title: Effect of CVX-060 treatment on hepatic gene expression of cirrhotic rats

city: Belvaux

first: Gaia

last: Zaffaroni

address: avenue du Swing, 6

country: Luxembourg

institute: Luxembourg Centre for Systems Biomedicine

summary: Currently, the therapeutic prospects for cirrhosis patients are limited to liver transplantation and, therefore, there is an urgent need to develop new therapeutic strategies for improved treatments. Cirrhosis was induced in male Wistar rats with CCl4 treatment, and RNA from the complete livers was extracted and quantified through microarray experiments. Angiopoietins signalling is a key pathway in blood vessel normalization. Angiopoietin 1 (Ang1)-Tie2 signalling stabilizes blood vessels, Angiopoietin 2 (Ang2) on the other hand is a context-dependent antagonist of Ang1 and decreases its stabilizing effect giving rise to immature blood vessels. Cirrhotic conditions are characterized by higher expression and activity of Ang2 than healthy conditions, resulting in the loss of blood vessels stability. Previous work showed that inhibition of Ang2 via CVX-060 enhances Ang1-Tie2 signalling, and can stabilize the vascular system in cirrhotic livers. We therefore performed RNA extraction after treatment of cirrhotic rats with CVX-060 during 4 weeks. We observed changes in expression state (expressed/not expressed) in key transcription factors previously implicated in cirrhosis.

overall_design: To induce cirrhosis, male Wistar rats were exposed to inhalation of CCl4, as previously described. Five cirrhotic rats were treated once a week with 10 mg/kg of CVX-060 (Pfizer, Inc., New York, NY, USA) for 4 weeks. CVX-060 was diluted in 500 l of saline solution and injected intravenously via the tail vein. In parallel, another group of cirrhotic rats (n=5) was injected with vehicle, as a treatment control. Gene expression in CCl4 and CCl4+CVX-060 treated livers was quantified using Affymetrix GeneChip Rat Genome 230.2 Array. The protocols comply with the criteria of the investigation and ethics committee of the Hospital Clínic Universitari and the University of Barcelona.

first: Satoshi

last: Okawa

first: Manuel

last: Morales-Ruiz

first: Antonio

last: del Sol


title: Genetic markers for temperature-sensitive neurons in mouse preoptic area

status: Public on Mar 23 2019

city: San Francisco

first: Lily

middle: Y

last: Jan

state: CA

address: 1550 4th Street, Room RH-484A

department: Physiology

country: USA

institute: UCSF

type: Expression profiling by high throughput sequencing

summary: This study combined single-cell RNA-seq with whole-cell patch-clamp recording to profile the neurons in mouse preoptic area with characterized temperature-sensitivity

overall_design: The temperature-sensitivity of 96 neurons in mouse preoptic area was characterized with whole-cell patch-clamp recording in freshly prepared brain slices, following which, the cell samples were harvested and subjected to single-cell RNA seq with an established protcol, Smart-seq2.

first: Tongfei

middle: A

last: Wang


title: Transcriptome analysis of Bacillus cereus strain F837/76 in response to porcine gastric mucin, accomplished by RNA sequencing

status: Public on Mar 25 2019

city: Oberschleißheim

first: Nadja

last: Jessberger

address: Schönleutnerstr. 8

department: Department of Veterinary Sciences, Faculty of Veterinary Medicine

country: Germany

institute: Ludwig-Maximilians-Universität München

summary: In the intestine, B. cereus comes in contact with the epithelial mucus layer. To investigate the overall response to that contact, total transcriptome analyses were performed using porcine gastric mucin (PGM), which is a commonly applied model for mucus interactions. Differential regulation of genes encoding enterotoxins and further virulence factors was of special interest.

overall_design: Reference strain F837/76 (=MHI 1505) was grown in triplicates in 50 ml mMOD minimal medium +/- 0.25 % PGM. Initial OD600 was 0.05. After 3 h, 10 ml samples were taken for total RNA preparation.

first: Erwin

last: Märtlbauer


title: Murine Marfan Syndrome Sildenafil Treatment

status: Public on Mar 19 2019

city: Hamilton

first: Nadia

last: Milad

state: Ontario

address: 1280 Main St W

country: Canada

institute: McMaster University

summary: Marfan syndrome (MFS) is a connective tissue disorder caused by mutations in the fibrillin-1 (Fbn1) gene. While aortic rupture is the major cause of mortality in MFS, patients also suffer from poorly understood pulmonary complications. Loss of basal nitric oxide (NO) production and vascular integrity are proposed to take part in MFS aortic root disease, yet their contribution to lung complications has yet to be determined. Due to its capacity to potentiate the vasodilatory NO/cyclic guanylate monophosphate signaling pathway, we assessed whether the phosphodiesterase-5 (PDE5) inhibitor sildenafil (SIL) could attenuate aortic root remodelling and emphysema in a mouse model of MFS. Despite increasing NO-dependent vasodilation, SIL unexpectedly elevated mean arterial blood pressure, failed to inhibit MFS aortic root dilation and exacerbated elastic fibrefiber fragmentation. In the lung, early pulmonary artery dilation observed in untreated MFS mice was delayed by SIL treatment, and severe emphysema-like alveolar destruction was prevented. In addition, improvements in select parameters of lung function were documented. Subsequent micro-array analyses showed changes to gene signatures involved in the inflammatory response in MFS lung treated with SIL, without significant downregulation of connective tissue or TGF-β signalling genes. Since PDE5 inhibition leads to improved lung histopathology and function, the effects of SIL against emphysema warrant further investigation in the settings of MFS despite limited efficacy on aortic root remodelling.

overall_design: n=6 per group, 4 groups, WT-Veh = wild-type vehicle treated controls, WT-SIL = wild-type sildenafil treated, MFS-Veh = Marfan mice vehicle treated, MFS-SIL = Marfan mice sildenafil treated

first: Zoe

last: White


title: Endogenous glucocorticoids suppress spontaneous gastric inflammation and spasmolytic polypeptide expressing metaplasia

status: Public on Mar 20 2019

city: Research Triangle Part

first: Jonathan

middle: T

last: Busada

state: NC

address: 111 TW Alexandar Drive

institute: NIEHS

summary: Adrenalectomy induced severe eosinophil and macrophage infiltration localized to the gastric corpus resulting in development of spasmolytic polypeptide expressing metaplasia (SPEM) and oxyntic atrophy. RNA sequencing analysis revealed significant upregulation of proinflammatory genes 3 days post-adrenalectomy, prior to leukocyte infiltration and histopathological changes.

overall_design: Examination of transcriptome under two different conditions (3day sham vs. 3day adrenalectomy)

first: Sivapryia

last: Ramamoorthy

first: Derek

middle: W

last: Cain

first: Xiaojiang

last: Xu

first: Donald

middle: N

last: Cook

first: John

last: Cidlowski


title: Gene expression profile in patients inoculated with Escherichia coli 83972

city: Lund

first: Ines

last: Ambite

address: Klinikgatan 28

department: Laboratory Medicine

country: Sweden

institute: Lund University

summary: Mucosal surfaces provide ideal living conditions for the normal flora but paradoxically, they also serve as attack sites for numerous bacterial pathogens that cause extensive morbidity and mortality. Understanding this dichotomy is critical for efforts to selectively target and remove pathogens without disturbing the commensal flora or its protective effects. The complex nature of disease predicts that virulence is multifaceted and that pathogens need multiple virulence factors to initiate tissue attack, disrupt immune homeostasis and create symptoms and pathology. The urinary tract supports ABU; a commensal-like state, which has been shown to prevent super-infection with more virulent strains. To reproduce this protective effect, we have established a protocol to create ABU, by inoculation with the ABU strain E. coli 83972. The therapeutic efficacy and safety of this procedure has been documented in placebo-controlled studies in patients with incomplete bladder voiding. Genome sequencing of E. coli 83972 has revealed a general “loss of virulence” phenotype, which includes fimbrial genes. E. coli 83972 lacks functional P or type 1 fimbriae, due to attenuating point mutations in the papG adhesin gene and a large, inactivating deletion in the fim gene cluster. Both fimbrial types have been proposed to enhance bacterial persistence in the urinary tract. In an attempt to increase the efficiency of E. coli 83972 inoculation and extend its use to include UTI-prone patients with complete bladder voiding, we restored P- and type 1-fimbrial expression and addressed how fimbriae affect the gene expression in inoculated human hosts.

overall_design: Prior to inoculation, patients were treated with antibiotics to sterilize their urine. E. coli was cultured overnight (16 h) in lysogeny broth, cells were harvested by centrifugation and re-suspended in PBS to a concentration of 10^5 cfu/ml. Patients were inoculated with 30 ml of the solution through a catheter, which was then removed. Blood samples were collected prior to inoculation, 3, 24 and 48 hours and at 1 and 2 weeks after inoculation.

first: Jenny

last: Grönberg-Hernández

first: Bela

last: Köves

first: Björn

last: Wullt

first: Catharina

last: Svanborg


title: Foxp1 is indispensable for ductal morphogenesis and controls the exit of mammary stem cells from quiescence [RNA-seq and ChIP-seq]

status: Public on Mar 22 2019

city: Parkville

first: Gordon

middle: K

last: Smyth

state: Vic

address: 1G Royal Pde

department: Bioinformatics

country: Australia

institute: Walter and Eliza Hall Institute of Medical Research

type: Genome binding/occupancy profiling by high throughput sequencing

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

overall_design: Refer to individual Series


title: Tumor-associated Reactive Astrocytes Aid the Evolution of Immunosuppressive Environment in Glioblastoma

city: Freiburg

first: Dieter

middle: Henrik

last: Heiland

address: Breisacherstr. 64

department: Department of Neurosurgery

institute: Medical Center Freiburg

summary: The role of activated astrocytes in glioblastoma environment

overall_design: RNA-seq of purified astrocytes

first: D

middle: H

first: O

last: Schnell


title: The non-canonical Notch ligand DNER regulates IFNγ in macrophages during COPD progression

city: Neuherberg

first: Johannes

last: Beckers

address: Ingolstaedter Landstr. 1

department: Institute of Experimental Genetics

institute: Helmholtz Zentrum Muenchen

summary: Chronic Obstructive Pulmonary Diseases (COPD) is the third leading cause of death worldwide with no curative therapy available. A novel non-canonical Notch ligand, DNER, has been identified in a GWAS to correlate with disease severity, but its function and contribution to COPD is completely unknown.   DNER localization and expression was determined in COPD patients and 6 month cigarette smoke (CS)-exposed mice. Microarray and GSEA of M1 and M2 bone marrow-derived macrophages (BMDM) from wild type (WT) and Dner deficient mice were performed. IFNγ levels and Notch activation were evaluated in 2 month CS-exposed WT and Dner deficient mice. Notch and NFκB pathways were evaluated by qPCR and Western Blot in BMDM.   DNER was increased in the lung of COPD patients and localized to macrophages in human and murine lung tissue. Upon pro-inflammatory conditions, WT BMDM and human macrophages exhibited increased Dner levels. Interestingly, IFNγ responses were abrogated in Dner deficient pro-inflammatory macrophages both in vitro and in vivo. LPS treated Dner deficient BMDM failed to trigger NFκB and Notch signalling cascades evidenced by the absence of nuclear active forms.   We provide the first molecular and functional insights into DNER, a novel Notch ligand that controls IFNγ secretion in lung recruited pro-inflammatory macrophages.

