title: Comparison of the transcriptional profile of PD1-treated CD4+ T cells with a Treg cell phenotype and Tconv cells

status: Public on Dec 31 2018

city: Bonn

first: Joachim

last: Schultze

state: NRW

address: Carl-Troll-Strasse 31

department: Genomics and Immunoregulation

country: Germany

institute: LIMES (Life and Medical Sciences Center Genomics and Immunoregulation)

summary: CD4+ T cells were activated in the presence of PD1. The transcriptional profile was compared to untreated CD4+ T cells as well as to regulatory T cells.

overall_design: Freshly isolated CD4+CD25low/intCD127+ T cells were analysed as well as CD4+ T cells and CD4+CD25+ Treg cells treated as indicated.

first: J

last: Chemnitz

first: M

last: Beyer

first: S

last: Classen


title: The impact of TGFb as well as PGE2 treatment on the expression of regulatory T cell specific genes

summary: Regulatory T cells (Treg) are potent inhibitors of the activation of the immune system. TGFb and PGE2 have been shown to be involved in the induction of regulatory T cells. The transcriptional profile of CD4+ T cells treated with TGFb as well as PGE2 was compared to untreated CD4+CD25- T cells as well as to regulatory T cells in order to determine the relationship of these cells to regulatory T cells.

overall_design: Freshly isolated CD4+ T cell were activated with various conditions and the transcriptional profiles were compared to CD4+ T cells separated into CD25 negative and positive subpopulations.

first: A

last: Gaarz


title: A comparison of the transcriptional profiles of CD4+ T cells treated with either IL-10 or VEGF.

summary: VEGF and IL-10 have been shown to play an inhibitory role on CD4+ T cells. Here we investigate the transcriptional expression changes in CD4+ T cells in response to IL-10 and VEGF treatment. The influence of these substances was investigated either immediately after T cell isolation or after previous short-time cultures.

overall_design: Freshly isolated CD4+ T cells were treated either immediately after isolation or after 12 hrs of cell culture with the indicated conditions.


title: A genome-wide comparison of gene expression patterns in CD4+ T cells under different T cell activating treatments

summary: In the literature, several conditions are described that lead to T cell activation. Within this experiment we compared the influence of various T cell activating conditions on the gene expression pattern of CD4+ T cells. T cell stimulation via anti-CD3 was compared to anti-CD3/anti-CD28 as well as to anti-CD3 and IL-2 stimulation.

overall_design: Freshly isolated CD4+ T cells and CD4+CD25- T cells activated with various conditions


title: Transcriptional profiling of CTLA-4 as well as TGFb treated CD4+ T cells vs. a Treg cell phenotype and Tconv cells

summary:
Comparison of the transcriptional profile of CTLA-4 as well as TGFb treated CD4+ T cells with a Treg cell phenotype and Tconv cells.
Since CTLA-4 and TGFb have been described as regulatory T cell inducing factors, CD4+ T cells were activated in the presence of CTLA-4 as well as TGFb. The transcriptional profile of these cells was compared to untreated CD4+CD25- T cells as well as to regulatory T cells in order to determine the relationship of these treated cells to regulatory T cells.

overall_design: Freshly isolated CD4+ T cells, CD4+CD25- as well as CD4+CD25+ Treg cells were treated as indicated and afterwards analysed by perfoming genome-wide expression analysis.


title: Expression profile of Pseudomonas putida KT2440 growing in myristic acid

city: Sevilla

first: Lorena

middle: Jiménez

last: Díaz

state: Sevilla

address: Energia Solar s/n

department: Biotechnology

country: Spain

institute: Abengoa Research

type: Expression profiling by high throughput sequencing

summary: We report the application of a high-throughput technique, RNA-seq, to study the transcriptomic pattern of P. putida KT2440 cultures using myristic acid as the sole carbon source at the exponential phase of growth compared with cultures grown with glucose as the sole carbon source. Thus, we can explore  the expression of genes involved in fatty acid degradation.

overall_design: P. putida KT2440 mRNA profiles growing in myristic acid or glucose as sole carbon source

last: Jiménez-Díaz

first: Antonio

last: Caballero

first: Natalia

last: Pérez-Hernández

first: Ana

last: Segura


title: FOXP3-dependent repression of a chromatin remodellimg enzyme ensures regulatory T-cell commitment

summary: Regulatory T (Treg) cells are involved in immune homeostasis and prevention of autoimmunity. Treg cells are characterized by the expression of the transcription factor FOXP3. Mutations in FOXP3 cause severe autoimmunity in mice and humans. However, the FOXP3-dependent molecular mechanisms leading to this severe phenotype are not well understood. Here we introduce a genome-wide transcription study of CD4+ T cells under different treatments in comparison to regulatory T cells. This study revealed a specific downregulation of SATB1 in Treg cells.

overall_design: Freshly isolated CD4+CD25intCD127+ T cells were analysed as well as CD4+ T cells and CD4+CD25+ Treg cells treated as indicated.


title: Activation dependent gene expression in Treg cells compared to various inhibitory factors

summary: Regulatory T (Treg) cells are involved in self tolerance and suppression of immunity to pathogens or tumours. FOXP3 is essential for Treg cell development and function. However, the FOXP3-dependent molecular mechanisms are not well understood. Here we compare the expression levels in CD4+ as well as Treg cells in reponse to different treatments in order to evaluate the Treg cell specific gene expression profile.


title: Genome-wide transcript profiling of human prostate stromal cells in response to genotoxic treatment and SASP inhibitors

status: Public on Dec 27 2018

city: Shanghai

first: Yu

last: Sun

address: 320 Yueyang Rd, Life Sciences Building A #1508

department: Shanghai Institute of Nutrition and Health

country: China

institute: Chinese Academy of Sciences

summary: Cancer develops in a complex environment that encompasses a wide spectrum of benign cell types, while the local microenvironment reduces the efficacy of multiple forms of cancer therapies. The DNA damage secretory program (DDSP) provoked by the side effects of genotoxic therapeutics results in cellular senescence and the senescence-associated secretory phenotype (SASP), the side effects of the latter frequently fueling advanced pathologies particularly therapeutic resistance. However, candidate approaches to prevent or circumvent the SASP development remains limited. We treated PSC27, a primary normal human prostate stromal cell line, with the genoxotic agents hereby represented by bleomycin, to investigate the relevant mechanisms. In order to control the SASP development, a group of potential SASP inhibitors were applied including p38MAPK, mTOR and TAK1 suppressors. The purpose was to compare the efficacy and effectiveness of these chemicals in combinatin with typical anticancer drugs in minimizing the secretory phenotype upon DNA damage that functionally remodels human stromal cells.

overall_design: ArrayStar human LncRNA Microarray v3.0 (8 x 60K, ArrayStar, Rockville, MD) was used to profile the whole genome transcripts of PSC27 cells treated with several forms of cancer agents to induce cell damage and/or control the ensuing SASP in vitro. Total RNA was isolated and amplified prior to hybridization in a one-color experiment. There were totally 5 groups of samples analyzed, each composed of 3 biological replicates, including controls and experimental groups.

first: Sun

last: Yu

first: Zhang

last: Boyi


title: Signature of circular RNAs in peripheral blood mononuclear cells (PBMCs) from patients with active tuberculosis

status: Public on Dec 29 2018

city: weifang

first: yurong

last: fu

address: No.7166, Baotong Xi (Western) Street, Weicheng District, Department of Laboratory Medicine, Shandong Provincial Key Laboratory of Clinical Laboratory Diagnostics, Weifang Medical University

institute: weifang medical universtiy

summary: The knowledge of circRNAs in tuberculosis (TB) remains limited. Aim of the present study was to characterize the expression profiles and potential function of circRNAs in human peripheral blood mononuclear cells (PBMCs) from patients with active TB.

overall_design: Sixty-one participants were recruited consecutively for this study: active TB patients (PTC group, n=31) and 30 healthy controls (PCR group, n=30). All patients were from Weifang Chest Hospital in Shandong Province, China. In order to have a relatively homogenous active TB patient population, only newly diagnosed active TB individuals with sputum smear or culture positive and without obvious lung cavities based on chest X-rays were included in the current study. Patients were excluded if they received any type of treatment or with other diseases. Age- and gender-matched healthy individuals who received regular health checkup at Affiliated Hospital of Weifang Medical University were enrolled as control subjects. Healthy controls with recent close contact of TB patient or history of TB were excluded from this study. Three PBMC specimens from each group (male/female=2/1; PTC group including PTC1, PTC2 and PTC3;PCR group including PCR1,PCR2 and PCR3) were randomly choosed and then used for microarray hybridization, and all of the PBMC samples were applied for subsequent RT-qPCR confirmation.

first: Yurong

last: Fu

first: Zhengjun

last: Yi

first: Jindong

last: Wang

first: Jinjuan

last: Qiao


title: Membrane protein overproduction stress in Bacillus subtilis

status: Public on Dec 30 2018

city: Coventry

first: Emma

middle: L

last: Denham

address: Gibbet Hill Road

department: Warwick Medical School

country: United Kingdom

institute: University of Warwick

type: Expression profiling by genome tiling array

summary: Comparison of the transcriptome of Bacillus subtilis under going membrane protein overproduction in the wild type, sigW and cssRS deletion strains. We demonstrate that the dynamics of the stress systems involved in membrane overproduction are far more complicated than was first hypothesised and that many more systems than SigW and CssRS are involved in membrane protein overexpression stress. Interestingly the cssRS genes are repressed in the sigW deletion strain.

sample_organism: Bacillus subtilis subsp. subtilis str. 168

overall_design:
RNA samples prepared from B. subtilis 168 amyE::spaRK pNZ8910 (empty plasmid), 168 amyE::spaRK pNS8910::B.plsY and mutants sigW amyE::spaRK pNZ8910::B.plsY and cssRS amyE spaRK pNZ8910::B.plsY were grown in Luria Bertani broth to O.D 600nm 1.0 before being induced with 1% subtilin and grown for a futher 2 hours were reverse transcribed, labeled and hybridized to tiling arrays.
All hybridizations were performed in triplicate using RNA isolated from independent cultures.

first: Jessica

last: Zweers

first: Pierre

last: Nicholas

first: Jan

last: Maarten van Dijl


title: High-throughput RNA sequencing of the goat peri-implantation endometrial epithelium

city: Harbin

first: hao nan

last: YU

state: Heilongjiang

address: Xiangfang District Wood Street No. 59

department: Life Science and Biotechnology Research Center

institute: Northeast Agricultural University

summary: RNA-sequencing and functional annotation revealed differentially expressed genes, pathways, and processes in the goat peri-implantation period, shedding new light on the early reproductive mechanisms in ruminants.

overall_design: Uterus mRNA profiles of 6-day old ,16-day old,19-day old generated by deep sequencing, in triplicate, using Life Technologies Ion Proton Analyzer.

first: Yun

last: Zhang

first: Yuanyuan

last: Xing

first: Bingnan

last: Li

first: Huili

last: Tong

first: Hua

last: Ni


title: RPPA profiling of ES8 Ewing sarcoma xenografts after Endoglin-targeting antibody-drug conjugate treatments

city: Houston

first: Joseph

middle: A.

