title: tRNA Modification Identification and Quantification through High Throughput Sequencing

city: Chicago

first: Tao

last: Pan

state: Illinois

address: 929 E. 57th Street

department: Biochemistry and Molecular Biology

institute: University of Chicago

summary: We report the identification and quantification of Watson-Crick modifications in tRNA and rRNA through the use of high throughput sequencing. We apply the recently published DM-tRNA-Seq method to generate demethylase treated and untreated 293T samples, and using computational methods we are able to flag sites using a modification index. This index allows us to generate site-resolved information about modification that we can use to identify and quantify Watson-Crick face modifications in tRNA and rRNA. With the demethylase treated samples, we are able to validate numerous nucleotide modifications from demethylase substrates, and the absence of demethylase action also serves to aid in identification. We find numerous novel modification sites in tRNA as well as striking comparisons between tissues cultures lines. Our study reports a comprehensive analysis of the tRNA modification landscape by identifying sites of modification as well as quantifying modification levels.

overall_design: Comprehensive comparative analysis of high throughput sequencing data to determine a quantitative metric of modification

first: Wesley

last: Clark

first: Guanqun

last: Zheng

first: Dan

last: Dominissini


title: Boron-deficiency-responsive microRNAs and their targets in Citrus sinensis leaves

status: Public on Feb 10 2017

city: Fuzhou

first: Chen

last: Lisong

address: Shangdian street NO.15

country: China

institute: Fujian Agriculture and Forestry University

type: Non-coding RNA profiling by high throughput sequencing

summary: Background: MicroRNAs play important roles in the adaptive responses of plants to  nutrient deficiencies. Here, we sequenced two small RNA libraries from B-deficient and  -sufficient (control) Citrus sinensis leaves, respectively, using Illumina sequencing in  order to identify the potential miRNAs related to the tolerance of citrus to B-deficiency.  Results: Ninety one (83 known and 8 novel) up- and 81 (75 known and 6 novel) downregulated miRNAs were isolated from B-deficient leaves. The great alteration of miRNA  expression might contribute to the tolerance of citrus to B-deficiency. The adaptive  responses of miRNAs to B-deficiency might related to several aspects: (a) attenuation  of plant growth and development by repressing auxin signaling due to decreased TIR1 level and ARF-mediated gene expression by altering the expression of miR393,  miR160 and miR3946; (b) maintaining leaf phenotype and enhancing the stress  tolerance by up-regulating NACs targeted by miR159, miR782, miR3946 and miR7539;  (c) activation of the stress responses and antioxidant system through down-regulating  the expression of miR164, miR6260, miR5929, miR6214, miR3946 and miR3446; (d)  decreasing the expression of major facilitator superfamily protein genes targeted by  miR5037, thus lowering B export from plants. Also, B-deficiency-induced downregulation of miR408 might play a role in plant tolerance to B-deficiency by regulating  Cu homeostasis and enhancing superoxide dismutase activity.  Conclusions: Our study reveals some novel responses of citrus to B-deficiency, which  increase our understanding of the adaptive mechanisms of citrus to B-deficiency at the  miRNA (post-transcriptional) level.

overall_design: Two libraries were constructed from C. sinensis leaves subjected to 0(B-deficient, Xa) or 10(B-sufficient,control, Xb) μM B   for 15 weeks, and sequenced by Illumina sequencing. Size fractionated small RNAs (16-30 bp) from total RNA extracts was ligated to 5' and 3' adapters, and reverse transcribed. After PCR amplification the sample was subjected to Solexa sequencing. The clean tags were used for further analysis.

first: Yi-Bin

last: Lu

first: Yi-Ping

last: Qi


title: Dynamic and flexible bridging of H3K9me3-nucleosomes via HP1β-dimerization  establishes a plastic state of condensed chromatin

city: Montreal

first: Carol

last: Chen

state: QC

address: 1001 Decarie Boulevard, Rm E01.4380

department: Human Genetics

country: Canada

institute: Research Institute of McGill University Hospital Centre

type: Genome binding/occupancy profiling by high throughput sequencing

summary: Histone H3 trimethylation of lysine 9 (H3K9me3) and heterochromatin proteins 1 (HP1) are hallmarks of heterochromatin, a state of compacted DNA essential for genome stability and long-term transcriptional silencing. The mechanisms by which H3K9me3 and HP1 contribute to chromatin compaction have been speculative and controversial. We demonstrate that mammalian HP1β is a prototypic HP1 protein exemplifying most basal chromatin binding and effects. These are caused by dimeric and dynamic interaction with highly enriched H3K9me3 and are modulated by various electrostatic interfaces. Via internucleosomal bridging HP1β specifically interacts with condensed chromatin, which we postulate stabilizes the compacted state. In agreement, HP1β genome-wide localization follows enrichment of H3K9me3 and bridging of chromatin fibers in a cellular context is sufficient for maintaining heterochromatic conformation. Overall, our findings define a fundamental mechanism for chromatin higher order structural changes caused by HP1 proteins, which may contribute to the plastic nature of condensed chromatin.

overall_design: HP1b ChIP-seq in mouse embryonic stem cells

first: Kyoko

last: Hiragami-Hamada

first: Szabolcs

last: Soeroes

first: Tuncay

last: Baubec

first: Miroslav

last: Nikolov

first: Bryan

last: Wilkins

first: Sarah

last: Kreuz

first: Hans

middle: M

last: Zenn

first: Nils

last: Kost

first: Wiebke

last: Pohl

first: Aleksandar

last: Chernev

first: Dirk

last: Schwarze

first: Thomas

last: Jenuwein

first: Matthew

middle: C

last: Lorincz

first: Bastian

last: Zimmermann

first: Peter

middle: J

last: Walla

first: Heinz

last: Neumann

first: Henning

last: Urlaub

first: Wolfgang

last: Fischle


title: The repressive regulatory role of H3K27me3 histone mark in bovine mastitis resistance to Staphylococcus aureus

city: Honolulu

first: Yanghua

last: He

state: HI

address: 1955 East West Road

department: Human Nutrition, Food and Animal Sciences

country: USA

institute: University of Hawaii at Manoa

summary: The regulatory effects of H3K27me3 on target genes expressions were analyzed by comparing S. aureus mastitis resistant and susceptible cows. The differentially expressed genes are mainly associated with immune and disease-related processes, which were negatively regulated by H3K27me3 modification on the up 2Kb regions relative to TSS in S. aureus mastitis cattle.

overall_design: Examination of H3K27me3 modifications in six cows.

first: Minyan

last: Song

first: Yi

last: Zhang

first: Xizhi

last: Li

first: Jiuzhou

first: Yuan

first: Ying

last: Yu


title: The Ski complex binds 80S ribosomes for 3’ to 5’ decay of mRNA

city: Munich

first: Markus

last: Pech

address: 25 Feodor-Lynen Str

department: Biochemistry

country: Germany

institute: Genzentrum, LMU

type: Expression profiling by high throughput sequencing

summary: Cytoplasmic degradation of eukaryotic mRNAs in 3’ to 5’ direction is catalyzed by the exosome complex together with the Ski complex and, in the yeast Saccharomyces cerevisiae, the Ski7 protein. This exosome-Ski-system also degrades ribosome-associated aberrant mRNAs lacking a stop codon, a pathway called non-stop-mRNA decay (NSD). However, the interplay between the Ski components and the ribosome is unknown. Here, we report that the Ski complex can associate with ribosomes in vitro and in vivo independently of Ski7. Ribosome profiling suggests that this association is important for NSD but also for general mRNA turnover. A cryo-electron microscopy structure reveals that the Ski complex binds near the mRNA entry site of the 40S subunit, facilitating the threading of the mRNA into the Ski2 helicase. Collectively, these results demonstrate an unanticipated role for the Ski complex in mRNA decay of ribosome-associated mRNAs, mediated by a direct interaction with the translation machinery.

overall_design: Ribosome profiling of 80S monosomes and in vivo pullouts of Ski complex associated 80S ribosomes. In vivo pullouts were performed using a yeast strain expressing C-terminally TAP (tandem affinity purification) tagged Ski3. Control mRNA from the total cell lysate and pull-down mRNA from the pullouts were also sequenced respectively.

first: Christian

last: Schmidt

first: Eva

last: Kowalinski

first: Vivekanandan

last: Shanmuganathan

first: Quentin

last: Defenouillère

first: Katharina

last: Braunger

first: Abdelkader

last: Namane

first: Otto

last: Berninghausen

first: Micheline

last: Fromont-Racine

first: Alain

last: Jacquier

first: Elena

last: Conti

last: Becker

first: Roland

last: Beckmann


title: Transcriptomic profiles reveal the genome-wide responses of the harmful dinoflagellate Cochlodinium polykrikoides (Cp) when exposed to the algicide copper sulfate

city: SEOUL

first: Jang-Seu

last: Ki

state: SEOUL

address: 20, Hongimun 2-Gil, Jongno-gu

department: Department of Life Science, College of Natural Sciences

country: South Korea

institute: Sangmyung University

summary: To identify the transcripome of dinoflagellate Cochlodinium polykrikoides that responded to algicide copper sulfate

overall_design: untreated cells that used as control (exponential stage of growth), the cells were treated with 1 mg CuSO4 and harvested at 12 h, 24h, and 48h after expousre  to CuSO4 (exponential stage of growth), untreated cells that harvest in stationary phase

first: Jang-Se

first: Ruoyu

last: Guo


title: Illumina Total RNA-seq in HeLa

city: Berlin

first: Dubravka

last: Vučićević

address: Ihnestraße 63-73

institute: Max Planck Institute for Molecular Genetics

summary: Purpose: Examine the effect of the long non-coding RNA PARROT on the transcriptome in HeLa cells.

overall_design: Total RNA-seq of  RNA from cells treated with the control knock-down (NK) or depleted of ENST00000046668 (PARROT) with two different siRNAs (si1 and si2) for 24h.

first: D

last: Vucicevic

first: U

middle: A

last: Orom


title: Identification and Differential Expression of MicroRNAs Associated with Fat Deposition in Wistar Rat Liver Using Solexa Sequencing

city: Taian

first: Yuqian

last: Wang

address: Daizong Street No. 61

institute: Shandong Agricultural University

summary: we analyzed the miRNAs expression in Wistar rat liver tissues, High glucose (HG)-induced NAFLD Wistar rats (NAFLD group, n=3) and normal Wistar rats (normal group, n=3).  Results provided the first global miRNAs in the NAFLD Wistar rat livers, and expanded the miRNAs repertoire in normal Wistar rat livers, which should be useful for further investigation into the biological functions and evolution of miRNAs in rats and other species. These findings suggest an important role of miRNAs in liver fat deposition, and implicate the participation of miRNAs in the NAFLD pathophysiological processes.

overall_design: Total RNA obtained from isolated NAFLD Wistar rat liver tissues compared to normal Wistar rat liver tissues.

first: Zhonghua

first: Deqing

last: Zhang


title: Gene expression of rhabdomyosarcoma cells infected with cytolytic and non-cytolytic variants of coxsackievirus B2 Ohio

city: Kalmar

first: Michael

last: Lindberg

address: Smalandsgatan 24

country: Sweden

institute: Linnaeus University

summary: In this study the gene expression in cells infected with lytic and non-lytic variants of coxsackievirus B2 Ohio (CVB2O) were analyzed using next generation sequencing. This approach was selected with the purpose of elucidating the effects of lytic and non-lytic viruses on host cell transcription. Total RNA was extracted from infected cells, next generation sequencing was performed, and the reads were subsequently mapped against the human and CVB2O genomes. The amount of intracellular virions was measured, showing a relative amount of virus RNA 13 times higher in the cells infected with the lytic variant, vVP1Q164K, compared to cells infected by the non-lytic CVB2Owt. Furthermore, differential gene expression in the cells infected with the two viruses was identified and a number of genes singled out as possible keys to the answer of how the viruses interact with the host cells, resulting in lytic or non-lytic infections.

