title: miRNA expression data from a cohort of Chilean Ulcerative Colitis human intestinal samples

first: NIEHS

last: Microarray Core

summary:
MicroRNAs have been associated with the pathogenesis of intestinal diseases such as colon cancer and are deregulated in the inflammatory environment of intestinal mucosa in UC patients. The effects of microRNAs on immunological factors have been described before, however, there is no evidence that they have an effect on alarmins that impact on the pathophysiology of UC. Our goal is to identify deregulated miRNAs to be paired with potential target mRNAs.
We used microarrays to compare inflamed and non inflamed mucosa from chilean ulcerative colitis patients

overall_design: Inflamed and non inflamed human Intestinal biopsies were obtained in colonoscopy from Ulcerative Colitis patients and total RNA were extracted and hybridized using Affymetrix Eukaryotic Target Hybridization Controls protocol. MicroRNAs were extracted and then hybridized with Affymetrix MicroRNA microarray was accomplished using the Affymetrix GeneChipTM Version 4 microRNA arrays following the Affymetrix hybridization protocols (ThermoFisher Scientific Santa Clara, CA).

first: Karen

last: Dubois-Camacho

first: John

last: Cidlowski

first: David

last: Díaz-Jimenez


title: Chromatin structure governs stalled replication fork processing and cohesin loading

status: Public on Oct 04 2019

city: Montpellier

first: romain

last: forey

address: 142 avenue de la Cardonille

country: France

institute: IGH

type: Genome binding/occupancy profiling by high throughput sequencing

summary: The progression of replication forks (RFs) can be challenged by obstacles of endogenous or exogenous origin. Stalled forks need to be readily stabilized and restarted in order to prevent genomic instability. Replication fork restart requires the recruitment of multiple enzymes and involves different DNA transactions. The MRX (Mre11-Rad50-Xrs2) complex plays a central role in this process. It has been implicated in the nucleolytic degradation of nascent DNA and in the loading of cohesin at stalled forks. However, little is known on how these functions are regulated. Here we show that MRX structural features are predominant on the nuclease activity of Mre11 for DNA resection at stalled replication forks. This results raise the question of the mechanisms by which MRX promotes nascent strand resection. At DNA double strand breaks (DSB) MRX promotes the binding of the chromatin remodeler RSC, from which the activity is required for 5’ end resection. Interestingly, MRX mutants exhibit increased nucleosome occupancy at stalled replication forks. This result suggest that a dynamic chromatin structure promoted by MRX could be required for the processing of stalled replication forks. Strinkingly the absence of two histones modifiers Gcn5 and Set1 recapitulates the phenotype of MRX mutants both on chromatin structure and nascent strand resection at stalled forks even though they are dispensable for its recruitment. Since nucleosomes also represent obstacles for the loading of SMC complexes on DNA, it is coherent that we observed that cohesin is no longer recruited at stalled forks in gcn5 and set1, as in MRX mutants. Together our data suggest that the regulation of chromatin structure at stalled replication forks is essential for their processing and to promote genome stability.

overall_design: NGS-based analysis of replication origin activity, chromatin architecture and cohesin recruitment in HU-arrested S. cerevisiae cells

first: Axel

last: Delamarre

first: Antoine

last: Barthe

first: Christophe

last: de la Roche Saint-André

first: Pierre

last: Luciano

first: Romain

last: Forey

first: Ismaël

last: Padioleau

first: Krzysztof

last: Ginalski

first: Vincent

last: Géli

first: Armelle

last: Lengronne

first: Philippe

last: Pasero


title: KLF15-Wnt–Dependent Cardiac Reprograming Up-Regulates SHISA3 in the Mammalian Heart

status: Public on Oct 07 2019

city: Goettingen

first: Laura

middle: C

last: Zelarayan

state: Lower Saxony

address: Robert-Koch Strasse 40

department: Institute of Pharmacology and Toxicology

country: Germany

institute: University Medical Center, Goettingen

type: Expression profiling by high throughput sequencing

summary:
Sustained cardiac stress promotes the transition from an adaptive response to heart failure. Understanding of mechanisms governing this transition will assist in identifying targets that prevent this progression. Our study revealed age-specific transcriptional functions mediated by KLF15 that are crucial for cardiac homeostasis. We report that postnatally, KLF15 continuously activates cardiac metabolism, but represses pathological, hypertrophic pathways associated with cardiomyocyte de-differentiation and endothelial cell (EC) remodeling in an age-dependent manner. Our integrative genomic and transcriptomic analyses identified novel target genes directly bound, and either activated or repressed by KLF15 in vivo in the adult heart. We identified a cooperative program inducing aberrant EC remodeling, caused by a reduction of KLF15 and a concomitant activation of Wnt signaling. Within this program, we further identified a so far uncharacterized cardiac gene - Shisa3, which is expressed in the developing heart and is upregulated in cardiac hypertrophy, ischemia and failure. Importantly, we demonstrate that the KLF15- and Wnt co-dependent, SHISA regulation occurs also in the human myocardium. Altogether, our results unraveled and characterized a previously unknown cardiac gene Shisa3, and attributed its significance to EC homeostasis of the adult heart, controlled by KLF15-Wnt dynamics.
Purpose: The aim of this study was to compare transcriptome profiles (RNA-seq) of heart tissue with a WT or KO Klf15 locus at different murine ages - postnatal day10 (p10), 4-week-old and 20-week-old mice.
Methods: Cardiac tissue total RNA profiles for different groups were obtained using deep sequencing, in triplicates, using Illumina HiSeq4000. The sequence reads that passed quality filters were analyzed at the transcript isoform level with TopHat, followed by DESeq2. qPCR validation was performed using TaqMan and SYBR Green assays.
Conclusions: Our study represents the first detailed analysis of the processes triggered upon Klf15 loss in hearts of different murine postnatal ages, which was so far not investigated. We report that this Klf15 loss first triggers Wnt canonical pathway activation, followed by activation of the non-canonical Wnt components, culminating in heart failure.

overall_design: Gene expression profiling from cardiac ventricles of P10, 4-week-old and 20-week-old mice with Klf15 wild type and loss of function.

first: Claudia

last: Noack

first: Lavanya

middle: M

last: Iyer


title: Prostaglandin E2-mediated T cell suppression requires expression of hydroxyprostaglandin dehydrogenase in regulatory T cells.

city: Bonn

first: Joachim

last: Schultze

state: NRW

address: Carl-Troll-Strasse 31

department: Genomics and Immunoregulation

institute: LIMES (Life and Medical Sciences Center Genomics and Immunoregulation)

summary: Prostaglandins are involved in maintaining tissue integrity under homeostatic conditions. However, in chronic inflammation and cancer prostaglandins have been linked to immune deviation including strong suppression of effector T-cell function. Yet, the molecular mechanisms underlyingimmunosuppression and the cell types involved are only purely understood. Here, we show for the first time that Treg cells are the critical cellular component exerting immunosuppressive effects in prostaglandin E2 (PGE2)-rich environments. Hydroxyprostaglandin dehydrogenase (HPGD), which catabolizes PGE2 into immunosuppressive metabolites, is the critical molecular link between prostaglandin accumulation, increased Treg-cell function and avoidance of tissue destruction.

overall_design: Conditional HPGD knockout mice were crossed to FOXP3-Cre-YFP mice and Treg and Tconv isolated from spleens of these mice were compared with Treg and Tconv cells from control animals.

first: Y

last: Thabet

first: K

last: Klee

first: J

middle: L

first: M

last: Beyer


title: Cell type purification by single-cell transcriptome-trained sorting

city: Utrecht

first: Aditya

last: Barve

address: Uppsalalaan 8

country: Netherlands

institute: Hubrecht Institute

type: Methylation profiling by high throughput sequencing

summary: Traditional cell type enrichment using fluorescence activated cell sorting (FACS) relies on methods that specifically label the cell type of interest. Here we propose GateID, a computational method that combines single-cell transcriptomics, for unbiased cell type identification, with FACS index sorting, to purify cell types of choice. We validate GateID by purifying various cell types from the zebrafish kidney marrow and the human pancreas without resorting to specific antibodies or transgenes.

sample_organism:
Danio rerio
Homo sapiens

platform_organism:
Danio rerio
Homo sapiens

overall_design: Single cell mRNA sequencing data of unenriched and enriched cells from zebrafish whole kidney marrow and human pancreas using GateID. For each cell, we provide libraries with transcriptome information. An unenriched sample is transcriptome data from a live single cell FACS sort, while an enriched library has transcriptome data for GateID enriched single cells for a given cell type.

first: Chloé

middle: S

last: Baron

middle: A

first: Mauro

middle: J

last: Muraro

first: Gitanjali

last: Dharmadhikari

first: Reinier

last: van der Linden

first: Anna

last: Lyubimova

first: Eelco

last: deKoning

first: Alexander

last: van Oudenaarden


title: Knockout of Staufen1 impairs the localization of specific subsets of mRNAs on the mitotic spindle of colorectal cancer cells

status: Public on Oct 05 2019

city: Montreal

first: Eric

last: Lecuyer

state: Quebec

address: 110 Pine Ave W

department: RNA biology

country: Canada

institute: IRCM

summary: Staufen1 (STAU1) is an RNA-binding protein involved in maturation, localization, translation and decay of mRNAs. STAU1 expression is modulated during the cell cycle and decreases during mitosis. In prometaphase, STAU155 binds specific classes of mRNAs that code for proteins implicated in transcription and cell cycle regulation. In this paper, we report that STAU155 co-localizes with microtubules on the mitotic spindle in human colorectal cancer cell line HCT116, and map the molecular determinant required for this association within the N-terminal 88 amino acids (aa 25-37). Interestingly, STAU1 co-purifies with ribosomal proteins and co-localizes with active sites of translation on the mitotic spindle. To characterize STAU1-dependent mRNA transport and localization on the spindle, we used RNAseq analysis to identify spindle-associated mRNAs on purified spindles of wild-type and STAU1-KO CRISPR cell lines. Our datasets identify 161 protein-coding transcripts that are less abundant on the mitotic spindle of STAU1-KO cells compared to WT, and 660 that are more abundant. Altogether, these data demonstrate that STAU1 controls the transport and the localization of specific sub-populations of mRNAs to the mitotic spindle of cancer cells and suggest that at least some spindle-localized mRNAs undergo local translation during mitosis.

overall_design: WT and STAU1-KO HCT116 cells were synchronized in mitosis with Taxol and RNAs purified from whole cell extracts and from mitotic spindle preparations. Biological replicates were analyzed.

first: Sami

last: Hassine

first: Louis

middle: P

last: Bouvrette

first: Luc

last: DesGroseillers


city: Tokyo

first: Norikazu

last: Saiki

address: 1-5-45 Yushima, Bunkyo-ku

department: Institute of Research

country: Japan

institute: Tokyo Medical and Dental University

summary: We report the continuous patterning and dynamic morphogenesis of hepatic, biliary and pancreatic structures, invaginating from a three-dimensional culture of human pluripotent stem cell (PSC). The boundary interactions between anterior and posterior gut spheroids differentiated from human PSCs enables autonomous emergence of hepato-biliary-pancreatic (HBP) organ domains specified at the foregut-midgut boundary organoids in the absence of extrinsic factor supply. The regional identity of the boundary region of anterior-posteior spheroids was analyzed by RNA-sequencing with micro-dissected boundary organoid into anterior, posterior, and boundary regions. Each region expressed the corresponding gut lineage markers. The early HBP specification markers including HHEX1 and PDX1 at the boundary were highly upregulated compared with the other two regions, indicating that the anterior-posterior boundary interactions autonomously generate HHEX and PDX1 positive cells in the absence of exogenous inductive factors. To delineate the HBP progenitor self-inductive mechanism, we evaluated the boundary specific expression profiles of known inductive signaling pathways that includes FGF, BMP, Hedgehog, NOTCH and retinoic acid (RA) signals, and found that the signal downstream of RA were activated prominently at the boundary region but not in the anterior or posterior regions.

