title: Microarray analysis of 48 histological architectures microdissected from lung adenocarcinoma specimens

city: Heidelberg

first: Ruprecht

last: Kuner

address: Im Neuenheimer Feld 460

department: Molecular Genetics

institute: German Cancer Research Center and National Center of Tumor Diseases

summary: Searching for lung adenocaercinoma architecture-specific gene signatures including therapeutic targets, oncogenic pathways and gene ontologies associated with disease prognosis

overall_design: Total RNA was obtained from different adenocarcinoma architectures upon laser capture microdissection of fresh frozen tumor samples

first: Holger

last: Sültmann

last: Fröhlich

first: Heike

last: Zabeck

first: Felix

last: Lasitschka

first: Michael

last: Meister


title: Sex differences in the synaptic genomic fabrics of the rat hypothalamic paraventricular node

status: Public on Dec 13 2018

city: Prairie View

first: Dumitru

middle: Andrei

last: Iacobas

state: TX

address: Ann Preston St

department: Undergraduate Medical Academy

country: USA

institute: Prairie View A&M University

summary: We profiled the whole transcriptomes of male and female rat hypothalamic paraventricular nodes to determine whether there are sex differences in the topology of the genomic fabrics responsible for the glutamatergic, GABAergic, dopaminergic, cholinergic and serotonergic transmission. Our Genomic Fabric Paradigm (GFP) is proposed as a transformative research approach to enhance the understanding of the brain transcriptomic circuitries. The genomic fabric of a particular synapse is the structured transcriptome associated with the most interconnected and stably expressed gene network responsible for that type of neurotransmission. GFP refines the description of functional pathways by selecting the most prominent genes and determining their networking.  Moreover, it quantifies the remodeling of functional pathways and their interplay in disease and recovery in response to a treatment. This experiment provides the absolute controls for a larger study on a rat model of autism spectrum disorder and its treatment with ACTH and PMX53.

overall_design: One tissue (hypothalamic paraventricular node) x two sexes (M, F) . Biological replicates: 4 PSNSM, 4 PSNSF.

middle: A

first: Tamar

last: Chachua

first: Sanda

first: Melissa

middle: J

last: Benson

first: Karin

last: Borges

first: Jana

last: Velíšková

first: Libor

last: Velíšek


title: Virus-mediated export of chromosomal DNA in plants

city: Birmingham

first: Marco

last: Catoni

address: Edgbaston

department: School of Biosciences

country: United Kingdom

institute: University of Birmingham

summary: The propensity of viruses to acquire genetic material from relatives and possibly from infected hosts makes them excellent candidates as vectors for horizontal gene transfer. However, virus-mediated acquisition of host genetic material, as deduced from historical events, appears to be rare. Here, we report spontaneous and surprisingly efficient generation of hybrid virus/host DNA molecules in the form of minicircles during infection of Beta vulgaris by Beet curly top Iran virus (BCTIV), a single-stranded DNA virus. The hybrid minicircles replicate, become encapsidated into viral particles, and spread systemically throughout infected plants in parallel with the viral infection. Importantly, when co-infected with BCTIV, B. vulgaris DNA captured in minicircles replicate and is transcribed in other plant species that are sensitive to BCTIV infection. Thus, we have likely documented in real time the initial steps of a possible path of virus-mediated horizontal transfer of chromosomal DNA between plant species.

sample_organism:
Arabidopsis thaliana
Beta vulgaris

platform_organism:
Arabidopsis thaliana
Beta vulgaris

overall_design: DNA re-sequencing of BCTIV-infected Arabidopsis and Beta vulgaris plants, and a healthy mock-inoculated Beet control.


title: Expression data from Ang II induced HUVECs

city: Shanghai

first: Xianxian

last: Zhao

state: China

address: 168 Changhai Road

country: China

institute: Shanghai Changhai Hospital

summary:
lncRNAs were associated with the cardiovascular diseases since
we used Affy lncRNA gene expression microarray  to analyze differentially expressed lncRNAs in both normal and Ang II induced HUVECs

overall_design: We incubated the HUVECs with Ang II of 1 μM for 48 h. Total RNA was harvested from HUVEC using TRIzol reagent (Invitrogen, Carlsbad, CA, USA) and the RNeasy Kit (Qiagen Co., Hilden, Germany) according to the manufacturer's instructions, including a DNase digest ion step.To identify potential molecular factors associated with Ang II induced injury in HUVECs, we used Affy lncRNA gene expression microarray (Affymetrix company, USA) to analyze differentially expressed lncRNAs in both normal and Ang II induced HUVECs

first: Songqun

last: Huang

first: Jingwen

last: Song


title: European sea bass brain DLB-1 cell line infected with NNV

city: MURCIA

first: ALBERTO

last: CUESTA

state: MURCIA

address: CAMPUS UNIVERSITARIO ESPINARDO, FACULTAD BIOLOGIA

department: CELL BIOLOGY AND HISTOLOGY

country: Spain

institute: UNIVERSITY OF MURCIA

type: Expression profiling by high throughput sequencing

summary: DLB-1 cell line were mock infected or infected with nervous necrosis virus (NNV).

overall_design: We examine the transcriptomic profile of DLB-1 cell line after infection with NNV.

first: A

last: Cuesta

last: Esteve-Codina

first: J

last: Gómez-Garrido


title: Fission yeast cells: control vs alkaline stress

status: Public on Dec 12 2018

city: Fukuoka

first: Yujiro

last: Higuchi

address: 744 Motooka

country: Japan

institute: Kyushu University

summary: Transcriptional profiling of fission yeast cells comparing control untreated cells with cells treated with alkaline stress

overall_design: Two-condition experiment, control vs alkaline-stressed cells. One replicate.

first: Kaoru

last: Takegawa


title: Molecular basis of complex heritability in natural genotype-to-phenotype relationships

city: Stanford

first: Christopher

middle: M

last: Jakobson

state: CA

address: 318 Campus Dr, Clark Center W350

department: Chemical and Systems Biology

institute: Stanford University School of Medicine

summary: The intrinsic complexity of quantitative traits was evident even before the molecular nature of the gene was understood. Yet we still lack a detailed molecular understanding of complex heritability. Here we alleviated statistical roadblocks to high-resolution genetic mapping by using an inbred population of diploid yeast with very low linkage disequilibrium and more individuals than segregating polymorphisms. We mapped over 18,000 quantitative trait loci, resolving more than 3,300 to single nucleotides. This allowed us to explore the molecular origins of complexity, hybrid vigor, pleiotropy, and gene ´ environment interactions and to rigorously estimate the distribution of fitness effects of natural genetic variation. Our results describe a comprehensive, high-resolution genotype-to-phenotype map and define general principles underlying the complexity of heredity.

overall_design: mRNA-seq performed on 2 parental diploid strains in 3 growth conditions in biological triplicate

first: Daniel

middle: F

last: Jarosz


title: Genome-wide analysis of long noncoding RNA expression profile in patients with Marjolin’s ulcer

status: Public on Dec 11 2018

city: Changsha

first: Zan

last: Liu

state: Hunan

address: Xiangya Road No. 81

institute: Xiangya Hospital, Central South University

summary: Marjolin’s Ulcer is an aggressive cutaneous malignancy that typically ensues over a period of time in the post-burned lesions and scars or any other chronic wound. Marjolin’s Ulcer makes up 1.2% of all skin cancers, it is reported that 2% of squamous cell carcinoma  and 0.03% of basal cell carcinoma originate in burn scars. Recent studies have shown that long non-coding (lncRNA) plays critical roles in a myriad of biological processes and human diseases,Since the roles of lncRNA in Marjolin’s Ulcer remain unknown,they were investigated in the study.Our findings indicate that the expression profiles of lncRNAs has changed in Marjolin’s Ulcer as compared with normal skin and para-cancerous scar, and may provide novel insight into the molecular mechanism underlying the disease and potential novel diagnostic or therapeutic targets for  Marjolin’s Ulcer.

overall_design: Microarray expression profiling of mRNAs and lncRNAs were conducted using RNA extracted from normal skin tissues, para-cancerous scar tissues and Marjolin’s Ulcer tissues in  three patients with Marjolin’s ulcer.

first: Liu

last: Zan

first: Zhang

last: Pihong

first: Ren

last: Licheng


title: miRNA sequencing of fat body collect from adult female locusts

city: Kaifeng

first: Jiasheng

address: Jinming RD

institute: Henan University

type: Non-coding RNA profiling by high throughput sequencing

summary: Using hight throughput sequencing and data processing, we identified miRNA and quantified their expression in the fat body of adult females of Locusta migratoria.

overall_design: Samples were collected from locusts at 0, 2, 4, 6 days post adult eclosion. And 3 samples were subjected for RNA sequencing for each time point.

first: Shutang

last: Zhou


title: Comparison of low-fat and high-fat diet on gene expression in muscle, liver and adipose tissue from mice of two genetic backgrounds

city: Boston

first: Hui

last: Pan

address: 1 Joslin Place

department: Bioinformatics and Biostatistics Core

institute: Joslin Diabetes Center

summary: Diet-induced obesity is the primary determinant of the current epidemic of diabetes. We have explored the role of genetics in this phenomenon, using C57Bl/6 (B6) and 129S6/SvEvTac (129) mice on a low- or high-fat diet. Microarray analysis indicated significant changes in expression levels between B6 and 129 mice in the chromosomal area of Wnt5a and protein kinase C delta (PKC-delta). Thus, caloric efficiency, i.e., the “thrifty gene,” is a dominant-acting genetic determinant of diet-induced obesity in mice and can be linked to a locus on chromosome 14, including genes linked to adipose development and insulin sensitivity.

overall_design: Skeletal muscle, liver, and epididymal fat pads were removed from B6 and 129 mice at the age of 6 months after the mice were maintained on a standard diet that contained 21% of calories from fat, 22% from protein, and 57% from carbohydrates. A total of 25 ug RNA pooled from two to three mice was used for cRNA synthesis and hybridization on Affymetrix microarray chips.

first: K

last: Almind

first: C

middle: R

last: Kahn


title: Identification of key pathways involved in the toxic response of the cyanobacterial toxin cylindrospermopsin on human hepatic HepaRG cells

city: Fougères

first: Antoine

last: Huguet

address: 10B rue Claude Bourgelat

country: France

institute: Anses

summary: Cylindrospermopsin (CYN), a hepatotoxin produced by several cyanobacterial species, has been implied in human intoxications following ingestion. Although some pathways involved in CYN toxicity have been reported, the whole process is certainly more complex. In order to identify the mechanisms related to CYN toxicity on liver, we studied the transcriptomic profile of HepaRG human hepatic cells exposed to a low concentration of CYN (0.8 µM for 24 hrs). The affected pathways were further confirmed through the expression of key genes by qPCR, and the investigation of toxicity markers by high content analysis (HCA) on a broader CYN concentration range. Also CYP450 activities and cell redox homeostasis were investigated after acute and repeated exposure to CYN. Our results revealed that CYN induced up-regulation of genes implied in RNA modification and maturation, but also down-regulation of genes involved in xenobiotic metabolism and cell cycle progress. There was cell cycle disturbance characterised by an accumulation of G1/S and G2/M cells, and an increase of phospho-H3 positive cells. The cell cycle arrest was linked to the induction of DNA damage pointed out by an increase of γH2AX positive cells, but also an accumulation of sub G1 cells indicating apoptosis not involving caspase 3. While GSH content decreased strongly after acute exposure to CYN, it increased after a repeated exposure reflecting an adaptive response of cell redox homeostasis when exposure to CYN was prolonged. However, our data suggested also that CYN induced a down-regulation of phase I and II metabolism gene products, and CYP450 activities were affected following both acute and repeated exposure to CYN. Our study indicated that repeated exposure of liver cells to low concentrations of CYN may affect their detoxification capacities.