sample_organism:
Homo sapiens
Coxsackievirus B2 (strain Ohio-1)

overall_design: 4 samples, two samples of one strain, one sample of a different strain, and one control sample

first: Anna

last: Sävneby


title: Pax6 links H3K4 methylase activity to transcriptional regulation of Plekha1 through its distal enhancer

city: Bronx

first: Ales

last: Cvekl

state: NY

address: 1300 Morris Park Avenue, Ullman 123

department: The Departments Ophthalmology and Visual Sciences, Genetics

institute: Albert Einstein College of Medicine

summary: We performed ChIP-seq on mouse lens epithelial cells (αTN4) and mouse newborn lens. Genome-wide binding sites of Pax6, H3K4me1, H3K4me2, H3K4me3, and RNA polymerase II were generated. We also performed RNA-seq on αTN4 cells treated with Pax6 and control shRNAs.

overall_design: Examination of correlation between Pax6 binding and histone H3K4 methylation distribution.

first: Jian

last: Sun

first: Shira

last: Rockowitz

first: Carola

last: Wilczek

first: David

last: Shechter

first: Deyou

last: Zheng


title: High-throughput sequencing identifies miRNAs and their targets involved in porcine muscle development

city: Guangzhou

first: Fan

last: Wu

state: Guangdong

address: Wushan Road

institute: South China Agricultral University

summary: To identify miRNAs involved in muscle development, three independent small RNA libraries from porcine skeletal muscle at the age of 63d、98d and 161d were constructed. A total of 4105184， 4606375 and 5113984 mappable small RNA sequences were generated in the three small RNA libraries, respectively, and 887 known and 472 new candidate miRNAs were obtained.

overall_design: sample 1: Examination of small RNA in porcine skeletal muscle at the age of 63d; sample 2: Examination of small RNA in porcine skeletal muscle at the age of 98d; sample 3: Examination of small RNA in porcine skeletal muscle at the age of 161d

first: Jianjun

last: Zuo


title: RNA sequencing of CACO-2 cells incubated with Bifidobacteria breve grown on human milk oligosaccharides.

city: Davis

first: Danielle

middle: G

last: Lemay

state: CA

address: 451 Health Sciences Dr

department: Genome Center

institute: University of California Davis

summary: Background: Breastfed human infants are predominantly colonized by bifidobacteria that thrive on human milk oligosaccharides (HMO).  The two most predominant species of bifidobacteria in infant feces are Bifidobacterium breve (B. breve) and Bifidobacterium longum subsp. infantis (B. infantis), both avid HMO-consumer strains. Our laboratory has previously shown that B. infantis, when grown on HMO, increase adhesion to intestinal cells and increase the expression of the anti-inflammatory cytokine interleukin-10. The purpose of the current study was to investigate the effects of carbon source—glucose, lactose, or HMO—on the ability of B. breve and B. infantis to adhere to and affect the transcription of intestinal epithelial cells on a genome-wide basis. Results: HMO-grown B. infantis had higher percent binding to Caco-2 cell monolayers compared to B. infantis grown on glucose or lactose. B. breve had low adhesive ability regardless of carbon source.  Despite differential binding ability, both HMO-grown strains significantly differentially affected the Caco-2 transcriptome compared to their glucose or lactose grown controls. HMO-grown B. breve and B. infantis both down-regulated genes in Caco-2 cells associated with chemokine activity.  Conclusion: The choice of carbon source affects the interaction of bifidobacteria with intestinal epithelial cells. HMO-grown bifidobacteria reduce markers of inflammation, compared to glucose or lactose-grown bifidobacteria. In the future, the design of preventative or therapeutic probiotic supplements may need to include appropriately chosen prebiotics.

overall_design: CACO-2 cells incubated with Bifidobacterium breve grown on (1) glucose, (2) lactose, or (3) human milk oligosaccharides. All experiments were run in triplicate.

last: Mills

first: Saumya

last: Wickramasinghe

first: Alline

middle: R

last: Pacheco


title: Phenazines regulated genes in Pseudomonas chlororaphis 30-84

city: Vernon Hills

first: DONGPING

last: WANG

state: IL

address: 777 Forest Edge Dr

department: Amlan

institute: OilDri Corporation of America

summary: Pseudomonas chlororaphis strain 30-84 is an effective biological control agent against take-all disease of wheat.  In this study, we conducted an RNA-seq analysis by comparing the wild type strain, PCA and O star with a phenazine deficient mutant. RNA-seq analysis identified over 800 genes differentially regulated by phenazines.

sample_organism: Pseudomonas chlororaphis subsp. aureofaciens 30-84

overall_design: A total of 8 samples were analyzed in AB medium + 2% casamino acids, Pseudomonas chlororaphis wild type strain (2 replicates);  Pseudomonas chlororaphis ZN mutant (2 replicates);  Pseudomonas chlororaphis PCA strain (2 replicates); Pseudomonas chlororaphis O star (2 replicates).

first: Dongping

first: Elizabeth

last: Pierson


title: Differential Analysis of L. buchneri Transcriptomes under anaerobic and aerobic conditions

city: Bielefeld

first: Felix

middle: Gregor

last: Eikmeyer

address: Universitaetsstrasse 25

department: Center for Biotechnology

institute: Bielefeld University

summary: The Lactobacillus buchneri CD034 strain, known to improve the ensiling process of green fodder and the quality of the silage itself was transcriptionally analyzed by sequencing of transcriptomes isolated under anaerobic vs. aerobic conditions. L. buchneri CD034 was first cultivated under anaerobic conditions and then shifted to aerobic conditions by aeration with 21% oxygen. Cultivations already showed that oxygen was consumed by L. buchneri CD034 after aeration of the culture while growth of L. buchneri CD034 was still observed. RNA sequencing data revealed that irrespective of the oxygen status of the culture, the most abundantly transcribed genes are required for basic cell functions such as protein biosynthesis, energy metabolism and lactic acid fermentation. Under aerobic conditions, 283 genes were found to be transcriptionally up-regulated while 198 genes were found to be down-regulated (p-value < 0.01). Up-regulated genes i. a. play a role in oxygen consumption via oxidation of pyruvate or lactate (pox, lctO). Additionally, genes encoding proteins required for decomposition of reactive oxygen species (ROS) such as glutathione reductase or NADH peroxidase were also found to be up-regulated. Genes related to pH homeostasis and redox potential balance were found to be down-regulated under aerobic conditions. Overall, genes required for lactic acid fermentation were hardly affected by the growth conditions applied. Genes identified to be differentially transcribed depending on the aeration status of the culture are suggested to specify the favorable performance of the strain in silage formation.

sample_organism: Lentilactobacillus buchneri subsp. silagei CD034

overall_design: 2 samples, 2 replicates

first: Stefan

last: Heinl

first: Hans

last: Marx

first: Alfred

last: Pühler

first: Reingard

last: Grabherr

first: Andreas

last: Schlüter


title: RNA sequencing of CACO-2 cells incubated with bifidobacteria grown on human milk oligosaccharides.

summary:
Background: Breastfed human infants are predominantly colonized by bifidobacteria that thrive on human milk oligosaccharides (HMO).  The two most predominant species of bifidobacteria in infant feces are Bifidobacterium breve (B. breve) and Bifidobacterium longum subsp. infantis (B. infantis), both avid HMO-consumer strains. Our laboratory has previously shown that B. infantis, when grown on HMO, increase adhesion to intestinal cells and increase the expression of the anti-inflammatory cytokine interleukin-10. The purpose of the current study was to investigate the effects of carbon source—glucose, lactose, or HMO—on the ability of B. breve and B. infantis to adhere to and affect the transcription of intestinal epithelial cells on a genome-wide basis.
Results: HMO-grown B. infantis had higher percent binding to Caco-2 cell monolayers compared to B. infantis grown on glucose or lactose. B. breve had low adhesive ability regardless of carbon source.  Despite differential binding ability, both HMO-grown strains significantly differentially affected the Caco-2 transcriptome compared to their glucose or lactose grown controls. HMO-grown B. breve and B. infantis both down-regulated genes in Caco-2 cells associated with chemokine activity.
Conclusion: The choice of carbon source affects the interaction of bifidobacteria with intestinal epithelial cells. HMO-grown bifidobacteria reduce markers of inflammation, compared to glucose or lactose-grown bifidobacteria. In the future, the design of preventative or therapeutic probiotic supplements may need to include appropriately chosen prebiotics.

overall_design: CACO-2 cells incubated with Bifidobacterium longum subsp. infantis grown on (1) glucose, (2) lactose, or (3) human milk oligosaccharides. All experiments were run in triplicate.


title: Transcriptome Analysis Reveals a Comprehensive Regulatory Network Involved in the Zebrafish Model of Diamond-Blackfan Anemia from RPL5 Deficiency

city: Beijing

first: yadong

last: yang

address: No.1-104 Beichen West Road, Chaoyang

institute: Beijing Institute of Genomics

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

overall_design: Refer to individual Series


title: ONSEN insertion site on Arabidopsis thaliana genome subjected to heat treatment

city: Yokohama

first: motoaki

last: seki

state: Kanagawa

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

department: CSRS

country: Japan

institute: RIKEN

summary: Identification of  the newly insertied site of heat-activaed ONSEN transposon on Arabidopsis thaliana

overall_design: ONSEN insertion site on a progeny of Arabidopsis thaliana (polIV mutant and wt:Col-0)  with heat treatment (37C) and without heat treatment (21C)

first: Hidetaka

last: Ito

first: Jong-Myong

last: Kim

first: Wataru

last: Matsunaga

first: Hidetoshi

last: Saze

first: Akihiro

last: Matsui

first: Takaho

last: Endo

first: Hiroki

last: Takagi

first: Yukari

last: Masuta

first: Seiji

last: Masuda

first: Junko

last: Ishida

first: Maho

last: Tanaka

first: Satoshi

last: Takahashi

first: Taeko

last: Morosawa

first: Tetsuro

last: Toyoda

first: Tetsuji

last: Kakutani

first: Atsushi

last: Kato

first: Motoaki

last: Seki


title: Transcriptome Analysis Reveals a Comprehensive Regulatory Network Involved in the Zebrafish Model of Diamond-Blackfan Anemia from RPL5 Deficiency [RNA-Seq]

first: yadong

last: yang

summary: In this study, we generated a zebrafish model of DBA with RPL5 morphants and implemented high-throughput RNA-seq and miRNA-seq to identify key genes, lncRNAs, and miRNAs during zebrafish development and hematopoiesis. We found that RPL5 is required for both primitive and definitive hematopoiesis processes that are partially mediated by the P53 pathway. Several genes such as cirh1a, noc2l, tars, and nol6 and miRNAs such as dre-miR-10a*, dre-miR-722, dre-miR-737, and dre-miR-142a-3p were significantly deregulated, and these changes may play a crucial role in hematopoiesis, ribosome biogenesis and development process. We also characterized the lncRNome in zebrafish with RPL5 deficiency. By constructing a comprehensive regulatory network, we identified central node genes in the network connected to the P53 pathway, almost all of which were targeted by the significantly deregulated miRNAs listed above. Our results therefore establish a regulatory network for critical genes and miRNAs involved in the RPL5-deficient zebrafish model and provide a comprehensive basis for the molecular pathogenesis of RPL5-mediated DBA and other ribosomopathies.

