title: Transcriptome analysis of human reninomas as an approach to understanding juxtaglomerular cell biology

city: Montreal

first: Timothy

middle: L

last: Reudelhuber

state: Quebec

address: 110 Avenue des Pins Ouest

country: Canada

institute: IRCM

summary: Renin, a key component in the regulation of blood pressure in mammals, is produced by the rare and highly specialized juxtaglomerular (JG) cells of the kidney. Although these cells line the media of the glomerular afferent arterioles and share some characteristics with contractile cells, they are filled with lysosome-like organelles where renin is activated and stored for regulated secretion in response to physiological and pathophysiological stimuli. Chronic stimulation of renin release results in a recruitment of new JG cells by the seeming conversion of adjacent smooth muscle cells along the afferent arterioles. Because JG cells rapidly de-differentiate when removed from the kidney, their developmental origin and the mechanism that explains their phenotypic plasticity remain largely unclear. In an effort to overcome this limitation, we have performed RNA expression analysis on four human renin-producing tumors. The most highly expressed genes that were common between the reninomas were subsequently used for in situ hybridization in mouse kidney. Our results add 40 new genes to the list that characterize renin-producing cells and reveal a significant variation in the expression patterns of developing, mature and recruited JG cells.

overall_design: RNA-Seq was performed with a HiSeq 2000 on three biopsies of a first reninoma from Paris (Par1B1-B3), one biopsy from a reninoma from Montreal (Mon), two biopsies from a reninoma from Rotterdam (RotB1, B2), and a second reninoma from Paris (Par2) along with a biopsy from adjacent supposedly normal tissue from the same patient (Par2N).

first: Lucie

middle: K

last: Xa

first: Marie

last: Lacombe

first: Chantal

last: Mercure

first: Alexis

last: Blanchet-Cohen

first: Benjamin

last: Haibe-Kains

first: Anton

last: van den Meiracker

first: Jan

middle: A

last: Danser

first: Kenneth

last: Gross

first: Michel

last: Azizi

first: Pierre

last: Corvol

first: Genevieve

last: Nguyen


title: Mapping Mouse Cell Atlas by Microwell-seq

status: Public on Feb 14 2018

city: hangzhou

first: guoji

last: guo

state: zhejiang

address: yuhangtang road 388

department: Center for Stem Cell and Regenerative Medicine

country: China

institute: Zhejiang University School of Medicine

summary: We developed Microwell-seq, a high-throughput and low-cost scRNA-seq platform using simple, inexpensive devices. Using Microwell-seq, we constructed a basic scheme for the Mouse Cell Atlas. We reveal single cell hierarchy for many tissues that have not been well previously characterized.  Our study demonstrates the wide applicability of the Microwell-seq technology and the Mouse Cell Atlas resource.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: Expression profiling by high throughput sequencing of major mouse organ types.

first: Xiaoping

last: Han

first: Renying

last: Wang


title: Cell-type specific sequencing of microRNAs from complex animal tissues V

city: Vienna

first: Chiara

last: Alberti

address: Campus-Vienna-Biocenter 1

country: Austria

institute: IMP

type: Non-coding RNA profiling by high throughput sequencing

summary: MicroRNAs (miRNAs) play an essential role in the post-transcriptional regulation of animal development and physiology. However, in vivo studies linking miRNA-function to the biology of distinct cell types within complex tissues remain challenging, partly due to the difficulties in achieving cellular resolution using available miRNA-profiling methods. Here, we report an in vivo small RNA-tagging approach that enables high-throughput sequencing of tissue- and cell type-specific miRNAs in animals, which we call microRNome by methylation-dependent sequencing, or mime-seq. The method combines orthogonal, cell-type-specific 3´ terminal 2’-O-methylation of animal miRNAs by the plant-specific methyltransferase HEN1, with oxidation-sensitive small RNA cloning and high-throughput sequencing. We show that mime-seq uncovers the miRNomes of rare cells within C. elegans and Drosophila at unprecedented specificity and sensitivity, enabling miRNA profiling with single-cell resolution in whole animals. Mime-seq overcomes the current challenges in tissue- and cell-type-specific small RNA profiling and provides novel entry points for understanding the function of miRNAs in spatially restricted physiological settings.

overall_design: 2 small RNA libraries from L1-staged C. elegans in two different conditions (untreated and treated with sodium periodate).

first: Raphael

last: Manzenreither

first: Ivica

last: Sowemimo

first: Thomas

middle: R

last: Burkard

first: Jingkui

first: Luisa

last: Cochella

first: Stefan

last: Ameres


title: Identification of miR-305, a microRNA that promotes ageing, and its target mRNAs in Drosophila

city: Fukuoka

first: Tetsuya

last: Sato

address: 3-1-1, Maidashi Higashi-ku

country: Japan

institute: Kyushu University

type: Expression profiling by high throughput sequencing

summary: MicroRNAs (miRNAs) are involved in the regulation of important biological processes. Here, we describe a novel Drosophila miRNAs involved in ageing. We selected eight Drosophila miRNAs, displaying high homology with seed sequences of ageing-related miRNAs characterized in other species, and investigated whether the overexpression of these miRNAs affected ageing in Drosophila adult flies. The lifespan of adults overexpressing miR-305, a miRNA showing high homology with miR-239 in C. elegans, was significantly shorter. Conversely, a reduction in miR-305 expression led to a longer lifespan than that in control flies. miR-305 overexpression accelerated the impairment of locomotor activity, and promoted the age-dependent accumulation of poly-ubiquitinated protein aggregates in the muscle, as flies aged. Thus, we demonstrate that the ectopic expression of miR-305 has a deleterious effect on ageing in Drosophila. To identify the targets of miR-305, we performed RNA-Seq. We discovered several mRNAs encoding antimicrobial peptides and insulin-like peptides, whose expression changed in adults upon miR-305 overexpression. We further confirmed, by qRT-PCR, that miR-305 overexpression significantly decreases the mRNA levels of four antimicrobial peptides. As these mRNAs contain multiple sequences matching the seed sequence of miR-305, we speculate that a reduction in target mRNA levels, caused by ectopic miRNA expression, promotes ageing.

overall_design: mRNA profiles of adults overexpressiong miR-305 and control male flies.

first: Makiko

last: Ueda

first: Yasuyuki

last: Ohkawa

first: Yoshihiro

middle: H

last: Inoue


title: Next Generation Sequencing  Analysis of ADHFE1 and vector control Transcriptomes in breast cancer cells

status: Public on Feb 16 2018

city: Bethesda

first: Prachi

last: Mishra

state: MD

address: 37 convent drive

country: USA

institute: National Cancer Institute

summary: Our study represents a detailed analysis of MCF10A and MCF7 transcriptomes, with biologic replicates, generated by RNA-seq technology

overall_design: Expression profiling of cell lines MCF10A and MCF7 that were untreated or treated with 1mM octyl-2HG, 1 mM control compound, transfected with empty vector or ADHFE1-overexpression construct.

last: Ambs

first: Wei

last: Tang


title: lncRNA expression profilings in ectopic and eutopic endometria of ovarian endometriosis.

city: Beijing

first: Luyang

last: Zhao

address: 28 Fuxing Road, HaiDian District

department: Department of Gynecology and Obstetrics

institute: People’s Liberation Army (PLA) Medical School, Chinese PLA General Hospital

summary: The etiology and pathophysiology of endometriosis remain unclear. Accumulating evidence suggests that aberrant mRNA and lncRNA expressions may be involved in the pathogenesis and development of endometriosis. This study therefore aims to survey key TFs, genes and lncRNAs and further understand the mechanism of endometriosis. Paired expression profiling of mRNA and lncRNA in ectopic endometria compared with eutopic endometria were determined by high-throughput sequencing techniques in eight patients with ovarian endometriosis. Our study presents a unique insight into the regulatory network of this enigmatic disorder and possibly provides clues regarding replacement therapy of endometriosis.

overall_design: Eight paired ectopic endometria (EC) and eutopic endometria (EU) from 8 patients with ovarian endometriosis obtained from Chinese PLA general hospitalwere selected and prepared for lnc RNA sequencing.All of the patients were confirmed by histological examination and diagnosed at the moderate to severe (III-IV) stage by the revised American Fertility Society (r-AFS) classification during laparoscopic surgery. EC were obtained during laparoscopy, and EU were obtained through curettage before the laparoscopic procedure. Only patients in the secretary phase of the menstrual cycle and without any hormonal treatment history were included in the study. Total RNA was isolated from frozen tissue. High quality RNA was subjected to Illumina HiSeq 2000 and 4000 platform in Annoroad Genome (Beijing, China).

first: Yuanguang

last: Meng

first: Chenglei

last: Gu


title: Alveolar Injury and Regeneration Following Deletion of ABCA3

status: Public on Feb 15 2018

city: Cincinnati

first: John

middle: M.

last: Snowball

state: OH

address: 3333 Burnet Ave

department: Pulmonary Research

institute: Cincinnati Childrens Hospital

summary: Surfactant deficiency, diffuse alveolar damage and respiratory failure caused by loss of Abca3 in AT2 cells was followed by remarkable proliferation of alveolar cells and selective survival of ABCA3 sufficient cells resulting in regeneration of alveolar structure and function, providing the conceptual framework for the development of therapies to ameliorate lung diseases caused by mutations in ABCA3 and other genes critical for AT2 cell function or surfactant homeostasis.

overall_design: Control and Abca3 cKO AT2 cell RNA-seq at 6 days post tamoxifen in adult mice.

first: Tara

last: Rindler

first: Courtney

last: Stockman

first: Alyssa

last: Filuta

first: Kari

middle: M

last: Brown

first: Wenjia

last: Zhou

first: Ruud

last: Veldhuizen

first: Erika

last: Zink

first: Sydney

middle: E

last: Dautel

first: Geremy

last: Clair

first: Charles

last: Ansong

first: Yan

last: Xu

first: James

middle: P

last: Bridges

first: Jeffrey

last: Whitsett


title: microRNA expression profilings in ectopic and eutopic endometria of ovarian endometriosis.

first: Luyang

last: Zhao

summary: The etiology and pathophysiology of endometriosis remain unclear. Accumulating evidence suggests that aberrant microRNA (miRNA) expression may be involved in the pathogenesis and development of endometriosis. This study therefore aims to survey key miRNAs and further understand the mechanism of endometriosis. Paired expression profiling of miRNA in ectopic endometria compared with eutopic endometria were determined by high-throughput sequencing techniques in eight patients with ovarian endometriosis. Our study presents a unique insight into the regulatory network of this enigmatic disorder and possibly provides clues regarding replacement therapy of endometriosis.

overall_design: Eight paired ectopic endometria (EC) and eutopic endometria (EU) from 8 patients with ovarian endometriosis obtained from Chinese PLA general hospitalwere selected and prepared for small RNA sequencing.All of the patients were confirmed by histological examination and diagnosed at the moderate to severe (III-IV) stage by the revised American Fertility Society (r-AFS) classification during laparoscopic surgery. EC were obtained during laparoscopy, and EU were obtained through curettage before the laparoscopic procedure. Only patients in the secretary phase of the menstrual cycle and without any hormonal treatment history were included in the study. Total RNA was isolated from frozen tissue. High quality RNA was subjected to Illumina HiSeq 2000 in Annoroad Genome (Beijing, China).


