title: Srf destabilizes cell identity (RNA-seq)

city: Kyoto

first: Takashi

last: Ikeda

address: 53 Shogoin Kawahara-cho Sakyo-ku

institute: Kyoto Univ.

summary: Multicellular organisms consist of multiple cell types, whose identities are maintained appropriately at locations where they are reside. The identity of each cell type is primarily maintained by cell-type-specific gene expression programs, but mechanisms that suppress these programs are poorly defined. Here we show that serum response factor (Srf), a transcription factor that is activated by various extracellular stimuli, can repress cell-type-specific genes and promote cellular reprogramming to pluripotency. Manipulations that decrease β-actin monomer resulted in nuclear accumulation of Mkl1 and the activation of Srf, which downregulated cell-type-specific genes and altered epigenetics in enhancers and chromatin organization. Mice overexpressing Srf exhibited various pathologies including an ulcerative colitis-like symptom and a metaplasia-like phenotype in the pancreas. Our results demonstrate an unexpected function of Srf via a mechanism by which extracellular stimuli actively destabilize cell identity and suggest Srf involvement in a wide range of diseases.

overall_design: Gene expressions comparing cells cultured on different stiffnesses

first: Takafusa

last: Hikichi

first: Takuya

last: Yamamoto

first: Keisuke

last: Okita

first: Shinji

last: Masui


title: Srf destabilizes cell identity (ATAC-seq)

status: Public on Apr 18 2018

country: Japan

type: Genome binding/occupancy profiling by high throughput sequencing

overall_design: Open chromatin regions determined by ATAC-seq analysis

first: Akira

last: Watanabe


title: Effect of β-adrenergic receptor antagonist and agonist on cardiac structure and function and whole body gene expression in Daphnia magna

status: Public on Apr 20 2018

city: Gent

first: Jana

last: Asselman

address: Coupure Links 653 (Building F, 2nd floor)

country: Belgium

institute: Ghent University

type: Expression profiling by high throughput sequencing

summary: Propranolol (PRO), a human β-AR (β-adrenergic receptor) antagonist, is considered to result in specific effects in a non-target species, D. magna, based on our previous studies. The present study investigated the effects of β-AR agents, including an antagonist and agonist using pharmacologically relevant endpoints as well as a more holistic gene expression approach to reveal the impacts and potential mode of actions (MOAs) in the model non-target species. Results show that the responses in cardiac endpoints and gene expression in D. magna are partially similar but distinguishable from the observations in different organisms. No effect was observed on heart size growth in PRO and isoprenaline (ISO) exposure. The contraction capacity of the heart was decreased in ISO exposure, and the heart rate was decreased in PRO exposure. Time-series exposures showed different magnitudes of effect on heart rate and gene expression dependent on the type of chemical exposure. Significant enrichment of gene families involved in protein metabolism and biotransformation was observed within the differentially expressed genes, and we also observed differential expression in juvenile hormone-inducible proteins in ISO and PRO exposure, which is suspected of having endocrine disruption potential. Taken together, deviation between the effects of PRO and ISO in D. magna and other organisms suggests dissimilarity in MOAs or attributes of target bio-molecules between species. Additionally, PRO and ISO may act as endocrine disruptors based on the gene expression observation. Results in the present study confirm that it is challenging to predict ecological impact of active pharmaceutical ingredients (APIs) based on the available data acquired through human-focused studies. Furthermore, the present study provided unique data and a case study on the impact of APIs in a non-target organism.

overall_design: The experiment is a 24 hour-exposure experiment, in which daphnia were exposed to different chemicals and their binary mixture. The concentrations were 1mg/L and 4mg/L for propranolol and 100mg/L for isoprenaline respectively. The concentrations in the exposure were chosen to be sufficiently high to observe clear time-series changes of heart rate and corresponding gene expression regulation within 24 hours. 20 individuals of 5 days old D. magna were exposed to different 35 ml chemical solutions separately and were harvested at 1, 6, and 24 hours of exposure. There were three replicates per treatment

first: Tae-Yong

last: Jeong

first: Karel

middle: A

last: De Schamphelaere

first: Filip

last: Van Nieuwerburgh

first: Dieter

last: Deforce

first: Sang

middle: D

last: Kim


title: A modular transcriptional signature identifies phenotypic heterogeneity of human tuberculosis infection [Berry_South Africa]

status: Public on Apr 19 2018

city: London

first: Akul

last: Singhania

address: 1 Midland Road

country: United Kingdom

institute: The Francis Crick Institute

summary: Whole blood transcriptional signatures distinguishing patients with active tuberculosis from asymptomatic latently infected individuals have been described but, no consensus exists for the composition of optimal reduced gene sets as diagnostic biomarkers that also achieve discrimination from other diseases.

overall_design:
We undertook RNA Sequencing (RNA-Seq) of our earlier Berry et al. 2010 (GSE19444 and GSE19442) cohorts and additionally set up a prospective cohort study at Leicester (UK) in subject groups of incident TB and recent TB contacts, respectively. In the Leicester cohort, we performed systematic longitudinal sampling and clinical characterisation first, to validate our TB signature using RNA-Seq in a new and independent cohort of individuals with active TB and LTBI, and secondly to provide longitudinal data in a low TB incidence setting.

43 of the 47 samples in this series were re-analyzed from GSE19442. These samples include links to the original sample at the foot of the page.

first: Raman

last: Verma

first: Christine

middle: M

last: Graham

first: Jo

last: Lee

first: Tran

last: Trang

first: Matthew

last: Richardson

first: Patrick

last: Lecine

first: Philippe

last: Leissner

middle: P

last: Berry

first: Robert

middle: J

last: Wilkinson

first: Karine

last: Kaiser

first: Marc

last: Rodrigue

first: Gerrit

last: Woltmann

first: Pranabashis

last: Haldar

first: Anne

last: O'Garra


title: Analysis of the long-lived responses induced by immunostimulants and their effects on a viral infection in zebrafish (Danio rerio)

city: Vigo

first: Patricia

last: Pereiro

state: Pontevedra

address: C/Eduardo Cabello, 6

department: Immunology and Genomics

country: Spain

institute: IIM-CSIC

summary:
In the last years, the innate immune response has gained importance since evidences indicate that, after an adequate priming protocol, it is possible to obtain some prolonged and enhanced immune response. Nevertheless, several factors, such as timing and method of administration of the immunostimulants need to be carefully considered. An inappropriate protocol can transform the treatments into a double-edged sword for the teleost immune system, resulting in a stressful and immunosuppressive status.
In this work, we analyzed the long-term effect of different stimuli (β-glucans, lipopolysaccharide and Polyinosinic:polycytidylic acid) on the transcriptome modulation induced by Spring Viraemia Carp Virus (SVCV) in adult zebrafish (Danio rerio) and on the mortalities caused by this infection. At 35 days post-immunostimulation the transcriptome was found to be highly altered compared to the control fish, and these stimuli also conditioned the response to SVCV challenge, especially in the case of β-glucans. No protection against SVCV was found with any of the stimuli and even non-significant higher mortalities were observed, especially with β-glucans. However, at short-term (a pre-stimulation with β-glucan and infection after 7 days) a slight protection was observed after infection. The transcriptome response in zebrafish kidney at 35 days post-treatment with β-glucans revealed a significant response associated to stress and immunosuppression. The identification of genes differentially expressed before and after the infection seem to indicate a high energy cost of the immunostimulation prolonged in time that could explain the lack of protection against the SVCV. The differential response to stress, alterations in the lipid metabolism, the tryptophan-kynurenine pathway and the interferon-gamma signaling seem to be some of the mechanisms involved in this particular response, which means the end of the trained immunity and the beginning of a stressful status characterized by immunosuppression.

overall_design: Four groups composed of 92 adult zebrafish/each were intraperitoneally (i.p.) injected with 20 µl of one of the following treatments: β-glucans (1 mg/ml), LPS (0.75 mg/ml), Poly(I:C) (1 mg/ml) and the control group with phosphate-buffered saline (PBS). After 35 days, half of the individuals were i.p. infected with 20 µl of a SVCV suspension (3 × 102 TDCI50/ml) and the remaining fish, which served as uninfected control, were inoculated with viral medium (MEM + 2% FBS + Primocin). For microarray hybridization, a total of 16 fish from each treatment (β-glucans-control, LPS-control, Poly(I:C)-control, β-glucans-SVCV, LPS-SVCV and Poly(I:C)-SVCV) were sacrificed at 24h post-infection and the kidney was removed, obtaining 4 pooled biological replicates (four fish/replicate).

first: Margarita

last: Álvarez-Rodríguez

first: Felipe

middle: E

last: Reyes-López

first: Lluis

last: Tort

first: Antonio

last: Figueras

first: Beatriz

last: Novoa


title: A modular transcriptional signature identifies phenotypic heterogeneity of human tuberculosis infection [Leicester progressor]

first: Akul

last: Singhania

overall_design: We undertook RNA Sequencing (RNA-Seq) of our earlier Berry et al. 2010 (GSE19444 and GSE19442) cohorts and additionally set up a prospective cohort study at Leicester (UK) in subject groups of incident TB and recent TB contacts, respectively. In the Leicester cohort, we performed systematic longitudinal sampling and clinical characterisation first, to validate our TB signature using RNA-Seq in a new and independent cohort of individuals with active TB and LTBI, and secondly to provide longitudinal data in a low TB incidence setting.

first: Raman

last: Verma

first: Christine

last: Graham

first: Jo

last: Lee

last: Trang


title: Differential expression of H3.3 genes and their role in modulating temperature stress response in Caenorhabditis elegans

city: Geneva

first: Florian

last: Steiner

address: 30, Quai Ernest-Ansermet

department: Department of Molecular and Cellular Biology

country: Switzerland

institute: University of Geneva

summary: We generated gene expression profiles of N2 (wild type) and strain FAS43 (Histone H3.3 null worms containing knockout alleles of all genes with homology to human histone H3.3: his-69, his-70, his-71, his-72, his-74) at embryonic and first larval instar stages.

overall_design: RNA was isolated from N2 and H3.3 null mixed-stage embryos and L1 larvae grown at 20°C using Trizol, in duplicates for all samples. RNA-seq libraries were prepared using the Illumina TruSeq protocol.

first: Kamila

last: Delaney


title: Characterization of lncRNAs involved in cold acclimation of zebrafish ZF4 cells

city: Hangzhou

first: Jiang

last: Penglei

address: Yuhangtang Road 866

department: School of basic medicine science

country: China

institute: Zhejiang University

summary: Long non-coding RNAs (lncRNAs) are increasingly regarded as a key role in regulating diverse biological processes in various tissues and species. So far, no data is available on screening and functional prediction of lncRNAs in cold acclimation in fishes. Here we compared expression profiles of lncRNAs in zebrafish embryonic fibroblast cells (ZF4) cultured at 28°C as control with that of cold acclimated cells cultured at 18°C for 30 days by high-throughput sequencing. There are 8363 novel lncRNAs were identified. Including known and novel lncRNAs, there are 347 lncRNAs up-regulated and 342 lncRNAs down-regulated in cold acclimated cells, compared with that of control cells at 28°C. Among differentially expressed lncRNAs, 74 and 61 were found only in control cells or in cold-acclimated cells, respectively. The Gene Ontology (GO) and Kyoto Encyclopaedia of Genes and Genomes (KEGG) enrichment analyses of genes adjacent to differentially expressed lncRNAs showed that enriched genes were involved in electron transport, cell adhesion, oxidation-reduction process, and so on. We predicted target genes of differentially expressed lncRNAs by looking for interactions between lncRNAs and mRNA, and constructed a complex interaction network. In summary, our genome-wide systematic identification and function prediction of lncRNAs in zebrafish cells, lays the foundation for future studies to elucidate crucial roles of lncRNAs in cold acclimation in fishes.