overall_design: Examination of mRNA expression profile in micro-dissected 3 different region from boundary organoid.

first: Takanori

last: Takebe

first: Hiroyuki

last: Koike

first: Kentaro

last: Iwasawa


title: Overexpression of small RNA MTS1338 M.tuberculosis (stationary phase)

city: Moscow

first: Artem

last: Grigorov

address: Ulitsa Miklukho-Maklaya, 16/10

department: Genomics and Postgenomic Technologies

country: Russia

institute: Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry

summary: We investigated the expression of MTS1338, a small non-coding RNA of  Mycobacterium tuberculosis in bacterial cultures, and demonstrated its significant contribution to host-pathogen interactions.

overall_design:
Trancriprtome profiles of control (pMV) and overexpressing MTS1338 (MTS1338_over) strains of M.tubercuilosis in stationary phase were generated by deep sequencing, in triplicate, using Illumina NovaSeq6000
This study describes transcriptome changes in M. tuberculosis strains with overexpression of MTS1388 small RNA  (stationary phase of growth).

first: Elena

middle: G

last: Salina


title: miRNA profile in the hippocampus of APP/PS1 transgenic mice

city: NANJING

first: XIAOLEI

last: ZHU

state: JIANGSU

address: 321 ZHONGSHAN ROAD

department: Neurology

country: China

institute: Nanjing Drum Tower Hospital

summary: To explore the miRNAs associated with the memory deficits in Alzheimer's disease, we detected the miRNA profiles in the hippocampus of  6-month-old male APPswe/PS1dE9 (APP/PS1) mice and age-matched wild type C57BL/6 mice.

platform_organism:
Homo sapiens
Human alphaherpesvirus 1
Human alphaherpesvirus 2
Macacine alphaherpesvirus 1
Human betaherpesvirus 5
human gammaherpesvirus 4
Herpesvirus saimiri (strain 11)
JC polyomavirus
Human immunodeficiency virus 1
Human betaherpesvirus 6B
Human gammaherpesvirus 8
Merkel cell polyomavirus
Betapolyomavirus hominis
Betapolyomavirus macacae

overall_design: Three 6-month-old male APPswe/PS1dE9 (APP/PS1) mice and 3 age-matched wild type C57BL/6 mice were used. The hippocampus were isolated and homogenized using a Tissue homogenizer, and the RNA was extracted for the miRNA microarray analysis.

first: Xiaolei

last: Zhu


title: Stereotyped transcriptomic transformation of somatosensory neurons in response to injury

city: Bethesda

first: Minh

middle: Q

last: Nguyen

state: MARYLAND

address: 9000, Rockville Pike

country: USA

institute: NIDCR/NIH

summary:
In mice, spared nerve injury replicates symptoms of human neuropathic pain and
induces upregulation of many genes in somatosensory neurons. Here we used single cell transcriptomics to probe the effects of partial infraorbital transection of the trigeminal nerve at the cellular level. Uninjured neurons were unaffected by transection of major nerve branches, segregating into many different classes. In marked contrast, axotomy rapidly transformed damaged neurons into just two new and closely-related classes where almost all original identity was lost. Remarkably, sensory neurons also adopted this transcriptomic state following various minor peripheral injuries. By genetically marking injured neurons, we showed that the injuryinduced transformation was reversible, with damaged cells slowly reacquiring normal gene expression profiles. Thus, our data expose transcriptomic plasticity, previously thought of as a driver of chronic pain, as a programed response to many types of injury and a potential mechanism for regulating sensation during wound healing.

overall_design: Nuclei from trigeminal ganglia from wildtype, spared nerve injury mice (2-, 7-, 21-, and 75 days after injury), chronic itch with facial lesions, and minor facial injury mice were isolated.  Neuronal nuclei were purified with anti-NeuN antibody and single nucleus RNA-seq were performed with either the Drop-Seq or 10x Genomics method.

first: Nick

last: Ryba


title: Transcriptome analysis on OVA-GA(10) immunized GA-CFP mice

city: Munich

first: Qihui

last: Zhou

address: Feodor-Lynen-Str. 17

institute: German Center for Neurodegenerative Diseases

summary: The goal of the study is to perform unbiased transcriptome analysis on spinal cord samples of immunized GA-CFP mice to configure the effect of OVA-GA(10) vaccination in a C9orf72 mouse model.

overall_design: RNA sequencing on WT or GA-CFP transgenic mice treated with either PBS or OVA-(GA)10 at age of 32 weeks.

first: Dieter

last: Edbauer


title: Integrative analysis identifies lincRNAs up- and downstream of neuroblastoma driver genes (PHOX2B)

city: Gent

first: Dries

last: Rombaut

address: Corneel Heymanslaan 10

department: Center for Medical Genetics

country: Belgium

institute: Ghent University

type: Non-coding RNA profiling by high throughput sequencing

summary: Long intergenic non-coding RNAs (lincRNAs) are emerging as integral components of signaling pathways in various cancer types. In neuroblastoma, only a handful of lincRNAs are known as upstream regulators or downstream effectors of oncogenes. Here, we exploit RNA sequencing data of primary neuroblastoma tumors, neuroblast precursor cells, neuroblastoma cell lines and various cellular perturbation model systems to define the neuroblastoma lincRNome and map lincRNAs up- and downstream of neuroblastoma driver genes MYCN, ALK and PHOX2B. Each of these driver genes controls the expression of a particular subset of lincRNAs, several of which are associated with poor survival and are differentially expressed in neuroblastoma tumors compared to neuroblasts. By integrating RNA sequencing data from both primary tumor tissue and cancer cell lines, we demonstrate that several of these lincRNAs are expressed in stromal cells. Deconvolution of primary tumor gene expression data revealed a strong association between stromal cell composition and driver gene status, resulting in differential expression of these lincRNAs. We also explored lincRNAs that putatively act upstream of neuroblastoma driver genes, either as presumed modulators of driver gene activity, or as modulators of effectors regulating driver gene expression. This analysis revealed strong associations between the neuroblastoma lincRNAs MIAT and MEG3 and MYCN and PHOX2B activity or expression. Together, our results provide a comprehensive catalogue of the neuroblastoma lincRNome, highlighting lincRNAs up- and downstream of key neuroblastoma driver genes. This catalogue forms a solid basis for further functional validation of candidate neuroblastoma lincRNAs.

overall_design: CLB-GA was transduced with control or inducible shPHOX2B. The cells were treated with doxycycline for 5 days.

first: Pieter

last: Mestdagh

first: Isabelle

last: Janoueix


title: Circular RNAs, mRNAs and lncRNAs associated with castration-related fat deposition

city: Zhengzhou

first: Jing

last: Wang

address: Huayuan Road No.116

institute: Institute of Animal Husbandry and Veterinary Science

summary: We firstly compared the expression file of circRNAs, mRNAs and lncRNAs in longissimus muscle (LM) between the castrated and intact Huainan male pigs to identify the key circRNAs, mRNAs and lncRNAs involved in the genetic basis of castration associated fat deposition.

overall_design: The longissimus muscle from three Huainan intact pigs.

first: Liushuai

last: Hua


title: Transcriptome Profiling for human Leydig cell-like cells, adrenal cell-like cells, and induced pluripotent stem cells

city: Los Angeles

first: Lu

last: Li

state: CA

address: Room 706, 1985 Zonal Ave

department: School of Pharmacy

institute: University of Southern California

summary: With the increasing common of reduced serum testosterone (T), or hypogonadism, in the male population, there is an urgent require for the approach of obtaining T-producing cells, which could be used to treat hypogonadism based on transplantation and reestablishment of T-producing cell lineage in the body. In human, T is mainly synthesized by the Leydig cells (LCs) that have been proposed to derive from mesenchymal cells of mesonephric origin. Although mesenchymal cells have been successfully induced into LCs, the limited source and possible trauma to donors hinders their wide applications in clinic therapies. Alternatively, human induced pluripotent stem cells (hiPSCs) that are highly expandable in cell culture and have the potential to differentiate into all somatic cell types become the emerging source of autologous cell therapies. In this study, we have successfully induced the differentiation of hiPSCs through mesoderm and early mesenchymal progenitors (EMPs) into either human Leydig cell-like cells (hLLCs) or human adrenal cell-like cells (hALCs) under different chemically defined culture systems. Factors that are critical for the normal development of LCs were added to both culture systems. hLLCs are expressed all steroidogenic genes and proteins that are important for T biosynthesis and are specific for LCs, synthesize T rather than cortisol (F), secret steroid hormones in response to db-cAMP and 22(R)-hydroxycholesterol, and display ultrastructural features resembling LCs. Differentially, hALCs synthesize F rather than T, and secret much less of steroid hormones than hLLCs. Thereafter, we performed microarray analyses to profile the whole gene expression pattern of hiPSCs and thier derivatives hLLCs and hALCs.

overall_design: The hiPSC line GM25256*B was induced to differentiate into human Leydig cell-like cells (hLLCs) and human adrenal cell-like cells (hALCs), respectively. Transcriptome profiling was performed using transcriptome microarrays. Each cell types including three replicates were collected and profiled.

first: Vassilios

last: Papadopoulos


title: Transcriptomic profiling of HeLa cells treated with miR-let-7i-3p and control-miR

city: Cologne

first: Konrad

middle: U.

last: Förstner

state: North Rhine-Westphalia

address: Gleueler Str. 60

department: Information Services

institute: ZB MED - Information Centre for Life Sciences

summary: To have a global picture of the targets of the mir-let-7i-3p, we assessed transcriptome changes, by deep-sequencing, of HeLa cells transfected with this miRNA or a control miRNA (cel-miR-231).

overall_design: Transcriptomic profiles of HeLa cells treated let-7i-3p and control-miR  were generated by deep sequencing, using Illumina HiSeq 2000.

first: Ana

last: Eulalio

first: Claire

last: Maudet


title: The Ccr4-Not complex regulates TORC1 signaling and mitochondrial metabolism by promoting vacuole V-ATPase activity

city: Memphis

first: Daniel

middle: Lee

last: Johnson

state: Tennessee

address: 71 S Manassas

department: Molecular Informatics Core

institute: UTHSC

summary: The Ccr4-Not complex is an effector of multiple signaling pathways controlling gene transcription and mRNA turnover.  Herein, we provide evidence that Ccr4-Not also activates nutrient signaling through the essential target of rapamycin complex 1 (TORC1) pathway.  Mechanistically, Ccr4-Not loss decreases TORC1 signaling due to reduced stability of the vacuole V-ATPase that is required to activate TORC1 when associated with the Gtr1 GTPase containing EGO complex.  Expressing a constitutively active Gtr1 in Ccr4-Not deficient cells bypasses the requirement for the V-ATPase and restores TORC1 signaling.  Transcriptome analysis reveals that Ccr4-Not loss activates TORC1 repressed retrograde signaling to remodel metabolism and enhance mitochondrial function.  Blocking retrograde signaling in a Ccr4-Not mutant further reduces TORC1 signaling, thus suggesting the enhanced mitochondrial metabolism due to Ccr4-Not loss is a metabolic adaptive response required to sustain TORC1 activity.  Therefore, Ccr4-Not is a critical activator of TORC1 signaling that regulates cellular metabolism.