title: Integrative Gene Network Analysis Identifies Key Signatures, Intrinsic Networks and Host Factors for Influenza Virus A Infections

city: New York

first: Christian

last: Forst

state: NY

address: One Gustave L. Levy Place

department: Genetics and Genomic Sciences

institute: Icahn School of Medicine at Mount Sinai

summary: Influenza A virus, with the limited coding capacity of 10 to 14 proteins, requires the host cellular machinery for many aspects of its life cycle. Knowledge of these host cell requirements not only reveals molecular pathways exploited by the virus or triggered by the immune system, but also provides further targets for antiviral drug development. To uncover novel pathways and key targets of influenza infection, we assembled a large amount of data from 12 cell-based gene-expression studies of influenza infection for an integrative network analysis. We systematically identified differentially expressed genes and gene co-expression networks induced by influenza infection. We revealed the dedicator of cytokinesis 5 (DOCK5) played potentially an important role for influenza virus replication. CRISPR/Cas9 knockout of DOCK5 reduced influenza virus replication, indicating that DOCK5 is a key regulator for the viral life cycle. DOCK5’s targets determined by the DOCK5 knockout experiments strongly validated the predicted gene signatures and networks. This study systematically uncovered and validated fundamental patterns of molecular responses, intrinsic structures of gene co-regulation, and novel key targets in influenza virus infection.

overall_design: Transcriptome profile of A549 WT and DOCK5 KO cells, mock infected and infected by H1N1 and H3N2 influenza strains, each in triplicates

middle: V

first: Bin

first: Minghui

last: Wang

first: Tsui-Wen

last: Chou

first: Guy

last: Mason

first: Won-min

last: Song

first: Eric

last: Schadt

first: Elodie

last: Ghedin

last: Zhang


title: m6A-irCLIP of mouse CD4+ T cell RNA

city: Stanford

first: Howard

last: Chang

state: CA

address: 269 Campus Drive

department: Dermatology

institute: Stanford University School of Medicine

type: Methylation profiling by high throughput sequencing

summary: Identify m6A modified residues by m6A-irCLIP in polyA selected RNA from mouse CD4+ T cells

overall_design: 2 replicates, polyA selected RNA

last: Broughton

first: Huabing

last: Li


title: Development of Novel Patient Derived Xenografts from Breast Cancer Brain Metastases

city: Aurora

first: Peter

last: Kabos

state: CO

address: 12801 E. 17th Avenue

department: Division of Medical Oncology

institute: University of Colorado School of Medicine

summary: Brain metastases are an increasing burden among breast cancer patients, particularly for those with HER2+ and triple negative (TN) subtypes. Mechanistic insight into the pathophysiology of brain metastases and preclinical validation of therapies has relied almost exclusively on intracardiac injection of brain-homing cells derived from highly aggressive TN MDA-MB-231 and HER2+ BT474 breast cancer cell lines. Yet, these well characterized models are far from representing the tumor heterogeneity observed clinically and, due to their fast progression in vivo, their suitability to validate therapies for established brain metastasis remains limited. The goal of this study was to develop and characterize novel human brain metastasis breast cancer patient-derived xenografts (BM-PDXs) to study the biology of brain metastasis and to serve as tools for testing novel therapeutic approaches. We obtained freshly resected brain metastases from consenting donors with breast cancer. Tissue was immediately implanted in the mammary fat pad of female immunocompromised mice and expanded as BM-PDXs. Brain metastases from 3/4 (75%) TN, 1/1 (100%) estrogen receptor positive (ER+), and 5/9 (55.5%) HER2+ clinical subtypes were established as transplantable BM-PDXs. To facilitate tracking of metastatic dissemination using BM-PDXs, we labeled PDX-dissociated cells with EGFP-luciferase followed by re-implantation in mice, and generated a BM-derived cell line (F2-7). Immunohistologic analyses demonstrated that parental and labeled BM-PDXs retained expression of critical clinical markers such as ER, progesterone receptor (PR), epidermal growth factor receptor (EGFR), HER2 and the basal cell marker cytokeratin 5 (CK5). Similarly, RNA sequencing analysis showed clustering of parental, labeled BM-PDXs and their corresponding cell line derivative. Intracardiac injection of dissociated cells from BM-E22-1, resulted in MRI-detectable macrometastases in 4/8 (50%) and micrometastases (8/8) (100%) mice, suggesting that BM-PDXs remain capable of colonizing the brain at high frequencies. Brain metastases developed 8 to 12 weeks after ic injection, located to the brain parenchyma, grew around blood vessels and elicited astroglia activation characteristic of breast cancer brain metastasis. These novel BM-PDXs represent heterogeneous and clinically relevant models to study mechanisms of brain metastatic colonization, with the added benefit of a slower progression rate that makes them suitable for preclinical testing of drugs in therapeutic settings.

overall_design: RNA-seq from three patient-derived breast cancer brain metastases.

first: Diana

last: Cittelly

first: Austin

last: Gillen


title: PITX1 Promotes Chondrogenesis and Myogenesis in Mouse Hindlimbs Through Conserved Regulatory Targets [RNA-Seq]

city: Dallas

first: Jialiang

state: TX

address: 5323 Harry Hines Blvd

institute: University of Texas Southwestern Medical Center

summary: The PITX1 transcription factor is expressed during hindlimb development, where it plays a critical role in directing hindlimb growth and the specification of hindlimb morphology. While it is known that PITX1 regulates hindlimb formation, in part, through activation of the Tbx4 gene, other transcriptional targets remain to be elucidated. We have used a combination of ChIP-seq and RNA-seq to investigate enhancer regions and target genes that are directly regulated by PITX1 in embryonic mouse hindlimbs. In addition, we have analyzed PITX1 binding sites in hindlimbs of Anolis lizards to identify ancient PITX1 regulatory targets. We find that PITX1-bound regions in both mouse and Anolis hindlimbs are strongly associated with genes implicated in limb and skeletal system development. Gene expression analyses reveal a large number of misexpressed genes in the hindlimbs of Pitx1-/- embryos. By intersecting misexpressed genes with genes that have neighboring mouse PITX1 binding sites, we identified 440 candidate targets of PITX1. Of these candidates, 68 exhibit ultra-conserved PITX1 binding events that are shared between mouse and Anolis hindlimbs. Among the ancient targets of PITX1 are important regulators of cartilage and skeletal muscle development, including Sox9 and Six1. Our data suggest that PITX1 promotes chondrogenesis and myogenesis in the hindlimb by direct regulation of several key members of the cartilage and muscle transcriptional networks.

overall_design: Hindlimb mRNA profiles of E9.5, E11.5 and E12.5 wild type (WT) and Pitx1-/- mice were generated by deep sequencing in triplicate.

middle: S

first: Carlos

last: Infante

first: Sungdae

last: Park

first: Douglas

middle: B

last: Menke


title: Genome-wide analyses of direct target genes of four rice NAC-domain transcription factors involved in 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: To understand the molecular mechanisms of drought tolerance, we performed ChIP-Seq and RNA-Seq analyses to identify direct target genes of the OsNACs using the RCc3:MYC-OsNACs roots. A total of 475 binding loci of 4 OsNACs were identified by cross-referencing the binding occupancy of OsNACs at promoter regions and expression levels of corresponding genes. The binding loci are distributed on promoter regions of 391 target genes that were directly up-regulated by OsNACs in four RCc3:MYC-OsNAC transgenic roots. The direct target genes were related to transmembrane/transporter activity, vesicle, plant hormone, carbohydrate metabolism, and transcription factors. The direct targets of each OsNAC are in a range of 4.0 to 8.7% of the genes up-regulated in RNA-Seq data sets. Thus, each OsNAC up-regulates of corresponding direct target genes that alters root system architectures of RCc3:OsNACs for drought tolerance.

overall_design: RNA-seq using roots of NT (nontransgenic plants), RCc3:myc-OsNAC5, 6, 9, and 10 transgenic plants that were generated by deep sequencing using Illumina Hiseq 2500.

first: Pil

middle: J

first: Ju-Kon

last: Kim


title: Transcriptomic study of single mutants hns, hns2 and double mutans hhahha2 and hnshns2 from enteroaggregative E. coli 042 by RNA-seq

city: Barcelona

first: Mario

last: Huttener Queiroz

address: Av. Diagonal 643

country: Spain

institute: Universitat de Barcelona

summary: Bacterial genomes encode in many instances more than one copy of genes coding for global modulators. In the Enterobacteriaceae, cells express the global modulator H-NS and its paralogue StpA. The enteroaggregative E. coli strain 042 encodes, in addition to the hns and stpA genes, an additional hns gene. We used RNA-seq to compare the transcriptome of the wt strain and its hns, hns2 and double hns hns2 derivatives, as well as of an hha null mutant (hhahha2). It is well known that the Hha protein co-modulates gene expression with H-NS. The results obtained have shown that the main role of H-NS2 is to modulate a subset of H-NS modulated genes, those that also are targeted by Hha, which are mainly HGT genes. When compared with H-NS, H-NS2 also shows a differential expression level and a different regulatory pattern.

overall_design: E. coli 042 and derivative mutants hns, hns2, hnshns2 and hhahha2 mRNA profiles were generated by Illumina RNA-seq. RNA extraction, DNase treatment, evaluation of RNA quality and cDNA libraries for Illumina sequencing were performed by Vertis Biotechnologie AG, Freising-Weihenstephan, Germany. Bacterial cells were grown until O.D.600 of 2,0 in LB medium at 37ºC with 200rpm of agitation. Three replicates were grown from each strain, 1 ml of each replicate was collected and bacterial pellets were maintained at -80ºC. Bacterial pellets were sent to Vertis Biotechnologie AG, Freising-Weihenstephan, Germany in dry ice. E. coli 042 wt was used as genome reference (NC_017626.1) for analysis.

first: A

last: Prieto

first: M

last: Bernabeu

first: S

last: Aznar

last: Ruiz-Cruz

last: Bravo

last: Hüttener

last: Juárez


title: HIF and HOIL-1L-mediated PKCζ degradation stabilizes plasma membrane Na,K-ATPase to protect against hypoxia-induced lung injury

city: Chicago

first: Jacob

middle: Iasha

last: Sznajder

state: IL

address: 240 East Huron

department: Medicine

institute: Northwestern University

summary: Exposure to hypoxia requires adaptive mechanisms for survival. During acute hypoxia, Na,K-ATPase endocytosis in alveolar epithelial cells (AEC) occurs via protein kinase C zeta (PKCζ) phosphorylation of α1- Na,K-ATPase independently of the hypoxia inducible factor (HIF). However, exaggerated Na,K-ATPase down-regulation leads to cell death. Here we report that during prolonged hypoxia plasma membrane Na,K-ATPase levels were maintained at ~50% of normoxic values due to HIF mediated regulation of HOIL-1L which targets PKCζ for degradation. Silencing HOIL-1L in the lung epithelium prevented PKCζ degradation causing Na,K-ATPase downregulation.  Accordingly, HIF regulation of HOIL-1L targets the phosphorylated PKCζ for degradation and serves as an hypoxia-adaptive mechanism to stabilize the Na,K-ATPase avoiding significant lung injury.

overall_design: ATII mRNA profiles of 8-10 weeks old wild-type (WT) and CreSPC/HOIL-1Lfl/fl mice were generated and sequenced by NextSeq 500 High Output reagent kit (Illumina Inc).

