title: PQR309 is a novel dual PI3K/mTOR inhibitor with antitumor pre-clinical activity in lymphomas as single agent and in combination

status: Public on Jan 24 2019

city: Bellinzona

first: Francesco

last: Bertoni

state: Ticino

address: Via V. Vela 6

department: Lymphoma & Genomics Research Program

country: Switzerland

institute: IOR

summary: assess the efficacy of dual PI3K/mTOR inhibitor with anti-lymphoma activity as single agent and in combination

overall_design: GEP analysis of 8 lymphoma cell lines with and without treatment

first: Chiara

last: Tarantelli

first: Eugenio

last: Gaudio

first: Andrea

last: Rinaldi

first: Luciano

last: Cascione


title: miRNA profiling in MMP-8 overexpressing MDA-MB-231 cells

status: Public on Jan 27 2019

city: Valbonne - Sophia-Antipolis

first: Kevin

last: Lebrigand

address: 660 route des lucioles

country: France

institute: IPMC/CNRS

summary: Matrix metalloproteinases (MMPs) have been traditionally implicated in cancer progression because of their ability to degrade the extracellular matrix. However, some members of the MMP family have recently been identified as proteases with antitumor properties. Thus, it has been described that collagenase-2 (MMP-8) has a protective role in tumor and metastasis progression, but the molecular mechanisms underlying these effects are unknown. We show herein that Mmp8 expression causes a decrease in miR-21 levels that in turn leads to a reduction in tumor growth and lung metastasis formation by MDA-MB-231 (4175) breast cancer cells. By using both in vitro and in vivo models, we demonstrate that the mechanism responsible for these MMP-8 beneficial effects involves cleavage of decorin by MMP-8 and a subsequent reduction of transforming growth factor ? (TGF-?) signaling that controls miR-21 levels. In addition, miR-21 downregulation induced by MMP-8 increases the levels of tumor suppressors such as programmed cell death 4, which may also contribute to the decrease in tumor formation and metastasis of breast cancer cells overexpressing this metalloproteinase. These findings reveal a new signaling pathway for cancer regulation controlled by MMP-8, and contribute to clarify the molecular mechanisms by which tumor-defying proteases may exert their protective function in cancer and metastasis.

overall_design: Dye swap-experiment comparing MMP8-overexpressing MDA-MB-231 cells  versus control MDA-MB-231 cells .

first: Bernard

last: Mari

first: Carlos

last: Lopez-Otin

first: Pascal

last: Barbry


title: Assessing chromatin accessibility in maize with ATAC-seq

status: Public on Jan 23 2019

city: Taipei

first: Pao-Yang

last: Chen

address: 128 Academia Road, Section 2, Nankang

department: Institute of Plant and Microbial biology

country: Taiwan

institute: Academia Sinica

type: Genome binding/occupancy profiling by high throughput sequencing

summary: Maize (Zea mays) is one of the most important crop in the world. Better understanding the maize chromatin architecture points to novel approaches to improve crop yield. Here, we describe the first ATAC-seq protocol to assess the maize genome. Fresh leaf tissue was gently chopped by a blade to release intact nuclei which later were fractionated using Percoll-sucrose gradient. The isolated nuclei were treated with a transposase that fragments and tags the genome; these fragments were subjected to two rounds of PCR to generate the ATAC-seq library. In the first round of PCR, these fragments were amplified with 5 cycles and sequencing barcodes were added. A fraction of the first PCR product was subjected to qPCR to determine the optimal amplification cycle number in the second round of PCR.  The library quality can be assessed by a Bioanalyzer prior to sequencing. The distinct bands indicated good quality. After sequencing, the computational analysis of fragment size distribution may show patterns of periodicity that is a characteristic to ATAC-seq libraries. In our preliminary analysis, we found that 85% percent of the identified regions deviate from closed regions previously identified by MNase-seq, suggesting that the ATAC-seq library preparation procedure described here is effective in identifying open chromatin regions of the maize genome.

overall_design: We extract the maize's nuclei to apply on Maize ATAC-Seq, provide a new way to study the role of chromatin accessibility. From the Library QC data, can show a successful ATAC-Seq library characteristics. 2500 nuclei is the best numbers for do maize ATAC-Seq.

first: Yi-Jing

last: Lee

first: Pearl

last: Chang

first: Jui-Hsien

last: Lu

first: Chung-Ju

middle: R

last: Wang


title: Expresssion data of Prdm14 KO ESCs expressing each orthologues.

status: Public on Jan 29 2019

city: Sanda

first: Yoshiyuki

last: Seki

state: hyogo

address: 1, Gakuen Uegahara

department: School of Biological and Environmental Sciences

country: Japan

institute: Kwansei Gakuin University

summary: Gene regulatory networks underlying cellular pluripotency are controlled by a core circuitry of transcription factors, including POU5F1 and NANOG in mammals. However, the evolutionary origin and transformation of pluripotency transcriptional networks have not been elucidated in deuterostomes. PR domain-containing protein 14 (PRDM14) is specifically expressed in pluripotent cells and germ cells, and is required for establishing embryonic stem cells (ESCs) and primordial germ cells (PGCs) in mice. Here, we compared the functions and expression patterns of PRDM14 orthologues within deuterostomes. Amphioxus PRDM14, zebrafish PRDM14, and the combination of sea urchin PRDM14 and CBFA2T compensated for disruption of the mouse Prdm14 gene in terms of maintaining mouse ESC pluripotency. Interestingly, Prdm14 was expressed in motor neurons, but not in germ cells in amphioxus embryos as observed in zebrafish embryos. Therefore, our results suggest that the integration of the PRDM14–CBFA2T complex into the transcriptional network for pluripotency may be essential for stabilizing pluripotency during the early amniote development.

overall_design: We anlalyzed 8 samples on two strip of microarray detected by GeneAtlas.


title: The antifibrotic activity of the selective IP receptor agonist ACT-333679 is mediated through inhibition of YAP/TAZ signaling

city: Allschwil

first: Axel

last: Klenk

address: Hegenheimermattweg 91

department: Research Informatics

institute: Idorsia Pharmaceuticals Ltd.

type: Expression profiling by high throughput sequencing

summary: Idiopathic pulmonary fibrosis (IPF) is a life-threatening and progressive scarring disease of the lung. Loss of alveolar epithelial cells, inflammation, activation of fibroblasts, appearance of myofibroblasts and excessive deposition of extracellular matrix (ECM) are central features of IPF pathogenesis, ultimately resulting in changes in tissue architecture and lung dysfunction. The two currently approved therapies, pirfenidone (Esbriet®) and nintedanib (Ofev®), significantly slow the rate of disease progression, but they do not halt or reverse tissue remodeling. Therefore, disease modifying strategies that influence (myo)fibroblast activity and ECM deposition could lead to promising new treatments.   Here we demonstrate potent and effective in vitro antifibrotic properties of the selective prostacyclin (IP) receptor agonist, ACT-333679, on TGFβ1-stimulated primary human lung fibroblasts from non-diseased and IPF donors. We demonstrate that ACT-333679 inhibited fibrotic processes through elevation of cAMP, inhibition of YAP/TAZ signaling and subsequent suppression of YAP/TAZ-induced gene transcription.    Our results describe attenuation of YAP/TAZ signaling through IP receptor activation as a novel mechanism that suppresses pro-fibrotic (myo)fibroblast activity and we offer a rationale to further explore the potential of IP receptor agonists for the treatment of IPF .

overall_design: Comparison of TGFβ1-stimulated primary human lung fibroblasts from IPF donors treated with or without the selective prostacyclin (IP) receptor agonist, ACT-333679 after 8 hours; 4 replicates per group

first: Katarina

last: Zmajkovicova

first: Yasmina

last: Bauer

first: Katalin

last: Menyhart

first: Berengere

last: Renault

first: Marie

last: Schnoebelen

first: Matthias

last: Bolinger

first: Oliver

last: Nayler

first: John

last: Gatfield


title: Urinary exosomal long noncoding RNAs may be novel biomarkers for the diagnosis of clear cell renal cell carcinoma

city: Shanghai

first: Jia

middle: yi

last: Liu

address: Fengyang road 458，Huangpu District

country: China

institute: Changzheng Hospital

type: Non-coding RNA profiling by high throughput sequencing

summary:
Background: Renal cell carcinoma, which presents no significant clinical manifestations at early stages, is one of the few tumors with an increasing worldwide incidence. This malignancy cannot be directly detected by tumor markers in body fluid without information from imaging examinations. Approximately 30–40% of patients with kidney cancer exhibit distant metastasis at diagnosis, and their 5-year survival rate is much lower than that of patients with early-stage renal cell carcinoma. Thus, the early diagnosis of renal cell carcinoma is extremely important. The aim of this study was to investigate the utility of urinary exosomal long noncoding RNA (lncRNA) as a new potential diagnostic marker for renal cell carcinoma.
Methods: Exosomes were isolated by ultracentrifugation from 50-ml urine samples from 10 patients with clear cell renal cell carcinoma and 10 matched healthy donors. Differentially expressed lncRNAs were analyzed by next-generation sequencing and further validated in kidney cancer cell lines, tissues and urinary exosomes. Then, we evaluated the sensitivity, specificity, clinical diagnostic value and stability of the selected lncRNAs.
Results: The levels of lncRNAs NR_040448 and NR_033390 in urinary exosomes can likely indicate the presence of renal cell carcinoma. In addition, RNA protected by exosomes was stable enough to serve as a biomarker.
Conclusion: Urinary exosomal lncRNA is a promising marker for the early diagnosis of renal cell carcinoma.

overall_design: Exosomes were isolated by ultracentrifugation from 50-ml urine samples from 10 patients with clear cell renal cell carcinoma and 10 matched healthy donors. Differentially expressed lncRNAs were analyzed by next-generation sequencing.

first: Jiayi

first: Bing


title: Next Generation Sequencing Facilitates Quantitative Analysis of Wild Type and carbamazepine-stressed E. coli K-12 LE392, P. putida KT2440, and RP4 plasmid Transcriptomes

city: Brisbane

first: Jianhua

last: Guo

address: Research Road, Level 4 Gehrmann Building

department: Australian Centre for Water and Environmental Biotechnology

country: Australia

institute: University of Queensland

summary: The goals of this study are to use Next-generation sequencing (NGS) to detect bacterial mRNA profiles of wild-type E. coli K-12 LE392, P. putida KT2440 and IncPα RP4 plasmid, and their mRNA response under the exposure of antiepileptic drug carbamazepine. Three concentrations of carbamazepine were applied, which were 0.05 mg/L, 10.0 mg/L and 50.0 mg/L (refer to low, medium and high, respectively). The group without dosing carbamazepine was the control group. Each concentration was conducted in triplicate. By comparing the mRNA profiles of experimental groups and control group, the effects of carbamazepine on transcriptional levels can be revealed. Illumina HiSeq 2500 was applied. The NGS QC toolkit (version 2.3.3) was used to treat the raw sequence reads to trim the 3’-end residual adaptors and primers, and the ambiguous characters in the reads were removed. Then, the sequence reads consisting of at least 85% bases were progressively trimmed at the 3’-ends until a quality value ≥ 20 were kept. Downstream analyses were performed using the generated clean reads of no shorter than 75 bp. The clean reads of each sample were aligned to the E. coli reference genome (NC_000913), P.putida reference genome (NC_002947), and IncPα plasmid reference genome (NC_00) using SeqAlto (version 0.5). Cufflinks (version 2.2.1) was used to calculate the strand-specific coverage for each gene, and to analyze the differential expression in triplicate bacterial cell cultures. The statistical analyses and visualization were conducted using CummeRbund package in R (http://compbio.mit.edu/cummeRbund/). Gene expression was calculated as fragments per kilobase of a gene per million mapped reads (FPKM, a normalized value generated from the frequency of detection and the length of a given gene.