overall_design: ZF4 cells were cultured at 28 °C as control and at 18 °C for 30 days, seperately. Each condition has three biological replica.

first: Penglei

last: Jiang

first: Yanwen

last: Hou

first: Xiaofan

last: Tao

first: Yutian

last: Sun

first: Hanxu

last: Lu

first: Juntao

last: Luo

first: Bingshe

last: Han

first: Junfang

last: Zhang


title: Transcriptional Profiling of Host Cell Responses to Virulent Haemophilus parasuis

city: Wuhan

first: shulin

last: fu

address: No. 68 Changqing Gardern

institute: Wuhan Polytechnic University

summary: we investigated the host cell responses involved in the molecular pathways interaction in porcine aortic vascular endothelial cells (PAVECs) induced by H. parasuis

overall_design: PAVECs  were  infected with H. parasuis SH0165 strain and the cells were collected for transcriptomic analysis. The control cells were infected with M-199 medium and treated in the same way. Three individual replicates were designed for the infection experiment.

first: Shulin

last: Fu

first: Jing

last: Guo

first: Ruizhi

last: Li

first: Yingsheng

last: Qiu

first: Chun

last: Ye

first: Yu

last: Liu

first: Zhongyuan

last: Wu

first: Ling

first: Yongqing

first: Chien-An

last: Hu


title: A modular transcriptional signature identifies phenotypic heterogeneity of human tuberculosis infection [Leicester non-progressor]

first: Akul

last: Singhania

first: Raman

last: Verma

first: Christine

last: Graham

first: Jo

last: Lee

first: Tran

last: Trang

first: Matthew

last: Richardson

first: Patrick

last: Lecine

first: Philippe

last: Leissner

last: Berry

first: Robert

last: Wilkinson

first: Karine

last: Kaiser

first: Marc

last: Rodrigue

first: Gerrit

last: Woltmann

first: Pranabashis

last: Haldar

first: Anne

last: O'Garra


title: Deep functional analysis of synII, a 770 kb synthetic yeast chromosome

city: Norwich

first: Conrad

last: Nieduszynski

address: Norwich Research Park

institute: Earlham Institute

summary: Herein we report the successful design, construction and characterization of a 770 kb synthetic yeast chromosome II (synII). Our study incorporates characterization at multiple levels, including phenomics, transcriptomics, proteomics, chromosome segregation and replication analysis to provide the most thorough and comprehensive analysis of a synthetic chromosome. Our “Trans-Omics” analyses reveal a modest but potentially significant pervasive up-regulation of translational machinery observed in synII is mainly caused by the deletion of 13 tRNAs. By both complementation assays and SCRaMbLE, we targeted and debuged the origin of a growth defect at 37°C in glycerol medium, which is related to misregulation of the HOG response. Despite the subtle differences, the synII strain shows highly consistent biological processes comparable to the native strain.

overall_design: Measurement of genome replication timing from a S. cerevisiae yeast strain with a 770 kb synthetic yeast chromosome II (synII). Two samples were analysed: a replicating sample (from S phase) and a non-replicating sample (from G2 phase).

first: Yue

last: Shen

first: Yun

last: Wang

first: Tai

last: Chen

first: Feng

last: Gao

first: Jianhui

last: Gong

first: Dariusz

last: Abramczyk

first: Roy

last: Walker

first: Hongcui

last: Zhao

first: Shihong

first: Wei

last: Liu

first: Yisha

last: Luo

first: Carolin

last: Müller

first: Adrien

last: Paul-Dubois-Taine

first: Bonnie

last: Alver

first: Giovanni

last: Stracquadanio

first: Leslie

last: Mitchell

first: Zhouqing

first: Yanqun

last: Fan

first: Baojin

last: Zhou

first: Bo

last: Wen

first: Fengji

last: Tan

first: Yujia

first: Jin

last: Zi

first: Zexiong

last: Xie

first: Bingzhi

last: Li

first: Kun

last: Yang

first: Sarah

first: Yingjin

last: Yuan

first: Christopher

last: French

first: Romain

last: Koszul

first: Adele

middle: L

last: Marston

first: Hui

last: Jiang

first: Jian

first: Joel

middle: S

last: Bader

first: Junbiao

last: Dai

first: Jef

last: Boeke

first: Xun

last: Xu

first: Yizhi

last: Cai

first: Huanming


title: A modular transcriptional signature identifies phenotypic heterogeneity of human tuberculosis infection

first: Akul

last: Singhania

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

overall_design: Refer to individual Series


title: Differential Gene Expression and Pathway Analysis in Juvenile Nasopharyngeal Angiofibroma Using RNA-Sequencing

city: Kansas City

first: Sufi

middle: Mary

last: Thomas

state: Kansas

address: 3901 Rainbow Blvd. Mail Stop 4031

department: Otolaryngology-Head & Neck Surgery

country: USA

institute: University of Kansas Medical Center

summary: We have identified a set of differentially expressed genes in the juvenile nasopharyngeal angiofibroma transcriptome and predict activation of the vascular endothelial growth factor and interleukin-6 signaling pathways, which represent potential molecular targets for therapy in patients with inoperable or persistent disease. These results implicate the role of fibroblasts as a tumor cell type driving disease progression.

overall_design: mRNA transcriptome profiles of cultured fibroblasts from two juvenile nasopharyngeal angiofibroma tumor explants and two fibroblast replicates cultured from normal adult tonsil tissue

middle: W

last: Jones

first: Jacob

last: New

first: Sumedha

last: Gunewardena


title: Differential expression of small RNAs in muscle tissue of patients with Amyotrophic lateral sclerosis and healthy controls

city: Ljubljana

first: Anja

last: Kovanda

address: Jamova 39

department: Dept. of Biotechnology

country: Slovenia

institute: Institute Jozef Stefan

summary: We report the differential expression of small RNAs in muscle tissue of patients with Amyotrophic lateral sclerosis and healthy controls

overall_design: Small RNA Seq of muscle samples from 11 ALS patients and 11 controls

first: Boris

last: Rogelj


title: 5hmC dynamically correlated with enhancer's activities during hES-to-Pancreatic endoderm cell differentiation (RNA-Seq)

city: Houston

first: Jia

last: Li

state: Texas

address: 2121 W HOLCOMBE BLVD

department: CEDP

institute: Guangzhou Medical University

summary: We generated 5hmC, WGBS and RNAseq of the cells in 5 stages during hES-to-pancreatic endoderm cell differantiation, and investigated the 5hmC correlation with 4 histones (H3K4me1, H3K4me3, H3K27ac and H3K27me3) during this process. Our results showed that 5hmC is dynamically correlate with enhancers' activities.

overall_design: Purpose: Determine the roles of 5hmC during hES to pancreatic endoderm cell differentiation process. The whole genome bisulfite sequencing, CMS-IP, ATAC-seq and RNAseq for the 5 stages (ES,DE,GT,FG,PE) have been sequenced.

first: Y

last: Huang

first: D

last: Sun

first: R

last: Xie

first: J


title: 5hmC dynamically correlated with enhancer's activities during hES-to-Pancreatic endoderm cell differentiation (ATAC-Seq)


title: Treatment of SW480 colon cancer cell induced xenografts with AZD and DBZ

city: Munich

first: Stefan

last: Krebs

address: Feodor-Lynen-Str. 25

department: Gene Center

country: Germany

institute: Ludwig-Maximilian University

summary: RNASeq data from replicates with and without treatment of SW480 colon cancer cells

overall_design: 3 biological replicates of xenografts treated with vehicle, AZD or DBZ

first: Eva

last: Schmidt

first: Helmut

last: Blum

first: David

last: Horst


title: 5hmC dynamically correlated with enhancer's activities during hES-to-Pancreatic endoderm cell differentiation

type: Methylation profiling by high throughput sequencing


title: 5hmC dynamically correlated with enhancer's activities during hES-to-Pancreatic endoderm cell differentiation (Bisulfite-Seq)


title: 5hmC dynamically correlated with enhancer's activities during hES-to-Pancreatic endoderm cell differentiation (CMS)


title: Single-cell sequencing of stage 4 chicken embryos

city: Madison

last: Vereide

state: WI

address: 330 North Orchard Street

department: Regenerative Biology

institute: Morgridge Institute for Research

summary: Abstract from Vermillion et al: During vertebrate development, progenitor cells give rise to tissues and organs through a complex choreography that commences at gastrulation. A hallmark event of gastrulation is the formation of the primitive streak, a linear assembly of cells along the anterior-posterior (AP) axis of the developing organism. To examine the primitive streak at a single-cell resolution, we measured the transcriptomes of individual chick cells from the streak or the surrounding tissue (the rest of the area pellucida) in Hamburger-Hamilton stage 4 embryos. The single-cell transcriptomes were then ordered by the statistical method Wave-Crest to deduce both the relative position along the AP axis and the prospective lineage of single cells. The ordered transcriptomes reveal intricate patterns of gene expression along the primitive streak.

overall_design: Examination of single-cells of stage 4 chicken embryos.

first: Katie

last: Vermillion


title: The effect of expression of the Agrobacterium tumefaciens virulence protein VirE3 on gene expression in Arabidopsis thaliana.

city: Leiden

first: Paul

last: van Heusden

address: Sylviusweg 72

department: Institute of Biology

country: Netherlands

institute: Leiden University

summary: During Agrobacterium-mediated transformation of plant cells a part of the tumour inducing plasmid, the T-DNA, is integrated into the host genome. In addition, a number of virulence proteins are translocated into the host cell. The virulence protein VirE3 binds to the Arabidopsis thaliana pBrp protein, a plant-specific general transcription factor of the TFIIB family. To study a possible role of VirE3 in transcriptional regulation, we stably expressed virE3 in A. thaliana under control of a tamoxifen-inducible promoter. By RNA sequencing we showed that upon expression of virE3 the RNA levels of 607 genes were increased more than three-fold and those of 132 genes decreased more than three-fold.

overall_design: An Arabidopsis line expressing virE3  and a control line were selected and the RNA from tamoxifen-induced and non-induced plantlets was analysed by Illumina RNA sequencing.

first: Xiaolei

last: Niu

first: G


title: Srf destabilizes cell identity (Hi-C-seq)

first: Takashi

last: Ikeda

summary: Multicellular organisms consist of multiple cell types, whose identities are maintained by the locations in which they reside. The identity of a cell is primarily maintained by cell-type-specific gene expression programs, but mechanisms that suppress these programs are poorly defined. Here we show that serum response factor (Srf), a transcription factor that is activated by various extracellular stimuli, can repress cell-type-specific genes and promote cellular reprogramming to pluripotency. Manipulations that decrease β-actin monomer quantity resulted in the nuclear accumulation of Mkl1 and the activation of Srf, which downregulated cell-type-specific genes and altered epigenetics in enhancers and chromatin organization. Mice overexpressing Srf exhibited various pathologies including an ulcerative colitis-like symptom and a metaplasia-like phenotype in the pancreas. Our results demonstrate an unexpected function of Srf via a mechanism by which extracellular stimuli actively destabilize cell identity and suggest Srf involvement in a wide range of diseases.

overall_design: To analyze the effect of Actb knockout and Srf overexpression on chromatin organization, Hi-C analyses of NPCs, NPCs with CRISPR/Cas9-based knockout of Actb and NPCs overexpressing Srf were performed.