overall_design: We performed gene expression microarray analysis of M0, M1 and M2 bone marrow-derived macrophages (BMDM) from wild type (WT) and Dner-deficient mice

first: Carolina

last: Ballester-López

first: Thomas

middle: M

last: Conlon

first: Zeynep

last: Ertüz

first: Flavia

last: Greiffo

first: Martin

last: Irmler

first: Isis

middle: E

last: Fernandez

first: Oliver

last: Eickelberg

first: Ali

middle: O

last: Yildirim


title: The transcription Factor Slug represses p16Ink4a and regulates murine muscle stem cell aging

city: Chicago

first: Pei

last: Zhu

state: IL

address: 1111 S Laflin Street, Apt314

department: Department of Biochemistry and Molecular Genetics

institute: university of illinois at chicago

summary:
Sustainable muscle regeneration necessitates proper maintenance of the quiescence-reversible SCs pool. Activation of p16Ink4a-associated senescence pathway during aging breaks muscle homeostasis and causes degenerative muscle disease by irreversibly dampening satellite cell (SC) self-renewal capacity.
We performed microarrays analysis to compare the genome-wide gene expression profiles of wild-type and Slug-deficient SCs and identified distinct classes of up-regulated genes upon deletion of Slug gene.

overall_design: Quiescent SCs were collected by FACS sorting of CD45-Sca1-CD11b-CD31-CD34+Integrin-α7+ cell population in mononucleated cells prepared from hindlimb muslces of adult wildtype and Slug knockout mice, respectively. RNA was extracted for Affymetrix microarrays analysis.

first: Chunping

last: Zhang

first: Yongxing

last: Gao

first: Furen

last: Wu

first: Yalu

last: Zhou

first: Wen-shu


title: MicroRNAs are important mediators of BMP-7 induced dendritic growth in sympathetic neurons

city: Moraga

first: Vidya

last: Chandrasekaran

address: 1928 Saint Mary's Road

department: Biology

institute: Saint Mary's College of California

summary: MicroRNA profiling of cultured sympathetic neurons from the superior cervical ganglia of E21 Sprague-Dawley rat pups following growth under control conditions or after treatment with BMP-7 at 50 ng/mL for 6 hours or 24 hours.

overall_design: Three conditions - Control, BMP-7 (50 ng/mL) for 6 hours, BMP-7 for 24 hours. Each RNA sample (called one biological replicate) was a pooled mixture of RNA samples from all the pups in a litter. Two such RNA samples per condition were used for the microarray analyses.

first: S

last: Thapa

first: P

middle: J

last: Lein

first: V


title: A Role for Chromatin Remodeling in Cohesin Loading onto Chromosomes

city: London

first: Sofía

last: Muñoz

address: 1 Midland Rd

country: United Kingdom

institute: The Francis Crick Institute

summary: The RSC chromatin remodeling complex recruits the cohesin loader Scc2-Scc4 by a direct protein interaction. Nucleosome-free DNA is the substrate for the cohesin loading reaction.

overall_design: MNase-seq analysis of the nucleosome positioning comparing wild type to Sth1Degron cells and Sth1Degron cells expressing either Sth1 wild type or Sth1K501R following Sth1 depletion.

first: Masashi

last: Minamino

first: Corella

middle: S

last: Casas-Delucchi

first: Harshil

last: Patel

first: Frank

last: Uhlmann


title: Acetyl-CoA carboxylase inhibition regulates microtubule dynamics and intracellular transport in cystic fibrosis epithelial cells

status: Public on Mar 18 2019

city: Cleveland

first: Aura

last: Perez

state: OH

address: 10900 Euclid Avenue

department: Pediatrics

institute: CWRU

summary: In this study, we hypothesize that acetyl CoA carboxylase (ACC) is an important intermediate in Cystic fibrosis (CF) inflammatory signaling cascade.  Here, we demonstrate that ACC inhibition mimics the cellular effects of ibuprofen promoting both redistribution of intracellular cholesterol and increased rates of microtubule reformation, while decreasing RhoA expression in CF epithelial cell models.  Inhibiting ACC polymerization with citrate increases RhoA expression and decreases microtubule reformation rates in wild-type epithelial cells, suggesting pro-inflammatory signaling.  Together, these findings demonstrate a novel mechanism of high-dose ibuprofen efficacy and point to a potential new therapeutic target for anti-inflammatory drugs in CF.

overall_design: Compare broader impact of ACC inhibition on TOFA-treated (5-(Tetradecyloxy-2-furoic acid) CF HNE cells

first: Sharon

last: Rymut

first: Calvin

middle: U

last: Cotton

first: Thomas

last: Kelley


title: Alterations of the MEK/ERK, BMP, and Wnt/b-catenin pathways detected in the blood of individuals with lymphatic malformations

city: Redwood City

first: Kavita

last: Sarin

address: 450 Broadway

department: Dermatology

institute: Stanford Medical School

summary: Lymphatic malformation (LM) is a developmental anomaly of the lymphatic system that may lead to disfigurement, organ dysfunction and recurrent infection. Though several treatment modalities exist, pharmacotherapy is often associated with side effects and recurrence is common following surgical interventions. Moreover, despite the recent discovery of PIK3CA mutations in lymphatic endothelial cells of LM patients, the full spectrum of molecular pathways involved in LM pathogenesis is poorly understood. Here, we performed RNA sequencing on blood samples obtained from ten LM patients and nine healthy subjects and found 421 differentially expressed genes that stratify LM subjects from healthy controls. Using this LM gene signature, we identified novel pathway alterations in LM, such as oxidative phosphorylation, MEK/ERK, bone morphogenetic protein (BMP), and Wnt/b-catenin pathways, in addition to confirming the known alterations in cell cycle and the PI3K/AKT pathway. Furthermore, we performed computational drug repositioning analysis to predict existing therapies (e.g. sirolimus) and novel classes of drugs for LM. These findings deepen our understanding of LM pathogenesis and may facilitate non-invasive diagnosis, pathway analysis and therapeutic development.

overall_design: RNA-sequencing of peripheral blooof 10 LM patients and 9 control subjects

first: Taehan

last: Kim

first: Elidia

last: Tafoya

first: Malcolm

last: Chelliah

first: Ramrada

last: Lekwuttikarn

first: Jiang

last: Li

first: Joyce

last: Teng


title: RNA-seq of Salmonlella Typhimurium variants

status: Public on Mar 21 2019

city: College Park

first: Jiqiang

last: Ling

state: MD

address: 2202 Microbiology Bldg., 4062 Campus Dr.

department: Cell Biology and Molecular Genetics

institute: The University of Maryland, College Park

summary: Next-gen RNA sequencing was performed on Salmonella variants with different levels of translational fidelity

sample_organism: Salmonella enterica subsp. enterica serovar Typhimurium str. ATCC 14028

overall_design: Salmonella cells were culture in Luria Broth at 37 degrees up to mid-log or stationary phase. Total RNA was extracted and sequenced with Illumina Hi-seq by Genewiz. Strand specific.

first: Ling

last: Jiqiang

first: Fan

last: Yongqiang


title: Identification of cancer drivers at CTCF insulators in 1,962 whole-genomes

status: Public on Mar 16 2019

city: New York

first: Ping

last: Chi

state: NY

address: 1275 York Ave

department: Medicine

institute: Memorial Sloan Kettering Cancer Center

summary: We report the genome wide CTCF binding sites in the human melanoma A375 cell line.

overall_design: ChIP-seq to identify CTCF binding sites in the human melanoma A375 cell line.

first: Elissa

last: Wong


title: The scaffolding role of RNA in ribonucleoprotein complexes: TRA2A recruitment in FXTAS disease

city: Barcelona

first: Magdalena

last: Arnal Segura

address: Carrer de Natzaret 113

country: Spain

institute: Vall d'Hebron Institute of Oncology

summary: To address the functional implications at highthroughput level of TRA2A recruitment in FXTAS nuclear inclusions we performed Clariom D splicing arrays with the COS-7 cell models. We compared the profiles of the cells upon CGG overexpression, TRA2A overexpression and knockdown, with the respective controls.

overall_design: 18 samples were analyzed: controls (n=3); cond1 (n=3);  cond2  (n=3);  cond3 (n=3);  cond4 (n=3); cond5 (n=3)

first: Teresa

last: Botta-Orfila

first: Mariona

last: Gelabert-Baldrich

first: Gian

middle: G

last: Tartaglia


title: Transcriptomic atlas of mushroom development reveals conserved genes behind complex multicellularity in fungi [Rickenella mellea]

city: Szeged

first: Laszlo

middle: G.

last: Nagy

state: Csongrad

address: Temesvari krt 62

department: Institute of Biochemistry, Synthetic and Systems Biology Unit

country: Hungary

institute: Biological Research Centre, Hungarian Academy of Sciences

summary: The evolution of complex multicellularity has been one of the major transitions in the history of life. In contrast to simple multicellular aggregates of cells, it has evolved only in a handful of lineages, including the animals, embryophytes, red and brown algae and fungi. Despite being a key step towards the evolution of complex organisms, the evolutionary origins and the genetic underpinnings of complex multicellularity are incompletely known. We constructed a reference atlas of mushroom formation based on developmental transcriptome data of six species and comparisons of >200 whole genomes, to elucidate the core genetic program of complex multicellularity and fruiting body development in mushroom-forming fungi (Agaricomycetes). Nearly 300 conserved gene families and >70 functional groups contained developmentally regulated genes from five to six species, covering functions related to fungal cell wall (FCW) remodeling, targeted protein degradation, signal transduction, adhesion and small secreted proteins (including effector-like orphan genes). Several of these families, including F-box proteins, expansin-like proteins, protein kinases, and transcription factors, showed expansions in Agaricomycetes, with from which many convergently expandedwere identified in multicellular plants and/or animals too, assuming convergent solutions to genetic hurdles imposed by complex multicellularity among independently evolved lineages. This study provides a novel entry point to studying mushroom development and complex multicellularity in one of the largest clades of complex eukaryotic organisms.

overall_design: 14 samples corresponding to 5 developmental stages were analyzed. Developmental stages contain 2-3  biological replicates.

first: Krisztina

last: Krizsan

first: Eva

last: Almasi

first: Zsolt

last: Merenyi

first: Neha

last: Sahu

first: Mate

last: Viragh

first: Tamas

last: Koszo

first: Stephen

last: Mondo

first: Brigitta

last: Kiss

first: Balazs

last: Balint

first: Ursula

last: Kues

first: Kerrie

last: Barry

first: Judit

last: Cseklye

first: Botond

last: Hegedus

first: Bernard

last: Henrissat

first: Jenifer

last: Johnson

first: Anna

last: Lipzen

first: Robin

last: Ohm

first: Istvan

first: Jasmyn

last: Pangilinan

first: Juying

last: Yan

first: Yi

last: Xiong

first: Igor

middle: V

last: Grigoriev

first: David

last: Hibbett


title: Transcriptomic atlas of mushroom development reveals conserved genes behind complex multicellularity in fungi

first: Laszlo

last: Nagy

sample_organism:
Schizophyllum commune
Coprinopsis cinerea
Lentinus tigrinus
Rickenella mellea
Phanerodontia chrysosporium


title: Transcriptomic atlas of mushroom development reveals conserved genes behind complex multicellularity in fungi [Phanerochaete chrysosporium]

overall_design: 8 samples corresponding to 3 developmental stages were analyzed. Developmental stages contain 2-3  biological replicates.

first: Krisztina

last: Krizsan

first: Eva

last: Almasi

first: Zsolt

last: Merenyi

first: Neha

last: Sahu

first: Mate

last: Viragh

first: Tamas

last: Koszo

first: Stephen

last: Mondo

first: Brigitta


title: Transcriptomic atlas of mushroom development reveals conserved genes behind complex multicellularity in fungi [Lentinus tigrinus]

overall_design: 27 samples corresponding to 9 developmental stages were analyzed. Developmental stages contain 3  biological replicates.

