title: Alterations in DNA replication timing identify TP63 as a novel marker of progeroid diseases [RepliSeq]

city: Tallahassee

middle: M

last: Gilbert

address: 319 Stadium Drive

department: Biology

institute: Florida State University

summary: Progeroid syndromes are rare genetic disorders that phenotypically resemble natural aging. Despite identification of causal mutations, mechanisms that generate their clinical manifestations remain elusive. Here, we identified a DNA replication timing (RT) signature that distinguishes progeroid syndromes from normal aging and identifies TP63 gene as a new disease marker. Abnormal TP63 RT appears early during differentiation of progeroid iPSCs and is associated with altered gene variant expression. Our findings demonstrate the utility of RT signatures to identify novel biomarkers not detected by other methods, reveal abnormal TP63 RT as an early event in progeroid disease progression and offer TP63 gene regulation as a potential therapeutic target.

overall_design: Genome-wide replication timing profiles were constructed from HGPS patients, normal individuals of different ages and cells entering cellular senescence.

first: JuanCarlos

last: Rivera-Mulia


title: Histone locus regulation by the Drosophila dosage compensation adaptor protein CLAMP

status: Public on Nov 15 2017

city: Boston

first: Michael

last: Tolstorukov

state: MA

address: 185 Cambridge Street

department: Molecular Biology

country: USA

institute: Massachusetts General Hospital

type: Expression profiling by high throughput sequencing

summary: The conserved histone locus body (HLB) assembles prior to zygotic gene activation early during development and concentrates factors into a nuclear domain of coordinated histone gene regulation. Although HLBs form specifically at replication dependent histone loci, the cis and trans factors that target HLB components to histone genes remained unknown. Here we report that conserved GA-repeat cis elements within the bidirectional histone3-histone4 promoter direct HLB formation in Drosophila. In addition, the CLAMP zinc-finger protein binds these GA-repeat motifs, increases chromatin accessibility, enhances histone gene transcription, and promotes HLB formation. We previously demonstrated that CLAMP also promotes the formation of another domain of coordinated gene regulation: the dosage-compensated male X-chromosome. Therefore, CLAMP binding to GA-repeat motifs promotes the formation of two distinct domains of coordinated gene activation located at different places in the genome.

overall_design: Examination of gene expression in 0-2 and 2-4 hour Drosophila embryos after clamp depletion by RNAi

first: Leila

middle: E

last: Rieder

first: Kaitlin

middle: P

last: Koreski

first: Kara

middle: A

last: Boltz

first: Guray

last: Kuzu

first: Jennifer

last: Urban

first: Sarah

last: Bowman

first: Anna

last: Zeidman

first: William

middle: T

last: Jordan III

middle: Y

middle: F

last: Marzluff

first: Robert

middle: J

last: Duronio

first: Erica

middle: N

last: Larschan


title: Comprehensive analysis of Long non-coding RNA expression in dorsal root ganglion reveals cell type specificity and dysregulation following nerve injury [rodent DRG]

status: Public on Nov 21 2017

city: Oxford

first: Georgios

last: Baskozos

address: Level 6, West Wing, John Radcliffe Hospital

department: NDCN

country: United Kingdom

institute: Oxford University

type: Non-coding RNA profiling by high throughput sequencing

summary: Dorsal root ganglion (DRG) neurons provide connectivity between peripheral tissues and spinal cord. Transcriptional plasticity within DRG sensory neurons after peripheral nerve injury contributes to nerve repair but also leads to maladaptive plasticity, including the development of neuropathic pain. This study presents tissue and neuron specific expression profiling of both known and novel Long Non-Coding RNAs (LncRNAs) in rodent DRG following nerve injury. We have identified a large number of novel LncRNAs expressed within rodent DRG, a minority of which were syntenically conserved between mouse and rat and which including both- intergenic and antisense LncRNAs. We have also identified neuron type-specific LncRNAs in mouse DRG, and LncRNAs that are expressed in human IPS cell-derived sensory neurons. We show significant plasticity in LncRNA expression following nerve injury, which in mouse is strain dependant. This resource is publicly available and will aid future studies of DRG neuron identity and the transcriptional landscape in both naïve and injured DRG.

sample_organism:
Mus musculus
Rattus norvegicus

platform_organism:
Mus musculus
Rattus norvegicus

overall_design: RNA-seq Illumina HiSeq4000 of mouse DRG SNI vs Sham (BALB/c and B10.D2 strains, males and females), Illumina HiSeq2000 of rat DRG (Wistar strain, males) SNT vs sham

first: David

last: Bennett


title: RNA-Seq in neutrophils from Antiphospholipid Syndrome

city: Ann Arbor

first: Amr

last: Sawalha

state: MI

address: 1150 W. Medical Center Drive

institute: University of Michigan

summary: Antiphospholipid antibodies are a leading cause of thrombosis. To further elucidate the role of neutrophils in APS, we performed a comprehensive transcriptome analysis using the total RNA of neutrophils isolated from 9 patients with primary APS and 9 age, sex and ethnicity-matched healthy controls using next-generation RNA-seq.

overall_design: Next-generation RNA-Seq of 9 APS (primary antiphospholipid syndrome) and 9 CON (healthy control) neutrophil samples matched by age, sex and ethnicity.

first: Patrick

last: Coit

middle: H


title: RNA transcriptome analysis during HSV-1 infection

city: Chicago

first: Michaela

middle: U

last: Gack

state: IL

address: 920 E 58th St

department: Microbiology

institute: The University of Chicago

summary:
For Samples 1-8 and 11-18: The innate immune sensor retinoic acid-inducible gene-I (RIG-I) detects double-stranded RNA derived from RNA viruses, and recent studies have demonstrated that RIG-I also plays a role in the antiviral response to DNA viruses. To identify the physiological RNA species that are recognized by RIG-I during HSV-1 infection, we purified the RNAs that co-immunoprecipitated with FLAG-tagged RIG-I in transfected human embryonic kidney (HEK) 293T cells that had been infected with a recombinant HSV-1 (hereafter referred to as HSV-1 mut) containing a mutation (K220A) in the viral serine/threonine protein kinase US3 that abolishes its catalytic activity, as the viral kinase is known to antagonize type-I IFN responses. As controls, RNA species bound to FLAG-RIG-I in uninfected cells and RNA bound to FLAG-GFP from both HSV-1 mut-infected and uninfected cells were also purified. RIG-I-bound RNA and total RNA extracted from uninfected and HSV-1 mut-infected cells were analyzed by RNAseq, and the resulting sequences were mapped to both the HSV-1F-strain and human genome (hg38). This analysis revealed that several human transcripts were highly enriched in the RIG-I-bound fraction from infected cells; in contrast, the enrichment of viral sequences was low. The cellular transcripts that were most abundant in the RIG-I fraction were predominantly non-coding RNAs from different subclasses, as well as some coding RNAs.
For Samples 9 and 10: HSV-1 infection is known to induces changes in the transcriptional profile of the infected cell. To analyze global changes in RNA transcript levels in infected cells, total RNA was extracted from HEK 293T cells that were infected with wild-type (WT) HSV-1. For comparison, total RNA was extracted from HEK 293T cells that remained uninfected. Next, RNAseq analysis was performed. The resulting sequences were mapped to the human genome, and gene inductions were calculated and normalized to uninfected samples to determine changes in gene expression upon infection.

overall_design: Cells, which were not infected or infected with either wildtype HSV-1 or mutated HSV-1 were either subjected to a pulldown isolating RLR/GFP associated RNA (8 samples) or the corresponding total RNA (8 samples) was extracted from the infected cells and sequenced. Additionally, non-transfected cells were infected and total RNA extracted and sequenced (2 samples)

first: Jessica

last: Chiang

first: Konstantin

last: Sparrer


title: Control of plant cell fate transitions by transcriptional and hormonal signals [RNA-seq: mock_vs_dex_14h]

city: Heidelberg

first: Jan

last: Lohmann

address: Im Neuenheimer Feld, 230

department: Stem Cell Biology

country: Germany

institute: Centre for Organismal Studies

summary: Plant meristems carry pools of continuously active stem cells, whose activity is controlled by developmental and environmental signals. After stem cell division, daughter cells that exit the stem cell domain acquire transit amplifying cell identity before they are incorporated into organs and differentiate.  In this study, we used an integrated approach to elucidate the role of HECATE (HEC) genes in regulating developmental trajectories of shoot stem cells in Arabidopsis thaliana. Our work reveals that HEC function stabilizes cell fate in distinct zones of the shoot meristem thereby controlling the spatio-temporal dynamics of stem cell differentiation. Importantly, this activity is concomitant with the local modulation of cellular responses to cytokinin and auxin, two key phytohormones regulating cell behaviour. Mechanistically, we show that HEC factors directly modulate auxin signal transduction by physical interaction with MONOPTEROS (MP), a key regulator of auxin signalling, and thus interfere with the autocatalytic stabilization of auxin signalling.

overall_design: p16:HEC1-linker-GR;inflorescence meristems; 14hours; mock1,mock2,mock3,dex1,dex2,dex3

first: Christophe

last: Gaillochet


title: Epigenome-wide Effects of Vitamin-D on Bronchial Epithelial Cells using ATAC-Seq and RNA-seq

city: Seattle

first: Ting

last: Wang

state: WA

address: 1100 Fairview Ave. N.

department: Clinical Research

institute: Fred Hutchinson Cancer Research Center

type: Genome binding/occupancy profiling by high throughput sequencing

summary: Vitamin D has been associated with viral respiratory infections, the main cause of severe asthma exacerbations in children. We used ATAC-Seq to evaluate the effect of vitamin D on chromatin accessibility in immortalized (BEAS-2B), normal (NHBEC), and asthma (AAEC) bronchial epithelial cells cultured and stimulated with calcitriol, poly I:C (to simulate viral infection), both, or sham (culture media), as well as the effect on gene expression.

overall_design: ATAC-Seq and total RNA-Seq were performed on 4 asthma human bronchial epithelial cell samples (AAEC), 4 normal human bronchial epithelial cell samples (NHBEC) and 4 immortalized (BEAS-2B) samples, respectively treated with calcitriol, poly I:C, both or sham (culture media).

first: Juan

middle: C

last: Celedon


title: Control of plant cell fate transitions by transcriptional and hormonal signals

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

overall_design: Refer to individual Series


title: Control of plant cell fate transitions by transcriptional and hormonal signals [RNA-seq: mock_vs_dex_3h]

overall_design: p16:HEC1-linker-GR;inflorescence meristems; 3hours; mock1,mock2,mock3,dex1,dex2,dex3


title: Control of plant cell fate transitions by transcriptional and hormonal signals [ChIP-seq]

overall_design: p35S:HEC1-linker-GFP, seedlings, WT1, WT2, 35S-HEC1-1, 35S-HEC1-2


title: Effects of oxidative stress on mitotic recombination and genomic stability in yeast

city: Hangzhou

first: Daoqiong

last: Zheng

state: Zhejiang

address: 866 Yuhangtang Road

department: Institute of Microbiology

country: China

institute: College of Life Sciences, Zhejiang University

summary: Oxidative stress is a common factor threating genomic stability in almost all aerobic organisms. Using a yeast screening system, we measured the frequency of mitotic recombination was greatly elevated after H2O2 treatment. H2O2 was able to break chromatid directly in G1 synchronized cells and homologous recombination was induced to repair DNA double stand breaks at S/G2 phase. By whole genome SNP microarray and sequencing, the patterns of H2O2 induced loss of heterozygosity (LOH; gene conversion and crossover), chromosomal rearrangement, and aneuploidy changes were revealed. LOH events were the most common genomic alterations induced by H2O2 and were randomly distributed throughout the genome.