overall_design: A total of six samples were analyzed.  Three samples were independent wild-type replicates and three were ccr4D mutant replicates

first: R

middle: N

last: Laribee


title: Rare pulmonary neuroendocrine cells are stem cells regulated by Rb, p53, and Notch

status: Public on Oct 03 2019

city: Stanford

first: Mark

last: Krasnow

address: 279 Campus Dr

department: Biochemistry

institute: Stanford University School of Medicine

summary: Pulmonary neuroendocrine (NE) cells are neurosensory cells sparsely distributed throughout the bronchial epithelium, many in innervated clusters of 20-30 cells. Following lung injury, NE cells proliferate and generate other cell types to promote epithelial repair. Here we show only rare NE cells, typically 2-4 per cluster, function as stem cells. These fully differentiated cells display features of classical stem cells. Most proliferate (self-renew) following injury, and some migrate into the injured area. A week later individual cells, often just one per cluster, lose NE identity (deprogram), transit amplify, and reprogram to other fates, creating large clonal repair patches. Small cell lung cancer (SCLC) tumor suppressors regulate the stem cells: Rb/p53 suppress self-renewal, whereas Notch marks the stem cells and initiates deprogramming and transit amplification. We propose that NE stem cells give rise to SCLC, and transformation results from constitutive activation of stem cell renewal and inhibition of deprogramming.

overall_design: Pulmonary neuroendocrine (NE, n=100) and non-NE (n=125) cells were purified from adult mouse lungs and analyzed by single-cell RNA-seq using Smart-Seq.

first: Youcef

last: Ouadah


title: Genome-wide miRNA analysis reveals different miRNAs between Tuberculous and viral Meningitis

status: Public on Oct 02 2019

city: Beijing

first: Liping

last: Pan

address: 97 Machang Road, Tongzhou District

institute: Beijing Chest Hospital, Capital Medical Universtiy.

summary: In order to identify the potential biomarkers for discriminating tuberculous meningitis (TBM) and viral meningitis (VM) and to reveal the different pathophysiological processes between TBM and VM, a genome-wide miRNA screenings of peripheral blood mononuclear cells (PBMCs) from TBM, VM, and healthy controls (HCs) using microarray assay was performed (12 samples). Twenty-eight differentially expressed miRNAs were identified between TBM and VM, and 11 differentially expressed miRNAs were identified between TBM and HCs. The 6 overlapping miRNAs detected in both TBM vs. VM and TBM vs. HCs were verified by qPCR analysis and showed a 100% consistent result with that in microarray test.

overall_design: Genome-wide miRNA profiling of PBMCs from tuberculous meningitis (TBM), viral meningitis (VM)  and healthy controls (HCs), were simultaneously measured using Agilent microarray technique. Four independent samples were included in each group (TBM, VM and HCs).


title: Harnessing the benefits of neuroinflammation: Generation of macrophages/microglia with remarkable remyelinating properties

city: Calgary

first: Manoj

middle: Kumar

last: Mishra

state: AB

address: 3330 Hospital Dr NW

department: Clinical Neuroscience

institute: Hotchkiss Brain Institute

summary: Excessive inflammation within the central nervous system is injurious, but an immune response is also required for its repair. Macrophages are versatile cells that adopt different properties depending upon their microenvironment. Exposing macrophages to interleukin-4 and -13 (IL4/IL13) has incurred interest for their reparative properties. Unexpectedly, while macrophages exposed to the classic pro-inflammatory signals (interferon-γ/lipopolysaccharide, IFN/LPS) killed neurons and oligodendrocytes in culture, the addition of LPS to IL4/IL13-treated macrophages profoundly elevated IL10, repair metabolites (lactate, ornithine), glucose metabolism and the oligodendrocyte-trophic heparin-binding epidermal growth factor (HBEGF); cells did not display pro-inflammatory or neurotoxic features.

overall_design: We subjected activated murine bone marrow derived macrophages (BMDMs) to microarray analysis to identify activation states of cells.  To determine the signature gene expression, BMDMs were treated with IFN gamma/LPS, IL4/IL13 and LPS/IL4/IL13 for 6h and subjected to microarray analysis.  Two (2) controls and 2 treatments (cytokines treated) samples were generated from BMDMs.  Thus, a total of 8 RNA samples from activated BMDMs were obtained for microarray analysis.

middle: K

first: V

middle: W

last: Yong


title: Integrated Paired-end Enhancer Profiling and Whole-Genome Sequencing Reveals Recurrent CCNE1 and IGF2 Enhancer Hijacking in Primary Gastric Adenocarcinoma [Capture-C]

city: Singapore

first: Wen Fong

last: Ooi

address: 60 Biopolis

country: Singapore

institute: Genome Institute of Singapore

summary: H3K27ac paired-end NanoChIP-seq, whole-genome sequencing, RNA-seq and Hi-C were integrated to reveal tumor-associated structural variants contributing to gastric cancer.

overall_design: H3K27ac paired-end NanoChIP-seq were generated from primary GC and matched normal samples to discover regulatory structural variations that occurred at cis-regulatory elements marking by H3K27ac mark.

first: Ooi

last: Fong

first: Kevin

last: Lim

first: Patrick

last: Tan


title: Transcriptome analysis of common and diverged circulating miRNAs between arterial and venous during aging

first: Hao

last: Wang

address: No.49 Huayuan North Road

institute: Peking University Third Hosptial

summary:
Background: miRNAs derived from peripheral venous blood gained extensive attention as clinical biomarkers, while arterial miRNAs exhibited slightly different expression profiles. We compared the expression profiles of venous- and arterial-derived plasma miRNA between young and aged male SD rats by next-generation sequencing, in order to explore whether peripheral venous miRNAs can represent entire circulating vessels in abnormal conditions like aging.
Results: MSigDB Hallmark Gene Set reference and TAM 2.0 server were used to investigate the enriched functions and associated diseases. The aging-related de-regulated miRNAs in artery and vein shown similar enriched functional terms. Of note, refer to the arterial-versus-venous differential-expressed miRNA profiles, only a few miRNAs shared between young and aged rats. Among them, miR-450a/b and miR-223 shown the similar tendency between young and aged rat, while miR-136 and miR-503 etc displayed the opposite direction under the same scenario. Since miRNAs are under the control of their specific transcriptional factors, we further analyzed upstream regulators which influence miRNAs level for vascular vessel location. TransmiR v2.0 tool was used and found enriched upstream transcription factors like NFκB and SIRT1. These transcriptional factors could be organ-specific expression and/or regulated in physiological and aging states as parts of plausible causal factors.
Conclusion: This study screened and analyzed the differential differential-expressed miRNA profiles in arterial and venous plasma under aging conditions, suggesting the importance of origin of candidate circulating miRNA biomarkers upon the certain scenario and its potential regulatory rule.

overall_design: Plasma miRNA profiles of 8-week-old and 22-month-old male SD rats (5 in each group) were generated by next-generation sequencing.

first: Yuan

last: Zhou

first: Zhongnan

last: Yin

first: Li

last: Chen

first: Ling

last: Jin

first: Qinghua

last: Cui

first: Lixiang

last: Xue


title: Expression analysis of wild type and CCP3 deficient LT-HSCs

first: Zhen

last: Xiong

address: 15 Datun Road, Beijing 100101, China

department: Institute of Biophysics

institute: Chinese Academy of Sciences

summary: All hematopoietic lineages are derived from a limited pool of hematopoietic stem cells (HSCs). Although the mechanisms underlying HSC self-renewal have been extensively studied, little is known about the role of protein glutamylation and deglutamylation in hematopoiesis. Here we show that carboxypeptidase CCP3 is most highly expressed in BM cells among CCP members. CCP3 deficiency impairs HSC self-renewal and hematopoiesis. Deubiquitinase BAP1 is a substrate for CCP3 in HSCs. BAP1 is glutamylated at Glu651 by TTLL5 and TTLL7, and BAP1-E651A mutation abrogates BAP1 glutamylation. BAP1 glutamylation accelerates its ubiquitination to trigger its degradation. CCP3 can remove glutamylation of BAP1 to promote its stability, which enhances Hoxa1 expression leading to HSC self-renewal. Bap1E651A mice produce higher numbers of LT-HSCs and peripheral blood cells. Moreover, TTLL5 and TTLL7 deficiencies sustain BAP1 stability to promote HSC self-renewal and hematopoiesis. Therefore, glutamylation and deglutamylation of BAP1 modulate HSC self-renewal and hematopoiesis.

overall_design:
Investigation of differentially expressed genes in CCP3 deficient LT-HSCs.
mRNA profiles of LT-HSCs (Lin–Sca-1+c-Kit+CD48–CD150+) from CCP3 deficient mice or WT littermates were generated by deep sequencing, using BGISEQ-500.

first: Z

first: P

last: Xia

last: Fan


title: Non-transmissible measles virus vector with segmented RNA genome establishes different types of iPSCs from hematopoietic cells

first: Kenzaburo

last: Tani

address: 4-6-1, Shirokanedai, Minato-ku

department: Project Division of ALA Advanced Medical Research

institute: The Institute of Medical Science, The University of Tokyo

summary: We established iPSCs from CD34+ HPCs or CD3+ T cells by transducing measles virus vectors encording reprogramming genes. HPC-derived iPSCs and T-cell-derived iPSCs showed naive-like and primed pluripotent cell properties, respectively.

overall_design: CD34+ and CD3+ cells were sorted from cord blood and transduced with measles virus vectors encoding OCT3/4, SOX2, KLF4 and L-MYC. The cells were cultured in regular human ESC culture media for 2-3 weeks. After development of colonies, the cells were harvested and dissociated, then cultured with in naive media or human ESC culture media. After several passages, total cell RNA was harvested and subjected to RNA seq.

first: Makoto

last: Takeda


title: Integrated Paired-end Enhancer Profiling and Whole-Genome Sequencing Reveals Recurrent CCNE1 and IGF2 Enhancer Hijacking in Primary Gastric Adenocarcinoma [4C-Seq]

summary: H3K27ac paired-end NanoChIP-seq, whole-genome sequecing, RNA-seq and Hi-C were integrated to reveal tumor-associated structural variants contributing to gastric cancer


title: Integrated Paired-end Enhancer Profiling and Whole-Genome Sequencing Reveals Recurrent CCNE1 and IGF2 Enhancer Hijacking in Primary Gastric Adenocarcinoma (Hi-C)

overall_design: Hi-C profiles were generated to interrogate for chromatin interactions and topological-associated domains.


title: The RNA helicase DDX6 regulates self-renewal and differentiation of human and mouse stem cells [RNA-seq]

city: Houston

first: Bruno

last: Di Stefano

state: TX

address: 1 Baylor Plaza

department: Molecular and Cellular Biology

institute: Baylor College of Medicine

summary: Analysis of human embryonic stem cells and induced pluripotent stem cells depleted for DDX6. Results provide insight into the regulation of human stem cell self-renewal and differentiation by the RNA-binding protein DDX6

overall_design: Human embryonic stem cells and induced pluripotent stem cells depleted for DDX6.

