title: Gene expression profile for male SD Rats upon fructose and DHA treatment by RNA-Seq

city: Los Angeles

first: Xia

last: Yang

address: 2000 Terasaki Life Sciences Bldg, 610 Charles E. Young Drive East

institute: UCLA

summary: To investigate the beneficial effects of DHA (omega-3) on affecting fructose induced brain dysfunction and metabolic disorders by sequencing the transcripome (RNA-Seq) in the hypothalamus and hippocampus of male SD rats.

overall_design: Male Sprague–Dawley (SD) rats of 2 months old were randomly assigned to an omega-3 fatty acid diet (n-3 diet) with or without fructose added in the drinking water (15%) for six weeks. The rats were sacrificed by decapitation. Hypothalamus and hippocampus were dissected out, flash frozen, and stored at -70°C for later transcriptome and DNA methylome sequencing experiments. All experiments were performed in accordance with the United States National Institutes of Health Guide for the Care and Use of Laboratory Animals and were approved by the University of California at Los Angeles Chancellor’s Animal Research Committee.

first: Qingying

last: Meng

first: Fernando

last: Gomez-Pinilla


title: STAT3 Regulates Adult Muscle Satellite Cell Maintenance During Injury-induced Muscle Regeneration

status: Public on Jul 13 2016

city: Hong Kong

first: Han

last: ZHU

address: Room 6312, Academic Building, HKUST

department: Department of Life Science

country: China

institute: HKUST

type: Expression profiling by high throughput sequencing

summary: We previously showed that STAT3 regulates myoblast differentiation in cell culture models, yet its role in adult muscle satellite cells (MuSC) in vivo was less well characterized. When Stat3 was conditionally deleted in MuSC, muscle development and adult MuSC formation were not affected. However, with repeated muscle injuries, the number of the quiescent MuSC in STAT3-null mice decreased and the regeneration was delayed, suggesting defective MuSC maintenance. Consistently, when we conditionally deleted Stat3 in MuSC of dystrophin-null mice, a mouse model for the fatal human Duchenne muscular dystrophy, the adult double knockout (dKO) mice displayed age-dependent reduction in the number of MuSC, and increase in muscle inflammation and fibrosis. Mechanistically, Stat3 ablation in dystrophin-null MuSC resulted in downregulation of several key myogenic genes including Pax7, upregulation of multiple pro-inflammatory and pro-fibrotic genes, and an increase in fibroadipogenic progenitor cells, which collectively contributed to defective MuSC maintenance and aggravated inflammation and fibrosis in dKO mice.

overall_design: We generate a condition STAT3 knockout mice (dKO) with mdx background (Dystrophin null, mouse model for human Duchenne muscular dystrophy). Three pairs of dKO and mdx (control) mice were used for muscle satellite cell FACS sorting, followed by RNA extraction and sequencing library construction. Pair end RNA sequencing was performed with Illumina HiSeq system.

last: Zhu

first: Zhenguo

last: Wu

first: Tom Hiu Tung

last: Cheung


title: The miR-17~92 microRNA cluster is a global regulator of tumor metabolism

status: Public on Jul 14 2016

first: Maxim

middle: N.

last: Artyomov

state: MO

address: 660 S. Euclid Avenue, Campus Box 8118

department: Immunology&Pathology

country: USA

institute: Washington University in St.Louis

summary: mRNA expression in Eμ-Myc lymphoma cells expressing or lacking miR-17~92

overall_design: Eµ-Myc B-cell lymphomas harboring conditional alleles of miR-17~92 were cultured with or without 4-OHT to generate isogenic tumour cells with homozygous deletion of miR-17~92. Wild type (fl) and miR-17~92-deleted (del) Eµ-Myc cells were cultured for 48 hours under regular growth conditions, and RNA isolated for sequencing analysis.

first: Said

last: Izreig

first: Bozena

last: Samborska

first: Radia

middle: M

last: Johnson

first: Alexey

last: Sergushichev

first: Eric

middle: H

last: Ma

first: Carine

last: Lussier

first: Ariel

middle: O

last: Donayo

first: Ping

last: Mu

first: Andrea

last: Ventura

first: Emma

middle: E

last: Vincent

middle: N

first: Thomas

middle: F

last: Duchaine

first: Russell

middle: G

last: Jones


title: Gene expression profile for male SD Rats upon fructose treatment by RNA-Seq

first: Xia

last: Yang

state: CA

department: IBP

overall_design: male SD Rats were feed with fructose for 6 weeks

first: Qingying

last: Meng

first: Fernando

last: Gomez-Pinilla


title: VDR ChIP-seq in PMA-differentiated macrophages (human M2-type like macrophages)

city: Kuopio

first: Carsten

last: Carlberg

address: Yliopistonranta 1D

department: Institute of Biomedicine

country: Finland

institute: University of Eastern Finland

type: Genome binding/occupancy profiling by high throughput sequencing

summary: We performed ChIP-seq in macrophage-type PMA-differentiated THP-1 cells after stimulation with the the natural VDR ligand 1,25dihydroxyvitamin D3 (1,25D). We identified in total 223 VDR binding locations on chromatin after 1,25D treatment. De novo analysis of VDR site sequences identified DR3-type binding sites as major motif.

overall_design: PMA-differentiated THP-1 cells were treated for 0, 1 and 2 h  with 100 nM 1,25D

first: Jussi

last: Ryynänen

first: Sami

last: Heikkinen

first: Antonio

last: Neme

first: Pauli

last: Tuoresmäki


title: Genomic analysis of human parthenogenetic haploid ESCs (hPGES), normal human ESCs(H9) and human forskin fibroblast

city: shanghai

first: cuiqing

last: zhong

address: yueyang road 320

institute: institute of biochemistry and cell biology

type: Methylation profiling by genome tiling array

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

overall_design: Refer to individual Series


title: Mismatch between mtDNA and nuclear DNA determines metabolism and healthy aging

city: Madrid

first: Fatima

last: Sanchez-Cabo

address: Melchor Fernandez Almagro

country: Spain

institute: CNIC

summary: We postulate here that the two singular characteristics of the mitochondrial oxidative phosphorylation system—the integration of three potentially antagonistic functions in the same structure and the double genetic origin of the components that assemble together in these molecular machines—make the evolution of an optimal system impossible. As a consequence the system is intrinsically mismatched and has to be continuously monitored, Adjusted and regulated in order to achieve the necessary and variable performance. Systematic transcriptomic, Metabolomic and biochemical evaluation of animals with identical nuclear DNA but different mtDNA haplotype strongly support the existence of intrinsic mismatch and reveals profound lifelong metabolic consequences on reactive oxygen species generation, Insulin signaling, Tendency towards obesity, And healthy ageing parameters, Including telomere atresia

overall_design:
Transcriptome analysis of conplastic mice versus WT mice in Liver and Heart tissues
Conplastic strains were obtained after 10 generations of backcrossing to create a new line harboring the nuclear genome of one strain and the mtDNA of another (C57BL/6 and NZB were purchased from Harlan Laboratories).

first: Jose

middle: A

last: Enriquez

first: Ana

last: Latorre


title: Genome-wide DNA methylation maps during dehydration in leaf tissues of Boea hygrometrica

city: Beijing

first: Lihong

last: Xiao

address: No.105 North Road of West 3rd-ring Road.Haidian District

institute: Capital Normal University

type: Methylation profiling by high throughput sequencing

summary: To examine the Boea hygrometrica genome methylation landscape and assess its functional significance during dehydration, we generated the first single-base resolution genome methylation maps for leaf tissues of hydrated, dehydrating to 70% RWC and dehydrating to 10% RWC (desiccating). The overall density of methyl-cytosine was not broadly altered by dehydration. There is, however, a small increase in intensity both for the whole genome and regionally during the first dehydration step (70% RWC) returning to near hydrated levels as leaves desiccate. We identified 5575 differentially methylated region-related genes during dehydration. The finding may provide an important clue for exploring molecular mechanisms and the regulation of desiccation tolerance at the whole-genome level.

overall_design: Examination of DNA methylation by BS-Seq in hydrated, dehydrating to 70% RWC and dehydrating to 10% RWC leaf tissues.


title: Impact of MEF2C on chromatin accessibility of mouse BM pre-B and myeloid cells

status: Public on Jul 12 2016

first: Wenyuan

last: Wang

state: cA

address: 651 Charles E Young Drive

summary: We analyzed the chromatin accessibility of control and Mef2c deficient mouse BM pre-B and myeloid cells by ATAC-seq analysis.

overall_design: Examination of chromatin accessibility of 2 cell types from both WT and Mef2c deficient mice.

first: Tonis

last: Org


title: Active histone markers landscape in mouse WT pre-B cells

summary: We analyzed the landscape of H3K4me3 and H3K27ac in WT mouse pre-B cells.

overall_design: Examination of 2 different histone modifications in 1 cell types.

first: Peter

last: Pioli


title: hiPSCs unravel aberrant TGFβ signaling as an etiology of left ventricular non-compaction

city: stanford

first: Kazuki

last: Kodo

address: campus street

institute: Stanford

summary: Left ventricular non-compaction (LVNC) is the third most prevalent cardiomyopathy in children and has a unique phenotype with characteristically extensive hypertrabeculation of the left ventricle, similar to the embryonic left ventricle, suggesting a developmental defect of the embryonic myocardium. However, studying this disease has been challenging due to the lack of an animal model that can faithfully recapitulate the clinical phenotype of LVNC. To address this, we show that patient-specific hiPSC-derived cardiomyocytes (hiPSC-CMs) generated from a family with LVNC recapitulated a developmental defect consistent with the LVNC phenotype at the single-cell level. We then utilized hiPSC-CMs to show that increased transforming growth factor beta (TGFβ) signaling is one of the central mechanisms underlying the pathogenesis of LVNC. LVNC hiPSC-CMs demonstrated decreased proliferative capacity due to abnormal activation of TGFβ signaling. Exome sequencing demonstrated a mutation in TBX20, which regulates TGFβ signaling, contributing to the LVNC phenotype. Our results demonstrate that hiPSC-CMs are a useful tool for the exploration of novel mechanisms underlying poorly understood cardiomyopathies such as LVNC. Here we provide the first evidence of activation of TGF signaling as playing a role in the pathogenesis of LVNC.

overall_design: mRNA expression profiles in human iPSC derived cardiomyocytes obtained from 2 independent unrelated control, 1 asymptomatic mild DCM (2 iPSC lines) and 3 LVNC patients (2 proband lines and 1 lines from 2 siblings) 2 weeks after starting cardiac differentiation.

first: Shijun

last: Hu

first: Kolsoum

last: InanlooRahatloo

first: Daniel

last: Bernstein

first: Joseph

middle: C

last: Wu


title: Next Generation Sequencing profile of leukemia from distinct cells-of-origin [ATAC-seq]

city: Bar Harbor

first: Jennifer

last: Trowbridge

state: ME

address: 600 Main Street

institute: The Jackson Laboratory

summary:
The goal of this study is to identify genomic signatures predicitve of cell-of-origin in acute myeloid leukemia
Cryopreserved leukemic bone marrow samples were thawed, and 50,000 LSCs (L-GMP; GFP+ Lin- Sca-1- c-Kit+ CD34+ FcγR+) were sorted by FACSAria (BD). Samples were placed at 37oC and 5% CO2 in IMDM plus 10% fetal calf serum for 30 minutes, then harvested, washed with 1X PBS, and ATAC-seq libraries were prepared. Quantitative PCR using the Library Quantitation kit (Kapa Biosystems) was used to estimate library concentrations. Libraries were sequenced on the Illumina HiSeq 2000 platform generating 2x150bp paired end reads at a sequencing depth of ~30-50 million reads per sample.
Libraries were sequenced on the Illumina HiSeq 2000 platform.