overall_design: JSC25 cells were grown in 7 mL YPD overnight to reach an OD600 of 0.2. Yeast cells (5×107) were collected by centrifugation and arrested in G1 in 1 mL YPD containing 2.5 μg α-factor at 300. After two hours, H2O2 was added into the cell culture. Cell culture was incubated at 300 for another hour. Yeast cells were then washed twice to remove α-factor and H2O2 before plating. Yeast  cells were cultured at 300  for 3 days and sectored colonies were selected for whole genome SNP microarray analysis.

first: Dao-Qiong

first: Thomas

middle: D

last: Petes


title: Melanoma therapeutic strategies that select against resistance by exploiting MYC-driven evolutionary convergence

status: Public on Nov 16 2017

city: Durham

first: Kris

last: Wood

state: NC

address: Box 3813 DUMC Department of Pharmacology and Cancer Biology

institute: Duke University

summary: Diverse pathways can drive resistance to BRAF and MEK inhibitors in BRAF mutant melanoma, suggesting that durable control of resistance will be a major challenge. By combining statistical modeling of genomic data from matched pre-treatment and post-relapse patient tumors with functional interrogation, we discovered that major pathways of resistance converge to activate the transcription factor c-MYC (MYC). MYC expression and pathway gene signatures were suppressed following initial drug treatment, then rebounded during tumor progression independent of the upstream pathway driving resistance. Suppression of MYC activity using either genetic approaches or BET bromodomain inhibition was sufficient to both sensitize diverse BRAFi/MEKi-resistant models and delay resistance in treatment naïve models. Although direct pharmacological inhibition of MYC remains difficult, the BRAFi/MEKi-resistant, MYC-activated state harbors “synthetic lethal” signaling and metabolic dependencies, including those involving SRC family and c-KIT tyrosine kinases as well as glucose, glutamine, and serine metabolic pathways, that can be targeted to create combination therapies that uniquely select against resistance evolution.

overall_design: Total RNA was isolated from A375 cells in biological triplicates in the following conditions: A375, A375-PLX4720 resistant clonal population, A375-MYC T58A, A375-PLX4720 resistant+shMYC

first: Katherine

middle: R

last: Singleton

first: Lorin

last: Crawford


title: Polyphosphate Metabolic Gene Expression Analyses Reveal Mechanisms of Phosphorus Accumulation and Release in Microlunatus phosphovorus Strain JN459

city: Jinan

first: Guangxiang

last: Cao

address: 18877 jingshi Road

institute: Shandong Academy of Medical Sciences

summary: The ability of Microlunatus phosphovorus to accumulate large amounts of polyphosphate (Poly-P) plays an important role in removing soluble phosphorus from wastewater. Our analyses indicate that Microlunatus phosphovorus  accumulates Poly-P under aerobic conditions but releases phosphorus under anaerobic conditions. To determine the mechanisms underlying Poly-P metabolism, we compared transcriptional profiles under aerobic and anaerobic conditions. Significant differences were detected in the expression levels of genes associated with Poly-P metabolism between aerobic and anaerobic conditions. These findings enhance our understanding of phosphate metabolism in a major bacterial species involved in wastewater phosphorus reduction.

overall_design: mRNA profiles of Microlunatus phosphovorus at 86 h and 92 h in SBR were generated by deep sequencing

first: Chuanqing

last: Zhong


title: Resident Macrophages are Locally Programmed for Silent Clearance of Apoptotic Cells

city: Berkeley

first: Jeffery

middle: S

last: Cox

state: CA

address: University of California, Berkeley Dept. of Molecular and Cell Biology 142 Weill Hall #3200

institute: University of California, Berkeley

summary: Although apoptotic cells (ACs) contain nucleic acids that can be recognized by Toll-like receptors (TLRs), engulfment of ACs does not initiate inflammation in healthy organisms. To better understand this phenomenon, we identified and characterized macrophage populations that continually engulf ACs in several distinct tissues. These macrophages share characteristics compatible with immunologically silent clearance of ACs, including high expression of AC recognition receptors, low expression of TLR9, and reduced TLR responsiveness to nucleic acids. When removed from tissues, these macrophages lose many of these characteristics and generate inflammatory responses to AC-derived nucleic acids, suggesting that cues from the tissue microenvironment are required to program macrophages for silent AC clearance. We show that KLF2 and KLF4 control expression of many genes within this AC clearance program. Coordinated expression of AC receptors with genes that limit responses to nucleic acids may represent a central feature of tissue macrophages that ensures maintenance of homeostasis.

overall_design: RNA sequencing on purified Tim-4+ peritoneal macrophages was performed on RNA isolated from macrophages immediately ex vivo (n=1) or after tissue culture for 60 hours (n=2) in two independent experiments. Tim-4+ peritoneal macrophages were stimulated + apoptotic cells (ACs) after tissue culture for 2 or 60 hours n=2 per experimental condition.

first: Allison

middle: W

last: Roberts

first: Bettina

middle: L

last: Lee

first: Jacques

last: Deguine

first: Shinu

last: John

first: Mark

last: Shlomchik

first: Gregory

last: Barton


title: Coop-Seq Analysis Demonstrates that Sox2 Evokes Latent Specificities in the DNA Recognition by Pax6

city: Munster

first: Veeramohan

last: Veerapandian

state: North Rhine-Westphalia

address: Röntgenstr. 20

department: Department Tissue Morphogenesis

institute: Max Planck Institute for Molecular Biomedicine

summary: Sox2 and Pax6 co-regulate genes in neural lineages and the eye by forming a ternary complex likely facilitated allosterically through DNA. We used the quantitative and scalable Cooperativity-by-sequencing (Coop-seq) approach to interrogate Sox2/Pax6 dimerization on a DNA library where five positions of the Pax6 half site are randomized yielding 1024 cooperativity factors. Consensus positions normally required for the high-affinity DNA binding by Pax6 need to be mutated for effective dimerization with Sox2. Out of the five randomized bases, a 5’ thymidin is present in most of the top ranking elements. However, according to structural models, this thymidin maps to a spacer region separating Sox and Pax half –sites and is not expected to directly interact with the binding proteins. Cooperative binding to the Coop-seq defined sequence signature was validated by classical EMSAs. Re-analysis of ChiPseq data identified several candidate elements in genomic regions co-bound by Sox2 and Pax6. A highly conserved Sox2/Pax6 bound site near the Sprouty2 locus consists of a prototype cooperativity signature. This element was verified to promote cooperative dimerization designating Sprouty2 as candidate target of Sox2/Pax6 in several mouse and human tissues including the brain and the eye. Collectively, the functional interplay of Sox2 and Pax6 demands the relaxation of high affinity binding sites and is enabled by alternative DNA sequences. We conclude that this binding mode evolved to warrant that a subset of target genes is only regulated in the presence of suitable partner factors.

overall_design: 1 Coop-seq experiment and 3 technical replicates.

first: Caizhen

last: Hu

first: Ralf

last: Jauch


title: Chromatin immunoprecipitation for genome-wide mapping of endogenous G-quadruplex DNA structures

city: Cambridge

first: Giovanni

last: Marsico

address: Robinson Way

institute: CRUK Cambridge Institute

summary: G-rich DNA sequences can form four-stranded G-quadruplex (G4) secondary structures and are linked to fundamental biological processes such as transcription, replication and telomere maintenance. G4s are also implicated in promoting genome instability, cancer and other diseases. Here, we describe a detailed G4 ChIP-seq method that robustly enables the determination of G4 structure formation genome-wide in chromatin. This protocol adapts traditional ChIP-seq for the detection of DNA secondary structures through the use of a G4-structure-specific phage display antibody with refinements in chromatin immunoprecipitation followed by high-throughput sequencing. Beginning with chromatin isolation and antibody preparation the entire protocol can be completed in less than 1 week including computational analysis.

overall_design: One cell line analysed with G4 ChIP-seq to detect the presence of G-Quadruplexes. Experiment performed in triplicates.

first: Robert

last: Hänsel-Hertsch

first: Jochen

last: Spiegel

first: David

last: Tannahill

first: Shankar

last: Balasubramanian


title: The HIV co-receptor CCR5, regulates the cellular architecture of osteoclast

city: Toon

first: Ji-Won

address: Shitsukawa

department: Proteo-Science Center

country: Japan

institute: Ehime University

summary: C-C chemokine receptor 5 (CCR5) is a co-receptor of HIV. Its ligand, CCL5 significantly augmented the number of wild-type osteoclasts but not Ccr5-deficient cells, indicating that CCL5 enhanced RANKL-induced osteoclastogenesis through CCR5. To investigate the changes in the transcriptional signatures induced by CCL5 in osteoclastogenesis, cultured osteoclasts at pOC stages were incubated with or without rmCCL5 for 2 days, and then subjected for RNA sequencing.

overall_design: mRNA profiles of primary bone marrow macrophages obtained from 7 weeks old C57BL6 mice were treated with recombinant CCL5, in triplicate, using Illumina Miseq.

first: Tadahiro

last: Iimura


title: SMAD2/3 binding pattern in a breast epithelial cell line, MCF10A MII [ChIP-seq]

city: Tokyo

first: Masato

last: Morikawa

address: 2-21-1 Kaga, Itabashi-ku

department: Advanced Comprehensive Research Organization

institute: Teikyo University

summary: We report that SMAD2/3 are redirected to novel binding sites on the genome after prolonged TGFβ stimulation.

overall_design: SMAD2/3 ChIP-seq analyses were performed in MCF10A MII cells at 2 different time points after TGFβ treatment.

first: Anders

last: Sundqvist

first: Eleftheria

last: Vasalaki

first: Daizo

last: Koinuma

first: Hiroyuki

last: Aburatani

first: Kohei

last: Miyazono

first: Hans

last: van Dam

first: Peter

last: ten Dijke


title: Regulation of the transition from mitosis to meiosis by the conserved RNA-helicase YTHDC2/BGCN [RNA-Seq]

city: Bethesda

first: Pedro

last: Batista

state: MD

address: 37 Convent Street Bldg 37

department: National Cancer Institute

institute: National Institutes of Health

summary: In the germline stem cell lineage, proliferating gonial cells switch from mitotic proliferation to meiotic prophase, marked by the onset of a cell-type-specific transcription program and a specialized cell cycle required to generate haploid gametes. The Drosophila gene benign gonial cell neoplasm (bgcn) encodes an RNA binding translational repressor required in fly testes for spermatogonia to stop dividing and transition to the spermatocyte state and meiosis. Here we show that the mammalian bgcn ortholog, YTHDC2, plays a key role in allowing a clean transition from mitosis to meiosis in both male and female germ cells in mouse, pointing towards a conserved role of post-transcriptional control of RNA translation and/or stability in this critical cell fate transition. Ythdc2-/- male germ cells undergo mitotic divisions but fail to properly execute meiotic prophase, instead attempting a mitotic-like division then undergoing cell death. Many meiotic markers were only weakly expressed in Ythdc2-/- testes compared to wild-type controls. Strikingly, the mitotic cyclin Cyclin A2, which is down-regulated prior to entry into meiotic prophase in wild-type, remained high in Ythdc2-/- germ cells that also expressed the meiotic marker SYCP3, suggesting that the mutant germ cells attempting to enter meiotic prophase have a mixed identity. YTHDC2 binds RNAs involved in both the mitotic cell cycle, including the mRNA Ccna2 that encodes Cyclin A2, as well as specific piRNA precursor RNAs and transcripts required for later stages of germ cell differentiation. YTHDC2-bound RNAs in testes were enriched for the m6A modification, suggesting that YTHDC2 may selectively regulate multiple target RNAs marked with m6A, to promote a clean transition from mitosis to meiosis and terminal differentiation.

