title: Neural Lineage Progression Controlled by a Temporal Proliferation Program

status: Public on Mar 08 2018

city: linkoping

first: shahrzad

last: Bahrampour

address: Campus HU: Lab 1, floor 13

department: IKE

country: Sweden

institute: Linkoping University

summary: Great progress has been made in identifying transcriptional programs that establish stem cell identity. In contrast, we have limited insight into how these programs are down-graded in a timely manner to halt proliferation and allow for cellular differentiation. Drosophila embryonic neuroblasts undergo such a temporal progression, initially dividing to bud off daughters that divide once (type I), then switching to generating non-dividing daughters (type 0), and finally exiting the cell cycle. We identify six early transcription factors that drive neuroblast and type I daughter proliferation. Early factors are gradually replaced by three late factors, acting to trigger the type I->0 daughter proliferation switch and eventually to stop neuroblasts. Early and late factors regulate each other and four key cell cycle genes, providing a logical genetic pathway for these transitions. The identification of this extensive driver-stopper temporal program controlling neuroblast lineage progression may have implications for studies in many other systems.

overall_design: We generated two quadruple transgenic UAS combinations: UAS-ase, -SoxN, -wor, -Kr (denoted UAS-Quad), and dominant-negative or -activated versions of three of the same of genes, UAS-ase-Vp16, -SoxN-EnR, -wor-EnR, with UAS-Kr encoding a wild type protein (denoted UAS-QuadD). UAS-Quad and UAS-QuadD misexpression were driven from da-Gal4. To analyze the transcriptomic effects of the Quad and QuadD misexpression, we conducted RNAseq analysis for two separate set of experiments: 1) da-Gal4/+ (control) VS da-Gal4/UAS-Quad), and 2) da-Gal4/+ (control) VS da-Gall4/UAS-QuadD. Within each experiment, we generated two biological replicates per genotype (control and gain-of-function). In total, we thus analyzed 8 samples (4 per each experiment; two replicates for control and two replicates for gain-of-function).

first: Shahrzad

first: Stefan

last: Thor


title: Dynamics of chromatin marks and the role of JMJD3 during pancreatic endocrine cell fate commitment

status: Public on Mar 14 2018

city: Beijing

first: Cheng-ran

last: Xu

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

department: School of Basic Medical Sciences

country: China

institute: Peking University

type: Expression profiling by high throughput sequencing

type: Genome binding/occupancy profiling by high throughput sequencing

summary: Pancreatic endocrine lineages are derived from pancreatic progenitors that undergo a cell fate transition requiring a switch from low to high Ngn3 expression. However, the underlying chromatin regulatory mechanisms are unclear. Here, we performed epigenomic analysis of gene regulatory loci featuring histone marks in cells with low or high level of Ngn3 expression. In combination with transcriptomic analysis, we discovered that in Ngn3-high cells, the removal of H3K27me3 was associated with the activation of key transcription factors and the establishment of primed and active enhancers. Deletion of Jmjd3, a histone demethylase for H3K27me3, at the pancreatic progenitor stage impaired the efficiency of endocrine cell fate transition and thereafter islet formation. Curiously, single-cell RNA-seq revealed that the transcriptome and developmental pathway of Ngn3-high cells were not affected by the deletion of Jmjd3. Our study indicates sequential chromatin events and identifies a crucial role for Jmjd3 in regulating the efficiency of the transition from Ngn3-low to Ngn3-high cells.

overall_design: The overall goal of this study was to understand the process of pancreatic endocrine cell specification and the chromatin regulations of endocrine cell fate transition. Specifically, we performed RNA-seq analyses on Ngn3-low and Ngn3-high cells from E13.5 Ngn3-GFP pancreata, and on nascent β-cells from E17.5 Ins1-RFP pancreata. To study the dynamic changes in the promoter and enhancer landscape during endocrine fate transitions, we performed ChIP-seq of promoter related histone modifications (H3K27me3 and H3K4me3) and enhancer related histone modifications (H3K4me1 and H3K27ac) in purified Ngn3-low, Ngn3-high and nascent β cells. To investigate the occupancy of NeuroD1 in endocrine progenitors, we performed NeuroD1 ChIP-seq of E14.5 whole pancreatic cells. To test the role of a histone demethylase, Jmjd3, in regulating endocrine lineage specification, we analyzed single-cell transcriptomes of Ngn3-low and Ngn3-high cells from Jmjd3-deleted pancreas.

first: Xin-Xin

last: Yu

first: Wei-Lin

last: Qiu

first: Liu

last: Yang

first: Lin-Chen

last: Li

first: Yu-Wei

last: Zhang


title: Gene expression profile in endotoxin stimulated murine primary macrophages

city: Univeristy Park

first: Gary

middle: H

last: Perdew

state: PA

address: 309A Life Sciences Building

country: USA

institute: The Pennsylvania State University

summary: We report high-throughput profiling of gene expression from murine primary macrophages. We profile mRNA in control and endotoxin stimulated macrophages, and examine the effect of AHR ligand (SGA360) under inflammatory status. This study provides a framework for understanding transcriptional changes caused by SGA360 during activated inflammatory signaling .

overall_design: Examination of gene expression in peritoneal macrophages under inflammatory stimulus and in the presence of AHR ligand.

first: Gulsum

middle: E

last: Muku

first: Tejas

middle: S

last: Lahoti

first: Iain

middle: A

last: Murray

first: Michael

last: Podolsky

first: Kayla

middle: J

last: Smith

first: Troy

middle: D

last: Hubbard

first: Guray

last: Kuzu

first: Krishne

last: Gowda

first: Shantu

middle: G

last: Amin


title: 4sU-seq of HFF exposed to salt and heat stress

city: München

first: Caroline

last: Friedel

address: Amalienstr. 17

department: Institut für Informatik

country: Germany

institute: Ludwig-Maximilians-Universität München

summary: Primary human foreskin fibroblasts (HFF) were exposed to either salt stress (80mM KCl) or heat stress (44ºC). Newly transcribed RNA was labelled by adding 500µM 4-thiouridine (4sU) to the cell culture media for 1h. Total cellular RNA was isolated using Trizol. Newly transcribed RNA was purified following the protocol described in Raedle et al. JoVE 2013.

overall_design: Newly transcribed RNA was labelled in one hour intervals during either salt or heat stress (prior to stress, 0-1h or 1-2h). All 4sU-RNA samples were sent for sequencing. Two independent biological replicates were analysed.

first: Thomas

last: Hennig

first: Marco

last: Michalski

first: Andrzej

last: Rutkowski

first: Lara

last: Djakovic

first: Adam

last: Whisnant

first: Marie-Sophie

last: Friedl

first: Bhaskar

last: Jha

first: Marisa

last: Baptista

first: Anne

last: L'Hernault

first: Florian

last: Erhard

first: Lars

last: Dölken

middle: C


title: Loss of integrin αvβ8 on murine hepatocytes accelerates liver regeneration

status: Public on Mar 09 2018

city: Edinburgh

first: Richard

middle: Sydney

last: Taylor

state: Midlothian

address: The University of Edinburgh, Easter Bush Campus

department: Roslin Institute

country: United Kingdom

institute: University of Edinburgh

summary: We assess the difference in overall gene expression levels post 2/3 hepatectomy in mouse livers as a result of loss of integrin αvβ8, through microArray experiments. We hypothesized that depletion of hepatocyte integrin αvβ8 would increase hepatocyte proliferation and accelerate liver regeneration following injury. Through use of microarray experiments we identify genes that are up/down regulated only in the mice with integrin αvβ8 depletion.

overall_design: Four replicates of β8flox/flox / Alb-Cre- baseline adult livers (uninjured) were compared to four replicates of β8flox/flox / Alb-Cre- remnant liver following 2/3 hepatectomy, and four replicates of β8flox/flox / Alb-Cre+ baseline adult liver (uninjured) compared with four relicates of β8flox/flox / Alb-Cre+ remnant liver following 2/3 hepatectomy. All samples are 24 hours post hepatectomy.

first: Stephen

middle: N

last: Greenhalgh

first: Kylie

middle: P

last: Matchett

first: Katherine

last: Huang

first: John

middle: T

last: Li

first: Koy

last: Saeteurn

first: Mhairi

last: Donnelly

first: Eilidh

middle: M

last: Simpson

first: Joshua

middle: L

last: Pollack

first: Amha

last: Atakilit

first: Kenneth

first: Jacquelyn

last: Maher

last: Iredale

first: Dean

last: Sheppard

first: Neil

last: Henderson


title: Loss of Asxl2 leads to myeloid malignancies in mice.

first: yanling

last: sun

state: Beijing

address: No.1, Beichen West Road  Chaoyang District

institute: Beijing Institute of Genomics

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

overall_design: Refer to individual Series


title: Single cell transcriptomics reveals new insights on the dynamical function of transcription factors during blood stem and progenitor cell formation

status: Public on Mar 20 2018

city: Monterotondo

first: Christophe

last: Lancrin

state: RM

address: Via Ramarini 32

department: EMBL Rome

country: Italy

institute: EMBL

sample_organism:
Homo sapiens
Mus musculus
other sequences


title: RNA sequencing of  human periodontal ligament stem cells (PDLSCs) with Illumina HiSeq2000

city: Hangzhou

first: Jianning

last: Liu

address: 866 Yuhangtang Road

institute: Zhejiang University

summary: To study the molecular mechanisms underlying PDLSC osteogenic differentiation, we developed RNA sequencing with Illumina HiSeq2000 to comprehensively identify RNA expression profiles in normal PDLSCs, osteogenic inductive PDLSCs and mechanical force-induced PDLSCs. Plenty of RNAs were found to be differentially expressed by RNA sequencing. Furthermore, the potential functions of these RNAs were investigated using bioinformatic analysis.

overall_design: The experiment included three samples: PDLSCs cultured with  normal media; PDLSCs cultured with osteogenic induction for seven days and PDLSCs stretched for 12h in a Flexcell® FX-5000™ Tension system.PDLSCs cultured with  normal media were considered as control group.

first: Fulan

last: Wei


title: Widespread transcriptional pausing and elongation control at enhancers

city: Boston

first: Karen

last: Adelman

state: MA

address: 45 Shattuck St. LHRRB-201a

department: Biological Chemistry and Molecular Pharmacology

institute: Harvard Medical School

summary: Regulation by gene-distal enhancers is critical for cell-type and condition-specific patterns of gene expression. Thus, to understand the fundamental basis of gene activity in a given cell type or tissue, we must be able to identify the precise locations of enhancers, and to functionally characterize their behaviors. Herein, we demonstrate that transcription is nearly universal feature of enhancers in Drosophila and mammalian cells, and that nascent RNA-sequencing strategies are optimal for identification of both enhancers and super-enhancers. We dissect the mechanisms governing enhancer transcription and discover remarkable similarities with transcription at protein-coding genes. We show that RNA polymerase II (RNAPII) undergoes regulated pausing and release at enhancers. However, as compared to mRNA genes, RNAPII at enhancers is less stable and more prone to early termination. Further, we find that the level of histone H3 Lysine 4 (H3K4) methylation at enhancers corresponds to transcriptional activity, such that highly-active enhancers display H3K4 tri-methylation rather than H3K4 mono-methylation considered a hallmark of enhancers. Finally, our work provides insights into the unique characteristics of super-enhancers, which stimulate high-level gene expression through rapid pause release; interestingly, this property renders associated genes resistant to loss of factors that stabilize paused RNAPII.

sample_organism:
Drosophila melanogaster
Mus musculus

platform_organism:
Drosophila melanogaster
Mus musculus

overall_design:
4sU experiments: 5 biological replicates were generated for Control (B-galactosidade treated) and Spt5-depletion (treated with double stranded RNA for Spt5) in S2 cells. 2 biological replicates were generated for Control and NELF-KO (4OHT treated) mouse embryonic stem cells. Start-seq: 2 biological replicates were generated for Control (B-galactosidase treated) and Spt5-depleted (treated with double stranded RNA targeting Spt5) S2 cells. 4 additional replicates of untreated samples were generated. ChIP-seq: 2 biological replicates using untreated cells were generated for all ChIP-seq datasets, with the exception of Pol II ChIP-seq for Control (B-galactosidade treated) and Spt5-dep. (Spt5 treated) S2 cells.