last: Ludwig

state: Texas

department: Sarcoma Medical Oncology

country: USA

institute: UT-MD-Anderson Cancer Center

summary: Endoglin (EDG) is a cell surface protein with an important role in the establishment of neo-angiogenesis and vasculogenic mimicry. EDG is part of the transforming growth factor-β (TGF-β) family, acting as an important co-receptor. EDG is shed from the cell surface into the extracellular compartment by matrix metalloproteinase 14 (MMP14), in its soluble form (sEDG). Both transmembrane and soluble forms of EDG exert important signaling functions in the development of new blood vessels and tumour progression. To better understand the role of EDG in Ewing sarcoma (ES), a deadly neoplasm of late childhood and adolescence, we test the efficacy of OMTX703, an endoglin-targeting antibody-drug conjugate in ES8 xenograft. Having determined an optimal dose for OMTX703, an additional experiment was conducted to assess the mechanism(s) of OMTX703 action and its potential mechanism(s) of resistance following a 2-week exposure to OMTX703 at 0, 10, 30, and 60 mg/kg; 246 proteins were assessed by reverse-phase protein array (RPPA). Analysis of variance (ANOVA), Pearson’s correlation as distance metric and Ward’s linkage as the clustering method using a false discovery rate (FDR) of 0.01, identified 60 proteins that discriminated between treatment groups (Matrix#1-Normalized Values). To investigate the proteomic changes associated with the heightened clinical activity of the 60 mg/kg dose, a secondary analysis was performed, which grouped the 10 mg/kg OMTX703 samples and the 10 mg/kg OMTX003 ones with the placebo-treated samples (Matrix#2-Normalized Values). Using a FDR of 0.0001, an absolute log2 fold change of 1.5, Pearson’s correlation as distance metric and Ward’s linkage as the clustering method, 22 proteins were discriminately identified between the 3 treatment groups (Matrix#2-Normalized Values). Notably, a protein regulator of altered metabolism (RPS6) was exclusively upregulated following OMTX703 (60mg/kg), and a second metabolism biomarker (LDHA) was down-expressed in the 30 and 60 mg/kg-treated groups. Conversely, BRD4 was one of about a dozen proteins that were preferentially down-regulated in samples treated only by 60 mg/kg.

overall_design: An RPPA analysis of ES8 xenografts treated with OMTX003 (n=8, a nacked mAb anti endoglin at 10 mg/kg), OMTX703 (an endoglin-targeting antibody-drug conjugate with cytolisin at 10, 30 and 60 mg/kg (n=8 each)) or control vehicle (n=7) were performed simultaneously using the same array. Lysates were processed, spotted onto nitrocellulose-coated FAST slides, probed with 300 validated primary antibodies, and detected using earlier methods. MicroVigene software program (VigeneTech) was used for automated spot identification, background correction, and individual spot-intensity determination. Expression data was normalized for possible unequal protein loading, taking into account the signal intensity for each sample for all antibodies tested. Raw log2 intensity values were normalized for global protein expression by median centering across 246 antibodies tested. Principal component analysis was used to check for a batch effect and feature-by-feature two-sample t-tests were used to assess differences between treatment and control groups. We also used feature-by-feature one-way analysis of variance (ANOVA) followed by the Tukey test to perform pair comparisons for all groups. Beta-uniform mixture models were used to fit the resulting p value distributions to adjust for multiple comparisons. The cutoff p values and number of significant proteins were computed for several different false discovery rates (FDRs).

first: Salah-Eddine

last: Lamhamedi-Cherradi

first: Pilar

last: Puerto-Camacho

first: Ana

middle: T

last: Amaral

first: Branko

last: Cuglievan

first: Brian

middle: A

last: Menegaz

first: Myriam

last: Fabre

first: Enrique

last: de Álava


title: RNA-seq sequencing of the transgenic plants seeds and leaves

city: Taian

last: Liu

state: Shandong Province

address: Daizong Street 61

department: College of Life Science

institute: Shandong Agricultural University

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

overall_design: Refer to individual Series


title: Site-specific microarray evaluation of spontaneous dermatitis in flaky tail mice I

status: Public on Dec 28 2018

city: Yufu-shi

first: Takashi

last: Sakai

state: Oita

address: 1-1 Idaigaoka, Hasama-machi,

department: Faculty of Medicine

country: Japan

institute: Oita University

summary: Flaky tail mice (FTM) with gene mutations to FLG and TMEM79 are known to spontaneously develop atopic dermatitis (AD)-like dermatitis with age. Interestingly, we have already reported that the spontaneous development of dermatitis exhibits site-specificity, i. e. , the face and neck develop spontaneous dermatitis, while the dorsal flank shows normal skin in old FTM. In fact, transepidermal water loss and stratum corneum (SC) pH increased, SC hydration decreased, and epidermis thickened in the neck, but not in the dorsal flank. The detailed pathogenic mechanisms of such site-specific emergence of dermatitis in AD remain unclear. To clarify the pathogenesis of site-specificity, we analyzed skin of the neck and flank in old FTM using a microarray.

overall_design: The gene expressions of neck compared to that of flank in FTM were analyzed.

first: Chinatsu

last: Aoki

first: Yasuko

last: Mori

first: Haruna

last: Matsuda-Hirose

first: Yutaka

last: Hatano


title: Whole genome expression in peripheral whole blood of chronic kidney disease patients having uncertain etiology (CKDu) compared to healthy controls

city: Kandy

first: Dhammika

last: Magana-Arachchi

state: Central

address: Hantana Road

department: Cell Biology

country: Sri Lanka

institute: National Institute of Fundamental Studies

summary: Chronic kidney disease of uncertain etiology (CKDu) is an increasing problem in Sri Lanka especially among the farming community. The etiologies although uncertain, have been associated with occupational and environmental factors. The expression pattern of genes in blood of these CKDu patients in an endemic region of Sri Lanka was analyzed compared to healthy individuals from a non-endemic region to see any expression changes that could be associated to environmental factors. Pattern of expression changes could lead to either strengthen or weaken current hypotheses for the causes.

overall_design: RNA extracted from blood of CKDu patients from a CKDu-endemic area were pooled stage-wise. Pooled RNA extracted from blood of healthy individuals of an area not endemic to CKDu were used as controls. Three technical replicates were performed for each of the pooled samples.

first: Saravanabavan

last: Sayanthooran

middle: N

first: Lishanthe

last: Gunerathne


title: MicroRNA-8073: Tumor suppressor and potential therapeutic treatment [mRNA]

city: Kamakura

first: Atsuko

last: Mizoguchi

state: Kanagawa

department: New Frontiers Research Laboratories

institute: Toray Industries, Inc.

summary: The introduction of miR-8073 into tumors could inhibit tumor growth, indicating its great potential as a therapeutic target for cancer.

overall_design: The mRNA expression of colorectal cancer cells transfected with either the miR-8073 mimic, microRNA-negative control sequence, or a blank were individually assayed.

first: Aiko

last: Takayama

first: Taiga

last: Arai

first: Junpei

last: Kawauchi

first: Hiroko

last: Sudo


title: Targets of miR-212/132 in doxorubicin-induced cardiotoxicity

city: Hannnover

first: Shashi

middle: Kumar

last: Gupta

address: Carl-Neuberg Strasse 1

department: IMTTS

institute: Hannover Medical School

summary: We overexpressed miR-212/132 by AAV9 in mouse model of doxorubicin-induced cardiotoxicity and wanted to identify myocardial targets of miR-212/132 in this model.

overall_design: AAV9-Control or AAV9-miR-212/132 was injected to mice by intravenous injection. Next day doxorubicin was injected at dose of 5mg/kg via ip route. Doxorubicin was further given at same dose once every week for four more consecutive weeks. Mice were sacrificed one week after the last doxorubicin injection. Heart was explanted and RNA isolation was done.

middle: K

first: Thomas

last: Thum


title: RNA-seq data of nox1 gene when T. guizhouense vs F. oxysporum

city: Nanjing

first: Youzhi

last: Miao

address: WeiGang NO.1

institute: Nanjing Agricultural University

summary: nox1 gene has effect on the production of H2O2 of T. guizhouense NJAU4742. In this experiment, WT, knockout mutant and overexpression mutant of nox1 gene for NJAU4742 were used to do confrantation with F. oxysporum FOC4 strain, and then the mycelum from NJAU4742 and FOC4 (before contact and after contact) were collected and used to detect the gene expression patterns in this progress by RNA-seq.

sample_organism:
Fusarium oxysporum
Trichoderma guizhouense

overall_design: confrantation experiment was based on GSM medium plate, then the mycelum before contact or after contact were scraped from the plates and used for RNA-seq

first: Jian

last: Zhang


title: RNA sequencing (RNA-seq) for identifing differentially expressed transcription factor genes during early plant growth

city: Shijiazhuang

first: Yanmin

last: Zou

state: Hebei

address: 286 Huaizhong Road

department: Center for Agricultural Resources Research

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

summary: The purpose of this study is to identify differentially expressed transcription factor genes during early plant growth. A total amount of 3 µg RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext® Ultra™ RNA Library Prep Kit for Illumina® (NEB, USA) following manufacturer’s recommendations and index codes were added to attribute sequences to each sample. We used an optimized data analysis workflow, and mapped about 45 million sequence clean reads per sample to the Arabidopsis genome and identified 33,685 transcripts in 2 and 6 dpg (day post germination) old wild type plant (Col-0). Among them, there are 9321 genes differentially expresses from 2- and 6-d-old plants, and 479 differentially expresses transcription factor (TF) genes. Of these genes, 344 TF genes up regulated and 135 down regulated in 6-d-old plants compared with 2-d-old plants, with a fold change ≥2, ≤0.6 and p value <0.05. The P values were adjusted using the Benjamini & Hochberg method. Corrected P-value of 0.005 and log2(Fold change) of 1 were set as the threshold for significantly differential expression. This study will facilitate analysis related with developmental study in early plant growth stage.

overall_design: RNA isolated from seedlings of 2- and 6-day old wild type arabidopsis plants(Col-0),and with 2 repeats of each sample

first: Dongping

last: Lu


title: A methylated-DNA-binding complex required for plant development mediates transcriptional activation of promoter methylated genes [Bisulfite-seq]

city: Beijing

first: xinjian

last: He

address: No. 7, zhongguancun life science park road, changping district

institute: National Institute of Biological Sciences

type: Methylation profiling by high throughput sequencing

summary: We found SUVH-SDJ complex occupies promoter methylated genes and promotes the expression of these genes.

overall_design: Examination of the DNA methylation level in Arabidopsis

first: Qiang-Qiang

last: Zhao

first: Xin-Jian


title: mRNAs and lncRNAs expression data of chondrogenic differentiated and undifferentiated murine chondrogenic cell line ATDC5 cells

city: Kunming

first: Wei

last: Wang

state: Yunnan

address: NO.1088, Haiyuan Middle Road,

department: Orthodontics

institute: Kunming Medical University

type:
Expression profiling by array
Non-coding RNA profiling by array

summary: Chondrogenic differentiation is a coordinated biological process regulated by various cell signalings at both transcriptional and post-transcriptional levels. In this study, microarray was performed to detect the expression profiles of lncRNAs and mRNAs during chondrogenic differentiation of murine chondrogenic cell line ATDC5.

overall_design: ATDC5 cells were treated by 1% ITS (0μg/ml recombinant human insulin, 5.5μg/ml human transferrin and 5ng/ml sodium selenite) for chondrogenic differentiation induction. After 14 days of chondrogenic induction, three pairs of differentiated ATDC5 cell samples (d-1, d-2, d-3) and undifferentiated ATDC5 cell samples (u-1, u-1, u-3) were harvested for RNA extraction and hybridization on Affymetrix microarrays.

