title: Nuclear mTOR acts as a transcriptional integrator of the androgen signaling pathway in prostate cancer progression [ChIP-seq]

city: Québec City

first: Etienne

last: Audet-Walsh

state: QC

address: 2705 boulevard Laurier

department: Molecular Medicine

institute: Université Laval

summary:
Whether the nuclear fraction of mTOR plays a role in prostate cancer (PCa) and can participate in direct transcriptional crosstalk with the androgen receptor (AR) is as yet unknown. The intersection of gene expression, DNA binding-events, and metabolic studies uncovered the existence of a nuclear mTOR-AR transcriptional axis dictating the metabolic rewiring and nutrient usage of PCa cells. In human clinical specimens, nuclear localization of mTOR was significantly associated with metastasis and castration-resistant PCa (CRPC), correlating with a sustained metabolic gene program governed by mTOR in that context. This study thus uncovers an unexpected function of mTOR and underscores a paradigm shift from AR to mTOR as being the master transcriptional regulator of cell metabolism during PCa progression.
We performed ChIP-seq of mTOR to study its role in LNCaP cells with or without androgen stimulation. The study was done twice independently; processed data are shown as a pool of either vehicle-treated samples or R1881-treated samples.

overall_design: Cells were seeded in media deprived from steroids. 48h later, cell were treated with 10nM R1881 or vehicle (EtOH) for 48h before crosslink and ChIP.

first: Étienne

first: Vincent

last: Giguère


title: A genome-wide transcriptome and translatome analysis of Arabidopsis transposons identifies a unique and conserved genome expression strategy for Ty1/Copia retroelements

status: Public on Jul 18 2017

city: San Francisco

first: Stefan

last: Oberlin

address: 505 Parnassus Ave

department: Department of Microbiology and Immunology

country: USA

institute: University of California, San Francisco

type: Expression profiling by high throughput sequencing

type: Non-coding RNA profiling by high throughput sequencing

summary: Retroelements, the prevalent class of plant transposons, have major impacts on host genome integrity and evolution. They produce multiple proteins from highly compact genomes and, similarly to viruses, must have evolved original strategies to optimize gene expression, although this aspect has been seldom investigated thus far. Here, we have established a high-resolution transcriptome/translatome map for the near-entirety of Arabidopsis thaliana transposons, using two distinct DNA methylation mutants in which transposon expression is broadly de-repressed. The value of this map to study potentially intact and transcriptionally active transposons in Arabidopsis thaliana is illustrated by our comprehensive analysis of the co-transcriptional and translational features of Ty1/Copia elements, a family of young and active retroelements in plant genomes, and how such features impact their biology. Genome-wide transcript profiling revealed a unique and widely conserved alternative splicing event coupled to premature termination that allows for the synthesis of a short subgenomic RNA solely dedicated to production of the Gag structural protein and preferentially associates with polysomes for efficient translation. Mutations engineered in a transgenic version of the Arabidopsis EVD Ty1/Copia element further show how alternative splicing is crucial for the appropriate coordination of full length and subgenomic RNA transcription. We propose that this hitherto undescribed genome expression strategy, conserved amongst plant Ty1/Copia elements, enables an excess of structural versus catalytic components, mandatory for mobilization.

overall_design: Total RNA-seq and 3'end mRNA-seq from total RNA and polysome associated RNA in transposon derepressed backgrounds. Complementary, sRNA-seq in one background with strong transposon reactivation was generated.

first: Alexis

last: Sarazin

first: Clément

last: Chevalier

first: Olivier

last: Voinnet

first: Arturo

last: Marí-Ordóñez


title: TRIM28 interacts with EZH2 and SWI/SNF to activate genes that promote mammosphere formation

city: Houston

first: Yuanxin

last: Xi

state: TX

address: 1400 Pressler St

department: Bioinformatics and Computational Biology

institute: The University of Texas MD Anderson Cancer Center

type: Genome binding/occupancy profiling by high throughput sequencing

summary: EZH2 is generally associated with H3K27 methylation and gene silencing. Mass spectrometry of the EZH2-interactome in MCF7 cells revealed EZH2-interactions with SWI/SNF subunits and TRIM28, which formed a complex with EZH2 distinct from PRC2. Transcriptome profiling showed that EZH2 primarily activates transcription in MCF7 cells and with TRIM28 co-regulates a set of genes associated with stem cell maintenance and poor survival of breast cancer patients. TRIM28 depletion repressed EZH2 recruitment and expression of this gene set, in parallel with decreased CD44hi/CD24lo mammosphere formation.  These results support PRC2-independent functions of EZH2 and TRIM28 in mammary stem cell enrichment and maintenance.

overall_design: TRIM28 ChIP-seq, EZH2 KD RNA-seq and TRIM28 KD RNA-seq in MCF7 cells

first: Jing

last: Li


title: Genome-wide maps of GlcNAc bound proteins and Pho ChIP-seq in Drosophila S2 cells and pupae.

city: Burnaby

first: David

last: Vocadlo

state: British Columbia

address: 8888 University Drive

department: Chemistry

country: Canada

institute: Simon Fraser University

summary: We developed a strategy to map GlcNAc modified proteins based on a chemical chromatin precipitation strategy. Drosophila S2 cells, as well as wild type (wt) and sxc null pupae, were fed with 100 uM Ac4GalNAz  and the resulting DNA was cross-linked, sonicated, and  purified. DNA strands cross-linked to GlcNAz proteins were isolated by congugating with alkyn-biotin by Staudinger ligation followed by streptavidin purification. The resulting DNA was constructed into libraries for sequencing. To asses the robustness of our strategy, we compared GalNAz ChIP-seq results in S2 cells with two other GlcNAc ChIP-seq strategies, using a mutant β-1,4-galactosyltransferase (GalT) and the lecting wheat germ agglutinin (WGA). Briefly, GalT was incubated with cross-linked, sonicated and purified DNA along with UDP-GalNAz. Ligation to biotin with click chemistry followed by streptavidin purification resulted in library ready material. For WGA and Pho ChIP-seq, cross-linked and purified DNA was incubated with pho antibody or WGA resin and purified followed by library preperation.

overall_design: Examination GlcNAc bound loci in Drosophila cells and pupae.

first: Ta-Wei

last: Liu

first: Mike

last: Myschyshyn

first: Don

last: Sinclair

first: Samy

last: Cecioni

first: Kevin

last: Beja

first: Barry

middle: M

last: Honda

first: Ryan

middle: D

last: Morin


title: Early flower development

city: Grenoble

first: Christel

last: Carles

state: Auvergne/Rhone Alpes

address: 17 rue des Martyrs, bât. C2

department: Laboratoire Physiologie Cellulaire Végétale (LPCV)

country: France

institute: University Grenoble Alpes

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

overall_design: Refer to individual Series


title: Heterogeneous responses of hematopoietic stem cells to inflammatory stimuli are altered with age - bulk

status: Public on Jul 19 2017

city: Cambridge

first: Carl

middle: G

last: de Boer

state: MA

address: 415 Main St

institute: The Broad Institute

summary: This includes bulk RNA-seq samples for sorted LT-HSCs, ST-HSCs, and MPPs stimulated (or not) with LPS+PAM. Samples taken at various time points.

overall_design: sorted LT-HSCs, ST-HSCs, and MPPs stimulated (or not) with LPS+PAM at various time points

first: Monika

last: Kowalczyk

first: Arnav

last: Mehta

first: Mati

last: Mann


title: Allelic genome-wide maps of open chromatin state in zygotes and early embryo

city: Boston

first: Lan

last: Jiang

state: Massachusetts

address: 200 Longwood Ave

institute: Boston Children Hospital

summary: Mammalian sperm and oocytes have different epigenetic landscapes and are organized in different fashion. Following fertilization, the initially distinct parental epigenomes become largely equalized with the exception of certain loci including imprinting control regions. How parental chromatin becomes equalized and how imprinted genes escape this wave of reprogramming is largely unknown. Here we generated high-resolution maps of parental allele-specific DNase I hypersensitive sites (DHSs) in zygotes and morula embryos by using physically-isolated parental pronuclei, as well as parthenogenetic (PG) and androgenetic (AG) embryos. Allelic transcriptome analyses revealed a high correlation between allelic DHSs and allelic gene expression not only in known imprinted genes but also in dozens of genes not previously known to be imprinted. Interestingly, we found that many paternally- expressed genes harbor paternal allele-specific DHSs (Ps-DHSs) that are highly enriched for histone H3K27 tri-methylation (H3K27me3) but devoid of DNA methylation in maternal allele. Importantly, ectopic removal of the H3K27me3 turns Ps-DHSs into bi- allelic DHSs and induces maternal allele derepression in genes that include maternal DNA methylation-independent imprinted genes Gab1, Sfmbt2, Slc38a4, and Phf17 (also known as Jade1). Thus, our study not only reveals parental allele-specific chromatin accessibility of preimplantation embryos, but also identifies maternal H3K27me3 as a DNA methylation- independent mechanism for genomic imprinting.

overall_design: Examination of DHSs in 3 cell types and gene expression in 2 cell types.


title: Expression profiling during early flower development [RNA-seq]

summary: We studied early events of flower formation with a temporal resolution by employing a floral induction  system to drive synchronised flower development from inflorescence meristem-like tissue (Wellmer et al. (2006)). We  generated a developmental time series including vegetative leaf tissue, young developing flowers at  zero (t0) and two days after induction of flower development (t2), and fully expanded inflorescences. We analysed histone mark dynamics at those time points and the transcriptomics data presented here served to compare histone mark dynamics to transcriptome dynamics.

overall_design: Transcriptome analysis in four different developmental stage/tissues in Arabidopsis thaliana using RNA-seq

first: Julia

last: Engelhorn

first: Robert

last: Blanvillain

first: Hugues

last: Parrinello

first: Marine

last: Rohmer

first: Cristel

middle: C


title: Two MicroRNAs and NF-kB Act in a Unique Regulatory Network to Ensure Precision of the Acute Inflammatory Response in Macrophages

city: Stanford

first: Georgi

middle: Kolev

last: Marinov

state: California

address: 279 Campus Drive West, Beckman Center, B-257A/259

department: Genetics

institute: STANFORD UNIVERSITY

summary: The innate inflammatory response must be tightly regulated to ensure effective immune protection while avoiding inflammation-related pathologies. The transcription factor NF-kB is a critical mediator of the inflammatory response, and its dysregulation has been associated with immune related malignancies. We herein show that miR-155, miR-146a and NF-kB form a regulatory network that tunes the macrophage inflammatory response in mice. We show that elevated miR-155 expression potentiates NF-kB activity in miR-146a deficient mice, thus leading to an overactive acute inflammatory response and chronic inflammation. Enforced miR-155 expression overrides miR-146a-mediated repression of NF-kB activation, thus emphasizing that miR-155 plays a dominant, downstream role in promoting inflammation. We further show that miR-155 deficient macrophages exhibit a suboptimal inflammatory response when exposed to low levels of inflammatory stimuli. Importantly, we demonstrate a temporal asymmetry between miR-155 and miR-146a expression during macrophage activation, which forms a combined positive and negative feedback network on NF-kB activity. This miRNA based regulatory network enables a robust and time-limited inflammatory response essential for functional immunity.