first: Takafusa

last: Hikichi

first: Hisashi

last: Miura

first: Ichiro

last: Hiratani

first: Keisuke

last: Okita

first: Shinji

last: Masui


title: MicroRNA biomarkers of tissue function

city: Easter Bush

first: Jason

last: Ioannidis

state: Midlothian

address: Easter Bush Veterinary Campus

department: Developmental Biology

institute: The Roslin Institute

type: Non-coding RNA profiling by high throughput sequencing

summary: In recent years circulating miRNAs have been proposed as biomarkers of several diseases in humans. However the origin of these potential biomarkers is not always investigated and recent studies have highlighted the importance of selecting biomarkers which are not blood-cell derived to ensure robust performance. The aim of this study was identify circulating miRNAs which are not blood-cell derived (highly expressed in plasma compared to whole blood cells in cow) and investigate the expression of a selection of those in a range of bovine tissues as a follow-up to these results.

overall_design: In this experiment a total of 8 bovine samples (4 blood cell samples and 4 plasma samples) were analysed using Illumina miRNA sequencing. These samples were collected from healthy cycling heifers during a normal oestrous cycle from each of 4 animals (the samples are paired). Therefore this study included 4 biological replicates for each of the two groups analysed.

first: Xavier

last: Donadeu


title: Srf destabilizes cell identity


title: GKAP acts as a genetic modulator of NMDAR signaling to govern tumor invasiveness

city: Cambridge

first: A

last: Bhutkar

state: MA

address: 77 Massachusetts Avenue

institute: MIT

summary: Genetic linkage analysis suggested that GKAP, a scaffold protein of the NMDA receptor (NMDAR), was a potential modifier of invasion in a mouse model of pancreatic neuroendocrine cancer (PanNET). Here we establish that GKAP governs invasive growth and treatment response of PanNET via its pivotal role in regulating the NMDAR pathway activity. Combining genetic knockdown of GKAP and pharmacological inhibition of NMDAR, we distilled gene expression signatures orchestrated by the NMDAR-GKAP axis, in addition to identifying two downstream effectors FMRP and HSF-1. Additionally, GKAP, FMRP, and HSF1 are functionally implicated in invasiveness of pancreatic ductal adenocarcinoma. Finally, gene expression signatures in tumors with low NMDAR activity are significantly associated with favorable patient prognosis in several cancer types.

overall_design: mPanNET tumors from different strain backgrounds: C57Bl/6 (B6) and C3HeB/Fe (C3H). Within B6 tumors, either treated with a potent NMDAR antagonist MK801 or untreated/saline-treated controls.

first: Leanne

last: Li

first: Qiqun

last: Zeng

first: Arjun

first: José

last: Galván

last: Karamitopoulou

first: Anamaria

last: Necsulea

first: Daan

last: Noordermeer

first: Alessandra

last: Piersigilli

first: Mei-Wen

last: Peng

first: Aurel

last: Perren

first: Inti

last: Zlobec

first: Hugh

last: Robinson

first: M

last: Iruela-Arispe

first: Douglas

last: Hanahan


title: Forniceal deep brain stimulation induces gene expression and splicing changes that promote neurogenesis and synaptic plasticity

status: Public on Apr 17 2018

city: Houston,

first: Hari Krishna

last: Yalamanchili

state: TX

address: 1250 Moursund St #1125,

institute: Baylor College of Medicine

summary: Clinical trials are currently underway to assess the efficacy of forniceal deep brain stimulation (DBS) for the improvement of memory in Alzheimer’s patients, and forniceal DBS has been shown to improve learning and memory in a mouse model of Rett syndrome (RTT), an intellectual disability disorder. The mechanism of DBS benefits has been elusive, however, so we assessed gene expression, splice isoform abundance, DNA methylation, and proteomic changes following acute forniceal DBS in wild-type mice and a mouse model lacking Mecp2, the gene whose loss of function causes RTT. We found that DBS upregulates genes involved in synaptic function, cell survival, and neurogenesis, and alters the proportions of different isoforms even for genes whose expression is unchanged. DBS rescued ~25% of the gene expression defects in Mecp2-null mice, particularly those involved in synaptic components, and it induced expression of 17-24% of the genes found to be downregulated in intellectual disability mouse models and in post-mortem human brain tissue from patients with Major Depressive Disorder. DBS could thus benefit individuals with a variety of neuropsychiatric disorders.

overall_design: There are 4 samples in this dataset. Two sham-treated samples (biological replicates; the sham samples are the control samples) and two DBS-treated samples (biological replicates; the DBS samples are the electrically stimulated samples).

first: Amy

last: Pohodich

first: Hari

middle: K

first: Ying

last: Wooi

first: Zhandong

last: Liu

first: Huda

middle: Y

last: Zoghbi


title: Systems approach elucidates convoluted transcriptional regulation on carbon metabolism [RNA-seq]

city: Ulsan

first: Donghyuk

last: Kim

address: 50 UNIST-gil, Eonyang-eup, Ulju-gun

department: Department of Chemical Engineering

country: South Korea

institute: UNIST

summary: The carbon metabolism in bacteria is regulated by two global TFs, CRP and Cra. While the regulon of CRP has been extensively studied, the complete definition of Cra has been missing. Thus, in vivo TF binding measurement with ChIP-exo and transcriptional expression measurement with RNA-seq for Cra was performed to define the Cra regulon.

overall_design: A total of twelve samples were analyzed. WT and Δcra mutant cells were cultured in M9 minimal media with 3 different carbon sources, glucose, fructose, and acetate.

first: Sang

last: Seo


title: Systems approach elucidates convoluted transcriptional regulation on carbon metabolism [ChIP-seq]

overall_design: A total of six samples were analyzed. cra-8myc tagged cells were cultured in M9 minimal media with 0.2% glucose, fructose, and acetate upto mid-log phase with biological duplicates.


title: Expression data of three Frankia strains under nitrogen-replete and nitrogen-defiecent conditions

city: Durham

first: Louis

last: Tisa

state: NH

address: 46 College Rd

department: MCBS

institute: University of New Hampshire

summary: Purpose: To compare RNASeq data of  Frankia strains (EAN1pec, EuIC and EUN1f) under nitrogen stress.   Frankia cultures were grown for 2 days under nitrogen replete (+NH4) or nitrogen- deficient (N2) conditions.  RNA-seq analysis provided insight into how the the bacteria responds to nitrogen stress.

sample_organism:
Parafrankia sp. EUN1f
Parafrankia sp. EAN1pec
Pseudofrankia inefficax

overall_design: mRNA profiles of bacteria from each Frankia strain (EAN1pec, EuI1c, EUN1f) grown under nitrogen-replete and niotrogen-defiencent conditions were generated by deep sequencing and mapped to their appropriate Frankia genome by CLC Gemonic Workstation.  The transcriptome profiles of the nitrogen stress cells were compared to the control nitrogen replete condition.

first: Sheldon

last: Hurst IV

first: Rediet

last: Oshone


title: PyMT 4 stages tumor progression ERRBS (Enhanced Reduced Representation Bisulphite Sequencing )

city: bronx

first: ying

last: cai

state: New York

address: 1300 morris park ave

institute: Albert Einstein College of Medicine

summary: We sequenced mammary tissues of PyMT mice from 4 stages (hyperplasia at week 6, adenoma/MIN at week 8, early carcinoma at week 10, and late carcinoma at week 12) during tumor progression. We also sequenced mammary tissues of age-matched FVB controls.

overall_design: We sacrificed 3 PyMT mice and 3 FVB control mice at each of the 4 stages, extracted genomic DNA and performed sequencing.

last: Cai

first: Jhih-Rong

last: Lin

first: Quanwei

last: Zhang

first: Kelly

last: O'Brien

first: Cristina

last: Montagna

first: Zhengdong


title: Tracking transcriptional changes in a species-specific manner during experimental hepatoblastoma progression in vivo

city: Bordeaux

first: Katarzyna

middle: B

last: Hooks

address: 146, rue Léo Saignat

department: CBIB

country: France

institute: Univ. Bordeaux

summary: Hepatoblastoma is a primitive liver cancer occurring mainly in infants with defined molecular alterations driving its progression, which is difficult to model in vivo. Here we present a new animal model for hepatoblastoma on the chick chorioallantoic membrane (CAM), which recapitulates relevant features of hepatoblastoma in patients. Expression of classic tumor-associated proteins such as β-catenin, EpCAM and CK19 was maintained in acini-like organized tumors on CAM, as was synthesis of AFP, a tumor marker used for monitoring patient response. RNA sequencing revealed an unexpected molecular evolution of hepatoblastoma cells on the CAM, with significant deregulation of more than 6000 genes including more than half of all HOX genes. Bioinformatic analysis could clearly distinguish between tumor cell-expressed genes and chick host genes, thereby shedding new light on the complex interactions taking place during experimental hepatoblastoma progression. Importantly, human tumor suppressive ribosomal genes were downregulated after implantation, whereas mitochondrial genes encoding for anti-apoptotic peptides were strongly induced in vivo. Meprin-1α expression was increased during evolution of CAM tumors and confirmed by immunohistochemistry. Cisplatin, a commonly used chemotherapeutic agent for hepatoblastoma, showed significant anti-tumoral effects in this model. Our results broaden the understanding of the molecular adaptation process of human cancer cells to the microenvironment and might help to elaborate novel therapeutic concepts for the treatment of this pediatric liver tumor.

sample_organism:
Gallus gallus
Homo sapiens

platform_organism:
Gallus gallus
Homo sapiens

overall_design: HuH6 cells and CAM mRNA profiles were generated by deep sequencing, in triplicate, using Illumina HiSeq 2500 and HiSeq 2000, respectively

first: Emilie

last: Indersi

first: Martin

last: Hagedorn


title: Next Generation Sequencing Facilitates Quantitative Analysis of Wild Type (WT) HSCs and  NHD13+ MDS HSCs Transcriptomes

city: New York

first: Haiming

last: Xu

state: NY

address: 1275 York Avenue

department: Cancer Biology and Genetics

institute: Memorial Sloan Kettering Cancer Center

summary:
Purpose: Next-generation sequencing (NGS) has revolutionized systems-based analysis of cellular pathways. To determine the molecular mechanism of severe cytopenia in NHD13+ Tg mice, we purified Lin-Sca-1+c-Kit+CD34-Flt3-CD150+ HSCs from WT and NHD13+Tg mice at 4 month of age and perform the RNA-seq analysis.

Methods: Trizol was used to extract RNA from FACS sorted CD150+CD34–Flt3–LSK viable cells. Total RNA was used for quality controls and for normalization of starting material. cDNA-libraries were generated with 10 ng of total RNA using the SMARTer Ultra Low RNA Kit for Illumina Sequencing according to the manufacturer’s indications. Sequencing was done using the Illumina Next-Gen Sequencing HiSeq platform with 30-45 million 75bp, paired-end reads.

Results: We found 597 genes with significantly differential expression in NHD13+ HSCs, compared to WT controls (p<0.001). The expression of NUP98-HOXD13 up-regulated the expression of HOX genes, including Hoxa3, Hoxa5, Hoxa7, Hoxa9, Hoxb6, Hoxc5, Hoxc6, Hoxc8, Hoxc9 and Hoxd3, the important myeloid transcription factor Pbx3, cell cycle regulators, Cdk6 and Cdc25C, as well as the transcripts encoding the Ly6d surface membrane protein. We then performed pathway analyses, which showed that DNA duplication, DNA damage response and cell cycle-related genes, were more highly expressed in NHD13+ HSCs than WT HSCs, while multiple metabolic process-related gene pathways were downregulated.