overall_design: ATAC-seq profiles of MLL-AF9 L-GMP AML samples to identify open chromatin signatures associated with leukemia cell-of-origin

middle: J


title: Discovery of a Drug that Targets a Diabetes Gene identified by GWAS

city: New York

first: Shuibing

last: Chen

state: NY

address: A 827B, 1300 York Ave

department: Surgery

institute: Weill Cornell Medical College

summary: A robust system using disease relevant cells to systematically evaluate the role in diabetes for loci identified through genome wide association studies (GWAS) is urgently needed. Toward this goal, we created isogenic mutant human embryonic stem cell (hESC) lines in GWAS-identified candidate diabetes genes including CDKAL1, KCNQ1 and KCNJ11, and used directed differentiation to evaluate the function of derivative human beta-like cells. The mutations did not affect the generation of insulin+ cells, but impaired insulin secretion both in vitro and in vivo, coinciding with defective glucose homeostasis. CDKAL1-/- insulin+ cells also displayed hypersensitivity to lipotoxicity. A high-content chemical screen identified a candidate drug that rescued CDKAL1-/--specific defects by inhibiting the AP1 (FOS/JUN) pathway. These studies establish a platform using isogenic hESCs to evaluate the function of GWAS-identified loci, and identify a drug candidate that rescues gene-specific defects, paving the way to precision therapy of metabolic diseases.A robust system using disease relevant cells to systematically evaluate the role in diabetes for loci identified through genome wide association studies (GWAS) is urgently needed. Toward this goal, we created isogenic mutant human embryonic stem cell (hESC) lines in GWAS-identified candidate diabetes genes including CDKAL1, KCNQ1 and KCNJ11, and used directed differentiation to evaluate the function of derivative human beta-like cells. The mutations did not affect the generation of insulin+ cells, but impaired insulin secretion both in vitro and in vivo, coinciding with defective glucose homeostasis. CDKAL1-/- insulin+ cells also displayed hypersensitivity to lipotoxicity. A high-content chemical screen identified a candidate drug that rescued CDKAL1-/--specific defects by inhibiting the AP1 (FOS/JUN) pathway. These studies establish a platform using isogenic hESCs to evaluate the function of GWAS-identified loci, and identify a drug candidate that rescues gene-specific defects, paving the way to precision therapy of metabolic diseases.

overall_design: RNA-seq was used to compare the gene expression in wildtype and CDKAL1-/- hESC derived insulin-GFP+ cells. In addiiton, RNA-seq was used to compare the gene expression in CDKAL1-/- hESC derived insulin-GFP+ cells cultured in control or high palmitate condition to examine the upregulation of ER stress pathway.

first: Hui

last: Zeng

first: Min

last: Guo

first: Ting

last: Zhou

first: Lei

last: Tan

first: ChiNok

last: Chong

first: Tuo

last: Zhang

first: Xue

last: Dong

first: Jenny

last: Xiang

first: Qibin

last: Qi

first: Todd

last: Evans

first: Johannes

last: Graumann


title: Analysis of embryonic development in the unsequenced axolotl: waves of transcriptional upheaval and stability

city: Cleveland

first: Peng

last: Jiang

state: OH

address: 2121 Euclid Ave

institute: Cleveland State University

summary: We performed whole transcriptome polyA+ RNA sequencing experiments on 17 stages of embryonic development

overall_design: The RNA-seq data consisted of three biological replicate samples from each stage (with the exception of stages 1 and 11, which only had two replicates), for a total of 49 samples.  RNA-seq data were paired-end with a read length of 101 bases.

first: Jeffrey

middle: D

last: Nelson

first: Ning

last: Leng

first: Michael

last: Collins

first: Scott

last: Swanson

first: Colin

last: Dewey

first: James

last: Thomson

first: Ron

last: Stewart


title: Cis-encoded sRNAs repress expression of polysaccharide utilization loci in Bacteroides fragilis 638R

city: Cologne

first: Konrad

middle: U.

last: Förstner

state: North Rhine-Westphalia

address: Gleueler Str. 60

department: Information Services

country: Germany

institute: ZB MED - Information Centre for Life Sciences

summary: The phylum Bacteroidetes is a major component of the human gut microbiota which has a broad impact on the development and physiology of its host, and a potential role in a wide range of disease syndromes. The predominance of Bacteroidetes and the genus Bacteroides in the distal gut is due in large part to the expansion of paralogous gene clusters, termed  Polysaccharide Utilization Loci (PULs), dedicated to the uptake and catabolism of host derived and dietary polysaccharides. It is generally thought that the diversity of PULs is key to Bacteroides successful competition for nutrients in the gut environment. The nutritive value of the available polysaccharides varies greatly and thus their utilization is hierarchical and strictly controlled. A typical PUL includes regulatory genes that control expression in response to the presence of specific glycan substrates. However the existence of additional regulatory mechanisms has been predicted to explain phenomena such as the hierarchical control, catabolite repression, and the fine tuning of gene expression to match catabolic activity. Using Bacteroides fragilis as a model organism, this report describes a previously unknown layer of regulatory control in which cis-encoded antisense small RNAs (sRNA) act as repressors of the PULs’ catabolic genes. Nearly 30% of B. fragilis PULs are subject to this type of sRNA control and these PULs tend to be more closely linked to the utilization of host-derived glycans than dietary polysaccharides. The findings described here indicate the presence of a global  control mechanism that underlies the known regulatory circuits which modulate PUL expression in response to substrate availability, and hence provide novel insight into regulation of the gut Bacteroidetes physiology.

overall_design: This was a simple, single sample study to establish a baseline transcriptome during balanced growth in complex media.

first: Yanlu

last: Cao

middle: U

first: Jörg

last: Vogel

first: Charles

last: Smith


title: Regulation of Choline Catabolism in Burkholderia thailandensis

city: Burlington

first: Matthew

last: Wargo

state: VT

address: 95 Carrigan Dr

department: Department of Microbiology and Molecular Genetics

institute: University of Vermont

summary: Burkholderia thailandensis is a soil-dwelling bacterium that shares many metabolic pathways with the ecologically similar, but evolutionarily distant, Pseudomonas aeruginosa. Among the diverse nutrients it can utilize is choline, which can be converted into the osmoprotectant glycine betaine and further catabolized as a source of carbon and nitrogen, similar to P. aeruginosa. Orthologs of genes in the choline catabolic pathway in these two bacteria showed distinct differences in gene arrangement as well as an additional orthologous transcriptional regulator in B. thailandensis. In this study, we showed that multiple glutamine amidotransferase1 (GATase1)-containing AraC-family transcription regulators (GATRs) are involved in regulation of the B. thailandensis choline catabolic pathway (gbdR1, gbdR2, souR).  Using genetic analyses and sequencing the transcriptome in the presence and absence of choline, we identified the likely regulons of gbdR1 (BTH_II1869) and gbdR2 (BTH_II0968). We also identified a functional ortholog for P. aeruginosa souR, a GATR that regulates the metabolism of sarcosine to glycine. GbdR1 is absolutely required for expression of the choline catabolic locus, similar to P. aeruginosa GbdR, while GbdR2 is important to increase expression of the catabolic locus. Additionally, the B. thailandensis SouR ortholog (BTH_II0994) is required for catabolism of choline and its metabolites as carbon sources, whereas in P. aeruginosa, SouR function can by bypassed by GbdR. The strategy employed by B. thailandensis represents a distinct regulatory solution to control choline catabolism and thus provides both an evolutionary counterpoint and an experimental system to compare the acquisition and regulation of this pathway during environmental growth and infection.

overall_design: Wild-type and transcriptional regulator deletion strains of B. thailandensis were grown in minimal media with and withouth choline using two biological replicates. RNA-Seq was performed obtaining single end reads to determine regulons for each transcription factor included in the study.

first: Adam

last: Nock


title: Next Generation Sequencing profile of leukemia from distinct cells-of-origin [Transcriptome profiles]

first: Jennifer

last: Trowbridge

summary:
The goal of this study is to identify genomic signatures predicitve of cell-of-origin in acute myeloid leukemia
50K bulk leukemia (GFP+) cells from the spleen of recipient mice were sorted directly into 350μl of RLT buffer (Qiagen) and flash-frozen.  Total RNA was isolated according to manufacturer’s protocols (Qiagen) including DNase treatment, and quality was assessed using an Agilent 2100 Bioanalyzer and RNA 6000 Nano kit. Amplified cDNA was sheared to approximately 300bp using a Covaris E220 Focused Ultrasonicator. RNA-seq library preparation used the TruSeq DNA sample prep kit v2 (Illumina).
Libraries were sequenced on the Illumina HiSeq 2000 platform.

overall_design: Transcriptome profiles of purified cell populations of hematopoetic stem and progenitor cells to identify transcriptomic singatures associated with leukemia cell-of-origin


title: Chameau Activates Transcription with Enhancer of Acetyltransferase Chameau (EAChm) in vitro

city: Nagasaki

first: TAKEYA

last: NAKAGAWA

address: 1-12-4 sakamoto

department: Biochemistry

country: Japan

institute: Nagasaki unversity

summary: We identified a novel co-activator EAChm which enhances histone acetyation and transcription with acetytransferase chameau.

overall_design: Drosophila S2 cell mRNA profile of control, EAChm and chameau K.D. were generated by deep sequencing in duplicate, using illumina MiSeq.

first: Masamichi

last: Doiguchi

first: Takashi

last: Ito


title: Next Generation Sequencing profile of leukemia from distinct cells-of-origin [ATAC-seq profiles]

summary:
The goal of this study is to identify genomic signatures predicitve of cell-of-origin in acute myeloid leukemia
Cryopreserved leukemic bone marrow samples were thawed, and 50,000 bulk leukemia (GFP+) cells were sorted by FACSAria (BD). Samples were placed at 37oC and 5% CO2 in IMDM plus 10% fetal calf serum for 30 minutes, then harvested, washed with 1X PBS, and ATAC-seq libraries were prepared. Quantitative PCR using the Library Quantitation kit (Kapa Biosystems) was used to estimate library concentrations. Libraries were sequenced on the Illumina HiSeq 2000 platform generating 2x150bp paired end reads at a sequencing depth of ~30-50 million reads per sample.
Libraries were sequenced on the Illumina HiSeq 2000 platform.

overall_design: ATAC-seq profiles of MLL-AF9 bulk AML samples to identify open chromatin signatures associated with leukemia cell-of-origin


title: Transcriptomic Analysis of the Serratia marcescens Response to Batrachochytrium dendrobatidis

status: Public on Jul 11 2016

city: Vermillion

first: Joseph

last: Madison

state: SD

address: 414 East Clark St

department: Biology

institute: University of South Dakota

summary: Global amphibian declines and extinction events are currently occurring at an unprecedented rate. While various factors are influencing these declines, one factor that is readily identifiable is disease. Specifically, the fungal pathogen Batrachochytrium dendrobatidis is thought to play a major role in amphibian declines in tropical and neotropical regions of the globe. While the effects of this chytrid fungus have been shown to be devastating, certain individuals and relict populations have shown resistance. This resistance has been attributed in part to the cutaneous microbiome. Many identified bacterial species that make up the microbiome have shown anti-B. dendrobatidis activity in vitro. One bacteria that is commonly associated as being a member of the amphibian microbiome across amphibian species and shows such anti-B. dendrobatidis activity is Serratia marcescens. Here, we look at transcriptomic shifts in gene expression of S. marcescens (high homology to strain WW4) in response to both live and heat-killed B. dendrobatidis.