overall_design: RNA-seq of wild-type and microRNA-146/155 knock-out bone marrow derived macrophages after LPS stimulation

middle: K

first: David

last: Baltimore


title: Analysis of gene expression in a ATRX loss-of-function line [RNA-seq]

city: Aubière

first: Céline

last: Duc

address: 10 Avenue Blaise Pascal

institute: CNRS

summary: Comparison between WT and atrx-1 mutant of genome expression to analyse the impact of loss of the ATRX chaperone

overall_design: 3 replicates for WT, 3 replicates for mutant were produced from 14d-old in vitro grown seedlings

first: Celine

first: Aline

last: Probst


title: Genome-wide dynamics of H3K27me3 and H3K4me3 during early flower development [ChIP-seq]

summary: We studied early events of flower formation with a temporal resolution by employing a floral induction  system to drive synchronized flower development from inflorescence meristem-like tissue (Wellmer et al. (2006)). We generated a developmental time series including vegetative leaf tissue, young developing flowers at  zero (t0) and two days after induction of flower development (t2), and fully expanded inflorescences. Although we found  very similar numbers of H3K27me3 and H3K4me3 target genes, many genes display quantitative  changes in those marks, especially between different tissue types (e.g. >60% of target genes change  quantitatively from leaf to t0).

overall_design: Examination of two different histone marks (H3K27me3 and H3K4me3) in four different tissues/developmental stages of Arabidopsis thaliana

last: Pose

first: Felix

last: Ott

first: Markus

last: Schmid


title: Characterization of microRNAs of Beta macrocarpa and their responses to Beet necrotic yellow vein virus infection [miRNA-seq]

status: Public on Jul 17 2017

city: Beijing

first: Junying

last: Liu

state: Beijing

address: yuan ming yuan weat road

department: Plant Pathology

country: China

institute: China Agricultural University

summary: Plant microRNAs (miRNAs) are a class of non-coding RNAs that play important regulatory roles in plant development, defense and abnormal disease symptom formation. Here, 547 known miRNAs, representing 129 miRNA families, and 282 potential novel miRNAs were identified in Beta macrocarpa using small RNA deep sequencing. Through a differential expression analysis, miRNAs responding to Beet necrotic yellow vein virus (BNYVV) infection were identified and confirmed using a microarray analysis. In total, 103 known miRNAs, representing 38 miRNA families, and 45 potential novel miRNAs were differentially regulated, with at least a two-fold change, in BNYVV-infected plants compared with the mock-inoculated control. These differentially expressed miRNAs were involved in hormone biosynthesis and signal transduction pathways, and enhanced axillary bud development and plant defenses. This work is the first to describe miRNAs of the plant genus Beta and may offer a reference for miRNA research in other species in the genus. It provides valuable information on the pathogenicity mechanisms of BNYVV.

overall_design: MicroRNAs of Beta macrocarpa and their responses to Beet necrotic yellow vein virus infection was investigated using systemic leaves of BNYVV-inoculated B. macrocarpa (15 dpi) as the experimental group and healthy plants as the control group by Illumina Hiseq2000.

first: Jun-ying

first: Cheng-gui

last: Han


title: SPOP mutation confers intrinsic BET inhibitor resistance in prostate cancer (ChIP-Seq)

status: Public on Jul 24 2017

city: San Antonio

first: Zhenqing

last: Ye

address: 8403 Floyd Curl Dr

department: 6Department of Population Health Sciences

institute: UT Health San Antonio

summary: Bromodomain and extraterminal domain (BET) protein inhibitors are emerging as promising therapeutics of cancers including prostate cancer.  The E3 ubiquitin ligase adaptor protein speckle-type POZ protein (SPOP) is implicated in human prostate cancers due to its frequent mutation.  Here we demonstrate that SPOP binds to the BET proteins BRD2, BRD3 and BRD4.  Wild-type SPOP, but not prostate cancer-associated mutants, promotes polyubiquitination and proteasome degradation of BET proteins by recognizing a common degron motif.  BET protein levels are highly elevated in SPOP-mutated prostate cancers in patients.  Expression of cancer-derived SPOP mutants upregulates cholesterol biosynthesis genes and confers resistance to the BET inhibitor in cultured prostate cancer cells and tumors in mice, and this effect can be overcome by the AKT inhibitor.  Our findings reveal BET proteins as proteolytic targets of SPOP and identify deregulated cholesterol biosynthesis as a downstream event of SPOP mutation-mediated tumorigenesis and therapy resistance in prostate cancer.

overall_design: Examination of BRD4 binding  in  SPOP wt and mutation stable cell lines with JQ1 treatment or in the BRD4 overexpression cells.

first: Yu

last: Zhao

first: Wang

last: Liguo

first: Haojie

last: Huang


title: Heterogeneous responses of hematopoietic stem cells to inflammatory stimuli are altered with age - single cell

first: Carl

last: de Boer

summary: This includes single cell RNA-seq samples for sorted LT-HSCs, ST-HSCs, and MPPs stimulated (or not) with LPS+PAM. Samples taken at 2 hours post stimulation (if applicable).

first: Monika

last: Kowalczyk

first: Arnav

last: Mehta

first: Mati

last: Mann


title: Nuclear mTOR acts as a transcriptional integrator of the androgen signaling pathway in prostate cancer progression

first: Etienne

last: Audet-Walsh


title: Heterogeneous responses of hematopoietic stem cells to inflammatory stimuli are altered with age


title: Defects in dosage compensation impact global gene regulation in the mouse trophoblast

city: Toyonaka

first: Koji

last: Nagao

state: Osaka

address: 1-1 Machikaneyama

department: Graduate School of Science

country: Japan

institute: Osaka University

summary: X chromosome inactivation (XCI) is critical for the development of the extraembryonic tissue as well as the embryonic tissue. Here we carried out transcriptomic analysis of the trophoblast isolated from two different Xist mutant embyros at E7.5 in comparison with wild-type.

overall_design: Allele-specific RNA-seq analysis of the trophoblast isolated from E7.5 embryos. Embryos were obtained from JF1 females crossed with B6 males carrying respective Xist mutations as well as B6 wild-type males.

first: Yuka

last: Sakata

first: Yuko

last: Hoki

first: Hiroyuki

last: Sasaki

first: Chikashi

last: Obuse

first: Takashi

last: Sado


title: Characterizing expression and processing of precursor and mature human tRNAs by hydro-tRNAseq and PAR-CLIP

city: New York

first: Tasos

last: Gogakos

state: NY

address: 1230 York Ave

institute: The Rockefeller University

summary: The participation of transfer RNAs (tRNAs) in fundamental aspects of biology and disease necessitates an accurate, experimentally confirmed annotation of tRNA genes, and curation of precursor and mature tRNA sequences. This has been challenging, mainly because RNA secondary structure and nucleotide modifications, together with tRNA gene multiplicity, complicate sequencing and sequencing read mapping efforts. To address these issues, we developed hydro-tRNAseq, a method based on partial alkaline RNA hydrolysis that generates fragments amenable for sequencing. To identify transcribed tRNA genes, we further complemented this approach with Photoactivatable Crosslinking and Immunoprecipitation (PAR-CLIP) of SSB/La, a conserved protein involved in pre-tRNA processing. Our results show that approximately half of all predicted tRNA genes are transcribed in human cells. We also report predominant nucleotide modification sites, their order of introduction, and identify tRNA leader, trailer and intron sequences. By using complementary sequencing-based methodologies, we present a human tRNA atlas, and determine expression levels of mature and processing intermediates of tRNAs in human cells.

overall_design: Four samples for hydro-tRNAseq in HEK293 cells. Two samples for SBB PAR-CLIP in HEK293 cells.

first: Thomas

last: Tuschl


title: Profiling Ssb-Nascent Chain Interactions Reveals Principles of Hsp70-Assisted Folding

city: Heidelberg

first: Kristina

last: Döring

address: Im Neuenheimer Feld 282

department: ZMBH

country: Germany

institute: Heidelberg University

summary: The yeast Hsp70 chaperone Ssb interacts with ribosomes and nascent chains to co-translationally assist protein folding. Here, we present a proteome-wide analysis of Hsp70 function during translation, based on in vivo selective ribosome profiling, that reveals mechanistic principles coordinating translation with chaperone-assisted protein folding. Ssb binds most cytosolic, nuclear, and mitochondrial proteins and a subset of ER proteins, supporting its general chaperone function. Position-resolved analysis of Ssb engagement reveals compartment- and protein-specific nascent chain binding profiles that are coordinated by emergence of positively charged peptide stretches enriched in aromatic amino acids. Ssbs’ function is temporally coordinated by RAC but independent from NAC. Analysis of ribosome footprint densities along orfs reveals that ribosomes translate faster at times of Ssb binding. This is coordinated by biases in mRNA secondary structure, and codon usage as well as the action of Ssb, suggesting chaperones may allow higher protein synthesis rates by actively coordinating protein synthesis with co-translational folding.

overall_design: Investigating the interaction of Ssb1 and Ssb2 with nascent polypeptide chains in four different strain backgrounds (WT, ssb1/2∆, RAC∆, NAC∆) and the translation speed in WT and ssb1∆ssb2 cells (all in replicates).

first: Nabeel

last: Ahmed

first: Trine

last: Riemer

first: Harsha

last: Suresh

first: Yevhen

last: Vainsthein

first: Markus

last: Habich

first: Jan

first: Matthias

middle: P

last: Mayer

first: Edward

last: O'Brien

first: Günter

last: Kramer

first: Bernd

last: Bukau


title: Tobacco mosaic virus infection alters phloem associated translatomes in Nicotiana benthamiana

city: College Park

first: James

middle: N

last: Culver

state: MD

address: 4291 Fieldhouse Dr.

department: Plant Science and Landscape Architecture

institute: University of Maryland, College Park

summary: In this study we used vascular specific promoters and a translating ribosome affinity purification strategy to identify phloem-associated translatome responses to infection by tobacco mosaic virus (TMV) in the systemic host Nicotiana benthamiana. Three different promoter:FLAG-RPL18 lines were used. These included two phloem specific promoters (pSUC2 and pSULTR2;2) as well as the more ubiquitously expressed cauliflower mosaic virus 35S promoter (p35S). Immunopurification of ribosome-mRNA complexes was accomplished by the method described in Reynoso et al. (Plant Functional Genomics: Methods and Protocols, 185-207; 2015).  The dataset includes samples from the leaves of 5-week-old plants inoculated with TMV (1 mg/mL) or mock inoculated with sterile water.

overall_design: 12 samples, 2 conditions (TMV or mock infected), 3 promoter lines, 2 biological replicates

first: Tamara

last: Collum


title: A genome-wide CRISPR activation screen identifies B4GALNT2 as an inhibitory host factor for influenza virus infection

city: Durham

first: Nicholas

last: Heaton

state: NC

address: 213 Research Drive, 426 CARL Building

department: Molecular Genetics and Microbiology

institute: Duke University School of Medicine

summary: Identification of factors to inhibit influenza virus infection

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: CRISPR activation technology was used to identify genes that rendered the cell refractory to infection. The complete sgRNA library (plasmid sample) were packaged into lentivirus and used to transduce A549 cells (transduced sample).  In three independent biological replicates, the transduced cells were infected with influenza virus, and the cells that were refractory to infection were collected and the sgRNAs enriched in those populations were sequenced (samples A, B, and C).

middle: S


title: p53 is essential for DNA methylation homeostasis in naïve embryonic stem cells, and its loss promotes clonal heterogeneity

city: Rehovot

first: Moshe

last: Oren

address: 234 Herzl St.

