title: Differentially expressed genes in the head of the 2nd instar pre-molting larvae of the nm2 mutant of the silkworm, Bombyx mori

city: Zhenjiang

first: Pingyang

last: Wang

state: Jiangsu province

address: Nanxu street

department: School of Biotechnology

institute: Jiangsu University of Science and Technology

summary: Molting is an important physiological process in the larval stage of Bombyx mori and is controlled by various hormones and peptides. The silkworm mutant that exhibits the phenotype of non-molting in the 2nd instar (nm2) is incapable of molting in the 2nd instar and dies after seven or more days. The ecdysone titer in the nm2 mutant is lower than that in the wildtype, and the mutant can be rescued by feeding with 20E and cholesterol. The results of positional cloning indicated that structural alteration of BmCPG10 is responsible for the phenotype of the nm2 mutant. To explore the possible relationship between BmCPG10 and the ecdysone titer as well as the genes affected by BmCPG10, digital gene expression (DGE) profile analysis was conducted in the nm2 mutant, with the wildtype strain C603 serving as the control. The results revealed 1727 differentially expressed genes, among which 651 genes were upregulated and 1076 were downregulated in nm2. BLASTGO analysis showed that these differentially expressed genes were involved in various biological processes, cellular components and molecular functions. KEGG analysis indicated an enrichment of these differentially expressed genes in 240 pathways, including metabolic pathways, pancreatic secretion, protein digestion and absorption, fat digestion and absorption and glycerolipid metabolism. To verify the accuracy of the DGE results, quantitative reverse transcription PCR (qRT-PCR) was performed, focusing on key genes in several related pathways, and the results were highly consistent with the DGE results. Our findings indicated significant differences in cuticular protein genes, ecdysone biosynthesis genes and ecdysone-related nuclear receptors genes, but no significant difference in juvenile hormone and chitin biosynthesis genes was detected. Considering the physiological characteristics of nm2 together with the results of DGE analysis, we speculate that there may be a relationship between BmCPG10 and ecdysone. In the mutant, the original function of BmCPG10 was lost due to the change in its protein structure. It appeared that BmCPG10 might influence the synthesis of ecdysone by controlling the production of substrate cholesterol. However, under a low titer of ecdysone, the expression of BmCPG10 was affected, as one of a series of effectors of the ecdysone signaling pathway. Blocking ecdysone biosynthesis resulted in non-molting silkworms and the formation of the nm2 mutant.

first: Qiaoling

last: Zhao


title: Transcriptome analysis of mouse IgG1 memory B cell subsets

status: Public on Jul 03 2017

city: Singapore

first: Vipin

last: Narang

address: Immunos #04-01, 8A Biomedical Grove, Singapore-138648

country: Singapore

institute: Singapore Immunology Network (SIgN)

type: Expression profiling by high throughput sequencing

summary: IgE plays an essential role in the pathogenesis of allergies and its production is strongly regulated. A transient IgE germinal center phase and lack of IgE memory cells limit the generation of pathogenic IgE, but this can be overcome by sequential switching of IgG1 cells to IgE. We investigated which population of IgG1 cells can give rise to IgE-producing cells in memory responses. We identified three populations of IgG1 memory B cells (DP:CD73+CD80+, SP:CD73-CD80+, DN:CD73-CD80-) that generate IgE plasma cells of high or low affinity, but none gives rise to IgE germinal center cells or IgE memory cells. The two memory IgG1 populations differ however in their ability to differentiate into IgG1 plasma cells and germinal center cells, and to expand the IgG1 memory B cell pool. To explore the molecular mechanisms that may explain the distinct functions of IgG1 memory B cell subsets we compared their expression by transcriptome analysis using next generation sequencing.

overall_design: mRNA profiles of quadruplicates of double positive (DP:CD73+CD80+), single positive (SP:CD73-CD80+), double negative (DN:CD73-CD80-) IgG1 memory B cells along with IgG1 germinal center (GC) cells and naïve B cells were generated using Illumina high throughput sequencing.

first: Jin-Shu

last: He

first: Maria

middle: A

last: Curotto de Lafaille


title: Amygdala transcriptome in rats prenatally exposed to valproic acid

city: Atlanta

first: Gregory

middle: K

last: Tharp

state: GA

address: 954 Gatewood Dr

department: Developmental and Cognitive Neuroscience

country: USA

institute: Yerkes National Primate Research Center

summary: The amygdala controls socioemotional behavior and has consistently been implicated in the etiology of Autism Spectrum Disorder (ASD). Precocious amygdala development is commonly reported in ASD youth with the degree of overgrowth positively correlated to the severity of ASD symptoms. However, surprisingly little is known about the cellular, molecular, or genetic changes that occur in the amygdala over development in ASD individuals or rodent models. We examined abnormalities in gene expression in the amygdala and socioemotional behavior across development in the valproic acid (VPA) rat model of ASD.

overall_design: Examination of unilateral amygdala micropunches from P10 and P21 male rats prenatally exposed to either saline or valproic acid.

first: Catherine

last: Barrett

first: Donald

last: Rainnie

first: Greg


title: α-ketoglutarate orchestrates macrophage activation through metabolic and epigenetic reprogramming

city: Epalinges

first: Ping-Chih

last: Ho

state: Vaud

address: Ch. des Boveresses 155

department: Department of Fundamental Oncology

country: Switzerland

institute: University of Lausanne

summary: We conducted gene expression analysis of naive and polarized macrophages from wild type C57BL6/J mice. In this project, we also compared how glutamine deprivation and production of alpha-ketoglutarate during LPS priming affects gene expression profiles in bone marrow-derived macrophages.

overall_design: Find unbiased transcriptomic changes affected by glutamine metabolism in endotoxin tolerant macrophage

first: Pu-Ste

last: Liu

first: Haiping

first: Xiaoyun

last: Li

first: Tung

last: Chao

first: Tony

last: Teav

first: Stefan

last: Christen

first: Giusy

last: Di Conza

first: Wan-Chen

last: Cheng

first: Chih-Hung

last: Chou

first: Magdalena

last: Vavakova

first: Charlotte

last: Muret

first: Koen

last: Debackere

first: Massimiliano

last: Mazzone

first: Hsien-Da

last: Huang

first: Sarah-Maria

last: Fendt

first: Julijana

last: Ivanisevic


title: Genome-wide identification of H3K9ac enriched regions in inner stem tissue of V2 seedlings and husks (maize B73) [ChIP-Seq]

city: Amsterdam

first: Maike

last: Stam

address: Science Park 904

department: Swammerdam Institute for Life Sciences

country: Netherlands

institute: University of Amsterdam

type: Genome binding/occupancy profiling by high throughput sequencing

summary:
Most cells in a multicellular organism carry the same genetic information; however, they can still differentiate to take up different functions in the organism.  This differentiation process involves tight regulation of gene expressions by regulatory sequences including transcriptional enhancers.  Enhancers can be located distantly from their target genes; this characteristic makes it difficult to identify enhancers only using experimental approaches.
Importantly, enhancers carry characteristic chromatin signatures such as low DNA methylation, high chromatin accessibility and histone modifications such as H3K9ac and H3K27ac.  Computational enhancer identification approaches often use machine learning methods in combination with a number of experimental genome-wide datasets to identify key enhancers features and scans the whole genome.
Limited knowledge on plant enhancers restricts us in available approaches we can use to perform genome-wide enhancer prediction in plant species.  In this work, we have integrated genome-wide low DNA methylation, chromatin accessibility and H3K9ac data from two tissues, inner stem tissue (V2-IST) from seedlings at the V2 stage and husk tissue, in the crop plant Zea mays.  This study identified approximately 1,400 candidate enhancers.
By comparing data from two different tissues, we determined tissue-specificity of the candidate enhancers.  We also have predicted putative target genes using gene expression data taking an advantage of having data from two tissues.

overall_design: Examination of H3K9ac in 2 tissue types.

first: Blaise

last: Weber

first: Rurika

last: Oka

first: Franziska

last: Turck


title: R-Spondin chromosome rearrangements drive Wnt-dependent tumor initiation and maintenance in the intestine

status: Public on Jul 01 2017

city: NEW YORK

first: Lukas

middle: Edward

last: Dow

state: New York

address: 413 East 69th Street, BB1318

department: Medicine

institute: Weill Cornell Medicine

summary: Defining the genetic drivers of cancer progression is key to understanding disease biology and developing effective targeted therapies. Chromosome rearrangements are a common feature of human malignancies, but whether they represent bona fide cancer drivers and therapeutically actionable targets, requires functional testing. Here, we describe the generation of transgenic, inducible CRISPR-based mouse systems to engineer and study recurrent colon cancer-associated EIF3E-RSPO2 and PTPRK-RSPO3 chromosome rearrangements in vivo. We show that both Rspo2 and Rspo3 fusion events are sufficient to initiate hyperplasia and tumor development in vivo, without additional cooperating genetic events. Rspo fusion tumors are entirely Wnt-dependent, as treatment with an inhibitor of Wnt secretion, LGK974, drives rapid tumor clearance from the intestinal mucosa without effects on normal intestinal crypts. Together, our study provides direct evidence that endogenous Rspo2 and Rspo3 chromosome rearrangements can initiate and maintain tumor development, and indicate a viable therapeutic window for LGK974 treatment of RSPO-fusion cancers.

overall_design: Examination of transcriptional changes associated with RSPO2 and RSPO3 gene fusions in intestinal organoid model.

first: Teng

last: Han


title: Repression of stress-induced LINE-1 expression protects cancer cell populations from lethal drug-exposures [ATAC-Seq]

city: South San Francisco

first: Suchit

last: Jhunjhunwala

state: CA

address: 1 DNA Way, MS-444A

institute: Genentech

summary: Establishing and maintaining phenotypic heterogeneity within cell and organismal populations is an evolutionarily conserved strategy that ensures survival of the population following stressful exposures. We previously identified a transient, reversible, drug-tolerant cancer cell subpopulation that survives otherwise lethal drug exposures. Here we show that these drug-tolerant persisters (DTPs) assume a highly heterochromatic state, which requires factors that modify or bind trimethylated H3 lysine 9 (H3K9me3). The increased H3K9me3 in DTPs is largely restricted to evolutionarily young Long Interspersed Repeat elements (LINEs). This transcriptionally repressive state, which decreases the expression of these retrotransposable elements, is critical for DTP survival, and disruption of this heterochromatic state results in re-expression of LINE elements and ablation of this subpopulation. Together, these findings establish a role for epigenetic silencing of transposable elements as a population survival strategy to maintain genomic integrity in subpopulations of cancer cells during lethal drug exposures.

overall_design: Investigation of chromatin structure by ATACseq in 1 cell type, 7 different conditions (heterogenous parental population, drug tolerant cells derived from the heterogenous parental population, drug tolerant cells following TSA-treatment, 2 subpopulations (ALDH_High and ALDH_Low) obtained from the heterogeneous parental population before or after drug treatment)

first: Gulfem

middle: D

last: Guler

first: Charles

last: Tindell

first: Marie

last: Classon


title: Drug-tolerant cancer cell persisters survive lethal exposures by silencing transposable elements [ChIP-Seq]

overall_design: Investigation of 2 histone modifications by ChIPseq in 1 cell type in control or drug-treated samples (2 treatments).


title: Genome-wide maps of gene transcription and chromatin state in mouse Setdb1 wildtype and CK-cre conditional knockout brain.