first: Wang

last: Wei


title: RNA-seq sequencing of the transgenic plants seeds

last: Liu

summary: To analyze influence of ZmDWF4 on seed development, we we chose 10DAP and 15DAP from the transgenic line L100 seed to RNA-seq sequence. Total RNA was extracted from the seeds (10 days after pollination, 10DAP, 15 days after of pollination,15DAP) of transgenic line L100 and wild type Q319. cDNA library was builded in the BIOMARKER, original reads were sequenced based on Illumina HiSeq2000, and through rRNA, low quality fragment DNA of filtering, ultimately, we obtained 99.30Gb high quality clean reads. Compared with reference gene sequence(AGPv3), according to genes function annotation, we found 463, 675 different expression genes, respectively.We classified the different expression genes according to Cellular Component, Molecular Function and Biological Process. It showed that BRs could affect many genes expression involved in different biological process in the seed development.

overall_design: Examination of the 10DAP and 15DAP seeds from transgenic line L100 and wild type Q319

first: Zhang

last: Xiansheng

first: Zhao

last: Xiangyu

first: Liu


title: ACTH-treated rats: a model to study IGFR-PI3K regulon

city: Sydney

first: Ruby

middle: CY

last: Lin

state: NSW

address: 176 Hawkesbury Road, Westmead

country: Australia

institute: The Westmead Institute for Medical Research

summary:
An increase in prevalence of metabolism-associated disorders worldwide poses an enormous financial burden on our current medical systems globally. This cluster of disorders includes obesity, insulin resistance, hypertension and coronary artery disease, collectively known as the metabolic syndrome disorders. The underlying pathogenesis is often attributed to interactions between genetic and environmental factors. Reliable biomarkers for early detection of these complex disorders have remained elusive. Genome-wide expression profiling is presented here in an attempt to identify high level interactions between genes and regulatory pathways. An unique 10K rat spotted oligonucleotide-array was used to identify transcriptome profiles of ACTH-treated compared with saline-treated Sprague-Dawley rats. This ACTH rodent model has been shown to exhibit traits and phenotypic manifestations of these disorders similar to those observed in humans. Heart and kidney profiles were analysed due to their high susceptibility to changes in homeostasis leading to metabolism-associated disorders. Quantitative RT-PCR was used to validate the microarray data. We have identified specific differential gene expression signatures as a result of ACTH administration. Gene annotation analyses have mapped those genes to a variety of cellular functions including signal transduction, carbohydrate/lipid metabolism, and cell organization and biogenesis. Interestingly, the majority of novel genes identified was mapped onto pathways involved in the signaling networks of insulin resistance and exerts an effect on regulation of intermediary metabolism and cell organization. The significance of this work is two fold; firstly, use of transcriptome based profiling at genomic level is feasible in identifying genetic signatures in these disorders, as is observed in oncology research and secondly, identification of novel candidate genes and networks associated with these disorders elucidate regulatory pathways that have potential to be developed further in clinical settings.
Keywords: disease state comparison

overall_design: Gene expression of ACTH-treated Sprague-Dawley rats (n=10) was compared to saline-treated SD rats (n=9, 1 died of complications). 4 replicates for heart and 6 replicates for kidney. For heart, randomly pooled (rat #1,3,5,7 etc) ACTH-treated samples (n=5) were hybridised to pooled saline-treated samples (n=9); and vice versa for kidney. This was to investigate biological differences in gene expression for an ACTH effect on the overall rat genome. Control arrays to look for within group differences were conducted prior to this (data not shown).

first: RubyCY

first: Yi

first: JackieKY

last: Lau

first: Mark

last: Cowley

first: Grace

last: Chong

first: Judith

last: Whitworth

first: Ian

middle: W

last: Dawes


title: Identification of primate renal salt-responsive gene networks that differ by blood pressure phenotype

city: San Antonio

first: Laura

last: Cox

department: Genetics

institute: Texas Biomedical Research Institute

summary: Sodium-lithium countertransport activity (SLC) is an intermediate phenotype for salt sensitive hypertension; elevated SLC corresponds to increased risk of hypertension. Genetic epidemiology studies indicate that SLC is heritable in humans and nonhuman primates; however, little is known about genetic determinants explaining variation in SLC. In this study we identified dietary salt-responsive gene networks in baboon kidneys and salt-responsive networks that differ between baboons with normal and high blood pressure phenotypes.

overall_design: Methods: Baboons with normal SLC (NSLC) or high SLC (HSLC) were subjected to a low sodium (LS) diet and a high sodium (HS) diet for 6 weeks each, kidney biopsies were collected after each diet and whole genome expression profile data were subjected to pathway and network analysis.

first: Robert

middle: E

last: Shade

first: Joseph

middle: R

last: Haywood

first: David

last: Rainwater

first: Jeremy

middle: P

last: Glenn

first: Kimberly

last: Spradling-Reeves


title: microRNA profiles of hADSC during replicative senescence

status: Public on Dec 26 2018

city: Madrid

first: Fatima

last: Sanchez-Cabo

address: Melchor Fernandez Almagro

institute: CNIC

summary: Microarray analysis of miRNAs from hADSC short passage cell vs long passage

overall_design: To determine the changes on miRNA repertoires in hADSC upon replicative cell senescence.

first: Silvia

last: García-López

first: Carmen

last: Albo

first: Rocio

middle: G

last: Urdinguio

first: Susana

last: Cañón

first: Fátima

last: Sánchez

first: Alberto

last: Martínez-Serrano

first: Mario

middle: F

last: Fraga

first: Antonio

last: Bernad


title: STAT3 secretion defect results in development abnormally

city: HangZhou City

first: Li

last: Xu

state: ZheJiang Province

address: BinWen Street  358#

institute: ZJTCMU

summary: Total RNA from embryos (12 days) of STAT3mut/mut, STAT3mut/wt and STAT3wt/wt mice which come from the same womb were extracted using TRIzol reagent (Invitrogen) following the manufacturer’s protocols.  RNA quantity, quality and integrity were analyzed with NanoDrop ND-1000 and standard denaturing agarose gel electrophoresis.  Sample labeling and array hybridization were performed according to the Agilent One-Color Microarray-Based Gene Expression Analysis protocol of Agilent Technology. The Whole Mouse Genome Oligo Microarray (Agilent 4*44k) represents all known genes and transcripts in the mouse genome (Kyoto Encyclopedia of Genes and Genomes, KEGG).  All the microarray experiments were performed by Kangchen Biotechnology Limited (Shanghai, China).

overall_design: Gene expression in embryos fromSTAT3-K177K180R mutant mice (wild type, heterozygous, and homozygous) were used for gene expression. Two independent experiments were performed at each group.


title: Gene Expressoin Profile in the Hypothalamus and Liver of Male Bgn_KO, FMOD_KO and WT Mice at 13 Weeks Old, With and Without DHA (omega-3) Treatment

city: Los Angeles

first: Xia

last: Yang

state: CA

address: 610 Charles E. Young Dr. East

institute: UCLA


title: RNA-seq sequencing of the transgenic plants leaves at the six-leaf stage

last: Liu

summary: To know BRs was how to cause transgenic line L100 leaves changed, we took the sixth leaves of transgenic line L100 to RNA-seq sequence. Total RNA was extracted from the sixth leaves of six-leaf stage of transgenic line L100 and wild type Q319. cDNA library was builded in the BIOMARKER, 100.20M original reads were sequenced based on Illumina HiSeq2000, and through rRNA, low quality fragment DNA of filtering, ultimately, we obtained 69.01M high quality clean reads. Compared with reference gene sequence(AGPv3), according to genes function annotation, we found 201 different expression genes. We classified the different expression genes according to Cellular Component, Molecular Function and Biological Process. It showed that BRs could affect many genes expression involved in different biological process.

overall_design: Examination of the sixth leaves transgenic line L100 and wild type Q319

first: Zhang

last: Xiansheng

first: Zhao

last: Xiangyu

first: Liu


title: RAW246.1 cells activation by internalized synthetic miR-122

first: Yanbo

last: Wang

address: 163 Xianlin Road

institute: Nanjing University

summary: Hepatic injury is often accompanied by pulmonary inflammation and tissue damage, but the underneath mechanism is not fully elucidated. Here we identify hepatic miR-122 as a culprit of pulmonary inflammation induced by various liver injuries. Analyses of acute and chronic liver injury mouse models confirm that liver dysfunction can cause pulmonary inflammation and tissue damage. Injured livers release large amounts of miR-122 in a microvesicle-independent manner into the circulation compared to normal livers. Circulating miR-122 is then preferentially transported to mouse lungs and taken up by alveolar macrophages, in which it binds toll-like receptor 7 (TLR7) and activates inflammatory responses. Depleting plasma miR-122 largely abolishes liver injury-induced pulmonary inflammation and tissue damage. Furthermore, alveolar macrophage activation by miR-122 is blocked by mutating the TLR7-binding UG-rich sequence on miR-122 or knocking out macrophage TLR7. Our findings reveal a novel causative role of hepatic miR-122 in liver injury-induced pulmonary dysfunction.

overall_design: To explore the molecular basis underlying the effect of hepatic miR-122 on alveolar macrophage inflammatory activation, we performed transcription profiling in macrophages treated with or without miR-122.

first: Ke

last: Zen


title: Genome-wide transcriptional and functional analysis of human T lymphocytes treated with benzo[a]pyrene

city: Rennes

first: Frédéric

last: Chalmel

state: France

address: 9 avenue du Pr. Léon Bernard

department: Physiology and physiopathology of the urogenital tract

country: France

institute: Inserm U1085-Irset

summary: Polycyclic aromatic hydrocarbons (PAHs) such as benzo[a]pyrene (B[a]P), are widely distributed carcinogenic and immunotoxic environmental contaminants, known to affect T lymphocytes. Despite extensive studies conducted, the molecular targets and pathways involved in their immunotoxic effects in human T lymphocytes remain unknown. Here, we analyzed the gene expression profile of primary human T lymphocytes treated with the prototypical PAH, B[a]P using a microarray-based transcriptome analysis. After a 48-h exposure to B[a]P, we identified 158 genes differentially expressed in T lymphocytes including not only genes well-known to be affected by PAHs such as the cytochromes P450 (CYP) 1A1 and 1B1, and the proto-oncogene c-KIT but also other ones not previously shown to be targeted by B[a]P such as genes encoding the gap junction beta-2 (GJB2) and beta-6 (GJB6) proteins. Functional enrichment analysis revealed that those candidates were significantly associated with the aryl hydrocarbon (AhR) and interferon (IFN) signalling pathways; it also revealed a clear alteration in essential biological functions, mainly those related to T lymphocyte recruitment. These data were confirmed by RT-qPCR assays for some selected genes such as the chemokine (C-C motif) ligand CCL3, and the cell adhesion protein like selectin L (SELL). Using functional tests in transwell migration experiments, B[a]P was shown to significantly decrease the chemokine (C-X-C motif) ligand 12 (CXCL12)-induced chemotaxis and transendothelial migration of T lymphocytes. Overall, the present study opens the way to unsuspected responsive pathway of interest, i.e., T lymphocyte migration, providing a broader understanding of the molecular basis of the immunotoxicity of PAHs.

overall_design: Independent T lymphocyte cultures isolated from 16 blood donors, each available in CTR (dimethylsulfoxide) and B[a]P-treated conditions were performed. Equal amounts of RNAs were pooled from these cultures to constitute four equimolar pools with four different blood donors per pool. Each pool was hybridized to Human Clariom™ S GeneChip.