country: Israel

institute: The Weizmann Institute of Science

type: Methylation profiling by high throughput sequencing

summary: Development of a zygote into a multicellular organism involves many tightly regulated cellular processes, including the epigenetic landscaping of chromatin. When embryonic stem cells (ESCs) are induced to undergo differentiation, the transcriptional network ensuring pluripotency is silenced partly by de novo 5mC DNA methylation. Oxidation of 5mC to hydroxymethylcytosine (5hmC) by the TET enzymes adds another layer of regulation to DNA methylation in ESCs. The increase in 5mC methylation along with a decrease in 5hmC methylation is essential for the cellular commitment towards lineage specification. Recently, crosstalk between the p53 tumor suppressor and DNA methylation was demonstrated, earning p53 the title ‘guardian of the epigenome’. However, the involvement of p53 in regulation of DNA methylation throughout development remained unclear. Here we show that p53 regulates the expression of DNA methyltransferases (DNMTs), which set and maintain 5mC methylation, as well as of TETs, which catalyze 5hmC. In the absence of p53, basal 5mC levels are markedly augmented while hydroxymethylation is compromised. p53 and TETs co-localize on putative enhancers and appear to maintain them unmethylated. Furthermore, p53-/- ESCs acquire an aberrant DNA methylation pattern upon induced differentiation. Importantly, this aberrant pattern is carried over into adult liver. Our results imply that p53 dysfunction may lead to abnormal methylation setting in both ESCs and adult tissue. Thus, loss of p53 function may facilitate cancer development not only by permitting genomic instability but also by enabling epigenetic promiscuity.

overall_design: DNA methylation profile of  WT and p53-/- mESCs either cultured in 2i+LIF medium (naïve state) or induced to differentiate by retinoic acid (RA) treatment for 4 days, and adult Liver tissue was generated using the RRBS protocol followed by deep sequncing.

first: Ayala

last: Tovy

first: Adam

last: Spiro

first: Ryan

last: McCarthy

first: Zohar

last: Shipony

first: Yael

last: Aylon

first: Kendra

last: Alton

first: Elena

last: Ainbinder

first: Noa

last: Furth

first: Amos

last: Tanay

first: Michelle

last: Barton


title: Tobacco mosaic virus infection alters phloem associated translatomes in Arabidopsis thaliana

summary: In this study we used vascular specific promoters and a translating ribosome affinity purification strategy to identify phloem-associated translatome responses to infection by tobacco mosaic virus (TMV) in the systemic host Arabidopsis thaliana ecotype Shahdara. Three different promoter:FLAG-RPL18 lines were used. These included two phloem specific promoters (pSUC2 and pSULTR2;2) as well as the more ubiquitously expressed cauliflower mosaic virus 35S promoter (p35S). Immunopurification of ribosome-mRNA complexes was accomplished by the method described in Reynoso et al. (Plant Functional Genomics: Methods and Protocols, 185-207; 2015).  The dataset includes samples from the leaves of 5-week-old plants inoculated with TMV (1 mg/mL) or mock inoculated with sterile water.


title: RNA-seq of inguinal adipose tissue of mice with selective ablation of Hdac3 in adipose tissue

city: Milano

first: Maurizio

last: Crestani

address: via Balzaretti 9

country: Italy

institute: University of Milano

summary: Selective ablation of Hdac3 in adipose tissue switches the metabolic signature of white adipose tissue by potentiating oxidative capacity and boosting browning. To investigate the genome-wide consequences of the lack of Hdac3 in adipose tissue, we used RNA-seq to profile the gene expression program of inguinal adipose tissue from mice with selective ablation of Hdac3 in adipose tissue (H3atKO) and their respective control (floxed).

overall_design: We examined two experimental groups: H3atKO and floxed mice, fed with chow diet (LFD) and maintained in standard housing conditions. For each experimental group we examined 3 RNA sample replicates, each consisting in a pool of RNAs extracted from inguinal adipose tissue of 2/3 mice.

first: Alessandra

last: Ferrari

first: Rui

last: Silva

first: Raffaella

last: Longo

first: Béatrice

last: Desvergne

first: Federica

last: Gilardi


title: Single-cell expression profiling reveals new roles for G-protein-coupled receptors in the regulation of Th17 pathogenicity

status: Public on Jul 15 2017

city: Bad Nauheim

first: Mario

last: Looso

address: Ludwigstrasse 43

institute: Max Planck Institute for Heart and Lung Research

summary: G-protein coupled receptors (GPCRs) are pivotal in regulating T cell responses in steady state and inflammation. GPCR expression was intensively studied in bulk cDNA of T cell populations, but limited data are available with respect to expression in individual cells. We here present an analysis of a selected set of 125 different GPCRs expressed on distinct single T cells under naive conditions and during experimental autoimmune encephalomyelitis (EAE), the mouse model of multiple sclerosis. We found that neuroinflammation induces characteristic changes in GPCR heterogeneity and patterning, and we identified functionally relevant subgroups with specific GPCR expression profiles among spinal cord-infiltrating CD4 T cells. In spinal cord-infiltrating T helper 17 (Th17) cells, for example, expression of receptors such as Cxcr3, Cxcr4, P2ry10, or S1pr1 was associated with reduced pathogenicity, and we show that these correlations also exists on the protein level. Using CXCR4 and S1P1 as examples, we demonstrate that pharmacological targeting of these receptors is able to modulate Th17 pathogenicity in vitro and in vivo. Taken together, GPCR single-cell expression analysis provides a basis for the development of new strategies for pharmacological modulation of pathogenic immune cell subtypes.

overall_design: Investigation of RNA expression in HUVEC in response to siRNA based Lphn2 knockdown, scrambled siRNA as control, two siRNA knockdowns for Lphn2 with two replicates each

first: D

last: Tischner

first: N

last: Wettschureck


title: Post-transcriptional regulation by the let-7 microRNA and the TRIM-NHL protein LIN41

city: Basel

first: Dimos

last: Gaidatzis

address: Maulbeerstrasse 66

country: Switzerland

institute: Friedrich Miescher Institute

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

overall_design: Refer to individual Series


title: Post-transcriptional regulation by the let-7 microRNA and the TRIM-NHL protein LIN41 [RNA-seq]

summary: We perform RNA sequencing and ribosome profiling time course experiments to examine the effect of fully dysregulating all let-7 targets (in let-7(n2853) animals), partially dysregulating only LIN41 (in lin-41(xe11) animals) or fully dysregulating all let-7 targets while partially dysregulating LIN41 in lin-41(xe11); let-7(n2853) double mutant animals. We conclude that effects on gene expression in let-7 mutant animals are largely and quantitatively explained by dysregulation of LIN41 as its primary target. Furthermore, we identify direct LIN41 target genes regulated on the level of translation or mRNA abundance.

overall_design: Total RNA-sequencing time course experiments sampling synchronized worm populations of different genetic backgrounds every two hours over the course of development from late L2/early L3 stage to late L4/Young adult stage.

first: Florian

last: Aeschimann

first: Helge

last: Großhans


title: Post-transcriptional regulation by the let-7 microRNA and the TRIM-NHL protein LIN41 [Ribosome footprinting]

overall_design: Ribosome profiling time course experiments sampling synchronized worm populations of different genetic backgrounds every two hours over the course of development from late L2/early L3 stage to late L4/Young adult stage.


title: The transcription factor Sox2 regulates AID expression in class switched B cells

first: Jayanta

last: Chaudhuri

address: 415 E 68th Street Z-1464

department: Immunology

institute: Memorial Sloan Kettering Cancer Center

summary: The transcription factor Sox2 is expressed in activated B cells following the initiation of immunoglobulin heavy chain class switch recombination (CSR), a reaction that deliberately introduces double strand breaks into the DNA. These lesions are generally highly toxic to the cell, so the reaction must be tightly controlled. This experiment used an overexpression model to test the hypothesis that Sox2 can regulate different aspects of the class switching reaction.

overall_design: B cells were isolated from mouse spleen and stimulated ex vivo with anti-CD40 and IL4. At 24 and 48h of stimulation, cells were retrovirally infected with pMIR or pMIR-Sox2 and sorted at 96h based on mCherry expression. Total RNA from pMIR-Sox2 cells was compared to pMIR control cells for changes in gene expression.

first: Lauren

middle: J

last: DiMenna

first: Wei-Feng

last: Yen

first: Zara

last: Saldanha

first: Rahul

last: Sharma


title: Targeted reconstruction of T cell receptor sequence from single cell RNA-seq links CDR3 length to T cell differentiation state

city: Berkeley

first: Shaked

last: Afik

state: CA

address: Stanley Hall

department: Computational Biology Graduate Group

institute: UC Berkeley

summary: The T cell compartment must contain diversity in both T cell receptor (TCR) repertoire and cell state to provide effective immunity against pathogens. However, it remains unclear how differences in the TCR contribute to heterogeneity in T cell state. Single cell RNA-sequencing (scRNA-seq) can allow simultaneous measurement of TCR sequence and global transcriptional profile from single cells. However, current methods for TCR inference from scRNA-seq are limited in their sensitivity and require long sequencing reads, thus increasing the cost and decreasing the number of cells that can be feasibly analyzed. We present TRAPeS, a publicly available tool that can efficiently extract TCR sequence information from short-read scRNA-seq libraries. We apply it to investigate heterogeneity in the CD8+ T cell response in humans and mice, and show that it is accurate and more sensitive than existing approaches. Coupling TRAPeS with transcriptome analysis of CD8+ T cells specific for a single epitope from Yellow Fever Virus (YFV), we show that the recently described “naive-like” memory population have significantly longer CDR3 regions and greater divergence from germline sequence than do effector-memory phenotype cells. This suggests that TCR usage is associated with the differentiation state of the CD8+ T cell response to YFV.

overall_design: We applied and tested TRAPeS to scRNA-seq data from a range of CD8+ T cell responses. These data sets were selected to include both mouse and human CD8+ T cells as well as those expected to have a range of TCR complexities. In mice, we used the lymphocytic choriomeningitis virus (LCMV) infection model, and profiled CD8+ T cells responding to either acute or chronic infection (using the Armstrong and Clone 13 strains of LCMV, respectively). In healthy human subjects we profiled naive CD8+ T cells, effector memory CD8+ T cells, and antigen-specific CD8+ T cells elicited by CMV infection; vaccination with the live attenuated yellow fever virus infection (YFV-17D); or by vaccination with adenoviral and modified vaccinia Ankara vectors encoding HCV proteins. We sorted up to 128 single CD8+ T cells from each dataset to a total of 565 cells, and generated scRNA-seq libraries with short (25-30bp) paired-end reads. To evaluate the accuracy of TRAPeS, we compared its output with that of directly sequencing the TCR sequence using long reads (in which reconstruction is not required). To that end, we sequenced libraries of epitope-specific cells for Clone 13, Armstrong and CMV, and naive T cells from the CMV donor with both short (25-30bp) paired-end and 150bp single-end sequence reads.