sample_organism:
Pseudomonas putida
Escherichia coli

platform_organism:
Pseudomonas putida
Escherichia coli

overall_design: Bacterial mRNA profiles of wild-type E. coli K-12 LE392, P. putida KT2440, and IncPα RP4 plasmid in response to 0.05, 10.0, and 50.0 mg/L carbamazepine for 2 hours, bacteria and plasmid without dosing carbamazepine are the control group, in triplicate, using Illumina HiSeq 2500

first: Yue

first: Ji

first: Likai

last: Mao


title: The long non-coding RNA LINC00941 and SPRR5 are novel regulators of human epidermal homeostasis

status: Public on Jan 28 2019

city: Regensburg

first: Christian

last: Ziegler

address: Universitaetsstrasse 31

country: Germany

institute: University Regensburg

summary: Several long non-coding RNAs (lncRNAs) act as regulators of cellular homeostasis; however, few of these molecules were functionally characterized in a mature human tissue environment. Here, we report that the lncRNA LINC00941 is a crucial regulator of human epidermal homeostasis. LINC00941 is enriched in progenitor keratinocytes and acts as a repressor of keratinocyte differentiation. Furthermore, LINC00941 represses SPRR5, a previously uncharacterized molecule, which functions as an essential positive regulator of keratinocyte differentiation. Interestingly, 54.8% of genes repressed in SPRR5 deficient epidermal tissue are induced in LINC00941 depleted organotypic epidermis, suggesting a common mode of action for both molecules.

overall_design: Investigating the impact of LINC00941 (on day 2 and day 3 of differentiation) or SPRR5 (on day 3 and day 4 of differentiation) depletion on the keratinocyte differentiation status in organotypic epidermal tissue cultures by high throughput sequencing.

first: Johannes

last: Graf

first: Stefan

last: Faderl

first: Jessica

last: Schedlbauer

first: Nicholas

last: Strieder

first: Bianca

last: Förstl

first: Rainer

last: Spang

first: Astrid

last: Bruckmann

last: Merkl

first: Sonja

last: Hombach

first: Markus

last: Kretz


title: Transcriptome analysis of rhesus monkey embryos

status: Public on Jan 31 2019

city: East Lansing

first: Uros

last: Midic

state: MI

address: 474 S. Shaw Lane

department: Animal Sciences

country: USA

institute: Michigan State University

summary: The goal of this study was to discover the underlying mechanisms that drive major changes in gene regulation during preimplantation development in the rhesus monkey. RNAseq data were collected from preimplantation stages (8-cell, morula, blastocyst), and used in conjunction with data from metaphase II stage oocytes to characterize individual gene expression profiles during preimplantation development, identify major groups of co-regulated genes, and identify likely upstream factors driving that gene regulation. Embryos were cultured following in vitro fertilization as described and lysed for analysis at specific stages.

overall_design: Transcriptomes of rhesus monkey MII oocytes, and 8-cell, morula, and blastocyst embryos were compared using RNAseq.

first: Meghan

middle: L

last: Ruebel

first: Peter

middle: Z

last: Schall

first: Kailey

middle: A

last: Vincent

first: Benjamin

last: Goheen

first: Catherine

last: VandeVoort

first: Keith

middle: E

last: Latham


title: Activity of afatinib in a window pre-operative EORTC study in patients with squamous cell carcinoma of the head and neck (HNSCC)

city: Milan

first: Loris

last: De Cecco

address: via Venezian 1

country: Italy

institute: IRCSS Istituto Nazionale Tumori

summary: Afatinib is a pan-HER inhibitor that improved progression-free-survival (PFS) in recurrent HNSCC versus methotrexate: median PFS 2.6 versus 1.7 months (LUX H&N 1 trial). This study is a translational research linked to  EORTC 90111  afatinib trial, an open-label, randomized, multicenter, phase II window of opportunity trial. Treatment-naïve HNSCC patients selected for primary curative surgery were randomized (5:1 ratio) to receive Afatinib during 14 days (day -15 until day -1) before surgery (day 0) or no treatment. Tumour biopsies, FDG/PET, and MRI were performed at diagnosis and at surgery. The primary end point was metabolic FDG-PET/CT response, defined according to EORTC guidelines.

overall_design: Eligible patients had to have a new histological diagnosis of HNSCC of the oral cavity, oropharynx, hypopharynx or larynx and be selected for primary curative surgery. The primary tumor needs to be ≥ 2 cm in their largest diameter measured bidimensionally by imaging done within two weeks prior to randomization.

first: Jean-Pascal

last: Machiels

first: Paolo

last: Bossi


title: Transcriptome analysis of the oriental fruit fly Bactrocera dorsalis early embryos

status: Public on Jan 25 2019

city: Wuhan

first: Wei

last: Peng

address: Shizishan Street No. 1, Hongshan District, Wuhan,Hubei  430070, P.R. China

institute: Huazhong Agricultural University

summary: We constructed three RNA libraries from embryos at 0-1, 2-4 and 5-8 post-oviposition (hpo) of Bactrocera dorsalis for deep sequencing. Using an Illumina HiSeq 2500 platform, we mapped more than 83, 85 and 98 million sequence reads from 0-1, 2-4 and 5-8 hour embryos respectively, and identified a total of 13,489 unigenes. 1683, 3201 and 3134 unigenes showed differential expression between the 0-1 and 2-4 hour embryos, the 0-1 and 5-8 hour embryos, and the 2-4 and 5-8 hour embryos respectively.

overall_design: RNA profiles from embryos at 0-1, 2-4 and 5-8 post-oviposition (hpo) of Bactrocera dorsalis were generated by Illumina deep sequencing.

first: Hongyu

last: Zhang


title: Genome-wide identification and characterization of transfer RNA-derived small RNAs in Plasmodium falciparum

city: Beijing

first: Zhensheng

last: Wang

address: Dongdan santiao

department: Microbiology and Parasitology

institute: Peking Union Medical College

summary: In this study, we performed deep sequencing and bioinformatics analyses of short RNAs from Plasmodium falciparum parasites to identify and characterize novel type of small RNAs. A total of 14,828,877 raw reads were produced from small RNA libraries. We detected a new type of small RNA from tranfer RNA known as tRFs.

overall_design: Plasmodium falciparum small RNAs of 18–30 nt in length were extracted and purified from the total RNA of blood staged parasites. Small RNA libraries were constructed and sequenced by Illumina solexa sequencing.

first: Zenglei

first: Heng


title: KDM6A improves the efficiency of nuclear transfer reprogramming in bovine

city: Yangling

first: Chuan

last: Zhou

state: Shaanxi

address: 3 Taicheng Road

department: College of Veterinary Medicine

institute: Northwest A&F University

summary: As a histone hallmark for transcription repression, Histone H3 lysine 27 trimethylation (H3K27me3) plays important roles in mammalian embryo development and induced pluripotent stem cells (iPSCs) generation. However, the expression profile and roles of H3K27me3 in bovine somatic cell nuclear transfer (SCNT) reprogramming remain poorly understood. In this study, we find SCNT embryos exhibit global hypermethylation of H3K27me3 from two-cell to eight-cell stage and its removal by ectopically expressed H3K27me3 demethylase-KDM6A could greatly improves SCNT efficiency. To illuminate the mechanism of improving SCNT reprogramming efficiency of KDM6A overexpression, we performed RNA sequencing of transcripts in SCNT morula with or without KDM6A overexpression. RNA-seq reveal that KDM6A overexpression could enhance transcription of genes mainly involved cell adhesion and cellular metabolism process, as well as X-linked genes. We first provides the transcriptome data of bovine SCNT morula with or without KDM6A overexpression. Meanwhile, we compared the differences of transcriptome between SCNT eight-cell embryos and morula. Our study provide a more promising approach to improving the efficiency of SCNT reprogramming and contribute to understanding the mechanism of first cell fate determine during embryo development in bovine.

overall_design: RNA-Seq profiles from pools of morula embryos from SCNT with (3 replicates) or without (3 replicates) KDM6A overexpression were generated using Illumina HiSeq 4000. SCNT morula without KDM6A overexpression are defined as the control. The RNA-seq data of SCNT eight-cell embryo were obtained from the Gene Expession Omnibus DataSets, accession number GSE99294

first: Yong

first: Jingcheng

first: Xin

last: Liu


title: Synthetic lethal siRNA screen for TN-IBC cell line SUM149PT using kinome library with EPA treatment

city: Houston

first: Yuan

last: Qi

state: TX

address: 1400 Pressler St

department: Bioinformatics & Computational Biology

institute: University of Texas M.D. Anderson Cancer Center

summary: Synthetic lethal siRNA screen using a kinome library containing 939 druggable genes in the TN-IBC cell line SUM149PT, in combination with EPA treatment.

overall_design: To identify a targetable candidate that would complement the antitumor effect of EPA, we performed a high-throughput, synthetic lethal siRNA screen using a kinome library containing 939 druggable genes in the TN-IBC cell line SUM149PT, in combination with EPA treatment.

first: Angie

middle: M

last: Torres-Adorno

first: Naoto

middle: T

last: Ueno


title: Global Gene Expression Changes in Cholangiocytes Treated with TGF-beta

city: Rochester

first: Aditya

last: Bhagwate

state: MN

address: 200 1st Street SW

institute: Mayo Clinic

summary: The growth factor, TGF-beta can have profound effect on global gene expression changes. Since TGF-beta signaling is not well studied in liver epithelia, RNA-seq analysis was performed to evaluate TGF-beta signaling in cholangiocytes.

overall_design: Cholangiocyte cell line, HIBEC,  were treated with Vehicle or TGF-beta for 48 hours to look at the gene expresson changes induced by TGF-beta

first: Nidhi

last: Jalan-Sakrikar

first: Robert

middle: C

last: Huebert


title: Profiling transcriptional changes in differentiating endoderm from mouse embryonic stem cells

city: Charleston

first: Jeremy

last: Barth

state: SC

address: 173 Ashley Ave, BSB 627

institute: MUSC

summary: Expression profiling was performed for endoderm differentiation in alpha-fetoprotein expressing cells differentiated from embryonic stem cells (ESCs) at 3 different stages of differentiation. Cells were sorted for alpha-fetoprotein expression at days 4, 7 and 21 of embryoid body differentiation and then subjected to Affymetrix DNA microarray analysis.

overall_design: Nine samples were analyzed; experimental groups were 3 replicates each (n=3) of Afp(+) cells collected at days 4, 7 and 21 of embryoid body differentiation.