first: Marie

last: Liamin

first: Hélène

last: Le Mentec

first: Bertrand

last: Evrard

first: Laurence

last: Huc

first: Elisa

last: Boutet-Robinet

first: Eric

last: Le Ferrec

first: Lydie

last: Sparfel


title: Site-1 protease function is essential for the generation of antibody secreting cells and reprogramming for secretory activity

city: York

first: Matthew

middle: Anthony

last: Care

state: North Yorkshire

address: Wentworth Way

department: Department of Biology

institute: The University of York

summary: The unfolded protein response (UPR) and activation of XBP1 is necessary for high secretory efficiency and functional differentiation of antibody secreting cells (ASCs). The UPR additionally includes a branch in which membrane-bound transcription factors, exemplified by ATF6, undergo intramembrane-proteolysis by the sequential action of site-1 (MBTPS1/S1P) and site-2 proteases (MBTPS2/S2P) and release of the cytoplasmic domain as an active transcription factor. Such regulation is shared with a family of CREB3-related transcription factors and sterol regulatory element-binding proteins (SREBPs). Of these, we identify that the CREB3 family member CREB3L2 is strongly induced and activated during the transition from B-cell to plasma cell state. Inhibition of site-1 protease leads to a profound reduction in plasmablast number linked to induction of autophagy. Plasmablasts generated in the presence of site-1 protease inhibitor segregated into CD38high and CD38low populations, the latter characterized by a marked reduction in the capacity to secrete IgG. Site-1 protease inhibition is accompanied by a distinctive change in gene expression associated with amino acid synthesis, steroid and fatty acid synthesis pathways. These result demonstrate that transcriptional control of metabolic programs necessary for secretory activity can be targeted via site-1 protease inhibition during ASC differentiation.

overall_design: B-cells were isolated from the peripheral blood of three adult donors and differentiated in vitro (see individual samples for culture conditions)

first: Muna

last: Al-Maskari

first: Gina

middle: M

last: Doody


title: Expression data from 40 lymphomas (Hodgkin, B cell, T cell)

city: TOULOUSE

first: Pauline

last: Gravelle

address: 1 Avenue Irène Joliot Curie

department: Anatomy-Pathology

institute: IUCT-ONCOPOLE

summary:
We produced and analyzed the transcriptomic profiles of 40 lymphoma patients. We used microarrays to compare the global gene expression profile between the different subtypes. These samples were analyzed with a tool predictive of immune escape mechanisms previously developped, IEGS33. Depending on lymphoma subtype, different immune escape signatures can be observed.
Therapeutic based on PD-1/PD-L1 blockade shows promising results in Hodgkin lymphoma (HL) and in some diffuse large B-cell lymphoma (DLBCL) patients but biomarkers predicting therapeutic response are still lacking. To gain understanding on the overall immune-escape (IE) mechanism, we recently developed a tool to score the transcriptional IE hallmarks in lymphoma samples and identified four stages of cancer immune-editing in DLBCL that correlated with overall survival. Through this method, we described here the IE profiles in HL and DLBCL from a meta-analysis of large series of microarrays. We observed that HL clustered together at the late equilibrium-early escape stage of cancer immune-editing with significant enrichment of genes involved in IE and T-cell activation as compared to DLBCL. Deconvolution of transcriptomes and immunohistochimistry showed that HL had higher CD3+ and CD4+ T-cells than all DLBCL and shared high abundance of CD8+ T-cells with DLBCL ABC and low infiltrates of CD68+CD163+ macrophages with DLBCL GC. HL and DLBCL shared the same cellular distribution of PD-1 and TIM3 staining but HL exhibited a higher expression of PD-L1 in tumor cells as well as LAG3 overexpression in ME as compared to DLBCL. Finally, our bioinformatic tools based on IEGS33 and T cell activation scores as global approach of immune escape mechanisms help to investigate in details the ME of HL. This method may be useful tool to identify HL as well as DLBCL patients who better benefit from immunotherapy strategies.

overall_design: Frozen biopsies of previously diagnosed lymphomas (B cell lymphomas, Hodgkin lymphomas, T cell lymphomas) were selected for RNA extraction and hybridization on GeneChip® Human Gene HTA_2.0 microarrays.

first: Sarah

last: Péricart

first: Camille

last: Laurent


title: MiRNA expression arrays from esophageal squamous cell carcinomas (ESCCs) and normal esophageal epithelia (Nes)

city: Guangzhou

first: Jing

last: Wen

address: 651 Dongfeng East Road

institute: Sun Yat-sen University Cancer Center

summary: To further study molecular mechanisms involving ESCC development, we have employed miRNA microarray expression profiling as a discovery platform to identify miRNAs differentially expressed between ESCCs and NEs.

overall_design: MiRNA expression analyses were performed on 30 ESCC and 10 NE samples without any anti-cancer treatment and using Agilent human miRNA microarrays based on miRBase (release 18.0) GeneChip®.

first: Jianhua

last: Fu


title: Profiling microRNA expression in Atlantic killifish (Fundulus heteroclitus) gill and responses to arsenic and hyperosmotic stress

city: Orono

first: Benjamin

last: King

state: ME

address: 5735 Hitchner Hall

department: Molecular and Biomedical Sciences

institute: University of Maine

type: Non-coding RNA profiling by high throughput sequencing

summary: The Atlantic killifish (Fundulus heteroclitus), native to estuarine areas of the Atlantic coast of the United States, has become a valuable ecotoxicological model due to its ability to acclimate to rapid environmental changes and adapt to polluted habitats. Killifish respond to rapid increases in salinity with an immediate change in gene expression, as well as long-term remodeling of the gills. Arsenic, a major environmental toxicant, was previously shown to inhibit the ability of killifish gill to respond to a rapid increase in salinity. We characterized miRNA expression in killifish gill under salinity acclimation with and without arsenic and identified a small group of highly expressed, well-conserved miRNAs as well as 16 novel miRNAs not yet identified in other organisms.

overall_design: Small RNA gene expression profiling in the gill during salinity acclimation (0, 1 and 24 hours post-transition to seawater) with and without 100 ug/L arsenic (sodium (meta)arsenite).

first: B


title: Rice stripe virus-derived siRNAs play different regulatory roles in host plant and vector insect [sRNA-Seq]

city: Fuzhou

first: Liu

last: Renyi

state: Fujian Province

address: Shangxiadian Road 15, Fujian University of Agriculture and Forestry, Fuzhou, Fujian, P.R.China

institute: Fujian Agriculture and Forestry University

summary: research was focus on the virus-derived sRNAs expression pattern in rice host or planthopper vector and host/vector gene expression pattern when infected with RSV

sample_organism:
Oryza sativa
Nilaparvata lugens

platform_organism:
Oryza sativa
Nilaparvata lugens

overall_design: The viruliferous and non-viruliferous small brown planthopper strains used in this work were derived from a rice field population in Hai'an, Jiangsu Province, China, and maintained in the laboratory for nearly nine years. The planthoppers were reared on 2 cm to 3 cm seedlings of rice (Oryza sativa Huangjinqing) in glass incubators, which were sealed with a nylon mesh, at 25 ± 1°C, 80% relative humidity, and 16 h of light per day. The planthoppers were transferred to fresh rice seedlings every 8 days to ensure sufficient nutrition.

first: Meiling

last: Yang

first: Zhongtian

last: Xu

first: Wan

last: Zhao

first: Qing

last: Liu

first: Qiong

last: Li

first: Renyi

first: Xiaoming

last: Zhang

first: Feng

last: Cui


title: Expression data from wheat root

city: Hangzhou

first: Li

last: Ruan

state: Zhejiang

address: Meiling South Road No. 9

institute: Tea Research Institute, Chinese Academy of Agricultural Science

summary:
Root foraging strategy of wheat for potassium (K) heterogeneity is based on special gene expressions. Low-K responsive genes, such as peroxidases, mitochondrion, transcription factor activity, calcium ion binding and respiration, up-regulated in Sp. NK rather than in Sp. LK. Methyltransferase activity, protein amino acid phosphorylation, potassium ion transport, protein kinase activity genes were found among down-regulated genes in Sp. LK.
We used microarrays to detail the global programme of gene expression underlying wheat root foraging strategy and identified distinct classes of up-regulated and down-regulated genes during this process.

overall_design: Based on the split-root system, wheat roots under K heterogeneity and homogeneity conditions were selected for RNA extraction and hybridization on Affymetrix microarrays. In order to simulate soil K heterogeneity environment, we used split-root system as test equipment of the present research. Two separated physical spaces, in which different K supply could be performed, were created in this split-root system. Three different K environments were performed as follows: (1) a homogeneous K-deprived condition (C. LK: both compartments had low K), (2) a homogeneous K-replete condition (C. NK: both compartments had normal K), and (3) a heterogeneous split condition (Sp. LK/Sp. NK: one compartment had low K, and the other had normal K).

first: Xiuli

last: Xin

first: Jiabao

first: Bingzi

first: Hao

last: Cheng

first: Congzhi

first: Donghao

last: Ma

first: Lin

last: Chen


title: Diethyldithiocarbamate, an anti-abuse drug, alleviates steatohepatitis and fibrosis in rodents

first: Tianhui

address: No. 95 Yong-an Road, Xi-cheng District

institute: Beijing Friendship Hospital, Capital Medical University

summary:
C57BL/6 mice received methionine/choline deficient (MCD) diet to establish the model of non-alcoholic fatty liver disease (NAFLD) with or without Diethyldithiocarbamate (DDC) treatment.
DDC improves hepatic steatosis, ballooning, inflammation and fibrosis in rodent models of NAFLD through modulating lipid metabolism and oxidative stress.

overall_design: In this study, mRNA in liver tissues from 2 normal control mice, 3 MCD-induced mice and 3 MCD-induced mice with DDC treatment were analyzed by microarray.


title: mRNA sequencing of samples coming from Translating Ribosome Affinity Purification (TRAP) using MSH1P::FLAG::RPL18

city: University Park

first: Hardik

last: Kundariya

state: PA

address: 361 N. Frear

institute: The Pennsylvania State University

summary: Col-0 transgenic plants expressing MSH1P::FLAG::RPL18 were generated in both msh1 homozygous mutant (SAIL-877-F01) and wild type backgrounds with cloned MSH1 sequence described in Xu et al. (2011) and with transformation by the floral dip method (Clough and Bent, 1998).  Positive transgenic lines were screened for FLAG tag by immunoblotting methods. Polysomal mRNA from MSH1-specific cells was obtained by ribosome purification using the TRAP method essentially as reported by (Reynoso et al., 2015) from floral stem tissues.

overall_design: Two samples from each Col-0 wild type TRAP, msh1 TRAP, Col-0 Total, and msh1 Total. Floral stem tissue was used.

first: Jesus

last: Beltran

first: Sally

last: Mackenzie


title: Rice stripe virus-derived siRNAs play different regulatory roles in host plant and vector insect

first: Liu

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

overall_design: Refer to individual Series


title: Rice stripe virus-derived siRNAs play different regulatory roles in host plant and vector insect [RNA-Seq]

first: Meiling

first: Zhongtian

first: Wan

first: Qing

first: Qiong


title: Elongation/termination factor exchange mediated by PP1 phosphatase orchestrates trancription termination

city: Oxford

first: Tea

last: Kecman

address: South Parks Road

department: Biochemistry

institute: University of Oxford

type: Genome binding/occupancy profiling by high throughput sequencing

summary: Termination of RNA polymerase II (Pol II) transcription is a key step, that is important for 3’end formation of functional mRNA, mRNA release and Pol II recycling. Even so, this underlying termination mechanism is not yet understood. Here, we demonstrate that the conserved and essential termination factor Seb1 interacts with Pol II near the end of the RNA exit channel and the Rpb4/7 stalk. Furthermore, the Seb1 interaction surface with Pol II largely overlaps with that of the elongation factor Spt5. Notably, Seb1 co-transcriptional recruitment is dependent on Spt5 de-phosphorylation by the conserved PP1 phosphatase Dis2, which also de-phosphorylates threonine 4 within the Pol II heptad repeated C-terminal domain. We propose that Dis2 orchestrates the transition from elongation to termination phase during the transcription cycle by mediating elongation to termination factor exchange and de-phosphorylation of Pol II C-terminal domain.