overall_design: Modulation of gene expression in differentiated HepaRG cells was measured at 24 hours after exposure to doses of 0 and 0.8 µM of cylindrospermopsin. Six independent experiments were performed, and 12 samples (6 controls and 6 exposed to cylindrospermopsin) had an RNA quality indicator ≥ 9 and were used for the microarray experiments.


title: Immunotherapy Utilizing NK cells and ADCC Mediating Agents with Poly (ADP-ribose) polymerase (PARP) Inhibition

city: bethesda

first: james

middle: w

last: hodge

state: md

address: 10/8b13, 9000 rockville pike

department: LTIB

institute: NCI

summary: Background: Poly (ADP-ribose) polymerase inhibitors (PARPi) prevent single-stranded DNA repair. Olaparib is a PARPi approved for the treatment of BRCA mutant ovarian and breast carcinoma. Emerging clinical data suggest a benefit of combining olaparib with immunotherapy in prostate cancer patients both with and without somatic BRCA mutations.   Methods: We examined if olaparib, when combined with IgG1 antibody-dependent cellular cytotoxicity (ADCC)-mediating monoclonal antibodies (mAbs) cetuximab (anti-EGFR), or avelumab (anti-PD-L1), would increase tumor cell sensitivity to killing by natural killer (NK) cells independently of BRCA status or mAb target upregulation. BRCA mutant and BRCA wildtype (WT) prostate carcinoma cell lines were pretreated with olaparib and then exposed to NK cells in the presence or absence of cetuximab or avelumab.  Results: NK-mediated killing was significantly increased in both cell lines and was further increased using the ADCC-mediating mAbs. Pre-exposure of NK cells to recombinant IL-15/IL-15RA further increased the lysis of olaparib treated tumor cells. In addition, olaparib treated tumor cells were killed to a significantly greater degree by engineered high-affinity NK cells (haNK). We show here for the first time that (a) olaparib significantly increased tumor cell sensitivity to NK killing and ADCC in both BRCA WT and BRCA mutant prostate carcinoma cells, independent of PD-L1 or EGFR modulation; (b) mechanistically, treatment with olaparib upregulated death receptor TRAIL-R2, and (c) olaparib significantly enhanced NK killing of additional tumor types, including breast, non-small cell lung carcinoma, and chordoma. Conclusions: These studies support the combined use of NK- and ADCC-mediating agents with correctly timed PARP inhibition.

overall_design: 2 prostate cancer cell lines were tested: 22rv1 and DU145. Each was treated with 20uM olaparib or vehicle. Samples were harvested at 6, 12 and 18h. Comparisons for gene changes were olaparib trated cells at a given timpoint versus the corresponding vehicle control trated cells.

first: James

middle: W

last: Hodge


title: Transcriptomic profiling of brassinosteroids response genes in moso bamboo (Phyllostachys heterocycla)

city: fuzhou

first: Zhe

last: Zhang

state: Fujian

address: No.15 Shangxiadian Road, Cangshan District, Fuzhou City, Fujian Province, China

department: Haixia Institute of Science and Technology

institute: Fujian Agriculture and Forestry University

summary: Brassinosteroids (BRs) are a group of plant steroid hormones that play crucial roles various of growth and developmental processes. Biological function and signal transduction pathway of BR has been well characterized in model plants like Arabidopsis and rice. However, their biological roles are still unclear in tree species, especially in an important non-timber plant moso bamboo, which has great ecological and economic value and distinguish fast-growth feature. Here we reported that reduce endogenous brassinosteroid by biosynthesis inhibitor propiconazole reduced both root and shoot growth in seedling stage. Exogenous BR application promoted shoot bract elongation and inclination of lamina joint and bract. Genome-wide transcriptome analysis were performed to identify hundreds of differential expressed genes by BR and propiconazole treatment in shoot and root parts of bamboo seedling, respectively. GO analysis revealed that BR regulates cell wall related genes, hydrogen peroxide catabolic genes and auxin related genes to promote bamboo root development and elongation. Our study identified BR response genes and provides a comprehensive resource for molecular mechanism research of bamboo growth.

overall_design: 18-day moso bamboo seedlings were transferred to 10 μM PPZ and mock medium for another 5 days. PPZ pre-treated seedlings were then treated with 1 μM BL or mock solution for 4 hours. Harvested seedling shoot and root separately, then isolated RNA was sequenced using Illumina Hiseq2500.

first: Xuelian

last: Yang

first: Wenfei

last: Wang

first: Qiang

last: Zhu

first: Lianfeng

last: Gu

first: Zhi-Yong


title: Next Generation Sequencing Facilitates Quantitative Analysis of root of original buckwheat (Fagopyrum hailuogouense) Transcriptomes

first: Moyang

address: dongchuan road 800

department: School of Agriculture and Biology

institute: Shanghai Jiao Tong University

summary: We generated 48.39 Gb of high-quality sequencing data (~8.07 Gb per sample). The analysis showed differences of transcriptomes between dormancy and growth stages of origina buckwheat roots. We identified numerous differentially expressed genes that exhibited distinct expression patterns. These genes have known or potential roles in development of origina buckwheat roots.  Therefore, we are appealing candidates for further investigation of the gene expression and associated regulatory mechanisms related to asexual reproduction character.

overall_design: Original buckwheat roots mRNA profiles of growth and dormancy stages were generated by deep sequencing, in  triplicate, using Illumina HiSeq 4000.


title: Therapeutic potential of targeting miR-141 in intervertebral disc degeneration: first steps toward the clinic

city: shanghai

first: jian

last: chen

address: shanghai pudong district minfeng road NO.351  Room 406  Building 1

summary: Understanding the molecular mechanisms regulating the maintenance and destruction of intervertebral disc may lead to the development of new therapies for intervertebral disc degeneration (IDD). Here we present evidence from miRNA microarray analyses of clinical data sets along with in vitro and in vivo experiments that miR-141 is a key regulator of IDD. Gain- and loss-of-function studies show that miR-141 drives IDD by inducing nucleus pulposus (NP) apoptosis. Furthermore, miR-141 KO in mice attenuated spontaneous and surgically induced IDD. Mechanistically, miR-141 promotes IDD development by targeting and depleting SIRT1, a negative regulator of NF-κB pathway. Therapeutically, upregulation or downregulation of miR-141 by nanoparticle delivery in IDD model aggravated or alleviated experimental IDD, respectively. Our findings reveal a novel mechanism by which miR-141, in part, promotes IDD progression by interacting with SIRT1/NF-κB pathway. Blockade of miR-141 in vivo may serve as a potential therapeutic approach in the treatment of IDD.

overall_design: To decipher the roles of miRNA in IDD, we examined the miRNA expression profiles with miRNA microarray on 3 NP tissues from IDD patients vs. 3 normal NP tissues from fresh traumatic lumbar fracture patients

first: Ming

middle: L

last: Ji

first: Jun

last: Lu


title: Urinary miRNAs contained in exosome of dogs and cats

status: Public on Dec 10 2018

city: Sapporo

first: Osamu

last: Ichii

state: Hokkaido

address: Kita 18-Nishi 9

department: Faculty of Veterinary Medicine

institute: Hokkaido University

summary: The purpose of this study was the identification of RNAs contained in the urinary exosome (UExo) from dogs and cats. The quality of total RNA in isolated urinary exosome (UExo)-derived total RNAs obtained from the column-based method (urine 1 mL) was checked by using a Bioanalyzer, and samples from normal renal function (NR) group and kidney disease (KD) group were pooled as one sample for each group.  We collected NR dogs  (n = 37), KD dogs (n = 47), NR cats (n=43), and KD cats (n = 45).  For the next generation sequencing, libraries were prepared according to the manufacturer’s protocols and sequenced using 50-base reads acquired by using a HiSeq 2000 platform. The December 2011 (GRCm38/mm10) mouse (Mus musculus) genome data were used as reference. As a result, we could identify the miRNA from these samples.

sample_organism:
Canis lupus familiaris
Felis catus

platform_organism:
Canis lupus familiaris
Felis catus

overall_design: Examination of NR dogs  (n = 37), KD dogs (n = 47), NR cats (n=43), and KD cats (n = 45) which were pooled as one sample for each group.


title: Comparative transcriptomics highlights new features of the iron starvation response in the human pathogen Candida glabrata

city: Paris

first: Antonin

last: Thiébaut

address: 7-9 quai Saint Bernard, building C, floor 3, room C321B

institute: Sorbonne Université

type: Genome binding/occupancy profiling by high throughput sequencing

summary: We conducted a network-based analysis of the Aft2 transcription factor involved in iron starvation response in Candida glabrata.

overall_design: We performed ChIPseq experiments using myc-tagged versions of Aft2 factor.

first: Médine

last: Benchouaia

first: Hugues

last: Ripoche

first: Thierry

last: Delaveau

first: Mariam

last: Sissoko

first: Jawad

last: Merhej

first: Laure

last: Fasseu

first: Sabrina

last: Benaissa

first: Geneviève

last: Lorieux

first: Laurent

last: Jourdren

first: Stéphane

last: Le Crom

first: Gaëlle

last: Lelandais

first: Eduardo

last: Corel

first: Frédéric

last: Devaux


title: Identification of Jun loss that promotes resistance to HDAC inhibitor Entinostat through Myc signaling in Luminal breast cancer [CGH]

city: Chapel Hill

first: Charles

middle: M.

last: Perou

state: NC

address: 12-044 Lineberger Comprehensive Cancer Center CB# 7295

department: Professor of Genetics, and Pathology & Laboratory Medicine; Lineberger Comprehensive Cancer Center

institute: University of North Carolina at Chapel Hill

summary: The histone deacetylase inhibitor Entinostat is in phase III trials for patients with metastatic estrogen receptor-positive breast cancer. Predictors of sensitivity and resistance, however, remain unknown.

overall_design: A total of 8 cell lines and 9 mouse models of breast cancer were treated with Entinostat. Luminal cell lines were treated with or without Entinostat at their IC50 doses, and MMTV/Neu luminal mouse tumors were treated with Entinostat until progression. We investigated these models using gene expression profiling by microarray and copy number by arrayCGH. We also utilized the network-based Dawnrank algorithm, that integrates DNA and RNA data, to identify driver genes of resistance. The impact of a number of candidate drivers was investigated in The Cancer Genome Atlas and the METABRIC

first: Maki

last: Tanioka

first: Daniel

middle: P

last: Hollern

first: Kevin

last: Mott

first: Chris

last: Fan

first: Matthew

middle: G

last: Soloway


title: Exoribonucleases coordinate degradation and expression of mRNAs in Escherichia coli at the stationary phase

city: Toulouse

first: Laurence

last: Girbal

address: 135 avenue de rangueil

institute: TBI

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

sample_organism: Escherichia coli str. K-12 substr. MG1655

overall_design: Refer to individual Series


title: Exoribonucleases coordinate degradation and expression of mRNAs in Escherichia coli at the stationary phase [transcriptome]

summary: Exoribonucleases are crucial for RNA degradation in Escherichia coli but the roles of RNase R and PNPase and their potential overlap in stationary phase are not well characterized. Here, we used a genome-wide approach to determine how RNase R and PNPase affect the mRNA half-lives compared to wild type (stabilome) in the stationary phase. The stabilome is an original dynamic transcriptome-based analysis to measure the rates of mRNA degradation at the genome scale. We have combined the analysis of stabilome with the steady state concentrations of mRNAs (transcriptome) to provide an integrated overview of the in vivo activity of these exoribonucleases at the genome-scale. The stabilome demonstrated that the mRNAs are very stable in the stationary phase and that the deletion of RNase R or PNPase caused only a limited mRNA stabilization. Intriguingly the absence of PNPase provoked also the destabilization of many mRNAs. These changes in mRNA half-lives in the PNPase deletion strain were associated with a massive reorganization of mRNA levels and also variation in several ncRNA concentrations. Finally, the in vivo activity of the degradation machinery was found frequently saturated by mRNAs in the PNPase mutant unlike in the RNase R mutant, suggesting that the degradation activity is limited by the deletion of PNPase but not by the deletion of RNase R. This work allowed the roles of RNase R and PNPase in coordinating E. coli RNA metabolism to be discussed and PNPase to be identified as a central player of the degradation machinery in stationary phase.

