaling in tumor cells and profound immunosubversion. Together with blood vessel spreading and normalization, neutrophil depletion was associated with T cell redistribution into tumor mass and sensitized tumors to anti-PD1 immunotherapy in this refractory model. Our observations illustrate a mechanism of immune exclusion protecting tumor cells from destruction that relies on neutrophil infiltration

overall_design: Comparison of samples between anti-Ly6G and control IgG treatment

first: Julien

last: Faget

last: Zangger

first: Etienne

last: Meylan


title: Transcriptome-wide survey of binding partner of slam protein in early Drosophila embryos

city: Goettingen

first: Gabriela

last: Salinas

state: Lower-Saxony

address: Kreuzbergring 57

department: Department of Pathology

country: Germany

institute: Universitaetsmedizin Goettingen

summary:
Purpose: Slam protein and RNA co-localize in early drosophila embryos. slam RNA specifically co-immunoprecipitates with its own protein from embryonic lysate as shown by RNA-IP and QRT-PCR. The goal of this study is to survey transcriptome wide (RNA-seq) targets of slam protein and validate the data from qRT–PCR analysis.
Methods: RNA-ip was performed for staged embryos (1.5 – 3 h after egg laying) Using slam antibody or GFP binder. RNA profiles in immune-predicates were generated by deep sequencing.
Results: Slam RNA specifically co-predicates with slam protein as shown by both next generation sequencing and RT-QPCR. No mRNA of other genes was detected in all independent experiments or showed the averaged enrichment in the same range.

overall_design: Compare the RNA profile from two independent experiments: Expt1. Wild type embryos, slam Ab (3x) and Diaphanous Ab (control, 4x)) for RNA pull down. Expt2. Wild type embryos (3x) and GFP-Slam transgenic embryos (2x), GFP-binder for RNA pull down.

first: Shuling

last: Yan

first: Joerg

last: Grosshans


title: Conventional and pioneer modes of glucocorticoid receptor interaction with enhancer chromatin in vivo

city: Bethesda

first: Razvan

middle: V.

last: Chereji

address: 6 Center Drive, Room 2A14

department: NICHD

institute: National Institutes of Health

summary: Here we show how chromatin structure is involved in glucocorticoid receptor (GR) binding in a mouse mammary cell line. We show that GR binds to accessible chromatin sites that are either nucleosome-free or contain a nucleosome.

overall_design: Performed micrococcal nuclease digests of 3134 cells along with high-throughput paired-end sequencing to precisely map nucleosome positions genome wide. Overlay this data with new and existing DNase-Sequencing and ChIP Sequecing data.

first: Thomas

last: Johnson

middle: V

first: Diana

last: Stavreva

first: Stephanie

last: Morris

first: Gordon

last: Hager

first: David

middle: J

last: Clark


title: EMC3 conditional KO in developing lung epithelium

city: Cincinnati

first: John

middle: M.

last: Snowball

state: OH

address: 3333 Burnet Ave

department: Pulmonary Research

institute: Cincinnati Childrens Hospital

summary: EMC3 is a critical component of an endoplasmic reticulum complex that mediates the processing and trafficking of surfactant associated proteins and lipids by AT2 cells and is required for lung function and respiration at birth.

overall_design: Lung E18.5 Epcam sorted KO vs. Control RNASeq

first: Xiaofang

last: Tang

first: Yan

last: Xu

first: Jeffrey

last: Whitsett


title: Transcriptome analysis of Wnt3a-treated Wild Type, Lrp5KO , Lrp6KO and Lrp5/6KO osteoblasts

city: Livermore

first: Aimy

last: Sebastian

address: 7000 East Ave

institute: Lawrence Livermore National Laboratory

summary: Wnt signaling is a major regulator of osteoblast differentiation and function. To investigate how Wnt3a signaling regulates osteoblastic gene expression and to identify the role of Lrp5 and Lrp6 in mediating Wnt3a signaling in osteoblasts, neonatal calvarial osteoblasts isolated from C57Bl6 (WT) and osteoblasts lacking Lrp5 (Lrp5KO), Lrp6 (Lrp6KO) and, both Lrp5 and 6 (Lrp5/6KO) were treated with Wnt3a for 24 hours and gene expression changes were quantified by RNA-seq.

overall_design: Transcriptome analysis to identify Wnt3a regulated genes in Wild Type, Lrp5KO , Lrp6KO and Lrp5/6KO osteoblasts

last: Loots


title: The metabolic response to a high-fat diet reveals obesity-prone and -resistant phenotypes in mice with distinct mRNA-seq transcriptome profiles

city: Gwangju

first: Ji-Young

last: Choi

address: 30, Chosundae 3-gil, Dong-gu

department: Food and Nutrition

country: South Korea

institute: Chosun University

summary: We investigated phenotypic differences underpinning obesity susceptibility or resistance based on metabolic and transcriptional profiling in C57BL/6J mice fed a high-fat diet (HFD)

overall_design: Total RNA of epididymal adipose tissues and liver was obtained from normal diet, high-fat diet-fed mice and mRNA expression-associated with lipid, and glucose metabolism was measured.

first: Myung-Sook


title: Regulation of cardiac cushion endocardial cells by KLF2

city: Philadelphia

first: Lauren

last: Goddard

address: 3400 Civic Center Boulevard

institute: UPENN

summary: Comparison of differential gene expression between controls and mice that lack the transciption factor KLF2 from the cardiac endocardium following Nfatc1 Cre deletion.

overall_design: E12.5 cardiac atrio-ventricular cushion mRNA profiles were generated from KLF2 fl/fl and Nfatc1 KLF2 fl/fl mice.

first: Mark

last: Kahn


title: Transcriptome analyses reveal metabolic syndrome of adulthood with intrauterine growth restriction in a pig model

status: Public on Nov 04 2017

city: Chengdu

first: Linyuan

last: Shen

state: Sichuan

address: 211# Huiming Road

department: College of Animal Science and Technology

institute: Sichuan Agricultural University

summary: Epidemiological data indicated intrauterine growth retardation (IUGR) is a risk factors for adult metabolic syndrome. However, the genetic mechanism underlying the phenotype in adulthood is not well characterized. Here, the present study employed adult normal and IUGR pigs as models to survey the difference of global gene expression in the liver using transcriptome sequence. The trancriptome libraries generated 104.54 gigabases data, 16,948 and 17,078 genes were expressed in normal and IUGR pigs, repectively. A total of 1,322 differentially expreesion genes (DGEs) were identified. An enrichment analysis of DGEs presented the top overrepresented GO terms and pathway were related to oxidoreductase activity, ATPase activity, amino catabolic process, glucose metabolism and Insulin signaling pathway. Finally, combined their phenotypes and gene expression patterns, we proved the adult IUGR pigs would obstruct the process of mitochondrial biogenesis and oxidative phosphorylation, which induced high oxidation press in adult IUGR. The increased gluconeogenic and decreased glycogen synthesis in liver resulted in reducing the capacity of glucose intolerance in IUGR. The decreased expression of insulin signaling genes (such as PI3K and AKT) implied a risk of diabetes in adult IUGR. Moreover, the capacity of fatty acid oxidation decreased in IUGR liver leaded to high content of triglyceride and free fatty acid in IUGR. Together, these findings provide a comprehensive understanding of the molecular mechanisms of adult IUGR pigs and valuable information for future studies of therapeutic intervention in IUGR metabolic syndrome.

overall_design: Liver mRNA profiles of adult IUGR and normal pigs were generated by deep transcriptome sequencing, in triplicate, using  HiSeq 2000 platform.