overall_design: Six samples were analyzed in this study. Three different treatments were utilized with two biological replicates of each. The three treatments included growth of Serratia marcescens with B. dendrobatidis, with heat-killed B. dednrobatidis, and without any B. dendrobatidis (control).

first: Oxana

last: Gorbatenko

first: Jacob

last: Kerby


title: Hormone induced repression of genes requires BRG1-mediated H1.2 deposition at target promoters

city: Barcelona

first: François

last: Le Dily

address: Dr. Aiguader, 88

institute: CRG-Centre for Genomic Regulation

summary: In this report we have discovered a new function of BRG1 during hormone-mediated gene repression. The ATPase BRG1 without the other subunits of the BAF complex is recruited by the hormone receptor to genomic sites marked by the pioneering factor FOXA1, where it remodels the target chromatin by interacting with linker histone H1.2 facilitating its deposition.

overall_design: T47D human breast cancer cells were incubated with the progestin R5020 for different times and prepared for RNA-seq and ChIP-Seq according published protocols.

first: Silvina

last: Nacht

first: Andy

last: Pohl

first: Roser

last: Zaurin

first: Daniel

last: Soronellas

first: Javier

last: Quilez

first: Priyanka

last: Sharma

first: Roni

last: Wright

first: Miguel

last: Beato

first: Guillermo

middle: P

last: Vicent


title: Topoisomerase 1 inhibition suppresses inflammatory genes and protects from death by inflammation (ChIP-Seq)

first: Ivan

last: Marazzi

address: 1468 Madison Avenue

department: Department of Microbiology

institute: Icahn School of Medicine at Mount Sinai

summary: The host innate immune response is the first line of defense against pathogens and is orchestrated   by the concerted expression of genes induced by microbial stimuli. Deregulated expression of   these genes is linked to the initiation and progression of numerous diseases associated with   exacerbated inflammation. Here, we identify Topoisomerase 1 (Top1) as a critical positive   regulator of RNA polymerase II (RNAPII) transcriptional activity at pathogen-induced genes.   Notably, depletion or chemical inhibition of Top1 suppresses the host response against   replicating Influenza and Ebola viruses as well as bacterial products. As a result, therapeutic   pharmacological inhibition of Top1 protects mice from death in experimental models of   chemical- and pathogen-induced lethal inflammation. Our results indicate that Top1 inhibition   could be used as therapy against life threatening infections characterized by an acutely   exacerbated immune response.

overall_design: We performed RNAPII ChIP on PR8ΔNS1 influenza infected and uninfected cells that had been treated with either DMSO or camptothecin.

first: Alex

last: Rialdi

first: Laura

last: Campisi

last: Zhao

first: Arvin

last: Lagda

first: Colette

last: Pietzsch

first: Jessica

middle: Y

last: Ho

first: Luis

last: Martinez-Gil

first: Romain

last: Fenouil

first: Xiaoting

last: Chen

first: Megan

last: Edwards

first: Giorgi

last: Metreveli

first: Stefan

last: Jordan

first: Zuleyma

last: Peralta

first: Cesar

last: Munoz-Fontela

first: Nicole

last: Bouvier

first: Miriam

last: Merad

first: Jian

last: Jin

first: Matthew

last: Weirauch

first: Sven

last: Heinz

first: Chris

last: Benner

first: Harm

last: van Bakel

last: Basler

first: Adolfo

last: García-Sastre

last: Bukreyev


title: Identification of ZEB1-regulated gene expression changes in HCC827 human lung adenocarcinoma cells

city: Rochester

first: Zhifu

last: Sun

state: MN

address: 200 1st ST SW

department: HSR-BSI

institute: Mayo Clinic

summary: We performed next-generation RNA sequencing for HCC827 human lung adenocarcinoma cells that are stably transfected with pcDNA3.1-ZEB1 or an empty pcDNA3.1 vector plasmid, in triplicate for each of the two HCC827 cell transfectants. The goal of this experiment is to identify putative downstream mediators of ZEB1 in human lung cancer cells. By successfully acquiring about 25 million reads for each sample, we identified more than 1,700 transcripts that are significantly regulated by ZEB1 (increased or decreased by ZEB1; p < 0.05). Among these genes, 87 of them are predicted direct targets for microRNA-200c, a well-established transcription target of ZEB1. Our results will be useful for further identification of genes that mediate the biological functions of ZEB1 in human lung cancer cells.

overall_design: Examination of gene expression differences between HCC827 cells expressing pcDNA3.1-ZEB1 and empty pcDNA3.1 vector by next-generation RNA sequencing

first: Yang

last: Yanan

first: Sun

last: Zhifu


title: Topoisomerase 1 inhibition suppresses inflammatory genes and protects from death by inflammation

first: Ivan

last: Marazzi

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

overall_design: Refer to individual Series


title: Epigenetic Plasticity Drives Adipogenic and Osteogenic Differentiation of Marrow-Derived Mesenchymal Stem Cells (RNA-seq)

city: Madison

first: Mark

middle: B

last: Meyer

state: WI

address: 1415 Linden Dr.

department: Nutritional Sciences

institute: University of Wisconsin-Madison

summary: Terminal differentiation of multipotent stem cells is achieved through a coordinated cascade of activated transcription factors and epigenetic modifications that drive gene transcription responsible for unique cell fate.  Within the mesenchymal lineage, factors such as RUNX2 and PPARγ are indispensable for osteogenesis and adipogenesis, respectively.  We therefore investigated genomic binding of transcription factors and accompanying epigenetic modifications that occur during osteogenic and adipogenic differentiation of mouse bone marrow-derived mesenchymal stem cells (MSC).  As assessed by ChIP-seq and RNA-seq analyses, we found that genes vital for osteogenic identity were linked to RUNX2, C/EBPβ, RXR, and VDR binding sites, whereas adipocyte differentiation favored PPARγ, RXR, C/EBPα, and C/EBPβ binding sites.  Epigenetic marks were clear predictors of active differentiation loci as well as enhancer activities and selective gene expression.  These marrow-derived MSCs displayed an epigenetic pattern that suggested a default preference for the osteogenic pathway; however, these patterns were rapidly altered near the Adipoq, Cidec, Fabp4, Lipe, Plin1, Pparg and Cebpa genes during adipogenic differentiation.  Surprisingly, we found that these cells also exhibited an epigenetic plasticity that enabled them to trans-differentiate from adipocytes to osteoblasts (and vice-versa) after commitment, as assessed by staining, gene expression, and ChIP-qPCR analysis.  The osteogenic default pathway may be subverted during pathological conditions leading to skeletal fragility and increased marrow adipocity during aging, estrogen deficiency and skeletal unloading.  Taken together, our data provide an increased mechanistic understanding of the epigenetic programs necessary for multipotent differentiation of MSCs that may prove beneficial in the development of therapeutic strategies.

overall_design: Marrow derived MSC cells were differentiated to day 7 or day 15 with osteogenic or adipogenic media.  These cells were then treated with vehicle or 100nM 1,25(OH)2D3 for 24 hours prior to mRNA isolation and sequencing.

first: Nancy

last: Benkusky

first: J

middle: W

last: Pike


title: Epigenetic Plasticity Drives Adipogenic and Osteogenic Differentiation of Marrow-Derived Mesenchymal Stem Cells (ChIP-seq)

overall_design: Marrow derived MSC cells were differentiated to day 7 or day 15 with osteogenic or adipogenic media.  These cells were then treated with vehicle or 100nM 1,25(OH)2D3 for 24 hours prior to ChIP assay, library creation and sequencing.


title: Topoisomerase 1 inhibition suppresses inflammatory genes and protects from death by inflammation (RNA-Seq)

overall_design: RNA seq was performed on Ebola (Wild type and mutant) infected or uninfected THP-1 cells in the presence of DMSO or Camptothecin

first: Alex

last: Rialdi

first: Laura

last: Campisi

last: Zhao

first: Arvin

last: Lagda

first: Colette

last: Pietzsch

first: Jessica

last: Ho

first: Luis

last: Martinez-Gil

first: Romain

last: Fenouil

first: Xiaoting

last: Chen

first: Megan

last: Edwards

first: Giorgi

last: Metreveli

first: Stefan

last: Jordan

first: Zuleyma

last: Peralta

last: Munoz-Fontela

last: Bouvier


title: Epigenetic Plasticity Drives Adipogenic and Osteogenic Differentiation of Marrow-Derived Mesenchymal Stem Cells

last: Meyer


title: Different promoter affinities account for specificity in MYC-dependent gene regulation

city: Wuerzburg

first: Martin

last: Eilers

address: Am Hubland

department: Chair for Biochemistry and Molecular Biology

institute: University of Wuerzburg

summary: Enhanced expression of the MYC transcription factor is observed in the majority of tumors. Two seemingly conflicting models have been proposed for its function: one proposes that MYC enhances expression of all genes, while the other model suggests gene-specific regulation. Here, we have explored the hypothesis that specific gene expression profiles arise since promoters differ in affinity for MYC and high-affinity promoters are fully occupied by physiological levels of MYC. We determined cellular MYC levels and used RNA- and ChIP-sequencing to correlate promoter occupancy with gene expression at different concentrations of MYC. Mathematical modeling showed that binding affinities for interactions of MYC with DNA and with core promoter- bound factors, such as WDR5, are sufficient to explain promoter occupancies observed in vivo. Importantly, promoter affinity stratifies different biological processes that are regulated by MYC, explaining why tumor-specific MYC levels induce specific gene expression programs and alter defined biological properties of cells.

overall_design: Gene expression profiling at different MYC levels in a human tumor cell line and ChIP-Sequencing of MYC in these cells.

first: Francesca

last: Lorenzin

first: Uwe

last: Benary

first: Apoorva

last: Baluapuri

first: Susanne

last: Walz

first: Lisa

last: Jung

first: Björn

last: von Eyß

first: Caroline

last: Kisker

first: Jana

last: Wolf

first: Elmar


title: PROP1 triggers epithelial-mesenchymal transition-like process in pituitary stem cells

city: ann arbor

first: Sally

last: Camper

state: MICHIGAN

address: 1241 E catherine st

institute: university of michigan


title: The C2H2-ZF transcription factor Zfp335 recognizes two consensus motifs using separate zinc finger arrays

city: Singapore

first: Brenda

middle: Yuyuan

last: Han

address: 61 Biopolis Drive, Proteos

country: Singapore

institute: Institute of Molecular and Cell Biology, A*STAR

summary: The complexities of DNA recognition by transcription factors with multiple Cys2-His2 zinc fingers (C2H2-ZFs) remain poorly studied. We previously reported a mutation (R1092W) in the C2H2-ZF transcription factor Zfp335 which led to selective loss of binding at a subset of targets, although the basis for this was unclear. We show that Zfp335 binds DNA and drives transcription via recognition of two distinct consensus motifs by separate ZF clusters, and identify the specific motif interaction disrupted by R1092W. Our work presents Zfp335 as a model for understanding how C2H2-ZF TFs may utilize multiple recognition motifs to control gene expression.