overall_design: Determine the differences of transcriptome between RPL5-deficient and MO control zebrafish embryos for understanding the complex molecular pathogenesis of mutant RPL5-mediated human diseases

first: Xiangdong

last: Fang


title: Transcriptional analysis of wild-type budding yeast microcolonies encapsulated in alginate particles

city: Solna

first: Vicent

last: Pelechano

address: Nobels väg 16

department: MTC

institute: ScilifeLab - Karolinska Institutet

summary: We analysed the transcriptomic signature associated to fast and slow growing microcolonies generated after the encapsulation of single cells belonging to a clonal wild-type population, in alginate microspheres. This allowed us to identify particular gene expression signatures associated to each subpopulation. In particular, we found that slow growing cells display an increased expression of respiratory genes even when growing in glucose rich media.

overall_design: S. cerevisiae cells were encapsulated in alginate particles using a Cellena microencapsulator (Ingeniatrics), as described (Gómez-Herreros et al, NAR 2011). Encapsulated cells were allowed to divide in rich media (YPD) and harvested. We analyzed 3 biological replicates of non-sorted particles (total), 3 biological replicates of big colonies (big) and 4 replicates of small particles (small). Due to the limited RNA amount, replicates 1 and 3 of the small colonies lead to very low sequencing quality and were excluded from the analysis. As control experiments we analysed biological duplicates from encapsulated cells not fixed with ethanol (nofix), and the same cells grown in batch without encapsulation at two different cell densities (YPD05 and YPD2).

first: Lidia

last: Delgado-Ramos

first: Sebastian

last: Chavez

first: Lars

last: Steinmetz


title: Analysis of gene expression among schistosoma japonicum from different hosts

city: shanghai

first: yang

middle: jian

last: mei

address: minhang district ziyue road No.518

institute: shanghai veterinary research institute

summary: The microarray analysis of gene expression difference between cattle,buffalo and goat,provide us a profiling as a new platform to discover the difference between their compatibility

overall_design: schistosoma japonicum were collected by hepatic portal vein perfusion from the cattle,buffalo and goat after they infected 49d,7weeks.Three animals were perfused for each host.And worms from each animal for each experiment.

first: Jianmei

last: Yang

first: Jiaojiao

last: Lin

first: Xingang

last: Feng

first: Chunxiu

last: Yuan

first: Zhiqiang

last: Fu

first: Yaojun

last: Shi

first: Jinming

last: Liu


title: Autocrine IGF1 signaling mediates pancreatic tumor cell dormancy in the absence of oncogenic drivers

status: Public on Feb 09 2017

city: Omaha

first: Kay-Uwe

last: Wagner

state: NE

address: 985950 Nebraska Medical Center

department: Eppley Institute for Cancer Research

institute: University of Nebraska Medical Center

summary: Mutant KRAS and c-MYC are oncogenic drivers and rational therapeutic targets for the treatment of pancreatic cancer. While tumor growth and homeostasis is largely dependent on these oncogenes, a few residual cancer cells are able to survive the ablation of mutant KRAS and c-MYC. By performing a genome-wide gene expression analysis of in vivo-derived bulk tumor cells and residual cancer cells lacking the expression of mutant KRAS or c-MYC, we have identified an increase in autocrine IGF1/AKT signaling as a common survival mechanism in dormant cancer cells. The pharmacological inhibition of IGF-1R reduced residual disease burden and cancer recurrence, suggesting this molecular pathway is crucial for the survival of cancer cells in the absence of the primary oncogenic drivers.

overall_design: Total RNA was extracted from flash-frozen pancreatic cancer tissues before or after doxycycline treatment of tumor transplanted athymic nude mice using the RNeasy Mini Kit (Qiagen).

first: Nirakar

last: Rajbhandari

first: Wan-chi

first: Barbara

middle: L

last: Wehde

first: Aleata

last: Triplett


title: A microRNA family exerts maternal control on sex determination in C. elegans

city: Bethesda

first: Katherine

last: McJunkin

state: MD

address: 50 South Drive, Building 50 Room 3148

institute: National Institutes of Health

summary:
Gene expression in early animal embryogenesis is in large part controlled post-transcriptionally. Maternally-contributed microRNAs may therefore play important roles in early development. We have elucidated a major biological role of the nematode mir-35 family of maternally-contributed, essential microRNAs. We show that this microRNA family regulates the sex determination pathway at multiple levels, acting both upstream and downstream of her-1 to prevent aberrantly activated male developmental programs in hermaphrodite embryos. The predicted target genes that act downstream of the mir-35 family in this process, sup-26 and nhl-2, both encode RNA binding proteins, thus delineating a previously unknown post-transcriptional regulatory subnetwork within the well-studied sex determination pathway of C. elegans. Repression of nhl-2 by the mir-35 family is not only required for proper sex determination but also for viability, showing that a single microRNA target site can be essential. Since sex determination in C. elegans requires zygotic gene expression to read the sex chromosome karyotype, early embryos must remain gender-naïve; our findings show that the mir-35 family microRNAs act in the early embryo to function as a developmental timer that preserves naïveté and prevents premature deleterious developmental decisions.

This SuperSeries is composed of the SubSeries listed below.

first: Victor

last: Ambros


title: Transcriptome Analysis Reveals a Comprehensive Regulatory Network Involved in the Zebrafish Model of Diamond-Blackfan Anemia from RPL5 Deficiency [miRNA-Seq]

first: yadong

last: yang

overall_design: Determine the differences of miRNome between RPL5-deficient and MO control zebrafish embryos for understanding the complex molecular pathogenesis of mutant RPL5-mediated human diseases

first: Xiangdong

last: Fang


title: Effects of LKB1/STK11 expression on MDA-MB-231 triple-negative breast cancer cells

city: New Orleans

first: Bridgette

last: Collins-Burow

state: LA

address: 1430 Tulane Ave, SL-78

department: Medicine

institute: Tulane University

summary: MDA-MB-231 cells transfected with pcDNA-vector or pcDNA-LKB1 were analyzed for changes in gene expression. Results provide insight into genes regulated by LKB1 signaling with implications in tumor and metastasis suppression in breast cancer.

overall_design: 4 samples, duplicates of -vector and -LKB1 stable cell lines

first: Lyndsay

middle: V

last: Rhodes

first: Matthew

middle: E

last: Burow

first: Elizabeth

last: Martin

first: Kenneth

middle: P

last: Nephew

first: Dave

middle: B

last: Miller

first: Aaron

last: Buechlein

first: Doug

last: Rusch

first: Hiaxu

last: Tang


title: Integrative analysis of sex-specific microRNA networks following stress in mouse nucleus accumbens

city: New York

first: Eddie

last: Loh

address: 1425 Madison Avenue

department: Department of Neuroscience

institute: Icahn School of Medicine at Mount Sinai

summary: Adult women are twice as likely as men to suffer from affective and anxiety disorders, although the mechanisms underlying heightened female stress susceptibility are incompletely understood. Recent findings in mouse Nucleus Accumbens (NAc) suggest a role for DNA methyltransferase-driven sex differences in genome-wide transcriptional profiles. However, the role of another epigenetic process—microRNA (miR) regulation—has yet to be explored. We exposed male and female mice to Subchronic Variable Stress (SCVS), a stress paradigm that produces depression-like behavior in female, but not male, mice, and performed next-generation mRNA and miR sequencing on NAc tissue. We applied a combination of differential expression, miR-mRNA network and functional enrichment analyses to characterize the transcriptional and post-transcriptional landscape of sex differences in NAc stress response. We find that male and female mice exhibit largely non-overlapping miR and mRNA profiles following SCVS. The two sexes also show enrichment of different molecular pathways and functions. Collectively, our results suggest that males and females mount fundamentally different transcriptional and post-transcriptional responses to SCVS and engage sex-specific molecular processes following stress. These findings have implications for the pathophysiology and treatment of stress-related disorders in women.

overall_design: miR and mRNA profiles in male and female mice exposed to SCVS were generated to identify sex differences in transcriptional and post-transcriptional stress response. Profiles were generated from 3 libraries per sex/stress condition (male control, male stressed, female control, female stressed), totaling 12 libraries for both the miR and mRNA analyses. Libraries for miR and mRNA sequencing were generated from separate size-enriched fractions of RNA isolated from nucleus accumbens (NAc) of 5 pooled samples per library. All female pools contained NAc from females in estrus or proestrus to control for the female estrous cycle.

first: Madeline

last: Pfau

first: Scott

last: Russo


title: RNASeq of juvenile keratinocytes, melanocytes, fibroblasts and whole skin

city: Tartu

first: Paula

last: Reemann

address: Ravila 19

department: Institute of Biomedicine and Translational Medicine, Department of Physiology

country: Estonia

institute: University of Tartu

summary: We used whole transcriptome sequencing (RNA-Seq) to assess differential gene expression of normal human melanocytes with respect to keratinocytes, fibroblasts and whole skin. We have identified a number of genes and pathways, which are characteristic or unique for MC compared to KC and FB. We also demonstrated the extent of the difference between genes detectable in MC culture and the whole skin. The present results reveal melanocytes as highly proliferative cells with stem cell-like properties.

overall_design: From each of the healthy juvnile skin tissue samples a whole skin sample was taken and three skin cell types (keratinocytes, melanocytes and fibroblasts) were harvested and cultivated. We chose 12 total RNA samples, extracted from 4 keratinocytes (Kc), 4 melanocytes (Mc), 2 fibroblasts (FB) and 2 whole skin samples for library preparation.

last: Reeman


title: Peripheral self-reactivity regulates antigen-specific CD8 T cell responses and cell division under physiological conditions

city: London

first: Eva

last: Frickel

address: 1 Midland Road

department: Host-Toxoplasma Interaction Laboratory

country: United Kingdom

institute: The Francis Crick Institute

summary: It is unknown how naïve CD8 T cells that harbour different and distinct T cell receptors to the same MHC-epitope combination differ in terms of their transcriptional expression profile.

overall_design: In this experiment we compared the expression profile of three naïve transnuclear CD8 T cell clones that differ in their T cell receptor and affinity to cognate peptide and self-reactivity. We find that the transcriptomes of these T cells differ with respect to readiness for cell cycle progression and T cell receptor signaling.

first: Lee

middle: K

last: Swee

first: Zhen

middle: W

last: Tan

first: Anna

last: Sanecka

first: Nagisa

last: Yoshida

first: Harshil

last: Patel

first: Gijsbert

last: Grotenbreg

first: Eva-Maria

first: Hidde

last: Ploegha


title: RNA-Seq analyse the virulence mechanism of rice pathogen Acidovorax avenae subsp. avenae strain RS-1 following ß-lactam antibiotics exposure

city: Hangzhou

first: Bin

last: Li

state: Zhejiang

address: Zijingang Campus, Nongshenghuan Building, C702

department: College of Agriculture and Biolechnology

institute: Zhejiang University

summary: This study investigated the transcriptomic response of rice pathogen Acidovorax avenae subsp. avenae (Aaa) strain RS-1 to ß-lactam antibiotics in particular Ampicillin (Amp) and the result highlights the importance of Amp-induced differentially expressed genes in the virulence of Aaa strain RS-1.

overall_design:
1 sample (Aaa strain under Amp (+) condition) with 2 biogical replicates;
our previous RNA-Seq squencing result of Aaa strain under Amp (-) condition [GSM1220690 and GSM1220691 in GSE50522] was used as the control.