first: Mailin

last: Gan

first: Yuan

last: Fan

first: Shunhua

last: Zhang

first: Jideng

last: Ma

first: Guoqing

first: Yanzhi

last: Jiang

first: Mingzhou

last: Li

first: Jinyong

last: Wang

first: Xuewei

first: Lianqiang

last: Che

first: Li

last: Zhu


title: Rice plants exhibiting bacterial blight resistance at high temperature suppress abiotic response

city: Fort Collins

first: Stephen

middle: Philip

last: Cohen

state: CO

address: 1177 Campus Delivery

department: Bioagricultural Sciences and Pest Management

institute: Colorado State University

summary:
Background: Plant disease is a major challenge to agriculture worldwide, and it is often exacerbated by abiotic environmental factors. During some plant-pathogen interactions, heat stress increases host susceptibility, a tendency which could spell disaster in light of the global warming trends associated with climate change. Despite the importance of this phenomenon, little is known about the molecular mechanisms that cause it. To better understand host plant responses during simultaneous heat and pathogen stress, we conducted a transcriptomics experiment for rice plants infected with Xanthomonas oryzae (Xo), an economically important bacterial pathogen of rice, during high temperature stress.
Results: Using RNA-Seq technology, 8,499 differentially expressed genes were identified as temperature responsive in one rice cultivar, IRBB61, experiencing susceptible and resistant interactions with Xo across three time points. Many genes with gene ontology terms associated with stress response were identified. Notably, genes in the plant hormone abscisic acid (ABA) biosynthesis and response pathways were identified as upregulated by high temperature in both mock-treated plants and plants in the susceptible interaction and suppressed by high temperature in plants in the resistant interaction. A DNA sequence motif similar to known ABA-responsive cis-regulatory elements was identified in the promoter region upstream of genes upregulated in susceptible but downregulated in resistant interactions.
Conclusions: The results of our study suggest that the plant hormone ABA is an important node for cross-talk between plant transcriptional response pathways to high temperature stress and pathogen attack. Genes in this pathway represent an important focus for future study to determine how plants evolved to deal with simultaneous abiotic and biotic stresses.

overall_design: RNA-Seq analysis of leaves from rice variety IRBB61 infiltrated with water at normal and high temperature regimes at 6 h post-infiltration, and rice leaves inoculated with Xanthomonas oryzae strain X11-5A carrying either an empty vector plasmid or a plasmid encoding the effector avrXa7 under normal and high temperature regimes over a time course (3, 12, 24 h post-inoculation).

first: Hongxia

last: Liu

first: Cristiana

middle: T

last: Argueso

first: Casiana

last: Vera Cruz

first: Valerie

last: Verdier

first: Jan

middle: E

last: Leach


title: Genes located in a chromosomal inversion are correlated with territorial song in white-throated sparrows

city: Atlanta

first: Donna

last: Maney

state: GA

address: 1510 Clifton Rd NE Rm 2006

institute: Emory University

summary: The genome of the white-throated sparrow (Zonotrichia albicollis) contains an inversion polymorphism on chromosome 2 that is linked to predictable variation in a suite of phenotypic traits including plumage color, aggression, and parental behavior. Differences in gene expression between the two color morphs, which represent the two common inversion genotypes (ZAL2/ZAL2 and ZAL2/ZAL2m), are therefore of potential interest toward understanding the molecular underpinnings of these phenotypes. To identify genes that are differentially expressed between the two morphs and correlated with behavior, we  quantified both behavior and gene expression in a population of free-living white-throated sparrows. We quantified behavioral responses to simulated territorial intrusions (STIs)  early during the breeding season. In the same birds, we then performed a transcriptomewide analysis of gene expression in two behaviorally relevant brain regions, the medial  amygdala and hypothalamus. Using network analyses, we identified modules of genes that were correlated with both morph and STI-induced singing behavior. The majority of these genes were located within the inversion, demonstrating the profound effect the inversion  has on the expression of genes captured by the rearrangement. Gene pathway analyses revealed that in the medial amygdala, the most prominent pathways were those related to  steroid hormone receptor activity. Within these pathways, the only gene encoding such a receptor was ESR1 (estrogen receptor alpha). Our results thus suggest that ESR1 and  related genes are important for behavioral differences between the morphs.

overall_design: RNA samples from the brain regions HYP and MeA were collected from a total of 19 male white-throated sparrows (10 WS and 9 TS). Free-living birds were collected during the peak of territorial behavior (May-June) the day after a simulated territorial intrusion using mist nets and song playback. For the MeA samples, MeA constituted the majority of the sampled tissue. For the HYP, samples included the caudal portion of the medial preoptic area (POM), the paraventricular nucleus (PVN),  the anterior hypothalamus, and the ventromedial hypothalamus (VMH).

first: W

last: Zinzow-Kramer

first: B

last: Horton

first: C

middle: D

last: McKee

first: J

last: Michaud

first: G

middle: K

last: Tharp

middle: W

last: Thomas

first: E

last: Tuttle

first: S

last: Yi

first: D


title: The effect of estrogen on microRNA expression in primary cultured rat neonatal cardiomyocytes

city: Shanghai

first: Xiao-Yan

address: 800 Xiangyin Rd

institute: Second Military Medical University

summary:
Dysregulation of miRs has been reported in a variety of cardiac diseases. In particular, it has reported that estrogen regulates a miRs network  in female cardiac fibroblasts, thereby modulating a spectrum of genes involved in cardiac fibrosis and remodeling. However, the estrogen-responsive miRs in cardiomyocytes still remain to be elucidated.
We used a microRNA microarray screening approach to address the miRs expression profiling in estrogen-treated cardiomyocytes.

overall_design: Primary cultured rat neonatal cardiomyocytes were treated with 17beta-estradiol (E2) for 24h. Cells were then used for microRNA extraction and hybridization on Affymetrix GeneChip miRNA 2.0 Array.

first: Jian-Qiang

last: Lu


title: Comparison between 3'-DGE and Conventional mRNA-Sequencing Methods

city: New York

first: Ravi

last: Iyengar

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

overall_design: Refer to individual Series


title: ATAC sequencing of developing cone photoreceptors

first: Botond

last: Roska

summary: We determined the accessible genome of postmitotic cone photoreceptors in the central region of the mouse retina on postnatal days P3, P6, and P10. At eachtimepoint we isolated GFP-labeled cells from three different Chrnb4-GFP mice (biological triplicates) using fluorescence-activated cell sorting. We then acquired reads of regions of  accessible DNA of the sorted cones using ATAC sequencing. Our data set contained 9 samples.

overall_design: ATAC-seq of isolated cone photoreceptors at 3 timepoints

first: Janine

last: Daum

first: Sjoerd

last: Holwerda

first: Özkan

last: Keles

first: Hubertus

last: Kohler

first: Michael

last: Stadler


title: Inhibition of H3K4 demethylation induces autophagy in cancer cell lines

city: Boston

first: Pin-Ji

last: Lei

state: Massachusetts

address: 100 Blossom Street

department: Department of Radiation Oncology

institute: Massachusetts General Hospital

summary: Epigenetic factors and related small molecules have emerged to be strongly involved in autophagy process. Here we report that two inhibitors of histone H3K4 demethylase KDM1A/LSD1, 2-PCPA and GSK-LSD1, are able to induce autophagy in multiple cell lines. The two small molecules induced accumulation of LC3II, formation of autophagosome, fusion of autophagosome with lysosome and SQSTM1/p62 degradation. 2-PCPA treatment inhibits cell proliferation through cell cycle arrest but not inducing cell death. Exogenous expression of KDM1A/LSD1 impaired the autophagic phenotypes triggered by 2-PCPA. The autophagy induced by 2-PCPA requires LC3-II processing machinery. But depletion of BECN1 and ULK1 with siRNA did not affect the LC3-II accumulation triggered by 2-PCPA. 2-PCPA treatment induces the change of global gene expression program, including a series of autophagy-related genes, such as SQSTM1/p62. Taken together, our data indicate that KDM1A/LSD1 inhibitors induce autophagy through affecting the expression of autophagy-related genes and in a BECN1-independent manner.

overall_design: Examination of RNA from U2OS cell with 10 kinds of small molecules treatment

first: Zhen

last: Wang


title: Transcriptome Profile of Lung Dendritic Cells after In Vitro Porcine Reproductive and Respiratory Syndrome Virus (PRRSV) Infection

status: Public on Nov 05 2017

city: Bonn

first: Dr. Maren

middle: Julia

last: Proell

address: Endenicher Allee 15

institute: Institute of Animal Science, University of Bonn

summary: Investigation of the transcriptome profile of lung dendritic cells (DCs) of two genetically different pig breeds (Pietrain and Duroc) after PRRSV infection in vitro and determination of the temporal changes in transcriptional profiles.