city: New York

first: Eddie

last: Loh

address: 1425 Madison Avenue

department: Department of Neuroscience

institute: Icahn School of Medicine at Mount Sinai

summary: We report locus-specific disintegration of megabase-scale chromosomal conformations after Kmt1e/Setdb1 histone H3-lysine 9 methyltransferase ablation in mouse brian. Histone modification, CCCTC-binding factor (CTCF), transcriptome and ‘3D genome’ (in situ Hi-C) mappings each identified a uniquely affected ~1Mb domain on chromosome 18 in cortical and striatal neurons, encompassing the Protocadherin cell adhesion gene clusters (cPcdh). Setdb1-deficient neuronal genomes showed de novo CTCF occupancies at thousands of cryptic binding sites and locus-specific disintegration of 1Mb cPcdh higher order chromatin. Loss of long-range repressive chromosomal conformations triggered massively increased proportions of neurons expressing specific cPcdh genes due to relaxation of stochastic constraint. Setdb1, shielding mature neuronal genomes from excess CTCF binding, maintains TAD integrity essential for mouse brain function.

overall_design: RNAseq, histone H3K9me3 ChIPseq, H3K27ac ChIPseq, CTCF ChIPseq, and in situ HiC on anti-NeuN+ neuronal nuclei from adult Setdb1 WT and KO cortex

first: Y

last: Jiang

first: E

first: P

last: Rajarajan

first: S

last: Chandrasekaran

last: Akbarian


title: Ten-Eleven Translocation 2 regulates adult neurogenesis through modulating 5mC oxidation dynamics at distinct regulatory elements

first: Bing

last: Yao

address: 615 Michael St. Rm 323

department: Human Genetics

institute: Emory University

type: Methylation profiling by high throughput sequencing

summary: Emerging evidence suggests that various epigenetic mechanisms play important roles in regulating adult neurogenesis. Ten-Eleven Translocation (Tet) proteins, the 5mC dioxygenases, could convert 5mC stepwise to 5-hydroxymethylcytosine (5hmC) and its further oxidation products, which constitute active DNA demethylation pathway. Here we show that unlike embryonic stem cells, 5hmC is acquired upon differentiation of adult neural stem cells (NSCs). The loss of Tet2 in proliferating NSCs significantly decreases their 5hmC abundance and partially blocks the acquisition of 5hmC upon differentiation, leading to the increased proliferation and reduced differentiation both in vitro and in vivo.  This impaired neurogenesis process results in a defect of learning and memory as well as depressive behavior in Tet2-/- animals. Biochemical and epigenomic analyses reveal that transcription factor Forkhead box O3 (Foxo3a) physically interacts with Tet2 and orchestrates with various forms cytosine modifications to regulate different cohorts of gene expression through distinct mechanisms. These data together establish a novel and fundamental role of Tet2 in neurogenesis by coordinating with Foxo3a to epigenetically regulate the expression of key genes involved in neurogenesis.

overall_design: Examine the roles of Tet2, Foxo3a and cytosine modifications in the neurogenesis process.


title: In vitro differentiation of human embryonic stem cells into ovarian follicle-like cells

status: Public on Jul 04 2017

city: Beijing

first: Kehkooi

last: Kee

state: Beijing

address: Room D110, Medical Science Building, School of Medicine, Tsinghua University

department: Basic Medical Sciences

country: China

institute: Tsinghua University

summary: Understanding the unique mechanisms of human oogenesis necessitates the development of an in vitro system of stem cell differentiation into oocytes. Specialized cell types and organoids have been derived from human pluripotent stem cells in vitro, but generating a human ovarian follicle remains a challenge. Here we report that human embryonic stem cells (hESCs) can be induced to differentiate into ovarian follicle-like cells in vitro. First, we find that two RNA-binding proteins specifically expressed in germ cells, DAZL and BOULE, regulate the exit from pluripotency and entry into meiosis. By expressing DAZL and BOULE with recombinant human GDF9 and BMP15, these meiotic germ cells are further induced to form ovarian follicle-like cells (FLCs), including oocytes and granulosa cells. This robust in vitro differentiation system will allow the study of the unique molecular mechanisms underlying human pluripotent stem cell differentiation into late PGCs, meiotic germ cells, and ovarian follicles.

overall_design: Including 6 samples，4 controls: ES_1, ES_2, SDE_1, SDE_2; 2 samples: FLC_1 (HSF6), FLC_2 (H9)

first: Dajung

last: Jung

first: Jie

last: Xiong

first: Min

last: Ye

first: Xunsi

last: Qin

first: Lin

last: Li

first: Shunfeng

last: Cheng

first: Mengyuan

last: Luo

first: Jia

last: Peng

first: Ji

last: Dong

first: Fuchou

last: Tang

first: Wei

last: Shen

first: Martin

middle: M

last: Matzuk


title: Trans-Generational Hormesis and the Inheritance of Aging Resistance

first: Jahnavi

last: Suresh

state: Singapore

address: 14 Medical Drive

department: Science

institute: Yale-NUS college

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

overall_design: Refer to individual Series


title: Trans-Generational Hormesis and the Inheritance of Aging Resistance [RNA-seq]

summary: Animals respond to dietary changes by adapting their metabolism to available nutrients through insulin and insulin-like growth factor signalling.  Restricting calorie intake generally extends life and health span, but Drosophila fed non-ideal sugars such as galactose are stressed and have shorter life spans.  Here, we report that although these flies have shorter life spans, their offspring show significant life extension if switched to a normal sugar (glucose) diet.  We define this as TGH or trans-generational hormesis, a beneficial effect that comes from a mild stress.  We trace the effects to changes in stress responses in parents, ROS production, effects on lipid metabolism, and changes in chromatin and gene expression.  We find that this mechanism is similar to what happens to the long lived Indy mutants on normal food, but surprisingly find that Indy is required for life span extension for galactose fed flies.  Indy mutant flies grown on galactose do not live longer as do their siblings grown on glucose, rather overexpression of Indy rescues lifespan for galactose reared flies.  We define a process where sugar metabolism can generate epigenetic changes that are inherited by offspring, providing a mechanism for how transgenerational nutrient sensitivities are passed on.

overall_design: Analyses of two differen sugar substrate fed dorosopila fly transcriptome with two replicates for each condition

first: Ng

middle: L

last: Fang

first: Krishna

last: Chaithanya

first: Xiao

last: Linfan

first: Tuan

middle: Z

last: Tan

first: Jan

last: Gruber

first: Nicholas

middle: S

last: Tolwinski


title: Trans-Generational Hormesis and the Inheritance of Aging Resistance [ChIP-seq]


title: Overexpression of NFIB and YBX1 in MCF-7 cells

city: Cambridge

first: Kerstin

last: Meyer

address: Robinson Way

department: Cancer Research UK Cambridge Institute

country: United Kingdom

institute: University of Cambridge

summary: Studying transcription factor (TF) interactions and gene regulatory networks in breast cancer, we have recently identified two distinct and opposing clusters of TFs associated with estrogen receptor-positive and -negative breast cancer and breast cancer risk. The relative activity of these two groups of TFs has a dramatic effect on patient outcomes and is likely to influence the phenotypic plasticity observed in breast cancer. We have identified two novel interactors (NFIB and YBX1) of the estrogen receptor (ESR1) using Rapid Immunoprecipitation Mass Spectrometry of Endogenous Proteins (RIME), co-immunoprecipitation and microscopy experiments. Both NFIB and YBX1 are members of the group of risk TFs that oppose the activity of the risk TFs associated with estrogen receptor-positive disease, and we have demonstrated that they both repress the transcriptional activity of ESR1. Here, we examine the effect of NFIB and YBX1 overexpression on the transcriptome of an estrogen receptor-positive breast cancer cell line to see if these risk TFs are able to repress the ESR1 regulon and drive cells towards a less estrogen-dependent phenotype.

overall_design: Data consists of three different cell lines (MCF-7 parental, MCF-7 stably overexpressing FLAG-tagged NFIB, and MCF-7 stably overexpressing FLAG-tagged YBX1), analysed to detect gene expression differences. Each cell line was tested in triplicate (biological replicates consisting of three separate clones of stable cells).

first: Tom

last: Campbell


title: Glucose impairs tamoxifen sensitivity modulating CTGF in breast cancer cells

city: Naples

first: Valerio

last: Costa

state: Italy

address: Via P. Castellino, 111

department: Institute of Genetics and Biophysics

country: Italy

institute: National Research Council

summary: Metabolic diseases, including type 2 diabetes and obesity are relevant negative prognostic factor in patients with breast cancer (BC). We have investigated the mechanisms through which elevated glucose levels affect tamoxifen sensitivity of estrogen receptor positive (ER+) BC cells. We found that MCF7 BC cell sensitivity to tamoxifen was 2-fold reduced in 25mM glucose (HG), a concentration mimicking hyperglycaemia, compared to 5.5 mM glucose (LG), resembling normal fasting glucose levels in humans. Shifting MCF7 cells from HG to LG ameliorated their responsiveness to tamoxifen. RNA-Sequencing revealed that glucose modified the transcriptome of MCF7 cells. In particular, cell cycle-related genes were affected by glucose. Combining gene specific knockdown and treatment with human recombinant proteins, we identified the Connective Tissue Growth Factor (CTGF) as glucose-induced factor able to reduce MCF7 cell sensitivity to tamoxifen. Moreover, we found that both CTGF expression levels and tamoxifen responsiveness were enhanced co-culturing MCF7 cells with human adipocytes through an Interleukin-8 (IL8)-mediated mechanism. Indeed, IL8 inhibition reduced CTGF levels and rescued tamoxifen sensitivity in MCF7 cells. Interestingly, CTGF immuno-detection in bioptic specimens obtained from women with ER+ BC correlated with distant metastases (P-value = 0.000), hormone therapy resistance (P-value = 0.000), reduced overall (P-value = 0.051) and disease free survival (P-value = 0.000). Thus, glucose affects tamoxifen responsiveness directly modulating CTGF in BC cells, and indirectly promoting the adipocytes’ release of IL8. Both CTGF and IL8 may represent potential targets in novel therapeutic strategies to increase tamoxifen sensitivity.

overall_design: The gene expression profile of MCF7 cells grown in high glucose and then shifted in low glucose (HG→LG; n=1) were compared to MCF7 cells grown in high glucose (HG; n=1).

first: Maria

middle: R

last: Ambrosio

first: Alfredo

last: Ciccodicola

first: Pietro

last: Formisano


title: RNA-biotin based pull down assay with Hela Nuclear Extract followed by RNA-seq

city: guangzhou

first: chengguo

last: yao

address: No. 74 zhongshan 2rd road

department: school of medicine

institute: sysu

summary: We aimed to discover trans-acting RNA molecules involved in mRNA 3’ processing. We reasoned that, if there exist such functional RNAs, they must directly associate with the key machinery responsible for mRNA 3’ processing. Therefore, it would be of great value to comprehensively identify RNAs interacting with pre-mRNA 3’ processing complex. To this goal, we took advantage of previously well-characterized system combined with high-throughput sequencing to investigate the target RNAs at the transcriptomic level.  Briefly, we used polyA site (PAS) RNA substrates, SV40 late (SVL), and corresponding control RNAs with point mutation (U to C) at the highly conserved cis-element AAUAAA. RNA substrates were first biotinylated at the 3’ end, and then bound to the streptavidin magnetic beads. After incubation with Hela Nuclear Extract (NE) under polyadenylation condition, the two wild type RNA substrates could specifically recruit mRNA 3’ processing factors in NE for complex assembly. The purification of the protein complex and its interacting RNAs were performed using biotin-streptavidin pull-down. We extracted RNAs from the pull-down sample, prepared the strand-specific RNA-Seq libraries and submitted them for deep-sequencing.

overall_design: SVL PAS and the point mutant RNA substrates RIP-seq were performed. Trimmed reads were mapped to human genome, fold enrichment were calculated based on the reads counts.