middle: I

first: Aaron

last: Ciechanover

first: Laura

last: Dada

first: Natalia

last: Magnani

first: Kishore

last: Anekalla

first: Alexander

last: Misharin


title: Genome-wide search for differentially expressed RNAs responsible for the effects induced by Ebola virus replication and transcription

first: zhongyi

last: wang

address: No.27, Taiping road, Haidian district, Beijing

institute: Academy of Military Medical Sciences

summary: In this study, we conducted a genome-wide screen to identify differentially expressed long noncoding RNAs (lncRNAs), circular RNAs (circRNAs), micro RNAs (miRNAs) and mRNAs during replication and transcription using a tetracistronic transcription and replication-competent virus-like particle (trVLP) system that models the life cycle of EBOV in 293T cells.

overall_design: P1 trVLPs were used to infect 293T cells and the TCID50 of P1 trVLPs was 10^-6.5/ml. Approximately 4×10^5 cells were present in each well of a 6-well plate, and P1 trVLPs used for infection in this experiment were applied in a volume of 2 ml per well. There were three wells per time point (0 hour, 24 hour, 48 hour, 72 hour and 96 hour) for the sequencing step. The samples in each well was used for independent experiments.

first: Zhongyi

last: Wang

first: Jun

last: Qian

first: Linna

last: Liu


title: Transcriptome sequencing reveals key potential long non-coding RNAs related to duration of fertility trait in the uterovaginal junction of egg-laying hens

city: Wuhan

first: Adeyinka

middle: Abiola

last: Adetula

state: Hubei

address: No. 1 Shizishan Road, Hongshan District

department: Animal genetics, Breeding, and Reproduction

institute: Huazhong Agricultural University

summary: Duration of fertility, (DF) is an important functional trait in poultry production and lncRNAs have emerged as important regulators of various process including fertility. In this study we applied a genome-guided strategy to reconstruct the uterovaginal junction (UVJ) transcriptome of 14 egg-laying birds with long- and short-DF (n = 7); and sought to uncover key lncRNAs related to duration of fertility traits by RNA-sequencing technology. Examination of RNA-seq data revealed a total of 9977 lncRNAs including 2576 novel lncRNAs. Differential expression (DE) analysis of lncRNA identified 223 lncRNAs differentially expressed between the two groups. DE-lncRNA target genes prediction uncovered over 200 lncRNA target genes and functional enrichment tests predict a potential function of DE-lncRNAs. Gene ontology classification and pathway analysis revealed 8 DE-lncRNAs, with the majority of their target genes enriched in biological functions such as reproductive structure development, developmental process involved in reproduction, response to cytokine, carbohydrate binding, chromatin organization, and immune pathways. Differential expression of lncRNAs and target genes were confirmed by qPCR. Together, these results significantly expand the utility of the UVJ transcriptome and our analysis identification of key lncRNAs and their target genes regulating DF will form the baseline for understanding the molecular functions of lncRNAs regulating DF.

overall_design: lncRNA expression profiling in the Utero-vaginal junction (UVJ) of long- and short-DF hens.

first: Li

last: Shijun

first: Zhao

last: Shuhong


title: mRNA-Seq profiling of human developing kidney

city: Los Angeles

first: Andrew

last: McMahon

state: California

address: 1425 San Pablo St, BCC 312

department: Stem Cell Biol & Regen Med

institute: University of Southern California

summary: To characterize the molecular features of human kidney development, and to capture timing of emergence of important kidney compartments, we generated mRNA-Seq data from human kidneys at various developing stages. In order to capture tissue representing the entire kidney, we sampled kidneys with a wedge spanning from the cortex to medulla region.

overall_design: Comparing gene expression profiles of human kidneys at different stages and find the features of early versus late kidneys in development

first: Tran

last: Trinh Khiet

first: Qiuyu

last: Guo

first: Nils

last: Lindstrom

last: McMcMahon


title: Leucine differentially regulates gene-specific translation in mouse skeletal muscle

city: Salt Lake City

first: Michael

middle: T

last: Howard

state: UT

department: Human Genetics

institute: University of Utah

summary: Mice received an oral gavage of either leucine or vehicle, and quadriceps muscle were harvested for ribosome profiling or RNA-Seq analysis.

overall_design: Gene expression analysis in the skeletal muscle of leucine treated or control mice.


title: Alcohol feeding promotes colonic permeability and changes in colonic organoid stem cell fate

city: Cleveland

first: Peter

last: Wilkinson

state: Ohio

address: 2103 Cornell Road

department: Pathology / Systems Biology & Bioinformatics

institute: Case Western Reserve University

summary: Alcohol increases intestinal permeability to pro-inflammatory microbial products including endotoxin and this is a key step in alcohol-induced organ damage such as alcoholic liver disease.  Elevated intestinal permeability is observed even after a period of sobriety. We sought to investigate mechanisms contributing to long-term effects of alcohol on intestinal permeability by testing the hypothesis that alcohol affects intestinal stem cells using ex vivo organoids generated from jejunum and colon from chronic alcohol fed mice.

overall_design: BL/6 mice were fed a control or an alcohol diet for eight weeks. Intestinal permeability was assessed in vivo and using ex vivo organoids  from colon and jejunum

first: CB

last: Forsyth

first: M

last: Shaikh

first: F

last: Bishehsari

first: G

last: Swanson

first: RM

last: Voigt

first: H

last: Dodiya

first: P

first: B

last: Tryniszewska

first: S

last: Song

first: A

last: Keshavarzian


title: Neural induction by the node and placode induction by head mesoderm share an initial state resembling neural plate border

city: London

first: Andrea

last: Streit

address: Centre for Craniofacial & Regenerative Biology, King's College London

country: United Kingdom

institute: Kings College London

summary:
Purpose:  The goal of this study is to identify similarities and differences in the induction of the central nervous system and the sensory placodes in chick.
Method: mRNA profiles for central and anterior pre-steak epiblast, neural plate, anterior and posterior pre-placodal region, non-neural epiblast, gastrula stage area opaca exposed to Hensen's node for 5 hours and control area of opaca from the same stage.  Deep sequencing was carried with Illumina HiSeq 2000. After filtering low quality reads, alignment was carried using TopHat2, differential expression analysis was done using R-package (easyRNA-seq and DSEq).
Results:  Despite the differences in inducing tissues (i.e. node and lateral head mesoderm) and in the final outcome (neural plate and pre-placodal region), the initial set of genes induced by both tissues is largely identical. We define this transcriptional signature as 'pre-neural state', and demonstrate its functional significance for both inductive processes.  An unbiased approach using GENEI3 and community clustering reveals  the gene regulatory modules characterising the transcirptional states of pre-neural, neural and placodal cells.
Conclusion:  Induction of the neural plate and the pre-placodal region initially share common features, and diverge later.  The pre-neural state is similar to the neural plate border and pre-streak epiblast state.

overall_design: Overall design:  mRNA profiles for 8 biological samples representing different stages in neural and pre-placodal induction were processed for deep sequencing data by Illumina HiSeq 2000.

first: Ravindra

last: Prajapati

first: Katherine

last: Trevers

first: Mark

last: Hintze

first: Natalia

last: Moncaut

first: Ramya

last: Ranganathan

first: Mohsin

middle: F

last: Khan

first: Claudio

middle: D

last: Stern


title: Transcriptome Analysis of Arabidopsis Root Development in Response to Treatment With Rhizobium sp. IRBG74

city: Milwaukee

first: Dazhong

last: Zhao

state: WI

address: 3209 N. Maryland Ave

department: Biological Sciences Department

institute: University of Wisconsin-Milwaukee

summary: To examine how the Arabidopsis root development responds to the Rhizobium sp. IRBG74 treatment at the molecular level, we performed RNA-seq experiments. Our RNA-seq results suggest that expression of genes mainly involved in auxin signaling, cell wall and cell membrane integrity and transport is altered in response to colonization by Rhizobium sp. IRBG74.

overall_design: Examination of Arabidopsis roots treated by Rhizobium sp. IRBG74 for 24 and 48 hours.

first: Jian

last: Huang


title: Analysis of Combined Transcriptomes Identifies Gene Modules Differentially Responding to Pathogenic Stimulation in Vascular Smooth Muscle and Endothelial Cells

city: Madison

first: Lianwang

last: Guo

address: 1111 Highland Avenue

department: Surgery

institute: University of Wisconsin at Madison

summary: Smooth muscle cells (SMCs) and endothelial cells (ECs) constitute vasculature media and endothelium, respectively. Current treatments for cardiovascular disease inhibit SMC hyperplasia but also damage the protective endothelial lining, predisposing patients to thrombosis. Therapeutics targeting SMCs without collateral damage to ECs are highly desirable. However, differential (SMCs versus ECs) disease-associated regulations remain poorly defined. We conducted RNA-seq experiments to investigate SMC-versus-EC differential transcriptomic dynamics, following treatment of human primary SMCs and ECs with TNFα or IL-1β, both established inducers of SMC hyperplasia and EC dysfunction. To analyze combined SMC/EC transcriptomes we developed customized algorithms. Induced by TNFα or IL-1β, 212 and 263 genes respectively showed greater up-regulation in SMCs than in ECs (SMC-enriched), while 140 and 204 genes showed greater up-regulation in ECs over SMCs (EC-enriched). Analysis of gene interaction networks identified 5 common hubs and 4 common bottlenecks in the two SMC-enriched gene sets, and 8 hubs and 3 bottlenecks shared in the EC-enriched gene sets. Significantly, four gene modules were formed with these hubs and bottlenecks. While the JUN module (including JUN, KLF5, HIF1A, CXCL8, FOSL1) and FYN module (FYN, JAK2, MAP2, PIK3R3, DAB2, ASAP2) were SMC-enriched, the SMAD3 (SMAD3, CDKN1A, TRAF1, BCL6, CEBPD, TRIB3, ANK3) and XPO1 (XPO1, ETS2, SSH2, NDRG1, GFPT2?) modules were EC-enriched. As these core subnetworks respond to pathogenic stimulation in a SMC-versus-EC differential manner, they may inform potential intervention targets for selective mitigation of SMC hyperplasia without endothelial damage.

overall_design: In this study, we performed RNA sequencing (RNA-seq) and global analyses of differential SMC-versus-EC transcriptomic responses, to the same pathogenic cytokine stimulant under stringently controlled conditions. The objective was to identify the gene modules (or subnetworks) that are highly up-regulated in SMCs yet little affected or regulated toward the opposite direction in ECs

first: Bowen

last: Wang

first: Xiaokang

last: Pan

first: Tiezheng

last: Yuan

first: Mengxue

last: Zhang

first: K

middle: C

last: Kent

first: Lian-Wang


title: Analysis of differential gene expression in the Streptococcus sanguinis ciaR mutant

city: Richmond

first: Ping

last: Xu

state: VA

address: 521 North 11th street

department: Philips Institute for Oral Health Research

institute: Virginia Commonwealth Univ. School of Dentistry

summary: Gene expression profile of the Streptococcus sanguinis two component system regulator, ciaR, deletion mutant compared to the wild-type strain SK36

overall_design: Experiment: ciaR mutant vs. wild-type SK36 and ciaR complementary strain vs. wild-type SK36. Biological replicates independently grown and prepared for each sample.