overall_design: In this study, we studied the effect of Dis2 deletion by ChIP-seq of Pol II CTD phosphomarks and termination factors. Samples were sequenced in duplicates and ChIP-Seq experiments include an input sample.

first: Krzystof

last: Kus

first: Dong-Hyuk

last: Heo

first: Katie

last: Duckett

first: Adrien

last: Birot

first: Sabrina

last: Liberatori

first: Shabaz

last: Mohammed

first: Lucia-Geis

last: Asteggiante

first: Carol

middle: V

last: Robinson

first: Lidia

last: Vasiljeva


title: Genome-wide transcriptional profiling of central amygdala and orbitofrontal cortex during incubation of methamphetamine craving

city: New York

first: Hannah

last: Cates

state: NY

address: 1425 Madison Ave, Box 6052

institute: Icahn School of Medicine at Mt. Sinai

summary: Methamphetamine (Meth) seeking progressively increases after withdrawal (incubation of Meth craving), but the transcriptional mechanisms that contribute to this incubation are unknown. Here we used RNA-sequencing to analyze transcriptional profiles associated with incubation of Meth craving in central amygdala (CeA) and orbitofrontal cortex (OFC), two brain areas previously implicated in relapse to drug seeking.  We trained rats to self-administer either saline (control condition) or Meth (10 days; 9 h/day, 0.1 mg/kg/infusion). Next, we collected brain tissue from CeA and OFC on withdrawal day 2 (when Meth seeking is low and non-incubated) and on day 35 (when Meth seeking is high and incubated), for subsequent RNA-sequencing. In CeA, we identified 10-fold more differentially expressed genes (DEGs) on withdrawal day 35 than day 2. These genes were enriched for several biological processes, including protein ubiquitination and histone methylation. In OFC, we identified many fewer expression changes than in CeA. Interestingly, there were more DEGs on withdrawal day 2 than on day 35. Several genes in OFC showed opposing expression changes on withdrawal day 2 (increase) when compared to withdrawal day 35 (decrease), which was further validated by qPCR. Our analyses highlight the CeA as a key region of transcriptional regulation associated with incubation of Meth seeking. In contrast, transcriptional regulation in OFC may contributes to Meth seeking during early withdrawal. Overall, these findings provide a unique resource of gene expression data for future studies examining transcriptional mechanisms in CeA that mediate Meth seeking after prolonged withdrawal.

overall_design:
Exp. 1 Genome-wide transcriptional profiling of CeA during incubation of Meth craving
We performed intravenous surgeries on two groups of rats (total n=26) and trained them to self-administer either saline (n=12) or Meth (n=14) as described above in 2 independent runs. We performed live decapitation on withdrawal days 2 and 35, and collected CeA tissue for mRNA preparation. We used the extracted mRNA for library preparation and RNA-sequencing. We pooled tissue from two rats as one biological replicate. The number of biological replicates in each group was: Day 2: Saline=3, Meth=4; Day 35: Saline=3, Meth=3.
Exp. 2 Genome-wide transcriptional profiling of OFC during incubation of Meth craving
As above, two groups of rats (total n=32) were trained to self-administer saline (n=16) or Meth (n=16) in 2 independent runs. We performed live decapitation on withdrawal days 2 and 35, and collected OFC tissue for mRNA preparation. We used the extracted mRNA either for library preparation and RNA-sequencing or for cDNA synthesis and qPCR. We pooled tissue from two rats as one biological replicate. The number of biological replicates in each group was: Day 2: Saline=4, Meth=4; Day 35: Saline=4, Meth=4.

first: Xuan

last: Li

first: Yavin

last: Shaham

first: Eric

middle: J

last: Nestler


title: Transcriptional analysis of P. gingivalis and A. baumannii

city: Louisville

first: Daniel

last: Miller

state: KY

address: 570 South Preston Street, Baxter 1, Room 224

institute: University of Louisville

summary: We examine the transcriptome of both P. gingivalis and A. baumannii in monotypic communities compared to heterotypic communities with both organisms. We identify a number of genes responsible for enhanced biofilm development as well as metabolic synergy.

sample_organism:
Acinetobacter baumannii
Porphyromonas gingivalis

overall_design: RNA-seq of mono-typic or hetero-typic communities following 3 hours of anaerobic incubation in PBS. The overall experiment was completed as two independent experiments comparing Pg to PgAb and a second experiment analyzing Ab to AbPg

first: Richard

last: Lamont


title: Expression profiling of CD8+ T-cells in peripheral blood (PB) of AML patients

city: Baltimore

first: Hanna

last: Knaus

state: Maryland

address: 1650 Orleans St

department: Oncology

institute: Johns Hopkins

summary:
1) Transcriptional profiles of highly purified (≥ 98%) PB CD8+ T-cells from newly diagnosed AML patients (pre-treatment) were compared to age-matched healthy controls and transcriptional profiles of PB AML CD8+ T-cells from patients who achieved complete remission (CR) versus non-responders (NR) longitudinally, at pre-treatment and upon recovery following induction chemotherapy (paired samples).
2) Transcriptional profiles of PB AML CD8+ T-cells from patients who achieved complete remission (CR) versus non-responders (NR) longitudinally, at pre-treatment (PRE) and upon recovery following induction chemotherapy (POST) (paired samples).

overall_design: 1)  AML patients vs. Healthy controls 2) AML patients induction chemotherapy responders (CR) versus non-responders (NR) at pretreatment (PRE) and upon recovery following induction chemotherapy (POST).

first: Leo

last: Luznik


title: Deregulation of growth-phase-dependent expression of SdsR causes cell death in Escherichia coli

city: Daejeon

first: Younghoon

last: Lee

address: KAIST 291 Daehak-ro, Yuseong-gu

department: Chemistry

country: South Korea

institute: KAIST

summary:
RNA-seq analysis of cells with pulsed overexpression of SdsR

Most small noncoding RNAs (sRNAs) are known to base pair with target mRNAs and regulate their stability or translation with the help of Hfq to trigger various changes in cell metabolism. SdsR (also known as RyeB), which is a member of the RpoS regulon, was reported as an abundant sRNA that represses tolC and mutS in E. coli. It is known to be specific to the stationary phase and is not expressed during the exponential phase, but no previous study had examined the importance of this growth phase-dependent regulation for cell growth and survival. In this study, we examined how forced expression of SdsR during the exponential phase alters cell growth and survival. We found that ectopic expression of SdsR during the exponential phase triggered a significant and Hfq-dependent cell death. This SdsR-driven cell death was alleviated by overexpression of RyeA, an sRNA transcribed on the opposite DNA strand, suggesting that SdsR/RyeA may represent a novel type of toxin/antitoxin (T/A) system in which both the toxin and the antitoxin are sRNAs. To identify target genes involved in the observed SdsR-driven cell death, we first performed RNA-seq analysis and used the RNA-seq data to predict which SdsR-targeted mRNAs could contribute to SdsR-driven cell death. We then examined whether repression of translation of each predicted target mRNA could cause the observed SdsR-driven growth defects, and found that the SdsR-driven cell death seen in our system was mainly caused by the SdsR-mediated repression of yhcB, which encodes an inner membrane protein.

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

overall_design: E. coli cells containing pHM4T, pSdsR, or pSdsR(45-103) were grown at 37℃ to an OD600 of 1.5~1.7. A final volume of 1 mM IPTG was added to the cell culture, followed by another 10 min and total RNAs were extracted using an RNeasy mini kit (Qiagen). For DNase treatment of 10 μg of total RNA, a Turbo DNA free kit (Ambion) was used according to the manufacturer’s guidelines. All RNA sequencing and alignment procedures were conducted by ChunLab. The Ribo-Zero rRNA removal kit (Epicentre) was used for ribosomal RNA depletion according to manufacturer instructions. Libraries for Illumina sequencing were generated using a TruSeq Stranded mRNA sample prep kit (Illumina) according to the manufacturer’s protocol. RNA sequencing was performed on the Illumina HiSeq 2500 platform using single-end 50 bp sequencing. The sequence data for the reference genome were retrieved form the NCBI database. Quality-filtered reads were aligned to the reference genome sequence using Bowtie2. The relative transcript abundance was measured in Relative Log Expression (RLE). To screen for mRNAs whose levels differed by more than two-fold versus that wild-type cells, we filtered for mRNAs with EdgeR p values < 0.05.

first: Jee

middle: S

last: Choi

first: Wonkyong

last: Kim

first: Shinae

last: Suk

first: Hongmarn

last: Park

first: Geunu

last: Bak

first: Junhyeok

last: Yoon


title: Maternally Expressed Genes Identified by Single-cell RNA Sequencing in Pre-implantation Development of Buffalo Parthenogenesis

city: Nanning

last: Chen

state: GuangXi

address: No. 100, East University Road

department: Animal Science and Technology

institute: Guangxi University

summary:
Background:Maternal mRNAs that accumulate in the oocyte during oogenesis play important roles during initial stages of embryonic development, before activation of the embryonic genome. Parthenogenesis of mammalian is a critical research modle for the function analysis of maternal genomics.
Results:Here we report comprehensive maternal transcriptome dynamics of single matured oocytes and pre-implantation embryos of buffalo parthenogenesis.Notably, more than half of the estimated 28659 bovine genes,15331 involved in more than 280 pathways, is expressed in oocytes and early embryos of parthenogenesis .The total numbers of genes expressed across stages are from 908 genes (morula/16cells)to 2603 genes(blastocyst/morula), and the nature of the expressed genes is also greatly different. A total of 3567 unique genes were identified to be differentially expressed between all consecutive stages of development(FPKM>0),of which the biggest expressed change was detected between the 8-and 16-cell stages, which demonstrated that parthenogenetic activation of embryonic development exist an embryonic genome activation process which is the same as the normal fertilization of embryos,also occurs between 8cells-16cells, consistent with the time of the development of the normal fertilized embryonic development,which suggesting that parthenogenetic embryonic development and normal fertilization embryo development may have a similar genome activation transcription regulation process.Besides,2726 genes were identified as only expressed/highly enriched in particular stages of development, suggesting their stage-specific roles in maternal genome during embryogenesis.Using weighted gene co-expression network analysis, we found 11 stage-specific modules of co-expressed genes that can be used to represent the corresponding stage of development. Furthermore, we identified 1530 hub genes of the maternally expressed gene networks.
Methods:Maternal mRNA profiles of pre-implantation development in buffalo parthenogenesis,using single-cell RNA  sequencing in IlluminaHiSeq platform. Sequencing adapters were trimmed using Cutadapt (https://code.google.com/p/cutadapt/) and the filtered reads were mapped to the reference genome sequence (ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/000/471/725/GCA_000471725.1_UMD_CASPUR_WB_2.0/)assembly using Tophat2 followed by Cufflinks.qRT–PCR validation was performed using SYBR Green assays.
Conclusions:This study provides a comprehensive examination of maternally expressed gene activities in buffalo oocytes and pre-implantation embryos of parthenogenesis for the first time,and find the special “EGA”between 8cells-16cells for parthenogenetic embry,and the study screen a number of specific stages hub gene with potentially important function.