first: Chunliu

last: Huang

first: Junjie

last: Shi

first: Yibin

last: Guo

first: Weijun

first: Siqi

last: Ming

first: Xingui

last: Wu

first: Rui

last: Zhang

first: Junjun

last: Ding

last: Zhao

first: Jie

last: Jia

first: Xi

first: Peng

last: Xiang

first: Yongsheng

first: Chengguo

last: Yao


title: Fip1 iCLIP-seq in Hela cells without treatment or treated with NC ASO, snoRD50a ASO

summary: We aimed to compare the Fip1/RNA interaction at transcriptomic level upon snoRD50a knockdown. To this goal, we utilized Fip1 iCLIP-seq protocol in both control and snoRD50a KD hela cells.

overall_design: Fip1 iCLIP-seq were performed in control and snoRD50a KD hela in Hela cells

first: Wei


title: Using hESCs to Probe the Interaction of CDKAL1 and MT1E, Two GWAS identified Diabetes Associated Genes

first: Shuibing

last: Chen

state: NY

address: A 827B, 1300 York Ave

department: Surgery

institute: Weill Cornell Medical College

summary: We report the RNA expression of insulin-GFP+ cells derived from CDKAL1-/- hESCs and CDKAL1-/-hESCs overexpressing MT1E

overall_design: Examination of RNA expression in 2 cell types.

first: Min

first: Hui

last: Zeng


title: PolyA site sequencing (PAS-seq) analysis of Hela cells treated with NC ASO or snoRD50a ASOs

first: chengguo

summary: Our RNA-seq experiment and subsequent in vitro analysis suggested that snoRD50a is a trans-acting RNA that can function in mRNA 3' processing. To test this hypothesis at transcriptomic level, we performed PAS-seq experiments to compare the polyA+ transcripts profile between negative control ASO (nc ASO) and snoRD50a ASO treated Hela cells

overall_design: ASO (antisense oligonucletode) technique is a commonly used technique to deplete nuclear RNAs. snoRD50a ASO is used to deplete endogenous snoRD50a. PAS-seq was performed in control and snoRD50a KD Hela cells

first: Chunliu


title: Pervasive epigenetic effects of Drosophila euchromatic transposable elements impact their evolution

city: Irvine

first: Grace

middle: Yuh Chwen

last: Lee

address: UCI

institute: University of California, Irvine

sample_organism:
Drosophila melanogaster
Drosophila simulans


title: Repression of stress-induced LINE-1 expression protects cancer cell populations from lethal drug-exposures [RNA-Seq]

first: Suchit

last: Jhunjhunwala

summary: DTP heterochromatin in genomic repeat regions protects the population from drug-induced death.

overall_design: Investigation of RNA expression changes in heterogenous parental populations as compared to drug treated and drugtolerant populations. Also included are TSA treated parental and drug-tolerant populations

first: Charles

last: Tindell

first: Gulfem

last: Guler

first: Marie

last: Classon


title: HTS-Seq analysis of Hela cells treated with NC ASO or snoRD50a ASOs

last: yao


title: The Stability of the Transcriptome during the Estrous Cycle in Four Regions of the Mouse Brain

city: Tallahassee

first: Cynthia

last: Vied

state: Florida

address: 1115 W. Call St

department: Translational Science Laboratory

institute: Florida State University

summary: We analyzed the transcriptome of the C57BL/6J mouse hypothalamus, hippocampus, neocortex, and cerebellum to determine estrous cycle-specific changes in these four brain regions.  We found almost 16,000 genes are present in one or more of the brain areas but only 210 genes, ~1.3%, are significantly changed as a result of the estrous cycle.  The hippocampus has the largest number of differentially expressed genes (DEGs) (82), followed by the neocortex (76), hypothalamus (63), and cerebellum (26).  Most of these DEGs (186/210) are differentially expressed in only one of the four brain regions.  A key finding is the unique expression pattern of growth hormone (Gh) and prolactin (Prl).  Gh and Prl are the only DEGs to be expressed during only one stage of the estrous cycle (metestrus).  To gain insight into the function of the DEGs, we examined gene ontology and phenotype enrichment and found significant enrichment for genes associated with myelination, hormone stimulus, and abnormal hormone levels.  Additionally, 61 of the 210 DEGs are known to change in response to estrogen in the brain.  50 genes differentially expressed as a result of the estrous cycle are related to myelin and oligodendrocytes and 12 of the 63 DEGs in the hypothalamus are oligodendrocyte- and myelin-specific genes.  This transcriptomic analysis reveals that gene expression in the female mouse brain is remarkably stable during the estrous cycle and demonstrates that the genes that do fluctuate are functionally related.

overall_design: Hypothalamus, hippocampus, neocortex, and cerebellum mRNA from adult female C57BL/6J (B6) mice were analyzed by RNA sequencing of 3 biological replicates for each of the 4 stages of the estrous cycle using an Illumina HiSeq 2500

first: Lisa

last: DiCarlo

first: Richard

last: Nowakowski


title: Pervasive epigenetic effects of Drosophila euchromatic transposable elements impact their evolution [ChIP-seq]

summary: We study the relatively unexplored evolutionary consequences of the epigenetic effects of transpoable elements (TEs) by providing the first genome-wide quantification of such effects in wild-derived D. melanogaster and D. simulans strains. Surprisingly, over half of euchromatic TEs show spread of repressive epigenetic marks to nearby DNA, resulting in differential epigenetic states of homologous genic alleles and, in return, selection against TEs. Interestingly, compared to D. melanogaster, the lower TE content in D. simulans is correlated with stronger epigenetic effects of TEs and higher levels of host genetic factors known to promote epigenetic silencing. We conclude that the epigenetic effects of euchromatic TEs, and host genetic factors modulating such effects, play a critical role in the population dynamics of TEs within and between species.

platform_organism:
Drosophila melanogaster
Drosophila simulans

overall_design: Examine the epigenetic effects of transposable elements

middle: Y

first: Gary

middle: H

last: Karpen


title: RNA-seq from four balanced translocation carriers in 1000 Genomes Project

city: Hong Kong

first: Zirui

last: DONG

address: Shatin, N.T.

department: Dept. of Obstetrics and Gynaecology

institute: The Chinese University of Hong Kong

summary: We performed RNA-seq for four balanced translocations' EB virus transformation cell line

overall_design: We identified four balanced translocaitons from 1000 Genomes Project and we performed RNA-seq from the cell line samples purchased from Coriell Institue

last: Dong

first: Chunyu

last: Geng


title: A phylogenetic framework to study the evolution of transcriptional regulatory networks

city: Madison

first: Sushmita

last: Roy

state: WI

address: 330 N. Orchard St.

institute: Wisconsin Institute for Discovery

sample_organism:
Schizosaccharomyces pombe
Saccharomyces cerevisiae
Candida albicans
Nakaseomyces glabratus
Naumovozyma castellii
Kluyveromyces lactis


title: VastDB: an Atlas of Alternative Splicing Profiles in Vertebrate Tissues and Cell Types

city: Barcelona

first: Manuel

last: Irimia

state: Barcelona

address: 88 Dr. Aiguader

department: MELIS

country: Spain

institute: Universitat Pompeu Fabra - Centre for Genomic Regulation

summary: Investigation of expression and alternative splicing in chicken stage embryos

overall_design: Chicken embryos at stage X of development were collected to perform high coverage RNA-Seq data

first: Miguel

last: Manzanares


title: Pervasive epigenetic effects of Drosophila euchromatic transposable elements impact their evolution [RNA-seq]


title: Patterns of host gene expression associated with harboring a foregut microbial community

city: Salt Lake City

first: Robert

middle: B

last: Weiss

state: UT

institute: University of Utah

summary: We compared gene expression in the foregut tissues of two rodent species: Stephen's woodrat (Neotoma stephensi), which harbors a dense foregut microbial community, and the lab rat (Rattus norvegicus), which lacks such a community. We found that woodrats have higher abundances of transcripts associated with smooth muscle processes, specifically a higher expression of the smoothelin-like 1 gene, which may assist in contractile properties of this tissue to retain food material in the foregut chamber. The expression of genes associated with keratinization and cornification exhibited a complex pattern of differences between the two species, suggesting distinct molecular mechanisms for this process in each of the two species. Lab rats exhibited higher abundances of transcripts associated with immune function, likely to inhibit microbial growth in the foregut of this species. Some of our results were consistent with previous findings in ruminants (high expression of facilitative glucose transporters, lower expression of B4galnt2), suggestive of possible convergent evolution, while other results were unclear, and perhaps represent novel host-microbe interactions in rodents. Overall, our results suggest that harboring a foregut microbiota is associated with changes to the functions and host-microbe interactions of the foregut tissues.

sample_organism:
Rattus norvegicus
Neotoma stephensi

platform_organism:
Rattus norvegicus
Neotoma stephensi

overall_design: Foregut tissue, polyA-containing mRNA profiles of Stephens' woodrats (Neotoma stephensi) and Sprague Dawley lab rats generated by deep sequencing, in triplicate, using the Illumina HiSeq 2000 platform.

first: Kevin

last: Kohl

first: M

last: Dearing


title: Antibiotics induce polarization of pleural macrophages to M2-like phenotype in patients with tuberculous pleuritis

first: Guangan

last: Hu

state: MA

address: 500 Main Street

department: Koch Institute

institute: MIT

summary: Purpose: To determine whether and how pleural macrophages change in phenotype, transcription and function in patients with tuberculous pleuritis following anti-TB antibiotic treatment.

overall_design:
Purifiy pleural macrophages from TB patients before and after antibiotics treatment
---------------
identities of antibiotics not provided

first: Sisi

last: Wang


title: IFN-γ Represses M2 Gene Expression in Human Macrophages by Suppressing and Disassembling MAF-binding Enhancers [RNA-seq]

first: Lionel

middle: B.

last: Ivashkiv

address: 535 East 70th Street

institute: Hospital for Special Surgery

summary: Mechanisms by which IFN-γ activates genes to promote macrophage activation are well studied, but little is known about mechanisms and functions of IFN-γ-mediated gene repression. We used an integrated transcriptomic and epigenomic approach to analyze chromatin accessibility, histone modifications, transcription factor binding, and gene expression in IFN-γ-primed human macrophages. IFN-γ suppressed basal expression of genes corresponding to an ‘M2’-like homeostatic/reparative phenotype. IFN-γ repressed genes by suppressing the function of enhancers enriched for binding by transcription factor MAF. Mechanistically, IFN-γ ‘disassembled’ a subset of enhancers by inducing coordinate suppression of binding by MAF, lineage-determining transcription factors, and chromatin accessibility. Genes associated with MAF-binding disassembled enhancers were suppressed in rheumatoid arthritis macrophages, revealing a disease-associated ‘negative IFN-γ signature’. These results identify enhancer inactivation and disassembly as a mechanism of IFN-γ-mediated gene repression, and MAF as a regulator of the macrophage enhancer landscape that is suppressed by IFN-γ to augment macrophage activation.

overall_design: RNA-seq in human macrophages stimulated with or without IFN-γ, RNA-seq of macrophages transfected with control or MAF-specific siRNA, and RNA-seq of macrophages transduced with control or MAF-expressing adenoviral particles.

first: Kyuho

last: Kang

first: Keunsoo


title: Total RNA sequencing of INS-GFP+ cells differentiated from HES3 hESCs treated with DMSO or H1152

first: Shuibing

last: Chen

summary: To systematically examine the cellular identity of INS+ cells derived after H1152 treatment, INSw/GFP HES3 hESCs were differentiated to a pancreatic progenitor population and treated with 10 µM H1152 for 8 days in sphere culture. The INS-GFP+ cells of H1152 or DMSO treated spheres were purified by cell sorting and transcripts profiled using RNA-seq.