Please note that [1] the 'processed_data_files.tar.gz' contains the processed data files for GSM2259961-GSM2259991; [2] the other Series supplementary files are associated with GSM2866861-GSM2866870; [3] the associated files are indicated in the corresponding sample description field.

first: Telmo

last: Henriques

first: Benjamin

last: Scruggs

first: Ryan

last: Flynn

first: Michiko

middle: O

last: Inouye

first: Ginger

middle: W

last: Muse

first: Adam

last: Burkholder

first: David

last: Fargo

first: Howard

middle: Y

last: Chang


title: Wild Type and two PtaDML10 RNAi lines, KD2 and KD5

city: Pozuelo de Alarcón (Madrid)

first: Daniel

last: Conde

address: Parque Científico y Tecnológico de la U.P.M. Campus de Montegancedo 28223

country: Spain

institute: Centre for Plant Biotechnology and Genomics U.P.M. – I.N.I.A

type: Methylation profiling by high throughput sequencing


title: Next Generation Sequencing Facilitates Quantitative Analysis of Wild Type and two PtaDML10 RNAi lines, KD2 and KD5 transcriptomes

summary: Purpose: we performed comparative RNA-seq analyses to identify differentially expressed genes between KD transgenic lines and Wild Type

overall_design:
wild type and two PtaDML10 RNAi lines, KD2 and KD5, were transferred to 3.5 L pots containing blond peat, pH 4.5. Before any photoperiodic treatments, the plants were grown in a chamber under LD controlled conditions (16h light, 21°C, 65% relative humidity and 150 µmol m-2 s-1 light intensity). After 4 weeks the plants were transferred to SD conditions (8h light, 19°C, 65% relative humidity and 150 µmol m-2 s-1 light intensity) for 12 weeks in order to induce apical bud formation.
To mimic winter conditions, dormant plants were kept under SD, 100 µmol m-2 s-1 light intensity and 4°C for 4 weeks.
Then plants were transferred to LD conditions to promote bud burst. The topmost bud of each plant, so-called apical, was collected when the first visual changes in bud developmental were evident. Buds with morphological changes indicating initial stages of bud break were removed, so all the apical buds were collected in stage 0. We collected 15 apical buds from 15 plants per each WT, KD2 and KD5 genotypes for RNA-seq analyses
Results: Using an optimized data analysis workflow, 2151 differentially expressed genes (DEG) were identified in KD lines, among which 764 were found upregulated and 1387 downregulated

first: Anne-Laure

last: Le Gac

first: Christopher

last: Dervinis

first: Matias

last: Kirst

first: Mariano

last: Perales

first: Stéphane

last: Maury

first: Pablo

last: González-Melendi

first: Isabel

last: Allona


title: Alterations in bronchial airway microRNA expression for lung cancer detection

first: Avrum

last: Spira

address: 72 E Concord Street

department: Computational Biomedicine

institute: Boston University

type: Non-coding RNA profiling by high throughput sequencing

summary: We have previously shown that gene-expression alterations in cytologically normal appearing bronchial epithelial cells can be used as a biomarker for lung cancer detection in smokers (Whitney et al., BMC Medical Genomics 2015; Silvestri et al., NEJM 2015). In this study, we have established that there are also alterations in bronchial microRNA-expression of smokers with lung cancer. Importantly, the performance of an existing bronchial mRNA-biomarker has been improved by integrating microRNA with mRNA expression.

overall_design: Using bronchial brushings collected from current and former smokers undergoing bronchoscopy for suspected lung cancer as part of the AEGIS-1/2 clinical trials, we profiled microRNA-expression via small-RNA sequencing in samples from 347 patients for which gene-expression data was also available. Patients were followed prospectively for up to one year until a final diagnosis of cancer (n=194) or benign disease (n=153) was made. After filtering-out 6 low-quality sequencing samples, we assigned 138 patients (AEGIS-1) to be used as a discovery set and the remaining 203 samples (AEGIS-1/2) were used as an independent test set.

first: Ana

middle: B

last: Pavel

first: Joshua

last: Campbell

first: Gang

last: Liu

last: Elashoff

first: Steven

last: Dubinett

first: Kate

last: Smith

first: Duncan

last: Whitney

first: Marc

last: Lenburg


title: A Domestication-Selected Retrotransposon for Quenching Genomic Immunity in Rice [Bisulfite-seq]

city: Shanghai

first: yiwen

last: Deng

state: Shanghai

address: 300 Fenglin Road

department: Institute of Plant Physiology and Ecology

institute: Shanghai Institute for Biological Sciences, Chinese Academy of Sciences

summary: Transposable elements (TEs) are genomic parasites that constitute the most abundant portions of higher plant genomes. However, whether TE selection occurred during crop domestication remains unknown. HUO is active under normal growth conditions, present at low copy numbers, inserts preferentially into regions capable of transcription, but absent in almost all modern varieties, indicating its removal during rice domestication and modern rice breeding. HUO triggers genomic immunity and dramatically alters genome-wide methylation levels and small RNA biogenesis, as well as global gene expression. Its presence specifically affects agronomic traits by decreasing yield performance and disease resistance but enhancing salt tolerance, which mechanistically explains its domestication removal. Thus, our study reveals a unique retrotransposon as a negative target for maintaining genetic and epigenetic stability during crop domestication and selection.

overall_design: Whole genome methylation maps of  WT line 308D and the HUO retrotransposon insertion lines 307T1 (1 copy) and 307T3 (3 copies) were generated using Bisulfite-seq.

first: Yiwen

first: Yingying

last: Zhang

first: Yu

last: Peng

first: Qun

last: Li

first: Zuhua

last: He


title: A Domestication-Selected Retrotransposon for Quenching Genomic Immunity in Rice [MeDIP-seq]

overall_design: Whole genome methylation maps of  WT line 308D and the 3 copies of HUO retrotransposon insertion lines  307T3  were generated using methylcytosine immunoprecipetation combined with Illumina sequencing (MeDIP-seq)


title: A Domestication-Selected Retrotransposon for Quenching Genomic Immunity in Rice [small RNA-Seq]

overall_design: The small RNA profiles of two-weeks seedling of WT line 308D and the HUO restrotransposon insertion lines 307T1 (1 copy) and 307T3 (3 copy) were generated by deep sequence dependent on illumina Hiseq2000.


title: A Domestication-Selected Retrotransposon for Quenching Genomic Immunity in Rice [RNA-Seq]

overall_design: The RNA profiles of two-weeks seedling of WT line 308D and the HUO restrotransposon insertion lines 307T1 (1 copy) and 307T3 (3 copy) were generated by deep sequence dependent on illumina Hiseq2000.


title: A Domestication-Selected Retrotransposon for Quenching Genomic Immunity in Rice


title: Ablation of the stress protease OMA1 protects against heart failure

city: Madrid

first: Carlos

last: Torroja

state: Madrid

address: Melchor Fernandez Almagro, 3

department: Bioinformatics Unit

institute: Centro Nacional de Investigaciones Cardiovasculares (CNIC)

summary: Heart failure (HF) is a major health and economic burden in developed countries. It has been proposed that the pathogenesis of HF may involve the action of mitochondria. Here we evaluate three different models of HF: tachycardiomyopathy, HF with preserved left ventricular (LV) ejection fraction, and LV myocardial ischemia and hypertrophy. Regardless of whether LVEF is preserved or reduced, our results indicate that the three models share common molecular features: an increase in mitochondrial ROS, followed by ultrastructural alterations in the mitochondrial cristae and loss of mitochondrial integrity that lead to cardiomyocyte death. We show that the ablation of the mitochondrial protease OMA1 averts cardiomyocyte death in all three experimental HF models, and thus, plays a direct role in cardiomyocyte protection. This finding identifies OMA1 as a potential target for preventing the progression of myocardial damage in HF associated to a variety of etiologies.

overall_design: Transcriptome analysis of 12-week-old wild type mice versus OMA1 KO mice under control (non-treated) or treated with Isoproterenol chronically (implanted minipumps) for 7 days in heart tissue. The nuclear genetic background for both genotypes is C57BL/6JOlaHsd.

first: Rebeca

last: Acin-Perez

middle: V

last: Lechuga-Vieco

first: Mª

last: del Mar Muñoz

first: Rocío

last: Nieto-Arellano

first: Fátima

last: Sánchez-Cabo

first: Concepción

last: Jiménez

first: Andrés

last: González-Guerra

first: Cristiane

last: Benincá

first: Pedro

last: Quiros

last: López-Otín

first: José

last: Castellano

first: Jesús

last: Ruíz-Cabello

first: Luis

last: Jiménez-Borreguero

last: Enríquez


title: SCO4117 ECF sigma factor pleiotropically controls secondary metabolism and morphogenesis in Streptomyces coelicolor

status: Public on Mar 07 2018

city: OVIEDO

first: Paula

last: Yagüe

state: ASTURIAS

address: JULIAN CLAVERIA SN

department: Biologia funcional

institute: Universidad de Oviedo

summary: Extracytoplasmic function (ECF) sigma factors are a major type of bacterial signal transducer whose biological functions remain poorly characterised in streptomycetes. In this work, we studied SCO4117, a conserved ECF sigma factor from the ECF52 family, a class of ECF sigma factors exclusive to Actinobacteria. We demonstrate that SCO4117 is a pleiotropic activator of secondary metabolism, germination, aerial mycelium differentiation and sporulation. The expression of genes encoding secondary metabolism pathways (deoxysugar synthases, actinorhodin biosynthetic genes), and genes involved in differentiation (bld, whi, rdl, chp, nepA, ssgB, scbR), was dramatically reduced (up to 300-fold) in a SCO4117 knockout strain. SCO4117 expression depends on its position in the chromosome, as the knockout mutant phenotype can only be fully complemented when the SCO4117 ORF is restored in the chromosome. A strain expressing a truncated version of SCO4117 harbouring only the ECF sigma factor domain, has an opposite phenotype to that observed in the knockout strain, consisting of overproduction of antibiotics (actinorhodin, CDA, cryptic antibiotics) and acceleration of differentiation (aerial mycelium differentiation and sporulation), suggesting a complex interaction between the SCO4117 domains that affects protein activity. Some genes from predicted secondary metabolite clusters (cryptic pathways) were up-regulated compared to the wild strain, indicating that this truncated version of the SCO4117 protein might be useful to activate cryptic pathways. Overall, in this work we demonstrate the pleiotropic effects on the regulation of secondary metabolism and differentiation of SCO4117, the first member of the ECF52 family to be characterised. SCO4117 is a conserved gene overexpressed during the substrate and aerial mycelium stages, showing complex regulation at the transcriptional and post-translational levels.

overall_design: Expression profiles from SCO4117 knockout strain, SCO4117::Tn5062 mutant, and wild type strain were obtained by Next Generation Sequencing from two biological replicates in two culture medium GYM.