overall_design: mRNA profiles for wild-type and YTHDC2/BGCN testis at P12 and P14 were generated by RNA sequencing. m6A modified transcripts were identified by immunopreciitation with an anti-m6A specific antibody followed by sequencing for P12 testes.

first: Alexis

last: Bailey

first: Rebecca

last: Gold

first: Y

middle: G

last: Chen

first: Dirk

last: de Rooij

first: Howard

last: Chang

first: Margaret

last: Fuller


title: Development and differentiation of early innate lymphoid progenitors

last: Cam

institute: NIH

summary: Early innate lymphoid progenitors (EILP) have recently been identified in the mouse adult bone marrow as a multipotential progenitor population committed to ILC lineages, but their relationship with other described ILC progenitors is still unclear. In this study, we examine the progenitor-successor relationships between EILP, IL-7R+ common lymphoid progenitors (ALP), and ILC precursors (ILCp). Bioinformatic, phenotypical, functional, and genetic approaches collectively establish EILP as an intermediate progenitor between ALP and ILCp. Our work additionally provides new candidate regulators of ILC development and clearly defines the stage of requirement of transcription factors key for early ILC development.

overall_design: transcriptional profiling of early ILC progenitors (EILP, ILCp), and common lymphoid progenitors (ALP) was performed by RNA sequencing

first: Christelle

last: Harly

first: Maggie

first: Jonathan

last: Kaye

first: Avinash

last: bhandoola


title: Chromatin state upon MSK1 downregulation by shRNA in dormant bone metastatic (DBM) cells.

city: Sabadell

first: Antoni

last: Berenguer-LLergo

state: Barcelona

address: Parc del Taulí, 1

department: A8G2 Group - Rheumatology Service

country: Spain

institute: Parc Taulí Research and Innovation Institute (I3PT)

summary: For many breast cancer (BCa) patients, symptomatic bone metastases appear after years or even decades of latency. How metastatic cells disseminate, and how micrometastatic lesions remain dormant and undetectable, are major questions in cancer research. Here we identify and functionally analyse a molecular mechanism involved in the bone metastatic latency of estrogen receptor (ER)+ BCa.

overall_design: ChIP-sequencing was performed on DBM shCTRL and DBM shMSK1 cells using antibodies recognizing 4 chromatin marks at histone H3 (H3K9ac, H3K9me3, H3K27ac, H3K27me3).

first: Sylwia

last: Gawrzak

first: Lorenzo

last: Rinaldi


title: Inhibition of ERG Activity in Patient Derived Prostate Cancer Xenografts using the Small Molecule Inhibitor YK-4-279

first: Ilsa

last: Coleman

address: 1100 Fairview Ave N, E2-112

department: Human Biology

institute: Fred Hutchinson Cancer Center

summary: ERG activity was blocked using YK-4-279 in three subcutaneously implanted ERG+ (LuCaP 23.1, 86.2, and 35) and one ERG- (LuCaP 96) PDX.  Tumor volume (TV), body weight (BW), serum prostate specific antigen (PSA), and overall survival (OS) were compared to vehicle treated controls.  Changes in gene expression were assessed by RNASeq and tissue microarrays were constructed to assess necrosis, proliferation, apoptosis, microvessel density, and ERG expression.

overall_design: RNA sequencing of tumors from from 16 animals (2 control, 2 treated from each of four patient derived xenograft lines) using Illumina HiSeq 2500.

first: Brian

last: Winters

first: Lisha

last: Brown

first: Holly

last: Nguyen

first: Tsion

middle: Z

last: Minas

first: Lori

last: Kollath

first: Valeri

last: Vasioukhin

last: Nelson

first: Eva

last: Corey

first: Aykut

last: Üren

first: Colm

last: Morrissey


title: JUNB is a critical AP1 component for SMAD2/3 binding after TGFβ stimulation [RNA-seq]

first: Masato

last: Morikawa

summary: We performed SMAD2/3 ChIP-seq analysis in MCF10A MII cells. To validate whether the changes in SMAD2/3 binding to the genome indeed resulted in changes in target gene expression, we performed RNA-seq transcriptome analysis after short and long periods of TGFβ stimulation (0, 1.5h and 16h) in MII cells. In addition, we revealed that JUNB is a critical AP1 component for SMAD2/3 binding after TGFβ stimulation. To assess the significance of JUNB for TGFβ-SMAD-target genes on a genome-wide scale, we also performed RNA-seq transcriptome analysis in JUNB-knock-downed MII cells.

overall_design: RNA-seq analysis in MCF10A MII cells with TGFβ stimulation and/or JUNB knock down

first: Anders

last: Sundqvist

first: Hans

last: van Dam

first: Peter

last: ten Dijke


title: The Unfolded Protein Response Regulator, ATF6, Promotes Mesodermal Differentiation

status: Public on Nov 14 2017

city: La Jolla

first: Evan

middle: Thomas

last: Powers

address: 10550 North Torrey Pines Rd

department: Chemistry

institute: The Scripps Research Institute

summary: ATF6 encodes a transcription factor that is activated during the Unfolded Protein Response to protect cells from ER stress. Loss of ATF6α and its paralog ATF6β, results in embryonic lethality, notochord dysgenesis, and in people, loss of ATF6α specifically, results in malformed neuroretina and congenital vision loss. These phenotypes implicate an essential role for ATF6 during vertebrate development. We investigated the function of ATF6 in development using human stem cells undergoing differentiation into multipotent germ layers, nascent tissues, and organs. We artificially activated ATF6 in stem cells with a recently identified small molecule ATF6 agonist, and we inhibited ATF6 using iPSCs from patients harboring ATF6 mutations. We discovered that ATF6 suppresses pluripotency, enhances differentiation, and surprisingly, guides stem cells toward mesodermal cell fates. Our findings reveal a novel role for ATF6 during differentiation and identify a new strategy to robustly create mesodermal tissues through modulation of the ATF6 arm of the UPR.

overall_design: Comparison of the transcriptomes of pluripotent stem cells before treatment and 13 days after treatment with either AA147 (a small molecule that activates the ATF6 pathway of the UPR) or RP22 (an inactive analog of AA147)

first: Heike

last: Kroeger

first: R

last: Wiseman

first: Jonathan

last: Lin


title: Regulation of the transition from mitosis to meiosis by the conserved RNA-helicase YTHDC2/BGCN

first: Pedro

last: Batista

overall_design: Refer to individual Series


title: Transcriptome sequencing of 15 normal lung parenchyma (NL), 17 atypical adenomatous hyperplasia (AAH) and 16 lung adenocarcinoma (LUAD) samples from 17 patients

city: Beirut

first: Humam

last: Kadara

address: Riad El Solh Street

department: Department of Biochemistry and Molecular Genetics, Faculty of Medicine

country: Lebanon

institute: American University of Beirut

summary: We sought to characterize expression profiles signifying the development of atypical adenomatous hyperplasia (AAH) from normal lung parenchyma (NL), and its progression to lung adenocarcinomas (LUAD).

overall_design: We performed transcriptome sequencing of 48 samples, comprising NLs, AAHs and LUADs, from 17 patients. Sequencing was performed using the Ion Torrent platform afterwhich gene profiles differentially expressed among the three groups were determined.

first: Smruthy

last: Sivakumar

first: Paul

last: Scheet


title: Control of plant cell fate transitions by transcriptional and hormonal signals [RNA-seq: cyc-mock_vs_cyc-dex_3h]

first: Jan

last: Lohmann

summary: Plant meristems carry pools of continuously active stem cells, whose activity is controlled by developmental and environmental signals. After stem cell division, daughter cells that exit the stem cell domain acquire transit amplifying cell identity before they are incorporated into organs and differentiate.  In this study, we used an integrated approach to elucidate the role of HECATE (HEC) genes in regulating developmental trajectories of shoot stem cells in Arabidopsis thaliana. Our work reveals that HEC function stabilizes cell fate in distinct zones of the shoot meristem thereby controlling the spatio-temporal dynamics of stem cell differentiation. Importantly, this activity is concomitant with the local modulation of cellular responses to cytokinin and auxin, two key phytohormones regulating cell behaviour. Mechanistically, we show that HEC factors directly modulate auxin signal transduction by physical interaction with MONOPTEROS (MP), a key regulator of auxin signalling, and thus interfere with the autocatalytic stabilization of auxin signalling.

overall_design: p16:HEC1-linker-GR;inflorescence meristems; 3hours; cyc-mock1,cyc-mock2,cyc-mock3,cyc-dex1,cyc-dex2,cyc-dex3

first: Christophe

last: Gaillochet


title: Insights into LMH cells response to fowl adenovirus serotype 4 (FAdV-4) infection by transcriptome analysis

city: Wuhan

first: Junqin

last: Zhang

address: Shizishan Street

institute: Huazhong Agricultural university

summary: To better understand the interactions between host and FAdV-4 infection at transcription level, and to explore the pathogenesis of this virus, a high-throughput RNA-seq technology was utilized in white leghorn male hepatocellular (LMH) cells at 12, 24, and 48 hours after FAdV-4 infection.

overall_design: The FAdV-4 infected and non-infected cells were collected at 12, 24, and 48 hpi. There were six groups: 12 h mock, 24 h mock, 48 h mock, 12 h infected, 24 h infected, and 48 h infected group. Each group had 3 biological replicates.

first: Zhong

last: Zou

first: Kun

last: Huang

first: Meilin

last: Jin


title: Characterisation of the effects of in situ fixation on DNA methylation levels

status: Public on Nov 13 2017

city: Paris

first: Rachel

last: Legendre

address: 28, rue du docteur Roux

department: Research and Resource Center for Scientific Informatics

country: France

institute: Institut Pasteur

type: Methylation profiling by high throughput sequencing

summary: Focusing on adult skeletal muscle stem cells, we have developed a protocol that circumvents the impact of the isolation procedures and captures the cells in their native quiescent state. We show that current isolation protocols induce major transcriptional changes accompanied by specific histone modifications, while having negligible effects on DNA methylation.