overall_design: A microarray study was performed to estimate genome wide mRNA concentrations in three E. coli K12 strains MG1655, MG1655_rnr) and MG1655_pnp), cultured in LB. Three hours after the entry in stationary phase, sampling was before the addition of rifampcin. Total RNA was then extracted from each sample. Each array measures the expression level of 4,254 genes from Escherichia coli MG1655 with eight 60-mer probes per gene in duplicates. Three independent repetitions were performed for each strain.

first: Clémentine

last: Dressaire

first: Vânia

last: Pobre

first: Sandrine

last: Laguerre

first: Cecilia

last: Arraiano

first: Muriel

last: Cocaign-Bousquet


title: A gene regulatory network driven by LIM homeobox 1 (LHX1) for embryonic head development (Microarray)

city: WESTMEAD

first: PIERRE

last: OSTEIL

state: NSW

address: 214 Hawkesbury Road

department: Embryology

country: Australia

institute: CMRI

summary: Development of the embryonic head is driven by the activity of gene regulatory networks of transcription factors. LHX1 is a homeobox transcription factor that plays an essential role in the formation of the embryonic head. The loss of Lhx1 function results in anterior truncation of the embryo caused by the disruption of morphogenetic movement of tissue precursors and the dysregulation of WNT signaling activity. Profiling the gene expression pattern in the Lhx1 mutant embryo revealed that tissues in anterior germ layers acquire posterior tissue characteristics, suggesting Lhx1 activity is required for the allocation and patterning of head precursor tissues. Here, we used LHX1 as an entry point to delineate its transcriptional targets and interactors and construct a LHX1-anchored gene regulatory network. Using a gain-of-function approach, we identified genes that immediately respond to Lhx1 activation. Meta-analysis of the datasets of LHX1-responsive genes and genes expressed in the anterior tissues of mouse embryos at head-fold stage, in conjunction with published Xenopus embryonic LHX1 (Xlim1) ChIP-seq data, has pinpointed the putative transcriptional targets of LHX1 and an array of genetic determinants functioning together in the formation of the mouse embryonic head.

overall_design: Total RNA obtained from anterior or posterior regions of E7.75 Lhx1epiCKO (Lhx1-/flox; Meox2+/Cre) and control (Lhx1+/flox; Meox2+/Cre) mouse embryos. There are three replicates per condition.

first: Tennille

last: Sibbritt

first: Chi

middle: K

last: Ip

first: Pierre

last: Osteil

first: Patrick

last: Tam

first: Nicolas

last: Fossat


title: Exoribonucleases coordinate degradation and expression of mRNAs in Escherichia coli at the stationary phase [stabilome]

overall_design:
A microarray study was performed to estimate genome wide mRNA half-lives in three E. coli K12 strains MG1655, MG1655(Δrnr) and MG1655(Δpnp), cultured in LB. Three hours after the entry in stationary phase, sampling was before the addition of rifampcin (500 µg/l) for transcrption arrrest and over the time after rifampcin addition. Total RNA was then extracted from each sample. Each array measures the expression level of 4,254 genes from Escherichia coli MG1655 with eight 60-mer probes per gene in duplicates. Three independent repetitions were performed for each strain.

Please note that there are variations between the samples of a given strain because there were sampled over the time (between Time 0 and Time 30 minutes) after transcription arrest. So there are repetitions of three kinetics rep1, rep2 and rep3 but these kinetics correspond to different time points except for time 0 which is in common in the three kinetics.


title: Identification of Jun loss that promotes resistance to HDAC inhibitor Entinostat through Myc signaling in Luminal breast cancer (expression)

first: Charles

last: Perou

first: Maki

last: Tanioka


title: Laser microdissection-based tissue specific transcriptome analyses reveals novel regulatory network of genes involved in heat-induced grain chalk in rice endosperm.

city: Niigata

first: Tsutomu

last: Ishimaru

address: 1-2-1 Inada, Joetsu, Niigata

institute: Central Region Agricultural Research Center, National Agriculture and Food Research Organization (CARC/NARO)

summary: Heat stress  occurrence during endosperm development and seed filling forms chalky portion in the limited zone of starchy endosperm of rice grains. In this study, isolation of aleurone, dorsal, central and lateral tissues of developing endosperm by laser-microdissection (LM) coupled with gene expression analysis of 44K microarray was performed to identify key regulatory genes involved in the formation of milky-white (MW) and white-back (WB) chalky grains during heat stress. Gene regulatory network analysis classified the genes changed under heat stress into five modules. the modules of genes changed in developing starchy endosperm corresponding to MW and WB portion under heat stress suggested different regulatory genes involved in each type of grain chalk. The most distinct expression pattern was observed in a M1 and M2 modules where most of the small heat shock proteins and cellular organisation genes being upregulated under heat stress in dorsal aleurone cells and dorsal starchy endosperm zones The histological observation supported the significant increase in cell number and size of dorsal aleurone cells in WB grains. With regard to the central zone of starchy endosperm, preferential downregulation of high molecular weight heat shock proteins (HMW HSPs) including a prominent member encoding for endoplasmic reticulum (ER) chaperones by heat stress were observed, while expression of starch-biosynthesis genes remained unaffected. Characterization of transgenic plants supressing endosperm lumenal binding protein (BiP1), an ER chaperone preferentially downregulated at MW portion under heat stress, showed an evidence of forming the chalky grains without disturbing the expression of starch-biosynthesis genes. The present LM-based comprehensive expression analyses provides novel inferences that HMW HSPs play important role in controlling the redox, nitrogen and amino aicd metabolism in endosperm leading to the formation of MW and WB chalky grains.Keywords ; developing endosperm, gene expression, grain chalkiness, heat stress, laser-microdissection, Oryza sativa.

overall_design: Microarray experiment was conducted based on the method of Takehisa et al. (2012). Total RNA (5.0 ng) was amplified to obtain complementary RNA (cRNA) using two-color Quick Amp Labeling kit (Agilent technologies), according to the modified manufacturer’s instruction. RNA extracted from control and high-temperature condition was labeled with cyanine-3 (Cy3)-CTP and cyanine-5 (Cy5)-CTP, respectively. Three biological replicates were prepared from high temperature conditions as well under control conditions. 1250 ng of labeled cRNAs were fragmented and hydridized on a slide glass of rice 4 × 44K microarray RAP-DB (G2519F#1524 ; Agilent Technologies). Slides were scanned on an Agilent G2505B DNA microarray scanner, and background of the Cy3 and Cy5 raw signals was corrected using the Feature Exraction (ver. 10.5.1.1, Agilent Technologies). The two channels Agilent microarray expression data of 12 microdissected samples of dorsal aluerone cells (AL), dorsal starchy endosperm (DSE), central starchy endosperm (CSE) and lateral starchy endosperm (LSE) at 7DAF from control and at 6DAF from heat stressed tissues consisting of three replicates was further processed (ratio computation, log transformation and baseline transformation) using the software GeneSpring GX version 12 (Agilent, Santa Carla, CA).

first: Sabiha

last: Parween

first: Yuhi

last: Saito

first: Takanari

last: Shigemitsu

first: Hiromoto

last: Yamakawa

first: Mikio

last: Nakazono

first: Takehiro

last: Masumura

first: Naoko

last: Nishizawa

first: Motohiko

last: Kondo

first: Nese

last: Sreenivasulu


title: Verticillium dahliae disease resistance and the regulatory pathway for maturity and tuberization in potato

city: Fredericton

first: Helen

middle: H.

last: Tai

state: New Brunswick

address: P. O. Box 20280, 850 Lincoln Rd.

department: Potato Research Centre

country: Canada

institute: Agriculture and Agri-Food Canada

summary:
Purpose: Verticillium dahliae is a fungal plant pathogen. The goals of the study are to examine gene networks involved in controlling resistance to V. dahliae in potato using expression quantitative trait loci (eQTL) mapping.
Methods: 91 clones from a diploid potato mapping population 15143 and the parental lines 07506-01 and 12120-03 from the Agriculture and Agri-Food Canada in Fredericton, New Brunswick, Canada were propagated in a V. dahliae-infested field in triplicate plots of five plants in a randomized complete block design. Tetraploid varieties Shepody, Hindenburg, Kennebec, Russet Burbank, Atlantic and Green Mountain were planted similarly and included in the analysis.  Green Mountain was also planted in additional plots and used a guard row clone.  Leaf samples were taken at 70 days after planting.  Two µg of total RNA per sample was used to construct DeepSAGE tag libraries using a modification to facilitate direct sequencing of the amplicons by Illumina sequencing. The samples from 91 clones were bar-coded with a different identification key.  Samples were diluted to a final concentration of 10 nM and were pooled.   Each of the three biological replicates was done in a separate pool.  Final pool concentrations were estimated using Quant-iT-PicoGreen prior to template DNA hybridization and sequencing on an Illumina Genome Analyzer II  according to the manufacturer's instructions.
Results: Tag count data were transformed to the relative unit of counts per million. Tags included in the analysis had to be present in at least one biological replicate. Clonal variation between samples was detected (p-value ≤ 0.05) using the exact test for a negative binomial distribution . Tags that did not have significant clonal variation were removed, leaving 6248 tags.  The LS mean of tag count was calculated for each tag for each clone.  The 21-nt tag sequences were aligned against PGSC S. tuberosum group Phureja DM1-3 transcripts (v3.4) using blastn.  Hits with E-value ≤ 0.5 were filtered in.   Where there were multiple blast hits meeting E-value criteria, only the one with the longest alignment was included.  4198 tags were assigned single-hit annotations in this manner and were used for eQTL analysis.
Conclusions: The results indicated that for most genes the eQTL controlling expression was mapped near the gene (cis-eQTL). There were also many trans-eQTLs, where were eQTLs for a gene that were found on another chromosome particularly on chromosome 5.

overall_design: Three sequencing runs were done in 8 channels.  RunA was a barcoded pool of all clones from block A/replicate 1.  RunB was a barcoded pool of all clones from block B/replicate 2.  RunC eas a barcoded pool of all clones from block C/replicate3

middle: H

first: Kare

last: Nielsen


title: Regulation of Glucose Uptake and Inflammation by FOXO1 and FOXO3 in Skeletal Muscle

city: Stockholm

first: Leonidas

middle: S

last: Lundell

state: Stockholm

address: Von Eulers Väg 4a

department: Physiology and Pharmacology

country: Sweden

institute: Karolinska Institute

summary:
Forkhead box class O (FoxO) transcription factors regulate whole body energy metabolism, skeletal muscle mass and substrate switching. To elucidate the role of FOXO in skeletal muscle, dominant negative (dn) constructs for FOXO1 (FOXO1dn) or FOXO3 (FOXO3dn) were transfected by electroporation into mouse tibialis anterior muscle and glucose uptake, signal transduction, and glucose stimulated gene expression profiles were assessed. Results were compared against contralateral control transfected muscle.
Transcriptomic analysis revealed major pathways affected by FOXO1dn or FOXO3dn revolve around metabolism and inflammation.