first: A

last: Manteca

first: M

last: López-García


title: Chromatin landscapes in mouse haploid stem cells [RRBS-seq]

first: Weisheng

last: Zheng

address: Siping Road, No.1239

department: Department of Bioinformatics

institute: Tongji University

summary: We generate histone modification profiles and DNA methylation profiles of mouse haploid embryonic stem cells. By comparison to mouse diploid ESCs and MEFs, we found the similar chromatin landscapes between haESCs and mESCs, which reveal the self-renew ability and pluripotency in haESCs. Besides, haESCs specific chromatin landscapes show its sperm-like functions.

overall_design: Methylation profiles of mouse haESCs

first: Qianshu

last: Zhu

first: Xinjie

last: Hu

first: Wenteng

last: He

first: Shaorong

last: Gao

first: Cizhong

last: Jiang


title: Chromatin landscapes in mouse haploid stem cells


title: Simultaneous host-pathogen transcriptional analysis of Clostridium perfringens murine myonecrosis infections

city: Melbourne

first: Jamie

last: Gearing

address: 27-31 Wright St

country: Australia

institute: Hudson Institute of Medical Research

summary: To obtain an insight into host-pathogen interactions in clostridial myonecrosis, we carried out comparative RNA-seq analysis measuring host genes in a murine C. perfringens infection model.  Analysis of the murine transcriptome from infected muscle tissues indicated that 270 genes were up-regulated compared to control mock-infected mice. KEGG pathway analysis of these genes revealed an enrichment of Toll-like receptor (TLR) and Nod-like receptor (NLR) signaling components.

overall_design: Examination of host gene expression 1.5 hours after infection or mock-infection (control) with Clostridium perfringens in triplicate using the AB SOLiD system.

first: Lee-Yean

last: Low

first: Paul

middle: F

last: Harrison

first: Jodee

last: Gould

first: David

middle: R

last: Powell

first: Jocelyn

last: Choo

first: Sam

last: Forster

first: Ross

last: Chapman

first: Jackie

middle: K

last: Cheung

last: Hertzog

first: Julian

middle: I

last: Rood


title: Loss of Asxl2 leads to myeloid malignancies in mice. [ChIP-Seq]

first: yanling

last: sun

summary: LK cells of each mouse genotype were fixed with 1% formaldehyde for 15 min and quenched with 0.125 M glycine. Chromatin was isolated by the addition of lysis buffer, followed by shearing with Bioruptor Pico with water cooler (Diagenode, Seraing, Belgium). The DNA was sheared to an average length of 300-500 bp. Genomic DNA regions of interest were isolated using antibodies against H3K27ac (Diagenode, C15410196), H3K4me1 (C15410194), and H3K4me2 (Abcam, ab32356). Complexes were washed, eluted from the beads with SDS buffer, and subjected to RNase and proteinase K treatment. Crosslinks were reversed by incubation overnight at 65°C, and ChIP DNA was purified by phenol-chloroform extraction and ethanol precipitation. After the measurement of DNA concentration with Qubit3.0, the libraries were prepared and sequenced on an Illumina NextSeq 500.

overall_design: To delineate the effect of ASXL2 in the maintenance of HSC self-renewal and cell fates, we performed RNA-seq on LK cells isolated from 6-week-old WT and Asxl2-/- mice with three biological replicates. To explore the impact of ASXL2 loss on histone modifications in HSC/HPCs, we performed Chromatin Immunoprecipitation (ChIP) assays followed by sequencing (ChIP-seq) using antibodies against H3K4me1, H3K4me2, and H3K27ac.

first: Jianping

last: Li

first: Fuhong

first: Peng

last: Zhang

first: Shi

last: Chen

first: Hui

last: Shi

first: Yanling

last: Sun

first: Ying

last: Guo

last: Yang

last: Man

first: Sarah

last: Greenblatt

first: Zhaomin

first: Zhengyu

first: Yuan

last: Zhou

first: Lan

last: Wang

first: Lluis

last: Morey

first: Sion

last: Williams

first: Xi

first: Qun-Tian

first: Stephen

last: Nimer

last: Yu

first: Qian-Fei

first: Mingjiang

last: Xu

first: Feng-Chun


title: Loss of Asxl2 leads to myeloid malignancies in mice. [RNA-Seq]

first: yanling

last: sun

summary: Total RNA was isolated from mouse Asxl2-/- and WT LK cells following standard protocol with TRIZol reagent (Life Technologies) followed by RNA library preparation with the Illumina TruSeq strand-specific mRNA sample preparation system. All RNA-seq libraries were sequenced with a read length of single-end 75bp using the Illumina NextSeq 500, and final of over 45 million reads per sample.

first: Jianping

first: Fuhong

last: He

first: Peng

first: Shi


title: Role of CD133 molecule in WNT response and renal repair

city: Groningen

first: Danny

last: Incarnato

state: Netherlands

address: Nijenborgh 7

department: Molecular Genetics

country: Netherlands

institute: University of Groningen

summary: Renal repair after injury is dependent on clonal expansion of proliferation competent cells. In the human kidney, the expression of CD133+ characterizes a population of resident scattered cells with resistance to damage and ability to proliferate. However, the biological function of the CD133 molecule is unknown. We found by RNA sequencing that cells undergoing cisplatin damage lost the CD133 signature and acquired metanephric mesenchymal and regenerative genes such as SNAIL1, KLF4, SOX9 and WNT3. CD133 was reacquired in the recovery phase. Lack of CD133 was specifically correlated with deregulation of the Wnt signalling and E-cadherin pathway and, functionally, limited cell proliferation after injury. By immunoprecipitation, CD133 appeared to form a complex with E-cadherin and β-catenin. In parallel, CD133-Kd cells showed lower β-catenin levels in basal condition and after Wnt pathway activation and reduced TCF/LEF promoter activation in respect to CD133+ cells. Finally, the lack of CD133 impaired generation of nephrospheres while favored senescence. These data indicate that CD133 may act as a permissive factor for beta-catenin signalling, preventing its degradation in the cytoplasm. Therefore, CD133 itself appears to play a functional role in renal tubular repair trough maintenance of proliferative response and control of senescence.

overall_design: Expression profiling by high-throughput sequencing

first: Alessia

last: Brossa

first: Elli

last: Papadimitriou

first: Federica

last: Collino

first: Salvatore

last: Oliviero

first: Giovanni

last: Camussi

first: Benedetta

last: Bussolati


title: RNA-seq profiles of wildtype and Ezh2 knockout mouse natural killer T cell subsets

city: Parkville

first: Gordon

last: Smyth

state: Vic

address: 1G Royal Pde

department: Bioinformatics

institute: Walter and Eliza Hall Institute of Medical Research

summary: Natural killer T (NKT) cells identified by CD1d-tetramer and TCRb were isolated from the thymi of wild type and Ezh2 knockout mice. The NKT cells were FACS sorted into different stages based on the surface expression of CD44 and NK1.1.

overall_design: For both wildtype and knockout mice, RNA was extracted from two biological replicates of CD44+ NK1.1- cells, one replicate of CD44+ NK1.1+ cells and one replicate of CD44- NK1.1- cells. Each RNA sample was divided into four and sequenced on four lanes of an Illumina HiSeq sequencer.

first: Aaron

last: Lun

first: Rhys

middle: S

last: Allan


title: Whole Genome Bisulfite Sequencing in wild type plants, and two RNAi transgenic lines, KD2 and KD5.

first: Daniel

last: Conde

summary: We report the application of Whole Genome Bisulfite Sequencing to identify differentially methylated regions (DMR) in two RNAi transgenic lines, with dowregulated expression of the demeter-like gene PtaDML10, in comparisson to wild-type plants of Populus tremula x Populus alba plants.

overall_design:
wild type and two PtaDML10 RNAi lines, KD2 and KD5, were transferred to 3.5 L pots containing blond peat, pH 4.5. Before any photoperiodic treatments, the plants were grown in a chamber under LD controlled conditions (16h light, 21°C, 65% relative humidity and 150 µmol m-2 s-1 light intensity). After 4 weeks the plants were transferred to SD conditions (8h light, 19°C, 65% relative humidity and 150 µmol m-2 s-1 light intensity) for 12 weeks in order to induce apical bud formation.
To mimic winter conditions, dormant plants were kept under SD, 100 µmol m-2 s-1 light intensity and 4°C for 4 weeks.
The topmost bud of each plant, so-called apical, was collected when the first visual changes in bud developmental were evident. Buds with morphological changes indicating initial stages of bud break were removed, so all the apical buds were collected in stage 0. We collected 15 apical buds from 15 plants per each WT, KD2 and KD5 genotypes for whole genome bisulfite sequencing analyses.

first: Anne-Laure

last: Le Gac

first: Christopher

last: Dervinis

first: Matias

last: Kirst

first: Mariano

last: Perales

first: Stéphane

last: Maury

first: Pablo

last: González-Melendi

first: Isabel

last: Allona


title: Dysregulation of the epigenetic landscape of normal aging in Alzheimer's disease [RNA-Seq]

city: Philadelphia

first: Gregory

last: Donahue

address: 3400 Civic Center Blvd, Bldg 421

department: Cell & Developmental Biology

institute: The University of Pennsylvania

summary: Aging is the strongest risk factor for Alzheimer's disease (AD), although the underlying mechanisms remain unclear. The chromatin state, in particular through the mark H4K16ac, has been implicated in aging and thus may play a pivotal role in age-associated neurodegeneration. Here we compared the genome-wide enrichment of H4K16ac in the lateral temporal lobe of AD individuals against both younger and elderly cognitively normal controls. We find that while normal aging leads to H4K16ac enrichment, AD entails dramatic losses of H4K16ac in the proximity of genes linked to aging and AD. Our analysis highlights the presence of three classes of AD-related changes having distinctive functional roles. Furthermore, we discover an association between the genomic locations of significant H4K16ac changes with genetic variants (SNPs) identified in prior AD genome-wide association studies (GWAS) and with expression quantitative trait loci (eQTLs). Our results establish the basis for an epigenetic link between aging and AD.

overall_design: RNA-seq in healthy and diseased human brains; using 8 young healthy brains (Young), 10 aged healthy brains (Old), and 12 aged diseased brains (AD)

first: Raffaella

last: Nativio

first: Greg

first: Amit

last: Berson

first: Sager

middle: J

last: Gosai

first: Jon

last: Toledo

first: Alex

last: Amlie-Wolf

first: Ferit

last: Tuzer

first: Claudio

last: Torres

first: John

middle: Q

last: Trojanowski

first: Li-San

last: Wang

first: Brian

middle: D

last: Gregory

first: F

last: Johnson

first: Nancy

last: Bonini

first: Shelley

last: Berger


title: Long-Range Enhancer Interactions Are Prevalent in Mouse Embryonic Stem Cells and Are Reorganized upon Pluripotent State Transition

city: Cambridge

first: Steven

middle: William

last: Wingett

state: Cambs

address: Francis Crick Avenue, Cambridge Biomedical Campus

department: Cell Biology

institute: MRC Laboratory of Molecular Biology

summary: Transcriptional enhancers, including super-enhancers (SE), form physical interactions with promoters to regulate cell type-specific gene expression. SE are characterised by high transcription factor occupancy and large domains of active chromatin, and are currently assigned to target promoters using computational predictions. How promoter–SE interactions change upon cell state transitions, and whether transcription factors maintain SE interactions, has not been reported. Here, we used promoter-capture Hi-C to identify promoters in close physical proximity to SE in mouse embryonic stem cells (ESCs). SE form complex, spatial networks in which individual SE contact multiple promoters, and a rewiring of promoter–SE interactions occurs between ESC and EpiSC pluripotent states. Long-range promoter–SE interactions are a hallmark of ESCs and are dependent on the transcription factor NANOG. These results provide new insights into the gene regulatory organization of pluripotent cells and demonstrate the requirement for transcription factors in maintaining a subset of SE interactions.