Conclusions: Our analyses demonstrate that the gene expression signature defined in murine NHD13+ MDS HSCs displays robust similarities with the gene expression profiles of human MDS cells, strongly suggesting that this murine MDS model can be used to accurately model human MDS.

overall_design: Lin-Sca-1+c-Kit+CD34-Flt3-CD150+ HSCs from WT and NHD13+Tg mice at 4 month of age were purified and used for the RNA-seq analysis. in duplicate.

first: Scott

last: Armstrong


city: Toronto

first: Norman

last: Rosenblum

state: ON

address: 686 bay st

country: Canada

institute: Hospital for sick children

summary:
Purpose: to analyze the mRNA content of highly purified HCN3+ urinary tract pacemaker cells compared to HCN3- neighboring cells
Methods: we sorted HCN3+ and HCN3- cells from E18.5 WT embryos and analyzed their content using RNA-seq
Results: Identified differentially expressed transcripts in HCN3+ cells compared to HCN3- cells
Conclusions: our study presents the first whole transcriptome analysis of HCN3+ urinary tract pacemaker cells that would provide a basis for the charactarization of the development and function of those cells

overall_design: RNA sequncing of HCN3+ urinary tract pacemaker cells in comparison to HCN3- cells

first: Meghan

last: Feeney

first: Samir

last: Iskander

first: Kirby

last: Yee


title: Systems approach elucidates convoluted transcriptional regulation on carbon metabolism

first: Donghyuk

last: Kim

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

overall_design: Refer to individual Series


title: Essential Roles of SETD7 as Transcriptional Activator and Co-regulator of H3K36me in Cardiac Lineage Commitment

city: Stanford

first: Joseph

last: Wu

state: Carlifornia

address: Stanford University School of Medicine

institute: Stanford University School of Medicine

summary: Coordinated epigenome alteration is fundamental for cardiac development. However, the precise mechanisms by which epigenetic modifying enzymes regulate cardiac development are still unclear. Here we identify SET domain containing protein 7 (SETD7) as a key regulator of cardiac differentiation. ChIP-seq reveals that SETD7 has distinct groups of target genes and regulates its stage-specific expression during cardiomyocyte differentiation, which is crucial for lineage commitment. We find SETD7 associates with stage-specific co-factors, such as SWI/SNF chromatin remodeling factors during mesodermal formation and transcription factor NKX2-5 in cardiac progenitor differentiation. Cross-analysis of epigenetic modifications shows that SETD7 recognizes and binds with active histone marker H3K36 methylation on gene-body region of its target genes. We further demonstrate SETD7 is required for functional properties of terminally differentiated cardiomyocytes. Together, our results suggest unidentified roles of SETD7 in cardiac lineage commitment and provide new insights into the crosstalk between epigenetic dynamics and epigenetic modifying enzymes.

overall_design: RNA-seq (n=8) and ChIP-seq (n=28) of the cardiac differentiation of H7 ESC.

first: Ning-Yi

last: Shao

first: JaeCheol

last: Lee


first: Ayush

middle: T

last: Raman

address: 75 Ames St

department: Epigenomics Program

institute: Broad Institute of MIT and Harvard

overall_design: There are 13 samples used for RNA-Sequencing, and each is a biological replicate. There are 5 sham (control) samples: 2 wild type sham samples and 3 MeCP2-null samples. There are 8 DBS samples: 4 wildtype and 4 MeCP2-null (KO) samples.

first: Huda

last: Zoghbi

first: Amy

last: Pohodich

first: Hari

last: Yalamanchili

first: Zhandong

last: Liu


title: De novo reconstruction of human adipose reveals conserved lncRNAs as regulators of brown adipogenesis

status: Public on Apr 16 2018

city: Singapore

first: Lei

last: Sun

address: 8 College Road

country: Singapore

institute: Duke-NUS

summary: Obesity has emerged as a formidable health crisis due to its association with metabolic risk factors such as diabetes, dyslipidaemia and hypertension. Recent work has demonstrated the multifaceted roles of lncRNAs in regulating mouse adipose development, but its implication in human adipocytes remain largely unknown at least partially due to the lack of a comprehensive lncRNA catalog, particularly those specifically expressed in brown adipose tissue (BAT).  In this study, we performed deep RNA-seq on adult subcutaneous, omental and fetal brown adipose tissues to de novo construct a catalog of 3,149 adipose active lncRNAs of which 1,351 are specifically detected in BAT. We further identified 318 lncRNAs conserved between human and mouse which, compared with non-conserved ones, are more broadly expressed in multiple cell types. One of these, lnc-dPRDM16, is transcribed divergently from Prdm16, tightly correlated with Prdm16 (R ≥ 0.7) in both mouse and human, and co-expressed (R ≥ 0.7) with protein-coding genes enriched in lipid and fatty acid catabolic processes. Loss of function of lnc-dPRDM16 led to a down-regulation of Prdm16 and an obvious reduction of adipogenesis in brown adipocyte culture. Together, our work has provided a comprehensive human adipose catalog built from diverse fat types, which when applied to our roadmap, identifies lnc-dPRDM16 as a promising modulator of adipose development for future clinical research.

overall_design: Transcriptome profiling of BAT, OME and SUB samples

first: Yen-Ching

last: Lim


title: Immune Profiling of Premalignant Lesions in Patients with Lynch Syndrome

first: Eduardo

last: Vilar

address: 1515 Holcombe Blvd., Unit 1360

department: Clinical Cancer Prevention

institute: The University of Texas MD Anderson Cancer Center

summary: mRNA expression from adenomas of patients with Lynch Syndrome and Familial Adenomatous Polyposis

overall_design: 24 adenoma samples analyzed


title: ETV1 binding sites in GIST and Melanoma cells

status: Public on Apr 15 2018

first: Yu

last: Chen

address: 1275 York Ave, Box 20

department: Human Oncology and Pathogenesis Program

summary: ETV1 is an oncogene in GIST and melanoma and a downstream transcriptional effector of MAP kinase signaling. Here, mapped the ETV1 binding sites in GIST and melanoma cell lines using ChIP-seq.

overall_design: ChIP-seq mapping of ETV1 binding sites in GIST and melanoma cell lines

first: Ping

last: Chi


title: Transcriptome analysis of chrysanthemum (Dendranthema grandiflorum) in response to low temperature stress

city: Beijing

first: Ke

last: Wang

address: No. 12 Nanfaxinfu Street, Shunyi District, Beijing

institute: Biomarker institute

summary: We used the RNA-Seq platform to perform a de novo transcriptome assembly to analyze chrysanthemum (Dendranthema grandiflorum) transcription response to low temperature. Using Illumina sequencing technology, a total of 86,444,237 high-quality clean reads and 93,837 unigenes were generated from four libraries: T01, controls; T02, 4 ℃ cold acclimation (CA) for 24 h; T03, -4 ℃ freezing treatments for 4 h with prior CA; and T04, -4 ℃ freezing treatments for 4 h without prior CA. In total, 7583 differentially expressed genes (DEGs) of 36462 annotated unigenes were identified.

overall_design: Transcriptome of  chrysanthemum leaves under four treatments was sequenced by the Illumina sequencing technology.  The four treatments are: T01, controls; T02, 4 ℃ cold acclimation (CA) for 24 h; T03, -4 ℃ freezing treatments for 4 h with prior CA; and T04, -4 ℃ freezing treatments for 4 h without prior CA.


title: Role of COP1 on MAP kinase transcriptional output in melanoma

summary: COP1 regulates MAP kinase dependent stability Pea3 transcription factors. We determined the role of COP1 in the regulation of MAP kianse transciptional output.  We generated A375 melanoma cells with CRISPR/Cas9 mediated COP1 (gene symbol RFWD) knockout. We treated control sgEGFP and COP1 loss sgCOP1 cells with vehicle, 1 µM vemurafinib, or 5 nM trametinib for 8 hours and isolated RNA for sequencing.

overall_design: Examination of transcriptome in COP1 intact and COP1 loss A375 melanoma cells in response to MAP kinase inhibition.


title: Next Generation Sequencing Facilitates Quantitative Analysis of  Bone Marrow Macrophages and Splenic Macrophages Transcriptomes in Mouse MLL-AF9 AML Leukemia

city: Tianjin

first: Guo Guang

last: Zheng

state: Tianjin

address: Blood Hospital,288 Nanjing Road,Heping District

department: Institute of Hematology & Blood Hospital

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

summary: The goals of this study aim to reveal functional and phenotypic diversity of leukemia-associated macrophages in response to the microenvironmental cues in mouse MLL-AF9 AML leukemia

overall_design: Compare transcriptomes of macrophages in mouse MLL-AF9 AML leukemia which are suggested as leukemia-associated macrophages (LAMs) with homeostasis and LAMs from mouse acute Myeloid leukemia.

first: Xiao

last: Yang

first: GuoGuang


title: Role of Epstein-Barr Virus (EBV) latency protein EBNA3C in EBV-induced lymphomagenesis in a cord blood-humanized mouse model

status: Public on Apr 13 2018

first: Shannon

middle: C

last: Kenney

address: 1111 Highland Avenue

department: Oncology

institute: University of Wisconsin-Madison

summary: This study compares cellular and viral gene expression in a cord blood-humanized (CBH) mouse model infected with wild-type Epstein-Barr virus (WT), versus a mutant EBV deleted in the latent viral EBNA3C gene (∆3C). EBV causes human B-cell lymphomas and transforms B cells in vitro. EBNA3C, an EBV protein expressed in latently infected cells, is required for EBV transformation of B cells in vitro. However, many EBV+ lymphomas in humans do not express this protein, suggesting that it may be less important in vivo or that cellular mutations and/or signaling pathways may obviate the need for EBNA3C. EBNA3C collaborates with EBNA3A to repress expression of the CDKN2A-encoded tumor suppressors, p16 and p14, and EBNA3C-deleted EBV transforms B cells containing a p16 germline mutation in vitro. We found that the ∆3C virus induced fewer lymphomas (occurring with a delayed onset) in comparison to the wild-type (WT) control virus, although a subset (10/26) of Δ3C-infected CBH mice eventually developed invasive diffuse large B cell lymphomas with type III latency. Both WT and ∆3C viruses induced monoclonal B-cell lymphomas (without somatic hyper-mutation) that were infiltrated by polyclonal T cells. In comparison to WT-infected tumors, ∆3C-infected tumors had greatly increased p16 levels, and RNA-seq analysis revealed a decrease in E2F target gene expression. However, we found that ∆3C-infected tumors expressed c-Myc and cyclin E at similar levels compared to WT-infected tumors, allowing cells to at least partially bypass p16-mediated cell cycle inhibition. Unexpectedly, ∆3C-infected tumors had increased T-cell infiltration, increased expression of T-cell chemokines (CCL5, CCL20 and CCL22) and enhanced type I interferon response in comparison to WT tumors. Together, these results reveal that EBNA3C contributes to, but is not essential for, EBV-induced lymphomagenesis in CBH mice, and suggest potentially important immunologic roles of EBNA3C in vivo.

overall_design:
Cord-blood humanized mice were infected with either wild-type B95.8 EBV or an EBNA3C mutant virus. Following euthanasia, RNA was isolated from the B-cell lymphoma tissue, and RNA-seq libraries were prepared and sequenced using an Illumina HiSeq2000 platform at the University of Wisconsin Biotechnology Center DNA Sequencing Facility. Mouse sequences were removed from analysis. Results from lymphomas infected with wild-type EBV (two different tumors) or EBNA3C mutant virus (two different tumors) are compared.
After the initial mapping/QC, the datasets 'wildtype_2' and 'dEBNA3C_3' were considered to be outliers. Therefore, these two sets of data were excluded from expression DEG analysis, and are not included here.

first: James

last: Romero-Masters

first: Makoto

last: Ohashi

first: Reza

last: Djavadian

first: Kate

last: Zhou

first: Eric

last: Johannsen


title: Role of COP1 on MAP kinase transcriptional output in gastrointestinal stromal tumor

summary: COP1 regulates MAP kinase dependent stability Pea3 transcription factors. We determined the role of COP1 in the regulation of MAP kianse transciptional output.  We transfected GIST882 cells with siRNA against a scrambled sequence and two sequences against COP1. We treated cells for 8 hours with vehicle or 100 nM PD0325901 in duplicate and isolated RNA for sequencing.

overall_design: Examination of transcriptome in COP1 intact and COP1 loss  GIST882 GIST cells in response to MAP kinase inhibition.


title: De novo transcriptome assembly for desiccation tolerance in intertidal seaweed species Ulva lactuca

city: Panajim

first: vishal

last: gupta

state: Goa

address: Dona Paula

department: Biological Oceanography

country: India

institute: CSIR-National Institute of Oceanography

summary: This study aimed at identification of genetic regulations for desiccation tolerance in intertidal seaweed species Ulva lactuca most commonly experienced phenomenon of intertidal communities.

overall_design:
The algal thalli were collected and acclamatised to laboratory. The experiments were designed for desiccation for different durations at a moisture condition of 20%. The thalli were desiccated for 24 h, 36 h and 72 h and investigated for transcriptomics by RNA-seq. Differential expression of genes determine the genetic regulations for desiccation tolerance in this lower group of aquatic plants.