last: Kiss

first: Balazs

last: Balint

first: Ursula

last: Kues

first: Kerrie

last: Barry

first: Judit

last: Cseklye

first: Botond

last: Hegedus

first: Bernard

last: Henrissat

first: Jenifer

first: Anna


title: Umbilical cord miRNA profile associated with catch-up growth in SGA infants

city: Salt

last: Bassols

address: C/ Dr. Castany s/n

institute: IDIBGI

summary: The aim of this study was to identify umbilical cord microRNA (miRNA) associated with catch-up growth in SGA infants. miRCURY LNA™ Universal RT microRNA PCR Human Panel I+II (Exiqon) were used to study the miRNA profile in umbilical cord tissue of 5 SGA infants with catch-up (SGA-CU), 5 SGA infants without catch-up (SGA-nonCU) and 5 control infants (appropriate-for-gestational-age, AGA). Catch-up differentially expressed miRNA were studied and validated in a larger cohort.

overall_design: qPCR gene expression profiling in umbilical cord from 15 subjects (5 SGA-CU, 5 SGA-nonCU and 5 AGA).

first: Abel

last: Lopez-Bermejo


title: Novel Upstream Regulators of YAP/TAZ Activation

city: Boston

first: Boston University

last: Microarray and Sequencing Resource

state: MA

address: 72 East Concord Street, E631

department: Microarray and Sequencing Resource

institute: Boston University

summary: The goal of this study was to determine if loss of STK25 or gain of miR-24-3p resulted in YAP/TAZ activation.

overall_design: Microarray analysis of hTERT-RPE-1 cells treated with either control siRNA, siSTK25 or pre-mir miR-24-3p.

first: Sanghee

last: Lim

first: Marc

last: Vittoria

first: Neil

last: Ganem


title: Single cell transcriptome analysis of quiescent versus reactivating Drosophila melanogaster larval central nervous system neural stem cells.

city: Plymouth

first: Claudia

last: Barros

state: Devon

address: The John Bull Building, Plymouth Science Park, 16 Research Way

department: School of Medicine

institute: University of Plymouth

summary: Single-cell transcriptome profile of Drosophila melanogaster larval brain quiescent versus reactivating (enlarged) neural stem cells, using whole-genome microarrays.

overall_design: Two condition experiment: single quiescent versus single reactivating (enlarged) Drosophila larval central nervous system neural stem cells. Biological replicates: 3 quiescent/reactivating cell pairs. Single cells independantly harvested directly from live 17h after larval hatching ventral nerve cords. One replicate per array.

first: Jon

last: Gil-Ranedo

first: Eleanor

last: Gonzaga

first: Karolina

last: Jaworek

first: Christian

last: Berger

first: Torsten

last: Bossing


title: Reassessment of Exosome Composition

city: Nashville

first: Jie

last: Ping

state: TN

address: 2525 West End Ave

institute: Vanderbilt University Medical Center

type: Non-coding RNA profiling by high throughput sequencing

summary: RNA-Seq of cellular and extracellular samples from DKO-1 and Gli36 cell lines. The distribution of extracellular RNA between microvesicles, and crude small extracellular vesicular vesicles fractionated based on flotation density in ioxdixanol is distinct between the different extracellular compartments.

overall_design: The extracellular release of RNA from two human cancer cells lines is examined based on separation of the samples into distinct extracellular compartments.

first: Dennis

last: Jeppesen

first: Robert

last: Coffey


title: Transciptome analysis of TP63 regulated pathways in HNSCC

status: Public on Mar 15 2019

city: Aurora

first: Maranke

last: Koster

address: 12800 E19th Avenue

institute: University of Colorado-Anschutz Medical Campus

summary:
Purpose: To identify TP63 expression regulated pathways in HNSCC
Methods: A recombinant lentivirus encoding either NS shRNA or TP63 shRNA was introduced into a HNSCC cell line, FaDu. SCCs were gene generated by implanting either FaDu-NS shRNA (n=3) or FaDu-TP63 shRNA into the tongue of athymic nude mice. Tongue SCCs harvested at the end of study were used for transcriptome analysis

overall_design: Identification of differentially expressed transcripts in TP63 knockdown SCCs compared to NS shRNA SCCs

first: Senthilnath

last: lakshmanachetty

middle: I


title: Tubulin mRNA stability is sensitive to change in microtubule dynamics caused by multiple physiological and toxic cues

first: Ivana

last: Gasic

address: 200 Longwood Avenue

institute: Harvard Medical School

summary: The goal of this study is to compare gene expression profiles in quiescent RPE1 hTert cells treated with microtubule-stabilizing (paclitaxel) and microtubule-destabilizing poisons (combretastatin A4)

overall_design: RPE 1 hTert cells were grown to full confluency, and maintained as such for 5 days to induce quiescence. Quiescent cells were treated with microtubule poisons combretastatin A4 and paclitaxel for 6 or 24 hours. Total RNA was collected and purified using the PureLink RNA Mini Kit (Invitrogen, Thermo Fisher Scientific, USA). RNA concentration and quality were determined using NanoDrop and Bioanalyzer respectively, and 500 ng of purified RNA was used as input for the Illumina TruSeq Stranded mRNA Library Prep Kit (Illumina, USA). Barcoded libraries were pooled and quantitated using KAPA, and single-end sequenced on an Illumina NextSeq (Illumina, USA). RNA-seq reads were mapped using STAR (version 2.1.0j) and processed using HTSeq-count (version 0.6.1). GRCh38 reference genome and transcript annotations were used for gene mapping; Entrez Gene identifiers and org.Hs.eg.db database were used for genome wide annotation. Differential gene expression and statistical analysis were performed using edgeR package. Genes with >50 reads per million and a fold change significantly different from zero in Wilcoxon signed-rank test (p< 0.05), were marked as differentially expressed genes, based on three biological replicates.

first: Timothy

last: Mitchison


title: Obesity expands a distinct population of adipose-resident T cells and increases vulnerability to infection

city: Chapel Hill

first: Joshua

last: Starmer

state: NORTH CAROLINA

address: 120 Mason Farm Road

department: Genetics

institute: University of North Carolina at Chapel Hill

summary: Obesity in humans is associated with worsened health outcomes following infections compared to non-obese individuals. Here, we examined the effects of adipose tissue and obesity on T cell responses to virus infection in mice. Lymphocytic choriomeningitis virus (LCMV) grew to high titer in adipose tissue. Virus-specific T cells enter the adipose tissue to resolve infection but then remain as a memory population distinct from memory T cells in lymphoid tissues. Memory CD4+ and CD8+ T cells residing in adipose were abundant, accounting for roughly 10% of all virus-specific memory T cells. Diet-induced obesity increased memory T cell number in adipose and spleen. Upon re-challenge infection, memory T cells caused severe pathogenesis, leading to sharply increased lipase levels, calcification of adipose tissue, pancreatitis, and reduced survival in obese mice but not lean mice. Thus, obesity leads to a unique form of viral pathogenesis involving memory T cell-dependent adipocyte destruction and collateral damage to other tissues.

overall_design: RNA-seq comparison of CD4+ T cells in spleen vs fat (with 10 mice pooled per replicate) and CD8+ T cells in spleen vs fat (with 5 mice pooled per replicate)

first: Misumi

last: Ichiro

first: Starmer

last: Joshua

first: Beck

last: Melinda

first: Magnuson

last: Terry

first: Whitmire

last: Jason


title: Screening in Human Cardiac Organoids Identifies a Requirement for the Mevalonate Pathway in Cardiomyocyte Proliferation

city: St Lucia

first: James

middle: E.

last: Hudson

address: Level 3, Skerman Building (65)

department: School of Biomedical Sciences

institute: The University of Queensland

summary:
Purpose: Induction of endogenous proliferation is a promising strategy for cardiac regeneration. We find that GSK3 inhibition activates a cell cycle network whereas MST1 inhibition drives the mevalonate pathway, with synergistic activation of proliferation. However, all GSK3 inhibitors tested also reduce contractile force in hCO. We screened for small molecule activators of cardiomyocyte proliferation that did not alter contractile force in hCOs. This was overcome by screening of a boutique compound library, identifying a p38 inhibitor, which activated a cell cycle network without reducing force. The screen also identified a TGFBR inhibitor that induces the mevalonate pathway and can also synergise to activate proliferation.  RNA sequencing was performed to investigate underlying mechanisms of action.
Methods: RNA samples were processed with Illumina TruSeq Stranded mRNA Library prep kit selecting for poly(A) taled RNA following the manufacturer’s recommendations. Libraries were quantified with Qubit HS (ThermoFisher) and Fragment Analyzer (Advances Analytical Technologies) adjusted to the appropriate concentration for sequencing. Indexed libraries were pooled and sequenced at a final concentration of 1.8 pM on an Illumina NextSeq 500 high-output run using paired-end chemistry with 75 bp read length. The sequencing data was demultiplexed using Illumina bcl2fastq2-v2.17. The quality of the reads was assessed thanks to FastQC. The reads were then processed and mapped to the human genome hg38 using the Bcbio-nextgen framework version 1.0.3. The aligner used was HISAT2 2.0.5.  Raw counts were normalised and analysed with DESeq2.
Results: Analysis of RNAseq data lead to the understanding that compound 3 regulated the cell cycle network, which was similar to GSK3 inhibitors, whereas compound 65 regulated the mevalonate network, which was similarly to MST1 inhibitors.
Conclusions: The current study adds to a growing body of evidence that alterations in cardiomyocyte metabolism may be a cause rather than a consequence of cardiomyocyte cell cycle arrest. Controlling cellular metabolism is emerging as a key strategy in the fight against cancer but the same pathways may conversely be required for the development of cardiac regenerative therapies.

overall_design: mRNA profiles of hCO samples (control and treated with three compounds selected from screen) were generated on an Illumina NextSeq 500 high-output run.

first: Richard

last: Mills

first: Benjamin

middle: L

last: Parker

first: Holly

last: Voges

first: Elise

last: Needham

first: Aurelie

last: Bornot

first: Mei

last: Ding

first: Henrik

last: Andersson

first: Magnus

last: Polla

first: Lauren

last: Drowley

first: Maryam

last: Clausen

first: Alleyn

last: Plowright

first: Ian

middle: P

last: Barrett

first: Qing-Dong

last: Wang

first: David

last: James

first: Enzo

middle: R

last: Porrello


title: Changes in DNA methylation patterns associated with Gulf War Illness

city: Fort Lauderdale

first: Lubov

last: Nathanson

state: Florida

address: 3321 College Ave.