first: Ann

last: Foley


title: Comparative genomic hybridization analysis in glycine max fast neutron mutants - seed composition in southern U.S. varieties

city: Saint Paul

last: Stupar

address: 411 Borlaug Hall, 1991 Upper Buford Circle

department: Agronomy and Plant Genetics

institute: University of Minnesota

summary: Four seed composition mutants (known as G15FN-109-1, G15FN-12-1, G15FN-23-3, and G15FN-54-3) were identified in a soybean fast neutron population developed in southern U.S. lines. The parent line for G15FN-109-1 is G00-3880, while the parent line for the other three mutants is G00-3213. Each mutant was compared to its respective parent line using CGH to identify the causative region/gene associated with the seed composition phenotypes.

overall_design: Four fast neutron mutant samples was analyzed. Each sample was compared to its wild type parent using Agilent CGH arrays.

first: Elizabeth

last: Prenger

first: Alexandra

last: Ostezan

first: Rouf

last: Mian

first: Travis

last: Glenn

first: Zenglu

last: Li

first: Adrian

last: Stec


title: Exploring the genes associated with male sterility mutant (msm) in Chinese cabbage (Brassica campestris ssp. pekinensis) using RNA-Seq

city: Shenyang

first: Shengnan

last: Huang

address: 120 Dongling Road Shenhe District Shenyang P.R. China

institute: Shenyang Agricultural University

summary: The hybrid seed production was performed using the male sterility line, which is an important way of heterosis utilization in Chinese cabbage. A stably inherited male sterile mutant msm was obtained from a Chinese cabbage DH line ‘FT’ using the isolated microspore culture combined with 60Co γ-rays mutagenesis. Compared to the wild type ‘FT’, the msm exhibited completely degenerated stamens and no pollen phenotype, and other characters had no significant difference except for stamen. The genetic analysis indicated that the msm mutant phenotype was controlled by a single recessive nuclear gene. Cytological observation showed that the stamen abortion of msm began at the tetrad period, and tapetum cells were abnormally expanded and highly vacuolated, leading to microspore abortion. Comparative transcriptome analysis on the flower buds of ‘FT’ and msm using RNA-Seq technology revealed a total of 1,653 differentially expressed genes (DEGs). Among which, a large number of genes associated with male sterility were found, including 64 pollen development and pollen tube growth-related genes, 94 pollen wall development-related genes, 11 phytohormone-related genes and 16 transcription factor-related genes, and the overwhelming majority of these genes were down-regulated in the msm vs. ‘FT’ comparison. Furthermore, KEGG pathway analysis indicated that a variety of carbohydrate metabolic and lipid metabolic pathways were significantly enriched, which may be related to pollen abortion. The expression patterns of 24 male sterility-related genes were analyzed using qRT-PCR. In addition, a total of 24,476 single nucleotide polymorphisms and 413,073 insertion-deletion events were specifically detected in msm. These results facilitate to elucidate the regulatory mechanisms of male sterility in Chinese cabbage.

overall_design: The RNA from the developing flower buds of a male sterility mutant (msm) and its wild type‘FT’at the full-bloom stage in Chinese cabbage were sequenced by RNA-Seq, in triplicate.

first: Shenling

last: Peng

first: Zhiyong

first: Chengyu

first: Chong

last: Tan

first: Runpeng

last: Yao

first: Danyang

first: Xiang

first: Li

last: Hou

first: Hui

last: Feng


title: MiR-146a downregulation contributes to sunitinib-induced cardiac dysfunction

city: Shijiazhuang

first: Shen

state: Hebei

address: Zhongshan Road 361

institute: Hebei Medical University

summary: The left ventricle tissue of mice underwent microarray assaying to reveal the miRNA alterations induced by SNT.

overall_design: Analysis of miRNA expression was performed with total RNA extracted from left ventricle tissue samples of mice administered vehicle or sunitinib.200 ng of total RNA extracted from the myocardium was fluorescent labeled with Cyanine3-pCp using miRNA Complete Labeling and Hyb Kit. The labeled samples were then concentrated and hybridized with the Hybridization Chamber gasket slides.

last: Shen

first: Congxi


title: Comparative transcriptome profiling of tomato (Solanum lycopersicum L.) pollen grains during maturation and in response to acquired thermotolerance conditions

city: Frankfurt am Main

first: GenXPro

last: GenXPro

address: Altenhöferallee 3

institute: GenXPro GmbH

summary: Global temperature increase poses a serious challenge for agricultural production worldwide, affecting yield in many crops including vegetable crops. While most crop plants can survive temperature increases during their vegetative growth periods, the reproduction phase is highly heat-stress (HS)-sensitive. Impaired pollen development and functioning under HS is implicated as the major cause for yield reduction. To better understand HS effect on pollen and identify pollen thermotolerance mechanisms, we established conditions that enable developing pollen grains to acquire thermotolerance (ATT conditions), using tomato as a model system. High-throughput sequencing at cDNA level was performed by Massive Analysis of 3’cDNA using Illumina HiSeq 2000 technology, generating a total of 6430 and 4660 transcripts differentially expressed (p ≤ 1e-05) during pollen development/maturation and following response of developing pollen to ATT, respectively. Gene Onthology functional analysis showed that transcripts related to maintenance of protein homeostasis (translation, proteolysis, protein folding) were enriched during pollen maturation and following the ATT treatment in our study, highlighting these processes as central for enabling pollen maturation and maintenance of pollen functioning under HS. The transcriptomic data was compared to available pollen proteomic data based on the same experimental setup and an overlap of 47% was detected between differentially expressed proteins and transcripts following ATT conditions, highlighting genes/proteins involved in protein folding, oxidation-reduction and translation, and validating transcriptomic results. Involvement of mitochondria and endoplasmic reticulum in pollen heat acclimation, and activation of several HSPs including sHSPs and HSP101, for protecting pollen cellular components including the translational machinery, are indicated. The results of this study can serve as a valuable resource of genes for future research on improving pollen thermotolerance.

overall_design: Establishment of the capacity of developing tomato pollen grains to acquire thermotolerance (ATT) using greenhouse-grown plants. Then, use of the established ATT conditions to test the effect on expression profiles of developing/maturing and mature pollen grains. Developing pollen grains are represented by pooling three developmental stages (3, 2 and 1 days before flower opening).

first: Nurit

last: Firon

first: Kamila

last: Bokszczanin

first: Sridharan

last: Jegadeesan

first: Nicolas

last: Krezdorn

first: Björn

last: Rotter

first: Avital

last: Beery

first: Adi

last: Doron-Faigenboim

first: Etan

last: Pressman

first: Peter

last: Winter

first: David

last: Honys


title: Long non-coding RNA Expression Profiling in Lung Cancer = Lung Adenocarcinoma (Lu-T) and in normal lung tissue (Lu-N)

city: Heidelberg

first: Sven

last: Diederichs

address: Im Neuenheimer Feld 280

department: RNA Biology & Cancer

institute: German Cancer Research Center (DKFZ)

summary:
The expression of long non-coding RNAs - lncRNAs - was profiled in the lung adenocarcinoma patient samples (LUAD, Lu-T) and in normal lung tissues adjacent to tumors (Lu-N) using the Invitrogen NCode Human lncRNA Array Platform.
will be published in: Anna Roth et al., Restoring LINC00673 expression triggers cellular senescence in lung cancer

overall_design: 27 tumor samples, 27 normal samples, data provided as log2 signal intensities quantile normalized with a minimum signal intensity (threshold 1.0)

first: Maria

last: Polycarpou-Schwarz

first: Anna

last: Roth

first: Arne

last: Warth

first: Philipp

last: Schnabel

first: Thomas

last: Muley

first: Michael

last: Meister

first: Heike

last: Zabeck

first: Hans

last: Hoffmann


title: Unregulated APC activation by T cells breaks self-tolerance

city: Pohang

first: Jaeu

last: Yi

country: South Korea

institute: POSTECH

summary: The absence of nTregs results in slight increase of B7 on dendritic cells (DC). Such slightly elevated B7 induce proliferation of T cells with intrinic high self-affinity: bidirectional T/DC interaction ensues, leading to progressive DC activation and reciprocal strong T cell activation.

overall_design: mRNA were purified from lymph node or spleen dendritic cells of germ-free Rag KO mice adoptively transferred with FACS-purifed naïve CD4 T cells or Tregs before a week.

first: J

last: Jung

first: S

last: Hong

first: D

last: Han

first: C

middle: D

last: Surh


title: Transcriptomic Predictors of Paradoxical Cryptococcosis-Associated Immune Reconstitution Inflammatory Syndrome

city: Minnespolis

first: Irina

last: Vlasova-St. Louis

address: 2001 6th St SE

department: Medicine

summary: Paradoxical cryptococcosis-associated immune reconstitution inflammatory syndrome

overall_design: Human samples: IRIS and control

last: St. Louis


title: Transcriptional correlates of falling in love

city: Los Angeles

first: Steve

last: Cole

state: CA

address: 11-934 Factor Bldg, UCLA

institute: UCLA School of Medicine

summary: Genome-wide transcriptome profiling of 111 peripheral blood mononuclear cells (PBMC) collected from 47 young women over the course of a 2-year longitudinal study of new romantic relationships.

overall_design: To characterize the impact of romantic love on human genome function, we conducted genome-wide transcriptome profiling of 111 samples of peripheral blood mononuclear cells (PBMC) collected from 47 young women over the course of a 2-year longitudinal study of new romantic relationships. Eligibility criteria included, 1) heterosexual female, 2) not pregnant or breastfeeding, 3) non-smoker, 4) no immune, cardiovascular, or psychiatric medication, 5) planning to remain in city for 6 mo, 6) in an exclusive (monogamous) romantic relationship for < 1 mo, and, 7) not yet in love with their partner. Following a baseline blod draw and survey, participants completed twice-monthly brief surveys until, 1) they reported falling in love with their partner, 2) they reported they and their partner had broken up, 3) they were selected as a yoked control participant for another participant that had fallen in love, or 4) 12 mo had elapsed. Any of these events triggered a 2nd blood sample and comprehensive survey. For those who had broken up, participation concluded after the 2nd blood draw. Those still in relationships continued to complete bi-weekly brief surveys until they either reported a break-up, they reported falling in love (if they were not in love at blood draw 2), or 12 mo had elapsed after blood draw 2. Participants were scheduled for a 3rd blood draw and comprehensive survey after any of these events .  Brief surveys assessed whether participants were in love with their partner (0=no;1=yes), sexual behavior (e.g., sexual intercourse frequency per week, oral sex frequency per week, semen exposure [0=no;1=yes]) and self-reported illness symptoms (0=none;1=present).