first: Kathleen

middle: B

last: Yates

first: Kevin

last: Bi

first: W

last: Haining

first: Nir

last: Yosef


title: Zebrafish zic2 controls formation of periocular neural crest and choroid fissure morphogenesis

status: Public on Jul 14 2017

city: Madison

first: Oleg

last: Moskvin

state: WI

address: 1220 Capitol Court

institute: University of Wisconsin-Madison

summary: RNA-seq transcriptome analysis identified an early requirement for zic2 in periocular neural crest as an activator of alx1, a transcription factor with essential roles in craniofacial and ocular morphogenesis in human and zebrafish

overall_design: Embryos derived from a zic2aGBT133/+; zic2bUW1127/+  incross were sorted by presence or absence of coloboma.  RNA was prepared from each individual embryo at ~ 25 hpf

first: Irina

last: Sedykh

first: Baul

last: Yoon

first: Laura

last: Robertson

first: Colin

last: Dewey

first: Yevgenya

last: Grinblat


title: The Ino80 complex mediates epigenetic centromere propagation via active removal of histone H3

city: Daejeon

first: Youngseo

last: Cheon

address: 291 Daehak-ro, Yuseong-gu

country: South Korea

institute: Korea Advanced Institute of Science and Technology

summary: Centromere is the chromosomal locus at which kinetochore is assembled to direct chromosome segregation. Histone H3 variant CENP-A epigenetically marks active centromeres; however, the mechanism by which CENP-A propagates at the centromere, replacing histone H3, remains poorly understood. Using fission yeast, we find that CENP-ACnp1 chromatin assembly at the centromere requires the Ino80 ATP-dependent chromatin remodeling complex which removes histone H3-containing nucleosomes from associated chromatin. CENP-ACnp1 chromatin actively recruits the Ino80 complex to centromeres to elicit eviction of histone H3-containing nucleosomes. Artificial targeting of Ino80 subunits to a non-centromeric DNA placed in a native centromere enhances the spreading of CENP-ACnp1 chromatin into the non-centromeric DNA. Based on these results, we propose that CENP-ACnp1 chromatin employs the Ino80 complex to mediate replacement of histone H3 with CENP-ACnp1, and thereby reinforces itself.

overall_design: ChIP-Seq samples of CENP-ACnp1, histone H3, Flag-tagged Ino80 subunits in wild type (wt) and various mutants were prepared using fission yeast.

first: Eun-Shik

last: Choi

first: Young-Seo

first: Keunsoo

last: Kang

first: Daeyoup

last: Lee


title: Gene expression profiling of continuous growth hormone infused (cGH) adult male mouse liver by RNA-seq analysis of rRNA-depleted liver RNA. [G137_G138]

city: Boston

first: David

middle: J.

last: Waxman

address: 5 Cummington Mall

department: Department of Biology and Bioinformatics Program

institute: Boston University

summary: rRNA-depleted RNA isolated from livers of intact male and female mice and from male mice treated with a continuous infusion of growth hormone for either 10 hr or 1 days was analyzed by RNA-seq

overall_design: Liver RNA was isolated from 8 week old male mice treated with a continuous GH infusion (cGH) for either 10 hours or 1 day. Sham pump males served as a control. RNA-seq data are compared to untreated adult females to identify genes that show sex differences in liver expression and also respond to cGH. RNA samples were pooled to make 3 biological replicates per condition comprised of 2-4 individuals each.

first: Dana

last: Lau-Corona

first: Alexander

last: Suvorov


title: Next generation sequencing of human monocyte derived dendritic cells stimulated for two hours with LPS, C5a and/or MSK inhibitor SB-747561

city: Amsterdam

first: Anouk

last: Zaal

state: NH

address: Plesmanlaan 125

department: Immunopathology

country: Netherlands

institute: Sanquin Research

summary: In order to determine the full breath of C5aR and TLR crosstalk in human DC, RNA sequencing analysis on human moDC stimulated in the absence or presence of C5a and TLR4 ligand lipopolysaccharide (LPS) was performed. To minimize interference of induced positive and negative feedback loops, we analyzed gene expression after two hours of DC activation. The involvement of CREB signaling in C5aR and TLR crosstalk was investigated by including moDC stimulated in the presence of MSK inhibitor.

overall_design: Human monocyte-derived dendritic cells of 4 independent donors were were sequenced on Illumina HiSeq 2000 platform

first: Anja

last: Ten Brinke

first: Kat

last: Moore

first: Benjamin

last: Nota


title: Transcriptional Profiling of the Chicken Tracheal Response to Virulent Mycoplasma gallisepticum Strain Rlow

city: Storrs

first: Edan

last: Tulman

state: CT

address: 61 North Eagleville Rd

institute: University of Connecticut

summary: The goal of this study was to provide a global assessment of the host's response to M. gallisepticum over a 7-day time course

overall_design: Differential gene expression was assessed between Rlow infected and Hayflick's only 'control chickens' on days 1, 3, 5, and 7 (5 infected per day, 4 controls on day 1, 5 controls  per days 3, 5, and 7), 39 total chickens assessed.

first: Jessica

middle: A

last: Beaudet

middle: R

first: Lawrence

last: Silbart

first: Steven

last: Geary


title: Variation in DNA methylation is not consistently reflected by sociality in Hymenoptera

city: Griffin

first: Brendan

middle: G.

last: Hunt

state: GA

address: 125 Redding Building, Griffin Campus, 1109 Experiment Street

department: Entomology

institute: University of Georgia

summary: We used pooled samples of adult females from 3 species of Hymenoptera to generate single-base resolution DNA methylation maps.

sample_organism:
Lasioglossum albipes
Dufourea novaeangliae
Neodiprion lecontei

overall_design: Mapping of 5-methylcytosine in 3 species of Hymenoptera by MethylC-Seq


title: ARID1A-mutated ovarian cancers depend on HDAC6 activity

city: Philadelphia

first: Priyankara

last: Wickramasinghe

state: PA

address: 3601 Spruce Street

department: Bioinformatics

institute: The Wistar Institute

summary: ARID1A, encoding a subunit of the SWI/SNF chromatin remodeling complex, is the most mutated epigenetic regulator in human cancers.   ARID1A and TP53 mutations are typically mutually exclusive.  Therapeutic approaches that correlate with ARID1A mutational status remain a challenge. Here, we show that HDAC6 activity is essential in ARID1A-mutated ovarian cancers.  Inhibition of HDAC6 activity using a clinically applicable small molecule inhibitor significantly improved the survival of mice bearing ARID1A-mutated ovarian tumors.  This correlated with the suppression of growth and dissemination of ARID1A-mutated, but not wild-type, tumors.  The dependence on HDAC6 activity in ARID1A-mutated cells correlated with a direct transcriptional repression of HDAC6 by ARID1A.  HDAC6 inhibition selectively promoted apoptosis of ARID1A-mutated cells.  HDAC6 directly deacetylated the Lysine 120 residue of p53, a pro-apoptotic post-translational modification.   Thus, ARID1A mutation inactivates p53’ apoptotic function by upregulating HDAC6.  These results indicate that pharmacological inhibition of HDAC6 is a novel therapeutic strategy involving ARID1A-mutation

overall_design: RNA-seq transcription profiling of samples with altered HDAC6 activity

last: Bitler

first: Rugang

last: Zhang


title: Nonsense-mediated mRNA decay in Tetrahymena is EJC independent and requires a protozoa-specific nuclease

city: wuhan

first: Wei

last: Miao

state: hubei

address: donghu south road #7

institute: Institute of hydrobiology, CAS

summary: Nonsense-mediated mRNA decay (NMD) is essential for removing premature termination codon (PTC)-containing transcripts from cells. Studying the NMD pathway in model organisms can help to elucidate the NMD mechanism of humans and improves our understanding of how this biologically important process has evolved. Protozoa are among the earliest branching eukaryotes. Their NMD mechanism is poorly understood and may be primordial. We demonstrate that highly conserved Upf proteins (Upf1a, Upf2, and Upf3) are involved in the NMD pathway of the ciliate, Tetrahymena thermophila. We further show that a novel protozoa-specific nuclease, Smg6L, is responsible for destroying many NMD-targeted transcripts. The transcriptome-wide identification and characterization of NMD-targeted transcripts in vegetative Tetrahymena cells showed that many have exon–exon junctions downstream of the termination codon. However, Tetrahymena homologs of exon junction complex (EJC) core components do not form a complex and are dispensable for NMD, suggesting that NMD is EJC independent in this early branching eukaryote.

overall_design: Examination of transcriptional variation associated with deletion of UPF1a, SMG6L, MAG1 genes and truncation of the NYN nucelase domain of Smg6L protein in Tetrahymena thermophila

first: Miao

last: Tian


title: Dnmt3a Regulates T-cell Development and Suppresses T-ALL Transformation (BiSulfite-seq)

city: Saint Louis

first: Bo

state: MO

address: 660 S. Euclid Avenue

department: Developmental Biology

institute: Washington University School of Medicine

summary: DNA methylation analysis of T-cell acute lymphoblastic leukemia blast cells from either control mice or Dnmt3a knockout mice carrying a Notch1 Intracellular Domain (NICD) retrovirus

overall_design: Comparison of DNA methylation between control and Dnmt3a-KO NICD-driven T-ALL

first: Grant

last: Challen


title: Genetic deletion or small molecule inhibition of the arginine methyltransferase PRMT5 exhibit anti-tumoral activity in mouse models of MLL-rearranged AML

status: Public on Jul 13 2017

city: Houston

first: Margarida

last: Almeida Santos

state: Texas

address: 1515 Holcombe Blvd Mail code 1000

department: Epigenetics and Molecular Carcinogenesis

institute: UT MD Anderson Cancer Center

summary: The hematological malignancies classified as Mixed Lineage leukemias (MLL) harbor fusions of the MLL1 gene to partners that are members of transcriptional elongation complexes. MLL-rearranged leukemias are associated with extremely poor prognosis and response to conventional therapies and efforts to identify molecular targets are urgently needed. Using mouse models of MLL-rearranged acute myeloid leukemia (AML), here we show that genetic inactivation or small molecule inhibition of the protein arginine methyltransferase PRMT5 exhibit anti-tumoral activity in MLL-fusion protein driven transformation. Genome wide transcriptional analysis revealed that inhibition of PRMT5 methyltransferase activity overrides the differentiation block in leukemia cells without affecting the expression of MLL-fusion direct oncogenic targets. Furthermore, we find that this differentiation block is mediated by transcriptional silencing of the cyclin-dependent kinase inhibitor p21 (CDKN1a) gene in leukemia cells. Our study provides pre-clinical rationale for targeting PRMT5 using small molecule inhibitors in the treatment of leukemias harboring MLL-rearrangements.

overall_design: RNA-seq data from 72h-treated DMSO and EPZ 015666 (PRMT5i) MLL-ENL/NrasG12D leukemia cells, three independent replicates.

first: Saakshi

last: Kaushik

first: Fan

last: Liu

first: Kylee

last: Veazey

first: Guozhen

last: Gao

first: Prosun

last: Das

first: Luís

last: Neves

first: Kevin

last: Lin

first: Yi

last: Zhong

first: Yue

last: Lu

first: Virginia

last: Giuliani

first: Mark

middle: T

last: Bedford

first: Stephen

last: Nimer


title: Nutrient sensing modulates malaria parasite virulence.

city: Almada

first: Ana

middle: Rita

last: Grosso

address: Campus de Caparica

department: Departamento Ciências da Vida

country: Portugal

institute: Unidade de Ciências Biomoleculares Aplicadas (UCIBIO)/Faculdade de Ciências e Tecnologia - Universidade Nova de Lisboa


title: Dnmt3a Regulates T-cell Development and Suppresses T-ALL Transformation

last: Zhang


title: Transcriptome data involved in Japanese flounder (Paralichthys olivaceus) albinism

city: Qingdao

last: Wang

state: Shandong

address: 106 Nanjing Road

institute: Yellow Sea Fisheries Research Institute, Chinese Academy Fishery Science

summary: In this study, a high-throughput sequencing strategy was employed to identify the mRNA involved in P. olivaceus albinism. Based on P. olivaceus genome, RNA-seq identified 21,787 know genes and 711 new genes by transcripts assembly. Of those, 235 genes exhibited significantly different expression pattern (fold change ≥2 or ≤0.5 and q-value≤0.05), including 194 down-regulated genes and 41 up-regulated genes in albino versus normally pigmented individuals. These genes were enriched to 81 GO terms and 9 KEGG pathways (p≤0.05). Among those, the pigmentation related pathways-Melanogenesis and tyrosine metabolism were contained.