overall_design: 3 ChIP-seq samples, 3 input samples from control Jurkat T cells or Jurkat cell lines overexpressing FLAG-tagged WT or bloto (R1092W) ZNF335

first: Chuan-Sheng

last: Foo

first: Shuang

last: Wu

first: Jason

last: Cyster


title: PROP1 triggers epithelial-mesenchymal transition-like process in pituitary stem cells [RNA-Seq]

summary: Mutations in PROP1 are the most common cause of hypopituitarism in humans; therefore, unraveling its mechanism of action is highly relevant from a therapeutic perspective. Our current understanding of the role of PROP1 in the pituitary gland is limited to the regulation of pituitary transcription factors Hesx1 and Pit1.  To elucidate the comprehensive PROP1-dependent gene regulatory network, we conducted genome wide analysis of PROP1 DNA binding and effects on gene expression in mutant tissues, isolated stem cells and engineered cell lines. We determined that PROP1 is essential for maintaining proliferation of stem cells and stimulating them to undergo an epithelial to mesenchymal transition-like process necessary for cell migration and differentiation. Genomic profiling reveals that PROP1 binds to and represses claudin 23, characteristic of epithelial cells, and it activates EMT inducer genes: Zeb2, Notch2 and Gli2.  Our findings identify PROP1 as a central transcriptional component of pituitary stem cell differentiation.

overall_design: Pituitary Colony forming cells mRNA of 13-day old wild type (Prop1 +/+), Prop1 mutants (Prop1df/df), wild type (Pit1+/+) and Pit1 mutants (Pit1 dw/dw) mice were generated by deep sequencing, in triplicates.

first: Maria

middle: I

last: Perez Millan


title: A conserved abundant cytoplasmic long noncoding RNA modulates repression of mRNAs by Pumilio proteins in human cells

city: Rehovot

first: Igor

last: Ulitsky

address: Hertzl St.

country: Israel

institute: Weizmann Institute of Science

summary: Thousands of long noncoding RNA (lncRNA) genes are encoded in the human genome, and hundreds of them are evolutionary conserved, but their functions and modes of action remain largely obscure. Particularly enigmatic lncRNAs are those that are exported to the cytoplasm, including NORAD - an abundant and highly conserved cytoplasmic lncRNA. Most of the sequence of NORAD is comprised of repetitive units that together contain at least 17 functional binding sites for the two Pumilio homologs in mammals. Through binding to PUM1 and PUM2, NORAD modulates the mRNA levels of their targets, which are enriched for genes involved in chromosome segregation during cell division. Our results suggest that some cytoplasmic lncRNAs function by modulating the activities of RNA binding proteins, an activity which positions them at key junctions of cellular signaling pathways.

overall_design: RNA-seq following perturbations of NORAD lncRNA and Pumilio proteins in U2OS cells

first: Ailone

last: Tichon


title: Next Generation Sequencing profile of leukemia from distinct cells-of-origin

first: Jennifer

last: Trowbridge


title: RNA-sequencing of tamoxifen resistant LY2 cells transfected with siRNA-HOXC11.

city: Dublin

first: Leonie

last: Young

address: York Street

country: Ireland

institute: Royal College of Surgeons, Ireland

summary: To assess the global effects of HOXC11 in endocrine resistant breast cancer cells we performed RNA-seq on LY2 cells which were transfected with either siRNA targeting HOXC11 (siHOXC11) or a scrambled negative control siRNA (scrHOXC11) in the presence of 4-OH-tamoxifen (10-8M).  Knockdown was verified by Taq-man qRT-PCR prior to library preparation.  RNA (10µg) was extracted using an Oligotex mRNA kit (Qiagen) as per manufacturer’s instructions (n=4). RNA was reverse transcribed followed by mRNA library preparation and sequencing based on a protocol outlined by Wilhelm et al., 2010.  Sequencing was performed on an Illumina Genome Analyzer II (GAII) (54 million reads per sample on average).

overall_design: Silencing of HOXC11 in tamoxifen resistant LY2 cells to identify putative HOXC11 target genes.

first: Yuan

last: Hao

first: Peadar

middle: O

last: Gaora

first: Damian

last: McCartan


title: Genetic Diversity Through RNA Editing: Apobec1-mediated RNA editing in bulk and single cell macrophages and dendritic cells

first: F.

middle: Nina

last: Papavasiliou

state: New York

address: 1230 York Ave.

institute: Rockefeller University

summary: RNA editing is a mutational mechanism that specifically alters the nucleotide content in sets of transcripts while leaving their cognate genomic blueprint intact. Editing has been detected from bulk RNA-seq data in thousands of distinct transcripts, but apparent editing rates can vary widely (from under 1% to almost 100%). These observed editing rates could result from approximately equal rates of editing within each individual cell in the bulk sample, or alternatively, editing estimates from a population of cells could reflect an average of distinct, biologically significant editing signatures that vary substantially between individual cells in the population. To distinguish between these two possibilities we have constructed a hierarchical Bayesian model which quantifies the variance of editing rates at specific sites using RNA-seq data from both single cells and a cognate bulk sample consisting of ∼ 106 cells. The model was applied to data from murine bone-marrow derived macrophages and dendritic cells, and predicted high variance for specific edited sites in both cell types tested. We then 1 validated these predictions using targeted amplification of specific editable transcripts from individual macrophages. Our data demonstrate substantial variance in editing signatures between single cells, supporting the notion that RNA editing generates diversity within cellular populations. Such editing-mediated RNA-level sequence diversity could contribute to the functional heterogeneity apparent in cells of the innate immune system.

overall_design: 26 samples were subjected to RNA-seq: 24 single WT macrophages, and 2 bulk samples (Apobec1 WT and KO macrophages), consisting of 500,000-1 million cells each.

first: Dewi

last: Harjanto

first: Violeta

last: Rayon-Estrada

first: F


title: NF-E2, FLI1 and RUNX1 collaborate at areas of dynamic chromatin to activate transcription in mature mouse megakaryocytes

city: Charlottesville

first: Chongzhi

last: Zang

state: VA

institute: University of Virginia

summary: Mutations in mouse and human Nfe2, Fli1 and Runx1 cause thrombocytopenia. We applied genome- wide chromatin dynamics and ChIP-seq to determine these transcription factors’ (TFs) activities in terminal megakaryocyte (MK) maturation. Enhancers with H3K4me2-marked nucleosome pairs were most enriched for NF-E2, FLI and RUNX sequence motifs, suggesting that this TF triad controls much of the late MK program. ChIP-seq revealed NF-E2 occupancy near previously implicated target genes, whose expression is compromised in Nfe2-null cells, and many other genes that become active late in MK differentiation. FLI and RUNX were also the motifs most enriched near NF-E2 binding sites and ChIP-seq implicated FLI1 and RUNX1 in activation of late MK, including NF-E2-dependent, genes. Histones showed limited activation in regions of single TF binding, while enhancers that bind NF-E2 and either RUNX1, FLI1 or both TFs gave the highest signals for TF occupancy and H3K4me2; these enhancers associated best with genes activated late in MK maturation. Thus, three essential TFs co- occupy late-acting cis-elements and show evidence for additive activity at genes responsible for platelet assembly and release. These findings provide a rich dataset of TF and chromatin dynamics in primary MK and explain why individual TF losses cause thrombopocytopenia.

overall_design: ChIP-Seq of key transcription factors in matured megakaryocytes

first: Annouck

last: Luyten

first: Ramesh

last: Shivdasani

first: Xiaole

middle: S

last: Liu


title: High Concentrations of Atmospheric Ammonia Induce Alterations of Gene Expression in the Breast Muscle of Broilers (Gallus gallus) Based on RNA-Seq

status: Public on Jul 10 2016

city: Beijing

first: Bao

last: Yi

address: No.2 Yuanmingyuan West Road

department: Institute of Animal Sciences

institute: Chinese Academy of Agricultural Sciences

summary:
Background: High concentrations of atmospheric ammonia are one of the key environmental stressors affecting broiler production performance, which causes remarkable economic losses as well as potential welfare problems of the broiler industry. Previous reports have demonstrated that high levels of ammonia can alter body fat distribution and meat quality of broilers. However, the molecular mechanisms and metabolic pathways in breast muscle altered by high concentrations of ambient ammonia exposure on broilers are still unknown.
Results: This study utilized RNA-Seq to compare the transcriptomes of breast muscles to identify differentially enriched genes in broilers exposed to high or low concentrations of atmospheric ammonia. A total of 267 promising candidate genes were identified by differential expression analysis, among which 67 genes were up-regulated and 189 genes were down-regulated. Bioinformatics analysis suggested that the up and down-regulated genes were involved in the following two categories of cellular pathways and metabolisms: Steroid biosynthesis (gga00100) and peroxisome proliferator-activated receptor (PPAR) signaling pathway (gga03320), which both participate in the lipid metabolism processes.
Conclusions: This study suggests that longtime exposure to high concentrations of aerial ammonia can change fat content in breast muscle, meat quality and palatability via altering expression levels of genes participating in important lipid metabolism pathways. This study maybe provides new information that could be used for genetic breeding and nutritional intervention in production practice of broilers industry in the future.

overall_design: Breast muscle mRNA profiles of 42-day old Arbor Acres male broilers exposed to 3 ppm (control) and 75 ppm (treatment) concentrations of atmospheric ammonia were generated by RNA sequencing, in triplicate, using Illumina HiSeq2000.

first: Liang

last: Chen


title: RNA sequencing of mechanically strained NHEKs and control NHEKs

city: Münster

first: Sara

last: Wickström

address: Röntgenstraße 20

department: Cell & Tissue Dynamics

institute: Max Planck Institute for Molecular Biomedicine

summary: We sequenced mRNA from NHEKs that had been subjected to cyclic biaxial mechanical strain at 100 mHz for 12h together with unstrained control NHEKs, 3 biological replicates each

overall_design: Examination of mRNA levels in control and mechanically strained NHEKs


title: Tissue damage signals repurpose NF-κB, AP-1 and Smad3 to direct a Rev-erb sensitive wound healing program in macrophages

city: La Jolla

first: Christopher

last: Glass

address: 9500 Gilman Dr.

department: CMM

institute: University of California, San Diego

summary: A complex damage signal promotes co-localization of NFκB and Smad3 at Rev-erb-sensitive enhancers and drives expression of genes characteristic of alternate polarization states in the same cells.

overall_design: Chromatin mark H3K27Ac, transcription factors PU.1, cFos, SMAD3, and p65 were assessed by ChIP-Seq and RNA-Seq was used to measure gene expression in C57BL/6 and ReverbDKO mice and in in-vivo wounds

middle: K


title: Assay for Transposase-Accessible Chromatin with high throughput sequencing (ATAC-Seq) reveals lncRNA MANTIS important for the angiogenic function of endothelial cells

city: Frankfurt

first: Matthias

last: Leisegang

address: Theodor-Stern-Kai 7

department: Institute for Cardiovascular Physiology

institute: Goethe-University

summary: The angiogenic function of endothelial cells is tightly regulated but the impact of long non-coding RNAs (lncRNA) remains unclear. The lncRNA yielded to be an epigenetically restricted endothelial lncRNAs. Here, the chromatin accessibility after knockdown of MANTIS was investigated. It revealed changes on chromatin accessibility on several promoters which are known to be important for endothelial angiogenic function.