first: Li

last: Bin


title: Involvement of Igf1r in Bronchiolar Epithelial Regeneration: Role During Repair Kinetics after Selective Club Cell Ablation

city: Logroño

first: Jose

middle: Garcia

last: pichel

state: La Rioja

address: Piqueras 98

department: Oncology

country: Spain

institute: FUNDACIÓN RIOJA SALUD - CIBIR

summary: Regeneration of lung epithelium is vital for maintaining airway function and integrity. An imbalance between epithelial damage and repair is at the basis of numerous chronic lung diseases such as asthma, COPD, pulmonary fibrosis and lung cancer. IGF (Insulin-like Growth Factors) signaling has been associated with most of these respiratory pathologies, although their mechanisms of action in this tissue remain poorly understood. Expression profiles analyses of IGF system genes performed in mouse lung support their functional implication in pulmonary ontogeny. Immuno-localization revealed high expression levels of Igf1r (Insulin-like Growth Factor 1 Receptor) in lung epithelial cells, alveolar macrophages and smooth muscle. To further understand the role of Igf1r in pulmonary homeostasis, two distinct lung epithelial-specific Igf1r mutant mice were generated and studied. The lack of Igf1r disturbed airway epithelial differentiation in adult mice revealed enhanced proliferation and altered morphology in distal airway club cells. During recovery after naphthalene-induced club cell injury, the kinetics of terminal bronchiolar epithelium regeneration was hindered in Igf1r mutants, revealing increased proliferation and delayed differentiation of club and ciliated cells. Amid airway restoration, lungs of Igf1r deficient mice showed increased levels of Igf1, Insr, Igfbp3 and epithelial precursor markers, reduced amounts of Scgb1a1 protein, and alterations in IGF signaling mediators. These results support the role of Igf1r in controlling the kinetics of cell proliferation and differentiation during pulmonary airway epithelial regeneration after injury.

overall_design:
Lung mRNA profiles of 3 months-old Igf1rfl/fl normal/control transgenic mice were generated by deep sequencing using Illumina GAIIx.
-------------------------------------------
Submitter states "we use data on the absolute transcription levels (FPKM) of same IGF system genes on the adult "normal" mouse lung to compare them with those reported in the human adult lung (expressed in both as FPKM) (http://www.proteinatlas.org/)".

first: Icíar

last: López

first: Sergio

last: Piñeiro-Hermida

first: Rosete

middle: S

last: Pais

first: Raquel

last: Torrens

first: Andreas

last: Hoeflich

first: José

last: Pichel


title: High concordance between Illumina HiSeq2500 and NextSeq500 for Reduced Representation Bisulfite Sequencing (RRBS)

city: Royal Parade

first: Andrew

last: Keniry

state: Victoria

department: Molecular Medicine

country: Australia

institute: The Waler and Eliza Hall Institute of Medical Research

type: Methylation profiling by high throughput sequencing

summary: Reduced representation bisulfite sequencing (RRBS) provides an efficient method for measuring DNA methylation at single base resolution in regions of high CpG density. This technique has been extensively tested on the HiSeq2500, which uses a 4-colour detection method, however it is unclear if the method will also work on the NextSeq500 platform, which employs a 2-colour detection system. We created an RRBS library and sequenced it on both the HiSeq2500 and NextSeq500, and found no significant difference in the base composition of reads derived from either machine.  Moreover, the methylation calls made from the data of each instrument were highly concordant, with methylation patterns across the genome appearing as expected. Therefore, RRBS can be sequenced on the Nextseq500 with comparable quality to that of the HiSeq2500.

overall_design: Examination of RRBS data produced on the HiSeq2500 and NextSeq500.


title: Morphological and molecular characterization of human dermal lymphatic collectors

city: Göttingen

first: Jörg

last: Wilting

address: Kreuzbergring 36

department: Anatomy and Cell Biology

institute: University Medical School Göttingen

summary: Millions of patients suffer from lymphedema worldwide. Supporting the contractility of lymphatic collectors is an attractive target for pharmacological therapy of lymphedema. However, lymphatics have mostly been studied in animals, while the cellular and molecular characteristics of human lymphatic collectors are largely unknown. We studied epifascial lymphatic collectors of the thigh, which were isolated for autologous transplantations. Our immunohistological studies identify additional markers for LECs (vimentin, CCBE-1). We show and confirm differences between initial and collecting lymphatics concerning the markers ESAM1, D2-40 and LYVE-1. Our transmission electron microscopic studies reveal two types of smooth muscle cells (SMCs) in the media of the collectors with dark and light cytoplasm. We observed vasa vasorum in the media of the largest collectors, as well as interstitial Cajal-like cells, which are highly ramified cells with long processes, caveolae, and lacking a basal lamina. They are in close contact with SMCs, which possess multiple caveolae at the contact sites. Immunohistologically we identified such cells with antibodies against vimentin and PDGFRα, but not CD34 and cKIT. With Next Generation Sequencing we searched for highly expressed genes in the media of lymphatic collectors, and found therapeutic targets, suitable for acceleration of lymphatic contractility, such as neuropeptide Y receptors 1, and 5; tachykinin receptors 1, and 2; purinergic receptors P2RX1, and 6, P2RY12, 13, and 14; 5-hydroxytryptamine receptors HTR2B, and 3C; and adrenoceptors α2A,B,C. Our studies represent the first comprehensive characterization of human epifascial lymphatic collectors, as a prerequisite for diagnosis and therapy.

overall_design: The transcriptome of 6 different normal human lymphatic collectors (Lyko1, Lyko 4-12, Lyko 5, Lyko12, Lyko13, Lyko26) from the dermis of the thigh of women between 44 and 61 years of age was compared to cultures of human dermal lymphatic endothelial cells (LEC1, LEC2, HD-LEC9A) and a mixture of 3 different human dermal blood endothelial cells (HD-BEC-CA) to identify potential drug targets in the media of the collectors.

first: Viktoria

last: Hasselhof

first: Anastasia

last: Sperling

first: Kerstin

last: Buttler

first: Philipp

last: Ströbel

first: Jürgen

last: Becker

first: Thiha

last: Aung

first: Gunther

last: Felmerer


title: Transcriptomic analysis of defense responses in Arabidopsis thaliana wild-type and mammalian guanylate cyclase-expressing transgenic plants in response to infection with an avirulent strain of Pseudomonas syringae pv. tomato

city: Verona

first: Andrea

last: Minio

address: Via dell'Artigliere 8

department: Applied Biotechnologies

country: Italy

institute: Università di Verona

summary: To decipher the role of cGMP during the hypersensitive response Arabidopsis thaliana transgenic lines have been produced which express a rat soluble guanylate cyclase. Transgenic plants display a higher constitutive amount of cGMP (4 to 50 fold) compared to wild-type. Both GC and wt genotypes were infected with PstAvrB and transcriptome profile was analyzed at 12 hours post-infection.

overall_design: Transcriptomic profile of wild-type and guanylate cyclase-expressing plants in basal conditions (mock) and at 12hpi with PstAvrB (107 cfu/mL)

first: Jamshaid

last: Hussain

first: Jian

last: Chen

first: Vittoria

last: Locato

first: Wilma

last: Sabetta

first: Smrutisanjita

last: Behera

first: Sara

last: Cimini

first: Francesca

last: Griggio

first: Silvia

last: Martínez-Jaime

first: Alexander

last: Graf

first: Mabrouk

last: Bouneb

first: Raman

last: Pachaiappan

first: Paola

last: Fincato

first: Emanuela

last: Blanco

first: Alex

last: Costa

first: Laura

last: De Gara

first: Diana

last: Bellin

first: Maria

last: de Pinto

first: Elodie

last: Vandelle

first: Massimo

last: Delledonne


title: Longissimus dorsi muscle transcriptome in pure and crossbred Iberian pigs at birth and growing stages

city: Madrid

first: Cristina

last: Ovilo

address: Ctra Coruña km 7.5

institute: INIA-CSIC

summary: Iberian ham production includes both purebred (IB) and Duroc-crossbred (IBxDU) Iberian pigs, which show important differences in meat quality and production traits, such as muscle growth and fatness. This experiment was conducted to investigate gene expression differences that could be associated with the observed phenotypic differences between IB and IBxDU pigs. Nine IB and 10 IBxDU pigs were slaughtered at birth, and seven IB and 10 IBxDU at four months of age (growing period).  Muscle transcriptome was analyzed on LD samples with RNA-Seq technology. We detected 261 differentially expressed genes between IB and IBxDU neonates and 113 at growth (p < 0.01 and Fold-Change > 1. 5). Newborns transcriptome reflected a highly proliferative developmental stage, while older pigs showed upregulation of catabolic and muscle functioning processes. Regarding the genetic type effect, IBxDU newborns showed enrichment of gene pathways involved in muscle growth, in agreement with the higher prenatal growth observed in these pigs. However, IB growing pigs showed enrichment of pathways involved in protein deposition and cellular growth, supporting the catch-up growth experienced by IB pigs during this period. Moreover, newborn and growing IB pigs showed more active glucose and lipid metabolism than IBxDU pigs.

overall_design: In total 24 longissimus dorsi samples were analyzed, 6 coming from purebred Iberian male newborns and 6 coming from crossbred male newborns (IberianxDuroc), at each stage (birth and four months of age)

last: Óvilo

first: Miriam

last: Ayuso


title: Inhibition of inflammatory gene transcription by IL-10 is associated with rapid suppression of LPS-induced enhancer activation [h3k27 ChIP]

city: Boston

first: Bruce

last: Horwitz

state: MA

address: 77 Ave Louis Pasteur

department: Pathology

institute: Brigham and Women's Hospital

summary: IL-10 limits the magnitude of inflammatory gene expression following microbial stimuli and is essential to prevent inflammatory disease, however, the molecular basis for IL-10 mediated inhibition remains elusive. Using a genome-wide approach we demonstrate that inhibition of transcription is the primary mechanism for IL-10-mediated suppression in LPS-stimulated macrophages, and that inhibited genes can be divided into two clusters.  Genes in the first cluster are inhibited only if IL-10 is included early in the course of LPS stimulation and is strongly enriched for interferon-inducible genes.  Genes in the second cluster can be rapidly suppressed by IL-10 even after transcription is initiated, and this is associated with suppression of LPS-induced enhancer activation. Interestingly, the ability of IL-10 to rapidly suppress active transcription exhibits a delay following LPS stimulation.  Thus, a key pathway for IL-10 mediated suppression involves rapid inhibition of enhancer function during the secondary phase of the response to LPS.

overall_design: 3 independent macrophage pools were stimulated with LPS for 195 min, LPS and IL-10 for 195 min, or LPS for 195 min with the adddition of IL-10 for the last 30 min. ChIP-Seq performed for H3K27ac

first: Evan

last: Conaway

first: Dalila

last: de Oliveira

first: Christine

last: McInnis

first: Scott

last: Snapper

middle: H


title: Inhibition of inflammatory gene transcription by IL-10 is associated with rapid suppression of LPS-induced enhancer activation