overall_design: RRBS analysis of muscle stem cells that were either live or fixed by 0.5% paraformaldehyde after the isolation procedure

first: Léo

last: Machado

first: Joana

last: Esteves de Lima

first: Odile

last: Fabre

first: Caroline

last: Proux

first: Anikó

last: Szegedi

first: Hugo

last: Varet

first: Lars

last: Ingerslev

first: Romain

last: Barrès

first: Frédéric

last: Relaix

first: Philippos

last: Mourikis


title: RNA-sequencing of mouse E14.5 embryonic neural stem cells transduced in vitro with a shRNA against Foxp1 or a scrambled shRNA

city: Utrecht

first: Paul

last: Coffer

address: Uppsalalaan 6

department: Regenerative Medicine Center

country: Netherlands

institute: UMC Utrecht

summary: Through RNA-sequencing we analysed the differentially expressed genes upon in vitro knockdown of Foxp1 in mouse E14.5 embryonic neural stem cells using one shRNA against Foxp1

overall_design: RNA-sequencing of mouse E14.5 embryonic neural stem cells transduced with lentivirus carrying 1 shRNA scrambled or 1 shRNA  against Foxp1 in biological duplicate (different passages)

first: L

last: Braccioli

first: S

last: Vervoort

first: P


title: Cohesin loss eliminates all loop domains [PRO-Seq]

city: Houston

first: Suhas

last: Rao

state: TX

address: 1 Baylor Plaza

department: Molecular and Human Genetics

institute: Baylor College of Medicine

summary: The human genome folds to create thousands of intervals, called “contact domains,” that exhibit enhanced contact frequency within themselves. “Loop domains” form because of tethering between two loci – almost always bound by CTCF and cohesin – lying on the same chromosome. “Compartment domains” form when genomic intervals with similar histone marks co-segregate. Here, we explore the effects of degrading cohesin. All loop domains are eliminated, but neither compartment domains nor histone marks are affected. Loss of loop domains does not lead to widespread ectopic gene activation, but does affect a significant minority of active genes. In particular, cohesin loss causes superenhancers to co-localize, forming hundreds of links within and across chromosomes, and affecting the regulation of nearby genes. We then restore cohesin and monitor the re-formation of each loop. Although re-formation rates vary greatly, many megabase-sized loops recovered in under an hour, consistent with a model where loop extrusion is rapid.

overall_design: we use in situ Hi-C, ChIP-Seq and PRO-Seq to probe nuclear architecture, the epigenome and transcription during cohesin loss and recovery. We performed PRO-Seq on HCT-116-RAD21-mAC cells before and after 6 hours of treatment with 500uM of the auxin hormone in order to measure acute effects of cohesin loss on nascent transcription. In addition, PRO-Seq was performed on HCT-117-CMV-OsTIR1 cells before and after auxin treatment to measure transcriptional changes in response to the auxin hormone.

first: Erez

last: Lieberman Aiden


title: Identification of quiescence and early activation histones modifications pattern in satellite cells

first: Rachel

summary: We report that the current stem cell isolation procedures induce important transcriptional and epigenetic modifications. Focusing on adult skeletal muscle stem cells (MuSCs), here we report the epigenome (Histone 3 modifications by ChIP-sequencing) of true quiescent MuSCs and compare it to early-activated MuSCs isolated by the conventional method.

overall_design: Histone 3 modifications (H3K4me3, H3K27ac, H3K27me3) ChIP-seq analysis of muscle stem cells that were either fixed in situ (T0) or isolated with the traditional dissociation protocol (T3).


title: Gene expression in green millet (Setaria viridis): developmentally regulated genes, transcription start sites, and stimulating introns

city: Chesterfield

first: Ian

last: Davis

state: MO

address: 700 Chesterfield Pkwy W

department: Biotechnology

institute: Monsanto Company

summary: Setaria viridis (green millet) is gaining popularity as a model C4 monocot due to its small size, rapid life cycle, and compact, sequenced genome. To analyze the structure and regulation of genes throughout development, the transcriptomes of 13 tissues at different stages of development were determined by RNA sequencing, and transcription start sites were mapped. Genes were identified that are differentially expressed in different developmental stages within the leaf, as well as in the apical meristem before and after the transition from vegetative to reproductive growth, and in panicles before and after anthesis. In a majority of genes, transcription initiated at the sequence YR within a narrow peak 20 – 40 nt downstream of a TATA box. Genes expressed in multiple tissues generally use the same transcription start site across all tissue types. Several introns were identified that increase gene expression. These results will increase understanding of plant development, improve the annotation of the Setaria genome, and provide tissue-specific or constitutive promoters for use in transgenic applications.

overall_design: RNA was isolated from wild-type Setaria viridis and sequenced from a total of 13 different samples at various stages during development, with three biological replicates per sample. Some replicates were sequenced more than once (a/b/…) to generate sufficient reads.

first: Alan

middle: B

last: Rose

first: Jennifer

middle: P

last: To

first: Matthew

last: Marengo

first: Tedd

last: Elich


title: Global gene expression analysis of two potato cultivars in response to “Candidatus Liberibacter solanacearum” infection

city: College Station

first: Cecilia

last: Tamborindeguy

address: Heep Center

institute: Texas A&M University

summary: In this study we compare the transcriptome response of two potato varieties Atlantic and NY138 to the infection by Candidatus Liberibacter solanacearum. Four weeks old potato plant grown in growth chamber were infested with potato psyllid to transmit the pathogen Candidatus Liberibacter solanacearum. Three weeks after infestation leaf samples were collected for RNA extraction and transcriptome analysis. This is the first transcriptome study on this potato disease.

overall_design: Two factorial design experiment with two potato varieites Atlantic and NY138, and two treatment: no infection compared to infection by Candidatus liberibacter solanacearum

first: Julien

last: Levy

first: Azucena

last: Mendoza

first: J

last: Miller Jr

first: Elizabeth

middle: A

last: Pierson


title: JNK promotes epithelial cells anoikis by transcriptional and post-translational regulation of BH3-only proteins

city: Worcester

first: Roger

address: 373 Plantation St Suite 309

institute: University of Massachusetts Medical School

summary: Developmental morphogenesis, tissue injury, and oncogenic transformation can cause the detachment of epithelial cells.  These cells are eliminated by a specialized form of apoptosis (anoikis).  While the processes that contribute to this form of cell death have been studied, the underlying mechanisms remain unclear.  Here we tested the role of the cJUN NH2-terminal kinase (JNK) signaling pathway using murine models with compound JNK-deficiency in mammary and kidney epithelial cells.  These studies demonstrated that JNK is required for efficient anoikis in vitro and in vivo.  Moreover, JNK-promoted anoikis required pro-apoptotic members of the BCL2 family of proteins.  We show that JNK acts through a BAK/BAX-dependent apoptotic pathway by increasing BIM expression and phosphorylating BMF leading to death of detached epithelial cells.

overall_design: In order to understand the role of the JNK pathway in anoikis, Rosa-CreER (Control) and Jnk1flox/flox Jnk2-/- Rosa-CreER (Jnk1-/-Jnk2-/-) cells were grown as attached monoloayers or suspended for 4 hours. RNA was isolated from these cells and subjected to RNASeq to measure differential gene expression.  Three separate samples from each condition were analyzed.

first: Nomeda

last: Girnius


title: Characterisation of the effects of paraformaldehyde fixation on transcript quality and composition in skeletal muscle stem cells (MuSCs)

last: Legendre

summary: We compared the transcriptome of isolated 0.5% paraformaldehyde-fixed MuSCs to Live (freshly isolated, not fixed) MuSCs by RNA-sequencing.

overall_design: RNA-seq analysis of muscle stem cells that were either live or fixed by 0.5% paraformaldehyde after the isolation procedure

first: Léo

last: Machado

first: Joana

last: Esteves de Lima

first: Odile

last: Fabre

first: Caroline

last: Proux

first: Anikó

last: Szegedi

first: Hugo

last: Varet

first: Lars

last: Ingerslev

first: Romain

last: Barrès

first: Frédéric

last: Relaix

first: Philippos

last: Mourikis


title: Arabidopsis thaliana sixth generation of mutant fas2 MNase-seq

city: Alicante

first: Angel

last: Barco

address: Ramon y Cajal

department: Neuro Plasticity

institute: NeuroSciences Institute of Alicante CSIC

summary: CAF-1 is a major nucleosome assembly complex, which functions particularly during replication and DNA-repair. Here, we studied how the nucleosome landscape changes in fas2 a mutant of the CAF-1 complex in the model plant Arabidopsis thaliana

overall_design: Comparison of nucleosome distribution between the sixth generation fas2 mutant and wt

last: Hennig

first: Rafael

middle: M

last: Viana


title: Regulation of the transition from mitosis to meiosis by the conserved RNA-helicase YTHDC2/BGCN [RIP-Seq]

first: Pedro

middle: J

last: Batista

summary: In the germline stem cell lineage, proliferating gonial cells switch from mitotic proliferation to meiotic prophase, marked by the onset of a cell-type-specific transcription program and a specialized cell cycle required to generate haploid gametes. The Drosophila gene benign gonial cell neoplasm (bgcn) encodes an RNA binding translational repressor required in fly testes for spermatogonia to stop dividing and transition to the spermatocyte state and meiosis. Here we show that the mammalian bgcn ortholog, YTHDC2, plays a key role in allowing a clean transition from mitosis to meiosis in both male and female germ cells in mouse, pointing towards a conserved role of post-transcriptional control of RNA translation and/or stability in this critical cell fate transition. Ythdc2-/- male germ cells undergo mitotic divisions but fail to properly execute meiotic prophase, instead attempting a mitotic-like division then undergoing cell death. Many meiotic markers were only weakly expressed in Ythdc2-/- testes compared to wild-type controls. Strikingly, the mitotic cyclin Cyclin A2, which is down-regulated prior to entry into meiotic prophase in wild-type, remained high in Ythdc2-/- germ cells that also expressed the meiotic marker SYCP3, suggesting that the mutant germ cells attempting to enter meiotic prophase have a mixed identity. YTHDC2 binds RNAs involved in both the mitotic cell cycle, including the mRNA Ccna2 that encodes Cyclin A2, as well as specific piRNA precursor RNAs and transcripts required for later stages of germ cell differentiation. YTHDC2-bound RNAs in testes were enriched for the m6A modification, suggesting that YTHDC2 may selectively regulate multiple target RNAs marked with m6A, to promote a clean transition from mitosis to meiosis and terminal differentiation.

overall_design: mRNA profiles for wild-type and YTHDC2/BGCN testis at P12 and P14 were generated by sequencing. m6A modified transcripts were identified by immunopreciitation with an anti-m6A specific antibody followed by sequencing for P12 testes. RNAs interacting with YTHDC2/BGCN were identified by immunoprecipitation with a anti-YTHDC2/BGCN specific antibody followe by sequencing for P12 testes. All experiments were performed in duplicates.

first: Alexis

last: Bailey

first: Rebecca

last: Gold

first: Y

last: Chen

first: Dirk

last: de Rooij

first: Howard

middle: Y

last: Chang

first: Margaret

middle: T

last: Fuller


title: Understanding lipid metabolism in high-lipid-producing Chlorella vulgaris mutants at the genome-wide level

city: Ann Arbor

first: mehmet

last: tardu

address: 930 N University Ave

institute: University of Michigan

summary: In this study, physical and chemical mutagenesis methods were applied to enhance lipid productivity in Chlorella vulgaris. Then, de novo RNA-seq was performed to observe lipid metabolism changes at the genome-wide level. Characterization of two mutants, UV-715 and EMS-25, showed marked increases in lipid contents, i.e., 42% and 45%, respectively. In addition, the biomass productivity of the UV-715 cells was 9% higher than that of wild-type cells. Furthermore, gas chromatography-mass spectrophotometry analysis showed that both mutants have higher fatty acid methyl ester (FAME) contents than wild-type cells. To understand the effect of mutations that caused yield changes in UV-715 and EMS-25 cells at a genome-wide level, we carried out de novo RNA-seq. As expected, the transcriptional levels of the lipid biosynthesis genes were up-regulated, while the transcriptional levels of genes involved in lipid catabolism were down-regulated. Surprisingly, the transcriptional levels of the genes involved in nitrate assimilation and detoxification of reactive oxygen species (ROS) were significantly increased in the mutants. The genome-wide analysis results highlight the importance of nitrate metabolism and detoxification of ROS for high biomass and lipid productivity.

