title: mRNA-seq Analysis of Transcriptomes of the PC9R and PC9 cells

status: Public on Mar 14 2018

first: FAN

last: ZHANG

state: Shanghai

address: 507 Zhengmin Road

institute: Clinical Translational Research Center, Shanghai Pulmonary Hospital, Tongji University School of Medicine

summary:
The goals of this study is to compare the whole genome transcriptome of gefitinib-resistant NSCLC cell line (PC9R) with its gefitinib-sensitive counterpart (PC9) using RNA-seq tecnology
Methods: Genome-wide mRNA profiles of the PC9R and PC9 cells were generated by deep sequencing, using Illumina Hiseq2000. The sequence reads that passed quality filters were analyzed in the following steps: 1) RNA-seq reads were aligned to the hg19 genome assembly using TopHat (http://bioinformatics.oxfordjournals.org/content/25/9/1105.short) with the default parameters; 2) Expression index was generated using GFOLD V1.0.9 job count (http://bioinformatics.oxfordjournals.org/content/early/2012/08/23/bioinformatics.bts515); 3) Differential expression were calculated using GFOLD V1.0.9 job diff.  Gene expression was quantified in rpkm (reads per kilobase of exon per million mapped sequence reads); 4) GFOLD, a generalized fold change, was used to rank the differentially expressed genes from the RNA-seq data. The GFOLD value can be considered as a reliable log2-fold change when only a single biological replicate is available
Results: We found that hundreds of genes were either down- or up-regulated in the PC9R cells compared with the PC9 cells. Specifically, 6% of the total detected genes (1487 genes) were up-regulated in the PC9R cells, with a GFOLD value over 1, and 5% of the total detected genes (1112 genes) were down-regulated, with a GFOLD value less than -1.
Conclusions: Our study reveals the differentially expressed genes in gefitinib-resistant NSCLC cells comparing with the sensitive cells in a genome-wide scale. This results help to provide the novel insight into the gefitinib-resistant mechanism.

overall_design: The genome-wdie transcriptome study of gefitinib-resistant NSCLC cells (PC9R) comparing with the sensitive cells (PC9) using mRNA-seq technology

first: Fan

last: Zhang

first: Dan

last: Li

first: Sujun

last: Chen


title: RNA-seq identifies circulating miR-125a-5p, miR-125b-5p and miR-143-3p as potential biomarkers for acute ischemic stroke

status: Public on Feb 22 2018

city: Munich

first: Bernd

middle: Henrik

last: Northoff

address: Marchioninistr. 15

department: Institute of Laboratory Medicine

country: Germany

institute: Ludwig-Maximilians-University Munich

type: Non-coding RNA profiling by high throughput sequencing

summary:
Rationale: Currently, there are no blood-based biomarkers with clinical utility for acute ischemic stroke (IS). microRNAs (miRNAs) show promise as disease markers due to their cell-type specific expression patterns and stability in peripheral blood.
Objective: To identify circulating miRNAs associated with acute IS, determine their temporal course up to 90 days post-stroke, and explore their utility as an early diagnostic marker.
Methods and Results: We used RNA sequencing to study expression changes of circulating miRNAs in a discovery sample of 20 IS patients and 20 matched healthy control subjects (HCs). We further applied qRT-PCR in independent samples for validation (40 IS patients and 40 matched controls), replication (200 IS patients, 100 HCs), and in 72 patients with transient ischemic attacks (TIA). Sampling of patient plasma was done immediately upon hospital arrival. We identified, validated, and replicated three differentially expressed miRNAs, which were upregulated in IS patients compared to both HCs (miR-125a-5p [1.8-fold; P=1.5x10-6], miR-125b-5p [2.5-fold; P=5.6x10-6], and miR-143-3p [4.8-fold; P=7.8x10-9]) and TIA patients (miR-125a-5p: P=0.003, miR-125b-5p: P=0.003, miR-143-3p: P=0.005). Longitudinal analysis of expression levels up to 90 days after stroke revealed a normalization to control levels for miR-125b-5p and miR-143-3p starting at day two, while miR-125a-5p remained elevated. Levels of all three miRNAs depended on platelet numbers in a platelet spike-in experiment, but were unaffected by chemical hypoxia in N2a cells and in experimental stroke models. In a random forest classification, miR-125a-5p, miR-125b-5p and miR-143-3p differentiated between HCs and IS patients with an area under the curve (AUC) of 0.90 (sensitivity: 85.6%; specificity: 76.3%), which was superior to multimodal cranial computed tomography obtained for routine diagnostics (sensitivity: 72.5%) and previously reported biomarkers of acute IS (neuron specific enolase: AUC=0.69, interleukin 6: AUC=0.82).
Conclusions: A set of circulating miRNAs (miR-125a-5p, miR-125b-5p, miR-143-3p) associates with acute IS and might have clinical utility as an early diagnostic marker.