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

overall_design: Refer to individual Series


title: Transcriptional regulation of male-sterility in 7B-1 male-sterile tomato mutant

city: Oxford

first: Irina

last: Mohorianu

address: Headington

department: Medical Sciences Division

institute: University of Oxford

summary: The 7B-1 tomato (Solanum lycopersicum L. cv Rutgers) is a male-sterile mutant with enhanced tolerance to abiotic stress, which makes it a potential candidate for hybrid seed breeding and stress engineering. Transcriptomic profiles of the 7B-1 male-sterile and wild type (WT) anthers were studied using mRNA sequencing (RNA-Seq). In total, 768 differentially expressed genes (DEGs) were identified, including 132 up-regulated and 636 down-regulated transcripts. Gene ontology (GO) enrichment analysis of DEGs suggested a general impact of the 7B-1 mutation on metabolic processes, such as proteolysis and carbohydrate catabolic process. Sixteen candidates with key roles in regulation of anther development were subjected to further analysis using qRT-PCR and in situ hybridization. Cytological studies showed several defects associated with anther development in the 7B-1 mutant, including unsynchronized anther maturation, dysfunctional meiosis, arrested microspores, defect in callose degradation and abnormal tapetum development. TUNEL assay showed a defect in programmed cell death (PCD) of tapetal cells in 7B-1 anthers. The present study provides insights into the transcriptome of the 7B-1 mutant. We identified several genes with altered expression level in 7B-1 (including beta-1,3 glucanase, GA2oxs, cystatin, cysteine protease, pectinesterase, TA29, and actin) that could potentially regulate anther developmental processes, such as meiosis, tapetum development, and cell-wall formation/degradation.

overall_design: RNA-seq analysis of anthers from wild type and 7B-1 male-sterile mutant tomato plants.

first: Vahid

last: Omidvar

first: Tamas

last: Dalmay

first: Yi

last: Zheng

first: Zhangjun

last: Fei

first: Anna

last: Claudia

first: Andrea

last: Mazzucato

first: Vendula

last: Vecerova

first: Michaela

last: Sedlarova

first: Martin

last: Fellner


title: Inhibition of inflammatory gene transcription by IL-10 is associated with rapid suppression of LPS-induced enhancer activation [RNA-Seq]

overall_design: 2 independent murine macrophage pools were stimulated with LPS and IL-10 compared against untreated macrophages

middle: C


title: The histone 3 lysine 4 methyltransferase Setd1b is a maternal effect gene required for the oogenic gene expression program

city: Dresden

first: Francis

last: Stewart

address: Tatzberg 47-49

institute: BIOTEChnology Center TU Dresden

summary: Germ cell development involves major reprogramming of the epigenome to prime the zygote for totipotency. Histone 3 lysine 4 (H3K4) methylations are universal epigenetic marks mediated in mammals by six H3K4 methyltransferases related to fly Trithorax, including two yeast Set1 orthologs: Setd1a and Setd1b. Whereas Setd1a plays no role in oogenesis, we report that Setd1b deficiency causes female sterility. Oocyte specific Gdf9iCre conditional knockout (Setd1bGdf9cKO) ovaries develop through all stages however follicular loss accumulated with age and unfertilized metaphase II (MII) oocytes exhibited irregularities of the zona pellucida and meiotic spindle. Most Setd1bGdf9cKO zygotes remained in the pronuclear stage and displayed polyspermy in the perivitelline space. Expression profiling of Setd1bGdf9cKO MII oocytes revealed (i) that Setd1b promotes the expression of the major oocyte transcription factors including Obox1, 2, 5, 7, Meis2 and Sall4; and (ii) two-times more up- than downregulated mRNAs suggesting that Setd1b also promotes the expression of negative regulators of oocyte development with multiple Zfp-KRAB factors implicated. Together, these findings indicate that Setd1b serves as maternal effect gene through regulation of the oocyte gene expression program.

overall_design: Oocyte RNA profiling for Setd1bGdf9cKO and control mice

first: David

last: Brici

first: Susanne

last: Reinhardt

first: Andreas

last: Dahl

first: Qinyu

last: Zhang

first: Kerstin

last: Schmidt

first: Neha

last: Goveas

first: Jiahao

last: Huang

first: Gavin

last: Kelsey

first: Konstantinos

last: Anastassiadis

first: A

middle: F

last: Kranz


title: Inhibition of inflammatory gene transcription by IL-10 is associated with rapid suppression of LPS-induced enhancer activation [stat3_ChIP]

first: Bruce

last: Horwitz

overall_design: Murine bone marrow derived macrophage pools were stimulated with IL-10 for 30 min, LPS for 195 min, or LPS for 195 min with the adddition of IL-10 for the last 30 min. ChIP-Seq performed for STAT3

first: Evan

middle: A

last: Conaway

first: Dalila

last: de Oliveira

first: Christine

last: McInnis

first: Scott

last: Snapper


title: Campylobacter concisus pathotypes induce distinct global responses in intestinal epithelial cells [UNSWCD]

city: Sydney

first: Nandan

last: Deshpande

state: NSW

address: Kensington Campus

department: School of Biotechnology and Biological Sciences

institute: Systems Biology Initiative

summary: We report the response of Caco-2 cells to infection by C. concisus strains or exposure to C. concisuszonula occludens toxin

overall_design:
Identification of differential transcript expression following C. concisus infection or exposure to zonula occludens toxin.
UNSWCD dataset.

first: Nadeem

middle: O

last: Kaakoush


title: Identification of transcriptomic drivers of squamous cell carcinoma development through a preneoplastic intermediate [human miRNA-Seq]

city: Houston

first: Kenneth

last: Tsai

state: TX

address: 2130 West Holcombe Blvd , LSP9.4218

department: Dermatology & Translational Molecular Pathology

institute: University of Texas MD Anderson Cancer Center

summary: Cutaneous squamous cell carcinoma (cuSCC) comprises 15-20% of all skin cancers, accounting for over 700,000 cases in the U.S. annually. Most cuSCC arise in association with a distinct precancerous lesion, the actinic keratosis (AK). In order to identify potential targets for molecularly targeted chemoprevention, we performed integrated cross-species genomic analysis of cuSCC development through the preneoplastic AK stage using matched human samples and a solar UV-driven Hairless mouse model. We identified the major transcriptional drivers of this sequence showing that the key genomic changes in cuSCC development occur in the normal skin to AK transition. Our data validate the use of this UV-driven mouse cuSCC model for cross-species analysis and demonstrate that cuSCC bears deep molecular similarities to multiple carcinogen-driven SCCs from diverse sites, suggesting that cuSCC may serve as an effective, accessible model for multiple SCC types and that common treatment and prevention strategies may be feasible.

overall_design: We sought to identify important genetic events that drive squamous cell carcinoma development through combined analysis of next generation sequencing of matched patient samples with a UV-driven mouse model to identify key pathways.

middle: Y

first: Kimal

last: Rajapakshe

first: Hussein

last: Abbas

first: Cristian

last: Coarfa

first: Weimin

last: Xiao

first: Preethi

last: Gunaratne

first: Li

last: Shen

first: Hao

last: Yui

first: Xiaoping

last: Su

first: Erika

middle: J

last: Thompson

first: Yoko

last: Takata

first: Jianjun


title: Campylobacter concisus pathotypes induce distinct global responses in intestinal epithelial cells [BAA]

overall_design:
Identification of differential transcript expression following C. concisus infection or exposure to zonula occludens toxin.
BAA dataset.


title: Identification of transcriptomic drivers of squamous cell carcinoma development through a preneoplastic intermediate

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus


title: NGS-mRNA in lung tissues in RAG1-/- and in RAG1-/- Sgo1-/+ mice

city: Oklahoma City

first: Hiroshi

last: Yamada

state: Oklahoma

institute: OUHSC

summary: We compared lung mRNA expression profiles between RAG1-/-  control and RAG1-/- Sgo1-/+ chromosome instability model mice. RAG1-/-Sgo1-/+ mice developed significantly more spontaneous lung tumors.

overall_design: Characterize influence of chromosome instability on lung


title: Campylobacter concisus pathotypes induce distinct global responses in intestinal epithelial cells


title: LTβR controls thymic portal endothelial cells for hematopoietic progenitor cell homing and T cell regeneration

city: Beijing

first: Mingzhao

last: Zhu

address: 15 Da Tun Rd, Chaoyang District

department: Key Laboratory of Infection and Immunity

institute: Institute of Biophysics, Chinese Academy of Sciences

summary: Continuous thymic homing of hematopoietic progenitor cells (HPCs) via the blood is critical for normal T cell development. However, the nature and the differentiation program of the specialized thymic endothelial cells (ECs) controlling this process remain poorly understood. Here, using conditional gene-deficient mice, we find that lymphotoxin beta receptor (LTβR) directly controls thymic ECs to guide HPC homing. Interestingly, T cell deficiency or conditional ablation of T-cell-engaged LTβR signaling results in a defect in thymic HPC homing, suggesting the feedback regulation of thymic progenitor homing by thymic products. Furthermore, we identify and characterize a special thymic portal EC population with features that guide HPC homing. LTβR is essential for the differentiation and homeostasis of these thymic portal ECs. Finally, we show that LTβR is required for T cell regeneration upon irradiation-induced thymic injury. Together, these results uncover a cellular and molecular pathway that governs thymic EC differentiation for HPC homing.

overall_design: Whole transcriptome sequencing of 3 subsets of thymic endothelial cells(ECs) defined by Ly6C and Selp, in duplicate, using Illumina HiSeq 2500.

first: Yaoyao

last: Shi

first: Yu

last: Hou


title: Expression profiling analysis of mouse P4 cerebellum in CitK mutant mice proficient or knockout for P53

city: Torino

first: Ugo

last: Ala

address: Via Nizza 52

department: Dept. of Molecular Biotechnology and Health Sciences

institute: University of Torino

summary:
Purpose: Citron kinase (CitK) knockout mice show a severe form of primary microcephaly, associated with ataxia and lethal epilepsy. This phenotype is caused by massive apoptosis occuring during embryonic and post-natal brain development, associated with cytokinesis failure. Cerebellum is the tissue showing highest sensitivity to CitK loss. The clinical phenotype of CitK knockout mice is significantly resued by P53 inactivation. In addition, CitK/P53 double knockout brains have almost normal levels of apoptosis, but display high percentage of binucleated and multinucleated cells. The aim of this study was to analyze the gene expression changes produced in developing neural tissue by CitK loss and to determine which alterations are P53-dependent. expression changes
Methods: We analyzed by RNA sequencing total RNA extracted from P4 cerebellum of mice characterized by the following genotypes: 1. CitK +/-, P53 +/- (CTRL);  2. CitK -/-, P53 +/- (CitK-KO); 3. CitK +/-, P53 -/- (P53-KO); 4. CitK -/-, P53 -/- (D-KO). Biological triplicates were analyzed per every genotype.
Conclusions: The loss of CitK leads to a strong reduction of the expression of pro-neural genes and induces a P53-related pro-apoptotic gene sets. The analysis of D-KO mice reveals that most of these changes are P53-dependent, but many genes implicated in growth arrest are induced through P53-independent mechanisms.

overall_design: Cerebellar mRNA profiles of 4-day old mice of CTRL, CitK-KO, P53-KO and D-KO mice  were generated by deep sequencing, in triplicate, using Illumina  HiScan SQ

first: Ferdinando

last: Di Cunto

first: Federico

last: Bianchi

first: Francesco

last: Neri


title: Identification of transcriptomic drivers of squamous cell carcinoma development through a preneoplastic intermediate [human RNA-Seq]

first: Kenneth

last: Tsai

first: Kimal

last: Rajapakshe

first: Hussein

last: Abbas

first: Cristian


title: Campylobacter concisus pathotypes induce distinct global responses in intestinal epithelial cells [Toxin]

first: Nandan

last: Deshpande

overall_design:
Identification of differential transcript expression following C. concisus infection or exposure to zonula occludens toxin.
Toxin dataset.

first: Nadeem

last: Kaakoush


title: RNA-seq (strand-specific library) of barley shoots and roots from control and heat conditions.