overall_design: The INS-GFP+ cells of H1152 or DMSO treated spheres were purified by cell sorting and transcripts profiled using RNA-seq. Rat insulin promoter driven ZsGreen-sorted beta cells from human islets were also assayed.

first: Zaniar

last: Ghazizadeh


title: GCTM-5 positive and negative cells in pancreatic adenocarcinoma cell lines

city: Suita

first: Kouichi

last: Hasegawa

state: Osaka

address: 6F Techno Alliance Bldg. 2-8 Yamadaoka

department: StemRIM Institute of Regeneration-Inducing Medicine

country: Japan

institute: Osaka University

summary:
Analysis of GCTM-5 positive and negative cells sorted from CFPAC-1 and SW1990 human pancreatic adenocarcinoma cell line.
Results provide insight into molecular characteristics of GCTM-5 positive cells.

overall_design: Gene expression analysis of CFPAC-1 and SW1990 human pancreatic adenocarcinoma cells presenting GCTM-5 antigen or not (each 3 replicates).

first: Tatsuhiko

last: Ikeda

first: Bhavana

last: Nayer

first: Subhanwita

last: Sarkar


title: Critical Roles of the Histone Methyltransferase MLL4/KMT2D in Murine Hepatic Steatosis Directed by ABL1 and PPARγ2

city: Portland

first: Jae

middle: W

last: Lee

state: OR

address: 3181 SW Sam jackson Rd

department: Pediatrics

institute: Oregon Health & Science University

summary: The pathophysiologic continuum of non-alcoholic fatty liver disease begins with steatosis. Despite great progress in understanding the gene regulatory program directing steatosis, how it is orchestrated epigenetically is unclear. Here we show that the histone H3-lysine-4-methyltransferase, MLL4/KMT2D, plays critical roles in overnutrition-induced murine steatosis via dual mechanisms. First, in response to high fat diet (HFD), MLL4 activates the expression of PPARγ2, an overnutrition-induced steatotic transcription factor. Second, HFD enables the coactivator function of MLL4 for PPARγ2, as overnutrition-activated ABL1 kinase phosphorylates PPARγ2 and enhances its association with MLL4, facilitating recruitment of MLL4 to steatotic target genes of PPARγ2, including the PPARγ2-encoding gene itself, and their transactivation via H3-lysine-4-methylation. Consistently, inhibition of ABL1 improves the fatty liver condition of ob/ob mice by suppressing the pro-steatotic action of MLL4. Our results uncover a critical regulatory axis in overnutrition-directed steatosis, and present this ABL1-PPARγ2-MLL4 axis as a new target for anti-steatosis drug development.

overall_design: RNA samples from wild-type and MLL4 het livers treated with normal chow or high fat diet were prepared for sequencing according to the Illumina protocol, and sequenced on the Illumina HiSeq 2000. We will then compare the transcriptome changes between chow diet and high fat diet in wild-type livers. And then we identified gene whose expression is altered by high fat diet in wild-type livers but less significantly in MLL4 het livers in order to identify MLL4-target genes regulated by high fat diet.

first: Ji-Sun

last: Kwon


title: Vitamin C induced epigenomic remodeling in IDH1 mutant acute myeloid leukemia

city: Vancouver

first: Martin

last: Hirst

state: British Columbia

address: 2125 East Mall

department: Department of Microbiology & Immunology

country: Canada

institute: University of British Columbia

summary: The genomes of myeloid malignancies are characterized by epigenomic abnormalities. Heterozygous, inactivating TET2 mutations and neomorphic IDH mutations are recurrent and mutually exclusive in acute myeloid leukemia (AML) genomes. Ascorbic Acid (vitamin C) has been shown to stimulate the catalytic activity of TET2 in vitro and thus we sought to explore its effect in a leukemic model expressing IDH1R132H. Vitamin C treatment induced an IDH1R132H dependent reduction in cell proliferation and an increase in expression of genes involved in leukocyte differentiation.   Vitamin C induced differentially methylated regions (DMRs) that displayed a significant overlap with enhancers implicated in myeloid differentiation and were enriched in sequence elements for the hematopoietic transcription factors RUNX1 and PU.1.     ChIP-seq of PU.1 and RUNX1 revealed a significant loss of PU.1 and increase of RUNX1 bound DNA elements accompanied by their demethylation following vitamin C treatment. Additionally, vitamin C induced an increase in H3K27ac flanking sites bound by RUNX1. Based on these data we propose a model of vitamin C induced epigenetic remodelling of transcription factor binding sites driving differentiation in a leukemic model.

overall_design: We describe the distribution of 5mC, 5hmC H3K4me1, H3K4me3, H3K27ac, Runx1 and PU.1 as well as the transcriptional profile of HOXA9 immortalized mouse bone marrow cells expressing IDH1 R132H mutant (and IDH1 wt for medip/hmedip)

first: Matthew

last: Mingay


title: Hearts from AE3-null mice - RNA-Seq

city: Cincinnati

first: Mario

last: Medvedovic

state: OH

address: 3223 Eden Av. ML 56

department: Department of Environmental Health

institute: University of Cincinnati

summary: The AE3 (Slc4a3) Cl/HCO3 exchanger is highly abundant in heart, but its function is not known. To assess its function we performed RNA Seq analysis of mRNA from hearts of AE3-null and wild-type mice. The patterns of differential gene expression indicate mild hypoxia, enhanced glucose metabolism, and reduced fatty acid metabolism in cardiac myocytes, which is consistent with the hypothesis that HCO3 extrusion by AE3 plays a role in carbon dioxide disposal.

overall_design: Total RNA was isolated from hearts of 4-month-old FVB/N wild-type and AE3-null male mice (n = 4 of each genotype). Samples were subjected to RNA Seq analysis using the Illumina HiSeq 1000 platform. Sequence reads were aligned to the reference mouse genome using TopHat aligner and statistical analysis to identify differentially expressed genes was performed using the negative-binomial model of read counts. Differential expression data, expressed as RPKM values, were analyzed using the GOrilla gene ontology program. Significantly affected GO categories were grouped according to function and additional genes relevant to the significant GO categories were identified using the PubMatrix literature search analysis program.

first: Gary

middle: E

last: Shull


title: Intra- and inter-specific variations of gene expression levels in yeast are largely neutral

city: Guangzhou

first: Jian-Rong

last: Yang

address: No. 74, Zhongshan 2nd Road

institute: Sun Yat-sen University

summary: It is commonly, although not universally, accepted that most intra- and inter-specific genome sequence variations are more or less neutral, whereas a large fraction of organism-level phenotypic variations are adaptive.  Gene expression levels are molecular phenotypes that bridge the gap between genotypes and corresponding organism-level phenotypes.  Yet, it is unknown whether natural variations in gene expression levels are mostly neutral or adaptive.  Here we address this fundamental question by genome-wide profiling and comparison of gene expression levels in nine yeast strains belonging to three closely related Saccharomyces species and originating from five different ecological environments.

sample_organism:
Saccharomyces cerevisiae
Saccharomyces paradoxus
Saccharomyces mikatae

overall_design: To answer whether variations in gene expression levels within and between species are largely neutral or adaptive, we compared the transcriptomes of nine yeast strains belonging to three closely related species sampled from five different ecological environments.  Importantly, we selected strains such that their genomic phylogenetic relationships mismatch their relationships at the environmental level.  For instance, some strains are phylogenetically relatively distant from one another but have similar ecological environments, whereas others are phylogenetically relatively close to one another but live in ecologically distinct environments.  If gene expression variations among these strains result from the accumulation of neutral mutations, the relationships of their transcriptomes should mimic the genome-based phylogenetic tree.  On the contrary, if the expression variations among these strains are largely shaped by adaptations to their respective environments, their transcriptomes should cluster according to their ecological environments.  Thus, our design allows a distinction between the neutral and adaptive hypotheses. Raw short read data available on SRA under accession SRP074509.

first: Jianzhi

last: Zhang


title: A phylogenetic framework to study the evolution of transcriptional regulatory networks [RNA-Seq]

first: Sushmita

last: Roy

summary: Comparative expression analysis of HOG1 KOs during osmotic stress in the ascomycete yeasts

sample_organism:
Schizosaccharomyces pombe
Saccharomyces cerevisiae
Candida albicans

overall_design: Gene expression was measured in  KO strains as well as WT strains of three ascomycete yeasts, S. cerevisiae, C. albicans, and S. pombe. Expression was measured in a wildtype strain of each species, as well as a sko1 knockout mutant for S. cerevisiae and C. albicans, an msn2/4 knockout mutant for S. cerevisiae, an mnl1 knockout mutant for C. albicans, and an hsr1 knockout mutant for S. pombe. Expression was measured under normal media at T=0, and under KCl stress at T=20. Two replicates were used for each experiment.

first: Christopher

last: Koch

first: Jay

last: Konieczka

first: Toni

last: Delorey

first: Ana

last: Lyons

first: Amanda

last: Socha

first: Kathleen

last: Davis

first: Sara

last: Knaack

first: Dawn

last: Thompson

first: Erin

last: O'Shea

first: Aviv

last: Regev


title: Co-chaperone Hop/dSTIP1 is required for piRNA biogenesis and transposon silencing

status: Public on Jun 30 2017

city: Charleston

first: Vamsi

last: Gangaraju

address: 173 Ashley Ave

institute: Medical University of South Carolina

type: Non-coding RNA profiling by high throughput sequencing

summary: piRNAs are 26-30nt germ-line specific small non-coding RNAs that have evolutionarily conserved function in mobile genetic element silencing and maintenance of genome integrity. It has been shown that Drosophila Hsp70/90 Organizing Protein Homolog (Hop) – a co-chaperone interacts with piRNA binding protein Piwi and mediates silencing of phenotypic variations. However, it is not known if Hop has a direct role in piRNA biogenesis and transposon silencing. Here, we show that knock down of Hop in the germ-line nurse cells (GLKD) of Drosophila ovaries leads to activation of transposable elements. Females without germ-line Hop can lay eggs but the eggs do not hatch into larvae. GLKD of Hop leads to accumulation of γ-H2Av foci in the germline indicating increased DNA damage in the ovary. We also show that Hop is required for efficient piRNA biogenesis. Based on these results, we conclude that Hop is a critical component of piRNA pathway and it maintains genome integrity by silencing transposable elements.

overall_design: Total mRNA profiles of ovaries from nos.Luc (Control) and Hop germline knockdown conditions. Total small RNA profiles of ovaries from nos.Luc (Control) and Hop germline knockdown conditions.


title: ZIKV can infect human CD14+ monocytes and update multiple cellular pathways

city: Reno

first: Subhash

middle: C

last: Verma

state: NV

address: 1664 N Virginia Street, MS 320

department: Microbiology and Immunology

institute: University of Nevada, Reno

summary: The objective of this assay was to determine the effect of ZIKV on host cellular pathways

overall_design: Purified human CD14+ monocytes were infected with two strains of ZIKV (PR and NIG) and RNA was subjected for differential gene expression by next generation sequence analysis.

first: Stephen

last: St. Jeor


title: Genome wide analysis of the transcription induced by estrogen and tamoxifen in MCF-7 cells

city: Oslo

first: Shixiong

last: Wang

address: Gaustadalléen 21

department: Centre for Molecular Medicine Norway

country: Norway

institute: University of Oslo

summary: The aim of this study is to understand the role of tamoxifen in the transcription regulation of estrogen receptor positive breast cancer cells using GRO-seq experiment. ER positive MCF-7 cells was depleted with lipid hormone in stripped culture media for 4 days, and stimulated with 17-β-estradiol (100nM), 4-OH-tamoxifen (1μM), and the combination of both for 40min. Each treatment was generated in duplicates. Then nuclei was isolated and used as the starting material for GRO-seq experiments. Sequencing data was analyzed and differential gene expression analysis was performed. A rapid induction of gene expression by 17-β-estradiol was observed as previous studies reported. While also a number of genes were also up-regulated by 4-OH-tamoxifen treatment which is considered as a ER antagnist. The data strongly indicate that as a recpressor of estrogen receptor induced transcription, tamoxifen could also perform as a partial agnist at the same time.