overall_design: ATAC-seq profiles after knockdown with scrambled or MANTIS siRNA in human umbilical vein endothelial cells (HUVEC).

first: Carsten

last: Künne

first: Stefan

last: Günther

first: Ralf

last: Brandes


title: PROP1 triggers epithelial-mesenchymal transition-like process in pituitary stem cells [ChIP-Seq]

first: Sally

last: Camper

overall_design: Streptavidin ChIP-Seq of biotinylated PROP1 in GHFT1 cells in 2 samples: GHFT1 Prop1Tag BirA expressing cells and GHFT1 BirA alone as negative control.

first: Maria

last: Perez Millan


title: Sucralose Promote Food Intake Through NPY and A Neuronal Fasting Response

city: Sydney

first: Qiaoping

last: Wang

state: NSW

address: Johns Hopkins Dr

department: Charles Perkins Centre

country: Australia

institute: University of Sydney

summary: Non-nutritive sweeteners like sucralose are consumed by billions of people. While animal and human studies have demonstrated a link between synthetic sweetener consumption and metabolic dysregulation, the mechanisms responsible remain unknown. Here we use a diet supplemented with sucralose to investigate the long-term effects of sweet/energy imbalance. In flies, chronic sweet/energy imbalance promoted hyperactivity, insomnia, glucose intolerance, enhanced sweet taste perception and a sustained increase in food and calories consumed, effects that are reversed upon sucralose removal. Mechanistically, this response was mapped to the ancient insulin, catecholamine, and NPF/NPY systems and the energy sensor AMPK, which together comprise a novel neuronal starvation response pathway. Interestingly, chronic sweet/energy imbalance promoted increased food intake in mammals as well, and this also occurs through an NPY-dependent mechanism. Together our data show that chronic consumption of a sweet/energy imbalanced diet triggers a conserved neuronal fasting response and increases the motivation to eat.

overall_design: RNA-seq on Drosophila head samples fed control and sucralose diet

first: Qiao-Ping

first: Yong

middle: Q

last: Lin

first: Lei

last: Zhang

first: Yana

last: Wilson

first: Lisa

last: Oyston

first: James

last: Cotterell

first: Yue

last: Qi

first: Thang

middle: M

last: Khuong

first: Noman

last: Bakhshi

first: Yoann

last: Planchenault

first: Duncan

middle: T

last: Browman

first: Man

last: Lau

first: Tiffany

last: Cole

first: Adam

last: Wong

first: Stephen

last: Simpson

middle: R

first: Josef

last: Penninger

first: Herbert

last: Herzog

first: G

middle: G

last: Neely


title: Transcriptomic profiling of alpha, beta, and delta cell populations provides new insights into the role of ghrelin in the pancreas

city: Cambridge

first: Brian

middle: Yee Hong

last: Lam

address: Box 289 Addenbookes Hospital, Hills Road

department: Metabolic Research Laboratories

country: United Kingdom

institute: University of Cambridge

summary: Intra-islet crosstalk between islet cells is critical in orchestrating the body’s response to changes in blood glucose levels, but is incompletely understood. In this study, we used transgenic mouse lines that allowed the purification and transcriptomic characterisation of alpha, beta, and delta cells, yielding an RNA-sequencing database that can be searched for regulatory proteins which are differentially expressed between cell types. As an illustrative example, we examined the expression of g-protein coupled receptors, and found that the ghrelin receptor, Ghsr, was highly expressed in delta cells compared to alpha and beta cells. GHSR excitation elicited increases in cytosolic calcium levels in primary delta cells. In the perfused pancreas, the application of ghrelin stimulated somatostatin secretion, correlating with a decrease in insulin and glucagon release, which was sensitive to somatostatin receptor antagonism. These results show that ghrelin acts specifically on delta cells within pancreatic islets to affect blood glucose regulation.

overall_design: Examination of transcriptomic profiles obtained from pancreatic alpha, beta and delta cells

first: Alice

middle: E

last: Adriaenssens

first: Giles

last: Yeo

first: Frank

last: Reimann

first: Fiona

last: Gribble


title: Evidence for proliferation and synaptogenesis impairments in neural cells derived from idiopathic autistic patients

city: Los Angeles

first: Daniel

middle: H.

last: Geschwind

state: California

address: 2309 Gonda Bldg, 695 Charles E. Young Dr. South

department: Neurology

institute: UCLA

summary: Reprogramming of human somatic cells to a pluripotent state (induced pluripotent stem cells or iPSC) has provided an exciting opportunity to produce relevant cellular models of human complex neurogenetic diseases. Here we show the generation and characterization of iPSC lines from 8 sporadic ASD patients with early brain overgrowth and 5 age/gender-matched control lines. These cells were used to derive neural progenitor cells and neurons in culture. We reveal molecular and phenotypic evidence that both cell proliferation and synaptogenesis are affected in this model system. Specifically, we detected altered cell cycle and altered levels of excitatory and inhibitory markers in neural cells at early stages of differentiation. This work demonstrates that in a heterogeneous condition such as ASD, selection of subjects based on phenotype can improve power to detect biologically relevant pathway disruption that may help guide development of novel therapies.

overall_design: mRNA profiles of iPSC-derived neural progenitors and neurons from 8 sporadic ASD patients with early brain overgrowth and 5 age/gender-matched controls

first: Maria

middle: C

last: Marchetto

first: Haim

last: Belinson

first: Yuan

last: Tian

first: Patrícia

last: Beltrao-Braga

first: Cleber

last: Trujillo

first: Ana

last: Mendes

first: Yanelli

last: Nunez

first: Jing

last: Ou

first: Himanish

last: Gosh

first: Kristen

last: Brennand

first: Karen

last: Pierce

first: Tiziano

last: Pramparo

first: Lisa

last: Eyler

first: Cindy

last: Barnes

first: Eric

last: Courchesne

first: Fred

middle: H

last: Gage

first: Anthony

last: Wynshaw-Boris

first: Alysson

last: Muotri


title: ELAVL2-regulated transcriptional networks in human neurons link atlernative splicing, autism and human neocortical evolution

city: Dallas

first: Genevieve

last: Konopka

state: TX

address: 5323 Harry Hines Blvd.

department: Neuroscience

institute: UT Southwestern Medical Center

summary: The role of post-transcriptional gene regulation in human brain development and cognitive diseases remains mostly uncharacterized. ELAV-like RNA binding proteins are a family of proteins that regulate several aspects of neuronal function including neuronal excitability and synaptic transmission. Here, we identify the downstream transcriptional networks of ELAVL2, an RNA-binding protein with unknown function in the brain. We knockdown expression of ELAVL2 in human neurons and conduct RNA-sequencing, identifying networks of differentially expressed and alternatively spliced genes with altered ELAVL2. These networks contain autism-relevant genes as well as previously identified targets of other RNA binding proteins implicated in autism spectrum disorders such as RBFOX1 and FMRP. ELAVL2-regulated coexpression networks are also enriched for synaptic genes as well as genes with human-specific patterns of gene expression in the frontal pole. Together, these data suggest that ELAVL2 regulation of transcript expression is critical for neuronal functions at risk in autism spectrum disorders and such mechanisms of post-transcriptional gene regulation may have contributed to human brain evolution.

overall_design:
We carried out RNA-sequencing (RNA-seq) of human neural progenitors cells. For the RNA-seq, 5 indipendent replicates were used for the neural progenitor cells.
Primary human neural progenitor cultures were derived from mid-gestation fetal brain. Cells were transduced with a lentivirus containing a specific shRNA to ELAVL2 or a control shRNA. Cells were differentiated into neurons for 4 weeks and then harvested.

first: Stefano

last: Berto

first: Brent

middle: L

last: Fogel


title: Global analysis of dorsoventral patterning in the wasp Nasonia

status: Public on Jul 08 2016

city: Chicago

first: Jeremy

middle: A

last: Lynch

state: IL

address: 900 S. Ashland Ave

department: Biological Sciences

institute: UIC

summary: Using RNA interference, we dorsalized and ventralized Nasonia embryos.  By comparing transcriptomes from the RNAi cases to each other and to controls, we identify >100 genes expressed along the embryonic DV axis

overall_design: 2 biological replicates of Toll signaling knockdown, BMP signaling knockdown, and water injected (control) were produced, and RNA was isolated and sequenced from resulting embryos


title: Aberrant downstream mechanisms following loss of KMT2C and KMT2D in Pancreatic Ductal Adenocarcinoma

status: Public on Jul 09 2016

city: London

first: Jun

last: Wang

address: Charterhouse Square

institute: Barts Cancer Institute, Queen Mary, London

summary: Genes encoding the histone H3 lysine 4 (H3K4) methyltransferases KMT2C and KMT2D are subject to deletion and mutation in pancreatic ductal adenocarcinomas (PDAC). We examined the functional and transcriptional consequences of loss of these methyltransferases in patients with PDAC. Patients with low KMT2C and KMT2D expression demonstrated a much-improved outcome compared with those expressing high levels. RNA-seq analysis of KMT2C or KMT2D loss in three cell lines (PANC1, SUIT2 and COLO357) identified 31 and 124 differentially expressed genes respectively, with 19 genes common to both methlytransferases. Gene set enrichment analysis, and correlation with publicly available patient gene expression (GEP) datasets, highlighted significant reductions in pathways relating to cell-cycle and cell growth, where gene expression correlated with KMT2C/D depletion. Furthermore, loss of Kmt2d in three murine cell lines increased sensitivity to the nucleoside analogue 5-fluorouracil (5FU). These experiments support critical, non-redundant, roles for KMT2D and KMT2C in PDAC, where depletion impacts cell-cycle to reduce cell proliferation, enhance response to specific chemotherapy, which may improve patient survival.

overall_design: Investigation of changes in whole transcriptomes with KMT2C/D loss by siRNAs using RNA-seq in three human cell lines

first: Joshua

last: Dawkins

first: Jude

last: Fitzgibbon

first: Richard

last: Grose


title: Oncogenic Enhancers from Small Genomic Insertions

last: Young

state: MA

address: 9 Cambridge Center

institute: Whitehead Institute for Biomedical Research

summary: The noncoding regions of tumor cell genomes harbor a considerable fraction of total variation, but the functional contribution of such variants to tumorigenesis is ill-defined.  Among these noncoding variants, somatic insertions are among the least well-characterized due to challenges with interpreting short-read DNA sequences.  To address this, we have identified enhancer-associated small insertion variants across a spectrum of tumor cells by using ChIP-seq to enrich and sequence enhancer DNA, and a computational approach with multiple alignment procedures to identify small insertions.  Among the 82 tumor genomes studied here, small insertions were frequently observed in enhancer DNA sequences located near known oncogenes.  Further study of one such insertion, found in primary leukemia tumor genomes, revealed that it nucleates formation of an active enhancer that drives expression of the LMO2 oncogene.  The catalogue of enhancer-associated small insertion variants described here provides a foundation for further investigating the functions of this class of variants across a range of human cancers.