department: INIM

institute: Nova Southeastern University

summary: Gulf War Illness (GWI) is a complex condition that involves multiple organ systems and is characterized by an abrupt or delayed onset of persistent/relapsing symptomatology such as memory and other neurological problems, muscle and joint pain, gastrointestinal issues, hormonal imbalance, immune dysfunction and debilitating fatigue. Currently, treatment of the condition relies solely on management of symptomatology and improvement in quality of life due to a lack of knowledgeof the underlying mechanisms of disease onset and progression. An improved understanding of the key mechanisms of GWI and dysfunction within regulatory systems will lead to more objective diagnosis methods and adequate management of patients by providing targeted approaches to treatment. Disruption of DNA methylation patterns has been tied to various immune, neurological and endocrine disease states; however, the status of this epigenetic mark in GWI remains uncertain. This study aimed at identifying biomarkers of GWI by gaining knowledge on DNA methylation patterns of GWI in an effort to determine therapeutic targets of disease activity and provide insight into disease onset and progression.  Methods: Genomic DNA from 10 GWI patients and 10 healthy controls [HC] (“experimental cohort”) prepared from PBMCs was analyzed with ELISA-based DNA methylation assays and Illumina MethylationEPIC microarrays. These arrays allow measuring the methylation status at 850,000 CpG sites. Methylation changes in promoter regions were separately analyzed and used as input data in ingenuity pathway analysis software to identify altered functional pathways. Relevant differentially methylated CpG sites (DMS) were validated by pyrosequencing.  Results: Global DNA methylation levels using the ELISA-based assay on the DNA isolated from PBMCs of GWI patients were similar to those of HC. However, deeper evaluation using microarray-based genome-wide technology allowed detection of DMS in GWI patients with respect to HC. As an overall 10,767 CpG sites presented with differential DNA methylation levels across promoters, gene regulatory elements and within coding regions of genes. Majority of these DMS were hypermethylated in GWI patients as compared to the HC, and more than half of these sites localized to promoters and gene regulatory elements, relative to distribution of DMSin the network as a whole, indicating gene regulatory potential. Functional pathway analysis of the 776 genes with differentially methylated promoters (DMPs) fulfilling FDR≤0.2 criteriafollowing a genomic region-based approachlinks GWI to defects in at least 15 different pathways mostly related to cell signaling with a strong immune component.  Conclusions: This is the first study that has explored genome-wide epigenetic changes associated with GWI using the new MethylationEPIC microarrays covering about 850,000 CpG sites; which builds on previous methylation preliminary reports. The data obtained are consistent with previous evidence for dysregulation of the immune system in GWI and suggests a role of this epigenetic modification on the DNA pathobiology of GWI. They are also consistent with previous reports showing a Th1- to Th2-mediated immune response shift in GWI in addition to altered immune system function. Future validation studies in larger cohorts of GWI patients and evaluation of the effects of these methylation patterns on gene expression regulation are granted.

overall_design: Genomic DNA from 20 peripheral blood mononuclear cells (PBMC) samples (10 GWI, 10 controls) were bisulfite-converted and hybridised to the Illumina MethylationEPIC microarrays. GenomeStudio idat files were generated and the data was analyzed using the RnBeads R package.

first: Malav

last: Trivedi

first: Maria

last: Abreu

first: Leonor

last: Sarria

first: Natasha

last: Rose

first: Vladimir

last: Beljanski

first: Mary

middle: A

last: Fletcher

first: Nancy

last: Klimas


title: Physiological role of 2’-O-methylation within prokaryotic and eukaryotic tRNA for innate immune activation via endosomal Toll-like receptors

city: Heidelberg

first: Tatjana

last: Eigenbrod

address: Im Neuenheimer Feld 324

department: Department of Infectious Diseases

institute: Heidelberg University Hospital

summary:
Bacterial RNA has emerged as important activator of innate immune responses by stimulating the endosomal Toll-like receptors TLR7 and TLR8 in humans. Guanosine 2’-O-methylation at position 18 (Gm18) in bacterial tRNA was shown to antagonize tRNA induced TLR7/8 activation, giving rise to a potential role of this modification as immune escape mechanism. This modification also occurs in eukaryotic tRNA, yet a physiological immune function remains to be established.
We therefore set out to investigate the physiological role of Gm18 in prokaryotic and eukaryotic microorganisms by using mutants deficient in the respective 2’-O-methyltransferase. In E. coli, lack of 2’-O-methyltransferase trmH enhanced immune stimulatory properties of both tRNA and whole cellular RNA. Yet, when using living microorganisms, trmH mutants did not differ from their wildtype counterparts in terms of immunostimulation although gene expression profiling demonstrated the induction of a TLR8/RNA dependent gene signature by E. coli in principle. In summary, the results demonstrate that Gm18 is a global immune inhibitory RNA modification across the kingdoms and contributes to RNA recognition by innate immune cells.

overall_design: Total RNA was isolated from four stimulation experiments (non-treated, LPS, WT E. coli and ΔtrmH E. coli) of transdifferntiated wild-type BlaER1 cells and four transdifferentiated ΔTLR8 BlaER1 cells. Each stimulation was performed three times (sample 1-3) in pooled triplicates.

first: Daniel

middle: K

last: Buhl

first: Isabel

last: Freund


title: Transcriptomic atlas of mushroom development reveals conserved genes behind complex multicellularity in fungi [Coprinopsis cinerea]

first: Laszlo

last: Nagy

overall_design: 29 samples corresponding to 9 developmental stages were analyzed. Developmental stages contain 3-4  biological replicates.

first: Krisztina

last: Krizsan

first: Eva

last: Almasi

first: Zsolt

last: Merenyi

first: Neha

last: Sahu

first: Mate

last: Viragh

first: Tamas

last: Koszo

first: Stephen

last: Mondo

first: Brigitta

last: Kiss

first: Balazs

last: Balint

first: Ursula

last: Kues

first: Kerrie

last: Barry

first: Judit

last: Cseklye

first: Botond

last: Hegedus

first: Bernard

last: Henrissat

first: Jenifer

last: Johnson

first: Anna

last: Lipzen

first: Robin

last: Ohm

first: Istvan

first: Jasmyn

last: Pangilinan

first: Juying

last: Yan

first: Yi

last: Xiong

first: Igor

last: Grigoriev

last: Hibbett


title: Revealing cellular and molecular transitions in neonatal germ cell differentiation using Single-cell RNA sequencing

city: Hong Kong

first: Jinyue

last: Liao

address: Room 38016, 1/F Lui Che Woo Clinical Sciences Building

department: Department of Chemical Pathology

country: Hong Kong

institute: The Chinese University of Hong Kong

summary: Neonatal germ cell development provides the foundation of spermatogenesis. However, a systematic understanding of this process is still limited. To resolve the cellular and molecular heterogeneity, we profiled single-cell transcriptomes of undifferentiated germ cells from neonatal mouse testes and employed unbiased clustering and pseudotime ordering analysis to assign cells to distinct cell states in the developmental continuum. We defined the unique transcriptional programs underlying the migratory capacity, resting cellular states and apoptosis regulation in transitional gonocytes. We also identified a subpopulation of primitive spermatogonia marked by CD87/uPAR, which exhibited a higher level of self-renewal gene expression and migration potential. We further revealed a differentiation-primed state within the undifferentiated compartment, in which elevated Oct4 expression correlates with lower expression of self-renewal pathway, higher Rarg expression, and enhanced retinoic acid responsiveness. Lastly, the knockdown experiment revealed the role of Oct4 in the regulation of gene expression related to the MAPK pathway and cell adhesion, which may contribute to stem cell differentiation. Our study thus provides novel insights into the cellular and molecular regulations during early germ cell development.

overall_design: Here, we performed single-cell RNA-Seq of germ cells from mouse testes on postnatal day (PND) 5.5. We also obtained transcriptomes of subpopulations marked by different levels of CD87 or Oct4-GFP, as well as SSC culture after Oct4 knockdown by bulk RNA-Seq.

first: Tin

last: Lee


title: Transcriptomic atlas of mushroom development reveals conserved genes behind complex multicellularity in fungi [Schizophyllum commune]

first: Laszlo

last: Nagy

first: Krisztina

last: Krizsan

first: Eva

last: Almasi

first: Zsolt

last: Merenyi

first: Neha

last: Sahu

first: Mate

last: Viragh

first: Tamas

last: Koszo

first: Stephen

last: Mondo

first: Brigitta

last: Kiss

first: David


title: Impact of depletion of groucho or notch on transcription in Drosophila intestinal stem cells (ISCs).

city: Beijing

first: huanwei

last: huang

address: 7 Science Park Rd., ZGC life science park

country: China

institute: NIBS

summary:
Purpose:  To analysis impacts of groucho and notch on transcription in Drosophila ISCs by mRNA-seq.
Methods: mRNA-seq of RNA extracted from FACS sorted Drosophila ISCs.
Results: Groucho loss in ISCs leads to disruption of lateral inhibition,and knocking down notch in ISCs down-regulates expression of e(spl) factors.

overall_design: Isolation and amplification of total mRNA of FACS sorted ISCs from Dl>UAS-GFP(Ctrl) and Dl>UAS-GFP, groucho-RNAi or  Dl>UAS-GFP, notch-RNAi guts, followed by deep sequencing analysis. Arcturus PicoPure RNA isolation kit (Applied Biosystems) and Arcturus RiboAmp HS PLUS RNA amplification kit were used for RNA extraction and amplification separately.

first: Xingting

last: Guo

first: Rongwen

last: Xi


title: Genome Wide Chromatin Mapping of H3K27me3 and H3K4me3 histone modifications in wild type and ASXL1-/- Osteoclast

status: Public on Mar 14 2019

city: St Louis

first: nidhi

last: rohatgi

state: MO

address: 660 S Euclid Ave

department: pathology and immunology

institute: washington university in st. louis

summary: We report a  novel role of ASXL1 protein in altering epigentic profile of osteoclast. ASXL1 is an ETP protein that bind to polycomb repressive complex. We asked if ASXL1 regulates osteoclast differentiation  by maintaining balance between positive and negative epigenetic regulators. To address this question, we performed ChIP-seq using H3K27me3 and H3K4me3 antbody in day2 osteoclast. Our data reveals that there was a global loss of H3K27me3 in ASXl1-/- osteoclast which includes loss of this repressive methylation of NFATc1 promoter, which is a master regulator of osteoclastogenesis.

overall_design: Examination of 2 different histone modifications in 2 different cell types

first: Nidhi

last: Rohatgi

first: Patrick

last: Collins


title: Phosphosugar stress in Bacillus subtilis: Intracellular accumulation of mannose 6-phosphate derepresed the glcR-phoC operon from repression by GlcR

status: Public on Mar 13 2019

city: Groningen

first: Anne

middle: de

last: Jong

address: Nijenborgh 7

department: Molecular Genetics

country: Netherlands

institute: university of Groningen

summary: Bacillus subtilis phosphorylates sugars during or after their transport into the cell.Perturbation in the conversion of intracellular phosphosugars to the central carbon metabolitesand accumulation of phosphosugars can impose stress on the cells. In this study, we investigated the effect of phosphosugar stress on B. subtilis. Preliminary experiments indicated that the non-matabolizable analogs of glucose were unable to impose stress on B. subtilis. In contrast, deletion of manA encoding mannose 6-phosphate isomerase (responsible for conversion of mannose 6-phosphate to fructose 6-phosphate) resulted in growth arrest and bulged cell shape in the medium containing mannose. Besides, an operon encoding a repressor (GlcR) and a haloic acid dehalogenase (HAD)-like phosphatase (PhoC; previously YwpJ) were upregulated. Integration of the PglcR-lacZ cassette into different mutational backgrounds indicated that PglcR is induced when (i) a manA-deficient strain is cultured with mannose or (ii) when glcR is deleted.GlcR represses the transcription of glcR-phoC bybinding to the A-type core elements of PglcR. Electrophoretic mobility shift assay showed no interaction between mannose 6-phosphate (or other phosphosugars) and the GlcR-PglcR DNA complex. PhoCwas an acid phosphatase mainly able to dephosphorylate glycerol 3-phosphate and ribose 5- phosphate. Mannose 6-phosphatewas only weakly dephosphorylated by PhoC. Since deletion of glcR and phoCalone or in combination had no effect on the cell duringphosphosugar stress,it is assumed that the derepression of glcR-phoC is a side effect of phosphosugar stress in B. subtilis.

overall_design:
We selected two  Bacillus Subtilis Strain KMO and KM283. Cells were grwon in triplicate on different sugars and total RNA was isolated followd by cDNA preparation as described in protocol section, and subsequently Miroarray Array data and analysis was done.