Please note that the current study represents the re-analysis of the GSE97769 samples (GSM2577150, GSM2577148, GSM2577151, GSM2577153) based on a different assembly.

first: Vishal

last: Gupta


title: Environment-dependent striatal gene expression in the BACHD rat model for Huntington disease

city: Saarbrücken

first: Julia

middle: Maria

last: Schulze-Hentrich

address: Campus, Building A2.4

department: Genetics and Epigenetics

institute: Saarland University

summary: We examined effects of early life stress (ELS) and environmental enrichment (EE) during development on BACHD rat striatal gene expression using RNA sequencing

overall_design: We used a 2×3 factorial design with two genotypes (wildtype, WT; transgene, TG) and three environmental conditions (standard environment, SE; enriched environment, EE; early life stress, ELS) to assess effects of environmental enrichment and early life stress on striatal gene expression of 2-month-old WT and BACHD rats

first: Thomas

last: Hentrich


title: A broad single-cell transcriptome view of the male mouse germ line

city: Erlangen

first: Soeren

last: Lukassen

address: Schwabachanlage 10

department: Institute of Human Genetics

institute: Friedrich-Alexander Universitaet Erlangen Nuernberg

summary: Single-cell RNAseq of 2550 cells from the testes of two mice.

overall_design: Single-cell RNAseq with two biological replicates

first: Andreas

last: Winterpacht


title: Transcriptome level regulations for desiccation and submergence tolerance in intertidal seaweed species Ulva lactuca

summary: This study aimed at identification of genetic regulations for desiccation and submergence tolerance in intertidal seaweed species Ulva lactuca which arisies periodically due to tidal rhythms.

overall_design: The algal thalli were collected and acclamatised to laboratory. The experiments were designed for desiccation for different durations at a moisture condition of 20%. The thalli were desiccated for 24 h, 36 h and 72 h and investigated for transcriptomics by RNA-seq. After each desiccation time point, the thalli were resubmerged in autoclaved seawater. After 1 h of resubmergence, thalli were collected and processed for RNA extraction and subsequent RNA-seq. The transtion of desiccation to submergence will determine the genetic regulations for submergence tolerance in this group of plants.


title: Regulation of flagellum biosynthesis in response to cell envelope stress in Salmonella Typhimurium

city: Braunschweig

first: Matthias

last: Preusse

address: Inhoffenstr. 7

institute: Helmholtz Centre for Infection Research

summary: Flagella-driven motility of Salmonella enterica serovar Typhimurium facilitates host colonization. However, the large extracellular flagellum is also a prime target for the immune system. As consequence, expression of flagella is bistable within a population of Salmonella, resulting in flagellated and non-flagellated subpopulations. This allows the bacteria to maximize fitness in hostile environments. The degenerate EAL-domain protein RflP (formerly YdiV) is responsible for the bistable expression of flagella by directing the flagellar master regulatory complex FlhD4C2 to proteolytic degradation. The environmental cues controlling expression of rflP and thus the bistable flagellar biosynthesis remain ambiguous. Here, we demonstrate that RflP responds to cell envelope stress and alterations of outer membrane integrity. Lipopolysaccharide (LPS) truncation mutants of Salmonella Typhimurium exhibited increasing motility defects due to downregulation of flagellar gene expression. Transposon mutagenesis and genetic profiling revealed that σ24 (RpoE) and Rcs phosphorelay-dependent cell envelope stress response systems sense modifications of lipopolysaccharide, low pH activity of the complement system. This subsequently results in activation of RflP expression and degradation of FlhD4C2 via ClpXP. We speculate that diverse hostile environments inside the host might result in cell envelope damage and would thus trigger the repression of resource-costly and immunogenic flagella biosynthesis via activation of the cell envelope stress response.

sample_organism: Salmonella enterica subsp. enterica serovar Typhimurium str. LT2

overall_design: S. Typhimurium planktonic cultures representing wildtype, ΔrfaL, ΔrfaG, ΔrfaD

first: Imke

last: Spöring

first: Sebastian

last: Felgner

first: Denitsa

last: Eckweiler

first: Manfred

last: Rohde

first: Susanne

last: Häussler

first: Siegfried

last: Weiss

first: Marc

last: Erhardt


title: Transcriptional effect of ETV1 knockdown in melanoma cells

first: Yu

last: Chen

summary: ETV1 is amplified in a subset of melanomas. Here, we performed RNA-seq on two BRAF V600E mutant melonoma cell lines transduced with a scrambed shRNA and two individual ETV1 shRNA

overall_design: Two melanoma cell lines (A375 and Colo800) were infected in duplicate with three shRNA viruses (Scrambled, ETV1sh1-B11TRCN0000013923, ETV1sh2-TRCN0000013925). Four days after infection, RNA was harvested for expression profiling.

first: Ping

last: Chi


title: Altered expression profile of long non-coding RNA and mRNA in mice cortex around injury focus after traumatic brain injury

city: Chongqing

first: Zhong

last: Jianjun

address: NO.1 Youyi Road, Yuzhong District, Chongqing

department: Neurosurgery Department

institute: The first Affiliated Hospital of Chongqing Medical University

summary: We report the altered expression profiles of lncRNA and mRNA in mice cortex afetr traumatic brain injury (TBI).Total of 27,457 transcripts were identified as mRNA and 37,073 transcripts were identified as lncRNA. Total of 823 lncRNAs and 1,580 mRNAs were significantly changed after TBI according to the criteria: |log2(fold change)|>1, P<0.05. In addition, total of 360 new mRNAs and 8,041 new lncRNAs were identified in current sequencing study.

overall_design: TBI was induced in C57BL/6 mice. The LncRNA and mRNA expression profiles in cortex of normal mice and TBI mice were examined by RNA-Seq.

first: Jianjun

last: Zhong

first: Xiaochuan

last: Sun

first: Yong

last: Jiang

first: Jianhua

last: Peng


title: Accelerating early anti-TB drug discovery by creating mycobacterial indicator strains that predict mode of action [Mycobacterium tuberculosis]

status: Public on Apr 12 2018

city: Thuwal

first: AMIT

middle: KUMAR

last: SUBUDHI

state: Thuwal

address: Level4, Builiding, 2, KAUST

department: BESE

country: Saudi Arabia

institute: King Abdullah University of Science and Technology

summary: Due to the rise of drug resistant forms of tuberculosis there is an urgent need for novel antibiotics to effectively combat these cases and to shorten treatment regimens. Recently, drug screens using whole cell analyses have shown to be successful. However, current high throughput screens focus mostly on stricto sensu life-death screening that give little qualitative information and often require the lengthy process of target and mode of action (MoA) identification. In doing so, promising compound scaffolds or non-optimized compounds that fail to reach inhibitory concentrations are missed. To accelerate early TB drug discovery, we performed RNA sequencing on Mycobacterium tuberculosis and Mycobacterium marinum to map the stress responses that follow upon exposure to sub-inhibitory concentrations of antibiotics with known targets: ciprofloxacin, ethambutol, isoniazid, streptomycin and rifampicin. The resulting dataset comprises the first overview of transcriptional stress responses of mycobacteria to different antibiotics. We show that antibiotics can be distinguished based on their specific transcriptional stress fingerprint i.e. DNA damage for ciprofloxacin and ribosomal stress for streptomycin. Notably, this fingerprint was more distinctive in M. marinum and we decided to use this to our advantage and continue with this model organism. A selection of diverse antibiotic stress genes was used to construct stress reporters. In total, three functional reporters were constructed for DNA damage, cell wall damage and ribosomal inhibition. Subsequently, these reporter strains were used to screen a small anti-TB compound library to predict the mode of action. In doing so we could identify the putative mode of action for three novel compounds, which confirms our approach.

overall_design: RNA expression profiles of Mycobacterium tuberculosis and Mycobacterium marinum was generated upon exposure to sub-inhibitory concentrations of antibiotics with known targets: ciprofloxacin, ethambutol, isoniazid, streptomycin and rifampicin for 4 hrs and 24hrs duration and compared with controls without any drug exposure

first: Maikel

last: Boot

first: S

last: Commandeur

first: Amit

last: Subudhi

first: A

last: Abdallah

first: M

last: van Gemert

first: J

last: Lelievre

first: L

last: Ballell

last: Speer

first: Arnab

last: Pain

first: Wilbert

last: Bitter


title: MicroRNA-125a-5p overexpression in human macrophages

city: Cincinnati

first: Mario

last: Medvedovic

state: OH

address: 3223 Eden Av. ML 56

department: Department of Environmental Health

institute: University of Cincinnati

summary: Systemic juvenile idiopathic arthritis (SJIA) is a severe childhood arthropathy with features of autoinflammation. Monocytes and macrophages in SJIA have a complex phenotype with both pro- and anti-inflammatory properties that combine features of several well characterized in vitro conditions used to activate macrophages.  An important anti-inflammatory phenotype is expression of CD163, a scavenger receptor that sequesters toxic pro-inflammatory complexes that is highly expressed in both active SJIA and macrophage activation syndrome (MAS).  CD163 is most strongly upregulated by IL-10 (M(IL-10)), and not by other conditions that reflect features seen in SJIA monocytes such as M(LPS+IC).  MicroRNA play key roles balancing and integrating cellular signals such as those in macrophage polarization, and as such we hypothesize microRNA regulate macrophage functional responses in SJIA including CD163 expression in vitro.  We find that two microRNA previously found to be elevated in active SJIA, miR-125a-5p and miR-181c, significantly reduced macrophage CD163 expression through two distinct mechanisms.  Neither microRNA was elevated in M(IL-10) with robust CD163 expression, but were instead induced in M(LPS+IC) where they restricted CD163 mRNA expression.  Mir-181 species directly targeted CD163 mRNA for degradation.  In contrast, transcriptome analysis of miR-125a-5p overexpression identified “cytokine-cytokine receptor interactions” as the most significantly repressed gene pathway, including decreased IL10RA, which is required for IL-10-mediated CD163 expression. Finally, overexpression of miR-181c inhibited CD163 anti-inflammatory responses to hemoglobin or high mobility group box 1 complexes. Together, these data show that microRNA utilize multiple mechanisms to integrate well characterized polarization phenotypes and regulate macrophage functional properties seen in SJIA.