overall_design: Transcriptome profiling of hormone depleted MCF-7 cells treated with vehicle (control), 17-β-estradiol (100nM), 4-OH-tamoxifen (1μM) and combination of both for 40min. 2 replicates for each

first: Antoni

last: Hurtado


title: Immunophenotyping and Transcriptomic Outcomes in PDX-Derived TNBC Tissue

city: Research Triangle Park

first: Rainer

last: Blaesius

state: NC

address: 21 Davis Drive

institute: Becton Dickinson Technologies

summary: Cancer tissue functions as an ecosystem of a diverse set of cells that interact in a complex tumor microenvironment. Genomic tools applied to biopsies in bulk fail to account for this tumor heterogeneity, whereas single-cell imaging methods limit the number of cells which can be assessed or are very resource intensive. The current study presents methods based on flow cytometric analysis and cell sorting using known cell surface markers (CXCR4/CD184, CD24, THY1/CD90) to identify and interrogate distinct groups of cells in triple-negative breast cancer clinical biopsy specimens from patient-derived xenograft (PDX) models. The results demonstrate that flow cytometric analysis allows a relevant subgrouping of cancer tissue and that sorting of these subgroups provides insights into cancer cell populations with unique, reproducible, and functionally divergent gene expression profiles. The discovery of a drug resistance signature implies that uncovering the functional interaction between these populations will lead to deeper understanding of cancer progression and drug response.

overall_design: Triple-negative breast cancer PDX-derived tumors were dissociated and sorted into subpopulations of CD24+/CD184 high and CD24+/CD184 low expressing cells using flow cytometry and the transcriptomes of these subpopulations were characterized using bulk RNAseq.

first: Eileen

last: Snowden

first: Warren

last: Porter

first: Friedrich

last: Hahn

first: Mitchell

last: Ferguson

first: Frances

last: Tong

first: Joel

last: Parker

first: Aaron

last: Middlebrook

first: Smita

last: Ghanekar

first: William

last: Dillmore


title: The biosynthesis of nitrous oxide in the green algae Chlamydomonas reinhardtii

city: Palmerston North

first: David

last: Wheeler

state: No State/International

address: Tennent Drive, Massey University (Turitea)

department: Institute of Fundamental Sciences

country: New Zealand

institute: Massey University

summary: This data was generated to identify the molecular pathways responsible for nitrous oxide synthesis by the green algae Chlamydomonas reinhardtii, when supplied with nitrite under aerobic conditions (oxia). RNA samples were collected at three time points, 15 min, 3 hours, and 24 hours after the start of the experiment. The control and treatment groups were grown under the same conditions, except treatment group was supplied with 10mM nitrite at time 0. Illumina TruSeq stranded RNA libraries were synthesised from the resulting RNA before sequencing on a HiSeq2500 (125bp). The resulting sequence run generated 241,151,809 paired-end 125bp reads, of which 200,946,839 remained following quality filtering. The short data was mapped to the published genome and read counts were generated with HT-Seq count with the default settings. The raw read count data was analysed by DESeq2 in order to identify genes differentially expressed during nitrous oxide production.

overall_design: Stranded RNA-seq libaries were synthesised from RNA collect at 15 minutes, 3 hours, and 24 hours after addition of 10 mM nitrite to the treatment group of Chlamydomonas reinhardtii. Controls were grown under identical conditions but not supplied with nitrite. Three growth flask were used for the control and treatment group to provide triplicates.

first: Benoit

last: Guieysse

first: Maxence

last: Plouviez


title: BET inhibitors suppress lytic DNA replication [Akata-Zta DNA-seq]

city: New York

first: JJ

last: Miranda

address: 3009 Broadway

institute: Barnard College, Columbia University

summary: Lytic infection by the Epstein-Barr virus (EBV) poses numerous health risks, such as infectious mononucleosis and lymphoproliferative disorder. We demonstrate that JQ1 and other BET inhibitors block two different steps in the sequential cascade of the EBV life cycle: expression of the immediate-early gene BZLF1 and lytic genome replication. This represents a novel mode of action for antiviral drugs that may increase efficacy and decrease emergence of resistance. The sequenced total DNA data below show that JQ1 and I-BET cause a decrease in EBV genome replication after induction.

sample_organism:
Homo sapiens
human gammaherpesvirus 4

platform_organism:
Homo sapiens
human gammaherpesvirus 4

overall_design: (A) Total DNA from Akata-Zta pretreated with JQ1 or vehicle, treated with doxycycline or vehicle, experiment performed in triplicate. (B) As in (A) but pretreated with I-BET or RVX-208.

first: Kristin

last: Keck

first: J


title: Investigating the genetic basis of RNA Editing in humans

city: Ann Arbor

first: Isabel

middle: Xiaorong

last: Wang

state: Michigan

address: 210 washtenaw ave

department: Pediatrics&Genetics

institute: HHMI/University of Michigan

summary: Adenosine deaminases acting on RNA (ADAR) are proteins that deaminate adenosine to inosine, which is then recognized by the ribosome as guanosine. To study the genetic basis of RNA editing efficiency by ADAR, we carried out deep RNA sequencing (RNA-Seq) in human B-cells and uncovered more than 100,000 RNA editing sites. Next, we evaluated the extent of individual variation in the RNA editing among unrelated individuals from Centre d'Etude du Polymorphisme Humain (CEPH) and found significant variation in the levels of editing. To understand whether there exists a genetic component to the variation in RNA editing levels, we obtained RNA-Seq data from 10 pairs of monozygotic twins. These results revealed that there exists a significant genetic component to variation in RNA editing.

overall_design: To identify RNA editing sites, we obtained RNA-Seq data for 2 unrelated individuals. To study individual variation in RNA editing, we analyzed RNA-Seq data in sets of 12 and 41 unrelated individuals. Lastly, to understand the genetic basis of variation in RNA editing, we studied related individuals, namely 10 pairs of monozygotic twins and large families.

first: Jonathan

last: Toung

first: Zhengwei

last: Zhu


title: Vitamin C Induces Specific Demethylation of H3K9me2 in Mouse Embryonic Stem Cells via Kdm3a/b

city: San Francisco

first: Miguel

last: Ramalho-Santos

state: CA

address: 35 Medical Center Way

department: Eli and Edythe Broad Center of Regeneration Medicine

institute: UCSF

summary: Histone methylation patterns regulate gene expression and are highly dynamic during development. The erasure of histone methylation is carried out by histone demethylase enzymes. We had previously shown that vitamin C enhances the activity of Tet enzymes in embryonic stem (ES) cells, leading to DNA demethylation and activation of germline genes. We report here that vitamin C induces a remarkably specific demethylation of histone H3 lysine 9 dimethylation (H3K9me2) in ES cells. Vitamin C treatment reduces global levels of H3K9me2, but not other histone methylation marks analyzed, as measured by Western blot, immunofluorescence and mass spectrometry. Vitamin C leads to widespread loss of H3K9me2 at large chromosomal domains as well as gene promoters and repeat elements. Vitamin C-induced loss of H3K9me2 occurs rapidly within 24 hours and is reversible. Importantly, we found that the histone demethylases Kdm3a and Kdm3b are required for vitamin C-induced demethylation of H3K9me2. Moreover, we show that vitamin C-induced Kdm3a/b-mediated H3K9me2 demethylation and Tet-mediated DNA demethylation are independent processes. Lastly, we document Kdm3a/b are partially required for the up-regulation of germline genes by vitamin C. These results reveal a specific role for vitamin C in histone demethylation in ES cells, and document that DNA methylation and H3K9me2 cooperate to silence germline genes in pluripotent cells.

overall_design: ChIP for H3K9me2 was performed on untreated and vitamin C-treated ES cells. ChIP DNA and Input DNA were subjected to paired-end sequencing.

first: Kevin

middle: T

last: Ebata

first: Kathryn

last: Mesh

first: Misha

last: Bilenky

first: Martin

last: Hirst


title: BET inhibitors suppress BZLF1 expression [MutuI RNA-seq]

summary: Lytic infection by the Epstein-Barr virus (EBV) poses numerous health risks, such as infectious mononucleosis and lymphoproliferative disorder. We demonstrate that JQ1 and other BET inhibitors block two different steps in the sequential cascade of the EBV life cycle: expression of the immediate-early gene BZLF1 and lytic genome replication. This represents a novel mode of action for antiviral drugs that may increase efficacy and decrease emergence of resistance. The RNA-seq data below show that the first block by JQ1 occurs before transcription of any EBV lytic genes (see wigs of EBV transcriptomes). A subset of the same RNA-seq data (three replicates each of Mutu+vehicle was compared to Mutu+JQ1) was examined for changes in the human transcriptome, and those results are presented in the spreadsheet "Differential_Expression_GEO"

overall_design: RNA-seq from MutuI pretreated with JQ1 or vehicle, treated with antibody or vehicle, experiment performed in triplicate


title: Reconstructing Lineage Hierarchies of Mice Uterus Epithelia Development using Single Cell Analysis

city: HangZhou

first: Bingbing

last: Wu

state: Zhejiang

address: 866 Yuhangtang Rd

department: School of Medcine

institute: Zhejiang University

summary:
Purpose:The endometrium layer comprises of luminal and glandular epithelia that both develop from the same simple layer of fetal uterine epithelia. Mechanisms of uterine epithelial progenitor self-renewal and differentiation are unclear.
Methods: This study aims to systematically analyze the molecular and cellular mechanisms of uterine epithelia development by single cell RNA-Seq
Results: An integrated set of single cell transcriptomic data of uterine epithelial progenitors and their differentiated progenies is provided. Additionally, the unique molecular signatures of these cells, characterized by sequential up-regulation of specific epigenetic and metabolic activities, and activation of unique signaling pathways and transcription factors, were also investigated. Finally, a unique subpopulation of early progenitor, as well as differentiated luminal and glandular lineages were identified. A complex cellular hierarchy of uterine epithelia development was thus delineated.
Conclusions: Our study therefore systematically decoded molecular markers and cellular program of uterine epithelia development that would shed lights on uterine developmental biology.

overall_design: 960 single CD326+ mice uterine epithelia from 5 developmental stages (post natal day 0, 7, 14, 28, 56) were isolated, pre-amplified and sequenced using Illumina Hiseq 2500, finally data from 714 single cells were collected

first: Xiaohui

last: Zou

first: Hongwei

last: Ouyang


title: A multi-scale model for hair follicle reveals heterogeneous skin domains drive rapid spatiotemporal hair growth patterning

city: Irvine

first: Maksim

middle: V

last: Plikus

state: California

address: 845 Health Sciences Road

department: Developmental and Cell Biology

institute: University of California, Irvine

summary: We report transcriptomes of whole skin from different anatomic regions, dorsum, ventrum, chin and ear pinna, as well as ear cartilage/muscle complex at different post-natal time points. Whole tissue was microdissected from wild type mice.

overall_design:
Examination of miscrodissected whole skin from dorsum, ventrum and chin at six consecutive time points of the hair cycle, and comparison of ear pinna telogen skin vs. ear cartilage/muscle complex vs. dorsal telogen skin.