overall_design: Prospective three-step case-control-study with discovery, validation, and replication step to examine circulating microRNAs after human ischemic stroke

middle: H

first: Lesca

middle: M

last: Holdt

first: Knut

last: Krohn


title: Developmental profiling of gene expression in embryos of the spider Parasteatoda tepidariorum

status: Public on Apr 05 2018

city: Takatsuki

first: Hiroki

last: Oda

state: Osaka

address: 1-1 Murasaki-cho

country: Japan

institute: JT Biohistory Research Hall

type: Expression profiling by high throughput sequencing

summary: The common house spider Parasteatoda tepidariorum is a chelicerate model organism for studying developmental mechanisms and their evolution in arthropods. In contrast to the well-studied model insect, Drosophila melanogaster, embryos of the spider undergo patterning in a cellular environment from early stages (at least after the number of the nuclei increase to 16). Use of spider embryos provide new opportunities to understand the evolution of developmental mechanisms underlying arthropod body plans. This analysis aims to generate genome-scale, developmental profiles of gene expression in embryos of the spider P. tepidariorum, which facilitate a wide range of studies using this spider species.

overall_design: The genome of P. tepidariorum has been sequenced, with gene models annotated (Schwager et al., 2017, BMC Biol. 15, 62). Embryonic development of P. tepidariorum has been divided into more than 10 stages (Akiyama-Oda and Oda, 2003, Development 130, 1735-1747; Mittmann and Wolff, 2012, Dev. Genes Evol. 222, 189-216). Two developmental series of mRNA (stage (st) 1, st2, st3, st4, st5 early, st5 late, st6, st7, st8, st10) were independently obtained from two pairs of parents and analyzed by RNA sequencing (RNA-Seq). Obtained reads were mapped to the genome assembly of P. tepidariorum (Ptep_1.0) and counted against AUGUSTUS gene models (Schwager et al., 2017, BMC Biol. 15, 62).

first: Sawa

last: Iwasaki-Yokozawa

first: Yasuko

last: Akiyama-Oda


title: 4sU metabolic labeled transcripts in mESCs

status: Public on Mar 17 2018

city: Lausanne

first: Jennifer

middle: Yihong

last: Tan

address: Rue du Bugnon 27

department: Department of Computational Biology

country: Switzerland

institute: University of Lausanne

summary: We carried out an extensive functional genomics analysis to elucidate the roles, if any, of splicing at enhancer-associated lincRNA loci (elincRNA). While we found little evidence supporting conservation of elincRNA exons, their splice sites and other splicing associated motifs accumulated significantly fewer mutations than neutrally evolving regions, suggesting that selection has acted to preserve their splicing. We showed that in contrast to other lincRNAs, not only were multi-exonic elincRNAs efficiently and rapidly spliced, they were also specifically associated with enhanced expression of proximal genes and increased local chromosomal interactions. Enrichment of chromatin signatures associated with high enhancer activity at these loci further supports the contribution of elincRNA splicing to enhancer function. Our results elucidate the previously observed evolutionary constraint at elincRNA splice sites, but not their exons, and corroborate the impact of elincRNA splicing modulation on neighboring gene expression regulation, highlighting an unexpected contribution of elincRNA splicing to enhancer function.