overall_design: 6 mice for FOXO1dn or FOXO3dn were electroporated in tibialis anterior with either construct or empty vector in contralateral leg. One week post-electroporation, mice were fasted for 4 h, and glucose uptake was measured in vivo using a modified oral glucose tolerance test. Mice were anesthetized with an intraperitoneal injection of Avertin, and electroporated tibialis anterior muscle was removed and snap-frozen. RNA was extracted from electroporated muscle utilizing the EZ RNA extraction kit, and hybridized to an Affymetrix Mouse Gene 2.1 ST array

first: Julie

last: Massart

first: Anna

last: Krook

first: Juleen

last: Zierath


title: Identification of Jun loss that promotes resistance to HDAC inhibitor Entinostat through Myc signaling in Luminal breast cancer

first: Charles

last: Perou

type:
Expression profiling by array
Genome variation profiling by array

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus


title: Identification of Jun loss that promotes resistance to HDAC inhibitor Entinostat through Myc signaling in Luminal breast cancer [cell line]

first: Maki

last: Tanioka

first: Daniel

last: Hollern

first: Kevin

last: Mott

first: Chris

last: Fan

first: Matthew

last: Soloway


title: Gene expression data of human small intestinal organoids

status: Public on Dec 06 2018

city: Tokyo

first: Masayuki

last: Fujii

address: 35, Shinanomachi, Shinjuku-ku

institute: Keio University

summary:
The usage of IGF1 and FGF2 instead of EGF and p38 inhibitor during human intestinal organoid culture enables to preserve differentiated cell populations.
We analyzed gene expression of human small intestinal organoids cultured with either IGF1/FGF2 or EGF/p38i.

overall_design: Gene expression of human healthy small intestinal organoids derived froma single patient were cultured in the following two conditions for ten days; 1. Wnt-3A, R-spondin, Noggin, A83-01, IGF1, IGF2; 2. Wnt-3A, R-spondin, Noggin, A83-01, EGF, SB202190.

first: Kohta

last: Toshimitsu


title: Screening of differentially expressed genes after DBDx treatment

status: Public on Dec 09 2018

city: Beijing

first: Yanbo

last: Zheng

address: 1# Tiantan Xili

institute: Institute of Medicinal Biotechnology

summary: The whole human genome microarray was used to analyze the differentially expressed genes in MIA PaCa-2 xenograft after DBDx treatment. A total of 255 genes were down-regulated and 212 genes were up-regulated by at least 2-fold between DBDx-treated and saline-treated group. The most obvious changes in Gene Ontology biolocial process classification were related to the immune system and tumor vasculature.

overall_design: NIH (nu/nu) athymic mice bearing MIA PaCa-2 xenografts(100 mm3) were treated orally with saline or DBDx at 242 mg/kg once daily, 5 consecutive days a week for 3 weeks. Three days after the last administration, mice were sacrificed and tumor tissues were used for gene expression analysis. Three mice per group.

first: Yan-bo

first: Xiu-jun

last: Liu


title: NF-κB p65 dimerization and DNA-binding is important for inflammatory gene expression

status: Public on Dec 08 2018

city: Marburg

first: Robert

last: Liefke

state: Hessen

address: Hans-Meerwein-Str. 2

department: Institute of Molecular Biology and Tumor Research (IMT)

country: Germany

institute: Philipps University of Marburg

summary: Increasing evidence shows that many transcription factors execute important biologic functions independent from their DNA-binding capacity. The NF-κB p65 (RELA) subunit is a central regulator of innate immunity. Here, we investigated the relative functional contribution of p65 DNA-binding and dimerization in p65-deficient human and murine cells reconstituted with single amino acid mutants preventing either DNA-binding (p65 E/I) or dimerization (p65 FL/DD). DNA-binding of p65 was required for RelB-dependent stabilization of the NF-κB p100 protein. The antiapoptotic function of p65 and expression of the majority of TNF-α–induced genes were dependent on p65’s ability to bind DNA and to dimerize. Chromatin immunoprecipitation with massively parallel DNA sequencing experiments revealed that impaired DNA-binding and dimerization strongly diminish the chromatin association of p65. However, there were also p65-independent TNF-α–inducible genes and a subgroup of p65 binding sites still allowed some residual chromatin association of the mutants. These sites were enriched in activator protein 1 (AP-1) binding motifs and showed increased chromatin accessibility and basal transcription. This suggests a mechanism of assisted p65 chromatin association that can be in part facilitated by chromatin priming and cooperativity with other transcription factors such as AP-1.

overall_design: p65 ChIP-Seq in HeLa after p65 KO and reconstitution with wildtype or mutant p65, before and after TNF stimulation (1x), RNA-Seq of the same cells (2x), RNA-Seq of p65 KO MEFs reconstituted with wt and mutant p65 (1x)

first: Tabea

last: Riedlinger

first: Johanna

last: Meier-Soelch

first: Liane

last: Jurida

first: Andrea

last: Nist

first: Thorsten

last: Stiewe

first: Michael

last: Kracht

last: Schmitz


title: Transcriptomics analysis of Aspergillus fumigatus co-cultivated with Pseudomonas aeruginosa

city: Jena

first: Vito

last: Valiante

address: Beutenbergstrasse 11A

department: Leibniz Research Group - Biobricks of Microbial Natural Product Syntheses

institute: Leibniz-Institute for Natural Product Research and Infection Biology

summary: We report a study conducted to investigate the variation on gene expression of the pathogenic fungus Aspergillus fumigatus upon co-cultivation with the pathogenic bacterium Pseudomonas aeruginosa. The study was conducted by investigating the gene expression variation at different time points (45, 90 and 180 minutes after co-incubation). As control, we used data obtained by cultivating the fungus either without bacteria, or with heat-inactivated Pseudomonas.

sample_organism:
Pseudomonas aeruginosa PAO1
Aspergillus fumigatus A1163

overall_design: Examination of Aspergillus fumigatus co-cultivated with Pseudomonas aeruginosa.

first: Sophia

last: Keller

last: Heinekamp

first: Axel

last: Brakhage


title: Gene expression profiling of ATP9A knockdown HepG2 cells

status: Public on Dec 07 2018

city: Amsterdam

first: Sander

last: Meisner

state: NH

address: Meibergdreef 69-71

department: Tytgat institute

country: Netherlands

institute: AMC

summary: Analyzing the molecular mechanism of extracellular vesicle release in ATP9A knockdown HepG2 cells by differences in the gene expression level.

overall_design: Total RNA was obtained from the ATP9A depleted HepG2 cells 72 hours after the transduction with short hairpin containing lentiviral construct. Gene expression microarray was performed by using Illumina bead array to study the diffences i gene expression pattern.

first: Vanesa

last: Muncan


title: Gene expression profiling of mobilized vs. Bone marrow (BM) resident hematopoietic stem and progenitor cells (LSK)

city: Frankfurt

first: Darja

last: Karpova

address: Sandhofstrasse 1

department: Cell Therapeutics

institute: German Red Cross Blood Donor Service

summary: Expression prolile of CWHM-823+tGro-b mobilized (3 mg/kg + 2.5 mg/kg, s.c. injection, timepoint 30 min) HSPC was compared to that of AMD3100 (5 mg/kg, 1 hr after s.c. injection) or G-CSF (100 ug/kg/injection, q12h, 5 days) mobilized as well as BM resident HSPC. Accordingly, the cells were isolated from the BM of untreated or from the peripheral blood (PB) of differentially mobilized mice.

overall_design: Mice were treated with G-CSF (5 days), AMD3100 (1 hr), CWHM-823+tGro-b or PBS. PB or BM was isolated, depleted of red blood cells and enriched for kit (CD117)+ progenitors. LSK cells (HSPC) were then flow sorted from the positive cell fraction.


title: PP2A inhibitors arrest G2/M transition through JNK/Sp1-dependent down-regulation of CDK1 and autophagy-dependent up-regulation of p21

city: Suzhou

first: Meng-Dan

last: Xu

address: Shizi Street

institute: the First Affiliated Hospital of Soochow University

summary: Protein phosphatase 2A (PP2A) plays an important role in the control of the cell cycle. We previously reported that the PP2A inhibitors, cantharidin and okadaic acid (OA), efficiently repressed the growth of cancer cells. In the present study, we found that PP2A inhibitors arrested the cell cycle at the G2 phase through a mechanism that was dependent on the JNK pathway. Microarrays further showed that PP2A inhibitors induced expression changes in multiple genes that participate in cell cycle transition. To verify whether these expression changes were executed in a PP2A-dependent manner, we targeted the PP2A catalytic subunit (PP2Ac) using siRNA and evaluated gene expression with a microarray. After the cross comparison of these microarray data, we identified that CDK1 was potentially the same target when treated with either PP2A inhibitors or PP2Ac siRNA. In addition, we found that the down-regulation of CDK1 occurred in a JNK-dependent manner. Luciferase reporter gene assays demonstrated that repression of the transcription of CDK1 was executed through the JNK-dependent activation of the Sp1 transcription factor. By constructing deletion mutants of the CDK1 promoter and by using ChIP assays, we identified an element in the CDK1 promoter that responded to the JNK/Sp1 pathway after stimulation with PP2A inhibitors. Cantharidin and OA also up-regulated the expression of p21, an inhibitor of CDK1, via autophagy rather than PP2A/JNK pathway. Thus, this present study found that the PP2A/JNK/Sp1/CDK1 pathway and the autophagy/p21 pathway participated in G2/M cell cycle arrest triggered by PP2A inhibitors. Quality-checked RNAs were then transcribed with the  First-Strand cDNA Synthesis Kit(Agilent)and their expression data obtained using Agilent 4×44 K Human Whole-Genome 60-mer oligonucleotide microarrays according to the protocols by the manufacturer.

overall_design: PANC-1 cells treated with 20μM cantharidin (CAN) or okadaic acid (OA) seperately

first: Wei

last: Li


title: RNA sequencing (RNA-seq) analysis of leaf and root of Col grown on 1/2 MS with or without PS-SO3H or PS-NH2 nanoplastics treatment

city: Jinan

first: Yuebin

last: Jia

address: 88 Cultural east road

institute: Shandong University

summary: The goals of this study are to find the differential expression genes after PS-SO3H or PS-NH2 nanoplastics treatment, to explain why the PS-SO3H or PS-NH2 nanoplastics have inhibited the root growth.

overall_design:
The RNA was extracted from 10-day-old leaf and root of Col grown on 1/2 MS with or without PS-SO3H or PS-NH2 nanoplastics treatment.
Library construction and sequencing were performed as described elsewhere, based on RNA extracted with the TRIzol reagent (Invitrogen, Carlsbad, CA, USA) from 10-day-old seedlings grown on 1/2 MS containing PS-SO3H or PS-NH2 nanoplastics. The RNA was purified by electrophoresis through a TBE-urea polyacrylamide gel. The gel regions harboring 18-30 nt fragments were excised and the RNA recovered. The resulting population of sRNAs was 5’ and 3’ RNA adaptor-ligated using T4 RNA ligase and amplified for 18 PCR cycles. The amplicons were purified and sequenced using an Illumina/Solexa Genome Analyzer (Beijing Genomics Institute, Shenzhen, China). Raw reads were trimmed by removing low-quality and adaptor sequences, and then they were aligned to the Arabidopsis genome using SOAP2 software. Transcript frequency was calculated using the reads per kilobase per million reads method. Differentially transcribed genes were identified using a method modified from Audic and Claverie (1997). Significance was based on the p value and the false discovery rate (FDR) (Audic and Claverie, 1997). The chosen thresholds were FDR ≤ 0.001 and |log2| ≥ 1. We identified 113 differentially expressed genes, of which 49 genes are up-regulated, and 94 genes are down-regulated.