overall_design: Promoter capture Hi-C of mouse ESCs,  EpiSCs  and Nanog-/- ESCs.  CHiP-Seq in mouse EpiSCs against Nanog, Oct4 and Sox2.  RNA-seq of EpiSCvsESC / ESCvsBT12

first: Clara

last: Novo

first: Biola-Maria

last: Javierre

first: Jonathan

last: Cairns

first: Anne

last: Segonds-Pichon

first: Paula

last: Freire-Pritchett

first: Mayra

last: Furlan-Magaril

first: Stefan

last: Schoenfelder

first: Peter

last: Fraser

last: Rugg-Gunn


title: Molecular and Pathological Interactions among Aβ42, Tau, TREM2, and TYROBP in Drosophila Models

city: New York

first: Bin

last: Zhang

state: NY

address: 1470 Madison Avenue

department: Genetics and Genomic Sciences

institute: Icahn School of Medicine at Mount Sinai

summary: Cerebral amyloidosis, neuroinflammation, and tauopathy are key features of Alzheimer’s disease (AD), but interactions among these features remain poorly understood. Our previous multiscale molecular network models of AD revealed TYROBP as a key driver of an immune- and microglia-specific network that was robustly associated with AD pathophysiology. Recent genetic studies of AD further identified pathogenic mutations in both TREM2 and TYROBP. In this study, we systematically examined molecular and pathological interactions among Aβ, tau, TREM2 and TYROBP by integrating signatures from transgenic Drosophila models of AD and transcriptome-wide gene co-expression networks from two human AD cohorts.

overall_design: We generated RNA-seq expression profiles for flies with "wild type", "glial expression of TREM2/TYROBP", "glial expression of TREM2/TYROBP and neuronal expression of Aβ" and "glial expression of TREM2/TYROBP and retinal expression of Tau".

first: Michiko

last: Sekiya

first: Minghui

first: Naoki

last: Fujisaki

first: Yasufumi

last: Sakakibara

first: Xiuming

last: Quan

first: Michelle

middle: E

last: Ehrlich

first: Eric

last: Schadt

first: Sam

last: Gandy

first: Kanae

last: Ando

first: Koichi

last: Iijima


title: Chromatin landscapes in mouse haploid stem cells [ChIP-seq]

first: Weisheng

last: Zheng

overall_design: Histone modification landscapes of mouse haESCs

first: Qianshu

last: Zhu

first: Xinjie

last: Hu

first: Wenteng

last: He

first: Shaorong

last: Gao

first: Cizhong

last: Jiang


title: Dysregulation of the epigenetic landscape of normal aging in Alzheimer's disease

first: Gregory

last: Donahue

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

overall_design: Refer to individual Series


title: Comparative RNAseq analysis of C. perfringens strain JIR325 grown in vivo and in vitro.

city: Clayton

first: Julian

last: Rood

state: VIC

address: Wellington Rd

department: Microbiology

institute: Monash University

summary: RNA-seq was employed for comparative analysis of the transcriptomes of both the pathogen and the host in C. perfringens-infected murine muscle lesions. The aim was to identify C. perfringens genes that were induced in the host environment and host signaling cascades that were activated in response to a C. perfringens infection.

overall_design: Three biological replicates of each treatment were analaysed.

first: Lee-Yean

last: Low

first: Paul

last: Harrison

first: David

last: Powell

first: Jackie

last: Cheung


title: VIRMA mediates preferential m6A mRNA methylation in 3'UTR and near stop codon and associates with alternative polyadenylation

city: Chicago

first: Xiaolong

last: Cui

state: IL

address: 680 N Lake Shore Drive

department: Department of Preventive Medicine

institute: Northwestern University

summary: N6-methyadenosine (m6A) is enriched in 3`UTR (3` untranslated region) and near stop codon of mature polyadenylated mRNAs in mammalian systems and has regulatory roles in eukaryotic mRNA transcriptome switch. Significantly, the mechanism for this modification preference remains unknown, however. Herein we report a characterization of the full m6A methyltransferase complex in HeLa cells identifying METTL3/METTL14/WTAP/VIRMA/HAKAI/ZC3H13 as the key components, and we show that VIRMA mediates preferential mRNA methylation in 3`UTR and near stop codon. Biochemical studies reveal that VIRMA recruits the catalytic core components METTL3/METTL14/WTAP to guide region-selective methylations. Around 60% of VIRMA mRNA immunoprecipitation targets manifest strong m6A enrichment in 3`UTR. Depletions of VIRMA and METTL3 induce 3`UTR lengthening of several hundred mRNAs with over 50% targets in common. VIRMA associates with polyadenylation cleavage factors CPSF5 and CPSF6 in an RNA-dependent manner. Depletion of CPSF5 leads to significant shortening of 3`UTR of over 2,800 mRNAs, 84% of which are modified with m6A. Together our studies provide insights into m6A deposition specificity in 3`UTR and its correlation with alternative polyadenylation.

overall_design: We used VIRMA KO/KD cell lines to test m6A deposition specificity in 3`UTR and its correlation with alternative polyadenylation.

first: Yanan

last: Yue

first: Jun

last: Liu

first: Chuan

first: Jianzhao


title: Epigenetic reprogramming enables the primordial germ cell-to-gonocyte transition (RNA-Seq)

city: London

first: Peter

last: Hill

address: Kensington

institute: Imperial College London

summary: Gametes are highly specialised cells that can give rise to the next generation through their ability to generate a totipotent zygote. In mouse, germ cells are first specified in the developing embryo as primordial germ cells (PGCs) starting around embryonic day (E) 6.25. Following subsequent migration into the developing gonad, PGCs undergo a wave of extensive epigenetic reprogramming at E10.5/E11.5, including genome-wide loss of 5-methylcytosine (5mC). The underlying molecular mechanisms of this process have remained enigmatic leading to our inability to recapitulate this step of germline development in vitro. Using an integrative approach, we show that this complex reprogramming process involves the coordinated interplay between promoter sequence characteristics, DNA (de)methylation, Polycomb (PRC1) complex and both DNA demethylation-dependent and -independent functions of Tet1 to enable the activation of a critical set of germline reprogramming responsive (GRR) genes involved in gamete generation and meiosis. Our results also unexpectedly reveal a role for Tet1 in safeguarding but not driving DNA demethylation in gonadal PGCs. Collectively, our work uncovers a fundamental biological role for gonadal germline reprogramming and identifies the epigenetic principles of the PGC-to-gonocyte transition that will be instructive towards recapitulating complete gametogenesis in vitro.

overall_design: RNA-Seq of mESCs

first: Petra

last: Hajkova

first: Zhiyi

last: Sun

first: Gopuraja

last: Dharmalingam


title: Genome-wide Studies of Chromatin Structure during Blood Cell Differentiation [HiC-seq]

city: Beijing

first: Yanjian

last: Li

address: Tsinghua University, Haidian District

institute: Tsinghua University

summary: Chromatin structure plays key role in regulating whole genome gene expression.The goal of this study are to compare chromatin structure of ATRA treated and control cells, finding the mechanism that how chromatin structure regulates gene transcription.

overall_design: HL-60 cells with ATRA or ethanol treated for 4 days were used to generate Hi-C library, in replicate.

last: LI

first: Michael

last: ZHANG

first: Yang

last: CHEN


title: Differential Gene Expression between ATRA treated and control HL-60 Cells [RNA-seq]

summary: These RNA-seq data were generated to correlate with genomic interaction data in a related Hi-C analysis. Analysis revealed differential expressed genes in ATRA treated and control HL-60 cells. Changes of gene expression with topological associated domains (TADs) were showd to be correlated with chromatin structure alteration

overall_design: HL-60 cells with ATRA or ethanol treated for 4 days were used to generate RNA-seq library, in replicate.


title: Assay for Transposase-Accessible Chromatin of ATRA treated and wild type HL-60 cell line [ATAC-seq]

summary: These ATAC-seq data were generated to correlate with genomic interaction data in a related Hi-C analysis. Analysis of ATAC-seq data revealed series of overlapping or specific open chromatin peaks in ATRA treated and control cells. Those specific peaks showed fewer overlapping with gene promoters than the overlapping peaks. Key transcription factor for blood cell differentiation GATA2 was found only bind in control specific peaks.

overall_design: HL-60 cells with ATRA or ethanol treated for 4 days were used to generate ATAC-seq, in replicate.


title: Chromatin structure alteration regulates key transcription factor expression during blood cell differentiation


title: Increased H3K9 methylation and impaired expression of Protocadherins are associated with the cognitive dysfunctions of the Kleefstra syndrome

city: Barcelona

first: giovanni

last: iacono

state: Spain

address: Baldiri Reixac, 4

department: single cell sequencing

institute: CNAG,Centro Nacional de Análisis Genómico

summary: Kleefstra syndrome, a disease with intellectual disability, autism spectrum disorders and other developmental defects is caused in humans by haploinsufficiency of EHMT1. Although EHMT1 and its paralog EHMT2 were shown to be histone methyltransferases responsible for deposition of the di-methylated H3K9 (H3K9me2), the exact nature of epigenetic dysfunctions in Kleefstra syndrome remains unknown. Here, we found that the epigenome of Ehmt1+/- adult mouse brain displays a marked increase of H3K9me2/3 which correlates with impaired expression of protocadherins, master regulators of neuronal diversity. Increased H3K9me3 was present already at birth, indicating that aberrant methylation patterns are established during embryogenesis. Interestingly, we found that Ehmt2+/- mice do not present neither the marked increase of H3K9me2/3 nor the cognitive deficits found in Ehmt1+/- mice, indicating an evolutionary diversification of functions. Our finding of increased H3K9me3 in Ehmt1+/- mice is the first one supporting the notion that EHMT1 can quench the deposition of tri-methylation by other Histone methyltransferases, ultimately leading to impaired neurocognitive functioning. Our insights into the epigenetic pathophysiology of Kleefstra syndrome may offer guidance for future developments of therapeutic strategies for this disease.

overall_design: Total of 199 sequenced samples. RNA-seq for wild type and Ehmt1+/- in multiple brain regions and developmental stages. H3k4me3 and H3k9me3 ChIP-seq for wild type and Ehmt1+/- in multiple brain regions and developmental stages. H3k36me3, H3k4me1, H3k27ac, H3k27me3, H3k9me2 for adult (P30) wild types, Ehmt1+/- and Ehmt2+/- hippocampus. DNA whole-genome bisulfate sequence for adult (P30) wild types, Ehmt1+/- and Ehmt2+/- hippocampus.

first: Giovanni

last: Iacono

first: Aline

last: Dubos

first: Marco

last: Benevento

first: Hans

last: van Bokhoven

first: Nael

last: Nadif Kasri

first: Yann

last: Herault

first: Henk

last: Stunnenberg


title: Dysregulation of the epigenetic landscape of normal aging in Alzheimer's disease [ChIP-Seq]

first: Gregory

last: Donahue

overall_design: ChIP-seq of H4K16ac in healthy and diseased human brains; using 9 young healthy brains (Young), 10 aged healthy brains (Old), and 12 aged diseased brains (AD); H4K16ac and input are included for each sample

first: Raffaella

last: Nativio

first: Greg

first: Amit

last: Berson

first: Sager

last: Gosai

first: Jon

last: Toledo

first: Alex

last: Amlie-Wolf

first: Ferit

last: Tuzer

first: Claudio

last: Torres

first: John

last: Trojanowski

first: Li-San

last: Wang

first: Brian

last: Gregory

first: F

last: Johnson

first: Nancy

middle: M

last: Bonini

first: Shelley

last: Berger


title: Genome-wide maps of chromatin state ATRA treated and control HL-60 cells [ChIP-seq]

first: Yanjian

last: Li

summary: These ChIP-seq data were generated to correlate with genomic interaction data in a related Hi-C analysis.The goal of ChIP-seq are to annotate active promoter and enhancer of ATRA treated and control HL-60 cells. After ATRA induction, H3K27ac peaks distal to gene promoters showed significant changes. Those changes were correlated with interaction intensity between promoters and enhancers.