Sample definition:
CCT		Chin skin, Competent telogen
CEA		Chin skin, Early anagen
CMA		Chin skin, Mid-anagen
CLA		Chin skin, Late anagen
CC		Chin skin, Catagen
CRT		Chin skin, Refractory telogen
VCT		Ventral skin, Competent telogen
VEA		Ventral skin, Early anagen
VMA		Ventral skin, Mid-anagen
VLA		Ventral skin, Late anagen
VC		Ventral skin, Catagen
VRT		Ventral skin, Refractory telogen
DCT		Dorsal skin, Competent telogen
DEA		Dorsal skin, Early anagen
DMA		Dorsal skin, Mid-anagen
DLA		Dorsal skin, Late anagen
DC		Dorsal skin, Catagen
DRT		Dorsal skin, Refractory telogen
ERST		Ear skin, Telogen
LC		Ear cartilage/muscle complex

first: Qing

last: Nie

first: Ji Won

last: Oh

first: Qixuan

first: Hyelim

last: Lee

first: Tao

last: Peng


title: Transcriptomic analysis of an archived bladder cancer cohort

city: Worcester

first: Yu

last: Liu

address: AS5-1018, 368 Plantation Street

department: Program in Systems Biology

institute: University of Massachusetts Medical School

summary: Establishment and application of RNAseq based transcriptome analayis on an archivaed bladder cancer cohort.

overall_design: Total RNA profilling 61 archived bladder cancer samples and comparison of 4 pairs of fresh frozen and FFPE bladder cancer samples.

first: Jeffrey

last: Wrana

first: Azar

last: Azad


title: Gene expression data from mouse colon. AOM+DSS induced colitis. Wild type or Cygb -/- mice

city: Copenhagen

first: Jorgen

last: Olsen

address: Blegdamsvej 3

department: Department of Cellular and Molecular Medicine

country: Denmark

institute: University of Copenhagen

summary: Cytoglobin is a member of the hemoglobin family and is thought to protect against cellular hypoxia and cellular oxidative stress. This function may be particularly important in inflammation induced cancer observed in e.g. patients with ulcerative colitis. In this study, we investigated the development of inflammation and tumors in the murine model of inflammation induced colorectal cancer using Azoxymethane treatment combined with Dextrane Sodium Sulphate.

overall_design: 29 samples were analyzed. Wild type, untreated (8 biological replicates); Wild type AOM+DSS (8 biological replicates); Cygb -/-, untreated (8 biological replicates); Cygb -/- AOM+DSS (8 biological replicates)

first: Jørgen

first: Mohammad

last: Yassin

first: Anders

last: Pedersen

last: Hay-Schmidt


title: Dermal fibroblasts play a central role in skin model protection against C. albicans invasion

city: Stuttgart

first: Christian

last: Grumaz

address: Nobelstr. 12

department: MBT

country: Germany

institute: Fraunhofer IGB

summary: This study shows that, in the presence of CD4+ T cells, dermal fibroblasts shift towards an antimicrobial phenotype leading to reduced dermal invasion by C. albicans. This is dependent on TLR2 activation and pro-IL-1β cleavage and results in expression of genes involved in defense against various classes of pathogens.

sample_organism:
Homo sapiens
Candida albicans SC5314

platform_organism:
Homo sapiens
Candida albicans SC5314

overall_design: Dual RNA-Seq of keratinocytes and fibroblasts with or without Candida albicans from infected humen reconstituted skin models with or without CD4+ T cells. Sequenced were fibroblasts, Keratinocytes and C. albicans isolated from these models. For each sample biological triplicates were analyzed.

first: A

last: Kühbacher

first: P

last: Stevens

first: C

first: H

last: Henkel

first: D

last: Finkelmeier

last: Burger-Kentischer

first: K

last: Sohn

first: S

last: Rupp


title: Gene profiling of human adult and pediatric liver cancer cells

city: Lausanne

first: Paolo

last: Angelino

address: Quartier Sorge, Bâtiment Génopode

department: BCF

institute: SIB Swiss Institute of Bioinformatics

summary: In an effort to comprehend some of the molecular differences between two cancers that originate in the same tissue, adult HCC and pediatric HB, we profiled four HCC and four HB cell lines using RNA sequencing. We identified an enhanced sugar uptake and usage in HB tumors compared to adult HCC, and two different metabolic subtypes of HB. We identified an enhanced sugar uptake and usage in HB tumors compared to adult HCC, and two different metabolic subtypes of HB. In particular, we showed that embryonal HB cell lines largely rely on glycolysis and express higher level of GLUT3, together with HK1, PFKP and LDHB coding for enzyme of glycolysis. On the contrary, fetal tumors express genes involved in gluconeogenesis, and as notable exception they express HK2, which is often over-expressed in adult solid tumors. Importantly, we found that the different utilization of HK isoforms renders the two HB subtypes sensitive to specific glycolysis inhibitors.

overall_design: HCC and HB gene profiles were generated by deep sequencing, in duplicates, using Illumina HiSeq 2500.

first: Etienne

last: Meylan

first: Jessica

last: Vazquez

first: Stefania

last: Crippa


title: Convergent roles of ATF3 and CSL in chromatin control of CAF activation [RNA-seq]

summary: Cancer associated fibroblasts (CAFs) play an important role in initiating and promoting epithelial cancers. The specific chromatin modifications involved in CAF activation remain to be elucidated. CSL, a constitutive transcriptional repressor and mediator of canonical Notch signaling, functions as a direct negative regulator of CAF effector genes and suppresses cancer/stromal cell expansion. We find that ATF3, a key stress responsive transcriptional repressor up-regulated in the acute UVA response of skin fibroblasts, is down-modulated in stromal cells of premalignant skin SCC lesions similarly to CSL. Increased ATF3 expression counteracts the consequences of compromised CSL, binding to a large set of overlapping target genes. At low basal levels, ATF3 converges with CSL in negative control of CAF activation, binding to a very small number of genomic loci that encompass mostly non-coding RNAs and pseudogenes. Silencing of ATF3 results in chromatin modifications and Pol II recruitment to many loci to which ATF3 does not bind, which are similarly affected by CSL silencing. The observed changes are of functional significance, as Bet inhibitors, which unlink activated chromatin from the basic transcription apparatus, have opposite effects of ATF3 or CSL silencing on all tested CAF effector genes. They exert a similar impact on clinically-derived CAFs both in vitro and upon topical in vivo treatment. Thus, ATF3 converges with CSL in global chromatin control of CAF activation with their loss eliciting epigenetic changes amenable to cancer and stroma-focused intervention.

overall_design:
Human Dermal Fibroblasts were infected with pInd-ATF3 viruses and treated for 3 days with doxyciclin at two different doses (100 and 500 ng/ml) in parallel with vehicle for 3 days, followed by RNA-Seq analysis.
Human Dermal Fibroblasts were transfected with two different siRNA against ATF3 in parallel with a control siRNA. Total RNA was extracted 3 days post-transfection, followed by RNA-Seq analysis (DEK32-37).
Cancer Associated Fibroblasts were treated with JQ1 (500nM) or vehicle (DMSO) for 48 hours, followed by RNA-Seq analysis (DMSO_1-3, JX_1-3).

first: Dong

last: Kim

first: Gian-Paolo

last: Dotto


title: Convergent roles of ATF3 and CSL in chromatin control of CAF activation

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

overall_design: Refer to individual Series


title: Convergent roles of ATF3 and CSL in chromatin control of CAF activation [HistoneMarkers ChIPseq]

overall_design: Examination of genome-wide H3K27ac, H3K4m3e, H3K27me3 histone modification and PolII binding in primary human dermal fibroblasts under normal (siCtrl) vs ATF3 (siATF3), CSL (siCSL) and CSL+ATF3 (siATF3+siCSL) silencing


title: Convergent roles of ATF3 and CSL in chromatin control of CAF activation  [ATF3 ChIP-seq]

overall_design: Examination of genome-wide over-expressed ATF3 binding sites in primary human dermal fibroblasts


title: The gene expression landscape of pine seedling tissues.

city: Malaga

first: Rafael

middle: A

last: Cañas

address: Facultad de Ciencias, Campus de Teatinos

department: Biología Molecular y Bioquímica

institute: Universidad de Málaga

overall_design: Gene expression analysis of the different tissues of one month old seedlings or Pinus pinaster. The tissue samples were isolated through Laser Capture Microdissection. The RNA was extracted and amplified using the CRA+ protocol (Cañas et al., 2014 Tree Physiol. 34:1278-1288). The cDNA was sequenced by 454 pyrosequencing in a GS-FLX+ platform.

first: Zhen

last: Li

first: M. Belén

last: Pascual

first: Vanessa

last: Castro-Rodríguez

first: Concepción

last: Ávila

first: Lieven

last: Sterck

first: Yves

last: Van de Peer

first: Francisco

last: Cánovas


title: Small RNA expression pattern in multiple inbred lines and their hybrids of maize embryo

city: Beijing

first: Yong-Xin

last: Liu

address: No.1 Beichenxi Road, Chaoyang District

department: State Key Laboratory of Plant Genomics

institute: Institute of Genetics and Developmental Biology, Chinese Academy of Sciences

summary: To investigate whether small RNAs (sRNAs) participate in the regulation of heterosis, we profiled the sRNA expression patterns in the germ seeds of five inbred lines and theirs three F1 hybrids using high-throughput sequencing technology.

overall_design: In this study, three hybrid varieties of maize, which were elite hybrids and widely cultivated in China that exhibited high heterosis for grain yield, and theirs five parental inbred lines were utilized.  The relationship of these varieties is as followed: Chang 7-2 (Paternal, P), Zheng 58 (Maternal, M), and Zhengdan 958 (Hybrid, H); Chang 7-2 (P), 9058 (M), and Lingdan 20 (H); 87-1 (P), Zong 3 (M), and Yuyu22 (H). Small RNA profile of eight maize varieties are generated by deep sequencing.

first: Xiu-Jie

last: Wang

first: Huabang

last: Chen


title: Hepcidin is regulated by promoter-associated histone acetylation and HDAC3

status: Public on Jun 29 2017

city: Oxford

first: Sant-Rayn

middle: Singh

last: Pasricha

state: Oxfordshire

address: John Radcliffe Hospital

department: MRC Human Immunology UnitC Human Immunology Unit

institute: University of Oxford

summary: We used NGS sequencing of RNA (RNA-Seq) in livers of mice treated with a 3 week low iron (2-6 parts per million) diet, and treatment with either RGFP966 (an HDAC3 specific inhibitor) or vehicle. Our primary interest is in the role of HDAC3 in expression of the iron regulatory hormone hepcidin (Hamp1 in mice).

overall_design: C57Bl/6 mice were treated with 3 weeks low iron diet, then treated with  2 doses of either RGFP966 20mg/kg i.p. or vehicle.

first: Hal

last: Drakesmith


title: Yellow-Leaf 1 encodes a magnesium-protoporphyrin IX monomethyl ester cyclase, involved in chlorophyll biosynthesis in rice (Oryza sativa L.)

city: Hangzhou

first: lv

middle: yu

last: song

address: CNRRI

institute: CNRRI

summary: We performed a transcriptomics analysis in the wild type and the mutant, and the expression levels of photosynthesis and chloroplast development genes were  affected in yl-1 mutant.

overall_design: RNA-sequencing analysis was performed on an Illumina Hiseq 4000 (LC Sciences, USA) following the vendor's recommended protocol

first: Zhonghua

last: Sheng

first: Yusong

last: Lv


title: Gene expression profile of regulatory T cell (Treg) subsets from CD28-deficient mouse

city: Noda

first: Ei

last: Wakamatsu

state: Chiba

address: 2669 Yamasaki

institute: Tokyo University of Science

summary: A comparative analysis of gene expression of CD4+ EGFP+ Nrp1+ (tTreg, thymus-derived Treg), CD4+ EGFP+ Nrp1- (pTreg, peripherally-derived Treg) and CD4+ EGFP- (Tconv, conventional T cell) in CD28-/- Foxp3EGFP and Foxp3EGFP mice.