title: ra12-02_aba-seed-ABA signaling in Arabidopsis seeds

city: evry

first: Soubigou-Taconnat

last: Ludivine

address: 2 rue gaston crémieux

department: URGV

institute: INRA

summary: ra12-02_aba-seed - ra12-02_aba-seed - Identification of ABA signaling factors and targets in Arabidopsis developing seeds by comparing ABA deficient and wild type genotypes - Transcriptome comparison of developing seeds harvested at 10 DAP from two ABA-deficient mutants (nced2 nced5 nced9 and nced2 nced5 nced6 nced9) and wild type (Columbia-0)

overall_design: 9 dye-swap - gene knock out,genomic comparison

first: José

last: Caius

first: Francois

last: Perreau

first: Annie

last: Marion-poll

first: Sandrine

last: Balzergue

first: Marie-Laure

last: Martin-Magniette


title: Gene expression associated with panitumumab efficacy in squamous cell carcinoma of head and neck

first: Loris

last: De Cecco

summary: Platinum-based chemotherapy plus cetuximab, an anti-Epidermal Growth Factor Receptor (EGFR) monoclonal antibody (Mab), is usually offered to recurrent/metastatic (R/M) head-neck squamous cell carcinoma (HNSCC) patients, with only a small portion experiencing durable responses.  The anti-EGFR-Mab panitumumab, was used as single agent in platinum pre-treated R/M-HNSCC patients in a phase II trial (PANI01). By analyzing gene expression profiles of a selected retrospective series of HNSCC patients treated with cetuximab, an anti-Epidermal Growth Factor Receptor (EGFR) monoclonal antibody (MAb), associated to chemotherapy, we were able to propose that long progression-free survival (PFS) cases consistently belong to defined molecular subtypes, such as Cluster3-hypoxia and Basal subtypes, respectively defined by De Cecco et al [DeCecco; Oncotarget, 2015] and Keck et al [Keck; CCR,2015], while short-PFS cases are characterized by an over-activation of RAS signaling

overall_design: Formalin-fixed, paraffin-embedded (FFPE) tumor specimens were collected from PANI01 trial: 20 samples were retrieved from primary tumors and five from R/M. RNA extraction, quality control and hybridization on DASL microarrays (Illumina) were performed as described [Bossi et al; CCR, 2016].


title: Differential gene expression of human natural killer cells following immobilized IgG1 stimulation

city: Baltimore

first: yang

last: song

state: MD

address: HSF-3, 3rd Floor; 670 W Baltimore St.

department: Department: Institute for Genome Sciences

institute: University of Maryland in Baltimore

summary: Analysis of human natural killer cells following stimulation with immobilized IgG1 for 4 and 24 hours. Results identified significantly differentially expressed genes in natural killer cells stimulated with immobilized IgG1 providing insight into how antibodies modulate the transcriptome in way that may contribute to cell activation and immune tolerance

overall_design: Natural killer (NK) cells from human peripheral blood mononuclear cells were stimulated for 4 or 24 hours in the presence of absence of immobilized IgG1. Following stimulation, NK cells were collected for total RNA extraction and hybridization to Illumina Human HT-12 v 4.0 Expression BeadChips.

first: E

last: So

first: Y

last: Song

first: R

last: Hertzano

first: Z

last: Zhang

last: Strome


title: Transcriptome response of Gluconobacter oxydans against five typical aldehyde inhibitors

city: Shanghai

first: Jie

last: Bao

address: 130 Meilong Road

institute: East China University of Science and Technology

summary: Toxic inhibitory compounds from lignocellulose pretreatment are the major obstacle to achieve high bioconversion efficiency in biorefinery fermentations. This study shows a unique glucose oxidation catalysis of Gluconobacter oxydans with its gluconic acid productivity free of inhibitor disturbance. The microbial experimentations and the transcriptome analysis revealed that both the activity of the membrane-bound glucose dehydrogenase (mGDH) and the transcription level of the genes in periplasmic glucose oxidation respiratory chain of G. oxydans were essentially not affected under the existence of inhibitory compounds. G. oxydans also rapidly converted furan and phenolic aldehyde inhibitors into the less toxic alcohols or acids. The synergy of the robust periplasmic glucose oxidation and the rapid inhibitor conversion of G. oxydans significantly elevated the efficiency of the oxidative fermentation in lignocellulose hydrolysate. The corresponding genes responsible for the conversion of furan and phenolic aldehyde inhibitors were also mined by DNA microarrays. The synergistic mechanism of G. oxydans provided an important option of metabolic modification for enhancing inhibitor tolerance of general fermentation strains.

overall_design: Two-condition experiment, aldehyde treated vs. untreated Gluconobacter oxydans cells. Biological replicates: 3 control replicates, 3 furfural treated replicates, 3 5-(hydroxymethyl)-2-furaldehyde (HMF) treated replicates, 3 4-hydroxybenaldehyde treated replicates, 3 syringaldehyde treated replicates, 3 vanillin treated replicates.

first: Pingping

last: Zhou


title: Principles and characteristics of the WRKY regulatory network of early MAMP-triggered immunity [RNA-Seq]

status: Public on Jan 22 2019

city: Cologne

first: Barbara

last: Kracher

address: Carl-von-Linné-Weg 10

department: Plant-Microbe Interactions

institute: Max Planck Institute for Plant Breeding Research

summary: During microbe-associated molecular pattern (MAMP)-triggered immunity (MTI) more than 5000 Arabidopsis genes are significantly altered in their expression and the question arises, how such an enormous reprogramming of the transcriptome can be regulated in a safe and robust manner? For the WRKY transcription factors, which are important regulators not only of this defense response, it appears that they act in a complex regulatory sub-network rather than in a linear fashion, which is much more vulnerable to gene function loss either by pathogen-derived effectors or by mutations. In this study we employed RNA-seq, mass spectrometry and ChIP-seq to find evidence for and uncover principles and characteristics of this network.

overall_design: Three biological replicates were analysed, each consisting of 4 conditions: plants of WT and wrky18 wrky40 wrky33 triple mutant genotype, each sampled at 0 h (untreated) and 2 h flg22 treatment.

first: Rainer

middle: P

last: Birkenbihl

first: Imre

last: Somssich


title: Principles and characteristics of the WRKY regulatory network of early MAMP-triggered immunity [ChIP-Seq]

overall_design: For each of two biological replicates we analysed 4 different conditions: plants of WT and wrky18 wrky40 wrky33 triple mutant genotype, each sampled at 0 h (untreated) and 2 h flg22 treatment. For each condition the IP was perfomred with an anti-allWrky antibody and input DNA served as negative control for the peak calling.


title: Distinct characteristics of Arabidopsis thaliana circular RNAs

city: Oldenburg

first: Sascha

last: Laubinger

address: Carl-von-Ossietzky-Str. 9-11

institute: University of Oldenburg

summary: In all living organisms, regulation of gene expression is fundamental for survival and adaptation. Gene expression can be modulated at various steps, including at the level of RNA processing. During the last few years, the importance of alternative splicing of mRNAs in controlling plant development and stress responses were emerged and highlighted its importance. Recently, an other type of alternative splicing has been reported which leads to the generation of circular RNAs (circRNAs), a novel class on endogenous noncoding RNAs. Several functions of circular RNAs have been proven or proposed, including functioning as microRNA or RNA-binding protein decoys, playing regulatory roles in gene expression or affecting transcriptional control via special RNA-RNA interactions. Despite the widening knowledge of circRNAs and their functional aspects in the animal kingdom, relatively little is known about circRNAs in plants.  In order to detect and classify circRNAs in Arabidopsis thaliana, we created a workflow that includes generation of Illumina libraries enriched for circRNAs and a comparison of biocomputational tools developed for detecting endogenous circular RNAs in other species. With the power of high-throughput sequencing and evaluation of algorithms, high-fidelity candidates were subjected for an analysis of their functional role in plant development and stress-related responses,  especially regarding the role of splicing, including alternative splicing events, splice site preference and strength variances and transcript composition and to comprehend the role of RNA processing in stress response.  Here we present an approach combining bioinformatic tools and molecular techniques to investigate the adaptability of  detection methods of circRNAs from other species to plant circular RNAs, and based on our high-fidelity results  identify and understand the characteristics of circRNAs in Arabidopsis thaliana.

overall_design: In order to identify and analyze circRNAs in plants, Arabidopsis thaliana liquid culture seedlings were subjected for NGS RNA library preparation. Plant material was treated with with the hormones salicylic acid and jasmonic acid, which mimic biotic stress conditions. Rnase R treatment, ribosomal and poly-A depletion were applied to enhance the signal. Libraries were done in triplicates.

first: Emese

middle: X

last: Szabo

first: Julian

last: Fratte

first: Margaux

last: Kaster


status: Public on Jan 19 2019

city: shanghai

first: manli

last: Yu

address: No.168 Changhai road

department: Department of Cardiology

institute: Changhai Hospital of Shanghai

summary: Diabetic hyperglycemia promotes reactive oxygen species (ROS) production to lead to oxidative stress and apoptosis responsible for progressive deterioration of the structure and function of organs. It has been indicated that factors and pathways regulating ROS production and the cellular redox state play a key role in the progression of diabetes and diabetes complications including cardiomyopathy. Recent studies had demonstrated that long non-coding RNAs (lncRNAs) played crucial roles on modulation of oxidative stress and apoptosis activity. In this study, we first established a high glucose induced oxidative stress and apoptosis model on primary rat cardiomyocytes. ROS formation and apoptosis activity were significantly increased at 24h/48h after high glucose stimulation. RNA sequencing analysis was applied to detect differentially expressed lncRNAs during cardiomyocytes oxidative stress and apoptosis.

overall_design: RNA-seq of a high glucose induced oxidative stress and apoptosis model on primary rat cardiomyocytes and control groups at 24h/48h.

first: Manli

first: Xianxian

last: Zhao


title: Whole blood transcriptome of childhood malaria

city: Tübingen

first: Angelica

last: Boldt

address: Wilhelmnstr 27

institute: Institute for Tropical Medicine

summary:
We aimed at finding differently expressed genes in whole blood cells of African children with asymptomatic Plasmodium falciparum infection (A), uncomplicated malaria (U), severe malarial anemia (A) and cerebral malaria (Ce) compared one to another and to healthy children (Co).
Understanding malarial immunopathology in the human host represents and enormous challenge for transcriptomic research. In this work, we used microarray and real-time RT-PCR technology to pursue deeper knowledge about the mechanisms underlying this disease in African children. To this end, we investigated the genomic transcriptional profiles in whole blood of healthy children and children with asymptomatic infection, uncomplicated malaria, malaria associated with severe anemia and cerebral malaria and compared them with previously published microarray results. We were able to discriminate between the different presentations of P. falciparum infection using supervised and unsupervised clustering of microarray data and unsupervised double-hierarchical clustering of real-time RT-PCR results of a set of 22 genes known to be expressed in at least one of the principal blood cell lineages. We further found considerable overlap between genes regulated in Kenyan and Gabonese children with symptomatic malaria, in contrast to adults with acute malaria from Cameroon. Different signatures for transcription factor binding sites in promoters of genes either up-regulated in symptomatic disease, specifically up-regulated in uncomplicated malaria or specifically down-regulated in cerebral malaria point out that similar gene expression in each of these clinical presentations is probably a result of common regulation at the transcriptional level. Immunoglobulin production, complement regulation and IFN beta signalling emerged as most discrepant features between uncomplicated malaria and all other investigated presentations, correlating with IRF7 and ISRE binding signatures in the corresponding genes. Down-regulation of several genes in cerebral malaria seems instead to be a response to hypoxia orchestrated by AhRF, GABP and HIF1 transcription factors. ARG1, BPI, CD163, IFI27, HP and TNFAIP6 transcript levels correlated positively with lactatemia and inversely with hemoglobin concentration and should be evaluated as prognostic markers to direct early therapeutic measures and prevent malarial disease evolution and death.