first: Xiaodong

last: Sun


title: Follicular helper T cells enhance autoimmunity through Ascl-2 in a murine model for Sjögren’s syndrome

status: Public on Dec 05 2018

city: Tokushima

first: Naozumi

last: Ishimaru

address: Kuramoto

department: Oral Molecular Pathology

institute: Tokushima University Graduate School

summary: We investigated how Tfh cells contribute to the breakdown of peripheral immune tolerance and the formation of autoimmune lesions in a murine model of SS. Our results indicate a yet unreported mechanism of autoreactive response through Tfh cells in a SS model mouse, and it will be supportive for understanding the pathogenesis of autoimmunity.

overall_design: Two-condition experiment, purified CD4+ CD25- T cells from spleen of non-thymectomied NFS/sld (Control) vs. purified CD4+ CD25- T cells from spleen of  thymectomied NFS/sld (SS model).

first: Kunihiro

last: Otsuka

first: Akiko

last: Yamada

first: Akihiro

last: Inagaki

first: Rieko

last: Arakaki

first: Aya

last: Ushio


title: High-throughput RNA sequencing on circular RNA profiles of human triple-negative breast cancer and adjacent normal tissues

city: Nan jing

first: kaixuan

last: zeng

address: Yuhuatai District, Communist Youth League Road No. 32

institute: southeast university

summary: In an attempt to search for metastasis-associated circRNAs, we performed RNA-sequencing on ribosomal RNA-depleted total RNA from three pairs of triple-negative breast cancer (TNBC) and adjacent normal tissues. A computational pipeline based on the anchor alignment of unmapped reads was used to identify circular RNAs. Taken together, 69,815 distinct circRNAs were found in this study and 87% were derived from exons, and the others were derived from introns, intergenic region and 3′ or 5′ UTR, etc. We further identified 5,033 differentially expressed circRNAs (fold change ≥ 2 and p < 0.05). Among them, 3,726 circRNAs were significantly down-regulated and 1,307 circRNAs were significantly up-regulated in TNBC tissues compared with adjacent normal tissues. These data indicate that circRNAs are abundant in human breast tissues and dysregulation of circRNAs may contribute to breast cancer progression.

overall_design: Circular RNAs profiles of three pairs of triple-negative breast cancer (TNBC) and adjacent normal tissues were generated by RNA deep-sequencing, using HiSeq3000, Illumina.

first: Kaixuan

last: Zeng

first: Shukui

last: Wang


title: Klf4 overexpression effect on P0 rat retina

status: Public on Dec 04 2018

city: Rio de Janeiro

first: Mariana

last: Silveira

state: Rio Janeiro

address: Av. Carlos Chagas Filho, 373. Ilha do Fundão., Centro de Ciências da Saúde, Bloco G, sala G2-004/019

department: Neurobiology

country: Brazil

institute: Institute of Biophysics Carlos Chagas Filho, Federal University of Rio de Janeiro

summary: Analysis of progenitor cells of P0 rats overexpressing Krüppel-like factor 4 (Klf4). Klf4 is a key transcriptional regulator of differentiation potential. Results provide insight into the role of Klf4 in the retina.

overall_design: Retinal explants were dissociated 39 h after in vitro electroporation and the transfected population (GFP+) was isolated by FACS. The transcriptome of the sorted GFP cells from control and Klf4-overexpressing cells were examined by microarray.

last: Souza da Silveira

first: Mauricio

last: Rocha-Martins


title: High concordance between SNPs identified by the porcine 60K BeadChip genotyping array (Illumina) and the whole-genome sequencing

city: ChengDu

first: Yu

last: Lin

state: SiChuan

address: GongPing

institute: Sichuan Agricultural University

type:
SNP genotyping by SNP array
Genome variation profiling by SNP array

summary: Crossbreeding has been an effective method to improve crossbred performance in pig industry. To have a global view of a classic three-way crossbreeding system of Duroc x (Landrace x Yorkshire) (DLY), we identified SNPs for each pig breed and crossbred individual originated from a DLY pig family to estimate the influence of purebreds on crossbred offspring using whole-genome sequencing. To confirm the accuracy of the SNPs identified by whole-genome sequencing, therefore, we performed the porcine 60K BeadChip genotyping array (Illumina) for each sequenced pig individual.

overall_design: To confirm the accuracy of SNPs identified by whole-genome sequencing, we performed the porcine 60K BeadChip genotyping array (Illumina) for ten pig individuals of a DLY pig  family.

first: Mingzhou


title: RNA-seq analysis asociated with the infection of bovine papillomavirus

city: São Cristóvão

first: Marcus

last: Batista

state: Sergipe

address: Av Marechal Rondon, s/n

department: Department of Biology

institute: Federal University of Sergipe

summary: Bovine papillomavirus (BPV) is the causative agent of papillomatosis in cattle. The disease causes cutaneous and mucosal lesions that can be minimized or lead to the appearance of malignant tumors. This study aims to identify possible molecular mechanisms that are behind the pathological processes associated with bovine papillomatosis through the identification of genes related to the development of the lesions. For this, next-generation RNA sequencing was used to assess differentially expressed genes in infected by BPV and non-infected bovines. Three animals with papillomatosis lesion and three without papillomatosis lesion were studied. The Galaxy platform was used to analyze the data generated by the sequencing. The Illumina output files were converted to FASTQ format. Quality evaluation was performed using FastQC and the sequence quality cut was performed using Trimmomatic. TopHat and Bowtie were used to map and align the reads with the reference genome. The abundance of the expressed genes was verified using Cuffilinks. Cuffdiff was used for differential expression analysis. Functional annotation of the differentially expressed genes was performed using Gene Ontology (GO) databases. RNA-sequencing generated a total of 121,722,238 of reads. In the gene expression analysis, a total of 13,421 genes expressed were identified and of these 1343 were differentially expressed. The functional annotation of differentially significant genes showed that many genes presented functions or they were related to metabolic pathways associated with the progression of papillomatosis lesions and cancer development in cattle. Although more studies are needed, this is the first study that focused on a large-scale evaluation of gene expression associated with the BPV infection, which is important to identify possible mechanisms regulated by the host genes that are necessary the development of the lesion

overall_design: Analysis of three BPV infected and three BPV non-infected samples

first: Gerlane

last: Barros

first: Debora

last: Barreto

middle: V


title: RF/6A Chorioretinal Cells do not Display Key Endothelial Phenotypes

city: Charlottesville

first: Stephen

last: Turner

state: VA

address: 1670 Discovery Drive

institute: Signature Science, LLC

summary: Purpose: The RF/6A chorioretinal cell line originally isolated from a fetal rhesus macaque in 1968 is widely used to model human retinal and choroidal endothelial cells in cell culture. We sought to determine the extent to which this line possesses endothelial cell-specific characteristics. Methods: RF/6A cells obtained from American Type Culture Collection were subjected to next-generation RNA sequencing. Transcriptomic-based cell type profiling was conducted using xCell. Validation of endothelial cell-specific marker expression was conducted by qRT-PCR and western blotting. Functional assays of acetylated low density lipoprotein uptake, TNF-?-induced adhesion molecule expression, shear stress alignment, and endothelial tube formation were assessed. Results: RF/6A transcriptomic profiles obtained de novo or from a publically available repository did not correspond to endothelial gene expression signatures. Expression of established endothelial markers (PECAM1, CDH5, KDR, VWF, ICAM2, ENG, or TEK) were very low or undetectable in RF/6A compared to primary human umbilical vein endothelial cells. Compared to primary endothelial cells, RF/6A were unable to uptake acetylated LDL, exhibit induction of E-selectin in response to TNF-? treatment, align in the direction of shear stress, or form regular capillary-like tubes in Matrigel. Conclusions: RF/6A do not exhibit key endothelial cell characteristics or behaviors. Therefore, caution should be employed in designing and interpreting studies using these cells as surrogates for choroidal or retinal endothelial cells.

first: Bradley

middle: D

last: Gelfand


title: Endo-siRNAs repress expression of SINE1B during in vitro maturation of porcine oocyte

city: Harbin

first: Xiaolei

last: Zhang

address: No.59 Mucai street

institute: Northeast Agricultural University

summary: We performed small RNA-seq on Dicer KD and control porcine oocyte, and report endo-siRNAs corresponding to SINE1B are significantly down-regulated by Dicer knockdown and are essential for in vitro maturation of porcine oocyte

overall_design:
Examination of samll RNA profiles in Dicer KD and control oocytes.
Please note that the processed data contains not other small RNAs, such as siRNAs, besides miRNAs. Therefore, small RNA sequences are included instead of miRNA IDs

first: Qingran

last: Kong

first: Jiaming


title: Aberrant alternative splicing profiling for myelodysplastic syndrome (MDS) patients

city: Tapei

first: Yi

middle: Tsung

last: Yang

address: No.7, Chung Shan S. Rd.（Zhongshan S. Rd.）, Zhongzheng Dist., Taipei City 10002, Taiwan (R.O.C.)

department: Internal Medicine

country: Taiwan

institute: National Taiwan University Hospital

summary:
Transcriptome analysis of total RNA from bone marrow (BM) mononuclear cells of MDS patients and normal dornors
Global gene expression and alternative splicing profiling among patients with myelodysplastic syndrome (MDS) compared with normal donors

overall_design: We analyzed bone marrow samples from 176 MDS patients and  20 healthy donors using the Affymetrix Human Transcriptome Array 2.0 platform

first: Yi-Tsung

first: Wen-Chien

last: Chou

first: Hwei-Fang

last: Tien


title: Transciptomic profiling of the uterii of laying and non-laying hens using RNA-seq

city: Honolulu

first: Nirvay

last: Sah

state: HI

address: 1955 East-west raod

department: Human Nutrition, Food and Animal Sciences

institute: University of Hawaii at Manoa

summary:
Purpose: With the advent of Next-generation sequencing (NGS), several novel genes/proteins and cellular pathways in wide variety of tissues has been discovered. The aim of this study are to perform uterine transcriptome profiling (RNA-seq) to determine differently expressed genes in laying and non-laying hens and to further validate the expression of candidate genes using real-time quantitative reverse transcription polymerase chain reaction (qRT–PCR)  in laying, non-laying and molting hens.

Methods: Uterine mRNA profiles of 35-60 weeks-old laying and non-laying hens, three each, were generated with NextSeq 500 sequencer in single-end mode with a read length of 1x76 bp. Raw sequencing reads were cleaned and trimmmed with Prinseq tool and good reads were aligned against the chicken reference gemone (Galgal 5.0) in Array Studio. Differential gene expression analysis was performed by the DESeq2 algorithm as implemented in Array Studio. The genes with at least two-fold change (FC) and Benjamini and Hochberg q-value < 0.05 were called differentially expressed.

Results: Using an optimized data analysis workflow, we mapped about 32 million reads from layers and 28 million reads from non-layers to the chicken genome. A total of 19,152 gene transcripts were annotated from Ensembl alignment which represents 50.24% of the chicken genome assembly. Differential gene expression analysis showed 616 were differentially expressed between layer and non-layer hens. 229 DEGs were significantly up-regulated and 286 were significantly down-regulated in the laying hens when compared to the non-laying hens. Twelve candiate genes, linked to calcium remodeling, were identified by gene function analysis and validated using qPCR. MEPE, CALCB, OTOP2, STC2 and ATP2C2 were confirmed to be highly expressed in laying hens as compared to molting and non-laying hens. RNA-seq and qPCR data for relative gene expression were highly correlated (R2 =0.99).