overall_design: ChIP-Seq for H3K27ac in cancer cell lines

first: Rhamy

last: Zeid

first: Matthew

last: Guenther

first: Heather

last: Hoke

first: Michael

last: McKeown

first: Ashley

last: Lau

first: Nicholas

last: Kwiatkowski

first: Lars

last: Anders

first: Denes

last: Hnisz

first: Zhaodong

last: Li

first: Brian

middle: J

last: Abraham

first: Abraham

last: Weintraub

first: Charles

first: Julia

last: Etchin

first: Nina

last: Weichart-Leahey

first: Sunniat

last: Rahman

first: Tong

middle: I

last: Lee

first: A

last: Look

first: Marc

last: Mansour


title: Intergenerational consequences of gene-environment induced epigenetic dynamics at rDNA in the mouse (Bis-PCR)

first: Robert

last: Lowe

address: 4 Newark Street

department: Blizard Institute

institute: QMUL

summary: The ability of environmental exposures in one generation to elicit phenotypic outcomes in subsequent generations suggests that DNA is not the sole vehicle of biological heredity. Such non-genetic inheritance has been demonstrated in a variety of non-mammalian species but, to date, has remained controversial and inadequately characterised in mammals. Here, we show that early life protein restriction (PR) in mice alters DNA methylation at specific genetic variants of multi-copy ribosomal DNA (rDNA), to produce a linear correlation with the extent of growth restriction induced by PR. These effects are common to soma and germ-line and are concomitant with changes in the relative abundance of the responsive rDNA genetic variant. Intergenerational pedigree analysis reveals that rDNA genetic correlations are abolished between directly exposed males and their unexposed offspring, and epigenetic correlations are gained. To the best of our knowledge, this is the first direct demonstration in mammals of epigenetic dynamics induced by gene-environment interactions. Our work confirms rDNA as an evolutionarily conserved target of nutritional insults and intergenerational effects in flies, yeast, and now mice.

overall_design: Bis-PCR profiling of rDNA for Protein restricted and control mice of G1 Sperm, G1 Liver and G2 Liver


title: The CENP-B fission yeast homolog, ABP1, is involved in the repression of cryptic transcription from the Tf2 and rRNA genes repeat

city: Barcelona

first: Oscar

last: Reina Garcia

state: Barcelona

address: C/Baldiri Reixac 10

department: Biostatistics and Bioinformatics

institute: IRB Barcelona

type: Non-coding RNA profiling by high throughput sequencing

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

overall_design: Refer to individual Series


title: Batch effects and the effective design of single-cell gene expression studies

first: John

middle: D

last: Blischak

address: 920 E. 58th Street, CLSC 317

department: Human Genetics

institute: University of Chicago

summary: Single cell RNA sequencing (scRNA-seq) can be used to characterize variation in gene expression levels at high resolution. However, the sources of experimental noise in scRNA-seq are not yet well understood. We investigated the technical variation associated with sample processing using the single cell Fluidigm C1 platform. To do so, we processed three C1 replicates from three human induced pluripotent stem cell (iPSC) lines. We added unique molecular identifiers (UMIs) to all samples, to account for amplification bias. We found that the major source of variation in the gene expression data was driven by genotype, but we also observed substantial variation between the technical replicates. We observed that the conversion of reads to molecules using the UMIs was impacted by both biological and technical variation, indicating that UMI counts are not an unbiased estimator of gene expression levels. Based on our results, we suggest a framework for effective scRNA-seq studies.

overall_design:
We collected single cell RNA-seq (scRNA-seq) data from three YRI iPSC lines using the Fluidigm C1 microfluidic system followed by sequencing. We added ERCC spike-in controls to each sample, and used 5-bp random sequence UMIs to allow for the direct quantification of mRNA molecule numbers. For each of the YRI lines, we performed three independent C1 collections; each replicate was accompanied by processing of a matching bulk sample using the same reagents. This study design allows us to estimate error and variability associated with the technical processing of the samples, independently from the biological variation across single cells of different individuals. We were also able to estimate how well scRNA-seq data can recapitulate the RNA-seq results from population bulk samples.

We combined the 96 single cell samples from each C1 chip into their own master mix and sequenced across three lanes of a HiSeq 2500 (3 individuals x 3 replicates x 96 wells x 3 lanes = 2592 files). We prepared two separate library preparations for each bulk sample, combined them all into one master mix, and sequenced across four lanes (3 individuals x 3 replicates x 2 library preparations x 4 lanes = 72 files).

first: Po-Yuan

last: Tung

first: Chiaowen

last: Hsiao

first: David

last: Knowles

first: Jonathan

last: Burnett

last: Pritchard

first: Yoav

last: Gilad


title: Intergenerational consequences of gene-environment induced epigenetic dynamics at rDNA in the mouse (RNA-Seq)

overall_design: RNA-seq profiling of Protein restricted mice and control mice of G2 Adult Liver


title: Intergenerational consequences of gene-environment induced epigenetic dynamics at rDNA in the mouse (RRBS)

overall_design: RRBS profiling of Protein restricted mice and control mice of G1 Sperm


title: Transcriptome Exploration in Anisodus acutangulus for Further Understanding of the Tropane Alkaloids Biosynthesis

city: SHANGHAI

first: Lijie

last: Cui

address: Guilin Road 100

institute: shanghai normal university

summary: We analyzed the transcriptome of A. acutangulus roots by deep RNA sequencing to dig TAs biosynthetic genes. KOG (Eukaryotic Orthologous Groups) and KEGG (Kyoto Encyclopedia of Genes and Genomes) pathway enrichment analyses identified 48 unigenes referring to the tropane, piperidine and pyridine alkaloid biosynthesis, 145 unigenes presumably involved in distribution of arginine to TAs biosynthesis, and 86 unigenes referring to the terpenoid backbone biosynthesis. Furthermore, 82 unigenes annotated as cytochrome P450 family members seemed to be involved in secondary metabolism pathways. Previously unknown TAs biosynthetic genes in A. acutangulus, which encode littorine mutase/monooxygenase (CYP80F1) and diamine oxidase (DAO), were identified by this study.

overall_design: A. acutangulus plants were collected from Yunnan Province of China, and the roots derived from the sterile A. acutangulus plants (2 months old) as the main tissue of TAs synthesis were collected and sequenced

first: Fenfen

last: Huang

first: Yuping

last: Lin

first: Dasheng

last: Zhang

first: Jie

last: Zong

first: Guoyin

last: Kai


title: The CENP-B fission yeast homolog, ABP1, is involved in the repression of cryptic transcription from the Tf2 and rRNA genes repeat [ChIP-Seq_CNAG]

summary: In Schizosaccharomyces pombe, Abp1 is homologous to mammalian CENP-B. Abp1 has various seemingly independent functions in the yeast nucleus. It binds to pericentromeric repeats and contribute to heterochromatin formation (ref). Abp1 is involved in regulating the directionality of mating-type switching by regulating the transcription of a member of the recombination-promoting complex (refs). Abp1 also preserves genome integrity by silencing the Tf2 retrotransposons and protecting replication forks during pausing (ref). The profile of the RNA extracted from abp1Δ cells shows an accumulation of RNA in size ranging between 100 and 200 bp. Solexa sequencing of these “little RNA” (liRNA) and comparison of their levels with the WT showed an increase in liRNA coming from various classes of genomic features. The biggest fold changes are attributed to liRNA coming from LTR retrotransposons and the rDNA genes repeats. We show that these liRNAs are targeted for degradation by the exosome and are the products of pervasive RNA Polymerase II transcription. Finally, we describe the genetic interactions of various transcriptional gene silencing effectors with the abp1 deletion in the silencing of the liRNA.

overall_design: ChIP-Seq peak calling of ABP1 in wild type Spombe cells

first: Anne

last: Daulny

first: Fernando

last: Azorin


title: The development and growth related transcriptome landscape of ovariectomized goat muscle

city: Yangling

first: Sihuan

state: Shaanxi

address: No. 22 Xinong Road

department: College of Animal Science and Technology

institute: Northwest A&F University

summary: In this study, ovariectomized and normal ewe longissimus thoracis were used to thoroughly explore the global transcriptome to reveal how the castrated ewes influence muscle development by Illumina2000 sequencing technology. As a result, 1,612 differently expressed unigenes were revealed between ovariectomized and normal ewe groups, which containing 718 up-regulated and 894 down-regulated genes in ovariectomized ewe muscle. Moreover, in the 1,612 unigenes, 903 genes were expressed commonly in the two groups, 288 and 421 genes were uniquely expressed in normal and ovariectomized ewe group, respectively. This study validated some differently expressed genes in samples by quantitative real-time PCR, and the results were consistent with the RNA-seq. Furthermore, this study revealed 24 and 11 differently expressed genes which associated with development and reproduction, respectively. These results were helpful for elucidating the molecular mechanism of muscle development of ovariectomized animal and the application of female castrated on fatting.

overall_design: Five female hybrid lambs with similar body weight at about 5 months old were randomly divided into treatment group (three lambs) and control group (two lambs). The goats in the treatment group were ovariectomized at the beginning of the experiment and the goats in control group were untreated. All the five goats were slaughtered at the 50th day.Two samples were derived from normal goat muscle and three samples were derived from ovariectomized goat muscle.Then total RNA was extracted from the five samples and sequenced by deep RNA sequencing method

first: Qing

last: Yang

first: Han

last: Xu

first: Lei

first: Chuanying

last: Pan

first: Chuzhao

last: Lei

first: Ruihua

last: Dang

first: Hong

last: Chen

first: Xianyong

last: Lan


title: Binding Profiles of Myc and RNA Polymerase II in Rat Neonatal Cardiomyocytes

city: Suita

first: Shuichiro

last: Higo

address: 2-2, Yamadaoka

department: Dpt. of Cardiovascular Medicine

institute: Osaka University

summary: During the progression of cardiac hypertrophy, cardiomyocytes accelerate RNA biogenesis to meet increasing metabolic demands under exogenous hypertrophic stimuli. We have elucidated the quantitative kinetics of RNA in c-Myc (Myc)-mediated hypermetabolic analytical model using cultured neonatal rat cardiomyocytes. Chromatin immunoprecipitation and high-throughput sequencing demonstrate that overexpressed Myc binds to a specific set of genes directly in cardiomyocytes and recruits RNA polymerase II to these genes.

overall_design: ChIP-sequence using rat neonatal cardiomyocytes transduced by adenovirus encoding Myc or LacZ control in duplicates.

first: Yuki

last: Masumura

first: Saki

last: Ishino


title: INO80 governs super-enhancer-mediated oncogenic transcription and tumor growth in melanoma [ChIP-seq_MiSeq]

status: Public on Jul 07 2016

city: Durham

first: Li

last: Wang

address: 111 T.W. Alexander Dr

institute: NIH

summary: Super-enhancers (SEs) are large genomic regions with high density of enhancer marks. In cancer, SEs are found near oncogenes and dictate cancer gene expression. However, how oncogenic SEs are regulated remains poorly understood. Here, we show that INO80, a chromatin remodeling complex, is required for SE-mediated oncogenic transcription and tumor growth in melanoma. The expression of Ino80, the SWI/SNF ATPase, is elevated in melanoma cells and patient melanomas compared to normal melanocytes and benign nevi. Furthermore, Ino80 silencing selectively inhibits melanoma cell proliferation, anchorage-independent growth, as well as tumorigenesis and tumor maintenance in mouse xenografts. Mechanistically, Ino80 occupies more than 90% of SEs, and its occupancy is dependent on transcription factors such as MITF and Sox9.  Ino80 binding reduces nucleosome occupancy and facilitates Mediator recruitment, thus promoting oncogenic transcription. Consistently, genes co-occupied by Ino80 and Med1 are specifically expressed in melanomas compared to melanocytes. Together, our results reveal an essential role of INO80-dependent chromatin remodeling in SE function, and suggest a novel strategy for disrupting SEs in cancer treatment.