overall_design: Nrp1+ Treg (tTreg), Nrp1- Treg (pTreg) and Tconv were sorted from Foxp3EGFP and CD28-/-Foxp3EGFP mice. Total RNAs were extracted from whole samples and analyzed by RNA-seq.

first: E

first: R

last: Abe


title: BET inhibitors suppress lytic DNA replication [Akata-Zta RNA-seq]

first: JJ

last: Miranda

summary: Lytic infection by the Epstein-Barr virus (EBV) poses numerous health risks, such as infectious mononucleosis and lymphoproliferative disorder. We demonstrate that JQ1 and other BET inhibitors block two different steps in the sequential cascade of the EBV life cycle: expression of the immediate-early gene BZLF1 and lytic genome replication. This represents a novel mode of action for antiviral drugs that may increase efficacy and decrease emergence of resistance. The RNA-seq data below show that the second block causes a decrease in expression of late but not early lytic genes.

overall_design: (A) RNA-seq from Akata-Zta pretreated with JQ1 or vehicle, then treated with doxycycline or vehicle, experiment performed in triplicate. (B) RNA-seq from Akata-Zta pretreated with I-BET, then treated with doxycycline or vehicle, experiment performed in triplicate.

first: Kristin

middle: M

last: Keck

middle: L


title: Tsc2 KO cells have a transcriptional signature found in bladder tumors with TSC1/2 deficiency and that is corrected by sirolimus and includes Lgals3 overexpression

city: Bethesda

first: Thomas

last: Darling

state: MD

address: 4301 Jones Bridge Road

department: Dermatology

institute: Uniformed Services University of the Health Sciences

summary: Use RNA-seq to obtain transcriptional signature of Tsc2 KO neonatal mouse dermal fibroblasts +/- sirolimus.  The resulting mTORC1 transcriptional signature is tested in the TCGA database of bladder cancers with non-silent mutations in TSC1/2.

overall_design: n = 3 WT vehicle, n = 3 KO vehicle, n = 3 WT sirolimus, n = 3 KO sirolimus

first: Peter

middle: J

last: Klover

first: Rajesh

last: Thangapazham

first: Jiro

last: Kato

first: Ji-an

first: Stasia

last: Anderson

first: Victoria

last: Hoffmann

first: Wendy

middle: K

last: Steagall

first: Shaowei

last: Li

first: Elizabeth

last: McCart

first: Neera

last: Nathan

first: Joshua

last: Bernstock

first: Matthew

middle: D

last: Wilkerson

first: Clifton

last: Dalgard

first: Joel

last: Moss


title: Transcriptomic analysis of Lactococcus lactis ssp. cremoris KW2 after ComX constitutive production

city: Louvain-La-Neuve

first: Pascal

last: Hols

address: Croix du Sud, 4-5, box L7.07.06

department: Institute of Life Sciences (ISV) Biochemistry, Biophysics and Genetics of Microorganisms (BBGM)

country: Belgium

institute: Faculty of Sciences Université catholique de Louvain

summary: Lactococcus lactis is one of the most important lactic acid bacterium used in the dairy industry. Activation of natural DNA transformation in this species would greatly improve the selection of novel strains with desired industrial traits. Here, we investigate the activation of natural transformation in L. lactis ssp. cremoris KW2, a strain of plant origin whose genome encodes the master competence regulator ComX and the complete set of essential late gene products required for natural transformation under its potential control. In absence of any information on the competence signaling system in this species, activation of natural DNA transformation by the constitutive production of ComX was attempted. Using a reporter strain of late competence phase activation and transcriptomic analyses, we show that all key genes for natural transformation can be induced in strain KW2. Then, we demonstrate that natural DNA transformation is functional in this strain and that this process requires the DNA uptake machinery dedicated to competence. Various chromosomal modifications such as point mutations or gene deletion/insertion could be quickly and efficiently achieved. These results are the first to report the functionality of natural DNA transformation in L. lactis and pave the way for the identification of molecular mechanisms activating competence development in this species.

overall_design: RNA-Seq comparison of wild-type and strain harboring a constitutive comX expression plasmid

first: Blandine

last: David

first: Amandine

last: Radziejowski


title: BET inhibitors suppress BZLF1 expression [MutuI DNA-seq]

first: JJ

last: Miranda

summary: Lytic infection by the Epstein-Barr virus (EBV) poses numerous health risks, such as infectious mononucleosis and lymphoproliferative disorder. We demonstrate that JQ1 and other BET inhibitors block two different steps in the sequential cascade of the EBV life cycle: expression of the immediate-early gene BZLF1 and lytic genome replication. This represents a novel mode of action for antiviral drugs that may increase efficacy and decrease emergence of resistance. The sequenced total DNA data in this series show that JQ1 causes a decrease in EBV genome replication upon antibody induction.

overall_design: Total DNA-seq from MutuI pretreated with JQ1 or vehicle, treated with antibody or vehicle, experiment performed in triplicate

first: Kristin

last: Keck


title: The regulatory network of OsNAC6 targets drought-related genes orchestrating rice drought tolerance (RNA-Seq)

city: Pyeongchang

first: Pil Joong

last: Chung

state: Gangwondo

address: Pyeongchang daero 1447

department: Crop Biotechnology Institute

country: South Korea

institute: Seoul National University

summary: OsNAC6 is a stress responsive NAC transcription factor in rice known as a regulator for the transcriptional networks of the drought tolerance mechanisms. However, little is known about the associated molecular mechanisms for drought tolerance. Here, we identified OsNAC6-mediated root structural adaptation such as increased root number and root diameter that was sufficient to confer drought tolerance. Multiyear (5 years) drought field tests clearly demonstrated that OsNAC6 overexpression in roots produced higher grain yield under drought conditions. Genome-wide analyses revealed that OsNAC6 directly up-regulated 13 genes. Taken together, OsNAC6 is a valuable candidate for genetic engineering of drought-tolerant high-yielding crops.

overall_design: RNA-seq using roots of NT and OsNAC6 transgenic plants

first: Pil-Joong

first: Ju-Kon

last: Kim


title: RNA sequencing of T-ALL (COG study)

city: Albuquerque

first: Ksenia

last: Matlawska

state: NM

address: 915 Camino de Salud

department: Pediatrics

institute: University of New Mexico

summary: The clinical and cytogenetic features associated with T-cell acute lymphoblastic leukemia (T-ALL) are not predictive of early treatment failure or relapse.  We investigated 213 newly diagnosed patients who were treated in the Children's Oncology Group (COG) T-ALL Studies 9404 and 0434 and identified a cluster cases characterized by increased expression of HOX9/10.  In samples with >8-fold HOXA9/10 deregulation, the presence of specific molecular lesions were confirmed through a systematic review of cytogenetic databases, FISH and PCR testing.  In cases with no identifiable lesions using the methods above, RNA sequencing was performed (Illumina and Ion Proton).  Fifteen cases selected for RNA sequencing met three criteria: HOXA9/10 expression ≥8-fold above the median, sufficient RNA, and an incomplete or absent molecular explanation for each sample’s HOXA9/10 deregulation.  Three cases were confirmed to have PICALM-AF10 fusions.  Two additional AF10-R cases showed DDX3X-AF10 lesions, one of which harbored a novel CASK gene fragment in a complex CASK-DDX3X-AF10 translocation.  Two cases harbored NUP98 fusions46 and one case each was identified for MLL-AF6, MLL-PICALM, HOXA10-(3’UTR)TRBC45, STAG2-LMO2, LOC338817-CCDC91.  We could not identify fusion transcripts in 3 cases.

overall_design: Identification of novel fusion transcripts in HOXA9/10-deregulated T-ALL


title: Analyses of T-ALL (COG study)


title: RNA-seq analysis of human cardiosphere cells with different tubule supportive potential

first: Emma

last: Harvey

summary: RNA-seq analysis of Cardiosphere derived cells from 6 patients, three were good supporters of angiogenesis and three were poor supporters of angiogenesis

overall_design: Cardiosphere derived cells were tested for their ability to support HUVEC supportive ability. 6 samples were expanded, RNA isolated and RNA-seq experiments carried out

first: Enca

last: Martin-Rendon

first: Mattia

last: Frontini


title: Global transcriptomic analyses of bronchial epithelial cells exposed to 5 ng/mL TGF-β1 and 10 nM Estrogen individually and in combination

status: Public on Jun 28 2017

city: Gainesville

first: Ley

middle: Cody

last: Smith

state: FL

address: 2187 Mowry Rd

institute: University of Florida

summary: To begin to identify downstream consequences of TGF-β1-induced reduction of estrogen receptor expression, we employed RNA-Seq.  Results of global transcriptomic analysis showed that TGF-β1 and E2 inversely modulated the expression of several genes involved in both known pro-fibrotic cellular processes such as extracellular matrix turnover and newly identified events including airway smooth muscle cell contraction and calcium flux regulation. We also report, for the first time, that E2 specifically modulated the expression of genes involved in chromatin remodeling pathways and that this regulation was absent in the presence of TGF-β1. Collectively, these results suggest that E2 influences pathways relevant to pulmonary fibrosis and highlights potential roles for E2 in the lung that may contribute to sex-specific differences in IPF.

overall_design: Four treatment groups were analyzed; cells exposed to vehicle control (n = 5), 5 ng/mL TGF-β1 (n = 5), 10 nM Estrogen (n = 3), or 5 ng/mL TGF-β1 and 10 nM Estrogen in combination (n = 4)

first: Tara

last: Sabo-Attwood


title: Lineage Reprogramming of Fibroblasts into Functional Neurons and Hepatocytes via Chemically Induced XEN-like State

first: Yan-Tao

last: Ma

address: No. 5 Yiheyuan Road

institute: Peking University

summary: Small-molecule based lineage reprogramming has newly emerged as a promising approach for generating functional cell types. We recently found that the chemical induction of iPSCs from fibroblasts pass through an extra-embryonic endoderm (XEN)-like state. In this study, we demonstrated that these chemically-induced XEN-like cells were not restricted to be reprogrammed to iPSCs, but feasible to be induced into functional neurons, bypassing the pluripotent stage. These induced neurons possessed neuron-specific expression profiles, formed functional synapses in culture dish and further matured after transplantation into brains of adult mice. Notably, by using similar principles, hepatocytes could also be induced from the XEN-like cells. Furthermore, the XEN-like cells are highly expandable (for at least 20 passages), retaining genome stability and lineage specifying potentials. Our study establishes a featured route of chemical lineage reprogramming and may provide a universal platform for generating large amounts of diverse functional cell types via the expandable XEN-like state.

overall_design: Total of 34 samples were analyzed, global transcriptional analysis of mouse fibroblasts, chemically-induced XEN-like cells, chemically-induced XEN-derived neuronal cells, chemically-induced XEN-derived hepatocyte-like cells, mouse primary neurons, mouse brain, mouse hepatocytes and mouse hepatic tissues by RNA-seq.

first: Xiang

last: Li

first: Defang

last: Liu

first: Yantao

first: Xiaomin

last: Du

first: Junzhan

last: Jing

first: Hongkui

last: Deng


title: Small RNA sequencing of mock treated or Sindbis virus-infected wild type and RNaseIII knockout cells

city: New York

first: Benjamin

last: tenOever

state: NY

address: 1468 Madison Avenue

department: Microbiology

institute: Ichan School of Medicine at Mount Sinai

summary: To assess the impact of endogenous RNaseIII nucleases on the small RNA profile in the presence and absence of virus infection.