overall_design: Examination of the ocular side skin of wild type and albinism Paralichtys olivaceus

first: Songlin

last: Chen


title: Connected gene communities underlie transcriptional changes in Cornelia de Lange Syndrome

city: Quebec

first: Steve

last: Bilodeau

state: Quebec

address: 2260 boul. Henri-Bourassa

institute: Centre de recherche du CHU de Québec-Université Laval

summary: Cornelia de Lange syndrome (CdLS) is a complex multisystem developmental disorder caused by mutations in cohesin subunits and regulators. While the precise molecular mechanisms are not well defined, they point toward a global deregulation of the transcriptional gene expression program. Indeed, cohesin is associated with the boundaries of chromosome domains in addition to enhancers and promoters connecting the 3D genome organization with transcriptional control and gene expression. Here we show that connected gene communities, built with noncoding regulatory elements and genes physically interacting in the 3D chromosomal space, provide a molecular explanation for the pathoetiology of CdLS. Indeed, NIPBL and cohesin are important constituents of connected gene communities, both being centrally positioned at active noncoding regulatory elements. Interestingly, mutations in SMC1A and NIPBL lead to coordinated gene expression changes in connected communities. Our findings suggest a model where CdLS is explained by coordinated modulation of connected gene communities.

overall_design: ChIP-seq of NIPBL, SMC1A and MED1 in GM12878 cells with whole cell extract controls.

first: Imène

last: Boudaoud

first: Éric

last: Fournier

first: Audrey

last: Baguette

first: Fabien

last: Lamaze

first: Maxime

last: Vallée

first: Arnaud

last: Droit


title: microRNA data involved in Japanese flounder (Paralichthys olivaceus) albinism

summary: In this study, a high-throughput sequencing strategy was employed to identify the miRNAs involved in P. olivaceus albinism. High-throughput miRNA sequencing identified a total of 475 miRNAs, including 64 novel miRNAs. Furthermore, 33 differentially expressed miRNAs containing 13 up-regulated and 20 down-regulated miRNAs were identified in albino versus normally pigmented individuals (fold change ≥1.5 or ≤0.67 and p≤0.05).


title: Dnmt3a Regulates T-cell Development and Suppresses T-ALL Transformation (RNA-seq)

first: Bo

summary: Gene expression analysis of T-cell acute lymphoblastic leukemia blast cells from either control mice or Dnmt3a knockout mice carrying a Notch1 Intracellular Domain (NICD) retrovirus

overall_design: Comparison of gene expression between control and Dnmt3a-KO NICD-driven T-ALL

first: Grant

last: Challen


title: Transcriptome and microRNA data involved in Japanese flounder (Paralichthys olivaceus) albinism

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

overall_design: Refer to individual Series


title: RNA-seq analysis of mouse liver transcriptome following exposure to TCPOBOP or PCN

first: David

last: Waxman

state: MA

summary: Changes in gene expression were assayed in mouse liver nuclear RNA following a single injection of the CAR agonist TCPOBOP (1,4-Bis-[2-(3,5-dichloropyridyloxy)]benzene) or the PXR agonist PCN (pregnenolone 16α-carbonitrile) in 7-week old mice. This study is part of a larger study entitled Sex-Differential Responses of Tumor Promotion-Associated Genes and Dysregulation of Novel Long Noncoding RNAs in Constitutive Androstane Receptor-Activated Mouse Liver (PMID: 28903501).

overall_design: Nuclear RNA was isolated from male and female CD1 mouse liver following either 3 hour exposure or 27 hour exposure to TCPOBOP; or from male liver following a 3 hour exposure to PCN. N=2-3 biological pools were sequenced per control or treatment group, with each pool comprised of nuclear RNA pooled from n=3-4 individual mouse livers.

first: Nicholas

last: Lodato


title: Effects of plasticizers (bisphenol A, bisphenol AF) and an herbicide in MCF7 human breast cancer cells

city: London

first: Matthew

last: Arno

state: LONDON

address: 150 Stamford Street

department: Genomics Centre

country: United Kingdom

institute: King's College London

summary: We studied alterations in gene expression profiles of the MCF7 human breast cancer cells caused by bisphenol A, bisphenol AF and glyphosate using Illumina RNA sequencing platform.

overall_design: Examination of endocrine disrupting effects of xenobiotics using the MCF7 cell line

first: Robin

last: Mesnage


title: High-resolution tissue-specific analysis of the Arabidopsis transcriptome in response to shade

city: La Jolla

first: Joanne

last: Chory

state: California

address: 10010 N Torrey Pines RD

department: Plant Biology Laboratory

institute: Salk Institute for Biological Studies

summary: cotyledon and hypocotyl specific whole-genome transcriptome (mRNA-Seq) analysis of Arabidopsis seedlings exposed to low and high R:FR ratio

overall_design: RNAseq analysis of the cotyledon and hypocotyl tissue in low and high red:far-red ratio

first: Ullas

last: Pedmale


title: Click chemistry enables comprehensive preclinical evaluation of targeted epigenetic therapies [RNA-seq]

city: Melbourne

first: Mark

last: Dawson

state: VIC

address: 305 Grattan Street

country: Australia

institute: Peter MacCallum Cancer Centre

summary: The success of targeted therapies hinges on our ability to understand the molecular and cellular mechanism of action of these agents. Here we modify various BET bromodomain inhibitors, an exemplar novel targeted therapy, to create functionally conserved compounds that are amenable to click-chemistry and can be used as molecular probes in vitro and in vivo. Using click-proteomics and click-sequencing we provide new mechanistic insights to explain the gene regulatory function of BRD4 and the transcriptional changes invoked by BET inhibitors. In mouse models of acute leukaemia, we use high resolution microscopy and flow cytometry to highlight the underappreciated heterogeneity of drug activity within tumour cells located in different tissue compartments. We also demonstrate the differential distribution and effects of the drug in normal and malignant cells in vivo. These data provide critical insights that reveal the cellular and molecular details for the efficacy and limitations of these agents. This study provides a framework for the pre-clinical assessment of other conventional and targeted therapies.

overall_design: RNASeq of MV4;11 cell treated with DMSO, JQ1 or JQ1–PA

first: Paola

last: Grandi

first: Dean

last: Tyler

first: Johanna

last: Vappiani

first: Enid

middle: Y

last: Lam


title: Click chemistry enables comprehensive preclinical evaluation of targeted epigenetic therapies [Click-Seq 2]

overall_design: Click-seq of K562 and MV4;11 cells


title: Click chemistry enables comprehensive preclinical evaluation of targeted epigenetic therapies [Click-Seq 1]

overall_design: Click-seq with JQ1-PA and JQ1-TCO in MV4;11 cells


title: Splicing activation by Rbfox requires self-aggregation through its tyrosine-rich domain

city: Los Angeles

first: Douglas

middle: L.

last: Black

address: 675 Charles E. Young Drive South

department: MIMG

institute: UCLA

summary: To determine how the higher order assembly of Rbfox proteins affect Rbfox-dependent splicing regulation, we expressed Rbfox wildtype and its mutant protein in Flp-In™ T-REx™ 293 Rbfox2-/- cells and extracted RNA from these cells to perform RASL-seq which profiles thousands of alternative splicing event.

overall_design: Flp-In™ T-REx™ 293 Cell Line (in triplicate) were transfected by Rbfox1 wildtype and its mutants, followed by Dox induction. Total RNAs were extracted and been analyzed by RASL-seq.

first: Yi

last: Ying

middle: L


title: Identifying ASCL1-mediated chromatin changes in primary GBM stem cell cultures [ATAC-seq]

city: Toronto

first: Peter

last: Dirks

state: ON

address: 686 Bay St

department: Arthur and Sonia Labatt Brain Tumour Research Centre and Division of Neurosurgery

institute: The Hospital for Sick Children

summary: ASCL1 mediates neuronal differentiation of GBM stem cell (GSC) cultures. We sought to identify chromatin changes upon induced ASCL1 expression in primary human GSC cultures. In this dataset, we include ATAC-seq data obtained from GSC cultures harbouring a CRISPR-deletion of ASCL1. We assessed differential ASCL1 binding between control and GSC cultures induced to overexpress ASCL1 after 14 days of doxycycline treatment.

overall_design: Glioblastoma cells with a genetic knockout of ASCL1 is compared to genetic knockout of ASCL1 overexpressing ASCL1 (n = 2 biological replicates; total = 4 samples)

first: Nicole

middle: I

last: Park

first: Kinjal

last: Desai


title: Click chemistry enables comprehensive preclinical evaluation of targeted epigenetic therapies [ChIP-seq 1]

overall_design: ChIPSeq for C/EBPα and β in MV4;11 cells


title: Vertical sleeve gastrectomy reverses diet-induced gene-regulatory changes impacting lipid metabolism

city: Duarte

first: Juan

last: Du

address: 1500 E. Duarte Rd

institute: Beckman Research Institute, City of Hope

summary: Vertical sleeve gastrectomy (VSG) produces sustainable weight loss, remission of type 2 diabetes (T2D), and improvement of nonalcoholic fatty liver disease (NAFLD). However, the molecular mechanisms underlying the metabolic benefits of VSG have remained elusive. We have previously demonstrated that diet-induced obesity leads to chromatin modifications in the liver of mice. We demonstrate here that VSG in C57BL/6J wild-type male mice can reverse these chromatin modifications and thereby impact the expression of key metabolic genes. Genes involved in lipid metabolism, especially omega-6 fatty acid metabolism, are up-regulated in livers of mice after VSG while genes in inflammatory pathways are down-regulated after VSG. Consistent with gene expression changes, regulatory regions near genes involved in inflammatory response displayed decreased chromatin accessibility after VSG. Our results indicate that VSG induces global regulatory changes that impact hepatic inflammatory and lipid metabolic pathways, providing new insight into the mechanisms underlying the beneficial metabolic effects induced by VSG.

overall_design: Chromatin accessibility and transcriptome profiles of VSG, Sham and Control mice liver in duplicates.

first: Jingyan

last: Tian

first: Lili

last: Ding

first: Candi

last: Trac

first: Brian

last: Xia

first: Siming

last: Sun

first: Dustin

middle: E

last: Schones

first: Wendong

last: Huang


title: Click chemistry enables comprehensive preclinical evaluation of targeted epigenetic therapies

first: Mark

last: Dawson


title: Ciliary Hedgehog signaling restricts injury-induced adipogenesis

city: San Francisco

first: Jeremy

last: Reiter

address: 555 Mission Bay Blvd South

institute: University of California, San Francisco

summary: Injured skeletal muscle regenerates, but with age or in muscular dystrophies, muscle is replaced by fat. Upon injury, muscle-resident fibro/adipogenic progenitors (FAPs) proliferated and gave rise to adipocytes. These FAPs dynamically produced primary cilia, structures that transduce intercellular cues such as Hedgehog (Hh) signals. Genetically removing cilia from FAPs inhibited intramuscular adipogenesis, both after injury and in a mouse model of Duchenne muscular dystrophy. Blocking FAP ciliation also enhanced myofiber regeneration after injury and reduced myofiber size decline in the muscular dystrophy model. Hh signaling through FAP cilia regulated the expression of TIMP3, a secreted metalloproteinase inhibitor, that inhibited MMP14 to block adipogenesis. A pharmacological mimetic of TIMP3 blocked the conversion of FAPs into adipocytes, pointing to a strategy to combat fatty degeneration of skeletal muscle. We conclude that ciliary Hh signaling by FAPs orchestrates the regenerative response to skeletal muscle injury.