first: Victoria

middle: N

last: Stone


title: Evolutionary recruitment of flexible Esrp-dependent splicing programs into diverse embryonic morphogenetic processes

first: Demian

last: Burguera

address: Diagonal 643

department: Genetics, Faculty of Biology

institute: University of Barcelona

summary: Epithelial-mesenchymal interactions are crucial for the development of multiple animal structures. Thus, unraveling how molecular tools are recruited in different lineages to control the interplay between these tissue types is key to understand morphogenetic evolution. Here, we studied Epithelial Splicing Regulatory Protein (Esrp) genes, which regulate extensive alternative splicing programs associated with cell adhesion and motility in human cells and are essential during mouse organogenesis. We found that Esrp genes are involved in the development of many structures in deuterostome organisms, often by conferring epithelial-associated cellular properties. However, this common employment of Esrp in morphogenetic functions was not mirrored at the exon level at the largest phylogenetic distances, as no Esrp-dependent exons appeared conserved between phyla. A remarkable phylum-specific event was observed in the Fgfr gene family, which was recruited as an Esrp target in stem chordates and subsequently co-opted into developmental programs of multiple novel traits in vertebrates.

sample_organism:
Strongylocentrotus purpuratus
Danio rerio

overall_design: mRNA profiles of zebrafish and purple sea urchin involving control and experimental impairment of Esrp genes functions during embryo development

first: Yamile

last: Marquez

first: Claudia

last: Racioppi

first: Jon

last: Permanyer

first: Antonio

last: Torres

first: Rosaria

last: Esposito

first: Beatriz

last: Albuixech

first: Lucía

last: Fanlo

first: Ylenia

last: D'Agostino

first: Enrique

last: Navas-Perez

first: Ana

last: Riesgo

last: Cuomo

first: Giovanna

last: Benvenutto

first: Lionel

middle: A

last: Christiaen

first: Elisa

last: Marti

first: Salvatore

last: D'Aniello

first: Antonietta

last: Spagnuolo

first: Filomena

last: Ristoratore

first: Maria

last: Arnone

first: Jordi

last: Garcia-Fernàndez

first: Manuel

last: Irimia


title: Identification of PARP1-RNA binding in-vivo using PAR-CLiP Sequencing

city: Louisville

first: Eric

middle: Christian

last: Rouchka

state: Kentucky

address: 522 East Gray Street

department: Biochemistry and Molecular Genetics

institute: University of Louisville

summary: Recent studies have implicated PARP1 in alternative splicing regulation. In addition, PARP1 has been shown to bind RNA in vivo suggesting that it is an RNA-binding protein (RBP). However, a detailed knowledge of the RNA-targets as well as the RNA binding region of PARP1 is unknown. We used Photoactivatable-Ribonucleoside-Enhanced Crosslinking and Immunoprecipitation (PAR-CLIP) in HeLa cells and identified a largely overlapping set ∼22142 of PARP1-RNA binding peaks mapping to mRNAs, of which ∼20484 sites are located in the intronic regions of genes. PARP1 preferentially bound RNA containing a Guanine-rich sequences. Using a bayesian model, we determined positional effects of PARP1 on exon skipping: PARP1 binding upstream and downstream to the skipped exons generally promoted exon inclusion, whereas binding on exons and closer to the skipped exon, promoted exon skipping. Finally, using truncation mutants, we narrowed the PARP1-RNA binding domain to the amino terminus region of the protein. Such studies on transcriptome-wide mapping of RNA-targets by PARP1, present the first step into understanding the role of PARP1 and RNA biogenesis. Our understanding of the role of PARPs and PAR in the transcriptional and post-transcriptional regulation of gene expression through modulation of RNA is still in the early stages. Continued identification and characterization of the functional interplay between PARPs and RNA may provide important insights into the role of PARPs in RNA regulation.

overall_design: 1 pooled sample combining PARP1 binding using PAR-CLiP Sequencing from 7 biological replicates

first: Manana

last: Mekishvilli

first: Julia

last: Chariker

first: Yvonne

last: Fondufe-Mittendorf


title: Modeling the pathogenesis of Charcot-Marie-Tooth disease type 1A using patient-specific iPSCs

city: Guangzhou

first: Weiqiang

last: Li

address: Zhongshan Road 2

institute: Sun Yat-sen university

summary: Here, human induced pluripotent stem cells (control-hiPSCs, CMT1A-hiPSCs, and PMP22-hiPSCs) were induced to differentiate to Schwann cells  (control-SCs, CMT1A-SCs, and PMP22-SCs) through neural crest stage (control-NCSCs, CMT1A-NCSCs, and PMP22-NCSCs). We sequenced mRNA samples from Schwann cell differentiation of human pluripotent stem cells at 3 different stage to generate the gene expression profiles of these cells.

overall_design: 7 samples, including undifferentiated hiPSCs (control-hiPSCs and CMT1A-hiPSCs), freshly isolated p75+/HNK1+ NCSCs  (control-NCSCs and CMT1A-NCSCs), and SCs (control-SCs, CMT1A-SCs, and PMP22-SCs) were analyzed.

first: Lihua

last: Huang

first: Andy

last: Xiang


title: Induced one gene overexpression and check the transcriptional expression

city: wuhan

first: juan

last: ling

address: lion street 1

summary: We have set up an Arabidopsis gain-of-function mutant pool overexpressing rapeseed full-length cDNAs under the control of chemically inducible promoter. This data comes from one mutant line

overall_design: the transcriptional expression profile of induced and non-induced mutant

first: Chunyu

last: Zhang

first: Juan

last: Ling


title: Transcriptomic responses to environmental temperature by turtles with thermosensitive and genotypic sex determination assessed by RNAseq inform the genetic architecture of embryonic gonadal development

city: Ames

first: Nicole

last: Valenzuela

state: IA

address: 251 Bessey Hal

institute: Iowa State University

summary: We report the expression profiles of putative genes involved in temperature-dependent sex determination across multiple developmental stages in turtles, and contrast this data with equivalent stages in turtles with sex chromosomes

sample_organism:
Chrysemys picta
Apalone spinifera

platform_organism:
Chrysemys picta
Apalone spinifera

overall_design: Total RNA sequencing from trunks, AKGs and gonadal tissue from Chrysemys picta and Apalone spinifera turtles, sequenced on Illumina HiSeq.

first: Radhakrishnan

last: Srihari

first: Literman

last: Robert

first: Neuwald

last: Jennifer

first: Severin

last: Andrew

first: Valenzuela

last: Nicole


title: RNA-Seq of Glioblastoma stem-like cell (GSC) NSC11 with and without 2Gy irradiation.

city: Bethesda

first: Philip

last: Tofilon

state: Maryland

address: 10 Center Drive-MSC 1002

department: Radiation Oncology

institute: NCI

summary: RNA-Seq analyses of GSC line NSC11 after 2Gy irradiation in the transcriptome and the translatome to evaluate radiation-induced changes in alternative splicing.

overall_design: Total Control (6), Total 2Gy1h (6), Polysome Control (6), Polysome 2Gy1h (6)

first: Amy

last: Wahba

first: Michael

last: Ryan

first: Uma

last: Shankavaram

first: Kevin

last: Camphausen


title: RNAseq data from Mesenchymal stem cells treated with TCDD or 1-methyl tryptophan

city: Atlanta

first: Gregory

middle: K

last: Tharp

state: GA

address: 954 Gatewood Dr

department: Developmental and Cognitive Neuroscience

institute: Yerkes National Primate Research Center

summary: Whole genome RNA-sequencing identified Nrf2, MAPK12 and IL-1a as important downstream targets of 1MT. We further demonstrate 1a1 and 1b1 activation by 1MT in IDO+ MSC following interferon-γ (IFNγ) activation, suggestive that 1MT-driven AHR signaling is uncoupled from IDO catalytic function. These observations support a novel paradigm by which AHR-activating compounds like 1MT can be used in cancer immunotherapy to stimulate a pro-inflammatory response, activating the body’s immune system to infiltrate and eradicate tumors.

overall_design: RNAseq analysis of MSCs to a common AHR ligand (TCDD) and comparisons with 1MT, to elucidate common signaling modalities.

first: Christopher

last: Lewis

first: Jacque

last: Galipeau

first: Steve

last: Bosinger

first: Greg


title: mRNA-Seq profiling SIX2+ and Foxd1+ cells in mouse embryonic and SIX2+ and SIX2-/MEIS1+ cells human fetal kidney

first: Andrew

last: McMahon

summary: To characterize the molecular features of human and mouse nephron progenitors and stromal cells we performed intracellular labeling for SIX2 and/or MEIS1 antibodies, FACS, and RNA-seq. Mouse interstitial progenitors were isolated by Foxd1-Tdt transgenic line, FACS, and RNA-seq

overall_design: Comparing gene expression profiles of human and mouse nephron progenitors and stromal cells

first: Albert

last: Kim

first: Qiuyu

last: Guo

first: Riana

last: Parvez

first: Nils

last: Lindstrom


title: Neuronal cytoskeletal gene dysregulation drives mechanical hypersensitivity in Rett Syndrome

city: Kansas

first: Aritra

last: Bhattacherjee

state: Kansas

address: 3901 Rainbow Blvd

department: Molecular and Integrative Physiology

institute: University of Kansas Medical Center

summary: This study investigated mechanisms of peripheral sensory abnormalities in Rett Syndrome using a MeCP2 knockout rat. Dramatic changes in peripheral innervation by DRG sensory neurons were observed in the knockout rats that strongly correlated with modality-specific sensory dysfunction. The cell-autonomous effect of MeCP2 mutation in DRG neurons disrupt axon growth mechanisms leading to the altered cutaneous innervation density. We performed RNA-Seq to compare the transcriptome of MeCP2 KO DRGs with that derived from wildtype littermates. This revealed profound impact of MeCP2 loss on axon growth regulatory pathways in sensory neurons. The findings will have significant impact on our understanding of sensory dysfunctions in Rett syndrome and Autism Spectrum Disorders at large.

overall_design: Comparison of dorsal root ganglia transcriptome of MeCP2 knockout rat and their wildtype littermates

first: Peter

middle: G

last: Smith


title: mRNA-Seq profiling nephron progenitor and stromal progenitor cells in mouse embryonic kidney

middle: P

summary: To characterize the expression profile of mouse nephron progenitors, we performed intracellular labeling of Six2 by antibody, followed by FACS and RNA-seq. To characterize the expression profile of mouse stromal progenitor cells, we isolated Tdt+ cells from Foxd1Cre;Tdt transgenic mice  kidney by FACS followed by RNA-seq.

overall_design: Comparing gene expression profiles of mouse nephron progenitors and stromal progenitor cells


title: Two functionally distinct human Pan3 isoforms regulate mRNA turnover across the transcriptome

city: Durham

first: Yarui

last: Diao

state: NC

address: 307 Research Drive, Box3709

institute: Duke University

summary: Human Pan3 protein has two functionally distinct isoforms required for proper decay of mRNA across the transcriptome.

overall_design: Time-course experiments were performed using actinomycin D to block transcription to study global mRNA decay upon depletion of different Pan3 isoforms.

first: Ann-Bin

last: Shyu

first: Chyi-Ying

last: Chen


title: H3K79me2 ChIP-seq profiling in melanoma

first: Xiaoyang

last: Zhang

address: 1950 CIrcle of Hope

type: Genome binding/occupancy profiling by high throughput sequencing

summary: To study the effect of DOT1L loss-of-function mutations in melanoma

overall_design: ChIP-seq of H3K79me2 in melanoma cells with and without shRNA-mediated DOT1L knockdown, as well as melanoma cells harboring DOT1L loss-of-function mutatioins.