overall_design: Mouse embryonic stem cells (mESCs) were labeled with 4-thiouridine for 15, 30 and 60 minutes in duplicates. Labeled and total RNA were sequenced on  Illumina HiSeq 2500.

middle: Y

first: Adriano

last: Biasini

first: Ana

middle: C

last: Marques


title: Transcriptome analysis of hypothalamuses from prepubertal and pubertal rats

status: Public on Mar 08 2018

city: Hefei

first: Fugui

last: Fang

state: Anhui

address: No. 130 of Changjiang West Road

department: College of Animal Sciences and Technology

country: China

institute: Anhui Agricultural University

summary: We applied RNA sequencing analysis to hypothalamuses from prepubertal and pubertal rats. The significant differential expression transcripts were screened out. In order to validate the RNA-seq data, the expression patterns in the samples of lncRNAs and mRNA genes were confirmed by qRT-PCR. This research provides an expression profile of lncRNAs to further research on puberty.

overall_design: LncRNA profiles of prepubertal and pubertal rats were generated by deep sequencing, three hypothalamuses for each group, using Illumina.

first: Lei

last: Luo


title: Beta-catenin maintains lung epithelial progenitors after lung specification

status: Public on Mar 01 2018

city: Houston

first: Edwin

middle: Justin

last: Ostrin

state: Texas

address: 1515 Holcombe Blvd, Unit 1465

department: Pulmonary Medicine

country: USA

institute: MD Anderson Cancer Center

summary: We performed RNA-seq on human embryonic stem cells raised in an established condition to produce 95% Nkx2.1 cells, with and without withdrawal of Wnt-agonist CHIR99021 or addition of Wnt-inhibitor IWP2

overall_design: Human lung progenitors were derived from RUES2 as described in Huang et al 2014, Huang et al 2015. Wnt agonist withdrawal or addition of Wnt inhibitor was done at day 12, with cell harvest for RNA-seq at day 12 (control) and day 15 (control and treatment)

middle: J

first: Jichao


title: Reduced Type I Interferon response signature detected in dendritic cells from prediabetic NOD mice compared to C57BL/6.g7 and Rag KO.

status: Public on Feb 28 2018

city: Bethesda

first: Kristin

middle: V

last: Tarbell

state: MD

address: 10 Center Dr, Bldg 10 5-5832

department: Diabetes, Endocrinology, and Obesity Branch

institute: NIH/NIDDK

summary: Investigating type I interferon in prediabetic stage of DCs from NOD mice compared to C57BL/6.g7 and Rag KO mice.

overall_design: RNAseq was used to study splenic cDC1, cDC2, pDC, moDC, and monocyte populations from 8-10 week old NOD and C57BL/6.g7 and Rag KO mice.

first: M

last: Rahman

first: Kameron

middle: B

last: Rodrigues


title: Comparison of Gene Expression between stromal vascular cells (SVC) and newly identified adipose precursor (SPA)

status: Public on Feb 21 2018

city: Gifu

first: Kazuo

last: Kajita

address: Yanagido 1-1

department: General Internal Medicine

institute: Gifu University Graduate School of Medicine

summary: We have identified proliferative cells in adipose tissue expressing adipocyte specific genes, which were named small proliferative adipocytes (SPA). Comparison of gene expression by microarray and real time PCR among stromal vascular cells (SVC), SPA and mature adipocyte (MA) revealed that adipocyte specific genes and several neuronal genes were increased in the order of SVC < SPA < MWA. However, proliferin 2 (PLF) was detected only in SPA. We found that SPA changed to lipid laden cells by incubation with differentiation medium containing insulin/dexamethasone/IBMX. In this study, we investigated the gene expression of differentiated SPA (D-SPA) comparing with differentiated SVC (D-SVC). Further study using microarrays and real time PCR revealed that uncoupling protein 1 (UCP1) and PLF were strongly expressed in D-SPA. These data suggested that SPA might be able to differentiate into beige cells.