overall_design: Transcriptomic profiling using RNAseq was performed on RNA derived from a bipotent, progenitor cell population, called fibro/adipogenic progenitors (FAPs), purified from tibialis anterior muscle 3 days post glycerol injury. Two populations of cells were sequenced, one from wild type muscle (FAP-ctrl) and another from cells in which cilia, using a floxed Ift88 allele, were conditionally deleted (FAP-no cilia). A total of five FAP-ctrl and 3 FAP-no cilia samples were used. The TruSeq Stranded Total RNA Library Prep Kit (Ilumina) was used to generate the library, which was subsequently sequenced using an Illumina 2500 SE 50bp platform and aligned to the GRCm38.78 whole genome using STAR RNAseq aligner. Individual read counts were normalized to the geometric mean read count across all samples using DEseq. Sequencing yielded ~314 million total reads with an average read depth of ~34.9 million reads per sample.

first: Daniel

last: Kopinke

middle: F


title: Identifying ASCL1 target genes in primary GBM stem cell cultures [ChIP-seq]

summary: ASCL1 mediates neuronal differentiation of GBM stem cell (GSC) cultures. We sought to identify genomic targets of ASCL1 in primary human GSC cultures. In this dataset, we include ChIP-seq data obtained from GSC cultures harbouring a CRISPR-deletion of ASCL1. We assessed differential ASCL1 binding between control and GSC cultures induced to overexpress ASCL1 after 18 hours of doxycycline treatment.

overall_design: Glioblastoma cells with a genetic knockout of ASCL1 is compared to genetic knockout of ASCL1 overexpressing ASCL1 (n = 3 biological replicates; n = 2 input samples; total = 8 samples)

first: Paul

last: Guilhamon

first: Mathieu

last: Lupien


title: Transcriptome of Plasmodium berghei wildtype parasites and KIN knockout parasites [RNA-seq]

first: Ana

last: Grosso

summary: The ability to sense, respond and adapt to changes in nutrient availability is a survival requisite. This might be particularly important for malaria parasites, which encounter major alterations in nutrients levels throughout infection. How these parasites deal with nutrient fluctuations and maintain infection without killing their hosts before transmission remains unknown. Here, we show that blood-stage malaria parasites respond to dietary-restriction through a rearrangement of their transcriptome accompanied by a significant reduction in their multiplication rate. A kinome analysis combined with chemical and genetic approaches identified KIN, a putative AMP-activated kinase homologue, as a master regulator that senses host nutrients both in vitro and in vivo, and mediates the transcriptional response to the host nutritional status. Diet-responsive genes include the plant-like ApiAP2 transcription regulators, which appear to act as downstream effectors of KIN. Overall, these findings reveal key components of a parasite nutrient-sensing mechanism that is critical to modulate replication and virulence in malaria parasites.

overall_design: Transcriptome alterations under dietary-restrictions in wildtype and KIN knockout parasites (3 biological replicates of each condition).

first: Liliana

last: Mancio-Silva

first: Katarzyna

middle: K

last: Modrzynska


title: Identifying ASCL1 target genes in primary GBM stem cell cultures [RNA-seq]

first: Peter

last: Dirks

summary: ASCL1 mediates neuronal differentiation of GBM stem cell (GSC) cultures. We sought to identify targets of ASCL1 in primary human GSC cultures. In this dataset, we include RNA-seq data obtained from GSC cultures harbouring a CRISPR-deletion of ASCL1. We assessed differential gene expression between control and GSC cultures induced to overexpress ASCL1 after 7 days of doxycycline treatment.

overall_design: Glioblastoma cells with a genetic knockout of ASCL1 is compared to genetic knockout of ASCL1 overexpressing ASCL1 (n = 3 biological replicates; total = 6 samples)

first: Nicole

last: Park


title: A single-cell transcriptomic analysis reveals precise pathways and regulatory mechanisms underlying hepatoblast differentiation

city: Beijing

first: Cheng-ran

last: Xu

address: NO.5 YIHEYUAN ROAD HAIDIAN DISTRICT, BEIJING, P.R.CHINA

department: School of Basic Medical Sciences

institute: Peking University

summary:
How the bi-potential hepatoblasts differentiate into hepatocytes and cholangiocytes remains unclear. Here, using single-cell transcriptomic analysis of hepatoblasts, hepatocytes, and cholangiocytes sorted from E10.5 to E17.5 mouse embryos, we found that hepatoblast-to-hepatocyte differentiation occurred gradually followed a linear default pathway. As more cells became fully differentiated hepatocytes, the number of proliferating cells decreased. Surprisingly, the proliferating and quiescent hepatoblasts exhibited homogeneous differentiation states at a given developmental stage. This unique feature enabled us to combine the single-cell and bulk-cell analyses to define the precise timing of the hepatoblast-to-hepatocyte transition, which occurs between E13.5 and E15.5. In contrast to hepatocyte development at almost all levels, hepatoblast-to-cholangiocyte differentiation underwent a sharp detour from the default pathway. New cholangiocyte generation occurred continuously between E11.5 and E14.5, but their maturation states at a given developmental stage were heterogeneous. Even more surprising, the number of proliferating cells increased as more progenitor cells differentiated into mature cholangiocytes. Based on an observation from the single-cell analysis, we also discovered that the protein kinase C (PKC)/mitogen-activated protein kinase (MAPK) signaling pathway promoted cholangiocyte maturation.
CONCLUSIONS:
Our studies have defined distinct pathways for hepatocyte and cholangiocyte development in vivo, which are critically important for understanding basic liver biology and developing effective strategies to induce stem cells to differentiate towards specific hepatic cell fates in vitro.

overall_design: The overall goal of this study was to define the precise road map and understand the underlying mechanisms for hepatobiliary lineages development. Specifically, we performed single-cell RNA-seq in sorted hepatoblasts, hepatocytes and cholangiocytes from E10.5-E17.5 mouse fetal livers. To precisely identify the time point of hepatoblast to hepatocyte transition, we performed bulk-cell RNA-seq using 2 × 10^5 sorted hepatoblasts/hepatocytes from E10.5 to E18.5. To study whether MAPK pathway promotes cholangiocyte maturation, we performed single-cell RNA-seq in sorted cells from liver explants treated with TPPB ((2S,5S)-(E,E)-8-(5-(4-(trifluoromethyl)phenyl)-2,4-pentadienoylamino) benzolactam, a PKC agonist) or U0126 (a MEK1/2 inhibitor).

first: Li

last: Yang

first: Wei-Hua

last: Wang

first: Wei-Lin

last: Qiu

first: Zhen

last: Guo


title: Host Transcriptomic responses to pneumonic plague reveal that Yersinia pestis inhibits both the initial adaptive and innate immune responses in mice

first: Zongmin

last: Du

address: No. 20, Fengtai Dongdajie Street

institute: Beijing Institute of Microbiology and Epidemiology

summary: Pneumonic plague is the most deadly form of infection caused by Yersinia pestis and can progress extremely fast. However, our understanding on the host transcriptomic response to pneumonic plague is insufficient. Here, we used RNA-sequencing technology to analyze transcriptomic responses in mice infected with fully virulent strain 201 or EV76, a live attenuated vaccine strain lacking the pigmentation locus. Approximately 600 differentially expressed genes (DEGs) were detected in lungs from both 201- and EV76-infected mice at 12 hours post-infection (hpi). DEGs in lungs of 201-infected mice exceeded 2,000 at 48 hpi, accompanied by sustained large numbers of DEGs in the liver and spleen; however, limited DEGs were detected in those organs of EV-infected mice. Remarkably, DEGs in lungs were significantly enriched in critical immune responses pathways in EV76-infected but not 201-infected mice, including antigen processing and presentation, T cell receptor signaling among others. Pathological and bacterial load analyses confirmed the rapid systemic dissemination of 201-infection and the confined EV76-infection in lungs. Our results demonstrate that fully virulent Y. pestis strongly inhibits both the innate and adaptive immune responses that are substantially stimulated in a self-limited infection, which update our holistic views on the transcriptomic response to pneumonic plague.

overall_design: We used RNA-sequencing technology to analyze transcriptomic responses in lungs, spleen and liver of  mice infected with fully virulent strain 201 or EV76 at 12, 48 and 72 hpi.

first: Tong


title: Gene Expression Changes in Definitive Endoderm in response to GATA6-depletion

city: Charleston

first: Stephen

last: Duncan

state: SC

address: 173 Ashley Avenue, BSB 6th Floor, Room 657A

department: Regenerative Medicine and Cell Biology

institute: Medical University South Carolina

overall_design: Refer to individual Series


title: Click chemistry enables comprehensive preclinical evaluation of targeted epigenetic therapies [ChIP-seq 2]

first: Mark

last: Dawson

overall_design: ChIPSeq of BRD4 in MV4;11 and K562 cells

first: Paola

last: Grandi

first: Dean

last: Tyler

first: Johanna

last: Vappiani

first: Enid

last: Lam


title: Deep sequencing of uncapped RNA in rdr1/2/6 and wild-type Arabidopsis plants

city: Yokohama

first: Motoaki

last: Seki

address: 1-7-22, Suehiro-cho, Tsurumi

institute: RIKEN CSRS

summary: Our previous experiment on biogenesis mechanisim of stress-inducible antisense RNAs showed that accumulation of antisense RNA in a drought-inducible gene, RD29A locus was decreased in rdr1/2/6 triple mutant. The RD29A antisense RNA did not have CAP structure and poly(A) tail. We applied deep sequencing of uncapped RNA using SOLiD to identify RDR1/2/6-mediated antisense RNAs in genome-wide. We identified 1) 975 RDR1/2/6-mediated antisense RNA loci on which no. of sequence tags is decreased in rdr1/2/6 and makes peak and 2) 1,613 RDR1/2/6-mediated antisense RNA loci on which no. of the tags is decreased in rdr1/2/6 and enriched on antisense strand of exons. They were grouped into 1,959 non-redundant loci.

overall_design: Untreated and 2hr drought stress-treated 2 weeks-old rdr1/2/6 and wild-type Arabidopsis thaliana plants were used. To determine 5’-end of uncapped RNA with and without poly (A), we developed Deep Sequencing of Uncapped RNAs (DSUR) with reference to PARE analysis (German et al. 2009, Nature Protocol 4:356-362) and applied DSUR using SOLiD to identify genome-wide RDR1/2/6-mediated antisense RNA loci in Arabidopsis.

first: Akihiro

last: Matsui

first: Kei

last: Iida

first: Maho

last: Tanaka

first: Junko

last: Ishida

first: Taeko

last: Morosawa

first: Katsushi

last: Yamaguchi

first: Shuji

last: Shigenobu

first: Norio

last: Kobayashi

first: Tetsuro

last: Toyoda


title: Deep sequencing of small RNAs

summary: Recently, we demonstrated that RDRs had a general function to synthesize antisense RNAs from sense transcripts of protein-coding genes. In this study, we analyzed whether RDR-mediated antisense RNAs were processed into small RNAs by deep sequencing using SOLiD. Deep sequencing identified 1,645 RDR1/2/6-mediated smRNA loci in drought stress and control conditions.

overall_design: Untreated and 2 hr-drought stress-treated 2 week-old rdr1/2/6 and wild-type Arabidopsis thaliana plants were used. smRNA libraries for SOLiD sequencing were constructed according to the protocol of SOLiD Total RNA-Seq Kit and subjected to SOLiD sequencing.