overall_design: Human melanoma cell line A375 cells were infected with shNT or shIno80, and total RNA was extracted 2, 3, 4 days after infection. The RNA was submitted to RNA-Seq subsequently. For ChIP-Seq, either wild type A375 and SK-MEL-147, or A375 infected with shNT or shIno80, was used for ChIP-Seq for corresponding factors.

first: Bingying

last: Zhou

first: Brian

last: Bennett

first: Adrienne

last: Cox

first: Guang

last: Hu


title: INO80 governs super-enhancer-mediated oncogenic transcription and tumor growth in melanoma


title: Intergenerational consequences of gene-environment induced epigenetic dynamics at rDNA in the mouse

first: Robert

last: Lowe

relation:
SuperSeries of: GSE72607
SuperSeries of: GSE72608
SuperSeries of: GSE72609


title: INO80 governs super-enhancer-mediated oncogenic transcription and tumor growth in melanoma [ChIP-seq_NextSeq]


title: The CENP-B fission yeast homolog, ABP1, is involved in the repression of cryptic transcription from the Tf2 and rRNA genes repeat [ChIP-Seq_BGI]

first: Oscar

last: Reina Garcia

overall_design: ChIP-Seq peak calling of Pol2Ser5 in wild type and ABP1d mutant Spombe cells

first: Anne

last: Daulny

first: Fernando

last: Azorin


title: INO80 governs super-enhancer-mediated oncogenic transcription and tumor growth in melanoma [ATAC-seq]


title: Tissue homogeneity requires inhibition of unequal gene silencing during development

city: College Park

first: Antony

middle: Merlin

last: Jose

state: MD

address: Rm 2136, Bioscience Research Building

department: Cell Biology and Molecular Genetics

institute: University of Maryland College Park

summary: Multicellular organisms can generate and maintain homogenous populations of cells that make up individual tissues. But, cellular processes that can disrupt homogeneity and how organisms overcome such disruption are unknown. We found that ~100-fold differences in expression from a repetitive DNA transgene can occur between intestinal cells in C. elegans. These differences are caused by gene silencing in some cells and are actively suppressed by parental and zygotic factors such as the conserved exonuclease ERI-1. If unsuppressed, silencing can spread between some cells in embryos, but can be repeat-specific and independent of other homologous loci within each cell. Silencing can persist through DNA replication and nuclear divisions, disrupting uniform gene expression in developed animals. Analysis at single-cell resolution suggests that differences between cells arise during early cell divisions upon unequal segregation of an initiator of silencing. Our results suggest that organisms with high repetitive DNA content, which include humans, could employ similar developmental mechanisms to achieve and maintain tissue homogeneity.

overall_design: The strain HC566 with the sur-5::gfp repetitive transgene was subjected to paired-end DNA-Seq, single read DNA-Seq, and poly-A-selected RNA-Seq using the Illumina HiSeq1500 platform. Deletions and inversions present in the sur-5::gfp transgenic DNA were detected by mapping DNA-Seq reads to the plasmid pTG96 using TopHat2. Deletions (or spliced forms) and inversions present in RNAs made from the transgene were detected by mapping the RNA-Seq reads to pTG96 using TopHat2.


title: Dis3l2-Mediated Decay Is a Quality Control Pathway for Noncoding RNAs

city: Boston

first: Peng

last: Du

address: 1 Blackfan Circle

institute: Boston Children’s Hospital, Harvard Medical School

summary: Mutations in the 3’-5’ exonuclease DIS3L2 are associated with Perlman syndrome and hypersusceptibility to Wilms’ tumorigenesis. Previously, we found that Dis3l2 specifically recognizes and degrades uridylated pre-let-7 microRNA. However, the widespread relevance of Dis3l2-mediated decay of uridylated substrates remains unknown. Here we applied an unbiased RNA immunoprecipitation strategy to identify Dis3l2 targets in mouse embryonic stem cells. The disease-associated long noncoding RNA (lncRNA) Rmrp, 7SL, as well as several other Pol III-transcribed noncoding RNAs (ncRNAs) were among the most highly enriched Dis3l2-bound RNAs. 3’-uridylated Rmrp, 7SL, and snRNA species were highly stabilized in the cytoplasm of Dis3l2-depleted cells. Deep sequencing analysis of Rmrp 3’ ends revealed extensive oligouridylation mainly on transcripts with imprecise ends.  We implicate the TUTases Zcchc6/11 in the uridylation of these ncRNAs, and biochemical reconstitution assays demonstrate the sufficiency of TUTase-Dis3l2 for Rmrp decay. This establishes Dis3l2-Mediated Decay (DMD) as a quality control pathway that eliminates aberrant ncRNAs.obtaining over four billion bases of sequence from chromatin immunoprecipitated DNA, we generated genome-wide chromatin-state maps of mouse embryonic stem cells, neural progenitor cells and embryonic fibroblasts. We find that lysine 4 and lysine 27 trimethylation effectively discriminates genes that are expressed, poised for expression, or stably repressed, and therefore reflect cell state and lineage potential. Lysine 36 trimethylation marks primary coding and non-coding transcripts, facilitating gene annotation. Trimethylation of lysine 9 and lysine 20 is detected at satellite, telomeric and active long-terminal repeats, and can spread into proximal unique sequences. Lysine 4 and lysine 9 trimethylation marks imprinting control regions. Finally, we show that chromatin state can be read in an allele-specific manner by using single nucleotide polymorphisms. This study provides a framework for the application of comprehensive chromatin profiling towards characterization of diverse mammalian cell populations.

overall_design: Systematic identification of mutant Dis3l2-bound RNAs in mouse embryonic stem cells

first: Mehdi

last: Pirouz


title: Transcriptional response to salinity stress in chickpea

city: New Delhi

first: Mukesh

last: Jain

state: New Delhi

address: New Mehrauli Road

country: India

institute: Jawaharlal Nehru University

summary: In this study, we aim to present a global view of transcriptome dynamics during salinity stress in different chickpea genotypes. We generated about 600 million high-quality reads from 16 libraries (control and stress samples for two chickpea genotypes for salinity stress at two developmental stages) using Illumina high-throughput sequencing platform. We mapped the reads to the kabuli chickpea genome for estimation of their transcript abundance in different tissue samples. The transcriptome dynamics was studied by differential gene expression analyses between stress treatment and control sample for each genotype.

overall_design: We collected roots of chickpea genotypes from vegetative and reproductive stage plants subjected to control (water) and salinity (irrigated with 80 mM NaCl solution) stress. Total RNA isolated from these tissue samples was subjected to Illumina sequencing. The sequenced data was further filtered using NGS QC Toolkit to obtain high-quality reads. The filtered reads were mapped to annotated chickpea genome using TopHat and fragments per exon kilobase per million (FPKM) was calculated using Cufflinks software for each gene in all the sample to measure their gene expression. Differential expression analysis was performed using Cuffdiff software. The differentially expressed genes during various stress conditions were identified.

first: Rohini

last: Garg


title: Single Cell Expression Profiling Resolves the Transcriptional Programs of Early Mesoderm Diversification

first: Evangelia

last: Diamanti

address: Wellcome Trust / MRC Building, Hills Road

department: Haematology

summary: We analyzed 1,205 cells from the epiblast and nascent mesoderm of gastrulating mouse embryos by single cell RNA-seq, representing the first transcriptome-wide in vivo view of mammalian gastrulation. Based on the distribution of key marker genes and their spatiotemporal expression patterns within the embryo, we identified 10 cell clusters corresponding to the epiblast and developing mesodermal populations. This enabled us to explore the global gene expression dynamics associated with the induction of Brachyury, anterior-posterior patterning of the primitive streak and the earliest stages of blood development.

overall_design: Examination of Gata1 binding in Runx1-ires-GFP+/Gata1-mCherry+ (primitive erythroid) cells derived from 5 days of differentiation of ESCs towards haematopoietic cells

first: Antonio

last: Scialdone

first: Yosuke

last: Tanaka

first: Wajid

last: Jawaid

first: Victoria

last: Moignard

first: Nicola

middle: K

last: Wilson

first: Iain

last: Macaulay

first: John

last: Marioni

first: Berthold

last: Göttgens


title: Host transcriptional reprogramming in response to the rice bacterial blight pathogen Xanthomonas oryzae pv. oryzae strain BLS354

city: Ithaca

first: Adam

last: Bogdanove

state: NY

address: 334 Plant Science Building

department: Plant Pathology and Plant-Microbe Biology

institute: Cornell University

summary: We performed RNA-Seq of leaves of Oryza sativa L. ssp. japonica cv. Nipponbare 48 hours after inoculation with Xanthomonas oryzae pv. oryzicola strain BLS354, the causal agent of bacterial leaf streak. Results provide insight into the molecular basis of bacterial leaf streak, particularly the role of transcription activator-like effectors in the disease.

overall_design: Examination of mRNA levels in Oryza sativa L. ssp. japonica cv. Nipponbare leaves at 48 hours after inoculation with Xanthomonas oryzae pv. oryzicola  strain BLS354 with three biological replicates compared to three replicates of mock inoculated O. sativa as the control.

first: Katherine

last: Wilkins

first: Li

last: Wang

first: Aaron

middle: W

last: Hummel

first: Andres

last: Cernadas


title: The CENP-B fission yeast homolog, ABP1, is involved in the repression of cryptic transcription from the Tf2 and rRNA genes repeat [smallRNA-Seq]

first: Oscar

last: Reina Garcia

overall_design: Strand-specific small RNA-Seq of wild type and ABP1d Spombe cells

first: Anne

last: Daulny

first: Fernando

last: Azorin


title: Transcriptional response to drought stress in chickpea

first: Mukesh

last: Jain

summary: In this study, we aim to present a global view of transcriptome dynamics during drought stress in different chickpea genotypes. We generated about 800 million high-quality reads from 14 libraries (control and stress samples for two chickpea genotypes for drought  stress at two developmental stages) using Illumina high-throughput sequencing platform. We mapped the reads to the kabuli chickpea genome for estimation of their transcript abundance in different tissue samples. The transcriptome dynamics was studied by differential gene expression analyses between stress treatment and control sample for each genotype.

overall_design: We collected roots of chickpea genotypes from vegetative and reproductive stage plants subjected to control (water) and drought (water withhelding till transpiration ratio reached 0.2) stress. Total RNA isolated from these tissue samples was subjected to Illumina sequencing. The sequenced data was further filtered using NGS QC Toolkit to obtain high-quality reads. The filtered reads were mapped to annotated chickpea genome using TopHat and fragments per exon kilobase per million (FPKM) was calculated using Cufflinks software for each gene in all the sample to measure their gene expression. Differential expression analysis was performed using Cuffdiff software. The differentially expressed genes during various stress conditions were identified.