overall_design: Epididymal fat from male C57/BL mice were digested with collagenase, and then centrifuged at 9 xg for 1 sec. The floating cells were separated from the lower phase (SVC). The floating cell fraction was centrifugazed at 226 xg for 3 min. The resultant floating cells and sediment cells were regarded as mature adipocytes (MA) and SPA, respectively. SVC and SPA were cultured in DMEM. When the cultured cells reached 90% confluency, they were harvested, and total RNA was extracted. To explore the characteristics of SPA, gene expression of SVC (S-3 2015.11.10), SPA (A-3 2015.11.10) and MA (A 2015.11.17) was compared with microarray. The number of samples was 3, the number of replication was one. The obtained results were confirmed by real time PCR and immunocytochemistry.

first: Koichiro

last: Taguchi


title: The single cell RNA seq of pulmonary alveolar epithelial cells

status: Public on Feb 05 2018

city: Beijing

first: huanwei

last: huang

address: 7 Science Park Rd., ZGC life science park

institute: NIBS

summary: The pulmonary alveolar epithelium which play key role in lung biological function is mainly composed of two types of epithelial cells: alveolar type I (AT1) and type II (AT2) cells. We know very little about developmental heterogeneity of the AT1 cell population. By using 10X genomics “Chromium Single Cell” technology, we performed single-cell RNA-seq (scRNA-seq) analyses of AT1 cells at postnatal day 3 (P3), P15, and P60, along with AT2 cells (P60) in mice. Our study identified a robust new genetic marker (Igfbp2) of postnatal AT1 cells. The study also provided the transcriptome information of AT1 cells during alveologensis.

overall_design: We performed 10X genomics single-cell RNA-seq at various developmental stages of  AT1 cells of lungs at postnatal (P)3, P15, and P60. We also performed 10X genomics single-cell RNA-seq of AT2 cells of P60 lungs.

first: Yanjie

last: Wang

last: Tang

first: Tao

last: Cai


title: Stereotyped p53 binding tuned by chromatin accessibility

status: Public on Jun 20 2018

city: Pittsburgh

first: Jacob

last: Stewart-Ornstein

state: PA

address: UPMC Hillman Cancer Center, 5117 Centre Avenue

department: computational and systems biology

institute: University of Pittsburgh, School of Medicine

type: Genome binding/occupancy profiling by high throughput sequencing

summary: We accessed the cell type specificity of p53 by directly measuring DNA binding in twelve cell lines in response to ionizing radiation.  We find that that vast majority of binding sites are occupied across all cells lines uniformly, in contrast to p53 regulated gene expression which shows great diversity in the same context.  We further identify a subset of p53 binding sites that are more restricted, appearing in one or a few cell lines.  We find that chromatin accessibility explains much of these differential binding events.

overall_design: p53 DNA binding was measured in twelve cell lines after IR by ChIPseq.  The transcriptional response of each of the twelve lines was also measured by mRNAseq.   To explore the influence of chromatin accessability p53 binding was compared to ATAC-seq data from two cell lines.