Conclusions: Our study reports the expression of four novel genes that are speculated to transport calcium ions across the uterine epithellium for eggshell mineralization. These genes can be used as quantitative basis of selecting hens with an improved eggshell quality.

overall_design: Uterine mRNA profile of three 35-60 weeks old laying and non-laying hens was genereted using Illumina NextSeq 500

first: Birendra

last: Mishra


title: Genome-wide chromatin analysis of Ewing sarcoma (ChIP-seq)

city: Guangzhou

first: Lehang

address: 107, West Yanjiang Road

institute: Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University

summary: As the second most common malignant bone tumor in children and adolescents, Ewing sarcoma is initiated and exacerbated by a chimeric oncoprotein, most commonly, EWS-FLI1. In this study, we apply epigenomic analysis to characterize the transcription dysregulation in this cancer, focusing on the investigation of super-enhancer and its associated transcriptional regulatory mechanisms. We demonstrate that super-enhancer-associated transcripts are significantly enriched in EWS-FLI1 target genes, contribute to the aberrant transcriptional network of the disease, and mediate the exceptional sensitivity of Ewing sarcoma to transcriptional inhibition. Through integrative analysis, we identify MEIS1 as a super-enhancer-driven oncogene, which co-operates with EWS-FLI1 in transcriptional regulation, and plays a key pro-survival role in Ewing sarcoma. Moreover, APCDD1, another super-enhancer-associated gene, acting as a downstream target of both MEIS1 and EWS-FLI1, is also characterized as a novel tumor-promoting factor in this malignancy. These data delineate super-enhancer-mediated transcriptional deregulation in Ewing sarcoma, and uncover numerous candidate oncogenes which can be exploited for further understanding of the molecular pathogenesis for this disease.

overall_design: ChIP-seq for MEIS1 in A673 Ewing sarcoma cells

first: Dechen


title: Gene expression profiling of PBMCs in dairy cows pre- and post-partum

city: Ithaca

first: Jennifer

last: Grenier

state: NY

address: 526 Campus Rd

department: Biomedical Sciences

institute: Cornell University

summary: The transition to lactation challenges dairy cows metabolically.  Immune dysfunction and infectious disease risk is the hallmark of this transition period. Transcriptome data of PBMC shows differentially expressed pathways postpartum. Metabolically stressed cows show upregulation of innate immune pathways and inflammation.

overall_design: Gene expression profiling of PMBCs from 6 dairy cows, each sampled 21 days prepartum and 7 days postpartum. Three cows (H1-3) showed signs of increased metabolic stress (by other assays) relative to the other three cows (L1-3).

first: Sabine

last: Mann

first: Anja

last: Sipka


title: Competitive RNA Pair Controls Gastric Cancer Metastasis by Regulating EphrinA1 Translation

status: Public on Dec 03 2018

city: Hangzhou

first: Tianhua

last: Zhou

state: Zhejiang

address: 866 Yuhangtang Road

department: School of Medicine

institute: Zhejiang University

summary: EphrinA1 overexpression-induced gene signature was significantly enriched in the cells with high expression of GMAN

overall_design: GMAN or EphrinA1 induced gene expression in HGC-27 gastric cancer cell was measured at 48h after transfection with pcDNA3.1 control vector or pcDNA3.1-GMAN or pcDNA3.1-EphrinA1 plasmid.

first: Wei

last: Zhuo

first: Yiman

last: Liu


title: Competitive RNA Pair Controls Gastric Cancer Metastasis

summary: To explor the role of lncRNAs in gastric cancer progression, we performed a microarray analysis to systematically screen the differential expression of lncRNAs between six human gastric cancer tissues and their matched non-tumor tissues

overall_design: Systematically screen the differential expression of lncRNAs between six human gastric cancer tissues and their matched non-tumor tissues


title: Gene expression (GE) data from differentiating equine satellite cells (ESC) culture incubated with phytochemical gamma-oryzanol (GO) and exposed to hydrogen peroxide

city: Warsaw

first: Tomasz

last: Sadkowski

address: Nowoursynowska 159

department: Department of Physiological Sciences

country: Poland

institute: Warsaw University of Life Sciences - SGGW

summary: Transcriptional profiling of GO-treated (24h) differentiating equine satellite cells (3rd day of differentiation) exposed to hydrogen peroxide (1h; last hour of pre-incubation with GO) compared to control GO-untreated cells. Goal was to determine the effects of GO pre-incubation on gene expression in equine satellite cells exposed to hydrogen peroxide.

overall_design: Two-condition experiment, GO-treated (24h) differentiating equine satellite cells and exposed to hydrogen peroxide (1h during 24h pre-incubation with GO) (3rd day of differentiation) vs. differentiating equine satellite cells without GO treatment (control). Biological replicates: 4 reps of examined condition , 4 control replicates

first: Anna

last: Ciecierska

first: Karolina

middle: A

last: Chodkowska


title: Transcriptomal analysis of the impact of ASAH1 inhibition on skin metastatic melanoma cells

city: Valbonne - Sophia-Antipolis

first: Kevin

last: Lebrigand

address: 660 route des lucioles

institute: IPMC/CNRS

summary: To assess the impact of ASAH1 inhibition skin metastatic melanoma, we transfected  three different human skin metastatic melanoma cell lines (501Mel, WM3912 and WM8) with a siRNA designed against ASAH1 (50nM) or a siRNA control (50nM) for 48h.

overall_design: 501Mel, WM3912 and WM8 cells transfected with siRNA against ASAH1 (siASAH1) or siRNA control (siCtl) experiments were performed in a one color design, for a total of 6 samples.

first: J

last: Leclerc

first: N

last: Nottet

first: C

last: Bertolotto

first: R

last: Ballotti


title: Effects of Intrauterine Growth Restriction on Ribosomal Subunit mRNA and Protein Expression in the Frontal Cortex of Near-Term Fetal Baboons

city: San Antonio

first: Laura

last: Cox

state: Texas

department: Genetics

institute: Texas Biomedical Research Institute

summary: Decreased fetal nutrient delivery is a major cause of developmental neuropathology.  Although intrauterine growth restriction spares fetal brain weight, we hypothesized that frontal cortices of fetuses of mothers nutrient restricted during pregnancy, would have decreased ribosomal protein expression. This could potentially result in compromised function since these cellular subunits play a central role in protein synthesis and cellular energetics. Fetal baboons from mothers fed as ad lib controls (CTR) or globally nutrient restricted (MNR) by 30% from 30 - 165 days of gestation (term ~ 184 days in length) were studied.  At necropsy, the average body weight of CTR mothers had increased by 11.3% while that of MNR mothers had decreased by 5.5% from before pregnancy.  Body weights of MNR fetuses were 17% smaller than CTR fetal weights, but fetal brains were not different. As measured by gene array, 24 of 75 ribosomal protein mRNAs detected were decreased.  Protein expression of 7 of 8 ribosomal proteins, assessed by semi-quantitative immunohistochemistry, was significantly (p< 0.05) or marginally (p > 0.05 < 0.1) decreased. The brains of growth-restricted fetuses are often assumed to be normal because of brain growth sparing. However, the present findings regarding ribosomal protein expression, strongly suggest that nutrient restriction in pregnancy, regardless of cause, inhibits protein synthesis in the fetal brain. In addition, these effects may be exacerbated if continued postnatally with possible effects on important protein dependent processes such as long-term memory storage.

overall_design: Total brain RNA obtained from 165dGA control (n=6) and nutrient restricted (n=6) pregnancies.

first: Thomas

middle: J

last: McDonald

first: Cun

last: Li

first: Peter

last: Nathanielsz


title: Gene expression in brown adipose tissue of interleukin-18 knockout mice at 6 and 12 weeks of age

city: Suita

first: Daisuke

last: Okuzaki

state: Osaka

address: Yamadaoka 3-1

department: Immunology Frontier Research Center

institute: Osaka univ.

summary: Interleukin-18 knockout mice had metabolic syndromes after 24 weeks of age. We examined gene expression profiles in mice brown adipose tissue using genome-wide microarray technology, and compared gene expression profiles between wild-type and interleukin-18 knockout mice. To verify responsible molecules involved in metabolic syndromes such as obesity, we compared the gene expression levels at 6 and 12 weeks of age, and picked up them whose expression was more than 2-fold increase or less than 1/2-fold decrease.

overall_design: The mouse whole brown adipose tissues derived from wild type and interleukin-18 knockout mice at 6 and 12 weeks of age were examined. Each strain was run in triplicate.

first: Kyosuke

last: Yamanishi


title: AKT1E17K activates focal adhesion kinase and promotes melanoma brain metastasis

status: Public on Dec 01 2018

city: Salt Lake City

first: Sheri

last: Holmen

state: UT

address: 2000 Circle of Hope Dr.

department: Surgery

institute: University of Utah

summary:
Goal: Comparison of protein and phospho-protein levels in primary tumors based on activation of different AKT paralogs
Methods: RPPA performed at the MD Anderson RPPA Core Facility. Detailed procedures available in methods section.
Results: Focus of study compared protein and phospho-protein levels of BRAFV600E;Cdkn2a-/-;Pten-/- and  BRAFV600E;Cdkn2a-/-;Pten-/-;AKT1E17K cohorts. P-FAK and paxillin were upregulated in tumors that express AKT1E17K compared with controls
Conclusion: AKT1E17K has a critical role in upregulating P-FAK and paxillin

overall_design: Thirty primary tumor samples included in analyses: Six BRAFV600E;Cdkn2a-/-, Six BRAFV600E;Cdkn2a-/-;Pten-/-, Six BRAFV600E;Cdkn2a-/-;Pten-/-;AKT1E17K,  Six BRAFV600E;Cdkn2a-/-;Pten-/-;AKT2E17K,  Six BRAFV600E;Cdkn2a-/-;Pten-/-;AKT3E17K

last: Holmes

first: David

last: Kircher

first: Christopher

last: M. Stehn

first: Grant

middle: M

last: Fischer


title: CD19 Chimeric Antigen Receptor Engineered NK92 Natural Killer Cells: Novel “Off the Shelf” Immunotherapy in Non-Hodgkin Lymphoma II

city: Mountain View

first: Afshin

last: Beheshti

state: CA

address: Moffett Blvd

institute: NASA Ames Research Center

summary: NK-92 a continuously growing cell line bioengineered to express human anti-CD19 chimeric antigen receptor (CAR) CD19.TaNK recognizing CD19+ B cells represents as potential “off the shelf” therapy candidate for B cell malignancies. The goal of this study was to establish the mechanistic rationale for CD19.TaNK therapy in B-cell NHL (bNHL) and to determine the therapeutic potency in vitro against a host of bNHL cell lines, patient derived primary cell lines (including anti-CD20 antibody resistant cell lines), and in in vivo mouse models. We utilized bNHL cell lines SU-DHL10, SU-DHL4, SU-DHL2 (DLBCL), HF-1 (follicular) and Raji (Burkitt’s) and Rituximab- (RR) and obinutuzumab (OR)-resistant bNHL cell lines (SU-DHL2, SU-DHL4, SU-DHL10), and patient derived primary cells (EL-5 and KSC) were investigated the cytolytic activity of CD19.TaNK. We observed significantly increased CD19.TaNK mediated cytolytic activity at E:T ratios (1:1-10:1) via LDH release in all bNHL cell lines and CD20 resistant bHNL cells. Further, the dynamic efficacy of CD19.TaNK determined using droplet based single cell microfluidics analysis of cell interactions (1:1) between CD19.TaNK and anti-CD20 sensitive or resistant bNHL cell showed that vast majority of the cells were killed by single contact >80% (SU-DHL 4, SUD-HL 4 -OR), 40% (SU-DHL10-RR), >60% (SU-DHL10, SUD-HL-10-OR) and 40% (SU-DHL10-RR) within first 40 minutes, while the remainder were killed through events requiring multiple contacts. Thus, suggesting that CD19.TaNK indiscriminately kills both anti-CD20 sensitive and resistant cells. Global transcriptome analysis performed using flow sorted bNHL co-cultured with CD19.TaNK at 1:1 ratio for two hours, revealed conserved activation of IFNγ signaling, execution of apoptosis, ligand binding, immunoregulatory or chemokine signaling pathways in these bNHL cells. Using proximity extension assay based 92-plex cytokine panel we observed increased secretion of various cytokines, granzymes and decreased secretions of ADA, HO-1, CD5, CD28, CD70, CD244, IFN and TNF consistently with anti-CD20 sensitive and resistant cells. Altogether these results demonstrate that CD19.TaNK inflicts mechanistically conserved killing activity against different bNHL cell lines, including in anti-CD20 refractory bNHL. Finally, in SCID mice experiments we observed marked reduction in the volume of SU-DHL10 derived tumor xenografts with infusion of CD19.TaNK compared to control. Overall, we observed potent anti-lymphoma activity with CD19.TaNK involving biologically conserved mechanisms indicating that CD19.TaNK could be equally active under untreated or refractory bNHL in the clinical settings.