overall_design: Pietrain and Duroc lung DCs were isolated and infected in vitro with PRRSV. Total cellular mRNA from non-infected (0 hours) and infected (3, 6, 9, 12 and 24 hours post infection) lung DCs was extracted and 12 lung DCs samples were used for the global transcriptome profile analysis (RNA-Seq).

first: Karl

last: Schellander

first: Maren

last: Pröll

first: Christiane

last: Neuhoff


title: Transmural pressure is a master regulator of airway branching morphogenesis

city: Princeton

first: Celeste

last: Nelson

address: 303 Hoyt Laboratory

department: Chemical & Biological Engineering

institute: Princeton University

summary: Mechanical forces are increasingly recognized to regulate morphogenesis, but how this is accomplished in the context of the multiple tissues present within a developing organ remains unclear. Here we use bioengineered “microfluidic chest cavities” to precisely control the mechanical environment of the fetal lung. We show that transmural pressure controls airway branching morphogenesis and regulates the frequency of airway smooth muscle contraction. Next-generation sequencing analysis shows that lungs held at higher pressure are more mature than lungs held at lower pressure. Timelapse imaging reveals that branching events are synchronized across distant locations within the lung, and are preceded by long-duration waves of airway smooth muscle contraction. Higher transmural pressure decreases the interval between systemic smooth muscle contractions and increases the rate of morphogenesis of the airway epithelium. These data reveal that the mechanical properties of the microenvironment instruct crosstalk between tissues to control the rate of development of the embryonic lung.

overall_design: (i) embryonic mouse lungs at E12.5 were cultured under low or high pressure for 48 hours prior to RNA extraction or (ii) embryonic mouse lungs were isolated from pregnant mice at E12.5, E13.5 and E14.5 prior to RNA extraction

first: Mei-Fong

last: Pang


title: The molecular basis of CD4 T-cell help for the cytotoxic T-cell response

first: Tomasz

last: Ahrends

address: 1230 York Ave

institute: The Rockefellere University

summary: CD4+ T cells optimize the cytotoxic T cell (CTL) response in magnitude and quality, by unknown molecular mechanisms. We here present the transcriptomic changes, resulting from CD4+ T-cell help during priming, as apparent in effector CTLs. This gene expression signature reveals that CD4+ T-cell help optimizes CTLs in the expression of cytotoxic effector molecules, but also in many other functions that ensure optimal efficacy of CTLs throughout their life cycle.

overall_design: Whole transcriptome analysis of effector CD8 T cells primed in the presence or absence of CD4 T cell help after vaccination or virus infection, or treated with agonistic CD27 or blocking CD70 antibody after vaccination.

first: Jannie

last: Borst


title: RNA-Seq based comparison of Staphylococcus aureus strains resistent and sensitive to MT02

city: Cologne

first: Konrad

middle: U.

last: Förstner

state: North Rhine-Westphalia

address: Gleueler Str. 60

department: Information Services

institute: ZB MED - Information Centre for Life Sciences

summary: A MT02 sensitive and resistant strain of Staphylococcus  LAC USA300 JE2 were exposed to MT02. From those cell RNA was extracted and anylsed by RNA-Seq

overall_design: Comparison of the expression profiles of Staphylococcus aureus strains resistent and sensitive to MT02

first: Ebaa

last: El-Hossary

first: Knut

last: Ohlsen

middle: U


title: A novel class of tRNA-derived small non-coding RNAs in response to myocardial hypertrophy and contribute to intergenerational inheritance

first: Linyuan

last: Shen

summary: tRNA-derived fragments (tRFs) have served as new class of non-coding RNA and played important role in regulating cellular RNA processing and protein translation, which was also proved have function on the intergenerational effects of paternal disease. However, there was no study reported the influence of tRFs on myocardial hypertrophy. In the current study, we explore the hypothesis that tRFs in response to myocardial hypertrophy and contribute to intergenerational inheritance.We used isoproterenol induced myocardial hypertrophy rat model. Small RNA (< 40 nt) tanscriptome sequencing was used to select differential expressed tRFs. We over-expressed the highest foldchange tRFs on H9c2 cell to check its function in enlarging cardiocytes surface area. We also compared the tRFs expression pattern in F0 sperm and F1 offspring heart between myocardial hypertrophy (Hyp) and control group (Con), as well as evaluated the phynotype of myocardial hypertrophy in F1 offspring. ISO successfully induced a typical cardiac hypertrophy model in our study. Small RNA-seq revealed tRFs were extremely enriched (84%) in Hyp heart. Overexpression tRFs1 and tRFs2 would both enlarge the surface area of cardiac cell and increase hypertrophic markers (ANF, BNP, and β-MHC) expression. tRFs1, tRFs2, tRFs3 and tRFs4 were also significantly high expressed in Hyp F0 sperm and in Hyp F1 offspring heart, but no function of tRFs7, tRFs9 and tRFs10. Compared to Con F1 offspring, Hyp F1 offspring had high expression levels of β-MHC and ANP genes, and increased fibrosis levles and apoptotic cell in heart.We demonstrate that tRFs are involved in regulating the response of myocardial hypertrophy, it might serve as novel epigenetic factor and contribute to intergenerational inheritance of cardiac hypertrophy.

overall_design: Heart small mRNA profiles  (15-40 nt) of ISO induced myocardial hypertrophy rats and control were generated by deep sequencing, in triplicate, using Illumina Hi-Seq 2000.

first: Mailin

last: Gan

first: Zhengdong

last: Tan

first: Xiao

last: Cheng

first: Dongmei

last: Jiang

first: Guoqing

last: Tang

first: Yanzhi

first: Mingzhou

last: Li

first: Xuewei

first: Shunhua

last: Zhang

first: Li

last: Zhu


title: Conventional and pioneer modes of glucocorticoid receptor interaction with enhancer chromatin in vivo

first: Razvan

last: Chereji

summary: Glucocorticoid hormone plays a major role in metabolism and many related diseases. The hormone-bound glucocorticoid receptor (GR) binds to a specific set of enhancers in different cell types, resulting in unique patterns of gene expression. GR-responsive enhancers have an accessible chromatin structure prior to hormone treatment (“pre-programmed”), whereas unresponsive enhancers specific to other cell types are inaccessible and inactive. Here we have addressed the role of chromatin structure in cell-specific GR-enhancer programming by precise mapping of nucleosome positions in mouse adenocarcinoma cells. We show that, before hormone treatment, some pre-programmed GR-enhancers are nucleosome-depleted, associated with the Brg1 chromatin remodeler and flanked by nucleosomes exchanging histones H2A.Z and H2A. However, most pre-programmed GR-enhancers are assembled into a nucleosome that exchanges H2A.Z and H2A, with little or no Brg1. After hormone treatment, nucleosomes at both types of pre-programmed GR-enhancer shift apart, coinciding with increased levels of Brg1, and continue to exchange H2A.Z and H2A. Hormone removal rapidly reverses these nucleosome shifts. In contrast, inactive GR-enhancers are nucleosomal, lack Brg1, do not exchange H2A.Z or H2A and do not respond to hormone. Thus, pre-programmed GR-enhancers are marked by a dynamic, mutable chromatin structure characterized by high levels of H2A.Z exchange. We propose that nucleosome-depleted GR-enhancers result from the binding of other transcription factors together with Brg1 to assist loading of GR after hormone treatment. At nucleosomal enhancers, GR binding may be directly facilitated by increased transient exposure of enhancer DNA associated with H2A.Z exchange.

overall_design: Performed micrococcal nuclease digests of nuclei prepared from 3134 cells and sequenced mono-nucleosomal DNA using paired-end sequencing to map nucleosome positions genome wide. These data are correlated with DNase-seq and ChIP-seq data.