first: Anthony

last: Anselmo

first: Ruslan

last: Sadreyev

first: Konrad

last: Hochedlinger


title: Gene expression profiling of kidneys derived from Pkd1 conditional knock-out (KO) mice treated by Salsalate

city: Toronto

first: York

middle: PC

last: Pei

state: Ontario

address: 8N838, 585 University Avenue

department: Department of Medicine

institute: University of Toronto

summary: Computational identification of gene expression pathways and key regulatory factors in the Pkd1 KO kidneys treated by Salsalate

overall_design: Using Affymetrix Mouse Gene 2.0 ST Arrays, the global gene profiling of 30 kidneys samples from wild type (n=7), KO (n=12) and KO mice treated by Salsalate (n=11) was performed

first: Xuewen

last: Song

first: Wouter

last: Leonhard

first: Dorien

last: Peters


title: Translational control of cardiac fibrosis (II)

first: Sonia

last: Chothani

address: 8 College Road

institute: Duke-NUS school of medicine

summary: Background: Fibrosis is a common pathology in many cardiac disorders and is driven by the activation of resident fibroblasts. The global post-transcriptional mechanisms underlying fibroblast-to-myofibroblast conversion in the heart have not been explored. Methods: Genome-wide changes of RNA transcription and translation during human cardiac fibroblast activation were monitored with RNA sequencing and ribosome profiling. We then used a RNA-binding protein-based analyses to identify translational regulators of fibrogenic genes. The integration with cardiac ribosome occupancy levels of 30 dilated cardiomyopathy patients demonstrates that these post-transcriptional mechanisms are also active in the diseased fibrotic human heart. Results: We generated nucleotide-resolution translatome data during the TGFβ1-driven cellular transition of human cardiac fibroblasts to myofibroblasts. This identified dynamic changes of RNA transcription and translation at several time points during the fibrotic response, revealing transient and early-responder genes. Remarkably, about one-third of all changes in gene expression in activated fibroblasts are subject to translational regulation and dynamic variation in ribosome occupancy affects protein abundance independent of RNA levels. Targets of RNA-binding proteins were strongly enriched in post-transcriptionally regulated genes, suggesting genes such as MBNL2 can act as translational activators or repressors. Ribosome occupancy in the hearts of patients with dilated cardiomyopathy suggested the same post-transcriptional regulatory network was underlying cardiac fibrosis. Key network hubs include RNA-binding proteins such as PUM2 and QKI that work in concert to regulate the translation of target transcripts in human diseased hearts. Furthermore, silencing of both PUM2 and QKI inhibits the transition of fibroblasts toward pro-fibrotic myofibroblasts in response to TGFβ1. Conclusions: We reveal widespread translational effects of TGFβ1 and define novel post-transcriptional regulatory networks that control the fibroblast-to-myofibroblast transition. These networks are active in human heart disease and silencing of hub genes limits fibroblast activation. Our findings show the central importance of translational control in fibrosis and highlight novel pathogenic mechanisms in heart failure.

overall_design: Ribosome profiling of left ventricle tissue of 30 end-stage DCM patients

first: Sebastian

last: Schafer

first: Eleonora

last: Adami

first: Stuart

last: Cook

first: Owen

last: Rackham


title: RNA-binding proteins govern neural progenitor hierarchy during development and tumorigenesis

city: Marseille

first: Daian

last: Fabrice

address: Case 907 - Parc Scientifique de Luminy

institute: CNRS

summary: The aim was to identify differentially expressed genes in Drosophila neural tumors caused by the combined knock-down of prospero and Syncrip, compared to tumors caused by the knock-down of prospero.

overall_design: Tumors were induced in the ventral nerve cords of larvae by mis-expressing UAS-RNAi constructs targeting prospero and Syncrip using poxn-GAL4. Adult ventral nerve cords containing bulk tumors were dissected, from which RNA was purified. Wild type tissue is also included in the dissected material. We have 3 different types of samples made in duplicate: [1] normal ventral nerve cords of approximately 6-day-old adults (wt1, wt2). They contain no NB; [2] Ventral nerve cords of approximately 6-day-old adults that contain prosRNAi NB tumors (cnt, cnt2); and [3] Ventral nerve cords of approximately 6-day-old adults that contain prosRNAi syncripRNAi NB tumors (Syp1, Syp2).

first: Sara

last: Genovese

first: Raphaël

last: Clément

first: Cassandra

last: Gaultier

first: Florence

last: Besse

first: Karine

last: Narbonne-Reveau

first: Fabrice

last: Daian

first: Sophie

last: Foppolo

first: Nuno

last: Miguel Luis

first: Cédric

last: Maurange


title: Essential roles of Windei and nuclear monoubiquitination of Eggless/SETDB1 in transposon silencing

city: Tokyo

first: Kaoru

last: Sato

address: 35-2 Sakae-cho, Itabashi-ku

institute: Tokyo Metropolitan Institute of Gerontology

summary: Eggless/SETDB1 (Egg), the only essential histone methyltransferase (HMT) in Drosophila, plays a role in gene repression, including piRNA‐mediated transposon silencing in the ovaries. Previous studies suggested that Egg is post‐translationally modified and showed that Windei (Wde) regulates Egg nuclear localization through protein–protein interaction. Monoubiquitination of mammalian SETDB1 is necessary for the HMT activity. Here, using cultured ovarian somatic cells, we show that Egg is monoubiquitinated and phosphorylated but that only monoubiquitination is required for piRNA‐mediated transposon repression. Egg monoubiquitination occurs in the nucleus. Egg has its own nuclear localization signal, and the nuclear import of Egg is Wde‐independent. Wde recruits Egg to the chromatin at target gene silencing loci, but their interaction is monoubiquitin‐independent. The abundance of nuclear Egg is governed by that of nuclear Wde. These results illuminate essential roles of nuclear monoubiquitination of Egg and the role of Wde in piRNA‐mediated transposon repression.

overall_design: Genome-wide examination of Egg binding regions and impact of depletion of Piwi and Wde on the Egg binding patterns in Drosophila ovarian somatic cells (OSCs).

first: Ken

last: Osumi

first: Mikiko

last: Siomi


title: Circular RNA expression profiles of mouse ovaries during postnatal development and the function of circular RNA epidermal growth factor receptor in granulosa cells

city: Shanghai

first: Ji

last: Wu

address: No.800, Dongchuan Road, Minhang District

institute: Shanghai Jiao Tong University

summary: Here, we explored the circRNA expression profiles of adult and neonatal mouse ovaries by high-throughput sequencing. A total of 28,000 circRNAs were identified in adult and neonatal ovaries The results showed that 343 circRNAs were up-regulated and 146 circRNAs were down-regulated in adult ovaries compared with neonate ovaries.

overall_design: Examination of  circRNA expression profiles in adult and neonatal mouse ovaries.

first: Wenchao

last: Jia


title: Inflammatory Stimuli Trigger Genome-Wide Shifts in Gene Expression, Increased Androgen Production and Proliferation in Rat Theca-Interstitial Cells

city: La Jolla

first: Antoni

last: Duleba

address: 9500 Gilman Drive

department: Ob/Gyn

institute: University of California San Diego

summary: The goals of this study are to compare the in vitro theca-interstitial cell transcriptome profile (RNAseq) between cells cultured with pro-inflammatory IL-1ß or LPS and control media.

overall_design: Theca cells were isolated and treated with IL1ß, LPS, or control media for 48 hours using 4 replicates for each treatment condition. RNA was isolated and sequenced using Illumina HiSeq.

first: Chelsea

last: Fox

first: Abhishek

last: Sohni

first: Miles

last: Wilkinson

first: Lingzhi

last: Zhang


title: Expression data from CD98hc null and wild type fibroblasts derived from embryonic stem cells

city: Barcelona

first: Camille

last: Stephan Otto Attolini

state: Select a State or Province

address: Baldiri Reixac 10

department: Biostatistics and bioinformatics Unit

country: Spain

institute: IRB Barcelona

summary:
CD98 is a heterodimeric protein comprising heavy (CD98hc) and light chains (LAT1, LAT2, xCT, y+LAT1, y+LAT2 and asc1) that confer substrate specificity to the amino acid exchanger. CD98hc-associated transporters have two well stablished biochemical functions: They are able to promote integrin-dependent signals and also function as amino acid transporters. CD98hc is overexpressed in highly proliferative cells and its deletion causes strong impairment of cell proliferation in vivo and in vitro.
We used RNA array to identify possible alterations that could take place in cells surviving loss of CD98hc which could lead to differently expressed gene sets.

overall_design: CD98hc null and wild type fibroblasts derived from embryonic stem cells were cultured in supplemented complete DMEM high glucose medium at 37 °C and 5% v/v CO2 in a humidified incubator. Total RNA was extracted from cultured cells, converted to cDNA and hybridized on Affymetrix microarrays.

last: Stephan-Otto Attolini

first: Sara

last: Cano

first: Manuel

last: Palacin


title: Identification of the role of polydom in neurofibromas

city: Suita

first: Daisuke

last: Okuzaki

state: Osaka

address: Yamadaoka 3-1

department: Immunology Frontier Research Center

institute: Osaka univ.

summary: Dermal neurofibromas in von Recklinghausen's disease (vRD) develop in the dermis. Therefore, we hypothesized that a dermal niche exists that promotes the development of dermal neurofibromas in subjects with vRD. We focused on polydom, a ligand for integrin α9β1 and known as a factor expressed in the nerve tissue of mice and human breast cancer and lung cancer, which is expressed around nerve tissue. There were fewer polydom-positive fibroblasts in dermal tissue surrounding neurofibromas than in the dermis of normal skin. However, the expression level of polydom mRNA was significantly higher in neurofibroma tissue than control tissue. In addition, quantitative reverse transcription-polymerase chain reaction (qRT-PCR) analysis of RNA purified from primary cultured dermal neurofibroma cells demonstrated that polydom mRNA expression was significantly higher in cells derived from the matrix of raised-type neurofibromas compared to normal human dermal fibroblasts. To investigate the role of polydom, RNA sequencing was used to compare the gene expression between cultured cells derived from dermal neurofibroma surrounding tissue with and without polydom knockdown.

overall_design: We performed an RNA sequencing used to compare the gene expression between cultured cells derived from dermal neurofibroma surrounding tissue with and without polydom knockdown in triplicates.

first: Tomo

last: Kamitani

last: Motooka

first: Hiroyuki

last: Murota


title: Gene expression in the striatum of Nestin-Cre (Foxp1-/-) mice in comparison to WT animals at embryonic day (E)18.5

city: Heidelberg

first: Henning

last: Froehlich

address: Im Neuenheimer Feld 366

institute: Institute of Human Genetics

summary: To define the genes and pathways which are influenced by Foxp1 in the striatum at embryonic stage (E)18.5 we performed a microarray expression study comparing gene expression in striatal tissue from WT and Nestin-Cre (Foxp1-/-) animals.

overall_design: We analyzed striatal tissue from 6 WT and 6 Nestin-Cre (Foxp1-/-) animals.

last: Fröhlich

first: Gudrun

last: Rappold


title: Transcriptome analysis of Botrytis cinerea in response to tea tree oil and its two characteristic components

city: Ningbo,

first: ZHENBIAO

last: LI

state: Zhejiang

address: No.818 Fenghua Road

institute: Ningbo University

summary:
Purpose: High-throughput RNA sequencing has been used to examine mRNA expression profiles in fungal cells treated with essential oils. The goals of this study are to analyze the global gene expression profiles in Botrytis cinerea with or without tea tree oil and its two characteristic components treatment by RNA-Seq.
Methods: The mRNA profiles of Botrytis cinerea with or without tea tree oil and its two characteristic components treatment were generated by deep sequencing, in triplicate, using Illumina HiSeq™ 2500 sequencing platform. The sequence reads that passed quality filters were analyzed at the transcript isoform level with two methods: Burrows–Wheeler Aligner (BWA) followed by ANOVA (ANOVA) and TopHat followed by Cufflinks. qRT–PCR  was performed to verified the sensitivity of the RNA-seq method.
Results: After high-throughput RNA sequencing, reads were filtered to yield 111.22 Gb of clean sequence data. The GC content for all samples exceeded 45%. The Q20 ratio (used to evaluate reads quality) was greater than 94%, and Q30 base percentage was at least 87.07%. Altered expression of 7 genes was confirmed with qRT–PCR, demonstrating the high degree of sensitivity of the RNA-seq method. Most differentially expressed genes (DEGs) from B. cinera cells treated with terpinen-4-ol participated in biosynthesis of secondary metabolites, and the metabolism of amino acid, carbohydrate and lipid. 1,8-cineole mainly affected DEGs involved in genetic information processing, and thus inducing cell death.
Conclusions: Terpinen-4-ol exerts antifungal activity mainly by blocking the expression of genes related to cell integrity and mitochondrial function. 1,8-cineole primarily affects genes involved in genetic information processing including DNA replication, transcription and repair. This study provides insight into the molecular mechanism by which tea tree oil acts against Botrytis cinerea based on the data from RNA-seq.