overall_design: mRNA profiles of wild type and mutant (UV-715 and EMS-25) Chlorella vulgaris SAG 211-12 cells were generated at stationary phase cell culture by deep sequencing, in two biological replicates, using Illumina MiSeq platform.

first: Mehmet

last: Tardu

first: Ehsan

last: Sarayloo

first: I

middle: H

last: Kavakli


title: Therapeutic Inhibition of Inflammatory Monocyte Recruitment Reduces Steatohepatitis and Liver Fibrosis

city: Cologne

first: Ali

last: Abdallah

address: Joseph Stelzmann Str. 26

department: Medical Faculty

institute: University of Cologne

summary: The CCR2/CCR5 inhibitor cenicriviroc blocks infiltration of inflammatory monocytes into the liver, thereby reducing NASH progression and fibrosis.

overall_design: The study demonstrates the hepatic accumulation of inflammatory CCR2+ macrophages in patients with NASH fibrosis and reveals that the dual CCR2/CCR5 inhibitor CVC effectively ameliorates steatohepatitis and fibrosis in mouse models by inhibiting the infiltration of monocytes during chronic liver injury. Thus, this study provides functional evidence for the successful therapeutic targeting of monocyte recruitment in steatohepatitis and fibrosis, mandating the clinical development of CCR2/CCR5 inhibitors in patients with NASH.

first: Oliver

last: Krenkel

first: Tobias

last: Puengel

first: Olivier

last: Govaere

first: Jana

middle: C

last: Mossanen

first: Marlene

last: Kohlhepp

first: Anke

last: Liepelt

first: Eric

last: Lefebvre

first: Tom

last: Luedde

first: Claus

last: Hellerbrand

first: Ralf

last: Weiskirchen

first: Thomas

last: Longerich

first: Ivan

last: Costa

first: Quentin

last: Anstee

first: Christian

last: Trautwein

first: Frank

last: Tacke


title: c-Maf-dependent transcripts in effector Tregs from Peyer's patches

status: Public on Nov 11 2017

city: Durham

first: Maria

last: Ciofani

address: 207 Research Drive, 128 Jones Building

department: Integrative Immunobiology

institute: Duke University School of Medicine

summary: We identify c-Maf as an essential factor regulating adoption of RORgamma t+ and T follicular regulatory phenotypes in effector Tregs. Differential expression analysis demonstrates reduced signatures of both ROR gamma t+ Tregs and T follicular regulatory cells following regulatory T cell-specific c-Maf deletion.

overall_design: Differential expression analysis of Peyer's patch effector Tregs (CD4+FoxP3+CD62L-) from 13-week old Maf+/+FoxP3-YFP-cre or Mafflox/floxFoxP3-YFP-cre mice, performed in duplicate.

first: Joshua

middle: D

last: Wheaton


title: Staufen1 inhibits MyoD translation to actively maintain muscle stem cell quiescence

status: Public on Nov 12 2017

city: Seattle

first: Cindy

last: van Velthoven

address: 615 Westlake Ave N

institute: Allen Institute

summary: Tissue regeneration depends on the timely activation of adult stem cells. In skeletal muscle, the adult stem cells maintain a quiescent state and proliferate upon injury. We show that muscle stem cells (MuSCs) use direct translational repression to maintain the quiescent state. High resolution single molecule and single cell analyses demonstrate that quiescent MuSCs express high levels of Myogenic Differentiation1 (MyoD) transcript in vivo, whereas MyoD protein is absent. RNA pulldowns and co-stainings show that MyoD mRNA interacts with Staufen1, a potent regulator of mRNA localization, translation, and stability. Staufen1 prevents MyoD translation through its interaction with the MyoD 3’UTR. MuSCs from Staufen1 heterozygous (Staufen1+/-) mice have increased MyoD protein expression, exit quiescence, and begin proliferating. Conversely, blocking MyoD translation maintains the quiescent phenotype. Collectively, our data show that MuSCs express MyoD mRNA and actively repress its translation to remain quiescent yet primed for activation.

overall_design: Anti-Staufen1 RIP-seq in quiescent MuSCs

first: T

last: Rando

first: A

last: de Morree

first: C


title: The food-borne pathogen Campylobacter jejuni responds to the bile salt deoxycholate with countermeasures to reactive oxygen species

city: Pullman

first: Michael

middle: E

last: Konkel

institute: Washington State University

summary: Bile plays an important role in digestion, absorption of fats, and the excretion of waste products, while concurrently providing a critical barrier against colonization by harmful bacteria. Previous studies have demonstrated that gut pathogens react to bile by adapting their protein synthesis. The ability of pathogens to respond to bile is remarkably complex and still incompletely understood. Here we show that Campylobacter jejuni, a leading bacterial cause of human diarrheal illness worldwide, responds to deoxycholate, a component of bile, by altering global gene transcription in a manner consistent with a strategy to mitigate exposure to reactive oxygen stress. More specifically, continuous growth of C. jejuni in deoxycholate was found to: 1) induce the production of reactive oxygen species (ROS); 2) decrease succinate dehydrogenase activity (complex II of the electron transport chain); 3) increase catalase activity that is involved in H2O2 breakdown; and 4) result in DNA strand breaks. Congruently, by adding 4-hydroxy-TEMPO (TEMPOL), a superoxide dismutase mimic, that reacts with superoxide to cultures under deoxycholate-mediated ROS stress, C. jejuni growth in the presence of deoxycholate was rescued. We postulate that continuous exposure of a number of enteric pathogens to deoxycholate stimulates a conserved survival response to this stressor.

sample_organism: Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819

sample_organism: Campylobacter jejuni subsp. jejuni 81-176

sample_organism: Campylobacter jejuni subsp. jejuni F38011

overall_design: Three C. jejuni strains were grown in Mueller-Hinton broth without deoxycholate for 12 hours, or with 0.05% deoxycholate for 14, 16, or 18 hours. Samples were generated in duplicate and transcriptional profiles of the different conditions and times were compared.

first: Nicholas

last: Negretti

first: Christopher

middle: R

last: Gourley

first: Geremy

last: Clair

middle: N

last: Adkins


title: Characterization of transcriptional and epigenetic changes during mouse alternative macrophage polarization [ChIP-Seq II]

status: Public on Nov 10 2017

city: Debrecen

first: Gergely

last: Nagy

address: Egyetem ter 1.

department: Department of Biochemistry and Molecular Biology

country: Hungary

institute: University of Debrecen

summary: The molecular basis of signal-dependent transcriptional activation has been extensively studied in macrophage polarization, however our understanding remains limited regarding the molecular determinants of repression. Here we showed that IL-4-activated STAT6 transcription factor is required for the direct transcriptional repression of a large number of genes during mouse alternative macrophage polarization. Repression results in decreased lineage-determining transcription factor, p300 coactivator and RNA polymerase II binding followed by reduced enhancer RNA expression, H3K27 acetylation and chromatin accessibility. In addition, STAT6-repressed enhancers showed extensive overlap with the NF-κB p65 transcription factor cistrome and exhibited decreased responsiveness to lipopolysaccharide after IL-4 stimulus on a subset of genes.

first: Attila

last: Horvath

first: Laszlo


title: scRNAseq reveals heterogeneity among mouse bone marrow Ly6Chi monocytes produced by GMPs and MDPs

city: Cincinnati

first: Nathan

last: Salomonis

state: OH

address: 3333 Burnet Avenue

department: Biomedical Informatics

institute: Cincinnati Children's Hospital

summary: Granulocyte-monocyte progenitors (GMPs) and monocyte-dendritic cell progenitors (MDPs) produce monocytes during homeostasis and in response to increased demand during infection. Both progenitor populations are thought to derive from common myeloid progenitors (CMPs), and a hierarchical relationship (CMP-GMP-MDP-monocyte) is presumed to underlie monocyte differentiation. Here, however, we demonstrate that mouse MDPs arose from CMPs independently of GMPs, and that GMPs and MDPs produced monocytes via similar, but distinct, monocyte-committed progenitors. GMPs and MDPs yielded classical (Ly6Chi) monocytes with gene expression signatures that were defined by their origins and impacted their function. GMPs produced a subset of “neutrophil-like” monocytes, whereas MDPs gave rise to a subset of monocytes that yielded monocyte-derived dendritic cells. GMPs and MDPs were also independently mobilized to produce specific combinations of myeloid cell types following the injection of microbial components. Thus, the balance of GMP and MDP differentiation shapes the myeloid cell repertoire during homeostasis and following infection.

overall_design: RNA-Seq of monocyte from mice

first: Alberto

last: Yáñez

first: Simon

last: Coetzee

first: Andre

last: Olsson

first: D

last: Muench

first: B

last: Berman

first: Dennis

last: Hazelett

first: H

middle: L

last: Grimes

first: Helen

middle: S

last: Goodridge


title: Transcriptomic and proteomic landscape of mitochondrial dysfunction reveals secondary coenzyme Q deficiency in mammals

city: Bentley

first: Irina

last: Kuznetsova

address: Building 304, Kent Street

department: The Centre for Crop and Disease Management

country: Australia

institute: Curtin University

summary: Differential gene expression in mouse models of mitochondrial dysfunction

overall_design: various mutants vs. wild type

first: Inge

last: Kuhl

first: Maria

last: Miranda

first: Ilian

last: Atanassov

first: Yvonne

last: Hinze

first: Arnaud

last: Mourier

first: Aleksandra

last: Filipovska

first: Nils-Goran

last: Larsson


title: Characterization of transcriptional and epigenetic changes during mouse alternative macrophage polarization [ChIP-Seq I]

first: Gergely

last: Nagy

first: Attila

last: Horvath

first: Laszlo


title: Large-scale low-cost NGS library preparation using a robust Tn5 purification and tagmentation protocol [i5i7]

city: Barcelona

first: Lars

last: Velten

address: C. Dr. Aiguader 88, P05

department: Bioinformatics and Genomics

institute: CRG

summary: In recent years, tagmentation-based library preparation using a hyperactive version of the Tn5 transposase gained more and more popularity. The limited hands-on time, robustness and high efficiency of the method are essential for the processing of next-generation sequencing libraries from little input material like single cells or the processing of hundreds of samples simultaneously. The hyperactive Tn5 is commercially available (Nextera XT DNA library preparation kit), however, high-throughput experiments with hundreds of samples are costly. Here, we present a highly reproducible Tn5 transposase purification strategy via an N-terminal His6-Sumo3 tag and the workflow for the tagmentation-based NGS library preparation. We demonstrate that NGS libraries processed with the in-house produced Tn5 are of the same quality like those processed with the Nextera XT DNA library preparation kit and that the purification of the transposase is reproducible across institutes. Producing the Tn5 transposase in-house allows for customized experimental design and reduces costs of large-scale experiments dramatically. We describe a novel single cell polyadenylation site mapping protocol that benefits from the fact that the in-house produced Tn5 can be loaded with any desired linker oligonucleotide for tagmentation.

overall_design: For samples labeled i5i7, full-length cDNA was amplified from 15pg of HeLa RNA using the smart-seq2 protocol. 75-225pg of cDNA was tagmented using various conditions as outlined in the sample specification. Samples were sequenced using a dual-indexed single read strategy, unless specified differently. Technical tagmentation replicates were processed from the same cDNA input.