Pleaes note that the values from multiple probes were combined and normalized further using TMM (Trimmed Media Mean) and provided in the Series supplementary file, Count.txt. For downstream analysis the Locus_tags (e.g. BSU00010, BSU00020 etc.) of Bacillus_subtilis_subsp_subtilis_str_168 (ASM904v1) are used, derived from GEO platform ORF column.

first: Kambiz

last: Heravi

first: Irfan

last: Manzoor

first: Hildegard

last: Watzlawick

last: de Jong

first: Oscar

last: Kuipers

first: Josef

last: Altenbuchner


title: Gene expression of 6 different mice strains

city: Tel Aviv

first: Amit

last: Frishberg

address: Haim Levanon

department: Cell Research & Immunology

country: Israel

institute: Tel-Aviv University

summary: Gene expression of 5 different Collaborative Cross mice strains and one C57BL/6 mouse

overall_design: Lungs gene expression of mice without any treatment.

first: Naama

last: Peshes-Yaloz

first: Ofir

last: Cohn

first: Diana

last: Rosentul

first: Yael

last: Steuerman

first: Liran

last: Valadarsky

first: Gal

last: Yankovitz

first: Michal

last: Mandelboim

first: Fuad

last: Iraqi

first: Ido

last: Amit

first: Lior

last: Mayo

first: Eran

last: Bacharach

first: Irit

last: Gat-Viks


title: Cell composition analysis of bulk genomics using single cell data

summary: Single-cell expression profiling is a rich resource of cellular heterogeneity. While profiling every sample under study is advantageous, such workflow is time consuming and costly. We devised CPM - a deconvolution algorithm in which cellular heterogeneity is inferred from bulk expression data based on pre-existing collection of single-cell RNA-seq profiles. We applied CPM to investigate individual variation in heterogeneity of murine lung cells during in vivo influenza virus infection, revealing that the relations between cell quantities and clinical outcomes varies in a gradual manner along the cellular activation process. Validation experiments confirmed these gradual changes along the cellular activation trajectory. Additional analysis suggests that clinical outcomes relate to the rate of cell activation at the early stages of this process. These findings demonstrate the utility of CPM as a mapping deconvolution tool at single-cell resolution, and highlight the importance of such fine cell landscape for understanding diversity of clinical outcomes.

overall_design: Lungs gene expression of Collaborative Cross mice taken 48h after the infection with either the influenza virus or PBS.


title: RIPChip ELAVL1 binding mRNA levels change by GnRH in LbetaT2 cells

status: Public on Mar 12 2019

city: San Diego

first: Tomohiro

last: Terasaka

address: 9500 Gilman DR LBR 332AA/BB

institute: UCSD

summary: Analysis of ELAVL1 binding mRNA with or without GnRH condition (30min) in LbetaT2 cells

overall_design: ELAVL1-RIP RNA obtained from LbetaT2 cells subjected to 30 minutes GnRH in vitro  compared to untreated control cells.

first: Taeshin

last: Kim

first: Mark

last: Lawson


title: Single cell sequencing of the parafascicular nucleus (PF) of the thalamus

first: Bernardo

last: Sabatini

summary: To examine the cellular heterogeneity in the PF, in mouse,  we used droplet-based single cell RNA sequencing technique developed by Klein et al. 2015, Cell 161, 1187–1201. doi:10.1016/j.cell.2015.04.044.

overall_design:
2 parafascicular nuclei and their surrounding tissue were dissected from 8 C57BL/6NCrl (Charles River Laboratories, Wilmington, MA, stock #027)  8 week old male mice and run using an  inDrops v3 pipeline and sequenced on a NextSeq 500

NOTE: the pf1_MATRIX.csv and MandelbaumProcessedData{*}.txt are derived from all the raw sequencing data files.

first: Gil

last: Mandelbaum

first: Daniel

last: Hochbuam


title: Epigenome analysis of depressed and control subjects. [subset]

city: Munich

first: Janine

last: Arloth

address: Kraepelinstr. 2-10

institute: Max Planck Institute of Psychiatry

summary: Genome wide DNA methylation profiling of depressed (n=324) and control subjects (n=209)  that were recruited at the Max Planck Institute of Psychiatry (MPIP). The Illumina Infinium 450k Human DNA methylation Beadchip was used to obtain DNA methylation profiles based whole blood samples.

overall_design: Bisulphite converted DNA from the 699 samples were hybridised to the Illumina Infinium 450k Human methylation Beadchip . Subset of samples from GSE125105.

first: Elisabeth

middle: B

last: Binder


title: The anti-sigma factor MucA of Pseudomonas aeruginosa: dramatic differences of mucA22 vs. DmucA mutants in anaerobic acidified nitrite sensitivity of planktonic and biofilm bacteria in vitro and during chronic murine lung infection

first: Michael

last: Schurr

state: CO

department: Microbiology

institute: University of Colorado School of Medicine

summary: In this study, the A-NO2- sensitivity of mucA22 mutant bacteria vs. a genome sequence-confirmed mucA deletion (∆mucA) mutant was determined. The ∆mucA is surprisingly more resistant to A-NO2- than mucA22 bacteria. The genes responsible for the disposal of nitric oxide (NO), a by-product of A-NO2-, were found to be near wild-type levels in the ∆mucA mutant yet were dramatically reduced in the mucA22 mutant.

overall_design: Pseudomonas aeruginosa wild-type (PAO1), mucA22 and ∆mucA bacteria were grown for 24 hr under anaerobic conditions in LBN (10g/l Tryptone, 5 g/l yeast extract, 5g/l NaCl, 100 mM KNO3), pH 6.5, followed by treatment of each organism with 15 mM A-NO2- for 20 min.

first: Warunya

last: Panmanee

first: Shengchang

last: Su

first: Gee

middle: W

last: Lau

first: Xiaoting

last: Zhu

first: Zhaowei

last: Ren

first: Cameron

middle: T

last: McDaniel

first: Long

last: Lu

first: Dennis

middle: E

last: Ohman

last: Muruve

first: Ralph

last: Panos

first: Hongwei

middle: D

last: Yu

first: Thomas

last: Thompson

first: Boo

last: Tseng

last: Hassett


title: Multiplexed primer extension sequencing: A targeted RNA-seq method that enables high-precision quantitation of mRNA splicing isoforms and rare pre-mRNA splicing intermediates

city: Ithaca

first: Jeffrey

last: Pleiss

address: 453 Biotech

institute: Cornell University

summary: The study of splicing has been greatly aided by the advent of RNA sequencing (RNA-seq), which can enable the genome-wide detection of discrete splice isoforms. Quantification of these splice isoforms requires analysis of splicing informative sequencing reads, those that unambiguously map to a single splice isoform, including exon-intron spanning reads corresponding to retained introns, as well as exon-exon junction spanning reads corresponding to either canonically- or alternatively-spliced isoforms. Because most RNA-seq experiments are designed to produce sequencing reads that uniformly cover the entirety of transcripts, only a comparatively small number of splicing informative reads are generated for any given splice site, leading to a decreased ability to detect and/or robustly quantify less abundant isoforms. To address this problem, we have recently described a method termed Multiplexed Primer Extension sequencing, or MPE-seq, which uses complex pools of thousands of reverse transcription primers to target sequencing to user selected loci. By targeting reverse transcription to pre-mRNA splice junctions, this approach can enable a dramatic enrichment in the fraction of splicing informative reads generated in an experiment, enabling an increase both in the precision with which splicing efficiency can be measured, and in the detection of splice isoforms including rare splicing intermediates. Here we provide a brief review of methods for calculating splicing efficiency with existing RNA-seq data, including the shortcomings associated with these approaches that drove our development of MPE-seq, as well as a detailed protocol for implementation of MPE-seq.

overall_design: MPE-seq of two WT S. pombe samples

last: Gildea

first: Zachary

last: Dwyer


title: Defining the transcriptome of T cells transduced with FOXP3fl or FOXP3d2

city: Stockholm

first: Nik

last: Kuznetsov

address: Nobels vag 16

institute: Karolinska Institute

summary:
Rationale - Regulatory T (Treg) cells suppress immune responses and have been shown to attenuate atherosclerosis. The Treg cell lineage specification factor FOXP3 is essential for Treg cells’ ability to uphold immunological tolerance. In humans, FOXP3 exists in several different isoforms, however, their specific role is poorly understood.
Objective - To define the regulation and functions of the two major FOXP3 isoforms, FOXP3fl and FOXP3Δ2, as well as to establish whether their expression is associated with ischemic atherosclerotic disease.
Methods and Results - Human primary T-cells were transduced with lentiviruses encoding distinct FOXP3 isoforms. The phenotype and function of these cells were analyzed by flow cytometry, in vitro suppression assays and RNA-sequencing. We also assessed the effect of activation on Treg cells isolated from healthy volunteers. Treg cell activation resulted in increased FOXP3 expression that predominantly was made up of FOXP3Δ2. FOXP3Δ2 induced specific transcription of GARP, which functions by tethering the immunosuppressive cytokine TGF-β to the cell membrane of activated Treg cells. RT-PCR was used to determine the impact of alternative splicing of FOXP3 in relation with atherosclerotic plaque stability in a cohort of over 150 patients that underwent carotid endarterectomy. Plaque instability was associated with a lower FOXP3Δ2 transcript usage, when comparing plaques from patients without symptoms and patients with occurrence of recent (<1 month) vascular symptoms including minor stoke, transient ischemic attack or amaurosis fugax. No difference was detected in total levels of FOXP3 mRNA between these two groups.
Conclusions - These results suggest that activated Treg cells suppress the atherosclerotic disease process and that FOXP3Δ2 controls a transcriptional program that acts protectively in human atherosclerotic plaques.

overall_design: In this experiment we have analyzed 3 groups of each 3 biological repliactes equalling 9 samples in total.

first: John

last: Andersson

first: Anne-Laure

last: Joly

first: Nikolai

last: Kouznetsov


title: Fibroblast RNA-Seq data from three genodermatoses (RDEB, XPC and KS)

city: Leganes

first: carlos

last: leon

state: Madrid

address: Avenida Universidad 30

department: Bioengineering

summary: Recessive dystrophic epidermolysis bullosa, Kindler syndrome and xeroderma pigmentosum C, are three cancer-prone genodermatoses whose causal genetic mutations cannot fully explain, on their own, the array of associated phenotypic manifestations. Recent evidence highlights the contributing role of the stromal microenvironment in the pathology of these disorders. To investigate common mechanisms that contribute to the pathogenic role played by dermal fibroblasts, we conducted a comparative gene expression analysis by RNA-Seq.

overall_design: 3 healthy controls, 9 RDEB, 3 XPC and 3 KS patients

first: Carlos

last: Leon

first: Marcela

last: del Rio


title: Global transcriptional responses to KI-MS2-008 treatment and Myc inactivation via doxycycline addition

city: Cambridge

first: Andrew

last: Chen

address: 500 Main St. Room 389

department: Biological Engineering

institute: Massachusetts Institute of Technology

summary: The Myc/Max heterodimer has crucial roles in normal cellular processes such as cell proliferation, metabolism, apoptosis, and differentiation, but its activity is often deregulated in a majority of human cancers. In an effort to explore alternative modes of Myc perturbation, we identified KI-MS2-008 as a small molecule that binds Max and modulates Myc-driven transcription, and in some cellular contexts, KI-MS2-008 treatment leads to a decrease in c-Myc protein levels. As the Myc/Max heterodimer controls many cellular processes, we expected that treatment with this small molecule would cause changes in the transcriptome. We found that treatment with 10 µM KI-MS2-008 resulted in global alterations in the transcriptome, mimicking direct Myc inactivation with doxycycline in P493-6, a B cell line with a Tet-Off system for c-Myc expression. We also discovered enrichment of various Myc target gene sets in the genes downregulated in response to KI-MS2-008 treatment in P493-6 cells. This trend was also observed in ST486 cells, but not in P3HR1 cells, which were chosen as non-engineered B cell lines that were sensitive and insensitive, respectively, toward KI-MS2-008 in cell viability assays.