first: Thomas

middle: A

last: Johnson

first: Diana

last: Stavreva

first: Stephanie

last: Morris

first: Gordon

last: Hager

first: David

last: Clark


title: Local Chromatin Features Including PU.1 and IKAROS Binding and H3K4 Methylation Shape the Repertoire of Immunoglobulin Kappa Genes Chosen for V(D)J Recombination

status: Public on Nov 03 2017

city: Cambridge

first: Felix

last: Krueger

address: Granta Park

country: United Kingdom

institute: Altos Labs

summary: Background: V(D)J recombination is an essential process for the generation of diverse antigen receptor (AgR) repertoires. In B cells, immunoglobulin kappa (Igk) light chain locus recombination follows recombination of the immunoglobulin heavy chain (Igh) locus. We recently developed the DNA-based VDJ-seq assay for the unbiased quantitation of Igh VH and DH repertoires. In conjunction with genome-wide datasets for several epigenetic features, we showed that two active chromatin states, located at the recombination signal sequences (RSS) of VH genes, are highly predictive of recombination. The contribution of chromatin features to Vk gene choice in recombination remains poorly understood. Results: We adapted the VDJ-seq assay to profile the Igk VkJk repertoire, and obtained a comprehensive readout of highly variable Vk gene usage in mouse bone marrow pre-B cells. We identified PU.1 binding at the RSS as highly predictive of whether a gene will actively recombine or not. Prediction of the frequency of recombination was more dependent on H3K4 methylation and IKAROS binding. Conclusions: Epigenetic features within the Vk region are able to explain much of the variation in Vk gene usage. Whilst PU.1 binding at the RSS appears to play a binary, all-or-nothing role, priming Vk genes for recombination, the frequency with which these genes recombine is shaped by the presence and enrichment of a number of other epigenetic features. In contrast to the Igh locus, the epigenetic landscape of the promoter as well as the RSS is predictive of Vk gene recombination.

overall_design: Three VkJk-seq sample replicates from flow-sorted ex vivo WT pre-B cells, and one VkJk-seq sample from flow sorted ex vivo Rag1-/- VH81X pre-B cells

first: Louise

middle: S

last: Matheson

first: Daniel

last: Bolland

first: Anne

last: Corcoran


title: Hemophilia mice treated with antisense oligonucleotides targeting either Upf1 or Upf3b

city: Carlsbad

first: Sagar

last: Damle

state: CA

address: 2855 Gazelle Ct

institute: Ionis Pharmaceuticals

summary: Hemophilia mice were treated for one month with ASOs targeting either Upf1 or Upf3b. The liver RNAs were extracted and analyzed

first: Lulu

last: Huang


title: High-intensity UV laser ChIP-seq for the study of protein-DNA interactions in living cells

city: Jena

first: Arndt

last: Steube

address: Adolf-Reichwein-Strasse 23

department: Cell and Molecular Biology

institute: Leibniz Institute for Natural Product Research and Infection Biology - Hans Knöll Institute (HKI)

summary: Genome-wide mapping of transcription factor binding is generally performed by chemical protein-DNA crosslinking, followed by chromatin immunoprecipitation and deep sequencing (ChIP-seq). Here we present the ChIP-seq technique based on photochemical crosslinking of protein-DNA interactions by high-intensity ultraviolet (UV) laser irradiation in living mammalian cells (UV-ChIP-seq). UV laser irradiation induces efficient and instant formation of covalent “zero-length” crosslinks exclusively between nucleic acids and proteins that are in immediate contact, thus resulting in a “snapshot” of direct protein-DNA interactions in their natural environment. We applied UV-ChIP-seq for genome-wide profiling of the sequence-specific transcriptional repressor B-cell lymphoma 6 (BCL6) in human diffuse large B-cell lymphoma (DLBCL) cells. Our approach resulted in sensitive and precise protein-DNA binding profiles, highly enriched in canonical BCL6 DNA sequence motifs. UV-ChIP-seq also revealed numerous previously undetectable BCL6 binding sites, particularly in more condensed, inaccessible areas of chromatin.

overall_design: Genome-wide mapping of BCL6-DNA interactions by replicate UV-ChIP-seq and corresponding control experiments. To control for enrichment of non-crosslinked protein-DNA interactions we performed ChIP-seq using non-irradiated cells (-UV control ChIP). Furthermore, unspecific antibody binding and input loading was controlled by sequencing of IgG enriched DNA fragments (UV IgG control) and input DNA fragments (UV input DNA) following UV irradiation, respectively. To compare photochemical (UV) with conventional chemical (FA) crosslinking, we performed BCL6 FA ChIP-seq and corresponding control experiments (FA input DNA, FA IgG control).

first: Hans

middle: P

last: Saluz


title: Whole transcriptome analysis identifies differentially regulated networks between osteosarcoma and normal bone samples

city: Perth

first: Sulev

last: Koks

state: Western Australia

address: 90 South Street

department: Centre for Molecular Medicine and Innovative Therapeutics

country: Australia

institute: Murdoch University

summary: We performed whole transcriptome analysis of osteosarcoma bone samples. Initially we sequenced total RNA from 36 fresh-frozen samples (18 tumoral bone samples and 18 non-tumoral paired samples) matching in pairs for each osteosarcoma patient. We also performed independent gene expression analysis of formalin-fixed paraffin-embedded (FFPE) samples to verify the RNAseq results. The use of FFPE samples allowed to analyse the effect of chemotherapy. Data were analysed with DESeq2 and Reactome packages of R. We found 6775 genes expressed differentially between the normal bone and osteosarcoma tissues with an FDR below 0.1, of which 4092 genes were up-regulated and 2683 were down-regulated. Among those genes, BTNL9, MMP14, ABCA10, ACACB, COL11A1 and PKM2 were expressed differentially with the highest significance between tumor and normal bone. Functional annotation with the Reactome identified significant changes in the pathways related to the extracellular matrix degradation and collagen biosynthesis. Analysis of independent FFPE samples largely verified our findings in fresh frozen samples, indicating that osteosarcoma is characterized by massive bone loss. We also found that chemotherapy induced the bone formation and reverses the bone loss caused by sarcoma. Taken together, our results indicate that changes in the degradation of extracellular matrix seem to be an important mechanism of osteosarcoma and efficient chemotherapy induces the genes related to bone formation.

overall_design:
36 samples, 18 from sarcoma and 18 from controls
15 FFPE samples, parffin sections [GSM2652426-40]

first: Dung

middle: X

last: Ho

last: Kõks

first: Phuong

last: Phung

first: Vab

middle: Q

last: Le

first: Van

middle: H

last: Nguyen

first: Ene

last: Reimann

first: Ele

last: Prans

first: Gea

first: Katre

last: Maasalu

first: Nghi

first: Le

last: Trinh

first: Hoang

middle: G

first: Aare

last: Märtson


title: Transcriptional profiling unravels enhanced xenobiotic metabolism in the skin of patients with atopic dermatitis but not with ichthyosis vulgaris

summary: Previous transcriptome analyses confirmed the major role of immunological and skin barrier abnormalities in atopic dermatitis (AD). We here aimed at identifying novel pathogenic pathways involved in AD by comparing AD patients stratified for filaggrin (FLG) mutations not only to healthy donors but also to patients with ichthyosis vulgaris (IV). We applied single-molecule direct RNA-sequencing to analyze the whole transcriptome of nonlesional skin. Six hundred and one genes (478 up-regulated and 123 down-regulated by greater than 2-fold) were differentially expressed when all AD patients were compared to healthy donors. Expression of genes involved in RNA/protein synthesis, RNA splicing, and ATP synthesis was enhanced. Interestingly, genes involved in cell death, response to oxidative stress, DNA damage/repair and xenobiotic metabolism were largely enriched. Two hundred and thirty-seven genes (216 up-regulated and 21 down-regulated by greater than 2-fold) were altered in the skin of IV patients when compared to healthy donors. Remarkably, enhancement of xenobiotic metabolism was only detected in AD skin. Moreover, increased expression of genes encoding for keratinocyte cross-linking (SPRR2) and S100 proteins characterizes the skin of patients with AD flare when compared to patients without. We did not find significant differences in gene profiling between AD patients with and without FLG mutations.This work reveals new putative pathogenic pathways related to xenobiotic metabolisms involved in AD.

overall_design: 29 samples, skin biopsies

first: Stefan

last: Blunder

first: Hubert

last: Hackl

first: Verena

last: Moosbrugger-Martinz

first: Matthias

last: Schmuth

first: Sandrine

last: Dubrac


title: Mechanisms of Myelocytic Nitric Oxide Synthases Against Hypoxia-Induced Pulmonary Hypertension

city: Kitakyushu

first: Takaaki

last: Ogoshi

state: Fukuoka

address: 1-1 Iseigaoka, Yahatanishi-ku

department: Department of Respiratory Medicine

country: Japan

institute: University of Occupational and Environmental Health,  Japan

summary: The goals of this study are to comprehensively identify genes controlled by myelocytic nitric oxide synthases in the lung against hypoxia-induced pulmonary hypertension, and to identify a novel alternative splicing mechanism.