title: A non-cell autonomous mechanism of beige adipocyte renaissance in subcutaneous adipose tissue

city: San Francisco

first: Biao

last: Wang

address: 555 Mission Bay Blvd South

department: CVRI

institute: University of California, San Francisco

summary: Two types of UCP1 positive cells-brown and beige adipocytes exist in mammals. Beige adipocytes are very plastic, and can be dynamically regulated by environment.Beige adipocytes formed postnatally in subcutaneous inguinal white adipose tissue (iWAT) lost thermogenic gene expression and multilocular morphology at adult stage, but cold could restore their “beigeing” characteristics, a phenomenon termed as beige adipocyte renaissance. Our results showed that beige cell maintenance and renaissance in adult mice were regulated by cAMP and HDAC4 signaling in white adipocytes non-cell autonomously. Genetic modulations of various components of this cAMP-HDAC4 cascade (e.g. LKB1) led to persistent browning and reduced adiposity independent of thermogenesis. To further study the mechanisms of beige adipocytes maintenance, we performed RNA-seq with samples from inguinal white adipose tissues of WT, AdipoqCre LKB1 F/F, and AdipoqCre LKB1 F/F; HDAC4 F/F mice.Our studies will move the beige adipocyte field forward and attract clinical applications to target beige adipocyte renaissance.

overall_design: Samples were divided into 3 groups: inguinal white adipose tissues from WT, AdipoqCre LKB1 F/F, and AdipoqCre LKB1 F/F; HDAC4 F/F mice. 5 mice/group. cDNA libraries were prepared using Ovation RNA-seq Systems V2 and Ovation Ultralow Library Systems V2 (Nugen) and subjected to sequencing using HiSeq 2500 System (Illumina).

first: Yangmeng

first: Esther

last: Paulo

first: Dongmei

last: Wu


title: Gene expression changes due to PARP knockdown in human cells

first: Eric

last: Rouchka

summary: To address the global impact of PARP-1 on the transcriptome, we knocked down PARP1 using siRNA from Dharmacon. Total RNA in three biological replicates from control (non-treated) and PARP-1 siRNA-treated cells were isolated. Sequencing of these RNAs on an Illumina NextSeq 500 yielded >56 million 75-bp RNA-seq reads. First we tested if PARP-1 KD was effective at the RNA-seq level. Reads aligning to the entire gene body of PARP-1 show a reduction in PARP-1 expression of about 1.5-fold (P-value < 0.0003), confirming that indeed PARP-1 was depleted after PARP-1 siRNA treatment. We next used these RNA-seq data sets (control and PARP-1 KD) to assess whether these treatments resulted in changes in gene expression and alternative splicing.

overall_design: mRNA profiles of three biological replicates (non-treated) and three PARP-1 siRNA knockdowns were compared using RNA-Seq on an IlluminaNextSeq 500.

first: Manana

last: Mekishvili

first: Julia

last: Chariker

first: Yvonne

last: Fondufe-Mittendorf


title: Genome-wide identification of mRNAs involved in potato response to drought exhibiting functional evolutionary conservation with Arabidopsis plants

city: Poznań

first: Marcin

middle: Andrzej

last: Pieczynski

address: Wieniawskiego 1

country: Poland

institute: Adam Mickiewicz University

summary: Drought is one of the main climate threats for crop plant production limitation. Climate change models predict constant global warming accompanied by strong reduction in water availability, especially for agricultural needs. Potato belongs to crop plants that are considered as sensitive to water shortage. Global estimation analyses show that drought may decrease potato yield by 18-32% in the period of 2040-2069 (Hijmans, 2003, Obidiegwu et al. 2015, Front in Plant science). Crop models predict that potato yields may reduce by ~30% as a result of water deficit in Poland (http://www.climateadaptation.eu/poland/agriculture-and-horticulture/). Genetic variability between potato cultivars has been described regarding their tolerance to drought (Soltys-Kalina et al. 2016). To diminish the effect of forecasted potato harvest losses, it is crucial to identify as many as possible potato plant strategies to withstand long drought periods during vegetative season. For this reason, we decided to analyse the expression differences in transcriptomes independently in two selected pairs of potato cultivars, Gwiazda/Oberon and Tajfun/Owacja. Cultivars in each pair are closely related to each other (having one parent in common or one grandparent in common, respectively) but differ in their sensitivity to drought conditions. In this paper, we identified at least 24 top selected genes whose expression profiles differ significantly during drought period when closely related studied cultivars are compared. Moreover, all but one of selected potato genes have their homologues in Arabidopsis plant genome. We found that A. thaliana mutants with mostly downregulated expression of seven selected homologous genes differ in their response to drought. To our knowledge, all of these genes were until now not reported as drought-related. Thus, our original approach and obtained results allowed to identify new players in plant response to drought.

overall_design: RNA-seq was performed for leaves from 4 potato cultivars from control and drought conditions (in triplicate for each condition).

first: Anna

last: Wyrzykowska

first: Kaja

last: Milanowska

first: Dominika

last: Boguszewska-Mankowska

first: Barbara

last: Zagdanska

first: Artur

last: Jarmolowski

first: Zofia

last: Szweykowska-Kulinska


title: Differential gene expression of human melanoma cells [ChIP-seq]

city: Worcester

first: Dr Yvonne

last: Edwards

state: MA

address: 373 Plantation Street

department: Program in Molecular Medicine

institute: University of Massachusetts Medical School

summary: We report the gene expression comparison of human A375 melanoma cells with GDF6 and BMP pathway modulation. These comparisons were used to determine the gene signature regulated by GDF6.

overall_design: Examination of gene expression in one cell type +/- GDF6 knockdown as well as +/- downstream pathway reactivation.

first: Arvind

middle: M

last: Venkatesan

first: Craig

last: Ceol

first: Sharvari

last: Gujja


title: Differential gene expression of zebrafish melanocytes and melanomas [RNA-seq]

summary: We report the gene expression comparison of zebrafish melanocytes and melanomas. These comparisons were used for integrative genomic studies that identified the BMP factor GDF6 as a new oncogene that is specifically expressed in melanomas.

overall_design: Examination of gene expression in two different cell types

first: Sagar

last: Chhangawala

first: Yariv

last: Houvras


title: Directional RNA-Seq on CD4+ T cells collected from children with asthma with/without obesity

city: Bronx

first: Deepa

last: Rastogi

address: 1300 Morris Park Ave

department: Pediatrics

institute: Albert Einstein College of Medicine

summary: We compare the CD4+ T cell transcriptome between obese and normal-weight children with asthma to identify molecules/pathways differentially expressed in obese asthmatic CD4+  T cells

overall_design: CD4+ T cell transcriptome generated using Directional RNA-Seq library preparatio; A=Normal-weight, B=obese

first: Rastogi

last: Deepa

first: Johnston

last: Andrew


title: Gene expression response to infection in self-fertilising fish

city: Swansea

first: Rebecca

middle: Jane

last: Pawluk

address: Swansea Univeristy

department: Biosciences

institute: Swansea Univeristy

summary: Parasites are strong drivers of evolutionary change and the genetic variation of both host and parasite populations can co-evolve as a function of the parasite's virulence and the host's immune resistance. The role of transcriptome variation in specific interactions between host and parasite genotypes has been less studied and can be confounded by high genotypic variability in natural populations. We have analysed gene expression between two inbred lines of a self-fertilising fish experimentally infected with a parasite under controlled conditions, in order to estimate the role of the genotype in the transcriptome responses to infection using RNA-seq.

overall_design: Analysis of gene expression in response to infection in 2 inbred fish lines

first: Sofia

last: Consuegra

first: Tamsyn

last: Webster


title: Inhibition of an Rgg-like Regulator in Streptococcus mutans by the Novel Peptide XrpA

status: Public on Feb 13 2018

city: Columbus

first: Justin

middle: Ray

last: Kaspar

state: OH

address: 305 W 12th Ave

institute: The Ohio State University

summary:
BACKGROUND: Streptococcus mutans, the etiological agent of human dental caries, displays complex regulation of natural genetic competence. Competence development in S. mutans is controlled by a peptide derived from ComS (comX inducing peptide, XIP); which along with the cytosolic regulator ComR controls the expression of the alternative sigma factor comX, the master regulator of competence development. ComR-XIP controls the expression of both PcomX and PcomS, with the latter creating a positive feedback loop. Recently, a gene embedded within the coding region of comX was discovered and designated xrpA (comX regulatory peptide A). XrpA was found to be an antagonist of ComX, but the mechanism was not established.  In this study, we began to dissect how XrpA exerts control over competence development in S. mutans.

METHODS: RNA-Seq was utilized to compare the transcriptomes of S. mutans wild-type strain UA159 (3 replicates), UA159 with addition of 2 uM sXIP (3 replicates) and with a mutant of xrpA (comX::T162C; 3 replicates). Strains were grown to OD600 nm = 0.5 in FMC medium before harvest. sXIP was added at OD600 nm = 0.2. Deep sequencing was performed at the University of Florida ICBR facilities (Gainesville, FL). Approximately 20 million short-reads were obtained for each sample. After removing adapter sequences from each short-read and trimming of the 3’-ends by quality scores (59), the resulting sequences were mapped onto the reference genome of strain UA159 (GenBank accession no. AE014133) using the short-read aligner.  Mapped short-read alignments were then converted into readable formats using SAMTOOLS.

RESULTS: Using an optimzed data analysis workflow, we mapped 14-19 million reads per sample to the genome of UA159. For viewing of the mapped reads aligned to the genome, .bam files were uploaded into the Integrative Genomics Viewer (IGV – version 2.3.55) (61). A .csv file containing raw read counts for each replicate (3) was then uploaded to Degust (http://degust.erc.monash.edu/) and edgeR analysis performed to determine Log2 fold change and a false discovery rate (FDR). Comparison of the transcriptome by RNA-Seq of the wild-type with the mutant lacking XrpA revealed 56 differentially expressed genes, with 34 upregulated in xrpA and 22 downregulated.  Many of the upregulated genes were competence-related genes, including comX and genes that are a part of the ComX regulon of S. mutans .  Since loss of xrpA caused upregulation of competence genes, we also analyzed the transcriptome of UA159 treated with 2 uM sXIP to induce competence, with UA159 treated with vehicle (DMSO) as a control. Cells treated with sXIP had 137 genes differentially expressed compared to the DMSO control.