overall_design: We hybridized each of 25 U133A and 25 U133B microarrays (Human Genome oligonucleotide array chip, designed by Affymetrix, Santa Clara, CA) with pooled cRNA from 4 of 20 Co individuals (C), 4 of 20 individuals with A, 4 of 20 individuals with U, 4 of 20 with S and 4 of 20 with Ce (i.e. 5 pools from each group) (but two U133B microarrays of A and one of Ce could not be further used due to low hybridization quality). The pools were statistically homogeneous with respect to age, weight, temperature, respiration rate, BCS, hemoglobin concentration, hematocrit, white cell count, glycemia and lactatemia average values.

middle: B

first: Martin

last: Grobusch

first: Maryvonne

last: Kombila

first: Arnaud

last: Dzeing

first: Cristina

last: Tena-Tomás

first: Michael

last: Bonin

first: Peter

middle: G

last: Kremsner

first: Jürgen

middle: F

last: Kun

first: Thomas

last: Engleitner

first: T

last: Velavan


title: Principles and characteristics of the WRKY regulatory network of early MAMP-triggered immunity

first: Barbara

last: Kracher

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

overall_design: Refer to individual Series


title: CRISPR/Cas9 genome editing demonstrates that CCM3 modulates endothelial miRNA expression

status: Public on Jan 18 2019

city: Hamburg

first: Matthias

last: Rath

address: Am Kaiserkai 1

department: Institute of Molecular Medicine

institute: MSH Medical School Hamburg

summary: CCM3 regulates blood-brain-barrier integrity and vascular maturation in vivo. CCM3 loss-of-function variants predispose to cerebral cavernous malformations (CCM). Various signalling pathways are deregulated upon CCM3 depletion in endothelial cells (ECs). In this study, we established a crRNA:tracrRNA:Cas9 RNP approach to efficiently knockout CCM3 in human ECs and studied the molecular and functional effects of its long-term inactivation.  Using small RNA sequencing, we show that CCM3 regulates the expression of aging‑associated miRNAs.

overall_design: Examination of the miRNA expression profile of 4 wild-type CI-huVEC lines and 4 clonal CCM3-knockout CI-huVEC lines

first: Konrad

last: Schwefel

first: Stefanie

last: Spiegler

first: Sabine

last: Ameling

first: Christiane

last: Much

first: Robin

last: Pilz

first: Oliver

last: Otto

first: Uwe

last: Völker

first: Ute

last: Felbor


title: RNA sequencing to determine gene expression changes in HMCES knockout cells

status: Public on Jan 17 2019

city: Nashville

first: David

last: Cortez

state: TN

address: 2215 Garland Avenue

department: Biochemistry

institute: Vanderbilt University School of Medicine

summary: The purpose of this study was to deteremine gene expression changes in when HMCES is inactivated. We found very few changes.

overall_design: Compare wild type and HMCES knockout U2OS cancer cells using RNA-seq.

first: Kareem

middle: N

last: Mohni


title: Arabidopsis thaliana seedlings: Wild type vs. sdg8, hub2 and sdg8hub2 mutants

status: Public on Jan 21 2019

city: Strasbourg

first: Wen-Hui

last: Shen

address: 12 rue du General Zimmer

institute: IBMP-CNRS

summary: Transcriptional profiling of 6-day-old seedlings of Arabidopsis wild type control and mutants is performed using Affymetrix IVT Arabidopsis ATH1 Genome Array.

overall_design: Seedlings of wild type control vs. Mutant sdg8, hub2 or sdg8hub2. Three biological replicates: 3 control, 3 each of the three mutants, independently grown under 16h light/ 8h dark photoperiods and harvested.

first: Wen

middle: H


title: 5-aza-2'-deoxycytidine alters DNA methylation patterns on a genome-wide scale.

city: St. Andrews

last: Shuker

address: Greenside Place

department: School of Biology

country: United Kingdom

institute: University of St Andrews

type: Methylation profiling by high throughput sequencing

summary: However, that work lacked direct evidence of the effects of 5-aza-dC on DNA methylation, and indeed the effect of the chemical has since been questioned in Nasonia. Here, using whole-genome bisulphite sequencing of more than 4 million CpGs, across more than 11,000 genes, we demonstrate unequivocally that 5-aza-dC disrupts methylation on a large scale across the Nasonia vitripennis genome.

overall_design: We employed a three by three factorial design whereby females were allocated to one of three 5-aza-dC exposure regimes and were harvested post-feeding at three time points. Exposure regimes were a) 20% sucrose for 24h, b) 20% sucrose supplemented with 10 µM 5-aza-dC for 24h and c) 20% sucrose supplemented with 10 µM 5-aza-dC for 48h. For each of the three regimes, females were harvested at 0, 24 or 48h post-exposure.

first: Nicola

last: Cook

first: Darren

middle: J

last: Parker

first: Eran

last: Tauber

first: Bart

last: Pannebakker


title: Identification of cis elements for temporal and spatial control of DNA replication [Capture Hi-C]

city: Tallahassee

last: Gilbert

state: FL

address: 319 Stadium Drive

department: Biology

institute: Florida State University

summary: DNA replication occurs in units of chromatin higher order organization (Topologically Associating Domains, or TADs; replication domains, or RDs), which self-organize in 3D into sub-nuclear compartments of early or late replicating chromatin. However, identification of cis-elements regulating replication timing (RT) and sub-nuclear compartments has been a major challenge in the field. Through an extensive series of CRISPR mediated deletion and inversions at a pluripotency associated domain (DppA2/4) in mouse embryonic stem cells (mESCs), we have identified cis-regulatory “early replication control elements” (ERCEs) that mediate early replication and A/B compartmentalization. We show that CTCF/cohesin loops, including the TAD boundaries, were dispensable, and multiple internal DNA segments were necessary for the domain’s early replication in a partially redundant fashion. These segments were also sufficient to maintain early replication in the context of large inversions, irrespective of TAD boundaries. High-resolution capture Hi-C of this region revealed three sites of major contact that also displayed prominent chromatin features. Targeted deletion of all three contact points, which do not include the major mapped replication origins, caused a complete shift to late replication and association with compartment B, equivalent to the switch during lineage commitment. Individual and pair-wise deletions confirmed their partial redundancy and interdependency in giving rise to domain-wise RT patterns, and suggest the importance of long-range interactions. ERCEs are enriched in properties of strong or super-enhancers, and regulate gene expression, although transcription itself is not sufficient in driving early replication. In sum, our results have revealed the first cis-elements regulating the temporal and spatial control of DNA replication that is independent of transcription.

overall_design: Capture Hi-C profiles in mESCs with a bait in DppA2/4 domain.

first: Jiao

last: Sima


title: The gene expression profiles in response to kanamycin antibiotics in Arabidopsis thaliana

first: haibin

last: wei

address: 294 Taiyuan Road

department: Institute for Nutritional Sciences

institute: Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences

summary: Arabidopsis grown in a plastic pot was used to investigate the kanamycin phytotoxicity to seedling growth. The seedlings was irrigated with solution of different kanamycin concentration. After ten days in treatment, the gene expression profiles was conducted to compare the pattern of antibiotics-induced genes.

overall_design: Arabidopsis seeds grew in a plastic pot at 23 °C and 60% humidity condition. After 21 days, the seedlings was irrigated with 0, 350, 700 and 1400 mg/L kanamycin solution. The treatments sustained ten days, and then the 4-week-old seedlings were selected to extract total RNAs from pooled leaf tissue from a mixture of all the 12 plants in a pot. The gene expression profiles was conducted by single-color microarrays in Agilent Bioanalyzer.

first: QuanHong

last: Yao

first: Chen

last: Chen


title: Transcriptome Analysis of Common Carp (Cyprinus carpio) Fed with Animal and Plant Diets

city: Chengdu

first: Jie

last: Luo

state: Sichuan

address: Huimin road

department: College of Animal Science and Technology

institute: Sichuan Agricultural University

summary:
purpose?To elucidate the relationship of utilization different type of diets in fish
method?enzyme activity determination and transcriptome sequencing were performed in common carp fed with single animal diet group (group AD), plant diet group (group PD) and mix diets group (group MD). Group MD as control group
results? 916 and 1296 differentially expressed genes were identified between group AD vs MD and PD vs MD. Protein digestion and absorption, bile secretion, hematopoietic cell lineage and intestinal immune network for IgA production pathways were significantly differentially expressed between common carp fed with single type of diet and mix diets.
Conclusion?common carp fed with mix diets had stronger immunity than common carp fed with single type of diets.

overall_design: mRNA profiles of  common carp fed with earthworm, earthworm + duckweed and duckweed were generated by deep sequencing, in duplicate, using Illumina Hiseq 4000 platform.

first: Song

last: Yang


title: Integrated multi-omics characterization reveals metabolic reprogramming associated with impaired mitochondrial function in clear cell renal cell carcinoma.

city: Bari

first: Fabio

last: Sallustio

state: Bari

address: Piazza G. Cesare N°11

institute: University of Bari

summary: An altered metabolism is involved in the development of clear cell - renal cell carcinoma (ccRCC), and in this tumor many altered genes play a fundamental role in controlling cell metabolic activities. In this study we delineated a large-scale metabolomic profile of human ccRCC, and  integrated it with transcriptomic data to connect the variations in cancer metabolism with gene expression changes. Moreover, to better analyze the specific contribution of metabolic gene alterations potentially associated with tumorigenesis and tumor progression, we evaluated the transcription profile of primary renal tumor cells. Untargeted metabolomic analysis revealed a signature of an increased glucose uptake and utilization in ccRCC. In addition, metabolites related to pentose phosphate pathway were also altered in the tumor samples in association with changes in Krebs cycle intermediates and related metabolites. Using an integrated multi-omics approach we identified NADH dehydrogenase (ubiquinone) 1 alpha subcomplex 4-like 2 (NDUFA4L2) as the most highly expressed gene in renal cancer cells and evaluated its role in sustaining angiogenesis, chemoresistance, and mitochondrial dysfunction. Finally we showed that silencing of NDUFA4L2 affects cell viability, increases mitochondrial mass, and induces ROS generation in hypoxia.  These findings delineate a ccRCC metabolic signature characterized by an anaerobic switch that favors rerouting of the sugar metabolism toward the PPP, and impairs the mitochondrial activity though the overexpression of NDUFA4L2. Thus, this protein could serve as a marker of ccRCC aggressiveness, as well as a potential novel therapeutic target.

overall_design: Total RNA obtained from isolated primary normal and neoplastic EPCAM+ renal cells

first: Giuseppe

last: Lucarelli

first: Grazia

last: Serino

first: Monica

last: Rutigliano

first: Michele

last: Battaglia


title: miRNA expression data from primary central nervous system lymphomas (PCNSL)

city: Kyoto

first: Ryuya

last: Yamanaka

address: 465 Kajii-cho, Kamigyoku

institute: Kyoto Prefectural University of Medicine

summary: Expression profiling of miRNA was performed on 27 PCNSLs. A gene classifier was developed.

overall_design: Twenty-seven PCNSL patients were selected for miRNA extraction and hybridization on Affymetrix microarrays.

first: Yasuo

last: Takashima


title: Incipient diabetic retinopathy - Early regulation of genes

city: Mannheim

first: Carsten

last: Sticht

address: Theodor-Kutzer-Ufer

department: ZMF

institute: University Heidelberg

summary: The development of diabetic retinopathy is well characterized on a histological level. Early vascular alterations involve the loss of pericytes. Earlier mechanisms leading to the phenotype of diabetic retinopathy, which involves the complete neurovascular unit, are not yet fully understood. The gene expression data presented here is derived from microarrays and gives further insights into early genetic regulation in incipient diabetic retinopathy.