overall_design: Samples were the lungs of the WT mice with triply n/i/eNOS-/- bone marrow transplantation and  the WT mice with triply n/i/eNOS-/- bone marrow transplantation after 3 days under the hypoxic exposure (4 samples for each groups).

first: Masato

last: Tsutsui


title: Telomere heterogeneity linked to metabolism and pluripotency state revealed by simultaneous measurement of telomere length and RNA-seq in the same human ES cell

first: Kunshan

last: Zhang

address: 389 Xincun Road

department: Stem cell Translational Research center

institute: Tongji Hospital, Tongji University

summary: Telomere length heterogeneity in various cell types including stem cells and cancer cells has been recognized. Cell heterogeneity also is found in pluripotent stem cells such as embryonic stem cells (ESCs). The implication and mechanisms underlying the heterogeneity remain to be defined. We have optimized a robust method that can simultaneously measure telomere length coupled with RNA-sequencing analysis (scT&R-seq) in the same human ES cell. Using this method, we show that telomere length varies with pluripotency state. Long telomere hESCs highly express TERF1/TRF1 as well as ZFP42/REX1, PRDM14 and NANOG for naïve pluripotency, in contrast to short telomere hESCs. hESCs express high telomerase activity as expected, and ubiquitously express NOP10 and DKC1, stabilizing components of telomerase complexes, regardless of telomere lengths. Moreover, new candidate genes such as MELK, MSH6 and UBQLN1 cluster with long telomeres and pluripotency network. Notably, short telomere hESCs exhibit higher oxidative phosphorylation primed for lineage differentiation, whereas long telomere hESCs show elevated glycolysis, another key feature for naïve pluripotency. Our data further suggest that telomere length is implicated in metabolism activity and pluripotency state of hESCs. Single cell analysis of telomere and RNA-sequencing can be exploited to further understand the molecular mechanisms of telomere heterogeneity.

overall_design: By combining the methods to amplify the telomere specific sequences and mRNA separately, 121 single hESCs were randomly selected for full-length RNA-seq using Smart-seq2.

first: Hua

last: Wang

first: Yifei

last: Liu

first: Yudong

last: Fu

first: Shan

last: Gao

first: Peng

last: Gong

first: Haiying

first: Zhongcheng

last: Zhou

first: Ming

last: Zeng

first: Zhenfeng

last: Wu

first: Yu

last: Sun

first: Tong

last: Chen

first: Siguang

last: Li

first: Lin


title: A general transcription co-factor, Smad3, potentiates master transcription factor mediated cell identity conversions [ATAC-seq]

city: Edinburgh

first: Keisuke

last: Kaji

state: Midlothian

address: 47 Little France Crescent

department: MRC Centre for Reproductive Health

institute: University of Edinburgh

summary: We have identified that expression of constitutive active Smad3 (Smad3CA) significantly enhanced reprogramming by Oct4, Sox2, Klf4, c-Myc. To investigate how Smad3CA expression impacts on chromatin opening, we performed ATAC-seq on day 3 of reprogramming in the presence or absence of Smad3CA expression.

first: Tyson

last: Ruetz

first: James

last: Ashmore

first: Kaji

last: Keisuke


title: Oncolytic reactivation of KSHV as a therapeutic approach for primary effusion lymphoma: RNA-sequencing of PEL cell lines during KSHV reactivation

city: Sacramento

first: Clifford

middle: G.

last: Tepper

address: 4645 2nd Avenue, Room 2300A

department: Biochemistry and Molecular Medicine

institute: UC Davis School of Medicine

summary: Primary effusion lymphoma (PEL) is an aggressive subtype of non-Hodgkin lymphoma caused by Kaposi’s sarcoma-associated herpesvirus infection, which is most commonly seen in HIV-positive patients. Induction of HIV reactivation by external stimuli in the presence of highly active anti-retroviral therapy (HAART) has been examined for its efficacy to eradicate latently infected HIV. Similary, lytic activation of viruses from latently infected tumor cells with anti-cancer drugs represents an effective strategy of anti-neoplastic therapy, through the induction of oncolysis by viral replication, stimulation of immune responses to the viral lytic antigens, and intrinsic effects of cancer drugs. Here we examined the combination of PEP005 with epigenetic drugs as a rational therapeutic strategy to target both in AIDS-associated KSHV-mediated malignancies. JQ1, a bromodomain and extra terminal protein (BET) inhibitor, in combination with a FDA-approved drug, PEP005, not only robustly induced KSHV lytic replication, but also inhibited IL-6 and VEGF production from PEL cells. This combination has been proposed for use in reactivation of HIV from latently infected T-cells, and the same combination and dosage inhibited PEL growth in vitro and delayed tumor growth in a PEL xenograft tumor model. Downstream activation of NF-B by PEP005 combined with sequestration of bromodomain-containing protein 4 (BRD4) by JQ1 robustly increased occupancy of RNA polymerase II onto the KSHV genome. RNA-sequencing analysis further revealed cellular targets of PEP005, JQ1, and the synergistic effects of both. We suggest that the combination of PEP005 with JQ1 should be considered as a rational therapeutic approach for HIV-associated PEL.

overall_design: A total of 12 samples were analyzed in this study. The study included three primary effusion lymphoma (PEL) cell lines, BC3, BCBL-1, HBL-6. Individual cultures of each cell line were cultured in medium containing vehicle control (DMSO), JQ1, PEP005, or the combination (JQ1 + PEP005). Following treatment of the cells for 24 hours, total RNA was isolated and then submitted fro RNA-sequencing analysis.

first: Yoshihiro

last: Izumiya

first: Feng


title: Targets of FRUITFULL in the pistil/silique [ChIP-Seq]

city: Wageningen

first: Marian

last: Bemer

address: Droevendaalsesteeg 1

department: Molecular Biology

country: Netherlands

institute: Wageningen University

summary: To learn more about the role of FRUITFULL (FUL), in pistil/silique development, we performed a ChIP-seq experiment to identify direct targets of FUL in the pistil/silique.

overall_design: We used a pFUL:FUL-GFP line to conduct chromatin immuno-precipitation experiments with GFP-specific antibodies followed by deep-sequencing (ChIP-seq) in order to determine FUL binding sites on a genome-wide scale. For the samples, pistils/siliques from flower stages 12-16 were harvested, fixed for 15-30’ and the immunoprecipitation was performed according to Kaufmann et al., 2010 (doi: 10.1038/ nprot.2009.244.).  Experiments were done in two biological replicates with the according input samples as controls.

first: Hilda

last: van Mourik

first: Gerco

middle: C

last: Angenent


title: A general transcription co-factor, Smad3, potentiates master transcription factor mediated cell identity conversions [ChIP-seq]

summary: We have identified that expression of constitutive active Smad3 (Smad3CA) significantly enhanced reprogramming by Oct4, Sox2, Klf4, c-Myc. Smad3 is known to interact with several master transcription factors and boost their activity during development. Therefore, we hypothesized that Smad3CA is recruited to Oct4 binding sites during reprogramming. To test this hypothesis, we investigated genome-wide Smad3 binding sites in the presence and absence of reprogramming factor expression.

overall_design: Oct4, Smad3 ChIP-seq on day 3 of reprogramming in the presence of Smad3CA expression, Smad3 ChIP-seq in MEFs with Smad3CA expression for 3 days.


title: Expression profiling and identification of targets of FRUITFULL in the Arabidopsis pistil/silique