overall_design: We collected the oocytes and early parthenogenetic activated embryos of buffalo in vitro （GV、MII、2cells、4cells、8cells、16cells、morula、blastocyst）to explore the dynamic changes of the maternal transcripts by single-cell RNA  sequencing,using IlluminaHiSeq platform.

first: F

first: M

last: Zhang

first: Q

last: Fu

first: L

last: Pu

first: Z

last: Hou

middle: Z

last: Xu

first: P

first: X

middle: L

last: Zhao


title: Primate fetal hepatic response to maternal obesity: epigenetic signaling pathways and lipid accumulation [gene expression]

city: San Antonio

first: Sobha

last: Puppala

state: TX

institute: Texas Biomedical Research Institute

summary: The liver is a major site for synthesis, storage and redistribution of carbohydrates, proteins and lipids. In addition, it is well-known that maternal obesity (MO) increases risk of offspring cardiovascular disease (CVD), diabetes and obesity. However, the mechanisms by which the MO intrauterine environment predisposes offspring to CVD and metabolic dysregulation are unknown. The goal of this study was to assess the impact of MO on primate fetal liver and identify underlying molecular mechanisms by which MO increases disease risk. The goal of this study was to identify candidate molecular mechanisms underlying MO in the near-term non-human primate (NHP) fetal liver. This is the first study of NHP fetal MO livers using unbiased transcriptome analysis to quantify hepatic gene expression, identify dysregulated signaling pathways and potential miRNAs regulating the disrupted metabolic processes. Unbiased gene (arrays) and microRNA (miRNA; small RNA-Seq) abundances were quantified in near-term (0.9 Gestation (0.9G)) baboon fetal livers (control (CON) = 6; MO = 5) and subjected to pathway and network analyses (GeneSifter, Ingenuity® Pathway Analysis (IPA)) to identify a coordinated molecular response to MO. Lipid and glycogen content (CON = 16; MO = 16) were quantified by Computer Assisted Stereology Toolbox (CAST) in 0.9G livers. Pairwise comparisons showed 933 differentially expressed genes between CON and MO livers: 350 genes were upregulated and 583 were downregulated. Pathway analysis revealed upregulation of Wnt/β-catenin signaling and downregulation of tricarboxylic acid (TCA) cycle, proteasome, oxidative phosphorylation and glycolysis pathways in MO fetal livers compared with CON. Inversely expressed miRNAs that target genes in these pathways provide additional support for the importance of these pathways in fetal liver metabolic regulation. Consistent with the observed pathway changes in MO, we found hepatic lipid content was threefold greater in MO than CON fetal livers (p=0.02). Molecular genetic analyses of CON and MO fetal baboon livers revealed dysregulation of Wnt/β-catenin signaling, TCA cycle, proteasome, oxidative phosphorylation and glycolysis pathways in MO livers, all of which are central to fatty acid metabolism and lipid storage. The marked lipid accumulation in MO fetal livers supports our hypothesis that dysregulation of these pathways detrimentally impacts lipid management. Furthermore, our findings demonstrate the detrimental impact of MO on fetal liver development and suggest impaired hepatic function prior to birth.

first: Cun

last: Li

first: Jeremy

last: Glenn

first: Amy

last: Quinn

first: Jennifer

last: Palarczyk

first: Edward

last: Dick Jr

first: Peter

last: Nathanielsz

first: Laura

middle: A

last: Cox


title: Gene Expression Profile in the Hypothalamus of Male Bgn_KO and WT Mice at 13 Weeks Old

first: Xia

last: Yang

address: 610 Charles E. Young Dr. East

institute: UCLA

summary: To investigate the effects of gene Bgn on affecting brain dysfunction and metabolic disorders by profiling the transcripome in the hypothalamus of male Bgn_KO and wild-type (WT, litter mate)  mice at 13 weeks old.

overall_design: All mice (male Bgn_KO (n=4) and WT (n=4)) were maintained in a temperature-controlled room with a 12-hour light and 12-hour dark cycle. Diet (Pico Lab 5053 rodent diet) and water were provided ad libitum. At 13 weeks old, mice were sacrificed. Hypothalamus and liver were dissected out, flash frozen, and stored at -80°C for later usage. All experiments were performed in accordance with the United States National Institutes of Health Guide for the Care and Use of Laboratory Animals and were approved by the University of California at Los Angeles Chancellor?s Animal Research Committee.

first: Qingying

last: Meng

first: Fernando

last: Gomez-Pinilla


title: Expression data from leaflets and roots of the tomato res mutant and its background genotype, wild-type (WT) (Solanum lycopersicum L. cv. Moneymaker), grown in control conditions and salt stress

city: Espinardo

first: Irene

last: Albaladejo

state: Murcia

address: Campus Universitario Espinardo

institute: CEBAS-CSIC

summary:
The res (restored cell structure by salinity) mutant exhibits a remarkable growth inhibition and morphological alterations in roots and leaves, which are suppressed when the mutant plants are exposed to salinity. The analysis of mutants like res may be very helpful in understanding how plants are able to coordinate the balance between growth and stress, a fundamental and not fully-understood question of important agronomical implications
In order to understand the molecular basis of phenotype recovery and tolerance induced by salt stress in res mutant, we carried out a comparative transcriptomic analysis between res and WT plants. This analysis revealed a constitutive alteration of an important number of genes involved in different pathways in res mutant, and identified genes specifically overexpressed under salt stress and responsible of both maintaining plant growth and promoting stress tolerance in res mutant.

overall_design: Gene expression was analysed in roots and leaves of WT and res plants in absence of stress (control) and when the phenotypic recovery of res mutant began to be observed after salt stress (5 days of 200 mM NaCl). Leaflets (from the first fully-expanded leaf) and roots were harvested and immediately frozen in liquid N2 for subsequent RNA extraction. Three biological replicates (each one including three plants) were considered for each genotype and treatment, resulting in a total of 24 samples. Microarrays analysis was performed using the GeneChip® Tomato Gene 1.1 ST Array Strip (Affymetrix).

first: Isabel

last: Egea

first: Belen

last: Morales

first: Francisco

middle: B

last: Flores

first: Carmen

last: Capel

first: Rafael

last: Lozano

first: Maria

middle: C

last: Bolarin


title: Gene Expressoin Profile in the Liver of Male WT and BGN_KO Mice at 13 Weeks Old

city: Los Angeles

summary: To investigate the effects of gene Bgn on affecting brain dysfunction and metabolic disorders by profiling the transcripome in the liver of male Bgn_KO and wild-type (WT, litter mate)  mice at 13 weeks old.

overall_design: All mice (male WT_liver (n=4) and male BGN_KO_liver (n=4)) were maintained in a temperature-controlled room with a 12-hour light and 12-hour dark cycle. Diet (Pico Lab 5053 rodent diet) and water were provided ad libitum. At 13 weeks old, mice were sacrificed. Hypothalamus and liver were dissected out, flash frozen, and stored at -80°C for later usage. All experiments were performed in accordance with the United States National Institutes of Health Guide for the Care and Use of Laboratory Animals and were approved by the University of California at Los Angeles Chancellor’s Animal Research Committee.


title: Gene expression profiles in the liver of liver-specific ROCK1 deficient mice

city: Pohang

first: Bhin

last: Jin-hyuk

address: Ji-gok research center, hyoja-dong, Nam-gu

department: Department of Chemical engineering

institute: POSTECH

summary: Liver-specific deletion of ROCK1 leads to a significant decrease in gene expression of key molecules invovled in lipid systhesis. The study was designed to determine whether hepatic ROCK1 plays a role in the regulation of fatty acid synthesis

overall_design: The control and liver-specific ROCK1 KO mice were fed a normal chow ad libitum for 16 weeks. RNA in livers of control and liver-specific ROCK1 KO mice was extracted to investigate hepatic gene expression profiles.

first: Young-Bum

last: Kim

first: Jinhyuk

last: Bhin


title: Kallikrein-related peptidases 4, 5, 6 and 7 regulate tumor-associated factors in serous ovarian cancer

city: London

first: Daniela

last: Loessner

address: Mile End Rd

institute: Queen Mary University of London

summary: Background: Tissue kallikrein-related peptidases 4, 5, 6 and 7 (KLK4-7) strongly increase the malignancy of ovarian cancer cells. By further deciphering the downstream effectors of KLK4-7, we aimed at finding new potential prognostic biomarkers and treatment targets for ovarian cancer patients. KLK4-7-transfected and vector-control OVMZ-6 (OV-KLK4-7 and OV-VC) ovarian cancer cells were established to select differentially regulated factors.  Methods: Three independent approaches, PCR arrays, genome-wide microarray and proteome analyses, were pursued leading to the identification of ten candidates (MSN, KRT19, COL5A2, COL1A2, BMP5, F10, KRT7, JUNB, BMP4, MMP1). Differential gene expression in OV-KLK4-7 versus OV-VC cells was validated by qPCR. To determine differential protein expression, Western blot analyses, immunofluorescence and immunohistochemistry were applied for four candidates (MSN, KRT19, KRT7, JUNB) in both cell lines and tumor xenografts.  Results: These experiments demonstrated that KLK4-7 distinctly regulate expression of MSN, KRT19, KRT7 and JUNB on the mRNA and protein levels in ovarian cancer cells and tissues. Protein expression of the top upregulated effectors, MSN and KRT19, was investigated by immunohistochemistry in a cohort of patients (n=66) afflicted with high-grade serous ovarian cancer and related to the immuno-expression levels of KLK4-7. Significant positive associations were found for KRT19/KLK4 (P=0.010), KRT19/KLK5 (P=0.030) and MSN/KLK7 (P=0.001); KRT19 and MSN immuno-expression showed a trend towards significance with KLK6.  Conclusions: These findings imply that KLK4-7 exert key modulatory effects on other cancer-related genes and proteins in ovarian cancer. The key downstream effectors of KLK4-7, MSN and KRT19, may represent important therapeutic targets associated with serous ovarian cancer.

overall_design: The dataset was derived from three biological repeats of each of the culture conditions: overexpression of KLK4-7 or empty vector control.

first: Ping

last: Wang

first: Viktor

last: Magdolen

first: Christof

last: Seidl

first: Julia

last: Dorn

first: Enken

last: Drecoll

first: Matthias

last: Kotzsch

first: Feng

first: Manfred

last: Schmitt

first: Oliver

last: Schilling

first: Anja

last: Rockstroh

first: Judith

last: Clements


title: The Virulence Effect of CpxRA in Citrobacter rodentium Is Independent of the Auxiliary Proteins NlpE and CpxP

city: St-Anne-de-Bellevue

first: Sebastien

last: Faucher

state: QC

address: 21,111 Lakeshore

department: Natural Resource Sciences

country: Canada

institute: McGill University

summary: Citrobacter rodentium is a murine pathogen used to model the intestinal infection caused by Enteropathogenic and Enterohemorrhagic Escherichia coli (EPEC and EHEC), two diarrheal pathogens responsible for morbidity and mortality in developing and developed countries, respectively. During infection, these bacteria must sense and adapt to the gut environment of the host. In order to adapt to changing environmental cues and modulate expression of specific genes, bacteria can use two-component signal transduction systems (TCS). We have shown that the deletion of the Cpx TCS in C. rodentium leads to a marked attenuation in virulence in C3H/HeJ mice. In E. coli, the Cpx TCS is reportedly activated in response to signals from the outer-membrane lipoprotein NlpE. We therefore investigated the role of NlpE in C. rodentium virulence. We also assessed the role of the reported negative regulator of CpxRA, CpxP. We found that as opposed to the ΔcpxRA strain, neither the ΔnlpE, ΔcpxP nor the ΔnlpE/ΔcpxP strains were significantly attenuated, and had similar in vivo localization to wild-type C. rodentium. The in vitro adherence of the Cpx auxiliary protein mutants, ΔnlpE, ΔcpxP, ΔnlpEΔcpxP, was comparable to wild-type C. rodentium, whereas the ΔcpxRA strain showed significantly decreased adherence. To further elucidate the mechanisms behind the contrasting virulence phenotypes, we performed microarrays in order to define the regulon of the Cpx TCS. We detected 393 genes differentially regulated in the ΔcpxRA strain. The gene expression profile of the ΔnlpE strain is strikingly different than the profile of ΔcpxRA with regards to the genes activated by CpxRA. Further, there is no clear inverse correlation in the expression pattern of the ΔcpxP strain in comparison to ΔcpxRA. Interestingly, 161 genes were downregulated in the ΔcpxRA strain while being upregulated or unchanged in all other Cpx auxiliary protein deletion strains. This group of genes include T6SS, ompF and the regulator for colanic acid synthesis, that may contribute to the loss of virulence of ΔcpxRA. Taken together, these data suggest that in these conditions, CpxRA activates gene expression in a largely NlpE- and CpxP-independent manner.