overall_design: THP-1 human monocytic cells were transfected in triplicate with negative control microRNA mimic or miR-125a-5p mimic. RNA extracted 24hours after transfection

first: Grant

last: Schulert

first: Thuy

last: Do

first: Mark

last: Bennett

first: Alexei

middle: A

last: Grom


title: Accelerating early anti-TB drug discovery by creating mycobacterial indicator strains that predict mode of action [Mycobacterium marinum]

overall_design: RNA expression profiles of Mycobacterium tuberculosis and Mycobacterium marinum was generated upon exposure to sub-inhibitory concentrations of antibiotics with known targets:ciprofloxacin, ethambutol, isoniazid, streptomycin and rifampicin for 4 hrs and 24hrs duration and compared with controls without any drug exposure


title: Whole Retina RNAseq after injury and Cyclopamine(C) treatment in zebrafish

city: Mohali

first: Rajesh

last: Ramachandran

state: Punjab

address: Knowledge city, Sector 81, SAS Nagar, Manauli

department: Department of Biological Sciences

institute: Indian Institute of Science Education and Research, Mohali

summary: several genes are being regulated after injury at various time points and after cyclopamine treatment.

overall_design: Examination of uninjured, 12hpi, 4dpi and cyclopamine treated 4dpi retinae with paired-end reads.

first: Simran

last: Kaur

first: Soumitra

last: Mitra


title: A three–microRNA signature as a potential biomarker for the early detection of oral cancer

city: HsinChu

first: Hsien-Da

last: Huang

address: 1001 University Road

department: Biological Science and Technology

country: Taiwan

institute: National Chiao Tung University

summary: Background: Oral squamous cell carcinoma (OSCC) is often diagnosed at a late  stage and may be malignantly transformed from oral leukoplakia (OL). This study aimed to identify potential plasma microRNAs (miRNAs) for the early detection of oral cancer.  Methods: Plasma from normal, OL, and OSCC patients were evaluated. Small RNA sequencing was used to screen differently expressed miRNAs among the groups. Next, these miRNAs were validated with individual samples by quantitative real-time polymerase chain reaction (qRT-PCR) assays. The possible physiological roles of the identified miRNAs were further investigated using bioinformatics analysis.  Results: Three miRNAs (miR-222-3p, miR-150-5p, and miR-423-5p) were identified as differentially expressed among groups; miR-222-3p and miR-423-5p negatively correlated with T stage, lymph node metastasis status, and clinical stage. A high diagnostic accuracy (Area under curve = 0.88) was demonstrated for discriminating OL from OSCC. Bioinformatics analysis reveals that miR-423-5p and miR-222-3p are significantly over-expressed in oral cancer tissues and involved in various cancer pathways.  Conclusions: The three plasma miRNA panel may be useful to monitor malignant progression from OL to OSCC and as potential biomarkers for early detection of oral cancer.

overall_design: Small RNA-seq analysis was performed on three different pooled samples (normal, oral leukoplakia and oral squmaous cell carcinoma) to identify differentially expressed miRNA.

first: Yi-An

last: Chang

first: Shun-Long

last: Weng

first: Shun-Fa

last: Yang

first: Chih-Hung

last: Chou

first: Wei-Chih

first: Siang-Jyun

last: Tu

first: Tzu-Hao

first: Chien-Ning

first: Yuh-Jyh

last: Jong


title: Effect of early calf-hood nutrition on the transcriptomic profile of the HPT axis in Holstein-Friesian bulls

city: Co. Meath

first: Anne-Marie

last: English

address: Dunsany

department: Department of Animal Bioscience

country: Ireland

institute: Teagasc Grange

summary: The aim of this study was to investigate the effect of early calf-hood nutrition on the transcriptomic profile of the arcuate nucleus of the hypothalamus, the anterior pituitary and the testes in Holstein-Friesian bulls and possible downstream effects on reproduction. Holstein Friesian bull calves with a mean (±S.D.) age and bodyweight of 19 (±8.2) days and 47.5 (±5.3) kg, respectively, were assigned to either a high (n=10) or low (n=10) plane of nutrition. Calves were fed in order to achieve an overall growth rate of 1.2 and 0.5 kg/day for the high and low plane of nutrition treatments, respectively.  At 126 days of age, the bulls were euthanized using an intravenous overdose of sodium pentobarbitone and arcuate nucleus of the hypothalamus, anterior pituitary and the parenchyma of the testes tissue samples were harvested and RNAseq analysis was performed. At the end of the trial period,

overall_design: 19 Holstein Friesian bull calves with a mean (±S.D.) age and bodyweight of 19 (±8.2) days and 47.5 (±5.3) kg, respectively, were assigned to either a high (n=10) or low (n=10) plane of nutrition. Calves were fed in order to achieve an overall growth rate of 1.2 and 0.5 kg/day for the high and low plane of nutrition treatments, respectively.  At 126 days of age, the bulls were euthanized using an intravenous overdose of sodium pentobarbitone and the arcuate nucleus, anterior pituitary and the parencyma of the testes tissue samples were harvested and RNAseq analysis was performed.

first: Paul

last: Cormican

first: Colin

last: Byrne

first: Sinead

last: Waters

first: David

last: Kenny

first: Sean

last: Fair


title: Effect of early calf-hood nutrition on the transcriptomic profile of subcutaneous adipose in Holstein-Friesian bulls

summary: The aim of this study was to investigate the effect of early calf-hood nutrition on the transcriptomic profile of subcutaneous adipose in Holstein-Friesian bulls and possible downstream effects on reproduction. Holstein Friesian bull calves with a mean (±S.D.) age and bodyweight of 19 (±8.2) days and 47.5 (±5.3) kg, respectively, were assigned to either a high (n=10) or low (n=10) plane of nutrition. Calves were fed in order to achieve an overall growth rate of 1.08 and 0.5 kg/day for the high and low plane of nutrition treatments, respectively.  At 126 days of age, the bulls were euthanized using an intravenous overdose of sodium pentobarbitone and subcutaneous adipose tissue samples were harvested and RNAseq analysis was performed. At the end of the trial period, there were 745 genes differentially expressed in adipose tissue of bulls on the high plane of nutrition relative to those on the low plane of nutrition (P<0.05; FDR<0.05; fold change >2.0). Plane of nutrition altered the expression of genes involved in energy production and branched chain amino acid degradation. Plane of nutrition was also found to down regulate genes such as leptin and adiponectin which are known to effect reproductive function. This study identifies some of the molecular mechanisms regulated by feeding bulls a high plane of nutrition, which may be incorporated into future breeding programmes for artificial insemination centres.

overall_design: 19 Holstein Friesian bull calves with a mean (±S.D.) age and bodyweight of 19 (±8.2) days and 47.5 (±5.3) kg, respectively, were assigned to either a high (n=10) or low (n=10) plane of nutrition. Calves were fed in order to achieve an overall growth rate of 1.2 and 0.5 kg/day for the high and low plane of nutrition treatments, respectively.  At 126 days of age, the bulls were euthanized using an intravenous overdose of sodium pentobarbitone and subcutaneous adipose tissue samples were harvested and RNAseq analysis was performed.


title: RNA-seq based transcriptomic profiling of the mouse small intestine response to lipopolysaccharide treatment

city: Chicago

first: Xiao-Di

last: Tan

state: IL

address: 2430 N Halsted St

department: Stanley Manne Children's Research Institute

institute: Ann & Robert H. Lurie Children's Hospital of Chicago

summary:
Purpose:Integrity of the intestinal mucosal barrier is important as a first line of defense against bacteria and endotoxin, we aim to characterize the activation response of intestinal mucosa to LPS exposure in a mouse model.
Methods:Intestinal mRNA profiles of LPS challenged and control mice were generated by deep sequencing, in triplicate, using Illumina HiSeq 2000
Results: Using an optimized data analysis pipeline(HISAT2/HT-Seq/DESeq2), 714 differentially expression protein-coding and noncoding genes (cut-off P <0.05) were identified in response to LPS treatment.
Conclusions: After LPS chanllenge, hundreds of genes are differentially regulated, and these genes participate in immuse defense, Inflammatory response as well as cell migration and proliferation (GO pathway analysis).

first: Xiao

middle: D

first: Hua

last: Geng


title: Analysis of Pol II position in asynchronous, G1- or G2/M-arrested cells

city: Oxford

first: Hannah

last: Mischo

address: South Parks Road

department: Dunn School of Pathology

institute: University of Oxford

summary: We sequenced RNA Pol II Flag pulldowns  (NET-seq) from five samples of W303 bar1D (asynchronous, alpha-Factor arrested, nocodazole arrested or transformed with a pGAL1 multicopy plasmid carrying either no ORF or the SEN1 ORF)

first: Kevin

middle: M

last: Harlen

first: Yujin

last: Chun

first: Brendan

last: Smalec

first: Somdutta

last: Dhir

first: Stirling

last: Churchman

first: Steve

last: Buratowski


title: Parasitic helminths repress the canonical intestinal stem cell program

city: San Francisco

first: Adam

last: Savage

state: CA

address: 513 Parnassus Ave

institute: University of California San Francisco

summary: The intestinal helminth parasite Heligmosomoides polygyrus initiates infection in mice by penetrating the duodenal mucosa, where it develops while surrounded by a multicellular granulomatous infiltrate before emerging into the intestinal lumen. We examined early H. polygyrus infection to assess the epithelial response to disruption of the mucosal barrier. Unexpectedly, intestinal stem cell markers, including Lgr5 and Olfm4, were completely lost in crypts overlying larvae-associated granulomas. We sought to identify the mechanism by which the H. polygyrus granuloma represses the activity of intestinal stem cells.

overall_design: CD45-negative EpCAM-positive CD44-positive crypt cells were sorted from duodenum of mice infected with H. polygyrus for six days. Crypt cells from granuloma punch biopsies was compared to crypt cells from non-granuloma punch biopsies.

first: Ysbrand

last: Nusse

first: Ophir

last: Klein

first: Richard

last: Locksley


title: Transcriptome of Varroa destructor life cycle

status: Public on Apr 11 2018

city: Avignon

first: Cédric

last: Alaux

address: Domaine Saint-Paul

department: UMR 406 Abeilles et Environnement

institute: INRA

summary: To study the underlying molecular mechanisms during the Varroa destructor life cycle, we carried out transcriptomic profiling of seven stages:  young mites (collected from P8  to P9 brood cells), phoretic mites (collected on adult bees), arresting mites (collected in unsealed L5 brood cells), pre-laying mites (collected from sealed brood cells containing moving larva), laying mites (collected from sealed brood cells containing pre-pupae), post-laying mites (collected from capped brood cells containing purple-eye and white-body pupae P5), emerging mites (collected from P8 to P9 brood cells). In addition, we sampled non-reproducing mites (collected from P5 brood cells, but without offspring), males (collected from P8 to P9 brood cells), and phoretic mites artificially reared in cages with adult bees. This study was performed using Apis mellifera L. honey bee colonies naturally infested by Varroa destructor mites. Adult mites were collected from 4 unrelated colonies.

overall_design: The transcriptomic profile of pools of 10 adult varroa were generated by deep sequencing. Adult mites from each life stage and conditions were collected from 4 unrelated colonies giving a total of 40 RNA-seq libraries.