title: Trascriptomic profiles of Lactobacillus plantarum strains isolated from cheeses

status: Public on Jul 12 2017

city: Bari

first: Maria

last: De Angelis

state: Italy

address: Via G. Amendola, 165/a

department: Department of Soil, Plant and Food Science, University of Bari Aldo Moro, Bari Italy

institute: University of Bari

summary: Analysis of Lactobacillus plantarum stains isolated from different cheese type

overall_design: Total RNA obtained from strains of Lactobacillus plantarum

last: Calasso

first: Francesco

middle: M

last: Calabrese


title: SUMOylation Regulates miR-34b/c Targeted Gene Expression Program

city: duarte

first: LU

last: YANG

address: 1500 duarte rd

institute: city of hope

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


title: Shotgun sequencing of 5-hydroxymethylcysotine circulating cell-free DNA from the blood distinguishes solid tumor tissues of origin

city: Chengdu

first: Dan

last: Xie

state: Sichuan

address: #17 Renmin Road

department: West China Hospital

institute: Sichuan University

summary: 5-Hydroxymethylcytosine (5hmC) is an important mammalian DNA epigenetic modification that has been linked to gene regulation and cancer pathogenesis. Here we explored the diagnostic potential of 5hmC in cell-free DNA (cfDNA), the circulating DNA found in human plasma which represents a noninvasive window into the health status of the body. We showed that the genome-wide 5hmC distribution in cfDNA can be reliably sequenced by chemical labeling-based 5hmC enrichment. We sequenced cell-free 5hmC from 49 patients of seven different cancer types and found distinct features that can be used for monitoring disease status and progression. Specifically, we discovered that lung cancer leads to a stage-dependent hypohydroxymethlation in cfDNA, whereas hepatocellular carcinoma (HCC) and pancreatic cancer lead to disease-specific changes in the cell-free hydroxymethylome. Our results demonstrate that cell-free 5hmC can be used not only to track the stage of cancer but also to identify tissue of origin in some solid tumors.

overall_design: 79 samples were sequenced and 130 datasets were generated

first: Chunxiao

last: Song


title: SUMOylation Regulates miR-34b/c Targeted Gene Expression Program [miRNA-seq]

summary: The microRNAs known as miR-34 family suppress the expression of a suit of proteins involved in oncogenesis and pluripotency, including c-Myc.  Their expression is frequently down regulated in cancers; however the regulation of their expression is not well understood. Through genome-wide miRNA profiling and mechanistic analysis, we identified an important role of SUMOylation in miR-34b/c expression, regulating the expression of c-Myc and all other tested miR-34 targets.

overall_design: We established HCT116 cell line that can be induced to express shRNA targeting the catalytic subunit of the SUMO E1 enzyme, SAE2 by adding doxocycline (DOX).  To rule out non-specific shRNA effects, we established two separate cell lines using two independent shRNAs Sh1 and Sh2.

first: Yi-Jia

last: Li

first: Li

last: Du

first: Grace

last: Aldana-Masangkay

first: Xiuli

last: Wang

first: Ryan

last: Urak

first: Stephen

last: Forman

first: Steven

last: Rosen

first: Yuan

last: Chen


title: Molecular pathogenesis of human prostate basal cell hyperplasia reveals a keratinocyte metaplasia

city: Dallas

first: Gervaise

middle: H.

last: Henry

address: 5323 Harry Hines Blvd, Mail Code:9110

department: Urology

institute: UT Southwestern Medical Center

summary: The incidence of basal cell hyperplasia (BCH) has been reported at 8-10%, but a molecular and cellular characterization has not been performed on this phenotype. Using freshly digested tissue from surgical specimens, we performed transcriptomic analysis of flow cytometry-purified basal epithelia from patients with and without a majority BCH phenotype. Gene set enrichment analysis revealed an increased expression of members of the epidermal differentiation complex, resembling the progression of other metaplastic diseases.

overall_design: In order to generate a clean molecular profile of BCH, free of contaminating signal from leukocytes, stroma and luminal epithelia, we performed RNA sequencing on bulk-isolated basal epithelia from 3 patients with basal hyperplasia and 4 patients without BCH

first: Douglas

middle: W

last: Strand

middle: H


title: Gene Expression Changes in Definitive Endoderm in response to GATA6-depletion (ChIP-seq)

last: Duncan

summary: GATA6 is required for proper definitive endoderm formation.  The mechanism of this process is poorly understood

overall_design: We used ChIP-Sequencing to identify genes that are direct targets of GATA6 during human endoderm specification using hES differentiation

first: Joseph

last: Fisher


title: SUMOylation Regulates miR-34b/c Targeted Gene Expression Program [RNA-seq]


title: ASCL1 mediates neuronal differentiation of primary GBM stem cell cultures upon Notch signalling blockade [RNA-seq]

first: Peter

middle: B

last: Dirks

summary: ASCL1 mediates neuronal differentiation of GBM stem cell (GSC) cultures upon Notch signalling inhibition. We sought to identify gene expression changes that were specific to ASCL1 function. In this dataset, we include RNA-seq data obtained from GSC cultures harbouring wildtype or CRISPR-deletion of ASCL1. We assessed differential gene expression between wildtype and ASCL1-knockout after treatment with gamma-secretase inhibitor for 7 days.

overall_design: Glioblastoma cells with a genetic knockout of ASCL1 is compared to wildtype ASCL1 glioblastoma cells treated with vehicle (DMSO) or gamma-secretase inhibitor (n = 3 biological replicates; total = 12 samples)

first: Nicole

last: Park


title: Yeast RNA-binding protein Nab3 regulations genes involved in nitrogen metabolism

city: Baltimore

first: Jonathan

last: Merran

state: Maryland

address: 725 N. Wolfe Street

department: Molecular Biology and Genetics

institute: Johns Hopkins University

summary: Termination of yeast RNA polymerase II (Pol II) transcripts occurs through two alternative pathways. Termination of mRNAs is coupled to cleavage and polyadenylation while non-coding transcripts are terminated through the Nrd1-Nab3-Sen1 (NNS) pathway in a process that is linked to RNA degradation by the nuclear exosome. Some mRNA transcripts are also attenuated through premature termination directed by the NNS complex.  In this paper we present the results of nuclear depletion of the NNS component Nab3. As expected many non-coding RNAs fail to terminate properly. In addition, we observe that nitrogen catabolite repressed genes are up-regulated by Nab3 depletion.

overall_design: Yeast Pol II genome wide positioning before and after Nab3-FRB tagged nuclear depletion using Illumina HI-Seq

middle: D

first: Jeffry

last: Corden


city: Lausanne

first: Pierre

middle: J

last: Fabre

address: Station 19

department: ISREC

institute: EPFL

summary: We performed ChIP-seq for CTCF using the autopod from E12.5 embryo and confirmed the binding pattern previously reported by a ChIP-on-Chip approach using the same embryonic tissue (Soshnikova et al., 2010). Our results show CTCF-mediated gating of long-range contacts at the HoxD locus.

overall_design: ChIP-seq analysis of CTCF in distal limbs at mouse E12.5 using anti-CTCF (Active motif REF# 61311)

first: L

last: Beccari

first: P

first: D

last: Duboule


title: Deep sequencing of small and uncapped RNA in rdr1/2/6 and wild-type Arabidopsis plants

first: Motoaki

last: Seki


title: Transcriptomic analysis of Drosophilalarval crystal cells

status: Public on Jul 20 2017

city: Toulouse

first: Lucas

last: Waltzer

address: 118 route de Narbonne

department: Centre de Biologie du Développement

institute: CNRS UMR5547

summary: Crystal cells are one of the 3 Drosophila blood cell lineages and represent less than 5% of the total hemocytes in wild type larvae. There development is notably controlled by mlf (myeloid leukemia factor), which regulate their number by stabilising the lineage-specific transcription factor Lozenge. To gain insight into the biology of this blood cell lineage and its regulation by mlf, we established the gene expression profile of the circulating crystal cells in wildtype and mlf mutant third instar larvae. This study provides a rich source of information to further characterise crystal cell function and regulation. In addition our data show that mlf is a major regulator of crystal cell gene expression programm and that mlf mutation leads to the accumulation of misdifferentiated crystal cells.

overall_design: RNA expression profiles of sorted lz-GAL4,UAS-GFP+ circulating blood cells from wild type and mlf-/- third instar Drosophila larvae were generated by deep sequencing, in triplicate, using Illumina HiSeq2500 sequencing platform.

first: Marion

last: Miller

first: Vanessa

last: Gobert

first: Benoit

last: Augé

first: Marc

last: Haenlin


title: Reconstructing blood stem cell regulatory network models from single-cell molecular profiles

city: Cambridge

first: Bertie

last: Gottgens

address: Jeffrey Cheah Biomedical Centre

institute: University of Cambridge

summary: The aim of this study was to validate networks for haematopoietic stem and progenitor cell networks, using ChIP-Seq data to assess and confirm the genomic binding sites of important haematopoietic transcription factors in a haematopoietic cell line.

overall_design: HoxB8-FL cells were fixed with either 1% or 0.4% formaldehyde for 10 mins. Chromatin was isolated, sonicated for 7 mins (30 sec on, 30 sec off), and specific antibodies were used to pull down the transcription factors of interest after a pre-clearing step. Chromatin was washed, de-crosslinked, amplified, size selected by gel purification and sequenced.

first: Sonia

last: Nestorowa

first: Fiona

last: Hamey

first: Sarah

last: Kinston

first: David

last: Kent

first: Nicola

last: Wilson

first: Berthold

first: Rebecca

last: Hannah


title: Human ES Cell-derived Hepatoblasts are an Optimal Lineage Stage for HCV Infection

first: yi

last: wang

address: 27(9) Taiping Road

institute: Beijing Institute of Transfusion Medicine

summary: Purpose: The hepatoblasts are found to be optimal stage, compared with hepatic stem cells (hHpSCs) and mature hepatocytes (hHeps). To identify the cellular determinants that correlated with HCV infection during hES cells’ differentiation, transcriptome profiling of cells at hHpSC, hHB, PreHep and hHep stages were compared with RNA sequencing.Results:  In general, the gene expression profile of cells at each stage clustered closer to the HCV infected cells at the same stages. The genes involved in regulation of liver development were up-regulated along with processes of maturation. Among the genes positively related to HCV replication, ABCB6, CEBPD, TNFRSF10C, GTF3A, HAS1, UBE2J1 were highly expressed in mature hHeps, while IGFBP6, SMAD6, ITGA7 etc. were highly expressed in progenitor hHB stage. Most of the 66 genes reported to be involved in HCV assembly and secretion remained unchanged, except CX3CL1 and PROX1 increased in mature hepatocyte and ARHGAF increased in rogenitors. Families of viral restriction factors reported involved in HCV infection were significantly enriched in hHeps. Conclusions: HCV does not change the transcription profile of induced cells and use different genes to support HCV replication in the cells from different stage. Low level of expression of viral restriction factors makes hHBs an optimal host for HCV infection.

overall_design:
Examination of transcriptome profiles of each stage of hepatic lineage cells differentiated from hESCs; Examination of HCV associated host factors during hepatic differentiation.
mRNA profiles of hHpSC, hHB, PreHep and hHep infected with or without HCV using Illumina GAIIx.

first: Fang

last: Yan

first: Yi

last: Wang

first: Yunfang


title: Phenotype-driven precision oncology in patient-derived tumor models predict therapeutic response in squamous cell carcinoma

city: Delhi

first: Debarka

last: Sengupta

state: Delhi

address: IIIT Delhi, Okhla Phase 3

department: Computational Biology and Computer Science

country: India

institute: Indraprastha Institute of Information Technology

summary: Comparison of single-cell transcriptomic profiles of cell lines obtained from the primary and metastatic tumor from a single patient.

overall_design: Analysis of single-cell transcriptomic profiles of cell lines derived from the primary squamous cell carcinoma tumor and a metastatic lymph node tumor isolated from a single patient.