overall_design: HL-60 cells with ATRA or ethanol treated for 4 days were used to generate Hi-C, in replicate.

last: LI

first: Michael

last: ZHANG

first: Yang

last: CHEN


title: Next Generation Sequencing Facilitates Quantitative Analysis of Wild Type Young and Old muscle Transcriptomes

first: Jie

last: Yin

address: 320 Yueyang Road

institute: Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences

summary:
Purpose: Next-generation sequencing (NGS) has revolutionized systems-based analysis of cellular pathways. The goals of this study are to compare Young and Old muscles transcriptome profiling (RNA-seq) to optimal high-throughput data analysis
Results: Using an optimized data analysis workflow, we mapped about 30 million sequence reads per sample to the mouse genome (build mm10) and identified 24799 genes. Among them, 95.7% of the genes displayed the similar expression level in both young and old muscles.2% of genes (501) were significantly up-regulated and 2.3% of genes (584) were significantly down-regulated. p value <0.05.

overall_design: Muscle mRNA profiles of 3-month old wild type (WT young) and 20-month old wild type mice  (WT Old) were generated by deep sequencing, in triplicate, using Illumina HiSeq 3000.

first: Ping

last: Hu

first: Bo

last: Xu

first: Liang

last: Xue


title: Pericyte-like cells generated from human pluripotent stem cells support hematopoietic stem and progenitors ex vivo

city: Los Angeles

first: Gay

middle: Miriam

last: Crooks

state: California

address: 610 Charles E. Young Drive, East

department: Pathology & Laboratory Med

institute: University of California Los Angeles

summary: Various mesenchymal cell types have been identified as critical components of the hematopoietic stem/progenitor cell (HSPC) niche. Although several groups have described the generation of mesenchyme from human pluripotent stem cells (hPSC), the capacity of such cells to support hematopoiesis has not been reported. Here we have demonstrated that distinct mesenchymal subpopulations co-emerge from mesoderm during hPSC differentiation. Despite co-expression of common mesenchymal markers (CD73, CD105, CD90, PDGFRβ), a subset of cells defined as CD146++CD140alow supported functional HSPC ex vivo while CD146-CD140a+ cells drove differentiation. The CD146++ subset expressed genes associated with the HSPC niche and high levels of the Wnt inhibitors. HSPC support was contact-dependent and was mediated in part through JAG1 expression. Molecular profiling revealed remarkable transcriptional similarity between hPSC-derived CD146++ and primary human CD146++ perivascular cells. The derivation of diverse pools of mesenchymal populations from hPSC opens potential avenues to model their developmental and functional differences and to improve cell-based therapeutics from hPSC.

overall_design: Our goal was to analyze and compare transcriptome of human pluripoten stem cell-derived mesenchyme (CD146++ and CD146-) with primary human lipoaspirate tissue-derived pericyte (CD146+) and CD146- mesenchymal populations.

first: Chee

last: Chin

first: Mirko

last: Corselli

first: David

last: Casero

first: Yuhua

last: Zhu

first: Chong

last: He

first: Reef

last: Hardy

first: Bruno

last: Péault


title: Identification and characterization of androgen receptor splice variants preferred bindings that drive prostate cancer progression [RNA-seq]

city: San Antonio

first: Zhenqing

last: Ye

state: TX

address: 8403 Floyd Curl Dr

department: 6Department of Population Health Sciences

institute: UT Health San Antonio

summary: Androgen receptor (AR) splice variants (ARVs) are implicated in developing castration-resistant (CR) prostate cancer (CRPC). Little is known about the ARV-mediated transcription program in CRPC. We identified ARV-preferred binding sites (ARV-PBS) and unique transcriptome in CRPC cells. ARVs preferentially bind to enhancers located in nucleosome-depleted regions with the full AR-response element (AREfull), while full-length AR (ARFL)-PBS are enhancers resided in closed chromatin regions with the composite FOXA1-nnnn-AREhalf motif. ARV-PBS exclusively overlapped with AR binding sites in CR patients. ARV-driven genes were up-regulated in abiraterone-resistant patient specimens and promote CRPC growth. We uncover distinct genomic and epigenomic characteristics of ARV-PBS and a unique ARV-dependent transcriptional program that not only drives CR progression but could also offer new targets for therapy. Increasing evidence suggests a pivotal role of ARVs in the acquisition of anti-AR therapy resistance in CRPC. It has been shown previously that ARVs possess unique structural and functional features such as completely lacking or only containing an impaired ligand-binding domain but constitutively active.  Our findings advance the understanding of ARVs by demonstrating that ARV-PBS exhibit distinctive DNA-binding motif, GC content, and nucleosome and epigenetic characteristics.  We further unravel that ARV-PBS exclusively overlap with AR bindings identified from castration-resistant patients and ARV activity is significantly increased in abiraterone-resistant patients.  Given that there is no drug available to target ARVs at present, identification of ARV-mediated unique downstream pathways opens new avenues for the development of effective therapeutics for CRPC.

overall_design: Androgen receptor splice variants (AR-V1, AR-V3, AR-V4 and AR-V7) were knocked down using siRNA in 22Rv1 cells (siARVs). RNA-seq experiments were then performed for both siARVs and control (siNT) samples in duplicates.  Differentially expressed genes were identified by comparing  siARVs with siNT.

first: Liguo

last: Wang

first: Ji

last: Lu


title: Epigenetic reprogramming enables the primordial germ cell-to-gonocyte transition (RRBS)

first: Peter

last: Hill

overall_design: Reduced representation bisulphite sequencing on PGCs between E10.5 and E14.5; male and female samples were treated separately following the initiation of sex specification (i.e. from E12.5)

first: Petra

last: Hajkova

first: Zhiyi

last: Sun

first: Gopuraja

last: Dharmalingam


title: Genetic Tagging During Human Mesoderm Differentiation Reveals Tripotent Lateral Plate Mesodermal Progenitors

summary: Although clonal studies of lineage potential have been extensively applied to organ specific stem and progenitor cells, much less is known about the clonal origins of lineages formed from the germ layers in early embryogenesis.  We applied lentiviral tagging followed by vector integration site analysis (VISA) with high-throughput sequencing to investigate the ontogeny of the hematopoietic, endothelial and mesenchymal lineages as they emerge from human embryonic mesoderm. In contrast to studies that have used VISA to track differentiation of self-renewing stem cell clones that amplify significantly over time, we focused on a population of progenitor clones with limited self-renewal capability. Our analyses uncovered the critical influence of sampling on the interpretation of lentiviral tag sharing, particularly among complex populations with minimal clonal duplication. By applying a quantitative framework to estimate the degree of undersampling we revealed the existence of tripotent mesodermal progenitors derived from pluripotent stem cells, and the subsequent bifurcation of their differentiation into exclusively bipotent endothelial/hematopoietic or endothelial/mesenchymal progenitors.

overall_design: Our goal was to analyze transcriptome changes of mesoderm commitment during human embyronic stem cells differentiation. RNA were extracted and sequenced from two populations, human embryonic stem cells (H1 line) and the human early mesodermal progenitors (hEMP) differentiated from H1.

first: Aaron

last: Cooper

first: Georgia

last: Lill

first: Denis

last: Evseenko

first: Matteo

last: Pellegrini

first: Donald

last: Kohn


title: NCoR/SMRT co-repressors cooperate with c-MYC to create an epigenetic barrier to somatic cell reprogramming

city: Shenzhen

first: Andrew

middle: P

last: Hutchins

address: 1088 Xueyuan Rd

institute: Southern University of Science and Technology


overall_design: RNA-Seq of PGCs from E10.5, E12.5, E14.5; male and female samples were treated separately following the initiation of sex specification (i.e. from E12.5)


title: Epigenetic reprogramming enables the primordial germ cell-to-gonocyte transition (AbaSeq)

overall_design: AbaSeq on PGCs between E10.5 and E12.5 to detect 5hmC; male and female samples were treated separately following the initiation of sex specification (i.e. from E12.5)


title: NCoR/SMRT co-repressors cooperate with c-MYC to create an epigenetic barrier to somatic cell reprogramming [ChIP-Seq]

summary: Changing the somatic cell transcriptome to a pluripotent state using exogenous reprogramming factors needs transcriptional co-regulators that help activate or suppress gene expression and rewrite the epigenome. Here, we show that reprogramming-specific engagement of the NCoR/SMRT co-repressor complex at key pluripotency loci creates an epigenetic block to reprogramming. HDAC3 executes the repressive function of NCoR/SMRT in reprogramming by inducing histone deacetylation at these loci. Recruitment of NCoR/SMRT-HDAC3 to pluripotency genes is facilitated by all 4 Yamanaka factors (OCT4, SOX2, KLF4 and c-MYC) but mostly by c-MYC. Class IIa HDACs further potentiate this recruitment by interacting with both the reprogramming factors and NCoR/SMRT. Consequently, depleting NCoR/SMRT-HDAC3 function enables high efficiency of reprogramming, while elevating NCoR/SMRT-HDAC3 recruitment at pluripotency loci by over-expressing constitutively active class IIa HDACs derails it. Our findings thus uncover an unexpected epigenetic mechanism involving c-MYC, whose manipulation greatly enhances reprogramming efficiency.

overall_design: ChIP-seq data consisting of NCoR or SMRT binding in ESCs, OSKM-transfected MEFs (Day 9) and H3K27ac ChIP-seq in OSKM-transfected MEFs (Day 5, 9 and 13) either co-transfected with a FLAG control or a HDAC3-Y298F deacetylase null mutant

first: Miguel

middle: A

last: Esteban

first: Qiang

last: Zhuang


title: Temporal epigenomic profiles of transition from hematopoietic multipotent progenitors to B committed cells [ChIP-seq]

status: Public on Mar 06 2018

city: Yokohama

first: Takaho

middle: A.

last: Endo

state: Kanagawa

address: 1-7-22 Suehiro, Tsurumi

department: IMS

country: Japan

institute: RIKEN

summary: To identify the “time-lapse” TF networks during B lineage commitment, we established multipotent progenitors harboring a tamoxifen-inducible form of Id3, an in vitro system where virtually all cells became B cells within 6 days by simply withdrawing 4-OHT. In this study, epigenomic analysis at multiple time points was performed using the culture system.

overall_design: Time-course epigenomic profiles of multipotent iLS cells toward B committed cells were analyzed by deep sequencing using Illumina Hiseq platform.

first: Tomohiro

last: Miyai

first: Tomokatsu

last: Ikawa


title: Temporal transcriptomic profiles of transition from hematopoietic multipotent progenitors to B committed cells [RNA-seq]

summary: To identify the “time-lapse” TF networks during B lineage commitment, we established multipotent progenitors harboring a tamoxifen-inducible form of Id3, an in vitro system where virtually all cells became B cells within 6 days by simply withdrawing 4-OHT. In this study, transcriptome analysis at multiple time points was performed using the culture system.

overall_design: Time-course transcriptomic profiles of multipotent iLS cells toward B committed cells were analyzed by deep sequencing, basically in triplicate, using Illumina Hiseq platform.