first: Fanny

last: Mondet

first: Andrea

last: Rau

first: Christophe

last: Klopp

first: Marine

last: Rohmer

first: Dany

last: Severac

first: Yves

last: Le Conte


title: Transcriptome analysis of immature and matured human oocytes from patients of young and advanced maternal age

city: Davis

first: Pablo

middle: Juan

last: Ross

address: 1 Shields Avenue

department: Animal Science Department

institute: UC Davis

summary:
Study Question: What effects do maternal age and oocyte maturation stage have on the human oocyte transcriptome that may be associated with oocyte developmental potential?
Summary Answer: Although polyadenylated transcript abundance changes during human oocyte maturation irrespective of age, young (YNG) and advanced maternal age (AMA) metaphase II (MII) oocytes exhibit divergent transcriptomes.
What is known already: Maternal age and maturation stage affect oocyte polyadenylated transcript abundance in human oocytes. Although RNA-Seq analysis of single human MII oocytes has been conducted, comparison of the germinal vesicle (GV) and MII oocyte transcriptomes has not been investigated using RNA-Seq, a technique that could provide novel insight into oocyte maturation and age-associated aberrations in gene expression.
Participants / materials, settings, methods: Patients undergoing infertility treatment at the Colorado Center for Reproductive Medicine (Lone Tree, CO, USA) underwent ovarian stimulation with FSH and received hCG for final follicular maturation prior to ultrasound guided egg retrieval. Unused GV oocytes obtained at retrieval were donated for transcriptome analysis. Single oocytes were stored (at -80°C in PicoPure RNA Extraction Buffer; Thermo Fisher Scientific, USA) immediately upon verification of immaturity or after undergoing in vitro oocyte maturation (24 hour incubation), representing GV and MII samples, respectively. After isolating RNA and generating single oocyte RNA-Seq libraries (SMARTer Ultra Low Input RNA HV kit; Clontech, USA), Illumina sequencing (100 bp paired-end reads in HiSeq 2500) and bioinformatics analysis (CLC Genomics Workbench, DESeq2, Weighted Gene Correlation Network Analysis (WGCNA), 3’UTR motif analysis, Ingenuity Pathway Analysis) were performed.
Main results and the role of chance: Within the 12,770 expressed genes in human oocytes (reads per kilobase per million mapped reads (RPKM) > 0.4 in at least 3 of 5 replicates for a minimum of one sample type), 458 and 3,506 genes significantly (adjusted p < 0.05 and log2 fold change > 1) increased and decreased in polyadenylated transcript abundance during oocyte maturation, respectively. The differentially expressed genes were enriched (FDR < 0.05) for biological functions and canonical pathways related to cell cycle and mitochondrial function. The majority (76%) and minority (25%) of up- and down-regulated transcripts with a complete 3’UTR were predicted to be targets of cytoplasmic polyadenylation (910 total genes), respectively. Differential gene expression analysis between young and advanced maternal age oocytes (within stage) identified 1 and 255 genes that significantly differed (adjusted p < 0.1 and log2 fold change > 1) in polyadenylated transcript abundance for GV and MII oocytes, respectively. These genes included CDK1, NLRP5, and PRDX1, which have been reported to affect oocyte developmental potential and be markers of oocyte quality. Despite similarity in transcript abundance between GV oocytes irrespective of age, divergent expression patterns emerged during oocyte maturation. These age-specific differentially expressed genes were enriched (FDR < 0.05) for functions and pathways associated with mitochondria, cell cycle, and cytoskeleton. Gene modules generated by WGCNA (based on gene expression) and patient traits related to oocyte quality (e.g. age and blastocyst development) were determined to be correlated (p < 0.05) and enriched (FDR < 0.05) for functions and pathways associated with oocyte maturation.
Limitations, reasons for caution: The human oocytes used in the current study were obtained from patients with varying causes of infertility (e.g. decreased oocyte quality and oocyte quality-independent factors), possibly affecting oocyte gene expression. Oocytes in this study were retrieved at the GV stage following hCG administration and the MII oocytes were derived by in vitro maturation of patient oocytes, which has the benefit of identifying intrinsic differences between samples, but may not be completely representative of in vivo matured oocytes. Thus, these factors should be considered when interpreting the results.
Wider Implications of the findings: Transcriptome profiles of young and advanced maternal age oocytes, particularly at the MII stage, suggest aberrant transcript abundance contributes to the age-associated decline in fertility.

overall_design: Study design, size, and duration: The effect of oocyte maturation (cross-sectional analysis) and age (longitudinal analysis) on polyadenylated transcript abundance were analyzed by examining single GV and single in vitro matured MII oocytes derived from five young (<30 years; average age 26.8; range 20-29) and five advanced maternal age (≥40 years; average age 41.6 years; range 40-43 years) patients. Thus, a total of 10 young (5 GV and 5 MII) and 10 advanced maternal age (5 GV and 5 MII) oocytes were individually processed for RNA-Seq analysis.

first: Juan

last: Reyes

first: Elena

last: Silva

first: James

last: Chitwood

first: William

last: Schoolcraft

first: Rebecca

last: Krisher


title: Mapping STAT1 pS727 occupancy and effect of cortistatin A (CA) on STAT1 occupancy in JAK2-driven neoplasms

city: Cambridge

first: Ioana

middle: Ilinca

last: Nitulescu

address: 12 Oxford St

institute: Harvard University

summary:
We characterized the marine natural product cortistatin A (CA) as an inhibitor of CDK8 to determine whether pharmacologic inhibition of CDK8 regulates super-enhancer function and inhibits AML proliferation.
In this series, we use ChIP-seq of STAT1 and STAT1 pS727 to examine how the localization of STAT1 is affected by inhibition of serine 727 phosphorylation

overall_design: ChIP-seq was carried out in SET-2 cells

middle: I

first: Madeleine

last: Lemieux

first: Matthew

last: Shair


title: A bacteriophage enzyme induces bacterial metabolic perturbation that confers a novel promiscuous function.

city: Uppsala

first: Dan

middle: I.

last: Andersson

address: Box 582

department: Department of Medical Biochemistry and Microbiology

country: Sweden

institute: Uppsala University

summary: One key concept in the evolution of new functions is the ability of enzymes to perform promiscuous side-reactions that serve as a source of novelty that may become beneficial under certain conditions. Here, we identify a mechanism where a bacteriophage-encoded enzyme introduces novelty by inducing expression of a promiscuous bacterial enzyme. By screening for bacteriophage DNA that rescued an auxotrophic E. coli mutant carrying a deletion of the ilvA gene, we show that bacteriophage-encoded S-adenosylmethionine (SAM) hydrolases reduce SAM levels. Via this perturbation of bacterial metabolism, expression of the promiscuous bacterial enzyme MetB is increased, which in turn complements the absence of IlvA. These results demonstrate how foreign DNA can increase the metabolic capacity of bacteria, not only by transfer of bona fide new genes, but also by bringing cryptic bacterial functions to light via perturbations of cellular physiology.

sample_organism: Escherichia coli str. K-12 substr. MG1655

overall_design: RNA-seq profiles of two plasmid constructs, inducible by IPTG, selected as providing metabolic rescue to E. coli ilvA-. The experiment was performed in duplicates with and without IPTG induction for the insert-bearing plasmids. A duplicate control experiment with empty plasmid in the same E. coli strain (with IPTG added) was also performed. Samples from the same experiments were processed both for RNA-seq and 10-plex TMT quantitative shot-gun proteomics. The TMT dataset is available at ProteomeXchange with identifier PXD005236.

first: Jon

last: Jerlström Hultqvist

first: Omar

last: Warsi

first: Annika

last: Söderholm

first: Michael

last: Knopp

first: Ulrich

last: Eckhard

first: Egor

last: Vorontsov

first: Maria

last: Selmer


title: RNA-seq analysis in MMTV-TGF- α Mice thymus

city: Istanbul

first: Nehir

last: Ozdemir Ozgenturk

address: Davutpasa/Esenler

department: Mol. Bio. and Genetics

country: Turkey

institute: Yildiz Technical University

summary: we report the comperative transcriptome analysis of the MMTV-TGF- α female mice thymus tissues

overall_design: 3 different fed types

middle: O

last: Ozgenturk


title: Genome-wide post-transcriptional dysregulation by microRNAs in human asthma as revealed by Frac-seq

city: London

first: Rocio Teresa

last: Martinez-Nunez

state: Greater London

address: 5th Floor Tower Wing, Guy’s Campus

department: Infectious Diseases

country: United Kingdom

institute: King's College London

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

overall_design: Refer to individual Series


title: Peripherally derived macrophages can engraft the brain independent of irradiation and maintain an identity distinct from microglia

status: Public on Apr 10 2018

city: Charlottesville

first: Christopher

last: Overall

state: Virginia

address: 409 Lane Road

department: Neuroscience

institute: University of Virginia


title: ER-464195-01 regulates the expression of inflammation-related genes in DSS-treated mice

city: Toyama

first: Jun-Dal

last: Kim

state: Toyama

address: 2630 Sugitani

department: Department of Complex Biosystem Research (CBR), Institute of National Medicine (INM)

country: Japan

institute: University of Toyama

summary:
We identified a small molecule, orally active ER-464195-01, inhibits the calreticulin binding to alpha integrins, and clearly suppresses the adherence ability of leukocytes. Our transcriptome analysis with the colon of dextran sodium sulfate (DSS)-treated mice reveals that the increased expression of pro-inflammatory genes was down-regulated by ER-464195-01.
Purpose: To gain insight into the molecular mechanisms underlying the prevention of DSS-induced colitis conferred by treatment of ER-464195-01, we performed a comprehensive analysis of ER-464195-01-mediated gene expression changes in DSS-induced colitis using RNA sequencing (RNA-Seq).
Methods: Male Balb/c mice (7 weeks) were allowed free access to distilled water (Otsuka Pharmaceutical) containing 2% DSS (molecular weight: 36,000–50,000; ICN Biomedicals) for 6 days to induce colitis. ER-464195-01 (10 mg/kg) or vehicle was orally administered once per day for 6 days.
Results: To investigate differentially expressed genes (false discovery rate (FDR) p<0.05, fold change >2) among three groups, we performed pairwise comparisons of RNA-Seq data using the CLC Genomics Workbench software. In comparison with the control, 5,570 (3,483 up- and 2,087 down-regulated) unique genes were significantly changed in the DSS-induced colitis group. Meanwhile, the data set of DSS-induced colitis with ER-464195-01 groups revealed significant changes in 1,808 (837 up- and 971 down-regulated) genes as compared with DSS alone. Notably, of 3,483 genes up-regulated by the DSS treatment, 894 transcripts of which were overlapped with 971 genes down-regulated genes by ER-464195-01.

overall_design: Intestinal mRNA profiles of control (normal water), DSS alone and DSS with ER-464195-01 mice were generated by RNA sequencing using the NextSeq 500 (Illumina).

first: Akiyoshi

last: Fukamizu


title: Multiple roles for Wwtr1 in cardiac wall maturation

city: bad nauheim

first: Stefan

last: Günther

address: ludwigtr. 43

institute: MPI for heart and lung research

summary: Cardiac trabeculation is a highly regulated process that starts with the delamination of cardiomyocytes from the compact wall to form stereotypical muscular ridges in the developing ventricle.  The Hippo signaling pathway has been implicated in cardiac development but many questions remain.  We investigated the role of Wwtr1, a nuclear effector of the Hippo pathway, in zebrafish and find that its loss results in hearts with reduced trabeculation.  However, in mosaic animals, wwtr1-/- cardiomyocytes contribute more frequently than wwtr1+/- cardiomyocytes to the trabecular layer of wild-type hearts.  To investigate this paradox, we examined the myocardial wall at early stages and find that loss of Wwtr1 leads to disruption of the compact wall architecture, as evidenced by the disorganized cortical actin structure and abnormal cell-cell junctions.  The mutant compact wall is not able to support trabeculation as, in mosaic animals, wild-type cardiomyocytes are more frequently in the compact layer of mutant than heterozygous hearts.  Therefore, we propose that Wwtr1 establishes the compact wall architecture necessary for trabeculation and that it also modulates a cardiomyocyte’s decision to enter the trabecular layer.