overall_design: Citrobacter rodentium DBS100 was grown in DMEM media at 37°C shaking to OD600 of 0.5-0.6 in triplicate. Samples were taken for analysis.

first: Natalia

last: Giannakopoulou

first: Nilmini

last: Mendis

first: Lei

last: Zhu

first: Samantha

last: Gruenheid

first: Hervé

last: Le Moual


title: Global characterization of the Dicer-like protein DrnB roles in miRNA biogenesis in the social amoeba Dictyostelium discoideum

city: Uppsala

first: Erik

last: Holmqvist

state: Uppland

address: Husargatan 3, Box 596, Uppsala University, Dept. of Cell and Molecular Biology

country: Sweden

institute: Uppsala University

summary: Micro (mi)RNAs regulate gene expression in many eukaryotic organisms where they control diverse biological processes. Their biogenesis, from primary transcripts to mature miRNAs, have been extensively characterized in animals and plants, showing distinct differences between these phylogenetically distant groups of organisms. However, little is known about miRNA biogenesis in organisms whose evolutionary position is placed in between plants and animals and/or in unicellular organisms. Here, we investigate miRNA maturation in the unicellular amoeba Dictyostelium discoideum, belonging to Amoebozoa, which branched out after plants but before animals. High-throughput sequencing of small RNAs and poly(A)-selected RNAs demonstrated that the Dicer-like protein DrnB is required, and essentially specific, for global miRNA maturation in D. discoideum. Our RNA-seq data also showed that longer miRNA transcripts accumulate in a drnB knock-out strain, generally preceded by a T-rich putative promoter motif. For two model miRNAs we defined the transcriptional start sites (TSSs) of primary (pri)-miRNAs and showed that they carry the RNA polymerase II specific m7G-cap. Different biogenesis pathways generate the 3’ ends of these pri-miRNAs, where pri-mir-1177 reads into the downstream gene, while pri-mir-1176 has a distinct non-polyadenylated end. This 3´-end is processed to shorter intermediates, stabilized in DrnB-depleted cells, of which some carry a short oligo(A)-tail. Furthermore, we identified 10 new miRNAs, all DrnB dependent and developmentally regulated. Thus, the miRNA machinery in D. discoideum shares features with both plants and animals, which is in agreement with its evolutionary position and perhaps also an adaptation to its complex lifestyle: unicellular growth and multicellular development.

overall_design: small and poly(A) enriched RNA-seq of D. discoideum AX2 WT and drnB- knock out strain from vegetative growing and 16h developed cells.

first: Zhen

last: Liao

first: Jonas

last: Kjellin

first: Marc

last: Höppner

last: Grabherr

first: Fredrik

last: Söderbom


title: Direct Targeting of MYCN Gene Amplification by Alkylating Pyrrole-Imidazole Polyamide and CRISPR/Cas9 in Neuroblastoma Cells (CHP-134)

status: Public on Dec 25 2018

city: Chiba

first: Jason

last: Lin

state: Chiba

address: 666-2 Nitona-cho, Chuo-ku

institute: Chiba Cancer Center Research Institute


title: Direct Targeting of MYCN Gene Amplification by CRISPR/Cas9 in Neuroblastoma Cells (CHP-134)

summary: Amplification of MYCN plays a pivotal role in multiple types of tumors and correlates with poor prognosis in high-risk neuroblastoma. Despite recent advances in the treatment of neuroblastoma, no approaches directly target the master oncogene MYCN. Difficulties in targeting the MYCN protein have inspired us to develop a new gene level inhibitory strategy using a sequence-specific gene regulator. Here we generated a MYCN-targeting pyrrole-imidazole (PI) polyamide, MYCN-A3, which directly binds to and alkylates DNA at homing motifs within MYCN transcript. Pharmacological suppression of MYCN inhibited the proliferation of cancer cells harboring MYCN amplification compared with MYCN non-amplified cancer cells. In neuroblastoma xenograft mouse models, MYCN-A3 specifically downregulated MYCN expression and suppressed tumor progression with no detectable adverse effects and resulted in prolonged overall survival. Moreover, we observed the copy number reduction of MYCN in neuroblastoma cells with MYCN amplification upon treatment with MYCN-A3 but not MYCN non-targeting PI polyamide. Expression microarray experiments were also performed to compare the genome-wide effect of MYCN-A3 with CRISPR/Cas9 silencing of MYCN (MYCNcr-a).

overall_design: CHP-134 cells were transfected with MYCNcr-a. After 6 hours, RNA was prepared for qPCR and microarray with 2x2 replicates per condition. Samples at 150 ng were labeled with RNA Spike-In Kit and analyzed on SurePrint G3 Human GE 8x60K V2 microarrays following Agilent Technologies’ recommendations. Arrays with sample were scanned on an Agilent SureScan microarray scanner. Expression analyses were performed by limma. Pairwise fold changes in expression (FC) are defined by differences between MYCNcr-a and CRISPR/Cas9 control. Gene symbols were additionally annotated by matching associated RefSeq mRNA and ncRNA as well as Ensemble accession codes in the array definitions.

first: Hiroyuki

last: Yoda

first: Atsushi

last: Takatori

first: Hiroki

last: Nagase


title: Direct Targeting of MYCN Gene Amplification by Alkylating Pyrrole-Imidazole Polyamide in Neuroblastoma Cells (CHP-134)

overall_design: CHP-134 cells were treated and transfected with MYCN-A3. After 6 hours, RNA was prepared for qPCR and microarray. Samples at 150 ng were labeled with RNA Spike-In Kit and analyzed on SurePrint G3 Human GE 8x60K V2 microarrays following Agilent Technologies’ recommendations. Arrays with sample were scanned on an Agilent SureScan microarray scanner. Sample replicates were as follows: MYCN-A3: 2+1; DMSO: 2. Expression analyses were performed by limma. Pairwise fold changes in expression (FC) are defined by differences between MYCN-A3 and DMSO. Gene symbols were additionally annotated by matching associated RefSeq mRNA and ncRNA as well as Ensemble accession codes in the array definitions.


title: Goat immune cells

city: Utrecht

first: Mariona

last: Baliu-Piqué

state: Utrecht

address: Lundlaan 6

department: Laboratory for Translational Immunology

country: Netherlands

institute: University Medical Center Utrecht

summary: Transcriptional profiling of goat immune cells in different tissues. Goal was to determine the global gene expression profiles of different immune cell subsets, and determine the differences in gene expression between the same immune cell subset in different organs.

overall_design: 10 cell subsets. Biological replicates: 3 or less replicates.

first: Lars

last: Ravesloot

first: Ad

last: Koets

first: Kiki

last: Tesselaar

first: José

last: Borghans


title: Transcriptome-wide analysis of gene expression using detached first-pair rosette leaves before culture (time 0), at 10min to 12h after detachment Col-0, coi1-2 and sdg8-2 seedlings.

city: Shanghai

first: Lin

last: XU

address: 300 Fenglin Road

department: Chinese Academy of Sciences

institute: Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences

summary: To reveal the early molecular events upon wounding during DNRR from Arabidopsis leaf explants cultured on B5 medium without exogenous hormones, we carried out an RNA-seq experiment using leaf explants before culture (i.e. time 0), at 10 and 30 min after detachment, and at 1 to 12 h after detachment. The results showed that the upregulation of JA-related genes occurred as an early response to wounding (mainly within 1 h), prior to the upregulation of auxin-related genes (from 2 to 12 h). These results indicated that JA responds rapidly to wounding and earlier than does auxin. To analysis whether SDG8-mediated H3K36me3 is generally involved in JA-mediated gene upregulation in response to wounding. We evaluated changes in the transcriptome in sdg8-2 and coi1-2 leaf explants (2 h vs. time 0) by analyzing RNA-seq data, and compared them with transcriptomic changes in wild-type.

overall_design: Arabidopsis seeds were germinated on ½ MS medium at 22°C under a 16-h light/8-h dark photoperiod. Detached leaf explants from 12-day-old seedlings were cultured on B5 medium without sucrose at 22°C under 24-h light conditions. Biological duplicates were performed for each timepoint analyzed.

first: Guifang

last: Zhang

first: Fei

last: Zhao

first: Lyuqin

last: Chen

last: Xu


title: Antibiofilm and antivirulence activities of 6-gingerol and 6-shogaol against Candida albicans due to hyphal inhibition

city: Gyeongsan-Si

first: Jintae

last: Lee

state: Gyeongsangbuk-Do

address: 214-1 Daedong

department: Chemical engineering

institute: Yeungnam University

summary: Candida albicans is an opportunistic pathogen and responsible for candidiasis. C. albicans readily forms biofilms on various biotic and abiotic surfaces, and these biofilms can cause local and systemic infections. C. albicans biofilms are more resistant than its free yeast to antifungal agents and less affected by host immune responses. Transition of yeast cells to hyphal cells is required for biofilm formation and is believed to be a crucial virulence factor. In this study, six components of ginger were investigated for antibiofilm and antivirulence activities against a fluconazole-resistant C. albicans strain. It was found 6-gingerol, 8-gingerol, and 6-shogaol effectively inhibited biofilm formation. In particular, 6-shogaol at 10 µg/ml significantly reduced C. albicans biofilm formation but had no effect on planktonic cell growth. Also, 6-gingerol and 6-shogaol inhibited hyphal growth in embedded colonies and free-living planktonic cells, and prevented cell aggregation. Furthermore, 6-gingerol and 6-shogaol reduced C. albicans virulence in a nematode infection model without causing toxicity at the tested concentrations. Transcriptomic analysis using RNA-seq and qRT-PCR showed 6-gingerol and 6-shogaol induced several transporters (CDR1, CDR2, and RTA3), but repressed the expressions of several hypha/biofilm related genes (ECE1 and HWP1), which supported observed phenotypic changes. These results highlight the antibiofilm and antivirulence activities of the ginger components, 6-gingerol and 6-shogaol, against a drug resistant C. albicans strain.

overall_design: Gene expression changes by 6-gingerol and 6-shogaol in Candida albicans

first: Jin-Hyung


title: Genome-wide Transcriptional Profiling of Nitrogen-Depleted E. coli Treated with Stapled Peptide Inhibitors of the Sigma-54 Promoters

city: Frederick

first: Jack

state: MD

address: SAIC-Frederick Miller Dr

institute: NIH

summary: We report the genome-wide effects of blocking the interaction between the sigma-54 bacterial transcriptional enhancer with its cognate promoter in E. coli under nitrogen-starvation conditions.