first: Zhenbiao

last: Li

first: Yingying

last: Wei

first: Jiayu

last: Xu

first: Feng

first: Hongfei

last: Wang

first: Xingfeng

last: Shao


title: A complex interplay between nitric oxide, quorum sensing and a unique secondary metabolite tundrenone constitutes hypoxia response in Methylobacter

status: Public on Oct 01 2019

city: Seattle

first: Mitchell

middle: William

last: Pesesky

state: WA

address: 616 NE Northlake Place

institute: University of Washington

summary: Methylobacter species, members of the Methylococcales, have recently emerged as some of the globally widespread, cosmopolitan species, appearing to play a key role in consumption of methane in a variety of environments and across gradients of dioxygen tensions. We approached the question of how Methylobacter copes with low dioxygen partial pressures that it encounters in its natural habitats, via laboratory manipulation. Through comparative transcriptomics of cultures grown under high dioxygen partial pressure and cultures starved for dioxygen, we identified a gene cluster encoding a hybrid cluster protein along with sensing and regulatory functions. Through mutant analysis we demonstrated that this gene cluster is involved in both oxidative and nitrosative stress responses and in NO reduction, while being responsive to NO, likely through direct sensing. Through additional transcriptomic analyses, we further uncovered a complex interconnection between the NO-mediated stress response and quorum sensing in turn controlling synthesis of the secondary metabolite tundrenone, these two systems being inversely regulated. Some of the key methylotrophy functions, such as the two alternative methanol dehydrogenases seem to be parts of the stress response regulatory cascade. One intriguing scenario that emerged from our analyses is that the main role of the respiratory denitrification pathway may be in producing the signaling molecule, NO, in response to hypoxia, rather than in serving as an energy-generating pathway. This novel and complex hypoxia stress response system is unique to Methylobacter tundripaludum, and it may play a role in the environmental fitness of these organisms and in their cosmopolitan environmental distribution.

sample_organism:
Methylobacter tundripaludum 21/22
Methylobacter tundripaludum 31/32

overall_design: 10 samples from Methylobacter tundripaludum 31/32 and 6 from M. tundripaludum 21/22 were processed with biological duplicates across a variety of conditions. In 31/32 the wild-type sequence was grown with either nitrate or ammonia as the provided nitrogen sources (2 samples). Also in 31/32, the wild-type and a deletion mutant in hcp/hcr were grown with and without low dioxygen stress, and with either nitrate or ammonia as the added nitrogen source (8 samples). In 21/22, the wild type and two mutant strains (one in the quorum sensing systema and one in the production of tundrinone) and the wild type were each grown in nitrate or ammonia as the proviced nitrogen source (6 samples).

first: Zheng

last: Yu

first: Lei

last: Zheng

first: Jing

last: Huang

first: Mari

last: Winkler

first: Ludmila

last: Chistoserdova


title: Regulation of tumor angiogenesis and mesenchymal–endothelial transition by p38α through TGF-β and JNK signaling

first: Camille

last: Stephan Otto Attolini

summary: The formation of new blood vessels is essential for normal development, tissue repair and tumor growth. Here we show that inhibition of the kinase p38α enhances angiogenesis in human and mouse colon tumors. Mesenchymal cells can contribute to tumor angiogenesis by regulating proliferation and migration of endothelial cells. We show that p38α negatively regulates an angiogenic program in mesenchymal stem/stromal cells (MSCs), multipotent progenitors found in perivascular locations. This program includes the acquisition of an endothelial phenotype by MSCs mediated by both TGF-β and JNK, and negatively regulated by p38α. Abrogation of p38α in mesenchymal cells increases tumorigenesis, which correlates with enhanced angiogenesis. Using genetic models, we show that p38α regulates the acquisition of an endothelial-like phenotype by mesenchymal cells in colon tumors and damage tissue. Taken together, our results indicate that p38α in mesenchymal cells restrains a TGF-β-induced angiogenesis program including their ability to transdifferentiate into endothelial cells.

overall_design: WT and p38α-null MSCs stimulated with TGFβ.

first: Raquel

last: Batlle

last: Stephan-Otto Attolini

first: Antonio

last: Berenguer Llergo


title: Transcriptional profiling of neurons in the ventral striatum of a Stard5-TRAP (JX5852) mouse line

city: New York

first: Laura

last: Kus

state: NY

address: 1230 York Avenue # 260

department: Heintz Laboratory

institute: The Rockefeller University

summary: TRAP translational profiling is a method that allows investigators to genetically characterize specific cell types in complex tissues such as mouse brain.  Using this technique we obtained RNA-Seq data from actively translating transcripts present in neurons in the ventral striatum of adult Stard5-EGFP/Rpl10a (JX5852) mice.

overall_design: TRAP-Seq of neurons in the ventral striatum of adult Stard5-EGFP/Rpl10a (JX5852) control mice

first: Jie

last: Xing

first: Cuidong

first: Nathaniel

last: Heintz


title: SNHG12 knockdown in Human Umbilical Vein Cells under ROS conditions.

city: Boston

first: Stefan

last: Haemmig

state: MA

address: 77 Avenue Louis Pasteur, NRB-742

department: Medicine

institute: Brigham and Women Hospital / Harvard Medical School

summary: Study the role of the lncRNA SNHG12 in human endothelial cells towards DNA damage triggers.

overall_design: Examination of  lncRNA SNHG12 loss in  cultured human endothelial cells under intrinsic stimuli for DNA damage such as H2O2 after transient knockdown.

first: Mark

last: Feinberg


title: mRNA expression data from oral squamous cell carcinoma patients

city: Chang Sha

first: Hao

last: Pan

address: Xiangya NO.72

department: Department of Periodontics

institute: Xiangya Stomatological Hospital & School of Stomatology, Central South University

summary: Oral squamous cell carcinoma (OSCC) accounts for the high mortality rate and morbidity in head and neck cancer. Data for analysis were obtained from the microarray data of 6 OSCC tissues, tissues adjacent to cancer, and contralateral normal tissues.We used the affy package under the R environment to preprocess and normalize the original gene chip data.

overall_design: Data for analysis were obtained from the microarray data of 6 OSCC tissues, tissues adjacent to cancer, and contralateral normal tissues. We used the affy package under the R environment to preprocess and normalize the original gene chip data. Differentially expressed genes were obtained by pre-processing gene expression profile data to construct a weighted gene co-expression network and identify key gene modules.

first: Yuhong

last: Wang

first: Zhangui

last: Tang


title: Integrated Paired-end Enhancer Profiling and Whole-Genome Sequencing Reveals Recurrent CCNE1 and IGF2 Enhancer Hijacking in Primary Gastric Adenocarcinoma [CapStarr-seq]

first: Wen Fong

last: Ooi

address: 60 Biopolis

institute: Genome Institute of Singapore

summary: H3K27ac paired-end NanoChIP-seq, whole-genome sequecing, RNA-seq and Hi-C were integrated to reveal tumor-associated structural variants contributing to gastric cancer

overall_design: H3K27ac paired-end NanoChIP-seq were generated from primary GC and matched normal samples to discover regulatory structural variations that occurred at cis-regulatory elements marking by H3K27ac mark.

first: Kevin

last: Lim

first: Patrick

last: Tan


title: Dual RNA-seq analysis unveils Trichoderma NoxR as an essential mediator of the molecular dialogue during interaction with Arabidopsis

city: Irapuato

first: Manuel

last: Villalobos-Escobedo

state: Guanajuato

address: Km 9.6 Libramiento Norte Carretera Irapuato-León Irapuato

department: Ingeniera Genetica

country: Mexico

institute: cinvestav

summary: Trichoderma species promote growth and strengthen immunity of Arabidopsis and crop species through multiple mechanisms. However, how fungal proteins mediate growth-defense tradeoffs is unknown. We analyzed the growth, root architecture, defense and global gene expression profiles in Arabidopsis seedlings co-cultivated with T. atroviride WT, and Δnox1, Δnox2, and ΔnoxR mutants, defective on the catalytic and regulatory subunits of NADPH oxidase, respectively. The gene expression profile in the fungus was also characterized in standard growth conditions and in the presence of plants.  The results revealed the critical role of Trichoderma NoxR in mediating growth-defense tradeoffs in Arabidopsis. The effects of T. atroviride WT in improving root branching and biomass production decreased in all three related NADPH defective mutants, particularly in ΔnoxR. In contrast, induction of jasmonic acid-related defense responses in roots and shoots were exacerbated in ΔnoxR compared to the WT strain. Transcriptome analyses showed a tight plant-fungus communication based on reactive oxygen species and availability of carbon resources. The ΔnoxR is unable to perceive changes in nutrient sources and activate signaling cascades, which suppresses the metabolic change from saprophyte to commensal. Thus we conclude that Trichoderma NoxR orchestrates fungal-induced development and defense tradeoffs in Arabidopsis and plays an important role in cross-kingdom plant-fungus communication.

sample_organism:
Arabidopsis thaliana
Trichoderma atroviride

overall_design: Transcriptional profile of Trichoderma atroviride during insteraction with Arabidopsis thaliana.

first: José

first: Saraí

last: Esparza-Reynoso

first: Ramón

last: Pelagio-Flores

first: Fabiola

last: López-Ramírez

first: León

middle: F

last: Ruiz-Herrera

last: López-Bucio

first: Alfredo

last: Herrera-Estrella


title: The RNA helicase DDX6 regulates self-renewal and differentiation of human and mouse stem cells

first: Bruno

last: Di Stefano

address: 1 Baylor Plaza

institute: Baylor College of Medicine

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

overall_design: Refer to individual Series


title: Expression data from human esophageal cancer cells

city: Urumqi

first: Zhang

last: Zegao

state: Xinjiang

address: 91 Tianchi Route

department: the Second Department of Radiation Oncology

institute: People’s Hospital of Xinjiang Uyghur Autonomous Region

summary:
When esophageal cancer cells are exposed to a certain dose of radiation, a series of biological process changes, including DNA damage, DNA repair, apoptosis, cell cycle, repopulation, mitotic disasters, etc. These changes may determine the radiotherapy sensitivity to esophageal cancer, as well as recurrence and metastasis after radiotherapy.
To clarify the changes in gene expression in esophageal cancer after radiotherapy, we used gene expression microarrays to screen for significant up-regulation and down-regulation of genes and to analyze associations with these biological processes.

overall_design: Test groups(T) and Control groups(C) were selected for RNA extraction and hybridization on Affymetrix Clariom S Assay. Test groups(T):  2 flasks of cells were given a radiation dose of 18 Gy at 6 frequencies. Control groups(C): 2 flasks of cells were cultured normally.

first: Zegao

last: Zhang

first: Jie

last: Yang

first: Ruozheng


title: Analyzing the transcriptomic response of MCF7 breast cancer cells to NR1H4 agonist GW4064

city: Atlanta

first: Jonathan

last: Mitchel

state: GA

address: 315 Ferst Drive

department: School of Biological Sciences

institute: Georgia Institute of Technology

summary:
Computational analysis identified NR1H4 as an active nuclear receptor in a xenograft model of breast cancer. Since there is evidence that NR1H4 agonist, GW4064, reduces MCF7 cell proliferation, here, we wanted understand the transcriptional changes induced by activating this nuclear receptor.
We measured changes in gene expression due to GW4064-treatment and applied gene set enrichment analysis to further understand the perturbed molecular pathways.