overall_design: larval hearts from mutants and WT siblings were manuall dissected out at 57-59 hpf.  A total of 23 hearts per biological replicate was collected.  RNA-sequencing was performed on three biological replicates for each genotype.

first: Jason

last: Lai

first: Michelle

last: Collins

first: Vanesa

last: Jiménez-Amilburu

last: Guenther

first: Hans-Martin

last: Maischein

first: Didier

last: Stainier


title: Bone density loci identified by genome-wide association studies segregate a lineage-specific PU.1-dependent gene regulatory network in osteoclasts

city: Charleston

last: Ostrowski

state: SC

address: 86 Jonathan Lucas street

department: Biochemistry and Molecular Biology

institute: Medical University of South Carolina

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus


title: Bone density loci identified by genome-wide association studies segregate a lineage-specific PU.1-dependent gene regulatory network in osteoclasts [ChIP-seq]

summary: Genome-wide association studies (GWASs) have been instrumental in understanding complex phenotypic traits. However, they have rarely been used to understand lineage-specific pathways and functions that contribute to the trait. In this study, by integrating publicly available lineage-specific enhancers from mesenchymal and myeloid compartments with bone mineral density loci, we were able to segregate osteoblast- and osteoclast (OC)-specific functions. Specifically, in OCs, a PU.1-dependent transcription factor (TF) network was revealed. Further we conducted functional genomic analysis PU.1 and MITF genome wide binding with corresponding gene expression analysis which revealed a TF network essential for OC differentiation. Several of these TFs were regulated by cooperative binding of PU.1 with BRD4 to form superenhancers. Further, PU.1 is essential for conformational changes in the superenhancer region of Nfatc1. In summary, our study demonstrates that utilizing GWASs with genome-wide binding studies as a filter helps to decipher lineage-specific pathways contributing to complex disease states.

overall_design: Analysis of MITF and PU.1 genomewide occupancy during murine osteoclast differntiation.

first: Sudarshana

last: Sharma


title: MicroRNAs underlie genome-wide transcriptome and translatome regulation in asthma as revealed by Frac-seq (RNA-Seq)

summary: Transcription and translation correlate poorly, as mRNA undergoes multiple regulatory steps such as alternative splicing and microRNA regulation that determine its translationability into protein. Measures of transcriptional mRNA levels may therefore misrepresent cellular activation. To test this hypothesis employing human physiological mRNA levels, we analyzed cytoplasmic and polyribosome-bound mRNA expression (Frac-seq) combined with microRNA profiling by small RNA-seq in bronchoepithelial cells from healthy and severe asthma (SA) donors, SA being a chronic inflammatory airways disease, poorly understood at the molecular level. We found 275 genes bound to polyribosomes differentially between healthy and severe asthma, of which only 11.64% overlapped with differentially expressed cytoplasmic mRNAs (226 genes). We found 335 alternatively spliced mRNA isoforms differentially bound to polyribosomes of which only ~8% were revealed by cytoplasmic mRNA analysis. Approximately two thirds of differentially expressed isoforms could not be found at the gene level in both cytoplasmic and polyribosome bound fractions, demonstrating the disruption of splicing in asthma. Only the analysis of differentially expressed isoforms bound to polyribosomes revealed disease-related pathways overlooked in total mRNA. We detected a network of 21 microRNAs differentially expressed, with 8 microRNAs accounting for more than 80% targeting observed in both cytoplasmic and polyribosome bound mRNA isoforms. Importantly, microRNAs target distinct cytoplasmic and polyribosome bound mRNAs. Hence this work, integrating deep-sequencing, subcellular fractionation and microRNA profiling, demonstrates the disruption of post-transcriptional regulatory processes as the main disease causing molecular mechanism in asthma, something that cannot be dissected employing more classic transcriptomics approaches alone.

overall_design: We performed cytoplasmic and polyribosome bound RNA-seq of bronchial epithelial cells from healthy controls and severe asthmatic patients. Small RNA-seq was also performed

first: Rocio

first: Peter

middle: H

last: Howarth

first: Tilman

last: Sanchez-Elsner


title: MicroRNAs underlie genome-wide transcriptome and translatome regulation in asthma as revealed by Frac-seq (miRNA-Seq)


title: Phosphorylation state of ZFP24 controls oligodendrocyte differentiation

first: Benayahu

last: Elbaz

address: Department of Neurology 5841 S. Maryland Ave

department: Neurology

institute: University of chicago

summary: The zinc finger protein ZFP24 is critical for CNS myelination. Nonetheless, the mechanism by which ZFP24 controls myelination is unknown. Here we use chromatin IP (ChIP) to map ZFP24 binding sites in oligodendrocyte progenitor cells (OPC) and differentiated oligodendrocytes (OLG). We find that ZFP24 directly binds the enhancer regions of genes important for oligodendrocyte differentiation and myelination and mediates their expression. We demonstrate that ZFP24 undergoes phosphorylation and dephosphorylation in oligodendrocyte lineage cells and that ZFP24 binding to DNA is controlled by its phosphorylated state such that only the non-phosphorylated form of the protein, predominantly found in mature oligodendrocytes, mediates expression of myelin protein genes. We have also identified key ZFP24 downstream target genes. Among these, we show that enforced expression of the crucial myelin transcription factor MYRF can rescue myelin proteins gene expression in ZFP24 -ablated cells. Our data also suggest that ZFP24 display overlapping genomic binding sites with the transcription factors MYRF, SOX10, and OLIG2 which are known to control terminal differentiation of oligodendrocytes. Though the human genome contains roughly 700 C2H2-containing zinc finger proteins, the DNA-binding sequences and the biological functions of the vast majority of them are unknown. Our findings provide a direct molecular mechanism by which dephosphorylation of ZFP24 mediates its binding to enhancer regions of genes important for oligodendrocyte differentiation and myelination, controls their expression, and as a result, regulates oligodendrocyte differentiation and CNS myelination.

overall_design: Chromatin IP for ZFP24 was performed on mouse Oligodendrocyte progenitor cells (OPC) and mature  (differentiated) oligodendrocyte (OLG). Corresponding Zfp24 null cells were used as control, as well as pooled chromatin input.

first: Sara

last: Isaac


title: HDAC1 and HDAC2 regulates TGF-b during Endothelial-to-Hematopoietic Transition [RNA-Seq]

city: Manchester

first: Roshana

middle: S

last: Thambyrajah

address: Wilmslow Road

department: Stem Cell Biology

institute: CRUK Manchester

summary:
The first hematopoietic stem cells originate from hemogenic endothelium (HE), that trans-differentiate into the lumen to form hematopoietic clusters. The molecular mechanisms driving this transition are only poorly understood. Here, we present a complete and comprehensive study that shows the requirement for Transforming Growth Factor beta (Tgfbeta) signalling as the master regulator of triggering EHT from HE, including Runx1-/- HE. We employed RNA-Seq data on Hdac deficient HE, together with ChIP-Seq for HDAC1 and HDAC2 and on wild type HE that indicated its importance in EHT. We tested our findings extensively on HE derived from different sites/origin. In all instances we observed an increase in the frequency of EHT by decreasing Tgfbeta levels.
Poly(A) RNA-sequencing on control and Hdac1 or Hdac2 deficient HE cells

overall_design: Hdac1 or Hdac2 deletion

first: Muhammad

middle: Z

last: Fadlullah

first: Martin

last: Proffitt

first: Shaun

last: Cowley

first: Valerie

last: Kouskoff

first: Georges

last: Lacaud


title: Single-cell RNA sequencing of sensory neurons in the mouse dorsal horn

city: Stockholm

first: Sten

last: Linnarsson

address: Scheeles väg 1

department: Medical Biochemistry and Biophysics

institute: Karolinska Institutet

summary: We have used large-scale single-cell RNA sequencing (RNA-seq) to classify sensory neurons in the mouse dorsal horn, with the purpose of identifying neuronal subclasses, in particular making a systematic and comprehensive molecular classification of spinal cord sensory neurons, providing the neuronal basis for somatic sensation.

overall_design: 1545 single cells from the mouse brain dorsal horn: 637 from strain C57/bl6, 537 from a vGat-cre-tdTomato line, and 371 from a vGlut2-eGFP line.

last: Häring

first: Amit

last: Zeisel

first: Patrik

last: Ernfors


title: Electromagnetic field-mediated direct lineage reprogramming into induced dopamine neurons in vivo for Parkinson's disease therapy

city: Goyang-si

first: Junghyun

last: Jung

state: Gyeonggi-do

address: Dongguk University Biomedi Campus 32, Dongguk-ro, Ilsandong-gu

department: Life Science

institute: Dongguk Uvi.


title: The transcriptomic profile of stem-cell derived neurons in 3D culture conditions and stem-cell derived astrocytic cells

status: Public on Apr 09 2018

first: Halil

last: Tekin

state: MA

address: 75 Ames St.

institute: Broad Institute of MIT and Harvard

summary: Understanding neurological diseases requires tractable genetic systems. Three-dimensional (3D) neural tissue systems are an attractive choice, but it is not well understood how the transcriptome profile of these tissues is affected by encapsulating materials. Here we characterize the effect of different culturing conditions on the transcriptomic profile of induced neuronal cells and develop a method for  rapid generation of 3D co-cultures of neuronal and astrocytic cells from hESCs. We perform transcriptome analysis of cells resulting from astrocytic cell differentiation. Using single-cell sequencing, we find that our system recapitulates transcriptional patterns of cell types in the human brain.

overall_design: Refer to individual samples.

first: Sean

last: Simmons

first: Beryl

last: Cummings

first: Linyi

last: Gao

first: Xian

last: Adiconis

first: Cynthia

last: Hession

first: Ayan

last: Ghoshal

first: Danielle

last: Dionne

first: Sourav

middle: R

last: Choudhury

first: Volkan

last: Yesilyurt

first: Neville

middle: E

last: Sanjana

first: Xi

last: Shi

first: Congyi

last: Lu

first: Matthias

last: Heidenreich

first: Jen

middle: Q

last: Pan

first: Joshua

last: Levin

first: Feng

last: Zhang


title: Accelerating early anti-TB drug discovery by creating mycobacterial indicator strains that predict mode of action

city: Thuwal

first: AMIT

last: SUBUDHI

address: Level4, Builiding, 2, KAUST

department: BESE

institute: King Abdullah University of Science and Technology

sample_organism:
Mycobacterium marinum
Mycobacterium tuberculosis H37Rv


title: Hepatic glucocorticoid receptor transcriptome profiling in normal and hypogonadal females

city: Research Triangle Park

first: Matthew

middle: Allan

last: Quinn

state: North Carolina

address: 111 T.W. Alexander Dr.

department: Signal Transduction Laboratory

institute: National Institute of Environmental Health Sciences

summary: We report the hepatic glucocorticoid receptor transcriptome is reprogrammed in the absence of ovarian hormones.

overall_design: Examination of transcriptome under two different conditions (vehicle vs. dexamethasone) under two different hormonal milieus (normal and hypogonadal).

first: Xiaojiang

last: Xu

first: John

last: Cidlowski