CONCLUSIONS: Collectively, these data reveal that the novel regulator XrpA exerts its influence over competence development by impacting ComRS functions, resulting in decreased expression of comX and late com gene expression that negatively impact transformability. These results highlight XrpA as a new negative regulator of competence signaling as well as broaden our understanding of the complex regulatory mechanisms that modulate competence and virulence in S. mutans.

overall_design: Streptococcus mutans mRNA profiles were generated for UA159, UA159 + 2 uM sXIP, and an xrpA mutant strain (comX::T162C) in FMC medium at OD600 nm = 0.5 by deep sequencing, in triplicate


title: RpoN-dependent global regulation in Pseudomonas aeruginosa PAO1

city: Hong Kong

first: Xin

last: Deng

address: To Yuen Building

department: Biomedical Sciences

country: Hong Kong

institute: City University of Hong Kong

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

sample_organism:
Pseudomonas aeruginosa
Pseudomonas aeruginosa PAO1

overall_design: Refer to individual Series


title: Differential gene expression of human melanoma cells [RNA-seq]

middle: J

first: Yvonne


title: Genetic intersection of Tsix and Hedgehog signaling during the initiation of X-chromosome inactivation

city: Boston

first: Brian

last: Del Rosario

address: 185 Cambridge St, CPZN-7250

department: Molecular Biology

institute: Massachusetts General Hospital

summary: X-chromosome inactivation (XCI) is the process that leads to silencing of one X-chromosome in female mammals. XCI is essential to peri-implantation development and is thought to be cell-autonomous, with all factors required to execute silencing being produced within each cell. Nevertheless, external cues to time XCI must exist in vivo, but such developmental signals have yet to be identified. Using multiple approaches to identify developmental regulators of XCI, we identify Indian Hedgehog (IHH) signaling as critical to this process.  We demonstrate that IHH signaling keeps XCI in check in pluripotent cells. HH signal transduction through GLI transcription factors regulates XCI by directly binding control elements at the 5’ end of Tsix, the antisense repressor of XCI. GLI binding potentiates Tsix expression and thereby impedes XCI. In vivo, mutating Ihh results in a sex ratio bias against females. Importantly, this female-specific lethality is rescued by a second-site mutation in Tsix.  We propose that XCI in the epiblast is regulated by IHH expressed from the visceral endoderm. Our data connect the HH and XCI pathways and support a role of cell-to-cell communication in the developmental timing of XCI.

overall_design: Anti-FLAG ChIP-seq from female mouse ES cell lines bearing doxycycline inducible transgenes for GLI1-3xFLAG and GLI2-3xFLAG

first: Amanda

first: Anthony

last: Anselmo

first: Peggy

middle: I

last: Wang

first: Ruslan

last: Sadreyev

first: Jeannie

last: Lee


title: Alternative splicing of differentiated myeloid cell transcripts after infection by Anaplasma phagocytophilum impacts a selective group of cellular programs

city: Baltimore

first: Amol

middle: Carl

last: Shetty

address: 670 W. Baltimore Street, Floor 3

department: Institute for Genome Sciences

institute: University of Maryland Baltimore

summary: Eukaryotic proteome diversity exceeds that encoded within individual genes, and results in part from alternative splicing events of pre-messenger RNA. The diversity of these splicing events can shape the outcome in development and differentiation of normal tissues, and is important in pathogenic circumstances such as cancer and some heritable conditions. A role for alternative splicing of eukaryotic genes in response to viral and intracellular bacterial infections has only recently been recognized, and plays an important role in providing fitness for microbial survival, while potentially enhancing pathogenicity. Anaplasma phagocytophilum survives within mammalian neutrophils by reshaping transcriptional programs that govern cellular functions. We applied next generation RNAseq to ATRA-differentiated HL-60 cells established to possess transcriptional and functional responses similar to A. phagocytophilum-infected human neutrophils. This demonstrated an increase in transcripts with infection and high proportion of alternatively spliced transcript events (ASEs) for which predicted gene ontology processes were in part distinct from those identified by evaluation of single transcripts or gene-level analyses alone. The alternative isoforms are not on average shorter, and no alternative splicing in genes encoding spliceosome components is noted. Although not evident at gene-level analyses, individual spliceosome transcripts that impact nearly all spliceosome components were significantly upregulated. How the distinct GO processes predicted by ASEs are regulated by infection and whether they are relevant to fitness or pathogenicity of A. phagocytophilum should be addressed in more detailed studies.

overall_design: RNAseq analysis of gene expression, transcript expression and transcript isoform expression in differentiated HL-60 cells infected or not by A. phagocytophilum.

first: J

middle: S

last: Dumler

first: Sara

last: Sinclair


title: GDF6-induced BMP signaling reawakens a neural crest identity in melanoma to prevent cell death and differentiation

first: Dr Yvonne

last: Edwards

sample_organism:
Danio rerio
Homo sapiens

platform_organism:
Danio rerio
Homo sapiens


title: Adult functions for the Drosophila DHR78 nuclear receptor

city: Salt Lake City

first: Carl

last: Thummel

department: Human Genetics

institute: University of Utah

summary: Here we study the adult functions of the single Drosophila member of this subfamily, DHR78, with the goal of defining its ancestral functions in the absence of genetic redundancy. We show that DHR78 mutants have a shortened lifespan and reduced motility. Mated DHR78 mutant females display reduced triglycerides along with a reduced feeding rate. Transcriptional profiling reveals a major role for DHR78 in promoting the expression of genes that are abundantly expressed in the midgut, suggesting that it contributes to nutrient uptake. We also identify roles for DHR78 in maintaining the expression of genes in the ecdysone and Notch signaling pathways.

overall_design: Comparison of the transcriptional profile of DHR78-transheterozygote female mutants in a btl>DHR78 background with genetically matched controls

first: Stefanie

last: Marxreiter


title: The role of microglia in maturation of adult-born neurons

city: Jerusalem

first: Raz

last: Yirmiya

address: Mount Scopus

country: Israel

institute: Hebrew University of Jerusalem

summary: Microglia depletion significantly lowered spine density in young (developing) but not mature adult-born-granule-cells (abGCs) in the olfactory bulb. PLX5622 significantly reduces microglia related gene transcripts.

overall_design: We tested mouse olfactory bulb transcription in WT mice versus mice treated with a PLX5622 diet (inducing a near-complete microglia depletion).

first: Neta

last: Rimmerman

first: Ronen

last: Reshef


title: Transcriptomic analysis of young and old erythrocytes of fish

city: Turku

first: Miriam

last: Goetting

address: Yliopistonmäki

department: Dept of Biology

country: Finland

institute: University of Turku

summary: Understanding gene expression changes over the lifespan of cells is of fundamental interest and gives important insights into processes related to maturation and ageing. This study was undertaken to understand the global transcriptome changes associated with ageing in fish erythrocytes. Fish erythrocytes retain their nuclei throughout their lifetime and they are transcriptionally and translationally active. However, they lose important functions during their lifespan in the circulation. We separated rainbow trout (Oncorhynchus mykiss) erythrocytes into young and old fractions using fixed angle-centrifugation and analyzed transcriptome changes using RNA sequencing (RNA-seq) technology and quantitative real-time PCR. We found 930 differentially expressed between young and old erythrocyte fractions; 889 of these showed higher transcript levels in young, while only 34 protein-coding genes had higher transcript levels in old erythrocytes. In particular ion binding, signal transduction, membrane transport, and various enzyme classes are affected in old erythrocytes. The transcripts with higher levels in old erythrocytes were associated with 7 different GO terms within biological processes and 9 within molecular functions and cellular components respectively. Our study furthermore found several highly abundant transcripts as well as a number of differentially expressed genes for which the protein products are currently not known revealing the gaps of knowledge in most non-mammalian vertebrates. Our data provide the first insight into changes involved in ageing on the transcriptional level and thus opens new perspectives for the study of maturation processes in fish erythrocytes.

overall_design: Examination of gene expression in young and old erythrocytes of fish

first: Mikko

last: Nikinmaa


title: Disruption of circadian clockwork in in vivo reprogramming-induced mouse kidney tumors

city: Kyoto

first: Kazuhiro

last: Yagita

address: Kawaramachi-Hirokoji, Kamigyo-ku

institute: Kyoto Prefectural University of Medicine

summary: The circadian clock, which regulates cellular physiology, such as energy metabolism, resides in each cell level throughout the body. Recently, it has been elucidated that the cellular circadian clock is closely linked with cellular differentiation. Moreover, the misregulation of cellular differentiation in mouse embryonic stem cells (ESCs) induced abnormally differentiated cells with impaired circadian clock oscillation, concomitant with the post-transcriptional suppression of CLOCK proteins. Here, we show that the circadian molecular oscillation is disrupted in dysdifferentiation-mediated mouse kidney tumors induced by partial in vivo reprogramming, resembling Wilms tumors. The expression of CLOCK protein was dramatically reduced in the tumor cells despite the Clock mRNA expression. We also showed that a similar loss of CLOCK was observed in human Wilms tumors, suggesting that the circadian molecular clockwork may be disrupted in dysdifferentiation-mediated embryonal tumors such as Wilms tumors, similar to the in vivo reprogramming induced mouse kidney tumors. These results support our previous reports and may provide a novel viewpoint for understanding the pathophysiological nature of cancers through the correlation between cellular differentiation and circadian clock.

overall_design: Examination of whole transcriptome in mouse kidney

first: Munehiro

last: Ohashi

first: Yasuhiro

last: Umemura

first: Nobuya

last: Koike

last: Yamada


title: Integrated transcriptomic analysis of Trichosporon asahii uncovers the core genes and pathways of fluconazole resistance

city: Beijing

first: Rongya

last: Yang

state: Beijing

address: 5 Nanmencang

department: Department of Dermatology

institute: PLA Army General Hospital

summary: We performed a series of fluconazole (FLC) perturbation experiments for two T. asahii strains, a clinical isolate stain CBS2479 (T2) and an environmental isolate strain CBS8904 (T8), to uncover potential genes and pathways involved in FLC resistance.

sample_organism: Trichosporon asahii var. asahii CBS 2479

sample_organism: Trichosporon asahii var. asahii CBS 8904

overall_design: We treated both types of T. asahii cells with two different doses of FLC for 5 different time points respectively, and then collected RNAs for gene expression profiling.

first: Haitao

last: Li

first: Yong

last: Chen


title: Transcriptome expression of WT, 160OE, arf10, arf16, and arf17 Arabidopsis seedlings treated with/without heat stress

city: Taipei

first: Jeng-Shane

last: Lin

address: No. 1, Sec. 4, Roosevelt Road

department: Plant Biology

country: Taiwan

institute: National Taiwan University

summary: 7-day-old seedlings were treated with heat stress at 44oC for 30 min. Total RNAs were isolated for library construction and analyzed by RNA-seq via Solexa platform. Raw sequences were obtained from the Illumina Pipeline software bcl2fastq v2.0 and expected to generate 20M (million reads or Gb) per sample.

overall_design: Examination of transcriptome expression in WT, 160OE, arf10, arf16, and arf17 treating with/without heat stress


title: Transcriptomic signature of spinal cord from SOD1 G86R mice

city: Strasbourg

first: Alexandre

last: Henriques

address: At U1118, 11 rue Humann

country: France

institute: Spedding Research Solutions, SAS

summary: We report transcriptomic dysregulations in the spinal cord of symptomatic SOD1 G86R mice by RNA sequencing. We found that genes related to immune system, lysosom, and sphingolipids had altered level of expression. These results were used to perform an integrated joint analysis with data from a metabolomic study.

overall_design: 5 spinal cord samples from SOD1 G86R mice and 5 spinal cord samples of non-transgenic control mice were analyzed.

first: Céline

last: Keime


title: RNA-Seq analysis of breast cancer cells after shikonin treatment

city: Kaohsiung

first: CHIA-YANG

last: LI

address: 100,Shih-Chuan 1st Road

department: Graduate Institute of Medicine

institute: Kaohsiung Medical University

summary: We performed RNA-seq analysis using differnt breast cancer cell lines (MCF-7, SK-BR-3 and MDA-MB-231) after shikonin treatment. We reported that shikonin enhances the expression of DUSP-1 and DUSP-2. Shikonin induces apoptosis and decreases the phosphorylation of JNK1/2 through activationg DUSP-1 and DUSP2.

overall_design: We treated three breast cancer cell lines with 10 μΜ shikonin for 6 hr. The gene expression profiling was performed using RNA-seq. Numbers of significantly differentially expressed (SDE) genes in different human breast cancer cell lines under shikonin treatment had been identified. We analyzed the functional annotation and performed the pathway analysis using 38 common SDE genes.