overall_design: MCF7 cells were plated in 6 well plates at a seeding density of 400,000 cells per well. The cells were grown in serum-free media for 24 hours before treatment. Cells were treated with GW4064 at IC50 concentration (9 µM) or vehicle only for 24 hours and then were harvested for microarray analysis. Three biological replicates were included in both the test and control groups.

first: Lilya

last: Matyunina

first: Jeffrey

last: Skolnick

first: John

last: McDonald


title: Integrated Paired-end Enhancer Profiling and Whole-Genome Sequencing Reveals Recurrent CCNE1 and IGF2 Enhancer Hijacking in Primary Gastric Adenocarcinoma

city: Singapore

first: Wen Fong

last: Ooi


title: mRNA expression in SIDS

city: Oslo

first: Ståle

last: Nygård

address: Institute for Experimental Medical Research, Oslo University Hospital - Ulleval

country: Norway

institute: University of Oslo

summary: Genetic predispositions in cases suffering sudden unexpected infant death have been a research focus worldwide the last decade. Despite large efforts there is still uncertainty concerning the molecular pathogenesis of these deaths. With genetic technology in constant development the possibility of an alternative approach into this research field have become available, like mRNA expression studies.  Methods: In this study we investigated mRNA gene expression in 14 cases that died suddenly and unexpectedly from infection without a history of severe illness prior to death. The control group included eight accidents, two cases of natural death, one undetermined, one case of medical malpractice and two homicides. The study included tissue from liver, heart and brain. The mRNA expression was determined using Illumina whole genome gene expression DASL HT assay.  Results: From the array, 19 genes showed altered expression in the infectious deaths compared to controls. The heart was the organ were most genes showed altered expression: 15 genes showed different mRNA expression compared to the control group. Conclusion: Down-regulation of KCNE5 in heart tissue from cases of infectious death was of particular interest. Variants of KCNE5 are associated with Brugada syndrome KCNE5 gene is known to give increased risk of cardiac arrhythmia and sudden death, and could be responsible for the fatal outcome in the group of infectious death.

overall_design: The purpose of this study was to investigate gene expression in infection cases and controls, in order to uncover genes that are differentially expressed in the two groups. Tissue from brain, heart and liver from 10 infection cases and 10 controls were included in this study, and mRNA expression was determined using the Illumina whole genome gene expression DASL HT assay.  The cases diagnosed as infectious death died suddenly and unexpectedly, without a history of severe illness prior to death.

first: Linda

last: Ferrante

first: Torleiv

last: Rognum


title: Integrated Paired-end Enhancer Profiling and Whole-Genome Sequencing Reveals Recurrent CCNE1 and IGF2 Enhancer Hijacking in Primary Gastric Adenocarcinoma (ChIP-seq)

first: Ooi

last: Fong

first: Kevin

last: Lim

first: Patrick

last: Tan


title: Targeting Spt5-Pol II small-molecule inhibitors uncouple distinct activities and reveal additional regulatory roles

city: Rehovot

first: Dena

last: Leshkowitz

department: Bioinformatics Unit, Life Sciences Core Facilities

country: Israel

institute: Weizmann Institute of Science


title: Genome-wide view of the impact of Spt5-Pol II inhibitors (SPIs) on mRNA levels [RNA-Seq 24h]

summary: We identified the first Spt5-Pol II inhibitors (SPIs). SPIs faithfully reproduced Spt5 knockdown effects on proximal-promoter-pausing, NF-κB activation and the expanded-repeat huntingtin gene in neuronal cells. We determined the global effect of short and long-term SPI-21 treatment by RNA-seq and compared the affected genes between the two treatments. The results revealed that temporary and constitutive Spt5-regulated genes can be distinguished by SPIs.

overall_design: HeLa cells were treated for 24 hours with either DMSO or SPI-21 (50μM). Then total RNA was extracted and subjected to RNA-seq.

first: Rivka

last: Dikstein

first: Anat

last: Bahat


title: Expression data from splenic cDC1, cDC2, and pDC from WT and Bcl6cKO mice

city: St. Louis

first: Kenneth

last: Murphy

state: MO

address: Clinical Science Research Building, 7th Floor, Room 7701A, Campus Box 8118

department: Department of Pathology

institute: Washington University School of Medicine

summary: We used microarray gene analysis to compare the transcriptional profiles between WT and Bcl6cKO splenic cDC1, cDC2, and pDCs.

overall_design: Splenic cDC1, cDC2, and pDCs from WT and Bcl6cKO mice were sorted and analyzed for microarray gene analysis.

first: Prachi

last: Bagadia


title: Genome-wide view of the impact of Spt5-Pol II inhibitors (SPIs) on mRNA levels [RNA-Seq 2h]

overall_design: HeLa cells were treated for 2 hours with either DMSO or SPI-21 (50μM). Then total RNA was extracted and subjected to RNA-seq.

first: Michael

last: Gershovis


title: ETS family proteins bind glucocorticoid receptor: relevance for treatment of Ewing sarcoma

first: Ido

last: Amit

address: 234 Herzl st.

department: Immunology

summary: Differential expression of gene was analyzed after FLI1 silencing in Ewing Sarcoma cell line A673.

overall_design: Cells were transfected with either siRNA -scrambeled (si-con) or siRNA-FLI1 oligonucleotide in 3 replicate. 48 h later, RNA was isolated and processed for RNA-seq.

first: Swati

last: Srivastava

first: Arunachalam

last: Sekar

first: Chamutal

last: Bornstein

first: Eyal

last: David

first: Yosef

last: Yarden


title: tRNA pool analysis of S. cerevisiae lacking Paf1 and Rtf1 using tRNA-HySeq

city: New Delhi

first: G Aneeshkumar

last: Arimbasseri

state: Delhi

address: Aruna Asaf Ali Marg

department: Molecular Genetics Laboratory

country: India

institute: National Institute of Immunology

summary: tRNAs isolated from log phase yeast cells were hydrolyzed, followed by adapter ligation and sequencing.

overall_design: tRNA from wild type yeast and yeast lacking Paf1 or Rtf1

first: Purnima

last: Bhargava

first: G


title: Next Generation Sequencing Facilitates Quantitative Analysis of Wild Type and Tbx1-nmf219/nmf219 inner ear Transcriptomes

city: Bar Harbor

first: Ken

last: Johnson

state: ME

address: 600 Main Street

institute: The Jackson Laboratory

summary:
Purpose: The goal of this study is to compare the expression profile of wild type and Tbx1-nmf219/nmf219 mice with NGS-derived inner ear transcriptome profiling (RNA-seq)
Methods: inner ear mRNA profiles of E16.5 wild-type (WT) and Tbx1-nmf219/nmf219mice were generated by RNA-seq
Results: Using an optimized data analysis workflow, we mapped about 30 million sequence reads per sample to the mouse genome and identified  transcripts in the inner ear of WT and Tbx1nmf219/nmf219 mice. Approximately 10% of the transcripts showed differential expression between the WT and Tbx1nmf219/nmf219 inner ear, with a fold change ≥1.5 and p value <0.05.
Conclusions: Our study represents the detailed analysis of inner ear transcriptomes, with biologic replicates, generated by RNA-seq technology.

overall_design: Inner ear mRNA profiles of E16.5 wild type (WT) and Tbx1-nmf219/nmf219 mice were generated by deep sequencing

middle: R

first: Cong

last: Tian


title: Gene expression signature of endometrial samples from women with and without endometriosis.

city: Moscow

first: Daniil

last: Nikitin

address: Miklucho-Maklaya

institute: Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry

summary: Endometriosis is a benign gynecological disease characterized by the presence of endometrial-like cells outside the uterus. The prevalence of this disease reaches 10-15% in women of reproductive age which accounts for approximately 200 mln of women worldwide. The existing therapeutic approaches include medications and surgical options, but the risk of post-treatment recurrence of endometriosis remains high. There are currently no effective biomarkers of endometriosis in clinical practice and laparoscopy remains the gold standard for its diagnosis. However, laparoscopy is highly invasive procedure that frequently leads to complications and cannot be used as a routine screening test. In this study we profiled by RNA sequencing 52 endometrial pathological samples and 12 corresponding normal human tissues. We performed two-step differential gene expression analysis of endometrial samples and lesions of patients with endometriosis in comparison with normal reproductive tissues. Based on this analysis we generated a characteristic signature of five genes downregulated in endometriosis with respect to healthy endometrium. The 5-gene expression signature identified had significant predictive power (AUC>0.85) thus suggesting that the marker gene set identified can be used for a low invasive molecular diagnostic of endometriosis. Our data also suggest that the statistical method of five-fold cross validation of differential gene expression analysis procedure can be used for the ability to generate robust gene signatures using real-world clinical data.

overall_design:
Next generation sequencing of endometrial samples and lesions of patients with endometriosis in comparison with normal reproductive tissues (healthy endometrium, ovary and cervix)
Please note that the normal Ovary (GSM3415785, GSM3415786, GSM3415852, GSM3415878) Cervix (GSM3415783, GSM3415784, GSM3415872, GSM3415855) data is available in GSE120795.

first: Aznaurova

last: Yana

first: Nikitin

last: Daniil

first: Garazha

last: Andrew

first: Suntsova

last: Maria

first: Sorokin

last: Maxim

first: Buzdin

last: Anton


title: Gene expression profile during odontogenic differentiation was analyzed using a microarray (miRNA).

city: Guangzhou

first: Zhao

last: Chen

state: Guangdong

address: Department of Stomatology, Nanfang Hospital, Southern Medical University, Guangzhou, Guangdong, P.R. China

department: Department of Stomatology

summary: The roles of microRNAs (miRNAs) in odontogenic differentiation of human dental pulp stem cells (hDPSCs) remain largely unexplored. In this study, the underlying molecular mechanism of osteogenic differentiation in hDPSCs is investigated using miRNA profifiling.

overall_design: Gene expression of hDPSCs at differentiated group were cultured with an odontogenic differentiation medium containing 50 mg/ml ascorbic acid, 100 nmol/L dexamethasone, and 10 mmol/L β-glycerolphosphate (Sigma, St Louis, MO, USA) for 14 days in 6-well plates. hDPSCs at undifferentiated group were cultured in 10 % FBS in DMEM with no supplements.

first: Fuchun

last: Fang


title: Combinatorial effect of ARTP mutagenesis and ribosome engineering on an industrial Streptomyces albus strain S12 for enhanced biosynthesis of salinomycin

city: Shanghai

first: Kuipu

last: Zhang

address: 130  Meilong Rd.

department: State  Key  Laboratory  of  Bioreactor  Engineering

institute: East  China  University  of  Science and Technology

summary: Streptomyces albus S12, TK and Tet30Chl25  are the parental strain , low-yield and high-yield of salinomycin mutant obtained by ARTP and ribosome engineering ,respectively. There are total 1602 differentially expressed genes (DEGs) show differences in expression between the mutant strain TK, Tet30Chl25 and the initial strain S12. KEGG pathway analysis of differentially expressed genes (DEGs) between the mutant strain TK, Tet30Chl25 and the initial strain S12 show that the relevant differential pathways affecting salinomycin production were mainly related to butanoate metabolism, starch and sucrose metabolism, glyoxylate metabolism. Besides , the transcription of genes in the salinomycin biosynthesis gene cluster and the transcription level of related genes in the precursors biosynthesis pathway were more active in the high-yield salinomycin production strain Tet30Chl25.  Furthermore, the transcription level ribosomal protein, string response, two component system and sigma factors are more active in high-yield of salinomycin mutants and that may involve in regulation  of salinomycin biosynthesis and may account for the high-yield of salinomycin.