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

overall_design: Refer to individual Series


title: Genome-wide identification of SUPPRESSOR OF GAMMA RESPONSE 1 (SOG1)-target genes in Arabidopsis

status: Public on Nov 02 2017

city: Ikoma

first: Nobuo

last: Ogita

state: Nara

address: 8916-5 Takayama-cho

department: Graduate School of Biological Sciences

institute: Nara Institute of Science and Technology

summary: NAC transcription factor SUPPRESSOR OF GAMMA RESPONSE 1 (SOG1) functions as a master regulator in DNA damage response of Arabidopsis. However, the signaling pathway controlled by SOG1 remains elusive. To identify target genes of SOG1, we used wild-type plants harboring the transgene ProSOG1:SOG1-Myc, which expresses the SOG1-Myc fusion gene under the 2-kb SOG1 promoter. It was previously demonstrated that SOG1-Myc can complement the sog1-1 mutation (Yoshiyama et al., 2013). After treatment of plants with 15 µM zeocin for 2 hours, chromatin fragments bound to SOG1-Myc were immunoprecipitated with the anti-Myc antibody, and were subjected to next generation sequencing. We identified 778 SOG1-binding peak summits, which displayed peak values 16-fold higher than those in wild-type plants without the transgene. The genomic regions between 5-kb upstream and downstream of each peak summit included 1514 genes among which we found SMR5, SMR7 and CYCB1;1 that were previously identified as SOG1 target genes (Yi et al., 2014; Weimer et al., 2016). Among 1514 genes identified by ChIP-sequencing, 146 genes were overlapped with the SOG1-regulated genes extracted from the microarray data (GSE106154); therefore, we concluded that the 146 genes are SOG1 ditrect target genes.

overall_design: 2 week-old WT and WT harboring ProSOG1:SOG1-Myc plants, grown in liquid MS medium under continuous light, were transferred to liquid MS medium with or without 15 µM zeocin and treated for 2 h. chromatin fragments bound to SOG1-Myc were immunoprecipitated with the anti-Myc antibody and were subjected to next generation sequencing.

first: Yoko

last: Okushima

first: Tetsuya

last: Kurata

first: Tomoaki

last: Sakamoto

first: Naoki

last: Takahashi

first: Masaaki

last: Umeda


title: Genome-wide identification of SUPPRESSOR OF GAMMA RESPONSE 1-regulated and 1 (SOG1)-target genes in Arabidopsis


title: Susceptible wheat cultivar infected with the wild type Puccinia graminis (isolate 99KS76A-1) and its mutants carrying knockout mutations in AvrSr35.

city: Manhattan

first: Eduard

last: Akhunov

state: Kansas

address: 2245 Buckingham St, Apt 10

department: Plant Pathology

institute: Kansas State University

summary: The assess the effect of AvrSr35 knock-out on host-pathogen interaction in the compatible host, we have performed time-course analysis of leaf transcriptomes obtained by infecting susceptible wheat cultivar Fielder with the wild type Puccinia graminis f.sp. tritici (Pgt) isolate 99KS76A-1 and its three mutants, M1, M4 and M7, that carry loss-of-function mutations in the AvrSr35 gene.

overall_design: The two-week seedlings of susceptible cultivar Fielder were used to perform leaf inoculation; leaf samples were collected at 24, 48 and 96 hours after inoculation in three biological replicates. As a control, mock inoculation was performed followed by sample collection after 24 hours (3 biological replicates). The RNA-seq library preparation was performed following the standard Illumina  protocols. Paired-end sequencing (2 x 100 bp) was performed on Illumina HiSeq 2500 by loading 6 barcoded libraries per lane of flow-cell.

last: Akhnuov


title: SMAD2/3 potentiate cell identity conversions with master transcription factors

first: Keisuke

last: Kaji

summary: The exogenous expression of master transcription factors (TFs) is a powerful and exciting approach to convert cellular identity. Yet, the generation of desired cell types is often plagued by inefficiency, slow kinetics and inability to produce mature cell types. Through investigations of the molecular mechanisms of induced plurpipotent stem cell generation, we discovered that expression of constitutively active Smad2/3 (Smad2CA/3CA), together with the Yamanaka factors, could dramatically improve the efficiency and kinetics of reprogramming. Mechanistically, SMAD3 interacted with both co-activators and reprogramming factors, bridging their interaction during reprogramming. Fascinatingly, SMAD2/3 interact with a multitude of master TFs in different cell types, and conversions of B cells to macrophages, myoblasts to adipocytes, and human fibroblasts to neurons were also markedly enhanced when their master TFs were co-expressed with Smad3CA. These results revealed the existence of shared molecular mechanisms underlying diverse TF-mediated cellular conversions, and demonstrated SMAD2/3 as a widely applicable booster.

overall_design:
84 samples were analysed. There are 10 sample groups: mouse embryonic fibroblasts (MEF), embryonic stem (ES) and 4 time points for each of two series;

MEF: Wild type 129 MEFs were grown to 80% confluence then harvested in Trypsin/EDTA, counted and 2500 cells were processed for sequencing identically to other samples. MEF cultured in Glasgow's Minimum Essential Medium (GMEM), 10% FCS, non-essential amino acids, 2 mM L-Glutamine, 1 mM sodium pyruvate, 100 U/ml penicillin/streptomycin, all from Life technologies) supplemented with 5 ng/ml FGF2 (Peptrotech) and 1 ng/ml heparin (Sigma-Aldrich).

ES: TNG-MKOS ES cells were grown to 80% confleunce, harvested in trypsin/EDTA, counted and then 2500 cells were processed for sequencing identically to other samples. ES mdeium is MEF medium supplemented with human LIF 100 U/ml.

d*_Sm3CA3: d* samples are reprogramming samples with over-expression of constitutive active Smad3 (Smad3CA), where d* reperesents the number of days since initiating reprogramming. At each time point, cells were lifted with Trypsin/EDTA, FACS sorted for mOrange expressing transgenic cells, and then 2500 cells were processed for sequencing. Reprogramming media consisted of ES medium supplemented with 300 ng/ml doxycycline (Sigma-Aldrich), with 10 ug/ml Vitamin C (Sigma-Aldrich)

d*_BFP1: The are the control reprogramming samples with control BFP expression vector infection, prepared the same way as Sm3CA samples.

Each sample group has three biological replicates, each of which has 2-3 technical replicates. All samples are present in three lanes of sequencing, reads from which were demultiplexed and provided here. Biological replicates in time series samples are paired within each series, such that d3_BFP1, for is paired with d8_BFP1. Sequencing is based on a platform that uses molecular tags, which are present with the barcodes in the read names in the format <6bp tag>.<8bp barcode>.es in the format <6bp tag>.<8bp barcode>.

Please note that technical replicates are indicated in the Sample titles (e.g. [A*] [B*] etc.). For the analysis in the paper, authors combined all reads from the technical replicates.

first: Ulrich

last: Pfisterer

first: Bruno

last: DiStefano

first: Jonathan

middle: R

last: Manning

first: Eleni

last: Chantzoura

first: Daniella

last: Rylander

first: Tian

last: Tian

first: Anna

last: Johnsson

first: Sten

last: Linnarsson

first: Thomas

last: Graf

first: Malin

last: Parmar


title: IL-1R8 is a checkpoint in NK cells regulating anti-tumor and anti-viral activity

city: Manchester

first: Santiago

last: Zelenay

state: UK

address: Alderley Park

institute: CRUK Manchester Institute

summary: We reported that IL-1R8 serves as a checkpoint for NK cell maturation and effector functions. Its genetic blockade unleashes NK-cell mediated resistance to hepatic carcinogenesis, hematogenous liver and lung metastasis and cytomegalovirus infection.

overall_design: RNA profile from splenic NK cells isolated by FACS sorting from wild-type and Il1r8-/- mice. NK cells were stimulated or not with murine IL-18 (20 ng/ml) for 4 hrs.

first: Eduardo

last: Bonavita

first: Martina

last: Molgora

first: Alberto

last: Mantovani

first: Cecilia

last: Garlanda


title: The novel heme-dependent inducible protein, SRRD regulates heme biosynthesis and circadian rhythms

city: Fukuoka

first: Tetsuya

last: Sato

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

institute: Kyushu University

summary: In order to investigate the function of heme in the regulation of gene expression, we herein examined variations in mRNA levels in ALA-treated cells from control conditions. A comprehensive anal- ysis by RNA sequencing showed marked changes in the expression of various genes. Among the different amounts of mRNA, we identified the novel heme-inducible protein, SRRD. The plant ho- mologue Sensitivity to Red Light Reduced (SRR1) was previously reported to be involved in the regulation of the circadian clock and phytochrome B signaling in Arabidopsis thaliana. We found that SRRD regulated not only heme biosynthesis, but also the expression of clock genes. The involvement of SRRD in the prolif- eration of cells was also demonstrated.