first: Bianca

last: Hennig

first: Ines

last: Racke

first: Chelsea

last: Tu

first: Matthias

last: Thoms

first: Hüseyin

last: Besir

first: Kim

last: Remans

last: Steinmetz


title: Transcriptional profiling of quiescent muscle stem cells in vivo

first: Cindy

last: van Velthoven

summary: Many stem cell populations exist in a quiescent state in vivo, exiting quiescence and entering the cell cycle in response to specific stimuli. In the case of skeletal muscle, the muscle stem cells (MuSCs, or “satellite cells”) are quiescent under normal homeostatic conditions and undergo activation and cell cycle entry in response to muscle fiber damage. Quiescent MuSCs are also much more potent than their proliferating progeny in assays of stem cell transplantation. In recent years, it has become increasingly apparent that the quiescent state is both actively maintained and dynamically regulated. However, most of the analyses of quiescent MuSCs have come from cells that have been removed from their niche in vivo, purified by fluorescence activated cell sorting, and then assay ex vivo. Although such cells are still in the quiescent state under these conditions, there is no doubt that significant biochemical changes will occur during the isolation and purification process. Thus, we have sought to examine the true in vivo quiescent state by analyzing the transcriptome of MuSCs. To achieve that, we have used techniques to label actively transcribing RNA in vivo using nucleoside analogs. In mice in which the enzyme uracil phosphoribosyltransferase (UPRT) is expressed specifically in MuSCs, administration of 4-thiouracil (4TU), which is converted to thiouridine (TU) by UPRT, resulted in labelling of MuSC transcripts, and the transcriptome could be analyzed following pull-down of TU-tagged RNA. Varying the timing of 4TU administration revealed the dynamic regulation of different subsets of transcripts. Notably, labeling transcripts during the isolation procedure revealed very active transcription of specific subsets of genes. Nevertheless, the ex vivo transcriptome remained largely reflective of the in vivo transcriptome. Using the transcriptional inhibitor, α-amanitin, we were also able to show that there was little difference between the steady-state transcript levels of the most highly expressed genes when comparing the ex vivo transcriptome with the in vivo transcriptome. Together, these data provide a novel view of the molecular regulation of the quiescent state at the transcriptional level, demonstrate the utility of these tools for probing transcriptional dynamics in vivo, and provide an invaluable resource for understanding stem cell state transitions.

overall_design: To examine nascent transcripts in MuSCs in vivo, Pax7CreER/+: UPRTHA/+ mice were injected with 4tU every 12 hours for 4 days (TU_4d), every 12 hours for 1 day (TU_1d), or 6 hours (TU_6h  in vivo) prior to harvesting of hindlimb muscles. Total RNA from hindlimb muscle (Input_muscle) was extracted and 4tU labelled transcripts were pulled down. In vivo labeling of MuSCs was compated to labeling nascent transcripts during the isolation procedure of MuSCs. During the ~6hr isolation procedure 4tU was added to the samples. Total RNA was isolated from purified MuSCs (Input_MuSC) and 4tU labeled RNA was pulled down (TU_sort ex vivo). The effect of nascent transcription on global RNA levels was determined by treating MuSC during the isolation procedure with the transcription inhibitor a-amanitin (MuSC_aAM) or DMSO control (MuSC_ctrlAM).

first: T

last: Rando

first: C


title: EZH2-bound RNAs associated with progression of prostate cancer

city: Rochester

first: LIGUO

last: WANG

state: MN

address: 200 1st St SW

department: Division of Computational Biology

institute: Mayo Clinic

summary: Through high-throughput RNA immunoprecipitation sequencing (RIP-seq), we discovered that EZH2 protein associates with messenger RNAs of a number of genes.

overall_design: Examination of EZH2-bound RNAs in 2 cell types (LNCaP, C4-2).

first: Haojie

last: Huang

first: Liguo

last: Wang

first: Liya

last: Ding


title: Single Cell RNA sequencing analysis of human haemopoietic lympho-myeloid progenitor populations (LMPP, MLP and GMP)

city: Cambridge

first: Evangelia

last: Diamanti

address: Wellcome Trust / MRC Building, Hills Road

department: Haematology

institute: University of Cambridge

summary: We performed single cell RNA sequencing of human haemopoietic lympho-myeloid progenitors with the aim to separate functionally and transcriptionally distinct progenitors within the heterogeneous GMP, LMPP and MLP populations. We performed RNA sequencing in a total of 415 single cells. From donors 1 (CB369) and 2 (CB431), 163/166 and 157/249 cells passed quality control.We further analysed the 320 single cells that passed quality control from two  different donors (157 and 163 from each donor; 91 LMPP, 110 MLP and 119 GMP). We performed clustering using Seurat package, which identified 3 clusters of cells.  We identified genes that were differentially expressed among cells of the different clusters. The majority of the cells in cluster 1 were MLP, the majority of cluster 3 were GMP while cluster comprised of LMPP and GMP cells. Cluster 1 showed high expression of lymphoid-affiliated genes. Conversely, cluster 3 showed increased expression of myeloid genes, while cluster 2 showed a mixed transcriptional signature. PCA analysis revealed a transcriptional continuum of LMPP, MLP and GMP populations.

overall_design: Transcriptional heterogeneity of LMPP, MLP and GMP human lymphomyeloid progenitors at the single cell level.

first: Fiona

last: Hamey

first: Dimitris

last: Karamitros

first: Bilyana

last: Stoilova


title: Anti-Warburg effect elicited by mitochondrial biogenesis drives differentiation of glioblastoma cells into astroglial cells

city: Guangzhou

first: Yizhao

last: Luan

state: Guangdong

address: Xianlie South Rd. 54, Yuexiu Dist

department: Zhongshan Ophthalmic Center

institute: Sun Yat-sen university

summary: Glioblastoma (GBM) is among the most aggressive of human cancers. Although differentiation therapy has been proposed to be potential approach to treat GBM, the mechanisms of induced differentiation remain poorly defined. Here, we established the induced differentiation model of GBM by using cAMP activators, which specifically directed GBM into astroglia. Next, transcriptomic and proteomic analyses uncovered oxidative phosphorylation and mitochondrial biogenesis were involved in induced differentiation of GBM. Further investigation showed dbcAMP reversed Warburg effect evidenced by increase of oxygen consumption and reduction of lactate production. Stimulated mitochondrial biogenesis downstream of CREB/PGC1α pathway triggered metabolic shift and differentiation. Blocking mitochondrial biogenesis by mdivi1 or silencing PGC1α abrogated differentiation, reversely over-expression of PGC1α elicited differentiation. In GBM xenograft models and patient-derived GBM samples, cAMP activators also induced tumor growth inhibition and differentiation. This study shows mitochondrial biogenesis and metabolic switch to oxidative phosphorylation drive the differentiation process of tumor cells.

overall_design: mRNA profiles of cell line DBTRG-05MG after 0h, 6h, 12h, 24h and 48h of dbcAMP treatment

first: Fan

last: Xing

first: Guangmei

last: Yan

first: Wenbo

last: Zhu


title: CD1c+ dendritic cell activation by Plasmodium falciparum-infected red blood cells

city: Saint Louis

first: Mei San

last: Tang

address: 660 S Euclid, Campus Box 8118

department: Pathology & Immunology

institute: Washington University in St Louis

overall_design: CD1c+ dendrtitic cells were purified from peripheral blood of 2 healthy donors and incubated with medium only, uninfected red blood cells, P. falciparum-infected red blood cells, or LPS for 6 hours

first: Anton

last: Goetz

first: Ana

last: Rodriguez

first: Mei


title: Context-dependent effects of Acf1 assessed in high throughput

city: Amsterdam

first: Bas

last: van Steensel

address: Plesmanlaan 121

department: division of Molecular Biology

institute: Netherlands Cancer Institute

summary: We applied a multiplexed genomic tethering assay (Brueckner, Epigenetics Chromatin, 2016; PMID:27777628) to elucidate the function of ACF1, the large subunit of the ACF nucleosome sliding complex in drosophila Kc167 cells. Targeting a Gal4DBD-ACF1 fusion to several hundred integrated reporters revealed a context-dependent repressive effect which is modulated by gene activity and chromatin state.

overall_design: TRIP assay in drosophila Kc167 cells combined with targeted recruitment of Gal4-Acf1 to integrated 5xGa4UAS-pMT-GFP reporters. Two technical replicate experiments of TRIP pool transfected with Gal4-Acf1, Gal4, Acf1 or Gal4-HP1 performed by day 2 after transient transfection.

first: Laura

last: Brueckner

first: Alessandro

last: Scacchetti

first: Peter

last: Becker


title: Defining lineage potential and fate behavior of precursors during pancreas development

summary: Pancreas development involves a coordinated process in which an early phase of cell segregation and patterning is proceeded by a longer phase of lineage restriction, expansion and extensive tissue remodeling. By combining quantitative clonal lineage tracing and whole-mount reconstruction with proliferation kinetics and single-cell transcriptional profiling, we define the functional basis of pancreas morphogenesis. Our results show that the large-scale organization of tissue can be traced to the activity of self-renewing precursors that localize at the termini of growing ductal branches and act collectively to drive serial rounds of stochastic ductal bifurcation balanced by termination. During this process, multipotent precursors give rise to self-renewing acinar-committed precursors, which are conveyed with growing ducts, as well as fate-restricted ductal progenitors that expand the trailing ducts and give rise to delaminating islet precursors. Together, these findings define quantitatively how the functional behavior and lineage progression of heterogeneous pools of the pancreatic precursors that define the organization of the organ.

overall_design: Single cell RNA sequencing of pancreatic E13.25 and E15.25 cells

first: Magdalena

last: Sznurkowska

first: Sonia

last: Nestorowa

first: Steffen

last: Rulands


title: Characterization of transcriptional and epigenetic changes during mouse alternative macrophage polarization

first: Gergely

last: Nagy

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

overall_design: Refer to individual Series


title: RNA Sequencing for reprogrammed beta cells

status: Public on Nov 09 2017

city: Pittsburgh

first: Xiangwei

last: Xiao

state: PA

address: 4401 Penn Ave

department: Surgery

institute: Children's Hospital of Pittsburgh

summary: Alpha-cell-derived INS+ cells (yellow cells) were isolated 1 month after AAV-PM (adeno-associated virus carrying pdx1 and mafA under the CMV promoter) infusion from ALX-treated GCG-Cre; R26RTomato; MIP-GFP mice, based on expression of tomato red (alpha-cell lineage) and GFP by flow cytometry. Sorted normal GFP+ beta cells and normal TOM+ alpha cells from GCG-Cre; R26RTomato; MIP-GFP mice without any treatment were used as controls.

overall_design: Examination of gene profile in reprogrammed mouse beta cells from alpha cells, compared to primary mouse beta cells and alpha cells

first: George

middle: K

last: Gittes


title: Characterization of transcriptional and epigenetic changes during mouse alternative macrophage polarization [GRO-Seq]

first: Attila

last: Horvath

first: Laszlo


title: Genomic imprinting of Xist by maternal H3K27me3

city: Boston

first: Lan

last: Jiang

state: Massachusetts

address: 200 Longwood Ave

institute: Boston Children Hospital

summary: Maternal imprinting at the Xist gene is essential to achieve paternal allele-specific imprinted X chromosome inactivation (XCI) in female mammals. However, the mechanism underlying the Xist imprinting is unclear. Here we show that the Xist gene is coated with H3K27me3 in mouse oocytes, which persists through preimplantation development. Ectopic removal of H3K27me3 induces maternal Xist expression and maternal XCI, indicating that maternal H3K27me3 is the imprinting mark of Xist.

overall_design: Examination of gene expression in 1 cell types.