overall_design: 6-weeks-old STZ-diabetic animals (DC6W), and age-matched controls (NC6W) were analyzed after 6 (@6W) weeks.

first: K

last: Kohl

first: M

last: Kolibabka

first: P

last: Friedrichs

first: H

last: Hammes


title: Balancing apelin and angiotensin-II signaling to reduce heart injury during weightlessness

city: suzhou

first: wenyi

last: yuan

address: renai road No.199

institute: IBMS

summary: In order to further develop gene expression methods for simulated weightlessness, genome-wide microarray expression profiles were used as a discovery platform to identify genes differentially expressed in mice after simulated weightlessness. After 28 days of tail suspension simulated weightlessness in 10-week-old male C57BL/6 mice, 706 genes were identified to distinguish tail suspension from control samples.

overall_design: After 28 days of tail suspension, the expression of simulated weightlessness-inducible genes in myocardium of mice was measured. The mice in the control group were not tail suspended, and the other feeding conditions were the same. Three mice in each group were used for repeated experiments.

first: Wenyi

last: Yuan

first: Tianqing

last: Peng


title: SNP array_YW-JTH_NCOMMS-18-17273A

city: New York

first: Yuxiang

last: Wang

state: NY

department: HOPP

institute: Memorial Sloan Kettering Cancer Center

summary: SNP array files of normal human astrocytes (NHA) with ATRX deficiency.

overall_design: NHA were cultured for 15 passages where the start point (P0), P5, P15 were collected along with their controls and subjected to Affymetrix SNP 6.0 microarray.

first: Jie

first: Aaron

last: Wild

first: Wei

last: Wu

first: Rachna

last: Shah

first: Carla

last: Danussi

first: Gregory

last: Riggins

first: Kasthuri

last: Kannan

first: Erik

last: Sulman

first: Timothy

last: Chan

first: Jason

last: Huse


title: Analysis of differentially expressed genes in KYSE450 cell line after tranfection with miR-107, miR-198 and miR-214.

city: jinan

first: Yanli

last: Ren

state: shandong

address: huaiyin street

institute: SDCH

summary: This study aimed to identify differential expressed genes before and after tranfection with miR-107, miR-198 and miR-214, using the KYSE450 esophagus cancer cell line as a model.

overall_design: There were a total of 4 samples examined.

first: Ming

last: Yang


title: Identification of cis elements for temporal and spatial control of DNA replication [Hi-C]

first: David

last: Gilbert

first: Jiao

last: Sima


title: Gene expression profiling of tumors harvested from mice exhibiting diet-induced obesity (DIO mice) relative to lean control mice (control mice)

status: Public on Jan 16 2019

city: Detroit

first: Emily

middle: A.

last: Teslow

address: 4100 John R St.

department: Oncology

institute: Wayne State University School of Medicine

summary: Gene expression profiling by microarray analysis of  tumors formed from inoculation of the established human breast cancer cell line MDA-MB-468 in two groups of mice: lean control and DIO mice.

overall_design: This two-condition experiment, comparing tumors harvested from lean control vs. DIO B6.Rag1-/- mice (Jackson Laboratory, Bar Harbor, ME), employed Agilent 2-color arrays to analyze  3 independent biological replicates in each group.

first: E

first: A

last: Bollig-Fischer


title: The intestinal intermediate filament network responds to and protects against microbial insults and toxins II

city: Aachen

first: Bernd

last: Denecke

state: NRW

address: Pauwelsstrasse 30

department: IZKF Aachen

institute: RWTH Aachen University

summary: The enrichment of intermediate filaments in the apical cytoplasm of intestinal cells is evolutionarily conserved, forming a sheath that is anchored to apical junctions and positioned below the microvillar brush border, which suggests a protective intracellular barrier function. To test this, we used Caenorhabditis elegans, the intestinal cells of which are endowed with a particularly dense intermediate filament-rich layer that is referred to as the endotube. We found alterations in endotube structure and intermediate filament expression upon infection with nematicidal B. thuringiensis or treatment with its major pore-forming toxin crystal protein Cry5B. Endotube impairment due to defined genetic mutations of intermediate filaments and their regulators results in increased Cry5B sensitivity as evidenced by elevated larval arrest, prolonged time of larval development and reduced survival. Phenotype severity reflects the extent of endotube alterations and correlates with reduced rescue upon toxin removal. The results provide in vivo evidence for a major protective role of a properly configured intermediate filament network as an intracellular barrier in intestinal cells. This notion is further supported by increased sensitivity of endotube mutants to oxidative and osmotic stress.

overall_design: 2 samples in triplicate were analyzed. We compared dissected intestines of Caenorhabditis elegans wild-type N2 strain with those intestines of strain BJ142 carrying the mutant allele ifo-1(kc2).

first: R

last: Coch

first: F

last: Geisler

last: Leube

first: B


title: The intestinal intermediate filament network responds to and protects against microbial insults and toxins I

overall_design: 2 samples in triplicate were analyzed. We compared Caenorhabditis elegans wild-type N2 strain grown on control JM103 Escherichia coli with those grown on Cry5B pore-forming toxin producing JM103.


title: The intestinal intermediate filament network responds to and protects against microbial insults and toxins

overall_design: Refer to individual Series


title: A single transcriptional factor Csa3b regulates CRISPR-Cas adaptation and interference in Sulfolobus

city: WuHan

first: Qing

last: Ye

state: HuBei

address: Shizishan street

department: state key laboratory of agricultural microbiology

institute: Huazhong Agricultural University

summary: Transcriptome sequencing was carried out on an Illumina HiSeq platform to investigate  CRISPR-Cas and DNA repair systems by Csa3b in Sulfolobus islandicus Rey15A. We compared the differently expressed genes in Sulfolobus islandicus Rey15A strain with csa3a overexpression vs. Sulfolobus islandicus Rey15A strain carrying an empty expression vector,We find thatcmr-α (SiRe_0890 ~ SiRe_0895) and cmr-β (SiRe_0597 ~ SiRe_0603)、the DNA double strand break (DSB)repair genes, including nurA, rad50, mre11, and herA (SiRe_0061 ~ SiRe_0064), as well as two subunits of DNA polymerase II (SiRe_0615 and SiRe_0617) that function in DNA repair, were significantly up-regulated. Our data indicated that the Csa3b regulator couples transcriptional activation of cmr genes, DNA repair genes.

overall_design: Examination of  different gene expression in 4 cell types.

last: Peng


title: RNA Polymerase II CTD Tyrosine 1 is Required for Efficient Termination by the Nrd1-Nab3-Sen1 Pathway (ChIP-chip)

city: Montreal

first: Francois

last: Robert

state: QC

address: 110 av des Pins Ouest

country: Canada

institute: IRCM

type: Genome binding/occupancy profiling by genome tiling array

summary: Transcription termination is key to gene regulation as it prevents transcription interference with neighboring genes. In Saccharomyces cerevisiae, termination at protein-coding genes is coupled to the cleavage of the nascent transcript, while most non-coding RNA transcription relies on a cleavage-independent termination pathway involving Nrd1, Nab3 and the helicase Sen1 (NNS pathway). In both pathways, the recruitment of termination factors involves phosphorylated forms of the RNA polymerase II C-terminal domain (CTD) but the contribution of individual CTD residues was never systematically investigated. Here, we investigated the impact of mutating phosphorylation sites in the CTD on termination. We observed widespread termination defects at protein-coding genes in mutants for Ser2 or Thr4 but rare defects in Tyr1 mutants for this class of genes. Instead, mutating Tyr1, or its phosphatase Glc7, led to widespread termination defects at non-coding genes known to terminate via the NNS pathway. These defects can be suppressed by slowing down transcription, suggesting that Tyr1 mediates termination via the regulation of elongation or pausing. Our work redefines the role of Tyr1 in termination at protein-coding genes in budding yeast and highlights its key role in termination by the NNS pathway.

overall_design: We took a systematic approach to examine the genome-wide distribution (using ChIP-chip) of various RNAPII CTD mutants. First, ChIPs were performed in a dual-tag system, where an ectopic rpb1 allele —carrying a desired CTD mutation—, tagged Flag, is expressed from a centromeric plasmid under the control of the RPB1 promoter in presence of the endogenous RPB1 allele tagged Myc. Both the mutant (Flag) and the endogenous WT (Myc) Rpb1 were assayed by ChIP-chip from the same extract, allowing direct comparison between the occupancy profile of RNAPII carrying a CTD mutation with that of a WT RNAPII. ChIPs (Cy5) were hybridyzed against Input (Cy3). Second, the project includes Pcf11, Rtt103, Nrd1 and Sen1 ChIP-chip in the various RNAPII CTD mutant cells where the endogenous Rpb1-FRB is anchored-away with the help of a rapamycin treatment. ChIPs (Cy5) were hybridized against a ChIP sample from an isogenic non-tagged strain (Cy3). Third, Rpb3 was profiled in WT, ctk1Δ, endo-S2A, sen1-R308W, nrd1ΔCID and rpb1-G1097D mutants and in cells where Nrd1 or Glc7 were anchored-away from the nucleus. ChIPs (Cy5) were hybridyzed against Input (Cy3). Finally, Tyr1-P was profiled in WT cells. ChIPs (Cy5) were hybridyzed against Input (Cy3). All ChIP-chip experiments were done in duplicates. Microarray data were normalized using the Lima Loess method and replicates were combined using a weighted average method as previously described (Pokholok et al., 2005).

first: Pierre

last: Collin

first: Célia

last: Jeronimo

first: Christian

last: Poitras

first: François


title: Expression data from colorectal adenoma tissue

city: Cologne

first: thomas

last: wunderlich

address: Gleueler Str. 50

institute: MPI for Metabolism Research

summary: Identification of altered gene expression in tumours of wildtype and FoxO1ADA mice after chemical-induction of CAC development

overall_design: Total RNA of one tumor per mouse was isolated and analyzed by Gene Array 2.0 ST microarray analysis

first: Anna

middle: L

last: Ostermann

last: Wunderlich


title: The dominant and poor penetrant phenotypes of the maize mutation Unstable factor for orange1 are caused by DNA methylation changes at a linked transposon

city: St. Louis

first: Blake

middle: C.

last: Meyers

state: MO

address: 975 N Warson Road

institute: Donald Danforth Plant Science Center

summary: Transcriptional analysis of the Ufo1-1 mutant allele and wild type plants were used to identify the candidate gene using a k-mer based approach. The transcriptome data also revealed the altered expression of carbohydrate metabolic genes, which translates into elevated levels of soluble sugars in leaves and light-induced lesions found in mature Ufo1-1 leaves.

overall_design: Genome-wide RNA and sRNA profiling was done by Illumina TruSeq sample preparation followed by high-throughput sequencing with Illumina HiSeq 2000 platform.