overall_design: RNA-seq characterizing three B cell lines: P493-6 (an engineered, KI-MS2-008 sensitive cell line), ST486 (a non-engineered, KI-MS2-008 sensitive cell line), and P3HR1 (a non-engineered, KI-MS2-008 insensitive cell line). P493-6 cells were treated with 0.1 µg/mL doxycycline, 1 µM KI-MS2-008, 10 µM KI-MS2-008, or 0.4% DMSO for 45 minutes or 8 hours. ST486 cells were treated with 1 µM KI-MS2-008, 10 µM KI-MS2-008 or 0.4% DMSO for 45 minutes or 8 hours. P3HR1 cells were treated with 10 µM KI-MS2-008 or 0.4% DMSO for 8 hours. 4 replicates were performed for each condition.

first: Robert

middle: M

last: Wilson

first: Vincent

last: Butty

first: Angela

middle: N

last: Koehler


title: Extensive recovery of embryonic enhancer and gene memory stored in hypomethylated enhancer DNA.

city: Boston

first: Ramesh

last: Shivdasani

address: 450 Brookline Ave. Dana 720D

department: Medical Oncology

institute: Dana Farber Cancer Institute

type: Methylation profiling by high throughput sequencing

summary: To understand how dynamics of enhancer features correlates with gene expression in adult tissue and during development, we analyzed histone modifications, chromatin accesibility, DNA methylation and gene expression at multiple time points during mouse development and adult mice.

overall_design: We conducted RNA-seq, ATAC-seq, ChIP-seq, and WGBS experiments using purified intestinal epithleal cells from mouse embryos and adult cells.

first: Unmesh

last: Jadhav

first: Alessia

last: Cavazza

first: Kushal

last: Banerjee

first: Huafeng

last: Xie

first: Nicholas

last: O’Neill

first: Veronica

last: Saenz-Vash

last: Herbert

first: Shariq

last: Madha

first: Stuart

middle: H

last: Orkin

first: Huili

last: Zhai


title: The long noncoding RNA Lnczc3h7a promotes TRIM25-mediated RIG-I antiviral innate immune response

city: hangzhou

first: Hongyu

last: Lin

address: Zijingang Campus of Zhejiang University, 866 Yuhangtang Road, Xihu District

institute: Zhejiang University School of Medicine

summary: In this study, we employed a combination of RIP-seq and iCLIP-seq technologies to identify long non-coding RNA associated with cytoplasmic TRIM25 and RIG-I protein in mouse macrophages cells.

overall_design: Two UV-RIP experiments were performed using anti-Flag antibody in RAW264.7 cells stably expressing Flag-tagged TRIM25 with or without VSV infection for 8 hr, then co-purified RNAs were analyzed using Illumina Xten. iCLIP experiment was performed using anti-TRIM25 antibody and anti-RIG-I antibody in RAW264.7 cells upon VSV infection for 8 hr and then was analyzed by Illumina HiSeq2500 SE50 sequencing.

first: Minghong

last: Jiang

first: Lun

last: Liu

first: Zongheng

last: Yang

first: Zhongfei

last: Ma

first: Shuo

first: Yuanwu

first: Lianfeng

last: Zhang

first: Xuetao

last: Cao


title: Release of paused RNA-Polymerase II at specific introns and chromatin domains favors spontaneous DNA double strand break formation and predicts cancer translocations

city: Milano

first: Pier Giuseppe

last: Pelicci

address: Via Adamello, 16

department: Department of Experimental Oncology

country: Italy

institute: European Institute of Oncology

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

overall_design: Refer to individual Series


title: Transcriptomic analysis of the interaction of choriocarcinoma spheroids with receptive vs. non-receptive endometrial epithelium cell lines: an in vitro model for human implantation

city: Barcelona

first: Adria

last: Caballe

address: C/ Baldiri Reixac 10

department: biostatistics

institute: IRB

summary: The aim of this study was to establish an in vitro model to investigate the initial stages of human implantation based on co-culture of a) immortalized cells representing the receptive (Ishikawa) or non-receptive (HEC-1-A) endometrial epithelium with b) spheroids of a trophoblastic cell line (JEG-3) modified to express green fluorescent protein. After co-culturing Ishikawa cells with trophoblast spheroids, 310 and 298 genes increased or decreased their expression compared to non-co-cultured Ishikawa control cells, respectively; only 9 genes (5 increased and 4 decreased) were differentially expressed in HEC-1-A upon co-culture with trophoblast spheroids. Compared to HEC-1-A, the trophoblast challenge to Ishikawa cells differentially regulated the expression of 495 genes. In summary, upon co-culture with the trophoblast spheroids, non-receptive epithelium is characterized by a muted transcriptional response which in turn fails to activate the full transcriptional response that trophoblast spheroids undergo when co-cultured with receptive epithelium.

overall_design: GFP expressing JEG-3 spheroids were co-cultured with confluent monolayers of receptive Ishikawa or non-receptive HEC-1-A epithelia. After 48 hours of co-culture, GFP+ (trophoblast JEG-3 spheroid cells) and GFP- cell fractions (receptive Ishikawa or non-receptive HEC-1-A epithelial cells) were isolated by fluorescence-activated flow cytometry (FACS). The specific transcriptional changes of the isolated cell populations were analyzed by RNA-seq profiling. Statistical significance of gene expression differences was set at an absolute log2 fold change (log2FC) ≥1 and an adjusted p-value <0.05.

first: Paula

last: Vergaro

first: Gustavo

last: Tiscornia

first: Rita

last: Vassena


title: Sam68 insures proper 3'-end pre-mRNA processing during germ cell differentiation

city: Paris

first: Pierre

last: de la Grange

address: 29, rue du Faubourg Saint-Jacques

department: Paris Biotech Santé

country: France

institute: GenoSplice technology

summary: Male germ cells express the widest repertoire of transcript variants in mammalian tissues. Nevertheless, factors and mechanisms underlying such pronounced diversity are largely unknown. The splicing regulator Sam68 is highly expressed in meiotic cells and its ablation results in defective spermatogenesis. Herein, we uncover an extensive splicing program operated by Sam68 across meiosis, primarily characterized by alternative last exon (ALE) regulation in genes of functional relevance for spermatogenesis. Lack of Sam68 preferentially causes premature transcript termination at internal polyadenylation sites.

overall_design: RNA‐Seq data for purified spermatocytes and spermatids isolated from Sam68+/+ and Sam68-/- mice.

first: Chiara

last: Naro

first: Livia

last: Pellegrini

first: Ariane

last: Jolly

first: Donatella

last: Farini

first: Eleonora

last: Cesari

first: Pamela

last: Bielli

first: Claudio

last: Sette


title: Therapeutic targeting of macrophages improves chemotherapy response and elicits neutrophil-dependent therapy resistance

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: Macrophages and neutrophils are almost invariably the most abundant intratumoral immune cells, and recent studies have revealed a sinister role for these cells in limiting chemotherapy efficacy. However, how these tumor-educated myeloid cells influence chemotherapy response is incompletely understood. Targeting tumor-associated macrophages by CSF-1 receptor (CSF-1R) blockade in a pre-clinical transgenic mouse model for breast cancer improved the anti-cancer efficacy of cisplatin. Importantly, our findings reveal that macrophage blockade in combination with cisplatin treatment evokes a compensatory neutrophil response limiting the therapeutic synergy of this therapy combination. Here we characterize neutrophils and macrophages gene expression profile from the tumor of mice treated with anti-CSF-1R, Control antibody, Cisplatin/anti-CSF-1R or cisplatin/control ab.

overall_design: Intervention studies combining anti-CSF1R and chemotherapy in a transgenic mouse model for breast cancer.

first: Camilla

last: Salvagno

first: Metamia

last: Ciampricotti

first: Sander

last: Tuit

first: Seth

last: Coffelt

first: Kelly

last: Kersten

first: Cheei-Sing

last: Hau

first: Chia-Huey

last: Ooi

first: Kim

last: Vrijland

first: Ji-Ying

last: Song

first: Jos

last: Jonkers

first: Carola

last: Ries

first: Karin

last: De Visser


title: The mSWI/SNF ATPase module mediates subcomplex identity and non-catalytic targeting in SCCOHT [ChIP-seq]

status: Public on Mar 11 2019

first: Cigall

last: Kadoch

state: Massachusetts

address: 450 Brookline Avenue

department: Pediatric Oncology

summary: Perturbations to mammalian SWI/SNF (mSWI/SNF) chromatin remodeling complexes have been widely implicated as driving events across cancers1. One such perturbation is the dual loss of the SMARCA4 and SMARCA2 ATPase subunits, which has recently been implicated in rare cancers such as small cell carcinoma of the ovary, hypercalcemic type (SCCOHT)2-5, SMARCA4-deficient thoracic sarcomas6 and dedifferentiated endometrial carcinomas7. The consequences of SMARCA4/2 dual loss on the biochemical composition of the complex, chromatin targeting and remodeling capabilities, and subcomplex identity (BAF vs. PBAF) in these cancers are unknown.  Here, we leverage SCCOHT cell lines to identify an unexpected ATPase module of mSWI/SNF subunits. Using biochemical and genome-wide profiling assays, we found that the incorporation of the ATPase module is a critical step in the functional specification of BAF and PBAF subcomplexes. Furthermore, by utilizing ATPase mutant variants, we found that the ATPase module mediates two separate and concurrent mSWI/SNF targeting mechanisms, evenly split between catalytically-independent targeting to primed enhancers/promoters and catalytically-dependent targeting to de novo enhancers. Finally, by linking these distinct sites to separate tumor-suppressive gene expression programs across ovarian tissues , we clarify the mechanistic consequences of SMARCA4/2 loss dual loss in these rare tumors.

overall_design: SMARCA4/2 deficient BIN-67 cells were treated to overexpress WT and mutant versions of the SMARCA4 ATPase subunit of the mSWI/SNF complex.

first: Joshua

last: Pan

first: Andrew

last: D'Avino


title: Release of paused RNA-Polymerase II at specific introns and chromatin domains favors spontaneous DNA double strand break formation and predicts cancer translocations [RNA-seq]

first: Pier Giuseppe

last: Pelicci

summary: Transcriptional activation leads to transient accumulation of DNA Double Strand Breaks (DSBs), which might promote formation of chromosomal translocations. We report here the genomic distribution of DSBs in non-transformed mammary cells grown under unperturbed conditions, using genome-wide Breaks Labeling In Situ and Sequencing (BLISS). We found thousands of high-confidence DSBs, which were enriched at the promoters of a subset of moderately- to highly-transcribed genes (fragile promoters) and co-localized with Topoisomerase II beta. Analyses of DSB-predictive features identified gene length and paused RNA Polymerase II, but not transcription, as critical factors (84% prediction accuracy). Analyses of DSB signaling and repair factors showed high levels of XRCC4, but not of gammaH2AX and NBS1, and no RAD51. Finally, the observed DSBs were predictive of a significant fraction of the recurrent translocations found in human breast cancers. These data suggest that, in normal cells, basal transcription from a specific class of promoters entails accumulation of TOP2B, leading to unresolved DSBs and increased probability of chromosomal translocations.

overall_design: To test the efficiency of BLISS in capturing genomic DSBs, we first studied induced DSBs, and identified the genomic AsiSI sites digested upon tamoxifen (4-OHT)-induced nuclear translocation of the AsiSI restriction endonuclease fused with the estrogen receptor-binding domain (AsiSIER). At this purpose, we performed ChIPseq experiments using a panel of antibodies against various DSB sensing and repair factors (i.e., NBS1, gammaH2AX, XRCC4 and RAD51), before and after AsiSI induction, and investigated the BLISS-positivity of the AsiSI sites showing increased ChIP signals of DSB sensing and repair factors, following 4-OHT administration. Since many DSB ends sequenced by BLISS were spread all along the genome (in addition to the AsiSI sites), even in the absence of 4-OHT treatment, we identified these endogenous DSB clusters by developing a bioinformatic pipeline that identifies genomic regions showing the concomitant presence of: i) a significant enrichment of BLISS signals over the total and local background at any given genomic site, and ii) ≥2 fold-enrichment of ChIPseq signals of at least one of three repair factors (NBS1, XRCC4, RAD51) within ±1 kb from the center of the BLISS signal, as compared to the input DNA (Tier1 DSBs). Finally, ChIP assays against Topoisomerase II beta and phosphorylated RNA Polymerase II were used to investigate the mechanisms underlying the generation of endogenous DSBs.