city: Poznań

first: Zofia

last: Szweykowska-Kulińska

address: Umultowska 89

department: Department of Gene Expression

country: Poland

institute: Adam Mickiewicz University

summary: Samples were collected after 1 h of the heat treatment. Samples were collected for control and heat stressed plants.

overall_design: RNA-seq was performed for shoot (in triplicate for each condition) and root (in duplicate for each condition)

first: Andrzej

last: Pacak

first: Maria

last: Barciszewska-Pacak

first: Aleksandra

last: Swida-Barteczka

first: Katarzyna

last: Kruszka

first: Paweł

last: Sega

first: Kaja

last: Milanowska

first: Iver

last: Jakobsen

first: Artur

last: Jarmolowski

last: Szweykowska-Kulinska


title: Identification of transcriptomic drivers of squamous cell carcinoma development through a preneoplastic intermediate [mouse miRNA-Seq]

last: Coarfa

first: Weimin

last: Xiao

first: Preethi

last: Gunaratne

first: Li

last: Shen

first: Hao

last: Yui

first: Xiaoping

last: Su

first: Erika

last: Thompson

first: Yoko

last: Takata

first: Jianjun


title: Molecular mechanism for stress-induced depression assessed by sequencing miRNA and mRNA in medial prefrontal cortex

first: Ke

last: Ma

state: Beijing

address: 15 Datun road,Chaoyang Strict,Beijing, China

department: Diseases Epigenetics

institute: Institute of biophysics, chinese academy of science


title: Global Profiling of the Cellular Alternative RNA Splicing Landscape During Virus-host Interactions

city: Sherbrooke

first: Martin

last: Bisaillon

state: Québec

address: 3201 rue Jean-Mignault

department: Biochimie

institute: Université de Sherbrooke

summary: Background  Alternative splicing (AS) is a central mechanism of genetic regulation which modifies the sequence of RNA transcripts in higher eukaryotes. AS has been shown to increase both the variability and diversity of the cellular proteome by changing the composition of resulting proteins through differential choice of exons to be included in mature mRNAs.   Results  In the present study, alterations to the global RNA splicing landscape of cellular genes upon viral infection were investigated through high-throughput RNA sequencing (RNA-seq) studies using mammalian reovirus as a model. Our study provides the first comprehensive portrait of global changes in the RNA splicing signatures that occur in eukaryotic cells following infection with a human virus. We identify modifications in the AS patterns of 240 cellular transcripts frequently involved in the regulation of gene expression and RNA metabolism. A significant number of the modified transcripts are also encoded by genes with important roles in viral infection/immunity. These modifications are expected to alter the functions of many cellular proteins. Finally, we used RT-PCR analysis in order to experimentally validate differential modifications in alternative splicing patterns that were observed through RNA-seq studies.  Conclusion  The present study demonstrated that viral infection can extensively modify the splicing patterns of numerous cellular transcripts. These findings provide additional insights into the complexity of virus-host interactions as these splice variants expand proteome diversity and function during viral infection. Finally, these data open new avenues of research for a better understanding of post-transcriptional events during virus infection and possible new targets toward the development of antiviral agents.

overall_design: mRNAs were isolated from L929 mouse cell line, 14 hours after infection with T3D-S Reovirus or T3D-S Mutant reovirus at a MOI of 50.  Control cells were uninfected.  The resulting libraries were multiplexed and paired-end sequenced using Illumina HiSeq.  Gene expression and alternative splicing were caracterized using Bowtie and RSEM.

first: M

first: G

last: Lemay

last: Scott


title: Genome-wide maps of CREB/CRTC binding in Drosophila mushroom body.

city: Nagoya

first: Kunio

last: Ihara

state: Aichi

address: Furo-cho 1, Chikusa-ku

department: Center for Gene Research

institute: Nagoya University

summary:
Purpose: Exploring the alteration in CREB/CRTC binding related to long-term memory
Methods: The nuclei of Drosophila mushroom bodies were purified and the histone acetylation and CREB/CRTC binding were examined by ChIP-seq using specific antibodies. The sequencing was performed using Miseq, and aligned to dm3 using CLCbio. The sequence reads that passed quality filters were analyzed by peak calling using PICS and ERD equipped on Strand NGS software. This method using two algorisms excludes false-positive calling of peaks. The PICS and ERD were run using a default setting except for the following parameters; for PICS, 120 bp as an average fragment length, 10 bp as a minimum distance between forward and reverse reads, 200 bp as a minimum distance between forward and reverse reads, 100 bp as a window width, with 5% false discovery rate; for ERD, 1.5 as an enrichment factor, 100 bp as a window size, 10 bp as a window slide size, 100 bp as a minimum region size. The peaks obtained by ERD analysis were filtered by an enrichment factor of 2, and a density of reads at 0.12 for CREB and 0.2 for CRTC. The CREB and the CRTC binding sites were determined as the peak-called region in at least 2 samples out of the three replicates. The CREB and the CRTC binding sites located 200 bp vicinity to each other were defined as the CREB/CRTC binding sites. In parallel, the read counts were obtained in the 1 kb window covering entire genome and analyzed by DESeq2, to determine the region enriched with CREB/CRTC in a specific group of samples. The region with increased or decreased CREB/CRTC binding were determined if the region were defined by the CREB/CRTC binding sites in the above criteria.
Results: Using an optimized data analysis workflow, the filtered reads amounted to 8-11million reads for CREB in each of 3 replicates, 8-17 million reads for CRTC in each of 3 replicates, and 4.4 million reads for input. Using anti-CREB antibody, we found 239 significant increases in CREB binding out of 4995 CREB/CRTC binding sites 1 day after training. Using anti-CRTC antibody, we found 4989 significant increases in CRTC binding out of 4995 CREB/CRTC binding sites 1 day after spaced training.
Conclusions: Our study shows that, although CREB binding is mostly unchanged, CRTC binding is significantly increased after long-term memory formation in Drosophila mushroom bodies.

overall_design: Examination of 2 different transcription factors (CREB and CRTC)

first: Yukinori

last: Hirano

first: Kunihiro


title: The beneficial effect of pterocarpan-rich extract from soybean leaf on metabolic syndrome in overweight and obese subjects: randomized controlled trial

city: Daegu

first: Ri

last: Ryu

address: 80 Daehak-ro

department: Food Science and Nutrition

institute: Kyungpook National University

summary: We investigated the effect of pterocarpan-rich extract from soybean leaf on metabolic syndrome and elucidated anti-inflammation mechanism based on RNA-seq transcriptomic profiles in overweight and obese subjects

overall_design:
Total RNA of peripheral blood mononuclear cells (PBMCs) was obtained from pterocarpan-rich extract soybean leaf (PT) and biomarkers associated with lipid, glucose metabolism and inflammation was measured.

Please note that raw data for the "after supplementation" samples have been lost and therefore were not provided,

first: Myung-Sook

last: Choi


title: Next generation sequencing (NGS) of exosomal-miRNA derived from human adipose mesenchymal stem cells (hAMSCs) conditioned medium (CM).

city: Seoul

first: Abu Musa Md Talimur

last: Reza

address: 604, Animal Science Building

department: Stem Cell and Regenerative Biology

institute: Konkuk University

summary:
Purpose: Relationship between mesenchymal stem cells (MSCs) and cancer cells became mysterious because of having sufficient evidences regarding both stimulatory and inhibitory role of MSCs to cancer cells. Certainly, there is debate on customary role of MSCs (inhibitory/stimulatory), however, the notable involvement of MSCs in cancer biology is undoubtedly clear. MSCs might support tumor development through immune suppression, epithelial to mesenchymal transition (EMT), angiogenesis, and serving as cancer stromal cells. In contrast, MSCs are also reported to play role in suppression of cancer by downregulating the cancer survival signaling pathways such as Wnt/β-catenin and/or Akt3. Now, it is a rational demand to investigate the mechanism behind these completely contradictory roles of MSCs in cancer biology. Incidentally, cytokines and soluble factors secreted by MSCs have been scrutinized thoroughly and most of the reports with few exceptions concluded that MSCs-secreted cytokines and soluble factors have stimulatory effect in the progression of cancer. While, role of exosomes which is a type of micro-vesicles having 30-200 nm diameters, secreted by all cells, could be up-taken by neighboring cells, containing many important components including RNAs, proteins, DNA and lipids, serving as efficient vehicles for cancer-stromal communication,  have been investigated very marginally and deserve to go for intensive investigation. Specially, cell-secreted miRNAs (18-22 nucleotides) are predominantly carried by exosomes and have been focused in recent years for its capacity in post-transcriptional regulation of gene expression through mRNA silencing.  Hence, understating the functions of MSCs-derived secretome (particularly exosomes) in cancer is very much important to comprehend the cross-talk between MSCs and cancer cell biology. In this research, next generation sequencing (NGS) was performed for enrichment analysis of miRNAs in hAMSCs-CM derived exosomes.
Methods: Exosomal-RNA was isolated from hAMSCs-CM derived exosomes, small RNA libraries were prepared through a series of processes such as adapter ligation, reverse transcription, PCR amplification, and pooled gel purification.Sequence quality was checked by FastQC experiment, unique sequences found for known miRNAs after clustering were verified with miRBase database (www.mirbase.org/) by blast, trimmed read might have considered as miRNA on condition of having 100% identical and whole length sequence of miRNA compare to the ones on miRBase database. Unmatched trimmed read excluded from miRBase were blast to ncRNA database Rfam (http://rfam.sanger.ac.uk/). Unmatched trimmed reads to any of non-miRNA on Rfam database were considered as a potential novel miRNA.
Result: The exosomal-RNA sequencing explored that exosomes contains a rich population of miRNAs and many of the obtained miRNAs are reported to have anti-cancer properties through targeting different cancer survival pathways.
Conclusion: Outwardly, we outlined that exosomal-miRNA is one of the conceivable reasons behind anti-proliferative effect of MSCs towards cancer cells.

overall_design: Exosomal-miRNA profiles were generated by NGS, in triplicate, by Illumina sequencing platforms.

first: AMMT

first: YJ

first: JH

last: Kim


title: Molecular mechanism for stress-induced depression assessed by sequencing miRNA and mRNA in medial prefrontal cortex (miRNA)

summary: Major depressive disorder is a common mood disorder. Chronic stressful life is presumably main etiology that leads to the neuron and synapse atrophies in the limbic system. However, the intermediate molecules from stress to neural atrophy remain elusive. Mice were treated by chronic unpredictable mild stress (CUMS) until demonstrating depression-like behaviors confirmed by the tests of sucrose preference, forced swimming and Y-maze. The sequencings of microRNA and mRNA from the medial prefrontal cortices were performed in CUMS-induced depression mice versus control mice to assess the molecular profiles of major depressive disorder. In the medial prefrontal cortices of depression-like mice, the levels of mRNAs that translated the proteins for the GABAergic synapses, dopaminergic synapses, myelination, synaptic vesicle cycle and neuronal growth were downregulated. miRNAs of regulating these mRNAs are upregulated. The deterioration of GABAergic and dopaminergic synapses as well as axonal growth is associated to CUMS-induced depression.