overall_design: Examination of ALA-treated versus untreated NIH3T3 cells.

first: Shigeru

last: Taketani


title: High-Throughput Drug Screening identifies Pazopanib and Clofilium tosylate as effective treatments for malignant rhabdoid tumors

city: Paris

first: Mamy

middle: Jean de Dieu

last: ANDRIANTERANAGNA

state: Ile de France

address: 26 rue d'Ulm

department: Centre de Recherche

institute: Institut Curie

summary: mRNA expression in two different cell lines (DEV and G401) and two conditions (CLOFILIUM and DMSO) were assessed using the Illumina HiSeq2500 plateform in order to detect genes that are differentially expressed in CLOFILIUM condition compared to control (DMSO)

overall_design: DEV and G401 cell lines were treated with CLOFILIUM and DMSO. mRNA were extracted 48 hours after treatment. 3 biological replicates were extracted for analysis.

first: Franck

last: Bourdeaut

first: Céline

last: Chauvin

last: Andrianteranagna


title: RNAseq of normal associate fibroblasts after treatment with large oncosomes from prostate cancer cells

city: Los Angeles

first: Sungyong

last: You

address: 8700 Beverly Blvd

institute: Cedars-Sinai Medical Center

summary: In order to detect the alteration in the transcriptomic profile of fibroblasts exposed to the large oncosomes and detemine the transcription factor responsible for those alteration we performed whole RNA sequncing with and without treatment with large oncosomes. Deep sequencing data were generated in duplicate using a NextSeq 500 platform (Illumina) using 75 single-end sequencing obtaining about 20 million reads per sample. Raw reads obtained from RNA-Seq were aligned to the custom human GRCh38 transcriptome reference (http://www.gencodegenes.org) using Bowtie (version 1.1.1) and RSEM (version 1.2.20) with default parameters. of 207 differentially expressed genes were identified between control and large oncosomes treated fibroblasts and master regulator analysis performed using TF-target interaction information collected from public databases revealed MYC and SPI1 as main transcription factors responsible for these alterations.

overall_design: mRNA profile in 2 different treatment conditions fibroblasts ctrl and fibroblasts treated with large oncosomes

first: Valentina

last: Minciacchi

first: Dolores

last: Di Vizio


title: MicroRNA regulation of type 2 innate lymphoid cell homeostasis and function in allergic inflammation

city: San Francisco

first: Heather

last: Pua

address: 513 Parnassus Ave, HSE-201, Box 0997

institute: UCSF

summary: MicroRNAs (miRNAs) exert powerful effects on immunity through coordinate regulation of multiple target genes in a wide variety of cells. Group 2 innate lymphoid cells (ILC2s) are tissue sentinel mediators of allergic inflammation. We established the physiological requirements for miRNAs in ILC2 homeostasis and immune function, and compared the global miRNA repertoire of resting and activated ILC2s and T helper type 2 (TH2) cells. Mice lacking the miR-17~92 cluster in ILC2s displayed reduced lung inflammation following exposure to the natural allergen papain.  Moreover, miR-17~92-deficient ILC2s exhibited defective growth and cytokine expression in response to IL-33 and TSLP in vitro. The miR-17~92 cluster member miR-19a promoted IL-13 production and inhibited expression of several target genes, including SOCS1 and A20, signaling inhibitors that limit IL-13 production. These findings establish miRNAs as important regulators of ILC2 biology, reveal overlapping but non-identical miRNA-regulated gene expression networks in ILC2s and TH2 cells, and reinforce the therapeutic potential of targeting miR-19 to alleviate pathogenic allergic responses .

overall_design: Gene expression analysis of ILC2 and Th2 cells in vitro and ex vivo isolated from the lung.

first: Priti

middle: B

last: Singh

first: Karl

middle: M

last: Ansel


title: Deubiquitinating Enzyme OTU5 Contributes to DNA Methylation Patterns and Is Critical for Phosphate Nutrition Signals

city: Taipei

first: Pao-Yang

last: Chen

address: 128 Sec. 2, Academia Rd, Nankang,

department: Institute of Plant and Microbial Biology

country: Taiwan

institute: Academia Sinica

summary: Phosphate (Pi) starvation induces a suite of adaptive responses aimed at recalibrating cellular Pi homeostasis. Plants harboring a mutation in OVARIAN TUMOR DOMAIN-CONTAINING DEUBIQUITINATING ENZYME5 (OTU5) showed altered DNA methylation of root hair-related genes and altered Pi-responsive root traits. Unlike the wild type, homozygous otu5 mutants did not respond to Pi starvation by increased lateral root formation and increased root hair length but formed very short root hairs when grown on low-Pi media. Under Pi-replete conditions, otu5 plants developed more root hairs than the wild type due to attenuated primary root growth, a phenotype that resembled that of Pi-deficient plants. Growth of plants on low-Pi media altered both H3K4 and H3K27 trimethylation levels at the transcriptional start site of a subset of genes encoding key players in Pi homeostasis, which was correlated with mRNA abundance changes of these genes. Pi starvation had a minor impact on DNA methylation. Differentially methylated regions were enriched in transposable elements, suggesting that DNA methylation associated with low Pi supply is required for maintaining genome integrity. It is concluded that DNA methylation and histone methylation constitute critical, interdependent regulatory components that orchestrate the activity of a subset of Pi-responsive genes.

overall_design: To understand the role of OTU5 in root development and in the alterations in root developmental programs induced by Pi starvation, we performed a comprehensive assessment of the transcriptional profiles and DNA methylation patterns of the otu5 mutant and its wild type under control and Pi deficient-conditions.

first: Ming-Ren

last: Yen

first: Fei-Men

last: Hsu

first: Der-Fen

last: Suen

first: Yi-Hsiu

last: Tsai

first: Hongyong

last: Fu

first: Wolfgang

last: Schmidt


title: Transcriptomics of adult human small bowel grafts

city: Madrid

first: Paloma

last: Talayero

address: Avenida de Cordoba s/n

department: Immunology

country: Spain

institute: Hospital 12 de Octubre

summary:
Objective: the objective of this work was to determine different gene expression patterns in small bowel grafts biopsies with “minimal changes” histology that could identify patients with high rejection risk
Methods: 24 samples (17 stable and 7 non stable grafts) from 8 adult patients with small bowel transplantation were included for RNA-Sequencing.Total RNA extracted from intestinal biopsies was used with the TruSeq RNA Sample Preparation v2 Kit to construct index-tagged cDNA libraries. Libraries were sequenced on the Genome Analyzer IIx following the standard RNA sequencing protocol with the TruSeq SBS Kit v5. Fastq files containing reads for each library were extracted and demultiplexed using Casava v1.8.2 pipeline. Sequencing adapter contaminations were removed from reads using Cutadapt software v1.6 and the resulting reads were aligned to the reference human genome (Ensembl gene-build GRCh37.75) using TopHat2 v2.0.13. Gene expression values were calculated as counts using HTSeq v0.6.1. Only genes with at least 1 count per million in all samples were considered for statistical analysis. Data were then normalized and differential expression tested using the R Bioconductor package edgeR. We selected all biopsies from 4 of the patients (18 biopsies, 11 stable and 7 non stable) as the discovery set. The other 6 biopsies from 4 patients (all stable) were used as the test set. Differences in the discovery set were tested by generalized linear model analysis,and results were considered significant when the Benjamini-Hochberg adjusted p-value was < 0,05.
Results: We obtained 816 differentially expressed genes (DEGs) between stable and non stable biopsies in the discovery set: 369 upregulated and 447 downregulated in the non stable group. The classification and prediction with the Nearest Shrunken Centroids method identified 5 genes (ADH1C, CYP4F2, PDZK1, SLC39A4 and OPTN) from the 816 DEGs that could classify both groups with an error rate of 11% and classified correctly all samples from the test set. These results were confirmed by Supoprted Vector Machine (SVM), bagSVM and Random Forest methods, showing high accuracy, sensitivity and specificity.
Conclusions: We identified 5 genes from the DEGs as possible biomarkers to classify patients with normal histology  that could be however in a higher risk of rejection. In this way, gene expression assays are powerful tools with high sensitivity that allow more accurate diagnosis.