first: Surinder

last: Chopra

first: Tzuu-fen

last: Lee

first: Kameron

last: Wittmeyer


title: Small RNA-seq analysis of human airway epithelium infected by Human Bocavirus 1

city: Kansas City

first: Jianming

last: Qiu

state: KS

address: 3901 rainbow blvd

department: Microbiology

institute: University of Kansas Medical Center

summary: Human Bocavirus 1(HBoV1), which belongs to the genus Bocaparvovirus of the family Parvoviridae, infects well differentiated human airway epithelium which is at mitotically quiescent state. To systematicaly investigate the host and viral small RNA expression after HBoV1 infection of primary human airway epithelium cultured at an air-liquid interface (HAE-ALI), small RNA-seq was applied to study the small RNA transcriptome profile of HAE-ALI infected by HBoV1.

sample_organism:
Homo sapiens
Human bocavirus

platform_organism:
Homo sapiens
Human bocavirus

overall_design: Primary human airway epithelial cells were cultured on collagen-coated, semipermeable membrane inserts of 0.33 cm2 and were polarized/differentiated at an ALI for 3-4 weeks. The well differentiated HAE-ALI cells were infected with HBoV1 at a multiplicity of infection (MOI) of 1,000 vgc/cell. At 7 days post infection, HBoV1 infected-cell were collected and RNA samples were prepared using the miRNeasy Mini Kit by following the manufacturer’s instruction. HAE cells from two Transwells were used as one RNA sample, totally 6 RNA samples from HBoV1 infected HAE-ALI cultures were performed for RNA isolation. All RNA samples were analyzed on an Agilent 2100 Bioanalyzer with an Agilent RNA 6000 Nano Kit to ensure an RNA Integrity Number (RIN) ≥ 8.0. Three RNA samples were chosen randomly for small RNA-seq.

first: Min

last: Xiong

first: Wei

last: Zou

first: Xuefeng

last: Deng


title: Comparative transcriptome and translatome analysis in rice revealed differential mRNA translation in Pokkali compared to IR29 under salt stress [polysomal RNA]

status: Public on Jan 15 2019

city: Kunming

first: Yun

last: Zheng

state: Yunnan

address: 452 Fengyuan Road

institute: Yunnan Agricultural University

summary: Soil salinity is one of the primary causes of yield decline in rice. Pokkali (Pok) is a highly salt-tolerant landrace whereas IR29, is salt-sensitive but a widely cultivated cultivar. Comparative analysis of these genotypes may offer better understandings of the salinity tolerance mechanism. The published reports largely underscored the importance of transcriptional regulation during salt stress in these genotypes, while, the regulation at translational level is also critically important. Therefore, simultaneous comparison of transcriptional and translational changes between IR29 and Pok could unravel molecular insights into gene regulatory mechanisms that differ between these contrasting genotypes. Using RNA-Seq, we analyzed transcriptome and translatome from the control and salt-exposed Pok and IR29 seedlings. Clear differences were evident both at transcriptional and translational levels between the two genotypes even under control condition. In response to salt stress, 57 DEGs were commonly upregulated both at transcriptional and translational levels in the two genotypes; the number of up/down regulated DEGs in IR29 was comparable at transcriptional and translational levels; whereas in Pok, the number of upregulated DEGs at translational level (544 DEGs) was considerably higher than that at transcriptional level (219 DEGs); contrastingly, the number of downregulated DEGs (58) at translational level was significantly smaller than that at transcriptional level (397 DEGs). We speculate that Pok is more capable of stabilizing mRNA as well as can efficiently load mRNAs on to polysomes for translation under salt stress. Functional analysis showed that Pok is more efficient in maintaining cell wall integrity, detoxifying reactive oxygen species (ROS), translocating molecules and maintaining photosynthesis under salt stress. The present study not only confirmed the known salt stress associated genes, but also identified a number of putative new salt-responsive genes. This study also showed the importance of translational regulation in salt stress and other stresses responsive mechanism.

overall_design: Using RNA-Seq, we analyzed transcriptome of the total RNA as well as the RNA-associated with the polysomes (PS) from the control and salt-exposed Pok and IR29 seedlings.

first: Yong-Fang

last: Li

first: Ramanjulu

last: Sunkar


title: Comparative transcriptome and translatome analysis in rice revealed differential mRNA translation in Pokkali compared to IR29 under salt stress [Total RNA]

overall_design: Using RNA-Seq, we analyzed transcriptome of the total RNA as well as the RNA-associated with the polysomes (PS) from the control and salt-exposed Pokkqli and IR29 seedlings.


city: Taipei

first: Yun-Wei

last: Kuo

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

department: Plant Biology

institute: National Taiwan University

summary: Plant microRNAs (miRNAs) have emerged as important regulators in developmental processes and stress responses in plants. To identify the wound-responsive miRNAs in the leaves of sweet potato, small RNA deep sequencing was conducted on unwounded and wounded leaves (30 min). Total RNAs were isolated for library construction and analyzed by RNA-sequencing via Illumina Genome Analyzer IIx platform. About 16 million total reads were obtained for each sample.

overall_design: Small RNAs deep sequencing from sweet potato in wounding stress.

first: Jeng-Shane

last: Lin

first: Min-Yao

last: Jhu

first: Yu-Chi

first: Shih-Tong

last: Jeng


title: Comparative transcriptome and translatome analysis in rice revealed differential mRNA translation in Pokkali compared to IR29 under salt stress

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


title: Argopecten irradians, gills, exposed to palmitoleic acid

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 palmitoleic acid at a concentration of 80 mg/L for 48 h.

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

first: Chi

last: Cheng


title: miRNA data from melanoma-derived exosomes and melanoma cell lines

city: Nantes

first: Delphine

last: Fradin

address: 8 quai Moncousu

institute: CRCI2NA, Inserm UMR1307, CNRS UMR6075

summary: Identify miRNAs enriched or overexpressed in melanoma-derived exosomes compared to melanoma cells. We analyzed the 2,578 human miRNAs located in the array according to two ways. The first one identified the differentially expressed miRNAs between melanoma-derived exosomes and their parent cells. In this way, we found 198 miRNAs up-regulated in melanoma cell lines compared to their exosomes and 206 miRNAs up-regulated in exosomes compared to their donor cells. The second way of analysis identifies the most expressed miRNAs in the melanoma-derived exosomes without assumption about their expression in parent cells. We defined two criteria; the first one is a RMA (Robust Multi-Array Average, a good alternative to gene expression value) above 5, corresponding to the mean expression level of the array and a SD ≤ 0.2 between all samples to discover miRNAs expressed uniformly between melanoma-derived exosomes M113 and M117. We identified 44 miRNAs under these criteria.

overall_design: We used microarray to identified miRNA enriched or overexpressed in melanoma-derived exosomes compared to their parent cells.

first: Fradin

last: Delphine


title: Genotype- and tissue-specific microRNA profiles and their targets in three alfalfa (Medicago sativa L) accessions

summary: Alfalfa (Medicago sativa L.) is a forage legume with significant agricultural value worldwide. MicroRNAs (miRNAs) are key components of post-transcriptional gene regulation and essentially control almost all aspect of plant growth and development. Although miRNAs have been reported from alfalfa but their expression profiles in different tissues and novel miRNAs as well as their targets have not been confirmed in this plant species. Therefore, we sequenced small RNAs in whole plantlets, shoots and roots of three different alfalfa genotypes (Altet-4, NECS-141 and NF08ALF06) to identify tissue-specific profiles. After comprehensive analysis using bioinformatics methods, we have identified 100 miRNA families, of which 21 belongs to the highly conserved families whereas the remaining 79 families are conserved between M. truncatula and M. sativa. The profiles of the six highly expressed conserved miRNA families (miR156, 159, 166, 319, 396, 398,) were relatively similar between the plantlets, roots and shoots of three genotypes. Contrastingly, the differenecs were robust between shoots and roots for miR160 and miR408 levels, which were low in roots compared to shoots. The study also has identified 17 novel miRNAs that also differed in their abundanecs between tissues of the alfalfa genotypes. Additionally, we have generated and analyzed the degradome libraries from three alfalfa genotypes that has confirmed 69 genes as targets for 31 miRNA families in alfalfa. The identification of conserved and novel miRNAs as well as their targets in different tissues of three genotypes not only enhanced our understanding of miRNA-mediated gene regulation in alfalfa but could also be useful for practical applications in alfalfa as well as related legume species.

overall_design: Identification and comprehensive analysis of conserved microRNAs and their targets in Alfalfa using Illumina HiSeq 2000 sequencer.

first: Maria

last: Monteros


title: Winter bear serum promotes muscle cell growth, increases protein content, and triggers metabolic switch and hibernation-like signatures in human myotubes

status: Public on Jan 14 2019

city: Pierre Bénite

first: emmanuelle

last: meugnier

address: Cens Eli Bat 2 D- Hopital Lyon Sud

summary: still unknown bear circulating factors have been reported to induce a 40% decrease of the net proteolytic rate in isolated rat muscles, accompanied by downregulation of expression levels of both lysosomal and ubiquitin-dependent proteolytic factors. Here we investigated the phenotype of cultivated human myocytes treated with hibernating bear serum, by disentangling impacts at the trophic, protein balance, and transcriptome and proteome levels. This study represents the first step towards characterization of the winter bear serum potential as a source of new therapeutic molecules to fight against human muscle atrophy.

overall_design: In vitro culture of fully differentiated human myotubes were treated during 48 hours with either winter or summer bear serum at a final concentration of 5%. After 48hours, cells were harvested for further analysis.

first: Etienne

last: Lefai

first: Sandra

last: Pesenti

first: Emmanuelle

last: Meugnier


title: Gene expression signatures for mSCLC cell lines derived from Rb/P53 mouse model

status: Public on Jan 13 2019

city: Shanghai

first: yujuan

last: jin

address: Yueyang Road 320#

institute: Shanghai Institutes for Biological Sciences, CAS

summary: To further decipher the molecular mechanisms involved in the non-SMC to SMCs transition process in SCLC, we performed the expression profiling of three paired non-SMCs and SMCs.

overall_design: Three paired non-SMCs and SMCs were selected for the analysis.

first: Yujuan

last: Jin

first: Hongbin

last: Ji


title: Tissue specific transcriptome atlas of early Brassica napus seed development

city: Winnipeg

first: Mark

last: Belmonte

state: Manitoba

address: 50 Sifton Rd

department: Biological Sciences

institute: University of Manitoba

summary: Tissues were isolated from the globular seed using laser microdissection. At least two bioreplicates are included for each tissue. Tissues examined are : the embryo proper (EP), micropylar endosperm (MCE), peripheral endosperm (PEN), chalazal endosperm (CZE), chalazal proliferating tissue (CPT), chalazal seed coat (CZSC), inner seed coat (ISC), and outer seed coat (OSC).

overall_design: RNA-seq of early Brassica napus seed tissues.

first: Dylan

last: Ziegler

first: Deirdre

last: Khan

first: Jenna

last: Millar

first: Michael

last: Becker


title: Comparison of the transcriptomes of immortalized Hertwig’s epithelial root sheath (HERS) cell line HERS-H1 and HERS-C2

city: Chengdu

first: Guoqing

last: Chen

address: No. 14, 3rd Sec., Ren Min Nan Road

department: West China Hospital of Stomatology

institute: Sichuan University

summary: We compared the transcriptome of the immortalized HERS cell line HERS-H1 and HERS-C2, using the Agilent Rat 4x44K Gene Expression Microarrays. We used primary Hertwig’s epithelial root sheath (HERS) cells as naïve cell reference.