overall_design: Expression profiles from Smutant TK, Tet30Chl25 and the parental strain strain were obtained by an Illumina HiSeq™2000 sequencing machine from samples taken at five day points in fermentation medium (0.8% germ powder, 0.5% soybean powder, 0.2% potassium chloride, 0.10% sodium chloride, 0.16% urea, 0.2% tartaric acid, 0.01% magnesium sulfate, 0.01% dibasic potassium phosphate, 0.5% calcium carbonate, 15% soybean oil, pH 6.6–6.9).

first: Ali

last: Mohsin

first: Yichen

last: Dai

first: Zhongbin

first: Yingping

last: Zhuang

first: Ju

last: Chu

first: Meijin

last: Guo


title: Analysis of gene expression in MEL cell before and after erythroid-like differentiation.

city: Hangzhou

first: Caiyong

address: 866 Yuhangtang Road

institute: Zhejiang University

summary: To promote the development and understanding of the in vitro erythroleukemia model, we analyzed the transcriptomes of mouse erythroleukemia (MEL) cells prior to and after erythroid-like differentiation induced by dimethyl sulfoxide (DMSO). A total of 348 protein-coding genes, including many known erythroid-enriched genes such as hemoglobin and heme synthesis genes, were upregulated upon erythroid-like induction in MEL cells

overall_design: The mRNA profiles of uninduced and DMSO-induced MEL cells were generated by deep sequencing, in duplicate, using Illumina HiSeq platform.


title: Altering sphingolipid metabolism attenuates cell death and inflammatory response after myocardial infarction

city: new york

first: Lior

last: Zangi

state: New York

address: 1470 Madison av

department: cardiovascular research center

institute: Icahn School of Medicine at Mount Sinai

summary: We performed transcriptomic analyses to evaluate changes in gene expression post MI. We investigated the effect of ACmodRNA function post MI. We found that several genes involved in de novo ceramide synthesis were upregulated. ACmodRNA treatment increased cell survival postMI. AC modRNA-treated mice had significantly better heart function, long term survival and smaller scar size than control mice 28 days post MI.

overall_design: mRNA profile of miouse heart tissu befor and after MI with or without AC modRNA treatmant.

first: Yoav

last: Hadas

first: Adam

last: Vincek

first: Elias

last: Youssef

first: Magdalena

middle: M

last: Żak

first: Elena

last: Chepurko

first: Nishat

last: Sultana

first: Mohammad

last: KSharkar

first: Ningning

first: Rinat

last: Komargodski

first: Ann

last: Kurian

first: Keerat

last: Kaur

first: Anthony

last: Fargnoli

first: Michael

last: Katz

first: Nadia

last: Hossain

first: Ephraim

last: Kenigsberg

first: Nicole

middle: C

last: Dubois

first: Eric

last: Schadt

first: Roger

last: Hajjar

first: Efrat

last: Eliyahu


title: RNase H dependent Antisense oligonucleotides in the nucleus causes transcription termination

city: Carlsbad

first: Sagar

middle: S

last: Damle

state: CA

address: 2855 Gazelle Ct

department: Functional Genomics

institute: Ionis Pharmaceuticals

summary: The aim of this study is to characterize Rnase H ASO mediated transcription events on chromatin.

overall_design:
chromatin associated RNA sequencing (chrRNA-seq): chromatin fraction were isolated from MHT cells after 24 hrs ASO free uptake. 14 different gapmer ASOs treatments targeting on 2 genes and 6 different controls were conducted for sequencing.
Precision nuclear run-on sequencing (PRO-seq): biotin labelled substrates were applied after ASO treatments.  6 different ASO treatments and 3 controls were applied for PRO-seq.

first: Fan

last: Lai


title: Filamentation is Associated with Reduced Pathogenicity of Multiple Non-albicans Candida Species

city: San Antonio

first: Yidong

last: Chen

state: Texas

address: 8403 Floyd Curl Drive, MSC 7784

department: Population Health Sciences

institute: UT Health Science Center at San Antonio

summary: Candidiasis affects a wide variety of immunocompromised individuals, including HIV/AIDS patients and cancer patients on chemotherapy. Candida albicans, a major human fungal pathogen, accounts for about 50% of all cases, while the remainder are caused by the less pathogenic non-albicans Candida species (NACS). These species are believed to be less pathogenic, in part, because they do not filament as readily or robustly as C. albicans, although definitive evidence is lacking.  To address this question, we used strains for two NACS, Candida tropicalis and Candida parapsilosis, that are genetically engineered to constitutively express the key transcriptional regulator UME6 and drive strong filamentation both in vitro and during infection in vivo. Unexpectedly, both strains showed a dramatic reduction in organ fungal burden and clearance of infection in response to UME6 expression. Consistent with these findings, we observed that a C. tropicalis hyperfilamentous mutant was significantly reduced and a filamentation-defective mutant was slightly increased for organ fungal burden. Comprehensive immune profiling did not reveal any significant changes in the host immune response to UME6 expression in the NACS.  Interestingly, however, whole-genome transcriptional profiling indicated that while genes important for filamentation were induced by UME6 expression in C. tropicalis and C. parapsilosis, other genes involved in a variety of processes important for pathogenesis were strongly down-regulated. Our findings are significant because they suggest fundamental evolutionary differences in the relationship between morphology and pathogenicity among Candida species and that NACS do not necessarily possess the same virulence properties as C. albicans.

sample_organism:
Candida parapsilosis
Candida tropicalis

platform_organism:
Candida parapsilosis
Candida tropicalis

overall_design: Examination of gene expression in 2 strains under 2 conditions  (presence and absence of doxycycline (Dox)) for 2 Candida species. There are two biological replicates for each strain grown under each condition (16 samples total).

first: David

last: Kadosh


title: The function of the Hedgehog signaling pathway in colonic adenomagenesis

city: Amsterdam

first: Barbara

middle: Florien

last: Westendorp

state: Noord-Holland

address: Meibergdreef 69-71

department: Tytgat Institute for Liver and Intestinal Research

institute: Academic Medical Center

summary:
The morphogen Indian Hedgehog plays a very important role during intestinal embryogenesis, but also maintains homeostasis in the adult gut. Intestinal Hedgehog is expressed by the intestinal epithelium and signals in paracrine manner
to fibroblasts in the stromal compartment. We studied the stromal changes upon simultaneous homozygous deletion of Ihh and the tumor-suppressor gene Apc in the colon.

overall_design: Epcam-CD45-CD31-gp38+ fibroblasts were isolated from induced VillinCre-ERT2-ZsGreen-IhhKO-ApcKO mice and RNA was isolated.

first: B

first: G

last: van den Brink


title: Gene expression profile during odontogenic differentiation was analyzed using a microarray (lncRNA).

first: Zhao

institute: Nanfang Hospital, Southern Medical University

summary: The roles of lncRNAs and mRNAs in odontogenic differentiation of human dental pulp stem cells (hDPSCs) remain largely unexplored. In this study, the underlying molecular mechanism of osteogenic differentiation in hDPSCs is investigated using miRNA profifiling.

first: Fuchun

last: Fang


title: A multi-omics analysis of the grapevine pathogen Lasiodiplodia theobromae reveals that temperature affects the expression of virulence- and pathogenicity-related genes

city: Gent

first: Laurentijn

last: Tilleman

address: Ottergemsesteenweg 460

institute: Ghent University

summary: A multi-omics approach was used to understand how temperature affects the molecular mechanisms of pathogenicity of Lasiodiplodia theobromae at different temperatures. The transcriptome (Illumina TruSeq) of LA-SOL3 strain grown at 25 °C and 37 °C was analysed.

overall_design: For RNA extraction, LA-SOL3 was inoculated into a 250 mL flask containing 50 mL of PDB and incubated at 25 °C or at 37 °C for 4 days. The transcriptome of LA-SOL3 was sequenced by Illumina TruSeq to characterise the differential expression at both temperatures.

first: Carina

last: Félix

first: Rodrigo

last: Meneses

first: Micael

last: Gonçalves

first: Ana

last: Duarte

first: Jesus

middle: V

last: Jorrín-Novo

first: Yves

last: Peer

first: Dieter

last: Deforce

first: Filip

last: Nieuwerburgh

last: Esteves

first: Artur

last: Alves


title: Human ANGIOGENIN is sufficient but not required for tRNA cleavage to generate tRNA fragments

city: Charlottesville

first: Anindya

last: Dutta

state: VA

address: 1340 Jefferson Park Ave

department: Department of Biochemistry and Molecular Genetics

institute: University of Virginia

summary: To identify tRNA fragments regulated by angiogenin (ANG, Rnase 5), we sequenced 15-50nt small RNAs upon ANG overexpression and ANG knockout.

first: Zhangli

last: Su


title: Hydrogen metabolism influences glycogen production in a verrucomicrobial methanotroph

city: Christchurch

first: Carlo

middle: Robert

last: Carere

address: University of Canterbury, Private Bag 4800,, Deliver to Carlo Carere, Link Building, room A311

department: Chemical and Process Engineering

country: New Zealand

institute: University of Canterbury

summary: Metabolic flexibility in aerobic methane oxidising bacteria (methanotrophs) enhances cell growth and survival in instances where resources are variable or limiting. Examples include the production of intracellular compounds (such as glycogen or polyhydroxyalkanoates) in response to unbalanced growth conditions and the use of some energy substrates, besides methane, when available. Indeed, recent studies show that verrucomicrobial methanotrophs can grow mixotrophically through oxidation of hydrogen and methane gases via respiratory membrane-bound group 1d [NiFe] hydrogenases and methane monooxygenases respectively. Hydrogen metabolism is particularly important for adaptation to methane and oxygen limitation, suggesting this metabolic flexibility may confer growth and survival advantages. In this work, we provide evidence that, in adopting a mixotrophic growth strategy, the thermoacidophilic methanotroph, Methylacidiphilum sp. RTK17.1 changes its growth rate, biomass yields and the production of intracellular glycogen reservoirs. Under nitrogen-fixing conditions, removal of hydrogen from the feed-gas resulted in a 14 % reduction in observed growth rates and a 144% increase in cellular glycogen content. Concomitant with increases in glycogen content, the total protein content of biomass decreased following the removal of hydrogen. Transcriptome analysis of Methylacidiphilum sp. RTK17.1 revealed a 3.5-fold upregulation of the Group 1d [NiFe] hydrogenase in response to oxygen limitation and a 4-fold upregulation of nitrogenase encoding genes (nifHDKENX) in response to nitrogen limitation. Genes associated with glycogen synthesis and degradation were expressed constitutively and did not display evidence of transcriptional regulation. Collectively these data further challenge the belief that hydrogen metabolism in methanotrophic bacteria is primarily associated with energy conservation during nitrogen fixation and suggests its utilisation provides a competitive growth advantage within hypoxic habitats.