overall_design: The sequencings of mRNA from the medial prefrontal cortices were performed in CUMS-induced depression mice(n=2) versus control (n=2)

first: Li

last: Guo

first: Aiping

last: Xu


title: Molecular mechanism for stress-induced depression assessed by sequencing miRNA and mRNA in medial prefrontal cortex (mRNA)


title: Profile of small interfering RNAs derived from Beet black scorch virus and its associated satellite RNA in Nicotiana benthamiana

first: Jin

address: Yuanmingyuan western road No.2

institute: China Agricultural University

summary: Co-infection of none-coding satellite RNAs (sat-RNAs) usually inhibits replication and attenuates disease symptoms of helper viruses. Here we find that the sat-RNA of Beet black scorch virus (BBSV) enhances both the accumulation and the systemic infection of its helper virus in the Nicotiana benthamiana (N. benthamiana). Besides, the infection of BBSV is higher efficient in low temperature (18ºC) than room temperature (25ºC), suggesting that BBSV is temperature sensitive. To explore the effect of temperature and sat-RNA on the silencing induced by BBSV, we cloned and sequenced the total small RNAs produced during infection of BBSV alone or with its sat-RNA under different temperature. Our results shows that the size profile of the siRNAs derived from either BBSV or coinfection with sat-RNA are 22 nucleotide (nt), followed by 21-nt reads and other length reads. Notably, more than 80% of the total small RNAs sequenced from plants infected with BBSV alone were BBSV-siRNAs, whereas the abundance of sat-RNA-derived siRNAs were higher than BBSV-siRNAs in the co-infected plants, indicating sat-RNA involved in gene silencing as a surrogacy of BBSV. Interestingly, the 5′ termini of siRNAs derived from BBSV and sat-RNA were dominated by Uridines (U) and Adenines (A), respectively. Consistently, the infection of BBSV alone or with sat-RNA induces high accumulation of Argonaute 1 (AGO1) and AGO2, respectively. Our work reveals the profiles of siRNAs of BBSV and sat-RNA and provides a new clue to investigate the complicated interaction between the helper virus and sat-RNA.

overall_design: analysis of small RNAs from Nicotiana benthamiana infected by BBSV alone or with its sat-RNA at two temperature conditions in compared with mock-inoculated plant.

first: Xianbing

last: Wang

first: Jialin

last: Yu


title: Analysis of Post-TBI Gene Expression Signature Reveals Tubulins, NFE2L2, NFkB, CD44, and S100A4 as Treatment Targets for Traumatic Brain Injury

city: Kuopio

first: Anssi

last: Lipponen

address: Neulaniementie 2

department: A. I. Virtanen Institute for Molecular Sciences

country: Finland

institute: University of Eastern Finland

summary: TBI was induced with lateral fluid-percussion injury in adult male rats. Genome-wide RNA-seq of the perilesional cortex, ipsilateral thalamus and dorsal hippocampus was performed at 3 months post-TBI. The data highlighted chronic transcriptional changes, particularly, in the perilesional cortex and thalamus. Genes showing a significantly altered expression both in the cortex and thalamus were submitted to the LINCS web query to identify novel pharmacotherapies to improve post-TBI outcome.

overall_design: TBI was induced to 5 rats, 5 sham operated served as a controls.

first: Jussi

last: Paananen

first: Noora

last: Puhakka

first: Asla

last: Pitkänen


title: RNA sequencing identifies differentially expressed genes in adult left ventricles following in utero caffeine exposure during embryonic day 6.5-9.5

city: Gainesville

first: Xiefan

last: Fang

state: Florida

address: 1200 Newell Drive, ARB R1-148

department: Pediatrics

institute: University of Florida

summary: Purpose: This study aims to identify the differentially expressed genes in adult left ventricles treated with caffeine during early embryogenesis. Methods: Pregnant CD-1 mice were treated with vehicle (normal saline) or 20 mg/kg caffeine via i.p. injection once daily during embryonic day (E) 6.5-9.5. Pups were born and raised to one year of age. Left ventricles from adult male mice were dissected and used for total RNA isolation with the RNeasy Plus Mini kit (Valencia, CA, USA). mRNA was isolated from total RNA using NEXTflex™ Poly(A) Beads (Bioo Scientific, Austin, TX, USA). Sequencing libraries were prepared with the NEBNext® mRNA Library Prep Master Mix Set for Illumina (NEB, Ipswich, MA, USA) and the NEBNext Multiplex Oligos for Illumina (NEB). Illumina-adapted libraries (n=3/treatment) were pooled at equal molar ratio and sequenced with one High Output 1x75 cycles run on a NextSeq500 sequencer (Illumina, San Diego, CA, USA). The fastq files generated from RNA-Seq were uploaded to the UF Research Computing Galaxy instance developed by the University of Florida. The data were cleaned with the following steps: removed sequencing artifacts, trimmed 5’ or 3’ ends with low scores, removed adaptor contamination, and filtered low quality reads by the FastQC program. The remaining high quality RNA-Seq reads were mapped to the mouse genome (mm10) with the Tophat2 tool. Counting of RNA-Seq reads were performed with HTSeq. Differential expression (DE) of genes between treatments was analyzed using R package EdgeR, with Ensembl Mus_GRCm38.79.gtf as the reference annotation. Genes with false discovery rate (FDR) less than 0.05 and absolute fold change greater than 1.5 were considered as significant. Results: DE analysis revealed that 85 genes were up-regulated, and 31 genes were down-regulated in the adult left ventricles treated with in utero caffeine.

overall_design: mRNA expression profiles in the adult left ventricles treated with vehicle or 20 mg/kg caffeine during E6.5-9.5 were generated by deep sequencing (n=3/treatment), using Illumina NextSeq500.

first: Scott

last: Rivkees

first: Christopher

last: Wendler


title: To a better understanding of the impact of vine nitrogen status on volatile thiols from plot to transcriptome level

city: Villenave d'Ornon

first: Pierre

last: Helwi

address: 210 chemin de Leysotte

country: France

institute: Bordeaux University

summary:
Purpose: The identification of genes in Sauvignon blanc berries which respond to nitrogen fertilization at (v+28) and at (v+35) and the identification of genes potentially involved in 3SH precursors biosynthesis.

Methods: Grape berries mRNA profiles of control vine (C) and vine fertilized with 100 U/ha of nitrogen (Soil N100) at (v+28) and at (v+35) in 2013 and 2014 were generated by deep sequencing, in triplicate.

Results: Genes in Sauvignon blanc berries at 2 stages ((v+28) and (v+35)) which respond to nitrogen supply were identified and genes potentially involved in 3SH precursors synthesis were described.

overall_design: Examination of the transcriptome of a control Sauvignon blanc vine versus a Sauvignon blanc vine supplied with 100 U/ha of nitrogen added to soil at 2 stages ((v+28) and (v+35)) in 2013 and 2014.

first: Sabine

last: Guillaumie

first: Celine

last: Keime


title: MicroRNAs circulate in the hemolymph of Drosophila and accumulate relative to tissue microRNAs in an age-dependent manner

city: Elk Grove

first: joseph

middle: M

last: dhahbi

state: ca

address: 9700 West Taron Drive

department: Medical Education

institute: California Northstate University College of Medicine

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

overall_design: Refer to individual Series


title: High throughput sequencing identifies misregulated genes in the Drosophila Polypyrimidine Tract-binding protein (hephaestus) mutant defective in spermatogenesis

city: Boulder

first: Ravinder

last: Singh

state: CO

address: UCB 347

department: MCD Biology

institute: Univ Colorado

summary: The Drosophila polypyrimidine tract-binding protein (dmPTB or hephaestus) plays an important role during spermatogenesis. The heph2 mutation in this gene results in a specific defect in spermatogenesis, causing aberrant spermatid individualization and male sterility. However, the array of molecular defects in the mutant remains uncharacterized. This study provides the first comprehensive list of genes misregulated in vivo in the heph2 mutant in Drosophila and offers insight into the role of dmPTB during spermatogenesis.

overall_design: Two samples; Control and the heph2 mutant

last: SIngh


title: MicroRNAs circulate in the hemolymph of Drosophila and accumulate relative to tissue microRNAs in an age-dependent manner [mRNA]

summary: In mammals, extracellular miRNAs circulate in biofluids as stable entities that are secreted by normal and diseased tissues, and can enter cells and regulate gene expression. Drosophila melanogaster is a proven system for the study human diseases. They have an open circulatory system in which hemolymph (HL) circulates in direct contact with all internal organs, in a manner analogous to vertebrate blood plasma. Here we show using deep sequencing that Drosophila HL contains RNase resistant, circulating miRNAs (HL-miRNAs). Limited subsets of body tissue miRNAs (BT-miRNAs) accumulated in HL, suggesting they may be specifically released from cells or particularly stable in HL. Alternatively, they might arise from specific cells such as hemocytes, in intimate contact with HL. Young and old flies accumulated unique populations HL-miRNAs, suggesting their accumulation is responsive to the physiological status of the fly. These HL-miRNAs may function in flies similarly to the miRNAs circulating in mammalian biofluids. The discovery of these HL-miRNAs will provide a new venue for health and disease-related research in Drosophila.

overall_design: Examination of mRNA levels in body tissues of young and old Drosophila melanogaster.

first: J

last: Dhahbi


title: Identifying genes differentially expressed in MDCK cells with scribble knock-down (scribKD)

city: Cambridge

first: Charles

last: Bradshaw

address: Tennis Court Road

department: Gurdon Institute

institute: University of Cambridge

summary:
Aim: To identify genes and pathways involved in elimination of scribKD cells by competition.
Methods: We carried out mRNA sequencing of MDCK-II cells carrying a tetracycline-inducible scribble shRNA construct.

overall_design:
We compared the transcriptomes of MDCK cells with scribble knock-down (scribKD+Tet) to that of control MDCK cells with wild-type scribble expression (scribKD-Tet) and to that of an isolate of scribKD cells that is resistant to cell competition (scribRES+Tet). The samples were obtained across at least two independent experiments.
Each experiment contained at least two replicates per condition.
mRNA profiles of three populations of MDCK-II cells were obtained by Illumina High-Throughput sequencing.

first: Maja

last: Goschorska

first: Eugenia

last: Piddini


title: Carcinoma-astrocyte gap junctions promote brain metastasis by cytosolic dsDNA response transfer

city: Philadelphia

first: Qing

last: Chen

state: PA

address: 3601 Spruce Street, Room 442

institute: The Wistar Institute

summary: Brain metastasis represents a substantial source of morbidity and mortality in various cancers, and is characterized by high resistance to chemotherapy. Here we define the role of the most abundant cell type in the brain, the astrocyte, in brain metastasis. Cancer cells assemble of carcinoma-astrocyte gap junctions composed of connexin 43 (Cx43). Cx43 in cancer cells support brain metastatic colonization.  We employ translating ribosome affinity purification (TRAP) to isolate translating mRNA from cancer cells in mixed asrtocyte co-cultures to determine the mechanism behind this Cx43-mediated brain metastatic growth. Once engaged with the astrocyte gap-junctional network, brain metastatic cancer cells employ these channels to transfer the cytosolic dsDNA response messenger cGAMP to astrocytes, activating the cGAS-STING pathway and production of inflammatory cytokines IFNα and TNFα. As paracrine signals, these factors activate the STAT1 and NF-κB pathways in brain metastatic cells, which support tumour growth and chemoresistance.

overall_design: TRAP mRNAs were isolated from MDA231-BrM2 (control or Cx43-depleted) after co-cultured with astrocytes. Gene expression profiles were generated by deep sequencing, in duplicate, using Illumina Illumina HiSeq 2000. Two independent replicates were done per condition (i.e. rep1 and rep2).

first: Adrienne

last: Boire

first: Joan

last: Massagué


title: Next Generation Sequencing Facilitates Quantitative Analysis of Wild Type and IFC （incompletely fused carpels） Maize Ovary Transcriptomes

city: zhengzhou

first: hongping

last: li

institute: Henan Agricultural University

summary: The goals of this study are to investigate transcriptional networks that are likely to regulate IFC ovaries and to better understand the molecular framework associated with carpel fusion in maize.