title: Characterization of transcriptional and epigenetic changes during mouse alternative macrophage polarization [ATAC-Seq]


title: Transcriptome analysis of canine (Canis familiaris) corpus luteum (CL) during non-pregnant late luteal phase compared with normal luteolyzing CL collected at prepartum progesterone (P4) decrease and following antigestagen treatment.

city: Zurich

first: Ge

last: Tan

address: Winterthurerstrasse 190

department: Functional Genomics Center Zurich

country: Switzerland

institute: University of Zurich

summary:
Next-generation sequencing (RNA-Seq) was performed on CL from the late luteal phase and compared with normally luteolyzing CL collected at the prepartum P4 decrease, and following antigestagen (Aglepristone)- treatment.
The analysis of transcriptomes presented herein supports the hypothesis describing luteal regression in non-pregnant dogs as a degenerative process devoid of the acute luteolytic principle and without an acute involvement of the immune system observed prepartum. The contribution of the immune system seems, however, to be critical in the PGF2alpha-mediated active prepartum luteolysis, which appears to be an acute immune process. The antigestagen-medited effects point towards the withdrawal of the luteotropic function of P4 with lesser involvement of immune system than during natural luteolysis.
In summary, a deeper insights have been obtained into possible endocrine, paracrine and autocrine mechanisms governing the luteal life span in the domestic dog during pregnancy and in non-pregnant cycles.

overall_design: Corpora lutea (CL) from clinically healthy, cross-breed bitches (aged 2-8 years) were used representing the following experimental groups: (Group-1) mid-pregnancy (days 35-40); (Group-2) active prepartum luteolysis; (Group-3) antigestagen-treated mid-gestation group (days 40-45); (Group-4) non-pregnant bitches at late CL regression (day 65 after ovulation). In all dogs the time of ovulation was determined by measurements of P4 (> 5ng/ml) and by vaginal histology. Pregnant dogs were mated 2 days after ovulation (Day 0). To determine active prepartum luteolysis (Group-2), P4 concentrations in peripheral blood plasma were measured at 6 h intervals beginning on day 58 of pregnancy; when P4 levels in 3 consecutive measurements decreased below 2-3 ng/ml, the tissue material was collected. In Group 3, prepartum luteolysis/abortion was induced with the antigestagen aglepristone (Alizine; 10mg/Kg bw, 2x/24 h apart) and the tissues were collected 24h after the second application. All dogs underwent routine ovariohysterectomy. For RNA preservation, immediately after surgery the CL tissue were trimmed of surrounding ovarian tissue, washed with phosphate-buffered saline (PBS) and placed in RNAlater® (Ambion Biotechnologie GmbH, Wiesbaden, Germany) for 24 h at +4°C, and then stored at  -80°C until use.

first: Sophie

last: Latter

first: Mariusz

last: Kowalewski


title: Combinatorial control of gene expression in Aspergillus niger grown on sugar beet pectin

city: Utrecht

first: Ronald

last: de Vries

address: Uppsalalaan 8

department: fungal physiology

institute: Centre of fungal biodiversity

summary: The aim of this study was to better understand the contribution of the transcriptional activators GaaR, RhaR and AraR in regulation of pectin degradation in A. niger.

overall_design: Single, double and triple mutants of gaaR, rhaR and araR were constructed and their phenotype and transcriptional response on pectin was analyzed.

first: Joanna

last: Kowalczyk

first: Ronnie

last: Lubbers

first: Mao

last: Peng

first: Evy

last: Battaglia

first: Jaap

last: Visser


title: Active brown fat engages fatty acid synthesis through AKT2 stimulated ChREBP activity, simultaneously with fatty acid oxidation, to maintain fuel storage

city: Worcester

first: Dr Yvonne

last: Edwards

state: MA

address: 373 Plantation Street

department: Program in Molecular Medicine

institute: University of Massachusetts Medical School


title: Genome-wide studies of sympathetic neuron development

city: Shanghai

first: Youqiong

last: Ye

address: 280 Chongqing south road

institute: Shanghai Jiao Tong University School of Medicine


title: The stress granule transcriptome reveals principles of mRNA accumulation in stress granules.

city: Boulder

first: Roy

middle: Robert

last: Parker

state: CO

address: 3415 Colorado Ave

department: Chemistry and Biochemistry

institute: University of Colorado at Boulder

summary: Stress granules are mRNA-protein assemblies formed on nontranslating mRNAs. Stress granules are important in the stress response, related to neuronal mRNP granules, and aberrant stress granules contribute to some degenerative diseases.  By RNA-Seq and single molecule FISH, we describe the stress granule transcriptome in both yeast and mammalian cells. This reveals that while essentially every mRNA, and some ncRNAs, can be targeted to stress granules, the efficiency of targeting can vary from <1% to 73%. mRNA accumulation in stress granules is increased by longer coding regions, poor translatability, and correlates with some RNA binding proteins. Standardizing the RNA-Seq analysis by single molecule FISH allows a quantitative description of the general and stress granule transcriptome. Approximately 15% of the bulk mRNA molecules accumulate in stress granules suggesting their effect will be limited primarily to subsets of mRNAs highly accumulating in stress granules

sample_organism:
Saccharomyces cerevisiae
Homo sapiens

platform_organism:
Saccharomyces cerevisiae
Homo sapiens

overall_design: To determine the RNAs in mammalian stress granules, we purified and performed RNA-Seq in triplicate on SG cores from U-2 OS cells isolated following 60’ of arsenite exposure, referred to as SGRNA. For each sample, 5% of the lysate was extracted for RNA-Seq on the total RNA population, referred to as TotalRNA.  To determine the RNAs in yeast stress granules, we purified and sequenced the mRNAs within SG cores from Saccharomyces cerevisiae after induction of SGs by sodium azidefor 30 minutes. SGRNA and TotalRNA were isolated from three independent biological replicates and sequenced.

first: Anthony

last: Khong

first: Tyler

last: Matheny

first: Saumya

last: Jain

first: Sarah

middle: F

last: Mitchell

first: Joshua

last: Wheeler


title: Mutational landscape of aggressive natural killer-cell leukemia and drug profiling highlight JAK-STAT signaling as a therapeutic target in NK-cell malignancies

city: Helsinki

first: Olli

last: Dufva

address: Haartmaninkatu 8

country: Finland

institute: University of Helsinki

summary: Cell lines derived from NK cell neoplasms were characterized using RNA sequencing and high-throughput drug sensitivity profiling to identify therapeutically actionable drivers in malignant NK cells.

overall_design:
RNA sequencing data was obtained from natural killer and T cell lines for gene expression profiling and mutation detection in parallel with drug sensitivity profiling.

The 'NK_cell_line_GEO_drug_sensitivity.txt' contains drug sensitivity scores of cell lines screened using 459 compounds.
Breifly, compounds were preprinted on 384-well plates (Corning) in five different concentrations covering a 10,000-fold concentration range with an acoustic liquid handling device (Echo 550, Labcyte Inc.) and dissolved in 5   l culture medium on a shaker for 10 min. 20   l of single-cell suspension of cell lines (3,000 cells per well) were dispensed using Multi-Drop Combi peristaltic dispenser (Thermo Scientific). Plates were incubated at 37   C and 5% CO2 for 72 h after which cell viability was measured using CellTiter-Glo 2.0 reagent (Promega) according to the manufacturer   s instructions with a Pherastar FS plate reader (BMG Labtech). Cell viability luminescence data were normalized to DMSO-only wells (negative control) and 100 mM benzethonium chloride-containing wells (positive control). The data were quantified using the drug sensitivity score (DSS) (Yadav et al., Scientific Reports 2014).

first: Satu

last: Mustjoki


title: Genome wide chromatin modification associated with brown adipose tissue.

city: Saint Lucia, Brisbane

first: Tony

last: Vuocolo

state: Queensland

address: 306 Carmody Road

institute: CSIRO

summary: Chromatin immunoprecipitation coupled with Next Generation Sequencing (NGS) was used to find regions enriched for  the histone modifications, H3K27ac in perirenal adipose tissue  in late gestation sheep fetuses, (i.e.~ 2 weeks before birth) .   This tissue has a primary role in maintaining thermogenesis in new-born mammals.

overall_design: Genome wide chromatin modification  profiles  for H3K27ac and H3K4me3 of perirenal adipose tissue from sheep fetuses at 132 days of gestation (132 d post conception (dpc); term =150±3d) were generated by deep sequencing using Illumina GA11X or HiSeq2000 sequencing platform. Two biological replicates were analysed. The sequence reads that passed quality filters were mapped to sheep genome  assembly OARv3.1.74 using the mapping protocol in the CLC Genomics Workbench (v7.0).

first: Ross

last: Tellam

first: Marina

last: Naval-Sanchez


title: Temperature adaptation effects on BAT metabolism

summary: We are reporting here the effects of adaptation to different ambient temperatures in the whole genome gene expression of interscapular BAT

overall_design: B6/J mice were adapted to three different ambient temperatures (30ºC, 22ºC and 6ºC) for a period of 4 weeks.

first: Juan

last: Sanchez-Gurmaches

first: David

last: Guertin


title: Temperature adaptation effects on BAT metabolism in BAT specific Akt2 knockout mice

summary: We are reporting here the effects of adaptation to different ambient temperatures in the whole genome gene expression of interscapular BAT of BAT specific Akt2 knockout mice

overall_design: Wildtype littermates and brown fat specific Akt2 KO mice (using UCP1-CreER) in B6/J background were adapted to 2 different ambient temperatures (30ºC, 22ºC) for a period of 4 weeks.


title: Transcriptional profiling of Drosophila melanogaster photoreceptors following nuclei affinity enrichment

city: WEST LAFAYETTE

first: Vikki

last: Weake

state: INDIANA

address: 175 S. University St.

department: Biochemisty

institute: Purdue University

summary: Purpose: The goal of this study was to globally characterize the transcript levels of genes in Drosophila photoreceptor neurons. Using transcriptome profiling of isolated photoreceptor nuclei from day 10 flies, we identified genes with enriched or reduced transcript levels post nuclei isolation relative to the starting pre-isolation material (whole head RNA extracts).

overall_design: Method: RNA extracted from photoreceptor nuclei of flies aged from 10 days post-eclosion was used to generate cDNA libraries using NuGen Ovation Drosophila RNA seq system. Samples were sequenced using  Illumina HiSeq2500 next generation sequencer. Three paired biological replicates were sequenced for post and pre-isolation samples.

first: Hana

last: Hall

first: Patrick

last: Medina

first: Jeremiah

last: Rounds

first: Christopher

last: Vincent

first: Rebecca

last: Doerge


title: RNA seq analysis of adipocyte precursor cells (APC) from Per3 KO mice

city: Palo Alto

first: Brian

last: Feldman

address: SIM1 Lokey Building

institute: Stanford University

summary: Understanding the differences in the transcriptome of adipocyte precuror cells in Per3 KO mice compared with wild type mice

overall_design: In order to understand the transcriptome of APCs from Per3 KO mice, we FACS sorted APCS and isolated RNA at ZT2 from young Per3 KO and littermate control WT mice.


title: Characterization of transcriptional and epigenetic changes during mouse alternative macrophage polarization [RNA-Seq II]

city: Debrecen

first: Gergely

last: Nagy

address: Egyetem ter 1.