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

overall_design: Bacterial mRNA profiles of E. coli grown in nitrogen-deficient media and treated with different sigma-54-based stapled peptides were generated by deep sequencing in triplicate

first: Sterling

last: Payne

first: Federico

last: Bernal


title: Transcriptome in Huh7 cells infected with 4 Ebolaviruses

city: Atlanta

first: César

last: Albariño

state: GA

address: 1600 Clifton Rd, MS G14

institute: Centers for Disease Control and Prevention

summary: we are reporting the transciptome of 4 Ebolaviruses from Huh7 infected cells, and harvested at 1-3 dpi

sample_organism:
Reston ebolavirus
Sudan ebolavirus
Bundibugyo virus
Ebola virus

overall_design: analysis of the abundance of each of the 7 viral mRNAs

first: Cesar


title: Transcriptional changes of influenza A/Hong Kong/1/68-H3N2 (HK68) infected A549 lung epithelial cells

city: Vermillion

first: Michael

last: Chaussee

state: SD

address: 414 E Clark St

department: Basic Biomedical Sciences

institute: University of South Dakota

summary: Typically viral infections make the host more susceptible to subsequent bacterial infections by mechanisms that are incompletely defined. To identify host changes that occur in response to HK68  infection, gene expression of A549 lung epithelial cells were identified. Changes included an increase in transcripts encoding proteins with fibronectin-type III (FnIII) domains, such as fibronectin (Fn), tenascin N (TNN), and tenascin C (TNC).  Results provide insight on the host response to IAV infection, including the production of a variety of ECM proteins, which can create an environment rich in host ligands for bacteria adherence

overall_design: Semi-confluent adenocarcinoma human alveolar basal epithelial cells (A549) cells were infected with influenza virus, A/Hong Kong/1/68-H3N2 (HK68) (5 X10^2  or 2 X 10^5 TCID50), or not (infection media only), and incubated for 30 minutes, 24 hours, or 48 hours at 37°C and 5% CO2.  RNA was extracted using Trireagent (LucernaChem) and RNaeasy MiNi Kit (Qiagen, Valencia, CA) as described by manufacturer’s instruction. RNA purity and quantity was confirmed with Agilent chips (Agilent RNA 600 Nano kit). To identify differently expressed genes, fold change was determined by comparing expression levels of IAV infected cells to those obtained with control treated A549 cells.  Two independent Codelink microarrays were completed.

first: Andrea

last: Herrera

first: Kathleen

last: Eyster

first: Victor

last: Huber


title: RNA Expression (log2) in preproB Cells from Two Cebpa +37 kb Enhancer(f/f) or Cebpa +37 kb Enhancer(f/f);Mx1-Cre Mice Exposed to pIpC 5 Weeks Earlier

city: Baltimore

first: Alan

middle: D

last: Friedman

address: 1650 Orleans St.

institute: Johns Hopkins University

summary: To gain insight into regulation of B cell development by C/EBPa, we compared gene expression in preproB cells with or without the +37 kb Cebpa enhancer.

overall_design: Gene expression was measured from FACS-sorted Lin-neg;B220+;CD43+BP1-;CD24- preproB cells 5 weeks after 3 doses of pIpC were given to Enh(f/f) vs Enh(f/f);Mx1-Cre mice


title: RNA Expression (log2) in Marrow Subsets fromTwo Cebpa-Enhancer/Promoter-hCD4 Mice

summary: To gain insight into regulation of B cell development by C/EBPa, we compared gene expression in hCD4- vs hCD4+ subsets of preproB and proB cells from Cebpa-Enh/prom-hCD4 mice, with preB cells and hCD4+ GMP also analyzed for comparison.

overall_design: Gene expression was measured from FACS sorted marrow subsets from Cebpa-Enh/prom-hCD4 mice.


title: Gene expression signatures for miR-26a over-expression and negative control in SMMC-7721 cells

status: Public on Dec 24 2018

city: Xi'an

first: Xiang

address: Changle west road #169

institute: the Fourth Military Medical University

summary:
To further development of our gene expression approach to microRNA-26a over-expression, we have employed whole mRNA microarray expression profiling as a discovery platform. SMMC-7721 cells at 70–80% confluence in 6-well plates were transfected using Lipofectamine 2000 (Invitrogen). Negative control mimics or miR-26a mimics (100nM) were transfected in each well. Cell extracts were prepared 48 h after transfection, total RNA was checked for a RIN number to inspect RNA integration by Affymetrix PrimeView™ Human Gene Expression Arrays.
We used microarrays to detail the global programme of gene expression underlying miR-26a over-expression and identified distinct classes of up-regulated or down-regulated genes during this process.

overall_design: SMMC-7721 cells at 70–80% confluence in 6-well plates were transfected using Lipofectamine 2000 (Invitrogen). Negative control mimics or miR-26a mimics (100nM) were transfected in each well. Total RNA was prepared 48 h after transfection.

first: Lin-Tao

last: Jia


title: RNA-seq analysis of Streptococcus pneumoniae during intraspecies competition in broth culture

city: Oxford

first: Angela

last: Brueggemann

address: Peter Medawar Building for Pathogen Research

department: Nuffield Department of Medicine

institute: University of Oxford

summary: Streptococcus pneumoniae (‘pneumococcus’) is a leading cause of morbidity and mortality worldwide and a frequent coloniser of the nasopharynx. Competition among bacterial members of the nasopharynx is believed to be mediated by bacteriocins: antimicrobial toxins produced by bacteria to inhibit growth of other bacteria. We have identified 14 newly-discovered bacteriocin gene clusters among pneumococci. Here, RNA-seq analysis was performed to investigate whether bacteriocin genes are transcriptionally active when two different strains are competing in broth culture. Pneumococcal reference strains PMEN3 (Spain9V-3) and PMEN6 (Hungary19A-6) were grown together in broth culture. Samples were taken at sequential time points and RNA was extracted and sequenced. The controls were prepared by growing each strain individually in identical experiential conditions and combining the RNA sequencing reads from each individual strain in silico. Differential expression analyses were performed by comparing reads generated when strains were competing in broth culture to those from when strains were grown individually.

overall_design:
Pneumococcal reference strains PMEN3 and PMEN6 were grown together in brain-heart infusion broth culture at 37°C + 5% CO2 for 6h. Broth cultures at five time points (2, 3, 4, 5 and 6 h of incubation) were sampled and RNA was extracted using the Promega Maxwell® 16 Instrument and LEV simplyRNA Cells purification kit, following the manufacturer’s protocol. Extracted RNA samples were sent to the Oxford Genomics Centre for processing. Library preps were made using RNA-Seq Ribozero kits (Illumina, Inc) and sequencing was performed on the MiSeq (Illumnia, Inc). The controls were prepared by growing each strain individually in identical experimental conditions and combining the RNA sequencing reads from each individual strain in silico. RNA-seq data for PMEN3 grown individually was previously published by us and retrieved from GEO (accession number GSE89200). A pseudo-reference genome was constructed using PMEN3 and PMEN6 reference genomes by sorting genes into three categories: those unique to PMEN3, those unique to PMEN6, and those shared between the two. RNA-seq reads from all time points were combined in silico and mapped to the pseudo-reference genome using Bowtie2 with the highest sensitivity option. Differential expression analyses were performed using the DESeq method by comparing reads generated when strains were competing in broth culture to those from when strains were grown individually. In theory, the control contained twice the number of reads compared to the in vivo competition experiment as it was compiled in silico from two sets of samples. Thus, although the downregulation of genes could not reliably be assessed, it could be assumed with a high level of confidence that upregulated genes are differentially expressed; nevertheless, this approach provides only relative values and actual fold-change ratios for the upregulated genes are likely to be underestimated using this method.

This series contains the re-analysis of samples from GSE89200.

first: Reza

last: Rezaei Javan

first: Andries

last: van Tonder

first: Caroline

last: Harrold


title: A single nucleotide polymorphism in the promoter of a hairpin RNA contributes to Alternaria leaf spot resistance in apple (Malus × domestica Borkh.)

city: Beijing

first: Tianzhong

last: Li

address: Yuanmingyuan Street No.2

department: Horticulture

institute: China Agricultural University

summary: Apple leaf spot caused by the Alternaria alternata f. sp. mali (ALT1) fungus is one of the most devastating diseases of apple (Malus × domestica). We identified a hairpin RNA (hpRNA)-mediated small RNAs, MdhpRNA277, from apple (cv. ‘Golden Delicious’) that is induced by infection with ALT1. MdhpRNA277 produces mdm-siR277-1 and mdm-siR277-2, which target five R genes, MdRNL1, MdRNL2, MdRNL3, MdRNL4, and MdRNL5, that are expressed at high levels in the resistant apple variety ‘Hanfu’ and at low levels in the susceptible variety ‘Golden Delicious’ following ALT1 infection. MdhpRNA277 is strongly induced in ‘Golden Delicious’ but was not induced in ‘Hanfu’ following ALT1 inoculation. The promoter activity of MdhpRNA277 was much stronger in ‘Golden Delicious’ than in ‘Hanfu’ after ALT1 inoculation. We identified a single nucleotide polymorphism (SNP) in the MdhpRNA277 promoter region between the susceptible variety ‘Golden Delicious’ (pMdhpRNA277-GD) and resistant variety ‘Hanfu’ (pMdhpRNA277-HF). The transcription factor MdWHy binds to pMdhpRNA277-GD, but not to pMdhpRNA277-HF. Transgenic ‘GL-3’ apple lines expressing pMdhpRNA277-GD: MdhpRNA277 were more susceptible to ALT1 infection than were those expressing pMdhpRNA277-HF:MdhpRNA277 due to induced mdm-siR277 accumulation and low levels of expression of the five target R genes. The failure of MdWHy to bind to pMdhpRNA277-HF might contribute to the low levels of MdhpRNA277 and mdm-siR277-1/-2 expression and the high levels of R gene expression and resistance to Alternaria leaf spot in resistant apple varieties. We confirmed that the SNP in pMdhpRNA277 is associated with Alternaria leaf spot resistance by analyzing the progeny of three additional crosses. The SNP identified in this study could be used as a marker to distinguish between apple varieties that are resistant or susceptible to Alternaria leaf spot.

overall_design: Small RNAs were induced  by  Alternaria alternaria f. sp. mali (ALT1) infection in apple by deep sequencing

first: Qiulei

last: Zhang


title: Genome-wide comparison of gene expression between biofilm and planktonic growth

city: Paris

first: Monot

last: Marc

address: 25, rue du docteur roux

department: Genomes and Genetics

institute: Institut Pasteur

summary: In this study, we used an original system to produce C. difficile anaerobic biofilms consisting in continuous-flow microfermentors, that is compared to planktonic growth culture.

overall_design: Two-conditions experiments, 630E strain Biofilm in Bioreactor and Planktonic growth at 24h in TY, 4 biological replicates for each condition

first: Isabelle

last: Poquet


title: Argopecten irradians, gills, exposed to okadaic acid

status: Public on Dec 21 2018

city: nanjing

first: Cheng

last: Chi

address: weigang road

institute: Nanjing Agricultural University

summary: Differential expression analysis of gill tissues of bay scallop (Argopecten irradians) exposed to okadaic acid at a concentration of 500 nM for 48 h.

overall_design: Each sample consists in total RNA was extracted from pooled tissues of 18 individuals

first: Chi

last: Cheng