overall_design: Chemostat cell samples (5 total) of Methylacidiphilum sp. RTK17,1 were grown methanotrophically under oxygen excess and oxygen limiting conditions in the presence of NH4+ or N2 as a usable nitrogen source with or without hydrogen gas supplementation into the feedgas

first: Ben

last: McDonald

first: Hanna

middle: A

last: Peach

first: Chris

last: Greening

first: Daniel

middle: J

last: Gapes

first: Christophe

last: Collet

first: Matthew

middle: B

last: Stott


title: Genome-wide DNA methylation profile analysis of human intervertebral disc degeneration

city: Tsu

first: Akihiro

last: Ikuno

state: Mie

address: 1577 Kurimamachiyacho

department: Bioresources

institute: Mie University

type: Methylation profiling by genome tiling array

summary: The pathophysiology of intervertebral disc (IVD) degeneration is not entirely understood; however, environmental and endogenous factors under genetic predisposition are considered to initiate the degenerative changes of human IVDs. Aberrant epigenetic alterations play a pivotal role in several diseases, including osteoarthritis. However, epigenetic alternations, including DNA methylation, in IVD degeneration have not been evaluated. The purpose of this study was to comprehensively compare the genome-wide DNA methylation profiles of human IVD tissues, specifically nucleus pulpous (NP) tissues, with early and advanced stages of disc degeneration. We conducted, for the first time, a genome-wide DNA methylation profile comparative study and observed significant differences in DNA methylation profiles between early and advanced stages of human IVD degeneration.  The overview of the DNA methylation profile in the current study revealed that differentially methylated loci were identified in many genes associated with known molecules that have been reported to be relevant to IVD degeneration. Importantly, changes in DNA methylation profiles were also found in genes that regulate the major signaling pathways, such as NF-κB, MAPK, and Wnt signaling, that are well known to be responsible for the pathogenesis of human disc degeneration.

overall_design: Human NP tissues obtained from spine surgeries were used in this study. The samples were divided into two groups: early stage degeneration (n=8, Pfirrmann’s MRI grade: I-III) and advanced stage degeneration (n=8, grade: IV). Genomic DNA was processed for genome-wide DNA methylation profiling using the Infinium MethylationEPIC BeadChip array ( Illumina, San Diego, CA, USA).  Raw IDAT files were processed using Methylation module (Version 1.90) in GenomeStudio software (V2011.1, Illumina) or the ChAMP package in R 3.4.3.

first: Koji

last: Akeda

first: Shin-ichiro

last: Takebayashi

first: Motomu

last: Shimaoka

first: Katsuzumi

last: Okumura

last: Sudo


title: Therapeutic benefit of rapamycin combined with clorgyline or rasagiline in an immunodeficient LAM model

city: Barcelona

first: Miguel Angel

last: Pujana

address: Gran Via 199

institute: Institut Catala d'Oncologia IDIBELL

summary: Inhibition of mechanistic target of rapamycin (mTOR) constitutes the standard of care of lymphangioleiomyomatosis (LAM). However, this treatment does not eradicate diseased cells and some patients show progressive decline of lung function. This study provides preclinical evidence for beneficial therapeutic approaches in combination with rapamycin. LAM tumorigenesis is reduced in vivo (ELT3-V3 tumor xenografts) using approved drugs for other human diseases and targeting monoamine oxidase A (MAO-A; clorgyline) or MAO-B (rasagiline).

overall_design: Six-week-old female NOD-scid mice were inoculated subcutaneously with ELT3-V3 cells (2×106 cells per injection/site/mouse), and when tumors reached 150-200 mmm3 randomized to control and treatment groups. RNA sequencing of control (n=2; 0.2% carboxymethylcellulose and 0.25% Tween-80), rapamycin (n=2; 0.25 mg/kg/day), rapamycin plus clorgyline (n=2; clorgyline 10 mg/kg/day), and rapamycin plus rasagiline (n=2; rasagiline 1 mg/kg/day). Total of eight tumors analyzed.

first: Miquel


title: RNAseq of Zcchc8 mutant mouse embryonic heads

city: Baltimore

first: Mary

last: Armanios

state: MD

address: 401 North Broadway

department: School of Medicine

institute: The Johns Hopkins University

summary: We identified a germline heterozygous loss-of-function mutation in ZCCHC8, an RNA exosome targeting component, in a family with autosomal dominant pulmonary fibrosis and telomerase RNA insufficiency. To understand the in vivo consequences of Zcchc8 loss, we targeted the gene locus. Zccchc8+/- showed no significant phenotypes but Zcchc8-/- mice showed severe neurodevelopmental defects and died early in adulthood by 60 days. To understand the causes underlying this neurodevelopmental defect, we performed RNAseq on embryonic mouse heads (including the brain). We found no significant changes in gene expression in Zcchc8+/- relative to Zcchc8+/+ embryos. In contrast, Zcchc8-/- mice had a skewed signature marked by upregulation of low abundant transcripts and short, single exon genes including replication-dependent histones. These genes, like telomerase RNA, had extended 3' ends consistent with ZCCHC8 playing a role in both telomerase RNA as well as histone gene post-transcriptional processing.

overall_design: We performed RNAseq on heads (including brains) of embryos with these genotypes: Zcchc8+/+ (n=5), Zcchc8+/- (n=3) and Zcchc8-/- (n=6) that were harvested on day E12.5.

first: Conover

last: Talbot Jr


title: Genome-wide view of the impact of Spt5-Pol II inhibitors (SPIs) on transcription [4sU-seq]

city: Rehovot

first: Dena

last: Leshkowitz

institute: Weizmann Institute of Science

summary: We identified the first Spt5-Pol II inhibitors (SPIs). SPIs faithfully reproduced Spt5 knockdown effects on proximal-promoter-pausing, NF-κB activation and the expanded-repeat huntingtin gene in neuronal cells. Using SPIs we identified Spt5 target genes that responded with profoundly diverse kinetics and a novel regulatory element of proximal-promoter-pausing. To validate that the effects of SPIs are at the transcriptional level, cellular RNA was metabolically labeled with 4-thio-uridine (4sU) for 2 hours in the presence of DMSO or SPI-21 in the presence or absence of TNFα. Newly synthesized labeled RNA was then purified and subjected to RNA-seq.

overall_design: Cellular RNA was metabolically labeled with 4-thio-uridine (4sU) for 2 hours in the presence of DMSO or SPI-21, in the presence or absence of TNFα.

first: Rivka

last: Dikstein

first: Anat

last: Bahat


title: Genome-wide view of the impact of Spt5-Pol II inhibitors (SPIs) on transcription [GRO-Seq]

summary: We identified the first Spt5-Pol II inhibitors (SPIs). SPIs faithfully reproduced Spt5 knockdown effects on proximal-promoter-pausing, NF-κB activation and the expanded-repeat huntingtin gene in neuronal cells. Using SPIs we identified Spt5 target genes that responded with profoundly diverse kinetics and a novel regulatory element of proximal-promoter-pausing. To obtain a genome-wide view of the impact of SPIs on transcription, we performed Global run-on sequencing (GRO-seq) using nuclei of HeLa cells treated with either DMSO (control) or SPI-21.

overall_design: Nuclei were isolated from HeLa cells pre-treated with either DMSO (control) or SPI-21 (50μM) for 1.5 hours


title: ELF4 is a target of miR-124 and promotes neuroblastoma proliferation and undifferentiated state

city: Austin

first: Vishy

last: Iyer

state: TX

address: 2500 Speedway Dr. MBB 3.212

department: Molecular Biosciences

institute: University of Texas at Austin

summary: We performed RNA-seq to identify the transcriptional targets of ELF4 in BE-(2)-C neuroblastoma cells.

overall_design: BE-(2)-C cells were treated in triplicates with either siControl or siELF4. 48 hours later, RNA was isolated and analyzed by RNA-seq.

first: Adam

last: Kosti

first: Haridha

last: Shivram

first: Luiz

last: Penalva


title: Comparison of the PU.1 interactome and transcriptome in human and mouse dendritic cells

city: Oviedo

first: Laura

last: Gutiérrez

state: Asturias

address: Avenida de Roma S/N

department: Medicine

institute: ISPA - University of Oviedo

summary: We have obtained data of the PU1-DNA binding locations in human and mouse inflammatory DC generated in vitro, with or without a TLR4 agonist stimulation.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: Biological replicates of human monocyte derived or mouse bone marrow derived inflammatory DC were cultured for 7 days, stimulated or not with LPS and collected at day 10. PU.1 ChIP Seq followed by High Throughput Sequecing was performed.

first: Maaike

last: Scheenstra

first: Pieter

last: de Bleser

first: Benjamin

last: Nota

first: Iris

last: De Cuyper

first: Petros

last: Papadopoulos

first: Vishal

last: Shalunke

first: Andrea

last: Woltman

first: Lianne

last: van de Laar

first: Wilfred

last: van Ijcken

first: Jeroen

last: Demmers

first: Erikjan

last: Rijkers

first: Sjaak

last: Philipsen

first: Timo

last: van den Berg

first: Taco

last: Kuijpers


title: Systemic effects of the long noncoding RNA COSMOC in autism spectrum disorders

city: Marseille

first: Madeleine

last: Erard-Garcia

address: 51 Blvd Pierre Dramard

institute: 1UMR 7051, INP, CNRS and Aix-Marseille University

summary: Autism Spectrum Disorders are complex neurodevelopmental disorders often attributed to specific mutated genes that collectively affect less than 10% of autists. We recently identified MOCOS, a molybdenum cofactor sulfurase-coding gene that was downregulated in stem cells of most autists of a cohort, disturbing redox homeostasis and synaptogenesis. We now report that, upstream of MOCOS, a divergent transcription generates an antisense long noncoding RNA called COSMOC. Remarkably, COSMOC expression is very low in all patients of this cohort. Knockdown studies indicates that loss of COSMOC reduces MOCOS expression, destabilizes lipid metabolism and affects energy metabolism of stem cells. Moreover, COSMOC deficiency is associated with defective neuronal maturation through the splicing regulator PTBP2 and the postsynaptic scaffold protein PSD95 involved in synaptic transmission. This dysregulation of COSMOC/MOCOS bidirectional unit might explain the origin of the disease for most autists

overall_design: Transcriptome analysis of two different primary cultures of human olfactory stem cells (OSC) isolated from two healthy individuals (C1 and C2) by microarray. Stem cells (used at a low passage number) were treated for 48 hours with siRNA against the lncRNA COSMOC and compared to controls. Samples include 8 OSC samples representing 4 groups with two replicates each.

first: Pauline

last: Rontani

first: Olivier

last: Perche

first: Louise

last: Greetham

first: Nicolas

last: Jullien

first: François

last: Erard

first: Valerie

last: Quesniaux

first: Bernhard

last: Ryffel

first: Emmanuel

last: Nivet


title: Inhibition of super enhancer downregulates the expression of KLF5 in basal-like breast cancers

city: Xiamen

first: Jiancheng

last: Ding

state: Fujian

address: School of Pharmaceutical Sciences, Xiamen University Xiang`an South Road

institute: Xiamen University

summary: The transcription factor KLF5 is highly expressed in basal-like breast cancer (BLBC). It promotes cell proliferation, survival, migration and stemness and serves as a potential therapeutic target. In this study, we first identified a super-enhancer (SE) located downstream of the KLF5 gene in BLBC. JQ-1, a BRD4-bromodomain inhibitor, inhibits the expression and activity of KLF5 in the HCC1806 and HCC1937 cell lines in time- and dose-dependent manners. A new BRD4 inhibitor, compound 870, is more potent than JQ-1 in terms of its ability to inhibit KLF5 and BLBC growth by inducing G1 phase cell cycle arrest. Additionally, a CDK7 inhibitor, THZ1, also inhibits KLF5 and BLBC growth. Our findings suggested that SE regulates KLF5 and that SE inhibitors could be an effective therapeutic strategy for treating BLBC.

overall_design: ChIP-seq performed in this study was designed to detect the signal of BRD4 and H3K27Ac around KLF5 gene

first: Ceshi

last: Chen

first: Wen

last: Liu

first: Chuanhuizi

first: Wenjuan

last: Zhang


title: SREBP2(N) Overexpression in Human Umbilical Vein Endothelial Cells

city: La Jolla

first: John

last: Shyy

state: California

address: 9500 Gilman Dr., BRF2 Rm 1217 Bay LL

institute: University of California, San Diego

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

overall_design: Refer to individual Series