overall_design: The study included 24 samples from 8 adult patients with small bowel transplantation. Samples correspond to RNA extracted from intestinal biopsies obtained at different post-transplantation time. All biopsies have an histological diagnosis of "minimal changes" and they were classified in two groups according their immunological stability (stable and non stable). Stable group comprised biopsies of patients that never rejected and biopsies obtained at least 15 days after rejection if no other rejection episode occurred in at least the next six months. Non stable group included biopsies obtained between rejection episodes (separated less than six months) and also those biopsies collected within the 15 days before the first rejection episode.

first: Lola

last: Alonso-Guirado

first: Haydee

last: Artaza

first: Guillermo

last: Padilla

first: Ana

last: Dopazo

first: Fátima

last: Sánchez-Cabo

first: Esther

last: Mancebo

first: Sarbelio

last: Rodríguez-Muñoz

first: Jorge

last: Calvo-Pulido

first: Mario

last: García-Lacoba

first: Estela

last: Paz-Artal


title: Sequencing analysis of proliferative heterogeneity in squamous cell carcinomas

city: New York

first: Markus

last: Schober

state: NY

address: 550 First Ave, Smilow 407

department: Dermatology

institute: New York University School of Medicine

summary: ChIP-seq, ATAC-seq and RNA-seq analyses were integrated to define direct, transcriptional Tgfβ targets in quiescent tumor propogating cells

overall_design: Differential gene expression analyses were performed between quiescent (CD71lo H2BGFPhi), proliferative (CD71hi H2BGFPlo) and double negative (CD71lo H2BGFPlo) cells in two independent tumors.  ATAC-seq analysis were compared between proliferative states depending on CD71 expression and H2BGFP label retention. Smad2/3 ChIP-seq analysis was performed on cells growth arrested in vitro with 5ng/mL TGFβ1. Copy number variation (CNV) analyses were done on input samples and nonsynonymous mutations were called from RNAseq data.

first: Jessie

last: Brown


title: Overexpression of TREM2 in human gastric cancer cells

status: Public on Nov 01 2017

city: HANGZHOU

first: YULONG

last: ZHENG

state: ZHEJIANG

address: 79 Qingchun Road

department: Department of Medical Oncology

institute: the First Affiliated Hospital, School of Medicine, Zhejiang University

summary: In order to investigate the molecular mechanisms underlying the role of TREM2 in gastric cancer, deep sequencing to profile global gene expression of MGC-803 cells with TREM2 overexpression was performed.

overall_design: To investigate the biological role of TREM2 in gastric cancer, MGC-803 cells with stable overexpression of TREM2 were established. Then deep sequencing to profile global gene expression of MGC-803 cells with TREM2 overexpression was performed.

first: Yulong

last: Zheng


title: MicroRNA Contents in Matrix Vesicles Produced by Growth Plate Chondrocytes Are Cell Maturation Dependent

city: Richmond

first: Barbara

middle: D.

last: Boyan

state: VA

address: 601 W. Main St.

department: School of Engineering

institute: Virginia Commonwealth University

summary: Chondrocytes at different maturation states in the growth plate produce matrix vesicles (MVs), membrane organelles found in the extracellular matrix, with a wide range of contents, such as matrix processing enzymes and receptors for hormones. We have shown that MVs harvested from growth zone (GC) chondrocyte cultures contain abundant small RNAs, including miRNAs. Here, we determined whether RNA also exists in MVs produced by less mature resting zone (RC) chondrocytes and, if so, whether it differs from the RNA in MVs produced by GC cells. Our results showed that RNA, small RNA specifically, was present in RC-MVs, and it was well-protected from RNase by the phospholipid membrane. A group of miRNAs was enriched in RC-MVs compared RC-cells, suggesting that miRNAs are selectively packaged into MVs. High throughput array and RNA sequencing showed that ~39% miRNAs were differentially expressed between RC-MVs and GC-MVs. Individual RT-qPCR also confirmed that miR-122-5p and miR-150-5p were expressed at significantly higher levels in RC-MVs compared to GC-MVs. This study showed that growth plate chondrocytes at different differentiation stages produce different MVs with different miRNA contents, further supporting extracellular vesicle miRNAs play a role as “matrisomes” that mediate the cell–cell communication in cartilage and bone development.

overall_design: miRNA expression profiles of resting zone chondrocyte cells and matrix vesicles

first: Zhao

last: Lin

first: Michael

middle: J

last: McClure

first: Junjun

last: Zhao

first: Allison

middle: N

last: Ramey

first: Niels

last: Asmussen

first: Sharon

middle: L

last: Hyzy

first: Zvi

last: Schwartz

middle: D


title: Paternal chromosome loss and metabolic crisis contribute to hybrid inviability in Xenopus

city: Ulsan

first: Taejoon

last: Kwon

address: 50 Unist-gil

department: Department of Biomedical Engineering

institute: Ulsan National Institute of Science and Technology

summary: Hybridization of eggs and sperm from closely related species can give rise to genetic diversity, or can lead to embryo inviability due to incompatibility. Although central to evolution, the cellular and molecular mechanisms underlying postzygotic barriers that drive reproductive isolation and speciation remain largely unknown. Species of the African Clawed frog Xenopus provide an ideal system to study hybridization and genome evolution. Xenopus laevis is an allotetraploid with 36 chromosomes that arose through interspecific hybridization of diploid progenitors, whereas Xenopus tropicalis is a diploid with 20 chromosomes that diverged from a common ancestor ~48 million years ago. Differences in genome size between the two species are accompanied by organism size differences, and size scaling of the egg and subcellular structures such as nuclei and spindles formed in egg extracts. Nevertheless, early development transcriptional programs, gene expression patterns, and protein sequences are generally conserved. Interestingly, whereas the hybrid produced when X. laevis eggs are fertilized by X. tropicalis sperm (le×ts) is viable, the reverse hybrid (te×ls) dies prior to gastrulation. Here, we applied cell biological tools and high-throughput methods to study the mechanisms underlying hybrid inviability. We reveal that two specific X. laevis chromosomes are incompatible with the X. tropicalis cytoplasm and are mis-segregated during mitosis, leading to unbalanced gene expression at the maternal to zygotic transition, followed by cell-autonomous catastrophic embryo death.

sample_organism:
Xenopus tropicalis
Xenopus tropicalis x Xenopus laevis

overall_design: Collect mRNA from whole embryos; three biological replicates were analyzed

first: Romain

last: Gibeaux

first: Rachael

last: Acker

first: Maiko

last: Kitaoka

first: Georgios

last: Georgiou

first: Ilavan

last: Kruijsbergen

first: Breanna

last: Ford

first: Edward

last: Marcotte

first: Daniel

middle: K

last: Nomura

first: GertJan

last: Veenstra

first: Rebecca

last: Heald


title: Selective endosteal remodeling of blood vessels in acute myeloid leukemia promotes malignancy at the expense of hematopoietic stem cells

first: Isabella

last: Kong

state: New York

address: 1300 York Ave

institute: Weill Cornell Medicine

summary: Hematopoietic stem cell (HSC) function requires bone marrow vascular niches, which have been proposed to be co-opted by leukemia cells to support their propagation. Acute myeloid leukemia (AML) cells produce angiogenic factors; however, anti-angiogenic therapies have not improved AML patient outcome. Using intravital microscopy we uncovered hierarchical vascular remodeling with AML progression. AML cells outcompete non-malignant hematopoiesis by gradual elimination of stroma cells, endosteal endothelium, and osteoblastic cells. While central marrow remains vascularized and splenic vascular niches expand, the remodeled endosteal regions lose the ability to retain HSCs. Overall, the endosteal endothelium microenvironment is altered by AML, yet by preserving it we rescue HSC loss and promote chemotherapeutic efficacy. Our findings suggest therapies targeting the endosteal vasculature may improve existing AML therapeutic regimes.

overall_design: RNA-Seq analysis on different AML clones versus HSC controls

first: Delfim

last: Duarte