first: Gaetano

last: Dellino

first: Fernando

last: Palluzzi

first: Andrea

last: Chiariello

first: Rossana

last: Piccioni

first: Simona

last: Bianco

first: Laura

last: Furia

first: Giulia

last: De Conti

first: Britta

last: Bouwman

first: Giorgio

last: Melloni

first: Davide

last: Guido

first: Luciano

last: Giacò

first: Lucilla

last: Luzi

last: Cittaro

first: Mario

last: Faretta

last: Nicodemi

first: Nicola

last: Crosetto

first: Pier

middle: G


title: Differentially Expressed Genes for Atrial Fibrillation Identified using RNA Sequencing from Paired Human Left and Right Atrial Appendages.

city: London

first: Alison

last: Thomas

state: London

address: WHRI, Charterhouse Square

institute: Dr

summary: Next Generation RNA Sequencing was carried out  on human paired left and right atrial appendages from patients with and without Atrial Fibrillation. EdgeR software was used to show a total of 247 genes were found to have significant differential expression between left and right atria.

overall_design: Left and Right atrial appendages from 5 patients in Sinus Rhythm and 5 patients in atrial fibrillation were subjected to RNA sequencing and differential gene expression using EdgeR.

first: Claudia

last: Cabrera


title: Constitutively Active YAP/TAZ Target Genes

first: Boston University

last: Microarray and Sequencing Resource

address: 72 East Concord Street, E631

department: Microarray and Sequencing Resource

institute: Boston University

summary: The goal of this study was to identify an active YAP/TAZ signature in the hTERT-RPE-1 cell line.

overall_design: Microarray analysis of hTERT-RPE-1 cells overexpressing either empty vectrol control, YAP-5SA or TAZ-4SA.

first: Ryan

middle: J

last: Quinton

first: Neil

last: Ganem


title: Gene expresssion profiles in PPARalpha-Serine280 phosphorylation mutants

city: Newark

first: Michinari

last: Nakamura

state: NJ

address: 185 South Orange Ave MSB-I543

department: Cell Biology and Molecular Medicine

institute: Rutgers New Jersey Medical School

summary: PPARalpha regulates cardiac fatty acid metabolism. GSK-3alpha phosphorylates PPARalpha at Serine 280, which increases PPARalpha transcriptional activity in cardiomyocytes.

overall_design: We transduced H9C2 cells with pDC316-YFP-PPARalpha-wild-type (WT), pDC316-YFP-PPARalpha-S280A phospho-resistant mutant, pDC316-YFP-PPARalpha-S280D phospho-mimicking mutant or pDC316-YFP alone for 2 days. Each n=2.

first: Seema

last: Husain

first: Junichi

last: Sadoshima


title: Release of paused RNA-Polymerase II at specific introns and chromatin domains favors spontaneous DNA double strand break formation and predicts cancer translocations [ChIP-seq & BLISS]

first: Pier Giuseppe

last: Pelicci

first: Gaetano

middle: I

last: Dellino

first: Fernando

last: Palluzzi

first: Andrea

last: Chiariello

first: Rossana

last: Piccioni

first: Simona

last: Bianco

first: Laura

last: Furia

first: Giulia

last: De Conti

last: Bouwman


city: Chicago

first: Yuanqing

last: Yan

state: IL

address: 303 E Superior Street

institute: Northwestern University

summary:
Investigation of whole genome-derived tiled peptide arrays to identify epitopes associated with autoantibody reactivity in NSCLC as a potential means for early detection. Arrays consisted of 2,781,902 tiled peptides representing 20,193 proteins encoded in the human genome.
The detailed analysis in this study is further described in Yan et al. Whole genome-derived tiled peptide arrays detect pre-diagnostic autoantibody signatures in non-small cell lung cancer. Cancer Res. 2019 Feb 5. pii: canres.1536.2018

overall_design: 2,781,902 16-mer   peptides with 12 amino acids   overlap representing the coding sequences in the genome and 4.5  47 scrambled peptides were   randomly  distributed  on  the  array.  Microarrays  were  synthesized    with  a  Roche-NimbleGen   Maskless  Array  Synthesizer  (MAS)  by  light-directed  solid-phase  peptide  synthesis  using  an   amino-functionalized  plastic  support  (Greiner  Bio-One)  coupled with  a  6-aminohexanoic  acid linker and amino acid derivatives carrying a photosensitive 2-(2-nitrophenyl) propyloxycarbonyl (NPPOC) protection group (Orgentis Chemicals)

last: Sun

first: Hong

last: Wang

first: Makoto

last: Kobayashi

first: Jon

last: Ladd

first: James

last: Long

first: Ken

middle: C

last: Lo

first: Jigar

last: Patel

first: Eric

last: Sullivan

first: Thomas

last: Albert

first: Gary

last: Goodman

first: Kim-Anh

last: Do

first: Samir

last: Hanash


title: Transcriptomic analysis of strains evolved for anaerobic xylose utilization [Y223_Y127_Y128]

city: Madison

first: Kevin

middle: S

last: Myers

state: WI

address: 5127 WEI, 1552 University Ave

department: Great Lakes Bioenergy Research Center

institute: University of Wisconsin - Madison

summary: Engineering microbes with novel metabolic properties is a critical step for production of biofuels and biochemicals. Synthetic biology enables identification and engineering of metabolic pathways into microbes; however, knowledge of how to reroute cellular regulatory signals and metabolic flux remains lacking. Here we used network analysis of multi-omic data to dissect the mechanism of anaerobic xylose fermentation, a trait important for biochemical production from plant lignocellulose. We compared transcriptomic, proteomic, and phosphoproteomic differences across a series of strains evolved to ferment xylose under various conditions.

overall_design: RNA-seq and transcriptome analysis of three evolved S. cerevisiae strains (Y22-3, Y127, Y128) grown aerobically or anaerobically in rich lab media with glucose, xylose, galactose, or sorbitol. Duplicates were collected on different days.

first: Audrey

last: Gasch


title: Transcriptomic analysis of strains evolved for anaerobic xylose utilization [Azf1]

overall_design: RNA-seq and transcriptome analysis of Azf1 deletion and over-expression (via MoBY 2.0 plasmid) in YPX -O2. Duplicate samples were collected on different days.


title: Purification of high-quality RNA from a small number of fluorescence activated cell sorted zebrafish cells for RNA sequencing purposes

city: Gent

first: Siebe

last: Loontiens

address: Corneel Heymanslaan 10

department: Center for Medical Genetics

country: Belgium

institute: Ghent University

summary: We provide a method for high quality RNA purification out of a small number (5000 - 100,000) of FACS sorted zebrafish cells followed by RNA sequencing

overall_design: RNA sequencing data from 6 RNA samples isolated from 20000 sorted fli:GFP zebrafish cells. 2 RNA samples isolated from whole embryo.

first: Lisa

last: Depestel

first: Suzanne

last: Vanhauwaert

first: Givani

last: Dewyn

first: Charlotte

last: Gistelinck

first: Karen

last: Verboom

first: Wouter

last: Van Loocke

first: Filip

last: Matthijssens

first: Andy

last: Willaert

first: Jo

last: Vandesompele

first: Frank

last: Speleman

first: Kaat

last: Durinck


title: Risk SNPs mediated promoter-enhancer switching promotes prostate cancer progression through lncRNA PCAT19

city: Toronto

first: Junjie

last: Hua

state: Ontario

address: 101 College Street

department: Princess Margaret Cancer Centre

institute: University Health Network


title: Gene expression profiles in GSK-3alpha Ser21Ala or GSK-3beta Ser9Ala knock-in mouse heart

first: Michinari

last: Nakamura


title: The ATPase module of mammalian SWI/SNF family complexes mediates subcomplex identity and catalytic activity-independent genomic targeting

first: Cigall

last: Kadoch


title: Gene expression profiles in GSK-3beta Ser9Ala knock-in mouse heart

summary: GSK-3 is a serine-threonine protein kinase and consists of two isoforms, GSK-3alpha and GSK-3beta. GSK-3alpha and GSK-3beta are inactivated by phosphorylation at Ser21 and Ser9, respectively. GSK-3alpha Ser21Ala and GSK-3beta Ser9Ala phosphorylation-resistant knock-in mice have constitutively active form of GSK-3.

overall_design:
Gene expression in GSK-3alpha Ser21Ala knock-in, GSK-3beta Ser9Ala knock-in, or wild-type mouse hearts were analyzed at baseline.
Please note that the wildtype samples were normalized twice for a separate analysis of GSK-3alpha vs wildtype and GSK-3beta vs wildtype. The wildtype samples are included on both series but are the same samples with identical CEL files.

first: Takahisa

last: Matsuda

first: Daniela

last: Zablocki

first: Junichi

last: Sadoshima


title: The mSWI/SNF ATPase module mediates subcomplex identity and non-catalytic targeting in SCCOHT [RNA-seq]

first: Joshua

last: Pan

first: Zach

last: McKenzie

first: Drew

last: D'Avino


title: Mouse skin samples after Zika virus-infected mosquito bites

status: Public on Mar 10 2019

city: New Haven

first: Ryuta

last: Uraki

state: CT

address: 300 Cedar Street

department: Internal Medicine

institute: Yale School of medicine

summary: Mouse skin bitten by Zika virus-infected mosquitoes were isolated and performed RNA-seq

overall_design: Examination of host responses after Zika virus-infected mosquito bites, in duplicate

first: Erol

last: Fikrig


title: Disruption of FBXL5-mediated cellular iron homeostasis promotes liver carcinogenesis

status: Public on Mar 09 2019

city: St. Louis

first: Yoshiharu

last: Muto

address: 660. S Euclid Ave., CB 8118

department: Medicine / Nephrology

institute: Washington University in St. Louis

summary: Hepatic iron overload is a risk factor for progression of hepatocellular carcinoma (HCC), although the molecular mechanisms underlying this association have remained unclear. We now show that the iron-sensing ubiquitin ligase FBXL5 is previously unrecognized oncosuppressor in liver carcinogenesis in mice. Hepatocellular iron overload evoked by FBXL5 ablation gives rise to oxidative stress, tissue damage, inflammation and compensatory proliferation in hepatocytes and to consequent promotion of liver carcinogenesis induced by exposure to a chemical carcinogen. The tumor-promoting effect of FBXL5 deficiency in the liver is also operative in a model of virus-induced HCC. FBXL5-deficient mice thus constitute the first genetically engineered mouse model of liver carcinogenesis induced by iron overload. Dysregulation of FBXL5-mediated cellular iron homeostasis was also found to be associated with poor prognosis in human HCC, implicating FBXL5 plays a significant role in defense against hepatocarcinogenesis.

overall_design: Total RNA was extracted from the nontumor and tumor tissue of an Alb-Cre/Fbxl5F/F male mouse (nontumor, n = 5; tumor, n = 5) or two littermate control Fbxl5F/F mice (nontumor, n = 6; tumor, n = 6) at 45 weeks of age.