overall_design: Three biological replicates were used for each of the samples (primary HERS cells, HERS-H1 cells and HERS-C2 cells). The primary Hertwig’s epithelial root sheath cells were isolated from the mandibular first molars of postnatal 8 days Sprague-Dawley rats. Immortalized HERS cell line HERS-H1 and HERS-C2 were derived from the primary Hertwig’s epithelial root sheath cells by retroviral introduction SV40 large T antigens.

first: Weidong

last: Tian


title: Iron regulation in Clostridioides difficile

city: Braunschweig

first: Denitsa

last: Eckweiler

state: Lower Saxony

address: Spielmannstr. 7

department: Institute of Microbiology

institute: Technische Universität Braunschweig

summary: The response to iron limitation of several bacteria is regulated by the ferric uptake regulator (Fur). The Fur-regulated transcriptional, translational and metabolic networks of the Gram-positive, pathogen Clostridioides difficile were investigated by a combined RNA sequencing, proteomic, metabolomic and electron microscopy approach. At high iron conditions (760 g/l) the C. difficile fur mutant displayed a growth deficiency compared to wild type C. difficile cells. Several iron transporters were found induced by Fur regulation during low iron (11 g/l) conditions. The major adaptation to low iron conditions was observed for the central energy metabolism. Most ferredoxin-dependent amino acid fermentations were found significantly down regulated (had, etf, acd, grd, trx, bdc, hbd). The substrates of these pathways phenylalanine, leucine, glycine and some initial intermediates (phenylpyruvate, oxo-isocaproate, 3-hydroxy-butanoyl-CoA, crotonyl-CoA) were found accumulated, while some end product like isocaproate and butanoate were found reduced. Flavodoxin (fldX) formation and riboflavin biosynthesis (rib) were found enhanced, most likely to replace the missing ferredoxins. Proline reductase (prd), the corresponding ion pumping RNF complex (rnf) and the reaction product 5-aminovalerate were significantly enhanced. An ATP forming ATPase (atpCDGAHFEB,) of the F0F1-type was found induced while the formation of a V-type, mostly proton-pumping, ATP-consuming ATPase (atpDBAFCEKI, was decreased. The [Fe-S] enzyme-dependent pyruvate formate lyase (pfl), formate dehydrogenase (fdh) and hydrogenase (hyd) branch of glucose utilization and glycogen biosynthesis (glg) were significantly reduced, leading to an accumulation of glucose and pyruvate. The formation of [Fe-S] enzyme carbon monoxide dehydrogenase (coo) was inhibited. An intensive remodeling of the cell wall was observed most likely to increase antibiotic resistance. Polyamine biosynthesis (spe) was found induced leading to an accumulation of spermine, spermidine and putrescine. The fur mutant lost most of its flagella. Finally, the CRISPR/Cas and a prophage encoding operon were downregulated. Fur binding sites were found upstream of 20 of the regulated genes. Overall, adaptation to low iron conditions in C. difficile focused on an increase of iron import, significant decrease in metabolic iron utilization and protection during the complex transition.

overall_design: Comparative examination of gene expression in Clostridioides difficile wildtype and fur mutant grown under high iron or low iron conditions.

first: Mareike

last: Berges

first: Annika-Marisa

last: Michel

first: Christian

last: Lassek

first: Dieter

last: Jahn


title: Comprehensive Study of Nuclear Receptor DNA Binding Provides a Revised Framework for Understanding Receptor Specificity

status: Public on Jan 12 2019

city: Boston

first: Trevor

last: Siggers

state: MA

address: 24 Cummington Mall

department: Department of Biology

institute: Boston University

summary: The type II nuclear receptors (NRs) function as heterodimeric transcription factors with the retinoid X receptor (RXR) to regulate diverse biological processes in response to endogenous ligands and therapeutic drugs. DNA-binding specificity has been proposed as a primary mechanism for NR gene regulatory specificity. We use protein-binding microarrays (PBMs) to comprehensively analyze the DNA binding of 12 NR:RXRα heterodimers. We find more promiscuous NR-DNA binding than has been reported, challenging the view that NR binding specificity is defined by half-site spacing.  We show that NRs bind DNA using two distinct modes, explaining widespread NR binding to half-sites in vivo. Finally, we show that the current models of NR specificity better reflect binding-site activity rather than binding-site affinity. Our rich dataset and revised NR binding models provide a framework for understanding NR regulatory specificity and will facilitate more accurate analyses of genomic datasets.

overall_design: Protein-binding microarray experiments were performed for type II Nuclear Receptors (NR) dimers. Purified or in-vitro transcribed translated (IVT) NR proteins were combined generate heterodimer and homodimers. NRs can bind half-sites sequences organized as direct repeats with a variable length spacer of 0-5 base pairs (bp) (DR0-DR5). To characterize both DNA-base preferences and the DR-spacing preferences, we measured NR binding to more than 1500 unique sequences at six DR spacer lengths (DR0-DR5). Specifically, for each DR spacer length, we measured NR binding to 24 sequences, which we refer to as seed sequences. These seed sequences exhibit a range of degeneracy from the consensus 5’-RGKTCA-3’ half-sites. To assay DNA base preferences for each seed sequence we also measured binding to all possible single-nucleotide variants (SNVs), with each SNV included as a separate probe on the PBM. To capture any binding preferences for flank and DR spacer sequences, we have included SNVs for the five nucleotides upstream and downstream of the DR and across the spacer sequence.

first: Ashley

last: Penvose

first: Jessica

last: Keenan


title: The Gene Response Mechanism Caused by Chinese-fir Fertilization by Transcriptome Technology.

city: Hangzhou

first: li

last: lei

address: xiashas street num 6

summary:
Objective: In order to study the change law of Chinese fir gene expression caused by fertilization, it provides scientific basis for Chinese fir fertilization theory and practice.
Method: Using Illumina HiSeq4000 high-throughput sequencing technology, sequencing sequences of four different fertilizer treatment materials (control CK1, nitrogen treatment N1, phosphorous treatment P1, and phosphorous and nitrogen mixture treatment NP1, each with three biological repeats) were obtained, and a series of comparative analysis of the differences were conducted. The experimental material was the 1-year clone cuttings of Chinese fir K62. At the end of 2017year, sand culture experiment was carried out in the plastic greenhouse of research institute of subtropical forestry,CAF. Because it was transcriptome sequencing without reference genome , sequencing reads need to be spliced into de  novo, unigene and transcripts are assembled, and then functional annotation, differential expression and other project analysis are conducted.
Result: In 12 samples, transcriptome sequencing produced clean reads5.0E+07nt to 7.1E+07nt, and the total splicing length was 724,341,090nt. BLASTX analysis was performed on clean reads in six databases (Nr, Swiss-prot,eggNOG, ,KEGG, Pfam, GO), and 74,288 genes were generated；The Venn diagram reveals the general overview of the gene response of different fertilization treatments: in the N1-VS-CK1 comparison group, NH4NO3 stimulation induced the opening expression of 3,295 genes, and CK1 produced 2,944 genes resistant to nitrogen; Similar results were obtained for other comparison groups. Chinese fir fertilization turns on and up-regulates the expression of some genes while shutting down or down regulating some genes of expression; Analysis of gene differential expression revealed that :720 differentially expressed genes were screened out in the N1-VS-CK1 comparison group, and 3,694 genes were found to be silenced by nitrogen application. Similar results were obtained in the other five groups: a number of differentially expressed genes were screened out, and a number of genes were silenced by nitrogen and phosphorus fertilizer; The results of the heatmap clustering graph of the six comparison groups were revealed that the genes between the same treatment  and the same comparison group are basically distributed in blocks: either high expression or low expression, and vice versa. The gene distribution between different treatments in the same comparison group was complementary. To fertilize Chinese fir, it is better to mix fertilizer with different types of fertilizers; The GO enrichment and functional classification has three major categories, namely, biological process BP, cell component CC and molecular function MF, with 50 small categories; Fertilization, whether single fertilizer or multiple fertilizers, has the greatest impact on the GO terms of Chinese fir:  chloroplasts, cytoskeleton, cell membrane, nucleus and cytoplasm. secondly molecular function, protein binding and biological process are affected. These results revealed that nitrogen and phosphorus can promote the absorption and metabolism of themselves and each other; KEGG enrichment analysis was performed in 6 comparison groups, and the most significant first 5 Pathway KEGG terms were selected in each comparison group, the comprehensive analysis results showed that after fertilizing Chinese fir, the most significant KEGG term was photosynthesis, nitrogen metabolism, carbon fixation and carbon metabolism, plant hormone signal transduction, plant-pathogen interaction, phenylpropanoid biosynthesis, pentose-phosphate pathway, porphyrin and chlorophyll metabolism, arginine biosynthesis and ect. Based on the above studies, the significantly up-regulated or down-regulated genes in important terms obtained by GO enrichment and classification and KEEG enrichment can be studied, and the results can guide the diagnosis of Chinese fir fertilization.
Conclusion: Illumina HiSeq4000 transcriptome sequencing is a quick and cheap way to study the molecular mechanisms of non-model plants, including coniferous trees with large genomes. Chinese fir fertilization can not only turn on some genes, but also turn off some genes. The growth and development of Chinese fir will be regulated in a way that is favorable for its adaptation to the environment, competitive resources and growth and development.

overall_design: Four different fertilizer treatment materials (control CK1, nitrogen treatment N1, phosphorous treatment P1, and phosphorous and nitrogen mixture treatment NP1, each with three biological repeats) were obtained,using Illumina HiSeq4000.

first: Q

middle: I

last: Ming

first: H

last: Guiping


title: Identification of the GATA2 transcriptome in the AR-V positive castrate-resistant prostate cancer cell line CWR22Rv1

city: Cambridge

first: Lewis

last: Chaytor

address: Hutchison/MRC Research Centre, Cambridge biomedical campus

department: Department of Oncology

institute: Cambridge University

summary: To interrogate the extent of overlap between GATA2 and AR-V regulated transcriptomes in castrate-resistant prostate cancer cells, we assessed global gene expression changes in GATA2-depleted CWR22Rv1 cells by microarray analysis using the Illumina Human HT-12 BeadChip array and compared GATA2 regulated genes to a previously generated AR-V regulated genset (Jones et al., 2015). We identified that AR-V transcriptional activity is dependant upon GATA2 at a subset of its target genes. GATA2 also regulated the expression of c-Myc and E2F1 regulated transcriptional targets amongst other oncogenic transcription factors. Transcripts regulated by GATA2 were highly enriched in the cell cycle.

overall_design: CWR22Rv1 cells were transfected with either a non-silencing scrambled control siRNA (siSCR) or a GATA2 targeting siRNA (siGATA2) 48 hours prior to harvest using Lipfectamine RNAiMAX (Invitrogen) to a final concentration of 25 nM in steroid depleted conditions. Cells were grown for 72 hours in steroid depleted conditions total -/+ 10 µM enzalutamide for 24 hours before RNA extraction using TRIzol (Life Technologies) and hybridization of triplicate samples to an Illumine HT-12 v4 BeadChip array.

first: Matthew

last: Simcock

first: Sirintra

last: Nakjang

first: Richard

last: Heath

first: Laura

last: Walker

first: Craig

last: Robson

first: Dominic

last: Jones

first: Luke

last: Gaughan