title: Regulation of gene expression after FGF2-induced gyrification of mouse brain

city: New Haven

first: Flora

last: Vaccarino

state: CT

address: 230 South Frontage Road

department: Child Study Center

institute: Yale University

summary: We analyze the cortical transcriptome under physiological or FGF2-perturbed conditions. Using system biology approaches (DGE, WGCNA and kinase enrichment analysis) we identify networks of co-expressed genes involved in neuronal differentiation and cortical patterning that are either up- or down-regulated in vivo after FGF2 perturbation.

overall_design: Total RNA was isolated from dorsal telencephalons of E13.5 embryos, from anterior brain regions  (rostral to the hippocampus). A total of 3 FGF-2 injected embryos were analyzed and compared to three age-matched vehicle-injected controls.

first: Tomasi

last: Simone

first: Gianfilippo

last: Coppola


title: Single-cell alternative splicing analysis with Expedition reveals splicing dynamics during neuron differentiation

city: La Jolla

first: Gene

last: Yeo

state: CA

address: 2880 Torrey Pines Scenic Dr. Room 3805/Yeo Lab

institute: UCSD

summary: Alternative splicing (AS) generates isoform diversity critical for cellular identity and homeostasis, yet characterization of this diversity in single cells remains limited. We developed Expedition, a computational framework to categorize and visualize the heterogeneity of AS from single-cell transcriptomes. Expedition consists of (i) outrigger, a de novo splice graph transversal algorithm to detect AS from single cell RNA-seq; (ii) anchor, a Bayesian approach to assign splicing modalities and (iii) bonvoyage, using non-negative matrix factorization to visualize modality changes. By applying Expedition to single iPSCs undergoing neuron differentiation, we discover that 25% of AS exons exhibit bimodality and are flanked by longer and more conserved introns harboring distinct cis-regulatory motifs. Bimodal exons are highly dynamic during cellular transitions, preserve translatability, enriched in recently emerged genes and have conserved AS in mammals. Applying Expedition (http://github.com/YeoLab/Expedition) in single cells redefines our estimates and understanding of AS in evolution and biology.

overall_design: Analysis of alternative splicing changes across motor neuron differentiation

first: Olga

last: Botvinnik

first: Yan

last: Song


title: Thrombin inhibition with dabigatran etexilate in C57BL/6 mice fed a high fat diet

city: East Lansing

first: James

last: Luyendyk

state: MI

address: 1129 Farm Lane

department: Pathobiology and Diagnostic Investigation

institute: Michigan State University

summary: Purpose: Determine the impact of thrombin inhibition with dabigatran etexilate on high fat diet-induced gene expression in livers of mice fed a high fat diet

overall_design: Examination of hepatic gene expression in 3 C57BL/6 mice fed a high fat diet and in 3 C57BL/6 mice fed a high fat diet containing 10 mg/g dabigatran etexilate

middle: P


title: RNA-Seq of regenerating DRG neurons

city: Columbus

first: Dario

last: Motti

state: Ohio [OH]

address: 700 Childrens Drive

department: Research

institute: Nationwide Children's Hospital

summary: To identify isoform differential expression underlying peripheral nerve regeneration we performed RNA-Sequencing on DRG neurons after axotomy.

overall_design: RNA was sequenced from peripheral Dorsal Root Ganglia (DRG) neurons from adult male mice 7 days after a conditioning lesion at the level of the sciatic nerve (Crushed samples) or after a sham surgery (Controls surgery).

first: Jessica

last: Lerch

first: Matt

middle: C

last: Danzi

first: Jared

last: Gans

first: Frank

last: Kuo

first: Richard

last: Morris

first: John

last: Bixby

first: Vance

last: Lemmon


title: Global mRNA translational landscapes in mouse bone-marrow-derived-macrophage-mediated response to LPS (lipopolysaccharide)

status: Public on Jul 11 2017

city: Rochester

first: Wenqian

last: Hu

state: Minnesota

address: 200 First St SW, GU16-01A

department: Biochemistry and Molecular Biology

institute: Mayo Clinic

summary: We performed ribosome profiling and RNA-seq on mouse bone marrow derived macrophages (BMDMs) treated with 100ng/ml LPS for 0hr, 1hr, 2hrs, 4hrs, 6hrs to obtain global mRNA translational landscapes during this inflammatory response.

overall_design: Examine transcriptomic and translatomic dynamics in mouse BMDMs' response to LPS treatment. Ribo-seq, RNA-Seq, CLIP-seq.


title: RNA-seq analysis of Kdm5c deficient brains in mice

city: Worcester

first: Rui

last: Li

state: Massachusetts

address: 364 Plantation Street, LRB

department: MCCB

institute: University of Massachusetts Medical School

summary: Kdm5c is an X-linked histone demethylase that acts as a transcriptional repressor via histone H3 lysine 4 (H3K4) – specific demethylation. In humans, KDM5C mutations cause intellectual disability and other neuropsychiatric comorbidities such as epilepsy, autism-like behavior, and aggression. To assess the role of Kdm5c in brain development and behavior, we generated mutant mice deficient for this enzyme and found cognitive deficits and other behavioral phenotypes (e.g. elevated aggression, reduced social interaction, low anxiety) in these mice. We then performed RNA-seq analysis of whole brain RNAs to determine the mis-regulated genes as listed in this dataset.

overall_design: Genome-wide gene expression was determined in the brain between 3 adult male Kdm5c deficient and 3 wild type littermate mice.

first: Jun

last: Xu

first: Yang

last: Shi


title: The developmental transcriptome profiling reveals an abundant GosB that regulates cell cycle, proliferation and apoptosis

city: Yangling

first: Hui

state: Shaanxi

address: College of Animal Science and Technology, Northwest A&F University, Yangling 712100, Shaanxi, China

institute: Northwest A&F University

summary: Background: In bovines, the development and growth of skeletal muscle involves many physiological processes and plays an extremely important role in the quality of beef, however, the regulatory mechanisms underlying the differences in meat quality are largely unknown. Therefore, a cattle muscle transcriptome analysis was performed to compare gene expression profiles between embryonic stage and adult stage. Results: Total RNAs from the Qinchuan cattle skeletal muscle at fetal and adult stages were used to construct libraries for Illumina next-generation sequencing using Ribo-Zero RNA sequencing (RNA-Seq) method. We found a total of 19,695 genes were expressed in the embryo and adult, and 3,299 and 433 genes were present only in the embryo and adult, respectively. Over 5,000 unigenes were significantly different (P < 0.05) when comparing fetal and adult patterns. We further characterized GosB, which was abundant in skeletal muscle, as the candidate gene to explore its role in cattle development. GosB increased the number of C2C12 myoblasts in S phase, and decreased the proportion of cells in G0/G1 phase. GosB promoted proliferation and protect the C2C12 cells from apoptosis via regulating Bcl-2 expression and controlling the intracellular calcium concentration. Conclusions: Modulation of GosB expression in muscle tissue may emerge as potent tool to control myoblast number in the cattle.

overall_design: Six longissimus muscle samples from Qinchuan cattles of two developmental states (embryonic, 90 d; and adult, 24 M old) were collected from Yiming abattoir, a local slaughterhouse of Xi’An, P.R. China.

first: Hong

last: Chen


title: Global mapping of miRNA-target interactions in cattle (Bos taurus)

city: Copenhagen N

first: Troels

middle: K H

last: Scheel

state: Copenhagen

address: Blegdamsvej 3

department: Institute for Immunology and Microbiology

country: Denmark

institute: University of Copenhagen

summary: With regulatory roles in development, cell proliferation and disease, micro-RNA (miRNA) biology is of great importance and a potential key to novel RNA-based therapeutic regimens. Biochemically based sequencing approaches have provided robust means of uncovering miRNA binding landscapes on transcriptomes of various species. However, a current limitation to the therapeutic potential of miRNA biology in cattle is the lack of validated miRNAs targets. Here, we use cross-linking immunoprecipitation (CLIP) of the Argonaute (AGO) proteins and unambiguous miRNA-target identification through RNA chimeras to define a regulatory map of miRNA interactions in the cow (Bos taurus). The resulting interactome is the deepest reported to date for any species, demonstrating that comprehensive maps can be empirically obtained. We observe that bovine miRNA targeting principles are consistent with those observed in other mammals. Motif and structural analyses define expanded pairing rules with most interactions combining seed-based pairing with distinct, miRNA-specific patterns of auxiliary pairing. Further, miRNA-target chimeras had predictive value in evaluating true regulatory sites of the miR-17 family. Finally, we define miRNA-specific targeting for >5000 mRNAs and determine gene ontologies (GO) for these targets. This confirmed repression of genes important for embryonic development and cell cycle progress by the let-7 family, and repression of those involved in cell cycle arrest by the miR-17 family, but it also suggested a number of unappreciated miRNA functions. Our results provide a significant resource for transcriptomic understanding of bovine miRNA regulation, and demonstrate the power of experimental methods for establishing comprehensive interaction maps.

overall_design: miRNA-target chimeras were identified in MDBK cells from standard AGO-CLIP or CLEAR-CLIP experiments as indicated. Experiments were included where cells had been exposed to infection with bovine viral diarrhea virus or tinyLNA-17 treatment. These are indicated. Processed reads were aligned to the host genome (BosTau7). Alignment statistics of CLIP reads are given in the processed data file "Table S1". A complete table of significant peaks from standard AGO-CLIP reads of the 39 data sets is given in "Table S2". This table additionally contains information regarding the associated CLIP read cluster (clustering of all CLIP reads) and potential overlapping miRNA-target chimeras, as well as genomic annotation. A complete list of individual miRNA-target chimeras is given in "Table S3". In the "RNA-seq: tinyLNA-17 vs. Mock" subseries, mRNA-seq was performed on two replicates each of MDBK cells treated with the miR-17 family inhibitor, tinyLNA-17. Differential gene expression analysis was performed and the associated data is given as processed data file "Table S5".

first: Michael

last: Moore

first: Joseph

last: Luna

first: Eiko

last: Nishiuchi

last: Fak

first: Robert

last: Darnell

first: Charles

last: Rice


title: Zika virus alters the microRNA expression profile and elicits an RNAi response in Aedes aegpyti mosquitoes

city: Galveston

first: Grant

last: Hughes

state: TX

address: 301 University Boulevard

department: Pathology

institute: University of Texas Medical Branch

summary: We sequenced the small RNA profiles in ZIKV-infected and non-infected Ae. aegypti mosquitoes at 2, 7 and 14 days post-infection. ZIKV induced an RNAi response in the mosquito with virus-derived short interfering RNAs dramatically increased in abundance post-infection. Further, we found 17 host miRNAs that were modulated by the ZIKV infection at all time points.

overall_design: Two-three day old female Aedes aegypti (Galveston strain) mosquitoes were infected with ZIKV (Mex 1-7) at 2 x 10 FFU/ml. At 2, 7 and 14 days post infection total RNA was extracted from infected and non-infected whole mosquitoes using mirVANA RNA extraction kit following the manufacturer’s protocol (Life Technologies). Small RNA libraries were created using the New England Biolabs small RNA library protocol (New England Biolabs) at the UTMB’s Next Generation Sequencing (NGS) Core (Galveston, TX). The purified cDNA libraries were sequenced using the rapid run platform and single end 50 base sequencing by synthesis on an Illumina Hi-Seq 1500 using the TruSeq SBS kit v3.

first: Miguel

middle: A

last: Saldaña

first: Kayvan

last: Etebari

last: Hart

first: Steven

middle: G

last: Widen

first: Thomas

last: Wood

first: Saravanan

last: Thangamani

first: Sassan

last: Asgari