first: Keiichi

last: Nakayama


title: Whole blood human transcriptome and virome analysis of ME/CFS patients experiencing post-exertional malaise following cardiopulmonary exercise testing

city: San Francisco

first: Charles

last: Chiu

state: CA

address: 185 Berry Street, Box 0134

department: Laboratory Medicine

institute: University of California, San Francisco

summary: Myalgic encephalomyelitis / chronic fatigue syndrome (ME/CFS) is a syndrome of unknown etiology characterized by profound fatigue exacerbated by physical activity, also known as post-exertional malaise (PEM). Previously, we did not detect evidence of immune dysregulation or virus reactivation outside of PEM periods. Here we sought to determine whether cardiopulmonary exercise stress testing of ME/CFS patients could trigger such changes. ME/CFS patients (n=14) and matched sedentary controls (n=11) were subjected to cardiopulmonary exercise on 2 consecutive days and followed up to 7 days post-exercise, and longitudinal whole blood samples analyzed by RNA-seq. Although ME/CFS patients showed significant worsening of symptoms following exercise versus controls, with 8 of 14 ME/CFS patients showing oxygen consumption (V̇O2) on day 2, transcriptome analysis yielded only 6 differentially expressed gene (DEG) candidates when comparing ME/CFS patients to controls across all time points. None of the DEGs were related to immune signaling, and no DEGs were found in ME/CFS patients before and after exercise. Virome composition (P=0.746 by chi-square test) and number of viral reads (P = 0.098 by paired t-test) were not significantly associated with PEM. These observations do not support transcriptionally-mediated immune cell dysregulation or viral reactivation in ME/CFS patients during symptomatic PEM episodes.

overall_design: RNAseq of whole blood samples from ME/CFS patients and controls following exercise.

first: Jerome

last: Bouquet

first: Tony

last: Li

first: David

last: Patrick

middle: Y


title: Neural stem cells of Parkinson’s disease patients exhibit aberrant mitochondrial morphology and functionality

city: Maastricht

first: Silvia

last: Bolognin

state: -- None selected --

address: Universiteitssingel 40,

institute: Maastricht University

summary: Emerging evidence suggest that Parkinson's disease (PD), besides being an age-associated disorder, might also have a neurodevelopment component. Disruption of mitochondrial homeostasis has been highlighted as a crucial cofactor in its etiology. Here, we show that PD patient-specific human neuroepithelial stem cells (NESCs) carrying the LRRK2-G2019S mutation recapitulate key mitochondrial defects previously described only in differentiated dopaminergic neurons. By combining high-content imaging approaches, 3D image analysis, and functional mitochondrial readouts we show that LRRK2-G2019S mutation caused aberrations in mitochondrial morphology and functionality compared to isogenic controls. LRRK2-G2019S NESCs displayed an increased number of mitochondria compared to isogenic control lines. However, these mitochondria were more fragmented and exhibited decreased membrane potential. Coherently, the release of total and mitochondrial redox oxidative species increased in LRRK2-G2019S NESC compared to controls. Functional alterations in LRRK2-G2019S cultures were also accompanied by a reduced mitophagic clearance via lysosomes. These findings support the hypothesis that preceding mitochondrial developmental defects contribute to the manifestation of the PD pathology later in life.

overall_design: Single-cell RNA-Sequencing experiments were performed on a total of 8 samples. These correspond to 4 time-points (Day 0, 10, 14 and 42). The time-point at 0 days refers to NESCs. The other time-points refer to Dopaminergic differentiation. Two cell-lines were analysed for each time-point: LRRK2-WT and LRRK2-G2019S.

first: Jonas

last: Walter

first: Suresh

last: Poovathingal

first: Luis

last: Salamanca

first: Stefano

last: Magni

first: Tomasz

last: Ignac

first: Jens

last: Schwamborn

first: Alexander

last: Skupin


title: The mSWI/SNF ATPase module mediates subcomplex identity and non-catalytic targeting in SCCOHT [ATAC-seq]

first: Cigall

last: Kadoch

institute: Dana Farber Cancer Institute

overall_design: SMARCA4/2 deficient BIN-67 cells were treated to overexpress WT and mutant versions of the SMARCA4 ATPase subunit of the mSWI/SNF complex. GFP was used as an expression control.

first: Joshua

last: Pan

first: Andrew

middle: R

last: D'Avino


title: Gene expression profiles in GSK-3alpha Ser21Ala knock-in mouse heart

first: Michinari

last: Nakamura

first: Takahisa

last: Matsuda

first: Daniela

last: Zablocki

first: Junichi

last: Sadoshima


title: Risk SNPs mediated promoter-enhancer switching promotes prostate cancer progression through lncRNA PCAT19 (ChIP-seq data set)

first: Junjie

last: Hua

summary: To determine the binding of H3K4me1 and H3K4me3 to PCAT19 locus, we performed ChIP-seq in 22Rv1 cells.

overall_design: Profiling H3K4me1 and H3K4me3 binding sites in 22Rv1 cells.

first: Housheng

last: He


title: The transcription factors TFEB and TFE3 link the FLCN-AMPK signaling axis to innate immune response and pathogen resistance [array]

status: Public on Mar 08 2019

city: Montreal

first: Alain

last: Pacis

state: QC

address: 740 Dr Penfield Ave

institute: Canadian Centre for Computational Genomics (C3G)

summary: TFEB and TFE3 are transcriptional regulators of the innate immune response, but the mechanisms regulating their activation upon pathogen infection are poorly elucidated. Using C. elegans and mammalian models, we report that the master metabolic modulator 5'-AMP-activated protein kinase (AMPK) and its negative regulator Folliculin (FLCN) act upstream of TFEB/TFE3 in the innate immune response, independently of the mTORC1 signaling pathway. In nematodes, loss of FLCN or overexpression of AMPK confers pathogen resistance via activation of TFEB/TFE3- dependent antimicrobial genes, while ablation of total AMPK activity abolishes this phenotype. Similarly, in mammalian cells, loss of FLCN or pharmacological activation of AMPK induces TFEB/TFE3-dependent pro-inflammatory cytokine expression. Importantly, a rapid reduction in cellular ATP levels in murine macrophages is observed upon lipopolysaccharide (LPS) treatment accompanied by an acute AMPK activation and TFEB nuclear localization. These results uncover an ancient, highly conserved and pharmacologically actionable mechanism coupling energy status with innate immunity.

overall_design: Gene expression profiles of wild-type and flcn mutant C. elegans.

first: Leeanna

last: El-Houjeiri

first: Elite

last: Possik

first: Tarika

last: Vijayaraghavan

first: Mathieu

last: Paquette

first: José

middle: A

last: Martina

first: Jalal

last: Kazan

first: Eric

last: Ma

first: Russell

last: Jones

first: Paola

last: Blanchette

first: Rosa

last: Puertollano

first: Arnim

last: Pause


title: The transcription factors TFEB and TFE3 link the FLCN-AMPK signaling axis to innate immune response and pathogen resistance [RNA-seq]

overall_design: Gene expression profiles of wild-type and aak-1(tm1944); aak-2(ok524) mutant C. elegans, after infection with S. aureus and OP50.


title: Transcriptomics modification consecutive to AS1842856 treatment in primary T lymphocytes

first: Marianne

last: Mangeney

address: rue Méchain

institute: CNRS/Inserm/Université Paris Descartes

summary: We have observed that the FOXO1 inhibitor AS1842856 induces a significant increase of both the bioenergetics and transcriptional activity of human T cells, together with a significant increase in their size, without any cell division. These modifications are accompanied by a decrease of p27 expression, contrasting with an increase of CDK2 cellular levels and by the phosphorylation of Rb and SAMHD1 proteins. As these changes are known to be characteristic of cells undergoing a G0 to G1 progression. To get an overall view of these changes in T-cell metabolism, we performed gene expression microarray analysis of PBT cultured during 7 days in the presence or not of AS1842856. We conclude that inhibition of FOXO1 by AS1842856 is sufficient to induce a profound reprogramming of human T lymphocytes, regulating their exit from quiescence.

overall_design: Primary T lymphocytes were cultured in the presence of 500 nM of AS1842856 or equivalent amount of DMSO. After 7 days of culture, cells were harvested and RNA was extracted and hybridized on Affymetrix microarrays.

first: Georges

last: Bismuth


title: Genome-wide maps of Twist2-binding, MyoD-binding and chromatin state in Twist2-overexpressing Twist2+ cells

city: Dallas

first: Stephen

last: Li

state: TX

address: 6000 Harry Hines Blvd

department: Molecular Biology

institute: University of Texas Southwestern Medical Center

summary: Integrated analysis of genome-wide ChIP-Seq and RNA-Seq data revealed the first dynamic chromatin and transcriptional landscape of Twist2 binding during myogenic differentiation. During differentiation, Twist2 competes with MyoD at shared DNA motifs to direct global gene transcription and repression of the myogenic program. Additionally, TWIST2 shapes the epigenetic landscape to drive chromatin opening at oncogenic loci and chromatin closing at myogenic loci.  These epigenetic changes redirect MyoD binding from myogenic genes towards oncogenic, metabolic, and growth genes.

overall_design: ChIP-Seq of Twist2, MyoD, H3K27ac, and H3K27me3 in Twist2-overexpressing Twist2+ myoblasts

first: Kenian

last: Chen

first: Spencer

last: Barnes

first: Venkat

last: Malladi

first: Lin

last: Xu


title: Single-cell profiling of glomerular cells provides a dynamic picture in experimental diabetic kidney disease

city: New York

first: Kemal

middle: Marc

last: Akat

state: NY

address: 1230 York Avenue

institute: The Rockefeller University

summary: Background: Recent single-cell RNA sequencing (scRNA-seq) analyses have offered much insight into cell-specific gene expression profiles in normal kidneys. However, in diseased kidneys, understanding of changes in specific cells, particularly glomerular cells, remains limited. Methods: To elucidate the glomerular cell–specific gene expression changes in diabetic kidney disease, we performed scRNA-seq analysis of isolated glomerular cells from streptozotocin-induced diabetic endothelial nitric oxide synthase (eNOS)–deficient (eNOS-/-) mice and control eNOS-/- mice. Results: We identified five distinct cell populations, including glomerular endothelial cells, mesangial cells, podocytes, immune cells, and tubular cells. Using scRNA-seq analysis, we confirmed the expression of glomerular cell–specific markers and also identified several new potential markers of glomerular cells. The number of immune cells was significantly higher in diabetic glomeruli compared with control glomeruli, and further cluster analysis showed that these immune cells were predominantly macrophages. Analysis of differential gene expression in endothelial and mesangial cells of diabetic and control mice showed dynamic changes in the pattern of expressed genes, many of which are known to be involved in diabetic kidney disease. Moreover, gene expression analysis showed variable responses of individual cells to diabetic injury. Conclusion: Our findings demonstrate the ability of scRNA-seq analysis in isolated glomerular cells from diabetic and control mice to reveal dynamic changes in gene expression in diabetic kidneys, with variable responses of individual cells. Such changes, which might not be apparent in bulk transcriptomic analysis of glomerular cells, may help identify important pathophysiologic factors contributing to the progression of diabetic kidney disease.

overall_design: Single-cell suspensions for single-cell RNAs-seq were prepared from whole glomeruli from 10-week old mice with diabetes or age- and sex-matched littermates. Glomeruli from 3 mice were pooled per condition and experiment, and two experiments were performed. The mice were eNOS deficient(eNOS-/-) on a C57BL/6 background. Diabetes was induced in 8-week old mice with streptozotocin injection over 5 consecutive days (50 μg/g body weight per day intraperitoneally. Age- and sex-matched littermates (controls) were injected with citrate vehicle. Single-cell RNA-seq was done on the Fluidigm C1 800-cell HT platform (v2), and sequenced paired-end on the Illumina NextSeq 500 platform.

first: Jia

last: Fu

first: Cijiang

last: He

first: Kim

last: Lee

first: Thomas

last: Tuschl