first: K

middle: H

first: M

middle: Y

last: Huang

first: W

last: Cheng

first: S

last: Wang

last: Fang

first: P

middle: L

last: Liu

first: C

last: Su

last: Shen

first: Y

middle: T


title: Transcriptomic and epigenetic responses to short-term nutrient-exercise stress in humans

city: Copenhagen

first: Lars

middle: Roed

last: Ingerslev

address: Blegdamsvej 3B

department: NNF Center for Basic Metabolic Research

country: Denmark

institute: Copenhagen University


title: Open housing drives the expression of immune-response genes in the nasal mucosa, but not the olfactory bulb

city: Leipzig

first: Torsten

last: Schöneberg

address: Johannisallee 30

department: Institute of Biochemistry, Medical Faculty

country: Germany

institute: Leipzig University

summary: Nasal mucosa and olfactory bulb are separated by the cribriform plate which is perforated by olfactory nerves. We have previously demonstrated that the cribriform plate is permissive for T cells and monocytes and that viruses can enter the bulb upon intranasal injection by axonal transportation. Therefore, we hypothesized that nasal mucosa and olfactory bulb are equipped to deal with constant infectious threats. To detect genes involved in this process, we compared gene expression in nasal mucosa and bulb of mice kept under specific pathogen free (SPF) conditions to gene expression of mice kept on non-SPF conditions using RNA deep sequencing. We found massive alterations in the expression of immune-related genes of the nasal mucosa, while the bulb did not respond immunologically. The absence of induction of immune-related genes in the olfactory bulb suggests effective defence mechanisms hindering entrance of environmental pathogens beyond the outer arachnoid layer. The genes detected in this study may include candidates conferring susceptibility to meningitis.

overall_design: Mice were kept for 1 or 2 weeks under specified-pathogen free (spf) or non-spf conditions respectively.

first: Carolin

last: Piotrowski

first: Vera

last: Lede

first: Anne

last: Butthof

first: Petra

last: Hirrlinger

first: Matthias

last: Tschöp

first: Ingo

last: Bechmann


title: A Chinese herbal formula, Gengnianchun, ameliorates β-amyloid peptide toxicity in a Caenorhabditis elegans model of Alzheimer’s disease

city: changchun

first: fanhui

last: meng

address: xinminstreet

institute: The First Hospital of Jilin University

summary: To further investigate the transcriptional effects of GNC treatment, we analyzed gene expression of C. elegans wild-type N2 in NGM supplemented with GNC (3.94 mg/mL) and nematodes maintained in control condition at the same age (old worms, 22-days old) using next-generation sequencing (NGS)

overall_design: Examination of C. elegans wild-type N2 in NGM supplemented with GNC (3.94 mg/mL) and nematodes maintained in control condition.

first: Fanhui

last: Meng

first: Wenjun

first: Yanqiu

last: Rao

first: Yan

last: Fu


title: Tet2 loss dysregulates the behavior of bone marrow derived mesenchymal stromal cells [RNA-seq]

city: Tianjin

first: Rong

last: Li

state: Tianjin

address: No.288, Nanjing Road,Heping District

department: Institute of Hematology and Blood Diseases Hospital

institute: Chinese Academy of Medical Sciences and Peking Union Medical College

summary: Bone marrow–derived mesenchymal stem/progenitor cell mRNA profiles of  WT and Tet2−/− mice were generated by deep sequencing.

first: Yuan

last: Zhou

first: Feng-Chun

last: Yang

first: Zhigang

last: Zhao


title: Transcriptomic analysis of normal and IPF lung fibroblast SSEA4+ and SSEA4- cells

city: Los Angeles

first: David

last: Habiel

state: CA

address: 8700 Beverly Blvd

department: Medicine

institute: Cedars-Sinai Medical Center

summary: Recently, SSEA4+ mesenchymal progenitor cells have been described in stromal cultures, where IPF (but not normal) progenitor cells show pathological properties both in vitro and in vivo. The purpose of this study is to determine differences between mesenchymal progenitor cells sorted from stromal cultures derived from the lung biopsies of IPF patients showing a slow progressive versus rapid progressive decline of lung function as previously defined (Trujillo, G et al Science trans med 2010). Further, both groups were also compared to their normal lung counterparts as well as SSEA4- mesenchymal progeny.

overall_design: SSEA4+ and SSEA4- cells were FACS sorted, RNA was extracted and sequenced.

first: Cory

last: Hogaboam


title: Transcriptomic and epigenetic responses to short-term nutrient-exercise stress in humans [RNA-seq]

first: Lars

last: Ingerslev

summary: High fat feeding is deleterious for skeletal muscle metabolism, while exercise has well documented beneficial effects for these same metabolic features. To identify the genomic mechanisms by which exercise ameliorates some of the deleterious effects of high fat feeding, we investigated the transcriptional and epigenetic response of human skeletal muscle to 9 days of a high-fat diet (HFD) alone (Sed-HFD) or in combination with resistance exercise (Ex-HFD), using genome-wide profiling of gene expression (by RNA-seq) and DNA methylation (by Reduced Representation Bisulfite Sequencing). HFD markedly induced expression of immune and inflammatory genes which was not attenuated by Ex. In contract, Ex markedly remodelled expression of genes associated with muscle growth and structure. We detected marked DNA methylation changes following HFD alone and in combination with Ex. Among the genes that showed significant association between DNA methylation changes and gene expression were glycogen phosphorylase, muscle associated (PYGM), which was epigenetically regulated in both groups, and angiopoiten like 4 (ANGPTL4), which was regulated only following Ex. We conclude that Short-term Ex does not prevent HFD-induced inflammatory response, but provokes a genomic response that may preserve skeletal muscle from atrophy. Epigenetic adaptation provides important mechanistic insight into the gene specific regulation of inflammatory and metabolic processes in human skeletal muscle.

overall_design: Sedentary or exercising human subjects undergo high-fat diet intervention.

first: Rhianna

middle: C

last: Laker

first: Christian

last: Garde

first: Romain

last: Barres


title: Transcriptomic and epigenetic responses to short-term nutrient-exercise stress in humans [RRBS-seq]


title: Induction of Cardiomyocyte Proliferation [tm-683-mouse]

city: San Francisco

first: Deepak

last: Srivastava

address: 1650 Owens St

institute: J David Gladstone Institutes

summary: Isolated adult cardiomyocytes from alpha-MHC MADM mice treated with 4 cell cycle genes to induce cardiomyocyte proliferation

overall_design: alpha MHC MERCREMER MADM Mice hearts were injected with adenoviruses encoding 4 cell cycle genes. 2 weeks later Cardiomyocytes were isolated and collected single and double colored cells

first: Tamer

last: Mohamed


title: Transcriptomic profiling of RCD1 and XLPRA2 retina at advanced stages of retinal degenerative disease

city: Philadelphia

first: William

middle: A.

last: Beltran

state: PA

address: 3900 Delancey Street, Ryan VHUP 2050

department: Clinical Studies

institute: University of Pennsylvania

summary: The retinal transcriptome of two non-allelic forms of retinitis pigmentosa (RP) in dogs, RCD1 and XLPRA2, was analyzed at clinically relevant advanced stages of the two diseases and compared to that of adult normal dogs.

overall_design: RNA-seq analysis of retina from 3 each RCD1 and XLPRA2 dogs with greater than 50% photoreceptor loss, compared to that of 3 normal adult dogs

first: Raghavi

last: Sudharsan

first: Daniel

last: Beiting

first: Gustavo

middle: D

last: Aguirre

middle: A


title: Global Analysis of Gene Expression Mediated By Orexin Receptor 1 Signaling in a Hypothalamic Cell Line

city: Jupiter

first: Thomas

last: Kodadek

state: FL

address: 130 Scripps Way

institute: The Scripps Research Institute

summary: The orexins/hypocretins and their cognate G-protein coupled receptors have been widely studied due to their associations with various behaviors and cellular processes. However, the detailed downstream signaling cascades that mediate these effects are not completely understood. We report the generation of a neuronal model cell line that stably expresses orexin receptor 1 and an RNA-Seq analysis of changes in gene expression seen upon receptor activation. Upon treatment with orexin, several related families of related transcription factors are transcriptionally regulated, including the early growth response genes (Egr), the Kruppel-like factors (Klf), and the Nr4a subgroup of nuclear hormone receptors. Furthermore, the transcriptional effects observed showed a degree of similarity with data from in vivo sleep deprivation microarray studies, supporting the physiological relevance of the data set. These results provide new insight into the molecular signaling events that occur during orexin receptor 1 signaling and support a role for orexin signaling in the stimulation of wakefulness during sleep deprivation studies.

overall_design: Differential gene expression was evaluated via RNA-Seq upon activation of OxR1 for 3 or 8 hours, compared to vehicle treated cells. All samples were done in triplicate.

first: Eric

last: Koesema


title: Macrophages and osteoclasts stem from a bipotent progenitor that lies downstream of the common macrophage/osteoclast/dendritic cell progenitor

city: Amsterdam

first: yanling

last: xiao

address: Plesmanlaan 121

country: Netherlands

institute: NKI

summary: Macrophages (MΦs), osteoclasts (OCs) and dendritic cells (DCs) are closely related, but the exact steps in their lineage commitment are unclear. We here dissect B220-CD11blow/negc-Kit+c-Fms+ mouse bone marrow (BM) cells into a CD27+Flt3+ progenitor popula

overall_design: Whole transcriptome analysis of CD27 low MOP and CD27 high MODP

first: Yanling

last: Xiao

first: Jannie

last: Borst


title: Expression data from infected skin and non-infected skin of Epinephelus coioides infected with Cryptocaryon irritans (C. irritans) and normal skin of E. coioides

city: Guangzhou

first: yazhou

last: hu

state: Guangdong

address: xingang west road no. 135

institute: Sun Yat-sen University

summary: To characterize the differentially expressed genes between infected skin with normal skin

overall_design: Using C. irritans-tail-infection method, infected skin (group Isk) and non-infected skin (group Nsk) of E. coioides infected with C. irritans and normal skin (group C) of E. coioides were sampled. Each group had 3 biological replicates

first: Anxing

last: Li

first: Yazhou

last: Hu


title: RNA-seq of peritoneal macrophages from wildtype and miR-33-/- mice under normal or hyperlipidemic conditions

city: New Haven

first: Nathan

last: Price

state: CT

address: 10 Amistad St Rm 320

department: CMED

institute: Yale University

summary:
Purpose:  Previous work has demonstrated that miR-33 is an important regulator of lipid metabolism and atherogenesis.  By performing bone marrow transplant experiments into LDLR-/- mice, our work demonstrates that the effects of miR-33 in macrophages play a major role in its ability to reduced atherosclerotic plaque burdon.  To have performed extensive additional characterization of the effects of miR-33 deficiency in macrophages icluding RNA-seq analysis of peritoneal macrophages from wildtype, miR-33-/-, LDLR-/-, and miR33-/-/LDLR-/- animals.
Methods:  Thioglycolate elicited peritoneal macrophages from WT and miR-33-/- mice were harvested by peritoneal lavage.  Cells were then plated for 2hr, then washed to remove non-adherant cells.  Macrophages were then scraped, pelleted and frozen at -80◦C. Total RNA from WT and miR-33-/- thioglycollate-elicited peritoneal macrophages was extracted and purified using a RNA isolation Kit (Qiagen) followed by DNAse treatment to remove genomic contamination using RNA MinElute Cleanup (Qiagen). The purity and integrity of total RNA sample was verified using the Agilent Bioanalyzer (Agilent Technologies, Santa Clara, CA). rRNA was depleted from RNA samples using Ribo-Zero rRNA Removal Kit (Illumina). RNA libraries from WT BMDMs were performed TrueSeq Small RNA Library preparation (Illumina) and were sequenced for 45 cycles on Illumina HiSeq 2000 platformm (1 x 75bp read length). The reads obtained from the sequencer are trimmed for quality using in-house developed scripts.  The trimmed reads are aligned to the reference genome using TopHat2.  The transcript abundances and differences calculated using cuffdiff.  The results were plotted using R and cummeRbund using in-house developed scripts.
Results:  Our RNA-seq analysis has allowed us to identify genes and pathways that are altered in miR-33 deficient peritoneal macrophages under hyperlipidemic conditions (LDLR-/- vs. miR33-/-/LDLR-/-).  Further analysis of gene expression changes that occur between wildtype and LDLR-/- animals has allowed us to identify which of these changes are likely due to differences in lipid loading and which are independent of these effects.