overall_design: For genome-wide expression profiling of SUDHL4, SUDHL4 rituximab resistant (RR), SUDHL4 obinutuzumab resistant (OR), SUDHL10, SUDHL10 rituximab resistant, SUDHL4 obinutuzumab resistant, Raji, EL-2, and EL-5 cells were co-cultured with CD19.TaNK cells, Human HT-12 BeadArray chips (Illumina, San Diego, CA) were used. RNA was isolated using RNeasy Minikit (Qiagen), following instructions recommended supplied by the manufacturer. Purity and the yield of isolated RNA was determined using Bioanalyzer. These experiments were performed in biological triplicates. All replicate samples were run individually. Total RNA of 500ng per sample was amplified using AmbionTotalPrep, and 1.5ug of the product was loaded onto the chips. Following hybridization at 55C, the chips were washed and then scanned using the Illumina iScan System. The data was checked with GenomeStudio (Illumina) for quality control. Data were corrected through COMBAT correction, quantile normalized, collapsed to genes from probes, then imported into MultiExperiment Viewer, MeV for analysis. Statistically significant genes were determined by applying a one-way ANOVA with an adjusted Bonferroni correction and false discovery rate (FDR) < 0.05 that resulted in a list of significant genes.

first: Ravi

last: Dashnamoorthy

first: Saheli

last: Sarkar

first: Sneha

last: Purvey

first: Frank

last: Passero

first: Laurent

last: Boissel

first: Tania

last: Konry

first: Andrew

last: Evens


title: Gene expression data of 135 patients presenting colorectal adenoma

city: Beerse

first: Joke

last: Reumers

address: Turnhoutseweg 32

department: DPDS

country: Belgium

institute: Janssen R&D

summary: Gene expression profiles of 135 patients presenting with colorectal adenomas during surgery or colonoscopy were obtained using Affymetrix U133+ arrays.

overall_design: Samples were obtained from Avaden Biosciences as FFPE blocks. Patients were selected from surgery and colonoscopy cases, excluding patients with hereditary cancer syndromes.

first: Stan

last: Gaj

first: Liesbeth

last: Van Wesenbeeck

first: Vinod

last: Krishna

first: Gerry

last: Chu

first: Ilse

last: Van den Wyngaert

first: Karin

last: Verstraeten

first: Gary

last: Borzillo

first: Karine

last: Smans

first: Pieter

last: Peeters

first: Janine

last: Arts

first: Kurtis

last: Bachman


title: Gene expression data of patients presenting with concurrent colorectal adenomas and colorectal tumors, including adjacent tissue to the tumor

summary: Gene expression profiles of 70 patients presenting with concurrent colorectal adenomas and colorectal tumors were obtained using Affymetrix U133+ arrays.

overall_design: Samples were obtained from Avaden Biosciences as FFPE blocks, from which sections were derived of the adenoma, tumor and tissue adjacent to the tumor. Patients were selected from surgery cases for where concurrent  adenoma and tumor were present, excluding patients with hereditary cancer syndromes.


title: A myogenic double reporter human pluripotent stem cell line allows prospective isolation of skeletal muscle progenitors

city: Houston

first: Annie

middle: W.

last: Shieh

address: 1825 Pressler St

department: Brown Foundation Institute Of Molecular Medicine

institute: University of Texas Health Science Center

summary: Myogenic differentiation of iPSCs has been done by gene–overexpression or directed differentiation. However, viral integration, long-term culture and the presence of unwanted cells are the main obstacles. By using CRISPR/Cas9n, a novel double reporter hESC line was generated for PAX7/MYF5, allowing prospective readout. This strategy allowed pathway screen to define efficient myogenic induction in hESC/iPSCs. Next, surface marker screen allowed identification of CD10 and CD24 for purification of myogenic progenitors. CD10 expression was also confirmed on human satellite cells and muscle progenitors. In vivo studies using transgene/reporter-free hESC/iPSCs further validated myogenic potential of the cells by dystrophin restoration and satellite cell engraftment in NSG-mdx4cv mice. In addition, side-by-side in vitro and in vivo comparison proved superior specificity of CD10/CD24 compared to recently reported markers (ERBB3/NGFR). This study provides new biological insights for myogenic differentiation using a new cell resource and identifies CD10 as a potential myogenic marker.

overall_design: hESCs were analyzed at 5 differentiation time-points (Day0, Day4, Day10-sorted for MYF5 EGFP positive or negative- and day20 myotubes after myogenic differentiation of MYF5 EGFP positive fraction). For each time-point, 3 independent biological replicates were harvested for further analysis. 1 x 106 cells were harvested / sorted at each time- point and RNA extracted using QIAGEN miRNeasy RNA isolation kit (217004, QIAGEN) according to manufacturer’s protocol. Each RNA sample was converted to cDNA using oligo-dT primers and was further converted into indexed sequencing libraries using Illumina kit. Indexed libraries were subsequently pooled together and then sequenced on an Illumina HiSeq 4000 for a 50 cycle single end run. To compare transcriptome profile of PAX7/MYF5 double reporter hESC derived myogenic cells to human skeletal myoblasts, we enlisted ENCODE polyA RNA-Seq data of the human skeletal muscle myoblasts from the Wold lab (GEO: GSM958744).

first: Sidney

last: Wang

first: Radbod

last: Darabi

first: Jianbo

last: Wu

first: Nadine

last: Matthias

first: Jonathan

last: Lo

first: Jose

last: Ortiz-Vitali


title: IFN-g producing Th1 cells induce different transcriptional profiles in microglia and astrocytes

city: Hannover

first: Chittappen Kandiyil

last: Prajeeth

address: Carl-Neuberg Str 1

department: Neurology

institute: Hannover Medical School

type:
Expression profiling by array
Third-party reanalysis

summary: Autoreactive T cells that infiltrate into the central nervous system (CNS) are believed to have a significant role in mediating the pathology of neurodegenerative diseases such as Alzheimer's disease, amyotrophic lateral sclerosis and multiple sclerosis. Their interaction with microglia and astrocytes in the CNS is crucial for the regulation of the neuroinflammatory process. Our previous work demonstrated that effectors secreted by Th1 and Th17 cells have different capacities to influence the phenotype and function of the glial cells.  We have shown that Th1 effectors altered the phenotype and function of both microglia and astrocytes whereas Th17 effectors induced direct effects only on astrocytes but not on microglia. Here we investigated if effector molecules associated with IFN-g producing Th1 cells induced different gene expression profiles in microglia and astrocytes. We performed a microarray analysis of RNA isolated from microglia and astrocytes treated with medium and Th1 culture supernatants and compared the gene expression data. By using the criteria of 2-fold change and a false discovery rate of 0.01 (corrected p-value < 0.01), we demonstrated that a total of 2106 and 1594 genes were differentially regulated microglia and astrocytes respectively in response to Th1-derived factors. We observed that Th1 associated effectors induce distinct transcriptional changes in microglia and astrocytes in addition to commonly regulated transcripts. These distinct transcriptional changes regulate distinct physiological functions and this knowledge can help in better understanding of T cell mediated neuropathologies.

overall_design:
microarray analysis of RNA isolated from astrocytes treated with medium and Th1 culture supernatants

Please note that in order to comparatively analyze this dataset with a previously generated, published microglia dataset [GSE45384], raw data from both studies were reprocessed and normalized together (as detailed in the sample data processing description) and the re-analyzed data is provided as a Series supplementary file:
GSM1103441-GSM1103452_re-analyzed_GSE45384_matrix.txt

first: Chittappen

first: Oliver

last: Dittrich-Breiholz

first: Steven

middle: R

last: Talbot

first: Jochen

last: Huehn

first: Martin

last: Stangel


title: Clinical treatment responsiveness in recurrent canine lymphoma correlates with Anaphase Promoting Complex activity

city: Saskatoon

first: Christopher

last: Eskiw

state: SK

address: 51 Campus Drive

department: Food and Bioproduct Science

institute: University of Saskatchewan

summary: The development of drug resistant cancer is a chronic threat to those undergoing cancer treatment. Why cells develop resistance to drugs has been studied extensively, with many molecular mechanisms driving the process now understood, yet it remains a chronic problem with few treatment options. In this study we treated companion canines presenting to the Western College of Veterinary Medicine in Saskatoon with drug resistant lymphoma with adjunct metformin along with their normal chemotherapy. We obtained repeated tumor samples from 4 canines undergoing this therapy and assessed RNA obtained from these samples by microarray. We identified a highly interconnected 201 gene set upregulated in the 4 dogs that was associated with tumor progression. This gene set was enriched in genes involved in mitotic progression and chromosome maintenance. We observed that mRNAs encoding substrates of the Anaphase Promoting Complex (APC) were integral to this gene set. Treatment with metformin lowered both protein and RNA levels of these substrates, while relapse resulted in elevated levels once again. The change in APC substrates clearly reflects disease progression, indicating that APC activity is critical for cellular homeostasis and loss of this activity can result in tumor progression.

overall_design: 15 samples isolated from canine tumors or control regions (skin biopsies); includes pre-treatment, remission and relapse of lymphoma

first: Troy

last: Harkness

first: Tera

last: Arnason

first: Anthony

last: Kusalik


title: identification of target genes regulated by cuc2 in a.thaliana shoot apical meristem.-Morphodynamics in Plants: from gene to shape.

city: Orsay

first: Stéphanie

last: Pateyron

address: Rue de Noetzlin _ Batiment 630

institute: IPS2_Institute of Plant Sciences Paris-Saclay

summary: au13-03_cuc2 - identification of target genes regulated by cuc2 in a.thaliana shoot apical meristem. - Identification of genes specifically targeted by the CUC2 transcription factor that defines the margins of the floral meristem of Arabidopsis thaliana. - identify genes specifically targeted by CUP-SHAPED COTYLEDON 2 (CUC2), a transcription factor required for embryonic shoot meristem formation and specification of the organ boundary in A.thaliana

overall_design: 3 dye-swap - genotype comparaison

first: My-Linh

last: Tran

first: Jan

last: Traas

first: Sandrine

last: Balzergue

first: Marie-Laure

last: Martin-Magniette


title: SigX ECF sigma factor deletion mutant expression profile in Pseudomonas aeruginosa H103 in LB medium

city: Evreux

first: Sylvie

last: Chevalier

address: 55, rue Saint Germain

department: Université de Rouen

institute: Normandie Université

summary: Analysis of a SigX knockout mutant of Pseudomonas aeruginosa H103 strain in LB.

overall_design: A deletion mutant of  sigX gene (PAOSX) has been studied at the phenotypic level and its expression profile was compared with parental strain Pseudomonas aeruginosa H103 in LB medium.  H103 and a sigX mutant were cultured until the milddle of the exponential growth phase. Three independant biological replicate were taken for the RNA extraction and hybridization on affymetrix array.