title: Global transcriptomic analysis of colons of wild type and NLRX1-/- mice with IBD

city: Blacksburg

first: Monica

last: Viladomiu

state: VA

address: 1015 Life Science Circle

department: Virginia Bioinformatics Institute

institute: Nutritional Immunology and Molecular Medicine Laboratory

summary: NLRX1 is a mitochondrial-associated NOD-like receptor that modulates antiviral immunity, cellular stress, autophagy, and reactive oxygen species (ROS) production. The role of NLRX1 in inflammatory bowel disease (IBD) remains largely unknown. This study aimed to characterize NLRX1-mediated mechanisms of protection from IBD.  We investigated the ability of NLRX1 to modulate global colonic gene expression, gut pathology, inflammation and immunity by using loss-of-function approaches in dextran sodiu sulfate (DSS) and CD4+CD45RBhigh transfer colitis models. Colons, spleens, and mesenteric lymph nodes (MLN) were excised for characterizing immune cell subsets, histological analyses, cytokine, RNA sequencing analyses, and autophagy expression, NF-κB activity, and ROS production. The loss of NLRX1 increased severity of disease and colonic histopathology in both models of IBD. Colons of NLRX1-/- mice had significantly increased epithelial ulceration and leukocyte infiltration mostly in the form of neutrophils, lymphocytes, and macrophages in the DSS model, while recipients of NLRX1-/- CD4+ T cells had increased leukocytic infiltration, proliferation, fibrosis, and crypt abscessation in both colon and ileum. The loss of NLRX1 increased numbers of effector T helper (Th1), Th17, and regulatory T cells (Treg) cells in the colonic mucosa and spleen, increased colonic NF-κB activity, upregulation of IL-17, IFNγ and TNF-α production, and increased ROS production. Global transcriptomic analyses demonstrates that NLRX1 regulates immunity and lipid metabolism pathways. NLRX1 ameliorates intestinal pathology during IBD by acting as an internal thermostat that modulates the balance of effector versus regulatory CD4+ T cell responses, and suppressing colonic NF-κB activity, inflammatory cytokine expression, lipid metabolism gene expression, ROS production and autophagy.

overall_design:
NLRX1 is a mitochondrial-associated NLR and has been proposed to act as an anti-inflammatory entity that prevents overzealous inflammation. Many important inflammatory pathways such as NF-κB modulation, ROS production, and autophagy have been linked to NLRX1, although exact mechanisms remain controversial. Given its multifactorial effects, NLRX1 presents as a highly powerful and novel molecule in the study of chronic immunologic diseases. In addition, the current controversy surrounding cellular and molecular mechanisms of action of NLRX1 sets the stage for further investigation.
We have developed a series of experiments characterizing the effect of NLRX1 deletion on sensitivity of mice to both acute and chronic models of inflammatory bowel disease, focusing not only on clinical and immunologic differences but also exploring several mechanisms by which NLRX1 provides protection from experimental IBD. First, we show that NLRX1 deletion promotes effector T cell phenotypes in murine models of IBD; an exciting finding opening new doors for NLRX1’s effects on immune-mediated disease. NLRX1 knockout mice are more sensitive to dextran sodium sulfate induced-colitis than their wild-type counterparts, and also that lack of NLRX1 in T cells in an adoptive transfer model results in similarly increased pathology at both the tissue level and immune cell level. Indeed, expression of NLRX1 in wild-type mice under active experimental IBD conditions is significantly suppressed, highlighting its importance as a potential regulatory molecule. We further analyze the molecular pathways influencing NLRX1 during IBD and show clearly that modulation of reactive oxygen species, NF-κB activity, inflammatory cytokine production, and autophagy are all implicated.  Thus, NLRX1 represents a novel and potential therapeutic target for IBD. Our findings are of great interest not only to researchers of IBD and other immune-mediated diseases, but also to the study of the lesser-known NLRs and their functions. This dataset was created using the acute DSS model.

first: Josep

last: Bassaganya-Riera

first: Pawel

last: Michalak

first: Raquel

last: Hontecillas

last: Leber

first: Cassandra

last: Philipson


title: Epigenetic reprogramming enables the primordial germ cell-to-gonocyte transition (WGBS)

first: Peter

last: Hill

overall_design: Whole genome bisulphite sequencing of PGCs between E10.5 and E12.5; male and female samples were treated separately following the initiation of sex specification (i.e. from E12.5)

first: Petra

last: Hajkova

first: Zhiyi

last: Sun

first: Gopuraja

last: Dharmalingam


title: Temporal transcriptomic and epigenomic profiles of transition from hematopoietic multipotent progenitors to B committed cells

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

overall_design: Refer to individual Series


title: RNA sequencing of drh-3(rrr2) mutants

city: Basel

first: Dimos

last: Gaidatzis

address: Maulbeerstrasse 66

country: Switzerland

institute: Friedrich Miescher Institute

summary: We found that the CSR-1 endoRNAi pathway functions in preventing a premature activation of embryonic transcription in developing Caenorhabditis elegans oocytes. An important component of this pathway is the dicer-related helicase DRH-3. To examine embryonic transcripts in the drh-3(rrr2) mutant on a global scale, we performed RNA sequencing on drh-3(rrr2) mutants and wild type animals. The RNA sequencing data of the wild type animals has been uploaded already under the accession number GSE62858, samples: GSM1534604 RNASeq_N2_1 and GSM1534605 RNASeq_N2_2.

overall_design: Total RNA sequencing was performed on RNA extracted from drh-3(rrr2) mutant animals in duplicates. Two samples in total.

first: Christina

last: Fassnacht

first: Rafal

last: Ciosk


title: Direct conversion of mouse fibroblasts into cholangiocyte progenitor cells

first: Kyungtae

last: Lim

address: Tennis Court Road

department: The Wellcome Trust/Cancer Research UK Gurdon Institute

institute: University of Cambridge

summary: We describe that Hnf1α and Foxa3 dramatically facilitate the robust generation of iHepSCs. Notably, the prolonged in vitro culture of Hnf1α and Foxa3 derived iHepSCs induce Notch signaling-mediated secondary conversion into cholangiocyte progenitor-like cells displaying the dramatically enhanced differentiation capacity into the mature cholangiocytes in vitro and in vivo. Our study provides the novel two-step approach for obtaining cholangiocyte progenitor-like cells using defined factors.

overall_design: Comparative analyses between induced hepatic stem-like cells (iHepSCs) generated from fibroblasts using two different combinations, 1a3 (Foxa3/Hnf1a) and 1b3 (Foxa3/Hnf1b; Yu et al. Cell Stem Cell 2013)

first: Kyung

middle: T

first: Dong

middle: W

last: Han


title: Regulation of RNA polymerase II processivity by Spt5 is restricted to a narrow window in elongation

city: Vienna

first: Tobias

last: Neumann

address: Campus-Vienna-Biocenter 1

country: Austria

institute: IMP

summary: Spt5 is a highly conserved RNA polymerase II (Pol II)-associated pausing and elongation factor. However, its impact on global elongation and Pol II processivity in mammalian cells has not been clarified. Here, we show that depleting Spt5 in mouse embryonic fibroblasts (MEFs) does not cause global elongation defects or decreased elongation rates. Instead, in the absence of Spt5, a fraction of Pol II molecules are dislodged during elongation thus decreasing the number of Pol II complexes that complete the transcription cycle. Most strikingly, this decrease is restricted to a narrow window between 15-20 kb from the promoter, a distance which coincides with the stage where accelerating Pol II attains maximum elongation speed and processivity. Consequently, long genes show a greater dependency on Spt5 for optimal elongation efficiency and overall gene expression than short genes. We propose that an important role of Spt5 in mammalian elongation is to promote the processivity of those Pol II complexes that are transitioning towards maximum elongation speed 15-20 kb from the promoter.

overall_design: For all experiments, we ablated the Supt5h gene in vitro by adding 4-hydroxy tamoxifen (4-HT) to primary Supt5hFl/- Rosa26ERT2-cre/+ mouse embryonic fibroblast (MEF) cultures for 72 hours. As controls, we used Rosa26ERT2-cre/+ primary MEFs treated with 4-HT for 72 hours (referred to as wild-type, WT).

first: Johanna

last: Fitz

first: Rushad

last: Pavri


title: Pairwise and higher order genetic interactions during the evolution of a tRNA

first: Julia

last: Domingo

address: 101 6th Av

institute: New York Genome Center

type: Genome variation profiling by high throughput sequencing

summary: A central question in genetics and evolution is the extent to which mutations have outcomes that change depending on the genetic context in which they occur. Pairwise interactions between mutations have been systematically mapped within and between genes, and contribute substantially to phenotypic variation amongst individuals. However, the extent to which genetic interactions themselves are stable or dynamic across genotypes is unclear. Here we quantify >45,000 genetic interactions between the same 87 pairs of mutations across >500 closely related genotypes of a yeast tRNA. Strikingly, all pairs of mutations interacted in at least 9% of genetic backgrounds and all pairs switched from interacting positively to interacting negatively in different genotypes (FDR<0.1). Higher order interactions are also abundant and dynamic across genotypes. The epistasis in this molecule means that all individual mutations switch from detrimental to beneficial in even closely-related genotypes. As a consequence, accurate genetic prediction requires mutation effects to be measured across different genetic backgrounds and the use of higher order epistatic terms.

overall_design: Experimental combinatorially complete fitness landscape of a tRNA by deep mutation scanning

first: Júlia

first: Guillaume

last: Diss

first: Ben

last: Lehner


title: Rational targeting of RNA structure in SMN2 transcripts reverses Spinal Muscular Atrophy molecular phenotypes

first: Roland

last: Schmucki

address: Grenzacherstrase

institute: F. Hoffmann - La Roche AG

summary: Marine natural compound homocarbonyltopsentin PK4C9 is a small TSL2-binding molecule which was identified to increase exon 7 splicing to therapeutic levels and rescue downstream molecular alterations in SMA cells. To assess the functionality of the restored SMN protein, we studied whether PK4C9 could modify SMN-mediated splicing events using RNA sequencing data from PK4C9-treated (40 microM, 24 h) vs. DMSO-treated GM03813C fibroblasts. The data was also used to find shared motifs amongst PK4C9-sensitive splicing events, in order to contribute to the description of the mechanism of action of PK4C9 and to help identify off-targets.

overall_design: Examination of 4 total-RNA replicates of DMSO-treated GM03813C fibroblasts (control) and 4 replicates of PK4C9-treated (40 microM, 24 h) GM03813C fibroblasts (GM03813C is a fibroblast cell line derived from a type I SMA patient).