overall_design: 12 samples total (3 replicates each sample type)

first: Carlos

last: Fernandez-Hernando


title: The role of Hdac3 in bone formation

city: Seattle

first: Pritha

last: Chanana

state: WA

address: 1100 Fairview Ave N, PO Box 19024

department: Shared Resources

institute: Fred Hutchinson Cancer Center

summary: Mice deficient for Hdac3 in mesenchymal progenitor cell (under the PRX1 promoter) die perinataly and exhibit severly short limbs. Here we analyzed the differentiational gene expression in the limbs of these mice. We observed that limbs from the CKO mice have higher expression of genes responsible for matrix degradation. In addition, we identified significant upregulation of FGF21 expression in CKO limbs.

overall_design: Hindlimbs and forearms were harvested from 1 day-old wildtype or Hdac3 CKOPRX1 for RNA-seq on bone tissue.

first: Marina

last: Feigenson

first: Lomeli

last: Shull

first: Elizabeth

middle: W

last: Bradeley

first: Jennifer

last: Westendorf


title: Regulation of Cell Cycle to Stimulate Adult Cardiomyocyte Proliferation and Cardiac Regeneration

first: Deepak

last: Srivastava

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

overall_design: Refer to individual Series


title: Methylation of Transcription Factor YY2 Regulates its Transcriptional Activity and Cell Proliferation

city: Ganzhou

first: Wenjuan

last: Zhang

state: Jiangxi

address: No. 23, Qingnian Road

department: First Affiliated Hospital

institute: Gannan Medical University

summary: Yin Yang 1 (YY1) is a multifunctional DNA-binding transcription factor shown to be critical in a variety of biological processes, and its activity and function have been shown to be regulated by multitude of mechanisms, which include but are not limited to post-translational modifications (PTMs), its associated proteins and cellular localization. YY2, the paralog of YY1 in mouse and human, has been proposed to function redundantly or oppositely in a context specific manner compared to YY1. Despite its functional importance, how YY2’s DNA binding activity and function is regulated, particularly by PTMs, remains completely unknown. Here we report the first PTM with functional characterization on YY2, namely lysine 247 mono-methylation (K247me1), which was found to be dynamically regulated by SET7/9 and LSD1 both in vitro and in cultured cells. Functional study revealed that SET7/9-mediated YY2 methylation regulated its DNA-binding activity in vitro and association with chromatin examined by ChIP-seq (chromatin immunoprecipitation coupled with sequencing) in cultured cells. Knockout of YY2, SET7/9 or LSD1 by CRISPR (clustered, regularly interspaced, short palindromic repeats) /Cas9-mediated gene editing followed by RNA-seq revealed that a subset of genes was positively-regulated by YY2 and SET7/9, but negatively-regulated by LSD1, which were enriched with genes involved in cell proliferation regulation. Importantly, YY2-regulated gene transcription, cell proliferation and tumor growth were dependent, at least partially, on YY2 K247 methylation. Finally, somatic mutations on YY2 found in cancer, which are in close proximity to K247, altered its methylation, DNA binding activity and gene transcription it controls. Our findings revealed the first PTM with functional implications imposed on YY2 protein, and linked YY2 methylation with its biological functions.

overall_design: The RNA-seq in this study was designed to reveal YY2, SET9 and LSD1 regulated genes in HeLa cells.

first: Wen

last: Liu

first: Wen-juan

first: Jian-cheng

last: Ding


title: Induction of Cardiomyocyte Proliferation [pz-822_human]

summary: hiPS derived cardiomycoytes treated with 4 cell cycle genes to induce cardiomyocyte proliferation and sorted for the different cell cycle stages according to FUCCI dye

overall_design: hiPS derived cardiomyocytes infected with adenovirus encoding 4 cell cycle genes in the presence or absence of TGFB inhibitor and Wee1 inhibitor (2i) to induce cardiomyocyte proliferation and sorted for the different cell cycle stages according to FUCCI dye. (-ve:G0 phase, Red:G1 phase, RedGreen: S phase, Green: G2/M phase).

first: Tamer

last: Mohamed


title: Multi-time series RNA-Seq analysis of Enterobacter lignolyticus SCF1during growth in lignin-amended medium

city: Richland

first: Lye Meng

last: Markillie

address: 902 Battelle Blvd

department: Biosystems Dynamics & Simulation

institute: Environmental Molecular Sciences Laboratory

summary: The production of lignocellulosic-derived biofuels is a highly promising source of alternative energy, but it has been constrained by the lack of a microbial platform capable to efficiently degrade this recalcitrant material and cope with by-products that can be toxic to cells. Species that naturally grow in environments where carbon is mainly available as lignin are promising for finding new ways of removing the lignin that protects cellulose for improved conversion of lignin to fuel precursors.

overall_design: Genome-wide transcriptomic analysis of cultures of SCF-1 were sampled along three times during batch anaerobic batch growth in lignin amended medium versus control (unamended medium).

first: Roberto

last: Orellana

first: Lye

middle: M

first: Hugh

last: Mitchell

first: Galya

last: Orr

first: Kristen

last: DeAngelis


title: Exploring the molecular mechanisms of positive and negative regulation of apoptosis post Orf virus infection in sheep

city: Wuhan

first: Dong

last: Chen

state: Hubei

address: 388 GaoXin 2nd Road, East Lake Hi-Tech Development Zone

department: Center for Genome Analysis

institute: ABLife, Inc.

summary: Contagious ecthyma (Orf) is a contagious disease with worldwide distribution, caused by the epitheliotropic Orf virus (ORFV), a member of the genus Parapoxvirus. In the current study, we collected the oral mucosa tissues samples (T0, T3, T7 and T15) from sheep at 0, 3, 7 and 15 days post ORFV infection, respectively. To explore the changes of comprehensive transcriptome of host cells from oral mucosa tissues post ORFV infection, the RNA-seq transcriptome comparisons were performed on these samples. It showed that 1928, 3219 and 2646 differentially expressed genes (DEGs) were identified among T3 vs. T0, T7 vs. T0, T15 vs. T0 respectively. Through Gene Ontology (GO) analyses of the DEGs from these comparisons, it revealed that  ORFV provoked the vigorous immune response of the host cells during the early stage of infection. Moreover, GO and network analysis revealed that positive and negative regulative mechanisms of apoptosis worked as whole in the host cells, in order to reach a homeostasis of oral mucosa tissues.

first: Haijie

last: Jia

first: Leilei

last: Zhan


title: RNAseq Analysis of Transcriptome expression profiles in E12.5 and E13.5 FACS sorted Osr2RFP/- (mutant)and Osr2RFP/+ (control) palatal mesenchymal cells

city: cincinnati

first: HAN

last: LIU

state: oh

address: 3333 burnet avenue

department: DEVELOPMENTAL BIOLOGY

institute: CINCINNATI CHILDREN'S HOSPITAL

summary:
Purpose:  The purpose of this study is to compare the transcriptome expression profiles of E12.5 and E13.5 Osr2RFP/- and Osr2RFP/+ palatal mesenchyme by using RNA-seq analysis.
Methods: Osr2RFP/+ male mice were crossed with Osr2+/- female mice. The embryos were harvested at E12.5 and  E13.5. The pair of palatal shelves were dissected from each Osr2-RFP positive embryo. The RFP+ palatal mesenchyme cells were isolated by using fluorescence-activated cell sorting (FACS). RNA-seq analysis was carried out using the FACS-isolated palatal mesenchyme from Osr2RFP/- and Osr2RFP/+  embryos, respectively.

overall_design: The transcriptome expression profiles of E12.5 and E13.5, Osr2RFP/- and Osr2RFP/+ palatal mesenchyme by using RNA-seq analysis,  in single pair (E12.5) or duplicates (E13.5), using Illumina HisEq 2000.

first: Jingyue

last: Xu

first: Han

first: Rulang

last: Jiang


title: Next Generation Sequencing of miRNAs in rat hepatic macrophage Kupffer cells.

city: Cleveland

first: Laura

middle: E

last: Nagy

address: 9500 Euclid Avenue

department: Pathobiology

institute: Cleveland Clinic

summary: We report the application of single-end-based sequencing technology for high-throughput profiling of miRNAs in Kupffer Cells.

overall_design: Examination of miRNA profile in Kupffer cells during chronic ethanol feeding to rat.

first: Paramananda

last: Saikia


title: Effect of corticision on orthodontic tooth movement in a rat model as assessed by RNA sequencing

city: nanjing

first: gu

last: qihui

address: zhongyang road

institute: Nanjing Stomatological Hospital

summary: Corticision is a common technique to accelerate orthodontic tooth movement; however, not much is known about the underlying mechanisms. In this study, we investigated the mechanism of alveolar tissue remodeling after corticision in a rat model of tooth movement (TM) by analyzing the differential transcriptome

overall_design: The transcriptomes of alveolus remodeling after corticision in a rat model of tooth movement and tooth movement without corticision were determined on RNA sequencing (RNA-Seq)

first: Qihui

last: Gu

first: Shuyu

last: Guo


title: H4K20me3 methyltransferase SMYD5 controls heterochromatin and chromosome integrity during embryonic stem cell differentiation

city: Detroit

first: Benjamin

last: Kidder

state: MI

address: 4100 John R St

department: Oncology

institute: Wayne State University

summary: Epigenetic regulation of chromatin states is thought to control gene expression programs during lineage specification. However, the roles of repressive histone modifications such as trimethylated histone lysine 20 (H4K20me3) in development and genome stability are largely unknown. Here, we show that depletion of SMYD5, a H4K20me3 methyltransferase, leads to decreased H4K20me3 and H3K9me3 ChIP-Seq levels, and de-repression of endogenous LTR/LINE elements during differentiation. SMYD5 depletion results in chromosomal aberrations and the formation of transformed cells that exhibit decreased H4K20me3 and H3K9me3 levels and an expression signature consistent with multiple human cancers. Moreover, dysregulated gene expression in SMYD5 cancer cells is associated with LTR/ERV elements and decreased H4K20me3. These findings implicate an important role for SMYD5 in maintaining chromosome integrity by regulating heterochromatin and repressing endogenous repetitive DNA elements during differentiation.

overall_design: ChIP-Seq for H4K20me3, H3K9me3 in murine shLuc and shSmyd5 embryoid body differentiated ES cells, and shSmyd5 cancer cells

first: Keji

last: Zhao