first: Maud

last: Fléchard

first: Rachel

last: Duchesne

first: Ali

last: Tahrioui

first: Emeline

last: Bouffartigues

first: Ségolène

last: Depayras

first: Julie

last: Hardouin

first: Damien

last: Tortuel

first: Cecil

middle: O

last: Azuama

first: Olivier

last: Maillot

first: Cécile

last: Duclairoir-Poc

first: Manuella

last: Catel-Ferreira

first: Gwendoline

last: Gicquel

first: Marc

last: Feuilloley

last: Lesouhaitier

first: Hermann

last: Heipieper

first: Groleau

last: Christine

first: Éric

last: Déziel

first: Pierre

last: Cornelis


title: Activation of nonsense-mediated mRNA decay protects against C9orf72 dipeptide-repeat neurotoxicity

city: shanghai

first: Wangchao

last: Xu

state: shanghai

address: 320 Yue Yang Road

institute: Institute of Neuroscience

summary: Amyotrophic lateral sclerosis (ALS) is a deleterious neurodegenerative disease without effective treatment options. Recent studies have indicated the involvement of the dysregulation of RNA metabolism in the pathogenesis of ALS. Among the various RNA regulatory machineries, nonsense-mediated mRNA decay (NMD) is a stress responsive cellular surveillance system that degrades selected mRNA substrates to prevent the translation of defective or harmful proteins. Whether this pathway is affected in neurodegenerative diseases is unclear. Here we report that the NMD pathway is inhibited in ALS patients with C9orf72 hexanucleotide repeat expansion (HRE), the most common cause of familial ALS. Bioinformatic analysis of multiple transcriptome profiles revealed significant overlap of upregulated genes in NMD-defective cells with those in the brain tissues, micro-dissected motor neurons, or induced pluripotent stem cell-derived motor neurons from ALS patients carrying C9orf72 HRE, suggesting the suppression of NMD pathway in these patients. In contrast, there are few overlapping upregulated genes in brain tissues from sporadic ALS patients with those in NMD-defective cells. Using Drosophila models expressing various C9orf72 HRE products, we have validated the suppression of the NMD pathway by C9orf72 HRE and identified arginine-rich dipeptide repeats (DPRs) generated from HRE as the main culprits of NMD inhibition. Furthermore, in human SH-SY5Y neuroblastoma cells and in mouse brains, expression of arginine-rich DPRs was sufficient to cause NMD inhibition. Remarkably, expression of UPF1, a core gene in the NMD pathway, efficiently blocked neurotoxicity caused by arginine-rich DPRs in both cellular and Drosophila models. Although not as effective as UPF1, expression of another NMD gene UPF2 also ameliorated the degenerative phenotypes in DPR-expressing flies, indicating neuroprotection by genetically reactivating the NMD pathway. Finally, after validating Tranilast as an NMD-activating drug, we demonstrated its therapeutic potential in cellular and Drosophila models of C9orf72 DPR neurotoxicity. Therefore, our study has revealed the suppression of NMD in C9orf72 ALS and has suggested that the restoration of the NMD pathway by Tranilast, an asthma drug with solid safety record, could be a promising therapeutic strategy for ALS.

overall_design: RNA sequencing of heads from 5-day-old female flies expressing PA36, PR36, (G4C2)36 or UPF1 RNAi.

first: Jin


title: CD19 Chimeric Antigen Receptor Engineered NK92 Natural Killer Cells: Novel “Off the Shelf” Immunotherapy in Non-Hodgkin Lymphoma I

first: Afshin

last: Beheshti

first: Ravi

last: Dashnamoorthy

first: Saheli

last: Sarkar

first: Sneha

last: Purvey

first: Frank

last: Passero

first: Laurent

last: Boissel

first: Tania

last: Konry

first: Andrew

last: Evens


title: A new model for long-range chromatin reorganisation linked to enhancer activation [ChIP-chip]

city: Edinburgh

first: Rob

last: Illingworth

state: Midlothian

address: Centre for Regenerative Medicine

department: Centre for regenerative Medicine

institute: The University of Edinburgh

type: Genome binding/occupancy profiling by genome tiling array

summary:
The most prominent model for long-range enhancer regulation involves direct enhancer-promoter interaction by looping out the intervening chromatin. Using a synthetic biology approach, we have determined that a chromatin unfolding between Shh and its enhancers is regulated specifically by the Shh-Brain-Enhancers and is mediated by the recruitment of Poly (ADP-Ribose) Polymerase 1. This ‘chromatin unfolding’ model represents a new mechanism of long-range enhancer-promoter communication in addition to the looping and tracking models.
ChIP-on-chip for H3K27me3 and H3K27ac on the Shh regulatory region on ESCs and transfected ESCs showed a gain of H3k27ac specifically on active enhancers and no loss of Polycomb marks upon Shh activation.

overall_design: Comparison of different Tale-Vp64 transfected ESCs. Tiling ChIP-chip for H3K27me3 and H3K27ac profiles across Shh and other candidate gene loci.

first: Nezha

last: Benabdallah

first: Iain

last: Williamson

first: Robert

first: Shelagh

last: Boyle

last: Therizols

first: Wendy

last: Bickmore


title: Molecular mechanisms and potential therapeutic drugs linking to cetuximab-resistance reactions in cancer cells

city: Chiba

first: Yuki

last: Sawai

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

department: Department of Oral Science

institute: Graduate School of Medicine, Chiba University

summary: To obtain differentially expressed genes associated with cetuximab resistance mechanism, we analyzed RNA samples using whole genome microarray expression profiling as a discovery platform to identify genes. Two kinds of RNA samples were extracted from SAS, Sa3, and HSC-3 cells: control cells and cetuximab-resistant cells.

overall_design: Cetuximab-resistant cells was established with three OSCC cells (SAS, Sa3, and HSC-3). The expression of cetuximab resistance mechanism gene was measured using control cells and cetuximab-resistant cells.

first: Katsuhiro

last: Uzawa


title: RNA-seq data of granulosa cells in chicken ovary

city: chengdu

first: qiang

middle: guo

last: zhu

state: sichuan

address: yihuanlu nanyiduan 24hao

institute: sichuan university

summary: Transcriptomics of granulosa cells from different developing stages (6mm, F5, F1) in chicken ovary

overall_design: three types of hen ovarian follicles (6mm, F5, F1) are linestones in follicle development, namely 6mm follicles prior to follcile selection, F5 follicles are early preovulatory follicles in fast growth, F1 follicles  prior to ovulation, late preovulatory follicles.

first: G

last: Zhu

first: J

last: Li


title: Mouse DC maturation by LPS

city: seoul

first: Seong Hwi

last: Hong

address: 120 Neungdong-ro

country: South Korea

institute: Konkuk University

summary: transcriptome during mouse DC maturation by LPS

overall_design: LPS treated on differentiated DC on day 6

first: Young

last: ParK

first: In

last: Jung

first: Jueng

last: You


title: Molecular charcterisation of Tangerine2 Mutant

city: Bangalore

first: Genotypic

last: technology

state: Karnataka

address: 259, Apoorva 4th cross,80 feet Road,RMV 2ND STAGE

country: India

institute: Genotypic Technology

summary: The tangerine2 mutant identified from Diepoxybutadiene (DEB) mutagenized population of Solanum lycopersicum and the biochemical studies revealed that mutant fruits accumulate prolycopene instead of lycopene in ripened fruits. We have developed whole genome microarray expression profiling as a discovery platform to identify differentially expressed genes in fruits tangerine2 mutant in comparison to Wild type. Tomato fruit tissue samples from different stages of fruit ripening like Mature green, Breaker, Turning and Ripening stages of tangerine2 mutant and wild type was used for microarray gene expression analysis. Carotenoid pathway analysis of both mutant and wild type reveals that the absence of expression of Carotenoid isomerase (CRTISO) gene in the tangerine2 mutant, the gene which is involved in the isomerisation of prolycopene to lycopene. Four genes (PSY, PDS, CRTISO, CYCB) of the carotenoid pathway was quantified in the same RNA samples by real-time PCR, confirming that the variation of the gene expression in Tangerine2 mutant.

overall_design: Organism : Solanum lycopersicum , Agilent Tomato Gene Expression  8x60k Array (AMADID: 065951) designed by Geotypic Technology Private limited

first: Osman

last: Basha

first: John

middle: E

last: Prasanth


title: Molecular characterization of unripening (ur) mutant

summary: Unripening mutant was identified from natural population of cv. Arka Vikas and the mutant was characterized with un ripened with light yellowish colour pericarp. Differential gene expression studies were carried out between unripening mutant and wild type using the whole genome microarray expression profiling as a discovery platform. Tomato fruit tissue samples from different stages of fruit ripening like Mature green, Breaker, Turning and Ripening stages of unripening mutant and wild type was used for microarray gene expression analysis. Carotenoid pathway analysis of both mutant and wild type reveals genes involved in the pathway altered in the unripening mutant. Four genes (PSY, PDS, CRTISO, CYCB) of the carotenoid pathway was quantified in the same RNA samples by real-time PCR, confirming that the variation of the gene expression in unripening mutant.

overall_design: wld type vs. mutant

first: P

last: Kumar


title: ColoCare Project: Gene expression analysis in colorectal cancer and adjacent mucosa tissues

city: Freiburg

first: Geoffroy

last: Andrieux

address: Breisacherstr 153

institute: University clinics Freiburg

summary: Within the ColoCare Project we obtained gene expression profiles from 77 tumor and 117 mucosa tissues using Illumina HumanHT12v4 gene chips. Including GSE101764, there are 77 tumor and 108 mucosa samples with matching DNA methylation profiles. The complex interplay between DNA methylation and gene expression was analysed by using both data sets.

overall_design: Colorectal cancer patients were recruited at the University Hospital of Heidelberg. Total RNA from 77 tumor and 117 mucosa samples were analyzed, including 68 tumor-mucosa pairs. There is matching DNA methylation data with the Accession number: GSE101764

first: Hauke

last: Busch

first: Melanie

last: Boerries


title: Transcriptome profile in Col and gvs1 during leaf senescence

city: Jeju-si

first: Jeongsik

last: Kim

state: Jeju

address: 102 Jejudaehakroe

department: Faculty of Science Education

institute: Jeju National University

summary:
Transcriptional profiling comparison between Col and gvs1-1 at DAE 14 and 28.
To understand the role of GVS1, a positive regulator of senescence, during senescence, we have employed transcriptional profiling of Col and gvs1-1 along aging (DAE 14 and 28). Agilent's Whole Arabidopsis Gene Expression Microarray (G2519F-021169, V4, 4x44K) was used.

overall_design: Transcription profile between Col and gvs1-1 at DAE14 and DAE 28 of the third and fourth leaves. 3 independent biological samples.

first: Jaeil

last: Lyu

first: Pyung Ok

last: Lim


title: Polycomb- and Methylation-Independent Roles of EZH2 as a Transcription Activator [microarray]

city: Atlanta

first: Jindan

last: Yu

state: GA

address: E330, 1760 Haygood Dr NE

department: Urology

country: USA

institute: Emory University

summary: EZH2 induces active transcription of the AR gene, thereby increasing AR level and promoting AR signaling. Importantly, EZH2-mediated activation of AR requires EZH2 protein occupancy at the AR gene promoter, but is independent of PRC2 as well as its histone methyltransferase activity

overall_design: LNCaP/C4-2B cells were treated with DMSO or EPZ6438 (1uM) for 3 days. LNCaP/C4-2B cells were transfected with sicontrol or siEZH2 (CDS) for 3 days

first: Jung