first: Rohini

last: Garg


title: ZNF224 binding profiles in HEK293 cells

city: Seoul

first: Tae-Young

last: Roh

state: --- Select One ---

address: 52 Ewhayeodae-gil, Seodaemun-gu

department: Life Sciences

country: South Korea

institute: Ewha Womans University

summary: ZNF224 is a Kruppel-associated box-containing zinc-finger protein which represses gene transcription by interacting with the KAP-1, WT1, PRMT5, and DEPDC1 co-repressors. In this study, we have found that ZNF224 functions as an oncogene in MCF7 cells. ZNF224 overexpression increases colony formation, cell growth, and cell survival against camptothecin (CPT) compared to control, and vice versa, upon siRNA knockdown of ZNF224. To examine the mechanism of ZNF224 as an oncogene, first we tried to identify DNA binding element (DBE) of ZNF224 through ChIP-sequencing, and found that ZNF224 could bind to elements containing 5'-CAGC-3' sequence, which was further confirmed by ELISA, SPR, qPCR, and luciferase activity assay. Based on these results, we found that ZNF224 binds to the MIR663A promoter. ZNF224 increased MIR663A transcription, which in turn binds to 3' UTR of p53 and p21 to decrease their expression. MIR663A antagonist abolished ZNF224-mediated suppression of p21 and p53, resulting in the enhanced apoptosis by CPT. The analyses using human breast ductal carcinoma tissues exhibited that the expression of ZNF224 and MIR663A was increased in cancer compared to its neighboring non-cancer region. Consequently, ZNF224 increases cell survival and decreases apoptosis by decreasing the expression of p53 and p21 via increasing the expression of MIR663A as a transcriptional activator. Taken together, we identified and characterized the DNA binding element of ZNF224 and its target genes, which provide novel insight into the role of ZNF224 in breast cancer.

overall_design:
The information of genome-wide ZNF224 binding sites in HEK293 cells transiently expressing the protein was generated by deep sequencing using Illumina GAIIx.

Note: The data for the sample immunoprecipitated with normal mouse IgG antibody was not provided by the submitter.

first: Tae

middle: Y

first: Chae

last: Lim

first: Sang

last: Park

first: Hong

middle: S

last: Kim


title: Genome-wide analysis of gene expression in MLL translocation transformed mouse leukemia cell lines

city: Ann Arbor

first: Andrew

middle: G.

last: Muntean

state: Michigan

address: 1301 Catherine St.

department: Pathology

institute: University of Michigan

summary: The purpose of this study is to investigate the transcriptional programs as it relates to disease latency initiated by different MLL fusion proteins, including: MLL-AF1p, MLL-AF6, MLL-Gas7, MLL-AF9 and MLL-ENL. Leukemia cell lines were established by transforming kit+ mouse bone marrow cells with retroviruses coding MLL-AF1p, MLL-AF6, MLL-Gas7, MLL-AF9 or MLL-ENL. At early phase after the cell lines were established, cells growing at exponential phase (cell density at 0.5~1x106/ml) were harvested for RNA extraction and sequencing purpose.

overall_design: Sequencing is performed on total RNA isolated from mouse leukemia cell lines generated from kit+ mouse bone marrow cells transduced with various MLL fusion proteins and is compared to control total RNA isolated from kit+ mouse bone marrow cells.

first: Lili

last: Chen

first: Yuqing

last: Sun

first: Jingya


title: Transcriptomic responses to Deepwater Horizon oil in mahi-mahi (Coryphaena hippurus) embryos reveals time and oil-dependent linkages between molecular initiating events and developmental toxicity

city: Charleston

first: Gary

last: Hardiman

state: SOUTH CAROLINA

address: 135 Cannon Street, Suite 303 MSC835

institute: MUSC

summary:
Purpose:To help identify molecular mechanisms and pathways potentially involved in the developmental toxicity for fish exposed to Deepwater Horizon (DWH) oil, transcriptomic profiles in mahi-mahi (Coryphaena hippurus) embryos exposed to different DWH oils (source and artificially weathered oil) were evaluated at different critical windows of development using High Throughput Sequencing (HTS).
Methods:Total mRNA profiles of 24, 48, 96 hpf mahi-mahi larvae after slick and source oil exposure were generated by deep sequencing, in triplicate, using Illumina HiSeq2500. qRT–PCR validation was performed using SYBR Green assays.
Results: Exposure to slick oil induced more pronounced changes in gene expression over time than did exposure to source oil. Predominant transcriptomic responses included alteration of E1F2 signaling, steroid biosynthesis, ribosome biogenesis, perturbation in eye development and peripheral nervous, and activation of P450 pathway.  Comparisons of changes of cardiac / Ca2+-associated genes with phenotypic responses revealed reduced heart rate and increased pericardial edema in larvae exposed to slick oil but not source oil.

overall_design: Total mRNA profiles of 24, 48, 96 hpf mahi-mahi larvae after slick and source (mass) oil exposure were generated by deep sequencing, in triplicate, using Illumina HiSeq2500.

first: Elvis

middle: G

last: Xu

first: Edward

middle: M

last: Mager

first: Martin

last: Grosell

first: Christina

last: Pasparakis

first: Lela

last: Schlenke

first: John

last: Stieglitz

first: Sean

last: Courtney

first: Daniel

last: Benetti

first: Graciel

last: Diamante

first: Juliane

last: Freitas

last: Hazard

last: Schlenk


title: INO80 governs super-enhancer-mediated oncogenic transcription and tumor growth in melanoma [RNA-seq]

first: Li

last: Wang

first: Bingying

last: Zhou

first: Brian

last: Bennett

first: Adrienne

last: Cox

first: Guang

last: Hu


title: High-resolution analysis of the m-xylene/toluene biodegradation subtranscriptome of Pseudomonas putida mt-2

city: Cantoblanco

first: Juan

middle: Carlos

last: Oliveros

state: Madrid

address: Darwin 3

institute: CNB, CSIC

type: Expression profiling by genome tiling array

overall_design: Refer to individual Series


title: Larval application of sodium channel homologous dsRNA restores pyrethroid insecticide susceptibility in a resistant adult mosquito population

status: Public on Jul 06 2016

city: Caesarea

first: Eyal

last: Maori

address: 17 Alon Hatavor street POB 3164

institute: Forrest Innovations Ltd

summary:
Mosquitoes host and pass on to humans a variety of disease-causing pathogens such as infectious viruses and other parasitic microorganisms. The emergence and spread of insecticide resistance is threatening the effectiveness of current control measures for common mosquito vector borne diseases, such as malaria, dengue and Zika. Therefore, the emerging resistance to the widely used pyrethroid insecticides is an alarming problem for public health. Among the new approaches implemented for pest control, one of the most promising is RNA interference (RNAi).
The aim of this study was to provide a feasible RNAi solution that can be applied on wild pyrethroid resistant mosquito populations in the near future. To achieve this, high dsRNA efficacy at economic quantities is required. It is recognized that the sodium channel transcript variability governs its functional diversity including the emergence of insecticide resistance. Therefore, to maximize the RNAi effect, we tiled a number of overlapping dsRNA constructs that together target about half of the voltage-gated sodium channel (VGSC) transcript variants annotated in this work. This strategy provided a refined dsRNA trigger that increased mortality with a three-fold decrease in dsRNA amounts compared to the primary VGSC dsRNA construct. Thus, we demonstrated the use of RNA interference (RNAi) to increase susceptibility of adult mosquitoes to a widely used pyrethroid insecticide.

overall_design: Small RNA sequences from 5 mosquitoes treated with Random or VGSC dsRNAs were generated using Illumina HiSeq 2500.

first: Ana

last: Dalla Bona

first: Rodrigo

middle: F

last: Chitolina

first: Marise

last: Lopes Fermino

first: Lisiane

last: de Castro Poncio

first: Avital

last: Weiss

first: José

middle: B

last: Pereira Lima

first: Nitzan

last: Paldi

first: Emerson

last: Soares Bernardes

first: Jonathan

last: Henen


title: RAG1 targeting in the genome is dominated by chromatin interactions mediated by the non-core regions of RAG1 and RAG2

city: Safed

first: Yaakov

last: Maman

address: Henrietta Szold 8

department: Azrieli Faculty of Medicine

institute: Bar-Ilan University

summary: The RAG1/RAG2 endonuclease initiates V(D)J recombination at antigen receptor loci but also binds to thousands of places outside of these loci.  RAG2 localizes directly to lysine 4 trimethylated histone 3 (H3K4me3) through a PHD finger.  The relative contribution of RAG2-dependent and RAG1-intrinsic mechanisms in determining RAG1 binding patterns is not known.  Through analysis of deep RAG1 ChIP-seq data, we provide a quantitative description of the forces underlying genome-wide targeting of RAG1.  Surprisingly, sequence-specific DNA binding contributes minimally to RAG1 targeting outside of antigen receptor loci.  Instead, RAG1 binding is driven by two distinct modes of interaction with chromatin:  the first is driven by H3K4me3, promoter-focused, and dependent on the RAG2 PHD, and the second is defined by H3K27Ac, enhancer-focused, and dependent on "non-core" portions of RAG1.  Based on this and additional chromatin and genomic features, we formulated a predictive model of RAG1 targeting to the genome.  RAG1 binding sites predicted by our model correlate well with observed patterns of RAG1-mediated breaks in human pro-B acute lymphoblastic leukemia. Overall, this study provides an integrative model for RAG1 genome-wide binding and off-target activity, and reveals a novel role for the RAG1 non-core region in RAG1 targeting.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: ChIP-seq profiles of RAG1 from mouse thymocytes, and H3K27Ac from human REH cell line

first: Grace

last: Teng

first: Rashu

last: Seth

first: Steven

last: Kleinstein

first: David

last: Schatz


title: High-resolution analysis of the m-xylene/toluene biodegradation subtranscriptome of Pseudomonas putida mt-2 [RNA-seq]

summary: Pseudomonas putida mt-2 metabolizes m-xylene and other aromatic compounds through the enzymes encoded by the xyl operons of the TOL plasmid pWW0 along with other chromosomally-encoded activities. Tiling arrays of densely overlapping oligonucleotides were designed to cover every gene involved in this process, allowing dissection of operon structures and exposing the interplay of plasmid and chromosomal functions. All xyl sequences were transcribed in response to aromatic substrates and the 3'-termini of both upper and lower mRNA operons extended beyond the ir coding regions, i.e., the 3’-end of the lower operon mRNA penetrated into the convergent xylS regulatory gene. Furthermore, xylR mRNA for the master m-xylene responsive regulator of the system was decreased by aromatic substrates, while the cognate upper operon mRNA was evenly stable throughout its full length. RNA-seq confirmed these data at a single-nucleotide level and refined the formerly misannotated xylL sequence. The chromosomal ortho route for degradation of benzoate (the ben, cat clusters and some pca genes) was activated by this aromatic, but not by the TOL substrates, toluene or m-xylene. We advocate this scenario as a testbed of natural 16 retroactivity between a pre-existing metabolic network and a new biochemical pathway implanted through gene transfer.

overall_design: Genome Analyzer IIx system (1x75bp) was used for sequencing total RNA extracted from P. putida (mt-2) containing the plasmid pWW0, in two different physiological states (treated with m-xylene and in C-runout condition).

first: Juhyun

last: Kim

first: Danilo

last: Pérez-Pantoja

first: Rafael

last: Silva-Rocha

middle: C

first: Victor

last: de Lorenzo