first: Amparo

last: Garcia-Lopez

first: Anna

last: Wacker

first: Francesca

last: Tessaro

first: Henry

last: Jonker

first: Christian

last: Richter

first: Arnaud

last: Comte

first: Nikolaos

last: Berntenis

first: Klas

last: Hatje

first: Daniel

last: Sciarra

first: Piotr

last: Konieczny

first: Guy

last: Fournet

first: Ignacio

last: Faustino

first: Modesto

last: Orozco

first: Ruben

last: Artero

first: Peter

last: Goekjian

first: Friedrich

last: Metzger

first: Martin

last: Ebeling

first: Benoît

last: Joseph

first: Harald

last: Schwalbe

first: Leonardo

last: Scapozza


title: Changes in gene expression following long-term in vitro exposure of Macaca mulatta trophoblast stem cells to biologically relevant levels of endocrine disruptors

city: East Lansing

first: Uros

last: Midic

state: MI

address: 474 S. Shaw Lane

department: Animal Sciences

institute: Michigan State University

summary: Trophoblast stem cells (TSCs) are key for embryo implantation and placentation. Environmental toxicants that compromise trophoblast function could compromise fetal viability, pregnancy outcome, and progeny health. Endocrine disrupting chemicals (EDCs) can epigenetically modify cells and alter their developmental properties.  Understanding the effects of low, chronic EDC exposures on TSCs and pregnancy is a priority in developmental toxicology.  Differences in placentation between primates and other mammals make a nonhuman primate model ideal for this.   We examined effects of chronic low-level exposure to five EDCs on rhesus monkey TSCs in vitro.  Two of the toxicants, ATR and TBT, exerted the strongest effects, with substantial overlap. Affected genes included some with obvious relevance to placentation and implantation (WNT7A, INHBA, and cytokines and their receptors).  Pathway analysis revealed significant reductions in the expression of genes related to cytokine signaling, a feature shared across all five EDCs tested.  Low-level chronic exposure of primate TSCs to EDCs may thus compromise trophoblast development in vivo, modify responses to pathogens and other challenges, and negatively affect embryo implantation and pregnancy rate.

overall_design: Effects of chronic exposure to low concentrations of 5 EDCs were tested in rhesus monkey trophoblast stem cells

first: Benjamin

last: Goheen

first: Kailey

last: Vincent

first: Catherine

last: VandeVoort

first: Keith

last: Latham


title: Dual RNA-sequencing of host and pathogen during Plasmodium berghei infection of hepatocytes in vitro

city: La Jolla

first: Elizabeth

last: Winzeler

address: 9500 Gilman Dr

institute: UCSD

summary: We report the dual RNA-sequencing of host and pathogen transcriptomes during Plasmodium berghei liver-stage development in vitro. Unlike traditional transcriptomic approaches that analyze RNA reads separately from host and pathogen, a dual-approach maps the mixed reads to each annotated genome within samples of pathogen-infected host cells. This is a powerful method, as host and pathogen transcriptomes can be analyzed simultaneously. We have taken advantage of this dual-RNA sequencing approach in order to gain insight into Plasmodium liver stage development within host hepatocytes. Huh7.5.1 hepatocytes were infected in vitro with P. berghei sporozoites freshly dissected from infected Anopheles stephansi mosquitos, and cells were collected throughout liver-stage development. This included samples collected at time zero (uninfected hepatocytes and sporozoites before infection), time 24 hours post infection (when the sporozoites have transformed into trophozoites), and time 48-50 hours post infection (when the trophozoites have transformed into liver-stage schizonts).

sample_organism:
Plasmodium berghei
Homo sapiens
mixed sample

overall_design: Dual RNA-sequencing of P. berghei-GFP and human RNA in infected and uninfected Huh7.5.1 cells

first: Justine

last: Swann

first: Nathan

last: Lewis

first: Alyaa

last: Abdel-Haleem

first: Shangzhong

last: Li


title: Changes in macrophage transcriptome associate with systemic sclerosis and mediate GSDMA contribution to disease risk

city: Singapore

first: Aida

last: Moreno-Moral

address: 8 College Road

country: Singapore

institute: Duke-NUS Medical School

summary: Integration of differential expression (DE) and expression QTL (eQTL) analysis in monocyte-derived macrophages (MDMs) from systemic sclerosis (SSc) patients and healthy controls reveals (i) changes in macrophage transcriptome as an important contributor in SSc and (ii) cis-regulation in GSDMA as a disease risk in macrophages, but not skin.

overall_design: We carried out RNA-sequencing and genome-wide genotyping in MDMs from 57 SSc patients and 15 controls. Our differential expression and expression QTL (eQTL) analysis in SSc was further integrated with epigenetic, expression and eQTL data from skin, monocytes, neutrophils and lymphocytes.

first: Marta

last: Bagnati

first: Jacques

last: Behmoaras

first: Enrico

last: Petretto


title: The regulartory role of ZCCHC24 in splicing machinery

first: Yu-Ting

last: Tseng

address: 650 Charles E. Young Drive South

department: Department of Microbiology, Immunology, & Molecular Genetics

institute: University of California, Los Angeles

summary: ZCCHC24, Zinc Finger, CCHC domain containing 24. Showed mesenchymal cell specific expression, but no known function or phenotype associated with it. It required for mesenchymal cell growth, KD in mesenchymal cells induces drastic growth arrest. Its role in splicing machinery is not known.

overall_design: 1 ug of total RNA was used for  for RNA-seq library preparation using the TruSeq™ Stranded mRNA LT Sample Prep Kit (Illumina). 100x2 bp paired-end RNA-seq reads were generated on a HiSeq 2000 sequencer.

first: Yi

last: Xing


title: Functional TRIM24 degraders via conjugation of ineffectual bromodomain and VHL ligands [RNA-Seq 2]

status: Public on Mar 05 2018

city: Boston

first: Nathanael

last: Gray

state: Massachusetts

address: 360 Longwood Ave

department: Cancer Biology

institute: DFCI

summary: The addressable pocket of a target protein is often not functionally relevant. This is particularly true for multidomain gene regulatory proteins, such as the bromodomain-containing transcriptional regulator TRIM24. TRIM24 has been posited as a dependency in numerous human cancers, yet potent and selective ligands for the TRIM24 bromodomain do not exert effective anti-proliferative responses. We therefore repositioned these probes as targeting features for heterobifunctional protein degraders.

overall_design: TRIM24 localization to chromatin with dTRIM24 in AML lines

first: Lara

last: Gechijian


title: Single-cell RNA-seq (Drop-seq) of MGE, CGE and LGE of E13.5 (MGE) and E14.5 (CGE, LGE) mouse embryos

city: New York

first: Christoph

last: Hafemeister

address: 101 Avenue of the Americas

summary: Single-cell RNA-seq to profile a developmental time course of interneuron development, measuring the transcriptomes of progenitors during their maturation in the ganglionic eminences.

overall_design: 10 samples: 3 CGE, 3 LGE, 4 MGE

first: Christian

last: Mayer

first: Rachel

middle: C

last: Bandler


title: Functional TRIM24 degraders via conjugation of ineffectual bromodomain and VHL ligands [RNA-seq]

overall_design: RNA-sequencing of MOLM-13 AML cells treated with DMSO, IACS-9571 or dTRIM24 for 4 or 24 hours.


title: Single-cell RNA-seq (Smart-seq2) of MGE of E13.5 mice

summary: Single-cell RNA-seq of mitotically enriched cells in the medial ganglionic eminence (Dlx6 negative), as well as labeled cells using FlashTag technology.

overall_design: 5 96 well plates of Dlx6 negative cells; 14 96 well plates using FlashTag: 3 replicates 3 hours after labeling, 3 replicates 6 hours after labeling, 3 replicates 12 hours after labeling, 5 replicates 24 hours after labeling


title: Developmental diversification of cortical inhibitory interneurons

summary: We applied massively parallel single-cell RNA-seq to profile a developmental time course of interneuron development, measuring the transcriptomes of over 60,000 progenitors during their maturation in the ganglionic eminences and embryonic migration into the cortex.


title: Single-cell RNA-seq (10X Genomics Chromium) of MGE, CGE, cortical and subcortical regions of E13.5, E18.5 and P10 mice

overall_design: Lhx6-GFP mice were used for E13.5 samples; for later stages, when cells have migrated out of the GEs, we used a Dlx6a-Cre; RCEloxP pan- GE fate mapping strategy to collect cortical interneurons at E18.5 and P10.


title: NCoR/SMRT co-repressors cooperate with c-MYC to create an epigenetic barrier to somatic cell reprogramming [RNA-seq]

first: Andrew

last: Hutchins

summary: Changing the somatic cell transcriptome to a pluripotent state using exogenous reprogramming factors needs transcriptional co-regulators that help activate or suppress gene expression and rewrite the epigenome. Here, we show that reprogramming-specific engagement of the NCoR/SMRT co-repressor complex at key pluripotency loci creates an epigenetic block to reprogramming. HDAC3 executes the repressive function of NCoR/SMRT in reprogramming by inducing histone deacetylation at these loci. Recruitment of NCoR/SMRT-HDAC3 to pluripotency genes is facilitated by all 4 Yamanaka factors (OCT4, SOX2, KLF4 and c-MYC) but mostly by c-MYC. Class IIa HDACs further potentiate this recruitment by interacting with both the reprogramming factors and NCoR/SMRT. Consequently, depleting NCoR/SMRT-HDAC3 function enables high efficiency of reprogramming, while elevating NCoR/SMRT-HDAC3 recruitment at pluripotency loci by over-expressing constitutively active class IIa HDACs derails it. Our findings thus uncover an unexpected epigenetic mechanism involving c-MYC, whose manipulation greatly enhances reprogramming efficiency.

overall_design: RNA-seq data consisting of Oct4, Sox2, Klf4, c-Myc (OSKM) transfected mouse embryonic fibroblasts co-transfected with one of shRNA targetting Luciferase (control), Ncor1 (NCoR) or Ncor2 (SMRT). Cells were assayd for total RNA on days 5 and day 9.

first: Miguel

last: Esteban

first: Qiang

last: Zhuang


title: De novo RNA-sequencing and transcriptome analysis of Aconitum carmichaelii to analyze key genes involved in the biosynthesis of diterpene alkaloids

status: Public on Mar 04 2018

city: Chiba

first: Mami

last: Yamazaki

address: Inohana 1-8-1, Chuo-ku

department: Graduate School of Pharmaceutical Sciences

institute: Chiba University

summary: In this study, we have performed Illumina based RNA sequencing to characterize the transcriptome and expression profiles of genes expressed in 4 tissues of A. carmichaelii. RNA sequencing and de novo transcriptome assembly fo A. carmichaelii  resulted in a total of 128,183 unigenes with 56,928 unigenes being annotated using NCBI-nr database. Transcriptome profile and analysis for 4 tissues of  A. carmichaelii showed that unigenes annotated as possible rate-determining steps of aconitine-type biosynthetic pathway were highly expressed in the root.

overall_design: Examination of 4 tissues of Aconitum carmichaelii using Illumina HiSeq paired end RNA sequencing

first: Kazuki

last: Saito

first: Nobuo

last: Kawahara

first: Hideyuki

last: Suzuki

first: Hiroki

last: Takahashi

first: Kayo

last: Yoshimatsu

first: Noriaki

last: Kawano

first: Amit

last: Rai

first: Megha


title: Allele-specific DNA methylation of disease susceptibility genes in Japanese patients with inflammatory bowel disease

city: Sendai

first: Yoichi

last: Kakuta

state: Miyagi

address: 1-1 Seiryo Aoba

institute: Tohoku University

summary: We determined cis-regulated allele-specific DNA methylation (ASM) around IBD susceptibility genes in CD4+ effector/memory T cells (Tem) in lamina propria mononuclear cells (LPMCs) in patients with IBD

overall_design: We performed MSNP analysis to detect allele specific methylation.


title: poly-A RNA profiling of Drosophila neural stem cells and tumor cells reveals genes involved in brain tumorigenesis.

first: Thomas

middle: Rainer

last: Burkard

address: Dr. Bohrgasse 7

institute: IMBA

summary: Acquisition of unlimited proliferation potential is a critical hallmark of tumor cells. Drosophila neural stem cells called neuroblasts asymmetrically segregate protein determinants such as Brat into one of their two daughter cells to prevent self-renewal and induce neuronal differentiation. Mutations in these fate determinants or defects in their asymmetric segregation result in a fate reversion of the differentiating daughter cells into proliferative ectopic neuroblasts, so-called tumor neuroblasts. Over time, these events result in the formation of large brain tumors that can be maintained indefinitely by transplantation into another fly host. Our transcriptome analysis identifies genes deregulated in these over-proliferative tumor brain cells.