institute: University of Debrecen

summary: The molecular basis of signal-dependent transcriptional activation has been extensively studied in macrophage polarization, however our understanding remains limited regarding the molecular determinants of repression. Here we showed that IL-4-activated STAT6 transcription factor is required for the direct transcriptional repression of a large number of genes during mouse alternative macrophage polarization. Repression results in decreased lineage-determining transcription factor, p300 coactivator and RNA polymerase II binding followed by reduced enhancer RNA expression, H3K27 acetylation and chromatin accessibility. In addition, STAT6-repressed enhancers showed extensive overlap with the NF-κB p65 transcription factor cistrome and exhibited decreased responsiveness to lipopolysaccharide after IL-4 stimulus on a subset of genes.

first: Attila

last: Horvath

first: Laszlo


title: Small transcriptome analysis in wild-type and exo2-delta strains of S. pombe

city: Paris

first: Maxime

last: Wery

address: 26 rue d'Ulm

institute: Institut Curie

summary: Antisense transcription can regulate sense gene expression. However, previous annotations of antisense transcription units have been based on detection of mature antisense long non-coding (aslnc)RNAs by RNA-Seq and/or micro-arrays, only giving a partial view of the antisense transcription landscape and incomplete molecular bases for antisense-mediated regulation. Here, we used Native Elongating Transcript sequencing to map genome-wide nascent antisense transcription in fission yeast. Strikingly, antisense transcription was detected for most protein-coding genes, correlating with low sense transcription, especially when overlapping the mRNA start site. RNA profiling revealed that the resulting aslncRNAs mainly correspond to cryptic Xrn1/Exo2-sensitive transcripts (XUTs). ChIP-Seq analyses showed that antisense (as)XUTs expression is associated with specific histone modifications patterns. Finally, we showed that asXUTs are controlled by the histone chaperone Spt6 and respond to meiosis induction, in both cases anti-correlating with levels of the paired-sense mRNAs, supporting physiological significance to antisense-mediated gene attenuation. Our work highlights that antisense transcription is much more extended than anticipated and might constitute an additional non-promoter determinant of gene regulation complexity.

overall_design: Small RNA-Seq in wild-type and exo2-delta strains of S. pombe

first: Camille

last: Gautier

first: Marc

last: Descrimes

first: Mayuko

last: Yoda

first: Hervé

last: Vennin-Rendos

first: Valérie

last: Migeot

first: Daniel

last: Gautheret

first: Damien

last: Hermand

first: Antonin

last: Morillon


title: H3K14 and H4 acetylation in wild-type cells of S. pombe

overall_design: ChIP-Seq (H3, H3K14ac and H4ac) analyses in wild-type cells of S. pombe.


title: Native Elongating Transcript Sequencing reveals global anti-correlation between sense and antisense nascent transcription in fission yeast


title: Identification of the key genes related to oxidation stress tolerance in yeast using RNA-Seq DGE method

city: Beijing

first: Hongwei

last: ZHAO

address: No.17 Tsinghua East Road, Haidian District

department: Food Science and Nutritional Engineering

institute: China Agricultural University

summary: The differentially expressed genes in mutation strain and control strain were analyzed using RNA-Seq DGE method to reveal the mechanism of the oxidation stress tolerance in yeast.

overall_design: The mutation strain and control strain were grown in SC-Ura medium with or without H2O2. After entering mid-exponential phase, the total RNA were isolated for RNA-Seq to identify the differentially expressed genes. Then the identified genes were enriched to Gene Ontology Database to find the gene functions.Besides, KEGG pathway enrichment were also conducted in this study to explore the related metabolic pathway.

last: Zhao

first: Beizhong

last: Han


title: RNA-seq analysis of gene expression in scramble and GPR126 knockdown colon cancer cells (HT-29)

city: coralville

first: Wenjie

last: Yu

state: Iowa

address: 512 7th Ave apt 2

institute: The University of Iowa

summary:
Purpose: Identify genes regulated by GPR126 in colon cancer cells by RNA-seq analysis
Methods: Use shRNAs to knock down GPR126 in HT-29 cells, total RNAs from scramble group (NC) and GPR126 knockdown group (Sh1) were subjected to RNA-sequencing.
Results: Around 700 transcriptomes were up-regulated in GPR126 knockdown HT-29 cells, and 14000 transcriptomes were down-regulated in GPR126 knockdown HT-29 cells.GPR126 mainly regualtes genes from DNA synthesis and cell cycle-related pathways.
Conclusions: Our study firstly showed the function of GPR126 regulating colon cancer cell proliferation by targeting genes invovled in DNA synthesis and cell cycle-related pathways.

overall_design: RNA interference in colon cancer cell line HT-29, knock down GPR126 expression, and conduct gene expression profiling by RNA-seq. Two groups, one sample from each group.

first: Yu

last: Wenjie

first: Li

last: Dali


title: Characterization of transcriptional and epigenetic changes during mouse alternative macrophage polarization [RNA-Seq I]

first: Gergely

last: Nagy


title: Transcriptome change caused by lowered intracellular S-adenosylmethionine level in the X63/0 mouse plasma cell line.

city: Sendai

first: Mitsuyo

last: Matsumoto

address: 2-1 Seiryo-machi Aoba-ku

department: Biochemistry

institute: Tohoku university school of medicine

summary: We aimed to examine the gene expression changes responding to a depletion of intracellular S-adenosylmethionine (SAM). The mouse plasma cell line X63/0 was treated with the SAM-synthetase inhibitor cycloleucine (cLEU), and the total RNA was isolated and analyzed by RNA-sequencing. As a result, we idntified 27 genes, including the ubiquitous SAM-synthetase MAT2A, whose expssions were up-regulated by two-fold or more.

overall_design: Total RNA was extracted from the mouse plasma cell line X63/0 before/after a three-hour treatment with 30 mM cycloleucine. This experiment was triplicated, and the resulting six samples were applied to RNA-sequencing.

first: Hiroki

last: Shima

first: Kazuhiko

last: Igarashi


title: Comparison of tbx5-positive ventricular cardiomyoctes with the rest of ventricular cardiomyocytes from adult zebrafish hearts

status: Public on Nov 08 2017

city: Madrid

first: Manuel

last: Gomez

state: Madrid

address: Melchor Fernández Almagro, 3

institute: CNIC

summary: In vertebrates, the heart has two main layers of cardiac muscle, a peripheral compact layer and an internal trabecular layer. Little is known on the differerences in gene expression between both layers. In zebrafish the outer layer is named cortical layer and the internal also trabecular layer. Here we used a double transgenic line labelling with GFP tbx5-positive cells and cardiomyoctes with nuclear DsRed (nucDsRed) to distinguish cortical from trabecular myocardium. Then, we compared the transcriptome of trabecular and cortical myocardium in the adult zebrafish. We describe that Tbx5a is a good marker of trabecular myocardium.

overall_design: Four paired biological replicates consisting on Tbx5-positive and Tbx5-negative adult zebrafish ventricular cardiomyocytes were analysed by RNA-seq to compare their transcriptomic profiles.

first: N

last: Mercader

first: H

last: Sánchez-Iranzo


title: mRNA Sequencing of Human PromoCells Using Random Primed mRNA-Sequencing Technique

city: New York

first: Ravi

last: Iyengar

state: NY

address: 1425 Madison Avenue, Room 12-70C

department: Pharmacological Sciences

institute: Icahn School of Medicine at Mount Sinai

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

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

first: Yuguang

last: Xiong

first: Magali

last: Soumillon

first: Jie

last: Wu

first: Jens

last: Hansen

first: Bin

last: Hu

first: Johan

middle: G

last: van Hasselt

first: Gomathi

last: Jayaraman

first: Ryan

last: Lim

first: Mehdi

last: Bouhaddou

first: Loren

last: Ornelas

first: Jim

last: Bochicchio

first: Lindsay

last: Lenaeus

first: Jennifer

last: Stocksdale

first: Jaehee

last: Shim

first: Emilda

first: Dhruv

last: Sareen

first: Clive

last: Svendsen

first: Leslie

last: Thompson

first: Milind

last: Mahajan

first: Eric

last: Sobie

first: Evren

middle: U

last: Azeloglu

first: Marc

last: Birtwistle


title: Native Elongating Transcript Sequencing (NET-Seq) in wild-type fission yeast cells

first: Maxime

last: Wery

overall_design: NET-Seq analysis in wild-type cells of S. pombe

first: Camille

last: Gautier

last: Descrimes

first: Mayuko

last: Yoda

first: Hervé

last: Vennin-Rendos

first: Valérie

last: Migeot

first: Daniel

last: Gautheret

first: Damien

last: Hermand

first: Antonin

last: Morillon


title: Gene expression prpfoling of the pathogen, Nautella italica R11, in response to its macroalagl host

city: Sydney

first: Nandan

middle: P

last: Deshpande

state: NSW

address: Kensington Campus

department: School of Biotechnology and Biological Sciences

institute: Systems Biology Initiative

summary: RNA-Seq analysis of bacterial cultures of Nautella italica R11, Wild type strain and a RaiR gene disruption strain in the presence and absence of the red macroalga Delisea pulchra

overall_design: mRNA sequencing of bacterial cultures collected after exposure to D. pulchra. 3 independent replicates of the WT bacterial strain and 3 independent replicates of RaiR gene disruption mutant bacterial strain were assessed along with triplicate replicates of cultures of each strain which were not exposed that were used as controls

first: Jennifer

last: Hudson

first: Suhelen

last: Egan


title: Accurate Design of Translational Output by a Neural Network Model of Ribosome Distribution

status: Public on Nov 07 2017

city: Berkeley

first: Robert

last: Tunney

state: CA

address: Barker Hall

department: Computational Biology

institute: University of California, Berkeley

summary: We present a ribosome profiling data set from S. cerevisiae as part of a larger study that models the elongation rate along transcripts as a function of local sequence neighborhoods. We then apply this model to design coding sequences that are optimized for translational output.

overall_design: Two lanes of sequencing from one ribosome profiling experiment

middle: J

first: Nicholas

last: McGlincy

first: Monica

last: Graham

first: Nicki

last: Naddaf

first: Lior

last: Pachter

first: Liana

last: Lareau


title: The transcription factor Isl1 is associated with multiple signalling pathways important during genital development

city: Athens

first: Carlos

middle: Rafael

last: Infante

state: GA

address: 500 D.W. Brooks Dr

department: Genetics

institute: University of Georgia

summary: To identify regulatory targets of the transcription factor Isl1 in the developing mouse genitalia, we performed ChIP-Seq using an anti-ISL1 rabbit monoclonal antibody on pooled chromatin isolated from multiple E14.5 mouse embryonic genital tubercles (GT). Our analysis identified more than 7,054 genomic regions enriched in both of two replicates. The majority of these binding sites are located more than 5 kb from the closest annotated transcriptional start site (TSS), with nearly one third of the binding sites more than 50kb away from the nearest TSS. A de novo motif search using HOMER demonstrated that GT Isl1 ChIP-seq peaks are enriched for a motif that matches the consensus sequence bound by Isl1 in other tissues. When compared to active enhancers in the GT identified using H3K27ac ChIP-Seq, we found that Isl1 binding sites are strongly enriched in the GT compared to other embryonic tissues. Further analysis of the location of Isl1 peaks revealed a strong association with genes implicated in limb and urogenital development. We conclude that there is a strong association between Isl1 regulatory activity and genes involved in genital development.

overall_design: Examination of Isl1 transcription factor binding in two replicates of chromatin isolated from the developing genital tubercles of E14.5 mouse embryos using ChIP-Seq.

first: Sungdae

last: Park

first: Douglas

middle: B

last: Menke