overall_design: miRNA profiles of 293T and RNaseIII null cells alone or treated with SINV for 24 hours

middle: R


title: Transcriptome profiling of primary murine fibroblast response to IFNB with or without prior Drosha depletion

summary: To assess the impact of Drosha on the response to IFNB

overall_design: Non-replicateive Adeno vectors were used to deliver either GFP or Cre to primary fibroblasts 3 days before a 6hr treatment with 100U IFNB.


title: Identification and mode of action of a plant natural product targeting human fungal pathogens

first: Dominique

last: Sanglard

address: Rue Bugnon 48

institute: University of Lausanne and University Hospital Center

summary: Candida albicans was subjected to treatment with tomatidine and samples were taken at 2 different time points (1h, 3h). The results show that tomatidine induces genes involved in ergosterol biosynthesis as compared to untreated controls.

overall_design: C. albicans SC5314 strain was exposed to 250 µM tomatidine and total RNA was extracted after 1 h or 3 h tomatidine/solvent exposure.

first: Stéphane

last: Dorsaz


title: Single-cell landscape of transcriptional heterogeneity and cell fate decisions during mouse early gastrulation

city: Cambridge

first: Felix

last: Krueger

address: Granta Park

department: Bioinformatics

institute: Altos Labs

summary: This study explores lineage and regulatory processes involved in early post implantation mouse embryos using single-cell RNA-seq

overall_design: Single cells from C57Bl/6Babr  mouse embryos at E3.5, E4.5, E5.5 and E6.5 were isolated and subjected to single-cell RNA-seq protocol.

first: Hisham

last: Mohammed

first: Irene

last: Hernando-Herraez

first: Wolf

last: Reik


title: Functional Characterization of Human Pluripotent Stem Cell-derived Arterial Endothelial Cells

city: Madiosn

first: Jue

last: Zhang

state: WI

address: 330 N orchard st

institute: Morgridge Institute for Research

summary: Single cell RNA-seq was performed from CD31+CD144+CD41-CD45- endothelial cells isolated from E11.5 mouse AGM

first: Scott

last: Swanson


title: Extracellular Vesicles Transfer the Receptor PD-1 in Rheumatoid Arthritis.

city: Aarhus N

first: Morten

last: Veno

state: DK

address: Aabogade 15

institute: Omiics ApS

summary:
Extracellular vesicles (EVs) isolated from cell cultures contain miRNAs associated with T cell co-inhibitory receptors. These are differently regulated in EVs from RA patients and
could contribute to the development of a chronic disease.

overall_design:
Peripheral blood (PBMC) and synovial fluid (SFMC) mononuclear cells were cultured from RA patients and HCs. EVs were collected by ultracentrifugation, and the miRNA
profile investigated

first: Yan

last: Yan

last: Venø

first: Stinne

last: Greisen


title: Polycomb Repressive Complex 1 regulates transcription of active genes [ChIPseq]

city: Saint Louis

first: Dale

last: Dorsett

state: MO

address: 1100 South Grand Boulevard

department: Biochemistry and Molecular Biology

institute: Saint Louis University School of Medicine

summary: Binding of RNA Polymerase, Spt5, and PRC1 subunits to chromosomes was measured by ChIP-seq

overall_design: Comparison of binding of RNA Polymerase, Spt5 and PRC1 subunits in untreated (Mock) cells and cells RNAi depleted for PRC1 subunits

first: Michelle

last: Pherson


title: A sexually dimorphic "pre-stressed" translational signature in CA3 pyramidal neurons of BDNF Val66Met mice

first: Jordan

last: Marrocco

address: 1230 York Avenue

institute: The Rockefeller University

summary: BDNF Val66Met mice, a model that is genetically susceptible to stress, recapitulated the translational effects of acute stress in the absence of applied stressors. However, unstressed heterozygous BDNF Val66Met mice did not display activation of immediate early genes, indicating a “pre-stressed” translational phenotype.

overall_design:
Examination of  the effect of stress and a SNP in male and female mice in CA3 neurons
Sample Title abbreviations: VV = Wild Type, VM = Heterozygous BDNF Val66Met , F = Female, M = Male, FST = acute forced swim stress, Hi = High Estradiol, Lo = Low estradiol, TRAP = Translating Ribosome Affinity Purification

first: Bruce

last: McEwen


title: Dynamic and stable enhancer-promoter contacts regulate terminal differentiation [UMI-4C]

city: Stanford

first: Paul

last: Khavari

address: 269 Campus Drive, CCSR 2150

institute: Stanford University

summary: Genome-wide chromosome conformation capture (Hi-C) and promoter-capture Hi-C (CHi-C) were performed during epidermal differentiation. These data indicate that dynamic and constitutive enhancer-promoter contacts combine to control gene induction during differentiation and that chromosome conformation enables discovery of new TFs with distinct roles in this process.

overall_design: Hi-C and CHi-C data from epidermal keratinocyte progenitor and differentiated cells.

first: Adam

last: Rubin

first: Brook

last: Barajas


title: Lentiviral Vectors Escape Innate Sensing but Trigger p53 In Human Hematopoietic Stem Cells

city: Milano

first: Davide

last: Cittaro

address: via Olgettina 58

department: Center for Traslational Genomics and Bioinformatics

institute: Ospedale San Raffaele

summary: In the context of lentiviral vector (LV)-mediated gene correction of hematopoietic stem and progenitor cells (HSPC), the viral origin of LV could trigger cellular responses with potential functional consequences that have not been investigated to date. Here, a time-course genome-wide transcriptional profiling of transduced human HSPC reveals a remarkably limited impact of LV on cellular gene expression, supporting some stealth features of the vector. In particular, LV efficiently escaped innate immune sensing that instead led to robust type I IFN signaling upon transduction with a gamma-retroviral vector. However, recognition of LV DNA prior to integration did trigger DNA damage responses that were activated also by non-integrating Adeno-associated vector DNA. As a consequence of this transient p53 activation, transduced HSPC showed increased apoptosis in vitro and reduced engraftment in vivo at limiting cell doses, but no long-term impact or competitive disadvantage were detected. Pharmacological inhibition of the LV signaling partially rescued both apoptosis and engraftment, potentially providing a novel strategy to further dampen the impact of ex vivo gene therapy on HSPC. Overall, our results shed light on the molecular mechanisms of viral vector sensing in HSPC and provide critical insight for the development of more stealth gene therapy strategies.

overall_design: RNA-seq of CD34+ cells transduced with different lentiviral vectors. Multiple time points were profiled in biological triplicates.

first: Francesco

last: Piras

first: Michela

last: Riba

first: Carolina

last: Petrillo

first: Dejan

last: Lazarevic

first: Ivan

last: Cuccovillo

first: Sara

last: Bartolaccini

first: Elia

last: Stupka

first: Luigi

last: Naldini

first: Anna

last: Kajaste-Rudnitski


title: Reprogramming methods influence DNA methylation and expression patterns of mouse induced pluripotent stem cells [RNA-seq]

city: Shanghai

first: Jian

last: Hu

address: 1239,Siping Road

institute: Tongji University

summary: Induced pluripotent stem cells (iPSCs) can be derived from somatic cells through ectopic expression of transcriptional factors or chemical cocktails. Chemical reprogramming might be safe than transcriptional factors since there is no integration of exogenous genes. However, there is still little direct evidence to prove this hypothesis. In this study, we have performed whole genome profiling of the DNA methylomes of mouse chemical iPSCs (CiPSCs), transcriptional factors induced iPSCs (TF-iPSCs) and embryonic stem cells (ESCs). We find that the methylation levels of high-CpG-density promoters (HCPs) and intermediate- CpG-density promoters (ICPs) have no significant difference among them, but low-CpG-density promoters (LCP) and three retrotransposons (LINEs, LTRs and SINEs) show preference to different methylation levels. Surprisingly, CiPSCs are hypomethylated than TF-iPSCs and the major difference of methylation levels lies in the intergenic regions while two iPSCs lines are generally hypermethylated compared to ESCs. Moveover, we find the methylation states of imprinting control regions (ICRs) and the expression of imprinted genes of CiPSCs are more resemble ESCs than TF-iPSCs. Our data first provide the epigenetic states of chemical induced pluripotent stem cells and compare the difference of mouse CiPSCs, TF-iPSCs and ESCs. These observations might affect ongoing choices of reprogramming methods for disease modeling and give some guides for potential therapeutic applications.

overall_design: Comparison of DNA methylation and genes expression patterns in 3 cell types


title: Reprogramming methods influence DNA methylation and expression patterns of mouse induced pluripotent stem cells [RRBS]


title: Reprogramming methods influence DNA methylation and expression patterns of mouse induced pluripotent stem cells

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

overall_design: Refer to individual Series


title: Deletion of Gas2l3 in mice leads to specific defects in cardiomyocyte cytokinesis during development

city: Wuerzburg

first: Stefan

last: Gaubatz

address: Am Hubland

department: Biochemistry and Cell Biology

institute: University of Wuerzburg

summary: Mammalian cardiomyocytes lose the ability to proliferate shortly after birth. This accounts for the limited regeneration capacity of the mammalian heart. A characteristic feature of growth arrested cardiomyocytes is binucleation, but the molecular mechanisms are not well understood. In rodents, binucleation of cardiomyocytes starts after birth and occurs through incomplete cytokinesis. Here we demonstrate an important and unexpected role of GAS2L3, a recently identified actin and tubulin binding protein, for cardiomyocyte cytokinesis during heart development in mice. Mice deficient in GAS2L3 die shortly after birth due to dilated cardiomyopathy. Cardiomyocyte-specific deletion of GAS2L3 confirmed that the phenotype resulted from the loss of GAS2L3 in cardiomyocytes. We show that a deficiency in GAS2L3 leads to a strong reduction in cardiomyocyte numbers due to reduced proliferation. In addition, the loss of Gas2l3 resulted in premature binucleation of cardiomyocytes and in induction of a p53-transcriptional program including the cell cycle inhibitor p21. Collectively, these data identify an important role for GAS2L3 in cardiomyocyte cytokinesis during development.

overall_design: Sequencing of mRNA extracted from hearts of E18.5 wildtype and Gas2L3 -/- mouse embryos , in triplicate, using Illumina NextSeq500.

first: Marco

last: Gründl

first: Björn

last: von Eyß

first: Elmar

last: Wolf


title: Characteristics of microRNA expression profile of equine sarcoid samples

city: Balice near Krakow

first: Klaudia

last: Pawlina-Tyszko

address: Krakowska 1

department: Deaprtment of Animal Genomics and Molecular Biology

country: Poland

institute: National Research Institute of Animal Production

summary: We report the application of next-generation sequencing for high-throughput profiling of microRNA expression characterictic for horse sarcoid, which is a skin tumor. With the use of HiScanSQ system (Illumina), we obtained over 124 million sequence reads from microRNA libraries. As a result, we identified over 200 known, as well as around 500 potentially novel, miRNA sequences. The analysis of differential expression of the identified miRNAs revealed that over 100 miRNAs were up- or downregulated in the sarcoid tissue in comparison to the control. The analysis of pathways showed e.g. pathways in cancer, viral carcinogenesis or transcriptional misregulation in cancer. Furthermore, microRNAs associated with carcinogenesis in humans were identified, such as: miR-10a, miR-21, miR-200 family. Concluding, our results suggest that microRNAs are largely involved in the neoplastic transformation of horse sarcoids.

overall_design: Identification of microRNAs expressed in sarcoid tissue samples and tumor-distant skin (control) samples obtained from five horses.

last: Pawlina

first: Artur

last: Gurgul

first: Tomasz

last: Szmatola

first: Christoph

last: Koch

first: Kathrin

last: Mahlmann

first: Maciej

last: Witkowski

first: Monika

last: Bugno-Poniewierska