overall_design: Comparison of transcriptomes of wild-type type II NBs and brat RNAi-triggered tumor type II NBs isolated by FACS from Drosophila melanogaster larval brains.

first: Francois

last: Bonnay

middle: R

first: Juergen

last: Knoblich


title: mRNA expression data from ESCs derived by polar body transfer reconstructed embryos (PBTESCs)

city: shanghai

first: cuiqing

last: zhong

address: yueyang road 320

institute: institute of biochemistry and cell biology

summary: Here we report the derivation of human PBTESCs from polar body transfer resconstructed embryos. We used RNA-seq to compare the gene expression levels among human parthenogenetic haploid ESCs (hPGES)、normal human ESCs (H9) and human forskin fibroblasts and identified that these cells express conventional ESCs pluripotent markers and most maternally imprinted genes were down-regulated.

overall_design: We collected fresh ESCs samples of 3 cell lines from PB1 transfer and 3 cell lines from PB2 transfer each at around 10^6 cells in similar passage. All the sample was lysised by 1 mL Trizol directly and stored at -80℃. DNA libraries building and sequencing was performed at the same time to reduce systematic error. Gene expression profiles of all the cell lines were analysed on illumina Hiseq 2500.

first: Zhi-Jiang

last: Chen

first: Jinsong

last: Li


title: Transcriptomic alterations in fibroblasts from Parkinson's disease patients carrying Parkin mutations

first: Mario

last: Ezquerra

state: Catalonia

address: Villarroel 170

department: Neurology

institute: Fundacio Clinic/IDIBAPS

summary: In this study, we evaluate the hypothesis that transcriptome pattern of a cell model of Parkinson’s disease (PD) could be altered compared to healthy individuals. We cultured fibroblasts from Parkin-associated PD (PRKN-PD; n=4) and healthy controls (HC; n=4) and analysed the transcriptome profile by using whole RNA sequencing.   We found 343 differentially expressed transcripts (DET) between patients and controls being 206 up-regulated and 137 down-regulated. These genes are related with the gene ontology terms cell adhesion, cell growth, aminoacid biosynthesis and folate metabolism amongst others. Our findings indicate that PRKN mutations are associated with global gene expression changes as observed in fibroblasts, and support an emerging view of PD as a systemic disease affecting also peripheral non-neural tissues such as the skin.

overall_design: Evaluation of transcript expression by RNA sequencing of fibroblasts from Parkin-associated Parkinson's Disease patients versus fibroblasts from healthy controls

first: Glòria

last: Garrabou


title: RNA-Seq analysis after spinal cord injury in lamprey reveals distinct transcriptional responses during functional recovery in spinal cord and brain

status: Public on Mar 03 2018

city: Lexington

first: Mark

last: Evers

state: Kentucky

address: 800 Rose Street

department: College of Medicine

institute: University of Kentucky

summary: The lamprey is a vertebrate that, unlike mammals, achieves spontaneous recovery after spinal cord transection. Despite anatomical, physiological, and behavioral data on spinal cord regeneration in lamprey, the molecular mechanisms underlying this capacity are largely unknown. To address this, we used RNA-Seq to obtain transcriptional profiles from uninjured animals and at 10 time points ranging from 6 hours to 12 weeks post injury. Overall, 4208 (spinal cord) and 3788 (brain) transcripts are differentially expressed (DE). Complex intraspinal and supraspinal responses were induced acutely and occurred even at chronic phases of recovery. Leveraging functional data for mammalian homologs of DE genes (via Enrichr) permitted identification of enriched conserved genes and pathways.  These included genes and pathways induced after mammalian peripheral nerve injury, such as those associated with regeneration, immune function, cell growth, proliferation and cell death. For example, ATF3, a transcription factor implicated in mammalian peripheral nerve regeneration, is highly expressed and enriched in lamprey spinal cord and brain after SCI. Other homologs of regeneration-associated genes that are differentially expressed after SCI include members of the WNT, HDAC, SOX, SMAD, KLF, and JUN families. This study provides the first comprehensive view of transcriptional responses during successful anatomical and functional recovery from spinal cord injury in lamprey, and reveals unexpectedly large changes in transcription in the brain, which is quite distant from the spinal lesion site.  Gene expression patterns associated with functional recovery in lamprey may be useful in guiding studies aimed at modulating mammalian responses to SCI.

overall_design: 22 samples were analyzed in total. RNA was extracted from uninjured animals (control brain and spinal cord tissue). There were 4-6 animals pooled per sample. Timepoints of sample collection post spinal cord injury are listed below.

first: Paige

last: Herman

first: Angelos

last: Papatheodorou

first: Stephanie

last: Bryant

first: Anthony

last: Arcese

first: Joseph

last: Herdy

last: Buxbaum

first: Jeremiah

last: Smith

first: Jennifer

last: Morgan

first: Ona

last: Bloom


title: Integrative analysis of reprogramming human fibroblast cells to naïve pluripotency [RRBS]

city: Shanghai

first: Shaorong

last: Gao

state: Shanghai

address: 1239 Siping Road, Yangpu District

department: School of life science and technology

institute: Tongji University

summary: Derivation of human naïve cells in the ground state of pluripotency provides promising avenues for developmental studies and therapeutic manipulations. However, the molecular mechanisms involved in establishment and maintenance of human naïve pluripotency remain poorly understood. Using the human inducible reprogramming system together with 5iLAF naïve induction strategy, we performed integrative analysis across the timeline from human fibroblasts to naïve iPSCs, which reveals ordered expression waves of gene networks sharing signatures with embryonic development process from post-implantation to pre-implantation stages. We also observed a significant transient re-activation of transcripts with 8-cell-stage-like characteristics in late naïve reprogramming stages. Moreover, combined quantitative proteomics analysis with transcriptional dynamics during naïve pluripotency induction, we identified ALPPL2 as the specific surface marker for human naïve pluripotency. Altogether, our study deepens the understanding of molecular mechanisms of human naïve pluripotency.

overall_design: RRBS profiles of transitioning cells at different time points in the naïve/primed reprogramming process were performed by deep sequencing.

first: Yuanyuan

last: Yang

first: Yixuan

last: Wang

first: Chengchen

last: Zhao

first: Yong

last: Zhang


title: Integrative analysis of reprogramming human fibroblast cells to naïve pluripotency [ChIP-seq]

overall_design: Examination of four different histone modifications (H3K4me2, H3K4me3, H3K27me3 and H3K9me3) during reprogramming.

first: Zhenzhen

last: Hou


title: Transcriptome and Translatome in Drosophila S2 cells treated by tsRNA transfection, serum deprivation, ago2 knockdown and rapamycin

status: Public on Mar 02 2018

city: Beijing

first: Jian

last: Lu

address: No.5 Yiheyuan Rd, Haidian District

institute: Peking University

summary: Transfer RNA-derived small RNAs (tsRNAs) are an emerging class of small RNAs, yet their regulatory roles have not been well understood.  Here we studied the molecular mechanisms and consequences of tsRNA-mediated regulation in Drosophila. By carrying out mRNA sequencing and ribosome profiling of S2 cells transfected with single-stranded tsRNA mimics and mocks, we show that tsRNAs recognize target mRNAs through conserved complementary sequence matching and suppress target genes by translational inhibition. Serum starvation experiments confirm tsRNAs participate in cellular starvation responses by preferential targeting the ribosomal proteins and translational initiation or elongation factors. Knock-down of AGO2 in S2 cells under normal and starved conditions reveals a dependence of the tsRNA-mediated regulation on AGO2. Our study suggests the tsRNA-mediated regulation might be crucial for the energy homeostasis and the metabolic adaptation in the cellular systems.

first: Shiqi

last: Luo

first: Feng

last: He

first: Junjie

first: Annan

last: Guo


title: RNASeq of OMP and TRPC2 neuronal population of zebrafish olfactory sensory neurons

city: PHILADELPHIA

first: Puneet

last: Dang

state: PA

address: 3610 Hamilton Walk

department: Neuroscience

institute: University of Pennsylvania

summary: RNASeq was performed on mRNA obtained from OMP expressing and TRPC2 expressing olfactory sensory neurons from 48hpf zebrafish embryos. Single-cell suspensions of 48hpf olfactory epithelia were FAC-sorted to obtain RFP expressing or venus expressing cells (RFP sample1: 3500 cells, RFP sample2: 5500 cells. Venus sample1: 676 cells, venus sample2:201 cells. RNA was extracted using QIAGEN RNEasy kit and cDNA was synthesized using a custom oligo-dT primer containing T7 promoter sequence courtesy of Jim Eberwine, University of Pennsylvanina. In vitro RNA amplification was carried out through one round for OMP:RFP neurons and through two rounds for TRPC2:venus neurons as per the protocol in Morris et al, 2011. Adapter-tagged libraries were synthesized using Illumina TruSeq v2.0 and deep-sequenced on HiSeq2500 to obtain ~100million reads per sample.

overall_design: Examination of mRNA expression profiles from 2 types of olfactory sensory neurons

first: Stephen

last: Fisher

first: Junhyong

last: Kim

first: Jonathan

last: Raper


title: MARS Seq data from human cortical organoids

city: Rehovot

first: Orly

last: Reiner

address: 234, Herzl Street,

department: Molecular Genetics

country: Israel

institute: Weizmann Institute of Science

summary: We analyze gene expression data of human organoid developmet

overall_design: Three developmental time points and two genotypes were examined

first: Eyal

last: Karzbrun

first: Aditya

last: Kshirsagar

first: Sidney

last: Cohen

first: Jacob

middle: H

last: Hanna


title: NHR-49/HNF4 integrates regulation of fatty acid metabolism with a protective transcriptional response to oxidative stress and fasting

city: Vancouver

first: Forum

last: Bhanshali

state: BC

address: 950 west 28th avenue

department: Medical genetics

country: Canada

institute: Centre for Molecular Medicine and Therapeutics, UBC

summary: Endogenous and exogenous stresses elicit transcriptional responses that limit damage and promote cell/organismal survival. Like its mammalian counterparts, Hepatocyte Nuclear Factor 4 (HNF4) and peroxisome proliferator-activated receptor a (PPARa), Caenorhabditis elegans NHR-49 is a well-established regulator of lipid metabolism. Here, we reveal that NHR-49 is essential to activate a transcriptional response common to organic peroxide and fasting, which includes the pro-longevity gene fmo-2/flavin-containing monoxygenase. These NHR-49-dependent, stress-responsive genes are also upregulated in long-lived glp-1/notch receptor mutants, and two of them contribute to increased oxidative stress resistance in wild-type worms and long-lived glp-1 mutants. Similar to its role in lipid metabolism, NHR-49 requires the Mediator subunit mdt-15 to promote stress-induced gene expression. However, NHR-49 acts independently from the transcription factor hlh-30/TFEB that also promotes fmo-2 expression. Similarly, activation of the p38 MAPK, PMK-1, which is important for adaptation to a variety of stresses, is only important for peroxide-induced expression of a subset of NHR-49-dependent genes, including fmo-2. Notably, we find that organic peroxide increases NHR-49 protein levels, apparently by a post-transcriptional mechanism that does not require PMK-1 activation. Together these findings establish a new role for the HNF4/PPARa-related NHR-49 as a stress-activated regulator of cytoprotective gene expression.

overall_design: Transcriptomes analysis of L4 stage wild-type (N2) and nhr-49(nr2041) worms (+/- tBOOH) using RNA sequencing in duplicate.

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