overall_design:
Examination of 2 different transcriptome changes in 2 ovary phenotypes.
Expression values obtained for the 25,368 genes expressed in at least one of the 2 sequenced samples.

first: Chaohai

last: Li

first: Hongping


title: Transcriptome analysis of 'Candidatus Liberibacter solanacearum' in its psyllid vector, Bactericera cockerelli [sexed insects]

city: College Station

first: Cecilia

last: Tamborindeguy

address: Heep Center

institute: Texas A&M University

summary: We sequenced mRNA from the bacterial pathogen 'Candidatus Liberibacter solanacearum" during its association with the psyllid vector Bactericera cockerelli.

overall_design: Total RNA was purified from psyllids, insect and bacterial rRNAs were depleted. PolyA RNA was purified using Dynabeads. PolyA purified RNA and depleted RNA were sequenced.

first: Freddy

last: Ibanez

first: Julien

middle: G

last: Levy


title: Epigenetic regulation of hematopoiesis by DNA methylation

city: Bethesda

first: Aniket

last: Gore

address: Bldg 6B center drive

institute: National Institute of child health and human development

summary: Purpose: RNA seq analysis from isolated zebrafish HSPCs at 48 hpf from control morpholino and dnmt3bb.1 morpholino injected embryos

overall_design:
HSPCs were isolated by FACS sorting using transgenic line Tg(kdrl:mApple, cmyb:GFP) as described by Bertrand et al 2010
Total RNA from isolated HSPCs at 48hpf

middle: V

first: Brant

last: Weinstein


title: Transcription Factor RFX2 Is a Key Regulator of Mouse Spermiogenesis

city: Beijing

first: Chunsheng

last: Han

address: 1-5 Beichen West Road, Chaoyang District

department: Institute of Zoology

institute: Chinese Academy of Sciences

summary: To identify RFX2-dependent genes during spermatogenesis, We chose 24-day-old wild-type and mutant testes samples. Spermiogenesis in mutants was normal before this time point while massive round spermatids detached from the tubules thereafter. RNAs were isolated from the total testicular cells.

overall_design: we carried out RNA-seq analysis using P24 wild-type and mutant testes samples.Two biological replicates were included for each genotype.

first: Yujian

last: Wu

first: Xiwen

last: Lin


title: A diversity of conserved and novel ovarian microRNAs in the Speckled Wood (Pararge aegeria)

city: Oxford

first: Peter

middle: W. H.

last: Holland

address: South Parks Road

department: Department of Zoology

institute: University of Oxford

summary: microRNAs (miRNAs) are important regulators of animal development and other processes, and impart robustness to living systems through post-transcriptional regulation of specific mRNA transcripts. It is postulated that newly emergent miRNAs are generally expressed at low levels and with spatiotemporally restricted expression domains, thus minimising effects of spurious targeting on animal transcriptomes. Here we present ovarian miRNA transcriptome data for two geographically distinct populations of the Speckled Wood butterfly (Pararge aegeria). A total of 74 miRNAs were identified, including 11 newly discovered and evolutionarily-young miRNAs, bringing the total of miRNA genes known from P. aegeria up to 150. We find a positive correlation between miRNA age and expression level. A common set of 55 miRNAs are expressed in both populations. From this set, we identify seven that are consistently either ovary-specific or highly upregulated in ovaries relative to other tissues. This ovary set includes miRNAs with known contributions to ovarian function in other insect species with similar ovaries and mode of oogenesis, including miR-989 and miR-2763, plus new candidates for ovarian function. We also note that conserved miRNAs are overrepresented in the ovary relative to the whole body.

overall_design: Ovarian RNAseq and small RNA sequencing from two geographically distinct populations of Pararge aegeria.

first: Shan

last: Quah

first: Casper

last: Breuker


title: Comparative transcriptomic analyses of vegetable and grain pea (Pisum sativum L.) seed development

city: Hangzhou

last: Liu

address: No.198, Shiqiao Road, Jianggan District

institute: Zhejiang Academy of Agricultural Sciences

summary: Pea (Pisum. sativum L.) is a traditional and important edible legume that can be sorted into grain pea and vegetable pea according to their harvested maturely or not. Vegetable pea by eating the fresh seed is becoming more and more popular in recent years. These two type peas display huge variations of the taste and nutrition, but how seed development and nutrition accumulation of grain pea and vegetable pea and their differences at the molecular level remains poorly understood. To understand the genes and gene networks regulate seed development in grain pea and vegetable pea, high throughput RNA-Seq and bioinformatics analysis were used to compare the transcriptomes of vegetable pea and grain pea developing seed. RNA-Seq generated 18.7 G raw data, which was then de novo assembled into 77,273 unigenes with a mean length of 930 bp. Functional annotation of the unigenes was carried out using the nr, Swiss-Prot, COG, GO and KEGG databases. There were 459 and 801 genes showing differentially expressed between vegetable pea and grain pea at early and late seed maturation phases, respectively. Sugar and starch metabolism related genes were dramatically activated during pea seed development. The up-regulated of starch biosynthesis genes could explain the increment of starch content in grain pea then vegetable pea; while up-regulation of sugar metabolism related genes in vegetable pea then grain pea should participate in sugar accumulation and associated with the increase in sweetness of vegetable pea then grain pea. Furthermore, transcription factors were implicated in the seed development regulation in grain pea and vegetable pea. Thus, our results constitute a foundation in support of future efforts for understanding the underlying mechanism that control pea seed development and also serve as a valuable resource for improved pea breeding.

overall_design: We used RNA-Seq to generate and compare the transcriptomes of the vegetable pea and the grain pea at early and late developmental stages. The objectives  were to gain an understanding of the molecular mechanisms for pea seed development, as well as their differences between vegetable and grain peas, and to establish a sound foundation for future molecular studies based on high throughput sequencing and the expression data.

first: Yaming

last: Gong


title: High throughput bisulfite sequencing of the MLH1 promoter in human hematiopoietic progenitor cell clones

city: Cleveland

first: Jonathan

middle: D

last: Kenyon

state: OH

address: 2103 Cornell

department: Pathology

institute: Case Western Reserve University

summary: Using single molecule ultra-deep bisulfite sequencing we characterized the CpG methylation landscape from –938 to –337 bp upstream of the MLH1 transcriptional start site position 0, from 30 hematopoietic colony forming cell clones (CFC) either expressing or not expressing MLH1.  We identify a correlation between MLH1 promoter methylation and loss of MLH1 expression. Additionally, using the CpG site methylation frequencies obtained in this study we are able to generate a classification algorithm capable of sorting the expressing and non-expressing CFC. Thus, as previously described for many tumor cell types, MLH1 promoter methylation in hematopoietic stem cell clones correlates with the loss of MLH1 expression, a critically important gene in the mismatch repair pathway.

overall_design: Examination of CpG methylation landscape upstream of the MLH1 transcriptional start site in human hematiopoietic progenitor cell clones

first: Gabrielle

last: Nickel

first: Yulan

last: Qing

first: Gabriela

last: Santos-Guasch

first: Ellen

last: Drake

first: Pingfu

last: Fu

first: Shuying

last: Sun

first: Xiaodong

last: Bai

first: David

last: Wald

first: Eric

last: Arts

first: Stanton

middle: L

last: Gerson


title: Variation in the expression of miRNAs and mRNAs in rice (Oryza sativa)

city: Guangzhou

first: Munan

last: Xie

state: Guangdong

address: No.135 Xin Gangxi Road, Haizhu District,

department: School of life sciences

institute: Sun Yat-sen University

summary: Changes in patterns of gene expression are believed to be responsible for the phenotypic differences within and between species. Although the evolutionary significance of functional mutations has been emphasized in rice domestication, little is known about the differences in gene regulation underlying the phenotypic diversification among rice varieties. MicroRNAs (miRNAs) are small regulatory RNAs that play crucial roles in regulating post-transcriptional gene expression. Here, we studied the variation in the expression of both miRNAs and mRNA transcripts in three indica and three japonica rice varieties using RNA sequencing (RNA-seq) to examine the miRNA regulatory effect on target gene expression in rice. In total, 71.0%, 9.2%, and 1.5% of the expressed mature miRNAs showed tissue, subspecies, and tissue-subspecies interaction-biased expression. Most of these differentially expressed miRNAs are evolutionarily weakly conserved. To examine the miRNA regulatory effect on global gene expression under endogenous conditions, we performed pair-wise correlation coefficient analyses on the expression levels of 240 mature miRNAs and 1178 messenger RNAs (mRNAs) both globally and for each specific miRNA-mRNA pair. We found that the deeply conserved miRNAs can significantly decrease the target mRNA abundance. In addition, a total of 109 miRNA-mRNA pairs were identified as significantly correlated pairs (Adjusted p<0.01). Of those, 41 pairs showed positive correlations, while 68 pairs showed negative correlations. Functional analysis elucidated that these mRNAs belonged to different biological pathways that could regulate the stress response, metabolic processes, and rice development. In conclusion, the joint interrogation of miRNA and mRNA expression profiles in this study proved useful for the study of the role of miRNA expression and regulation in the plant transcriptome.

sample_organism:
Oryza sativa Indica Group
Oryza sativa Japonica Group

overall_design: 12 small RNA samples from seeds and seedlings of O.sativa subspecies indica and japonica were analyzed. The small RNAs were sequenced by Illumina Genome Analyzer II. After triming the adapters, the 18-30 nt sequences were extracted for further study. 6 transcriptome samples of seedlings were also analyzed.

first: M

last: Wen

first: L

last: He

first: S

last: Shi

first: T

last: Tang


title: HeLa transcriptome induction by IFN gamma and indoleamine 2,3-dioxygenase (IDO)

first: Stephen

last: Taylor

address: Headington

institute: CBRG

summary: We describe the modulation of gene expression by IDO induction in HeLa cells.

overall_design: The RNA-seq transcriptome profile of IFN gamma-treated and IDO1-transduced HeLa cells was compared to that of untreated WT and GFP-transduced HeLa cells, respectively.

last: Silk

first: Qi

last: Zhao

first: Robert

last: Strausberg

first: Vincenzo

last: Cerundolo


title: Investigation about Monocytes in metastatic breast cancer patients under chemotherapy +/- Avastin

city: Fribourg

first: Rüegg

last: Curzio

address: Albert-Gockel 1

department: Département de Médecine 3

country: Switzerland

institute: Université de Fribourg

summary: The goal of this study was to determine if blood circulating monocytes of metastatic breast cancer patient would express a different activation profile compared to healthy donors, in order to use this specific changesas biomarkers to monitor then response to therapy

overall_design: CD11b+ cells were extracted from all blood of 4 healthy donors and 4 metastatic breast cancer patients using magnetic beads separation (Miltenyi). CD11b+ cells were then lysed and mRNA was extracted to perform RNASeq.

first: Curzio

last: Rüegg

first: Sarah

last: Cattin

first: Sylvain

last: Pradervand


title: RNA-seq analysis of glyoxylate cycle-dependent genes

city: Seoul

first: Ingyu

last: Hwang

address: Kwanak Gu Daehak Dong

department: Agricultural Biotechnology

institute: Seoul National University

summary: Comparision of transcriptome between Burkholderia glumae wild type BGR1 and isocitrate lyase mutant BICL39

overall_design: 3 samples examined

first: Lim

last: Jae Yun

first: Goo

last: Eunhye

first: Hwang

last: Ingyu