first: Antonina

last: Hafner

first: Galit

last: Lahav


title: Spatial and single-cell transcriptional profiling identifies functionally distinct human dermal fibroblast subpopulations

status: Public on Feb 12 2018

city: London

first: Magnus

middle: David

last: Lynch

address: 28th Floor, Tower Wing, Guy's Campus

department: Centre for Stem Cells and Regenerative Medicine

country: United Kingdom

institute: King's College London

summary: Fibroblasts synthesize the extracellular matrix of connective tissue and play an essential role in maintaining tissue integrity. We have previously shown that mouse skin connective tissue, the dermis, is comprised of functionally distinct fibroblast lineages. However, the extent of fibroblast heterogeneity in human skin is unknown. Here, using a combination of spatial transcriptional profiling of human and mouse dermis and single cell transcriptional profiling of human dermal fibroblasts, we show that there are at least four distinct fibroblast populations in adult human skin. We define markers permitting prospective isolation of these cells and show that although marker expression is rapidly lost in culture, different fibroblast subpopulations retain distinct functionality in terms of Wnt signalling, T cell communication and the ability to support human epidermal reconstitution in organotypic culture. Furthermore, while some fibroblast subpopulations are spatially segregated, others are not. These findings have profound implications for normal wound healing and diseases characterized by excessive fibrosis, and suggest that ex vivo expansion or in vivo ablation of specific fibroblast subpopulations may have therapeutic applications.

overall_design: Spatial RNA sequencing of human papillary versus reticular dermis for 3 individuals, and single cell RNA sequencing of dermal fibroblasts for a single individual.

middle: D

first: F

last: Watt


title: Gene expression in islets from control (WT) or transgenic (MYC) animals

status: Public on Jan 01 2018

city: San Francisco

first: Sapna

last: Puri

state: CA

address: 513 Parnassus avenue

institute: UCSF

summary: We report changes in gene expression in mouse islets that express c-MYC in pancreatic beta cells as compared to control cells that lack such ectopic expression.  The goal of the study is to identify the MYC-dependent changes that occur in beta cells that affect cellular fate and function.

overall_design: 2 WT and 4 MYC samples were processed for RNA-seq by using KAPA kits for library preparation after RNA integrity was confirmed. Sequencing was carried out on the Illumina platform.

first: Matthias

last: Hebrok


title: Suppression of RGSz1 function optimizes the actions of opioid analgesics by mechanisms that involve the Wnt/β-catenin pathway

status: Public on Jan 12 2018

city: New York

first: Aarthi

last: Ramakrishnan

state: New York

address: 1425 Madison Avenue

department: Neuroscience

institute: Icahn School of Medicine at Mount Sinai

summary: Regulator of G protein signaling z1 (RGSz1), a member of the RGS family of proteins, is present in several networks expressing mu opioid receptors (MOPR). By using genetic mouse models for global or brain region-targeted manipulations of RGSz1 expression, we demonstrate that the suppression of RGSz1 function increases the analgesic efficacy of MOPR agonists in male and female mice and delays the development of morphine tolerance while decreasing the sensitivity to rewarding and locomotor activating effects. Using biochemical assays and next-generation RNA sequencing, we identified a key role of RGSz1 in the periaqueductal gray (PAG) in morphine tolerance. Chronic morphine administration promotes RGSz1 activity in the PAG, which in turn modulates transcription mediated by the Wnt/β-catenin signaling pathway to promote analgesic tolerance to morphine. Conversely, the suppression of RGSz1 function stabilizes Axin2-Gaz complexes near the membrane and promotes β-catenin activation, thereby delaying the development of analgesic tolerance. These data show that the regulation of RGS complexes, particularly those involving RGSz1-Gaz, represents a promising target for optimizing the analgesic actions of opioids without increasing the risk of dependence or addiction.

overall_design: Understanding the impact of morphine tolerance and the influence of RGSz1 on gene expression in the PAG

first: Sevasti

last: Gaspari

first: Immanuel

last: Purushothaman

first: Li

last: Shen

first: Venetia

last: Zachariou


title: Effect of ultra-small silica nanoparticles (USSNs) on gene expression of peripheral blood mononuclear cells

status: Public on Apr 13 2018

city: Thunder Bay

first: Bradley

last: Vis

address: 955 Oliver Rd

country: Canada

institute: Lakehead University

summary: Humans are exposed to high levels of amorphous silica particles daily, as they are used in food, cosmetic and pharmaceutical products, and recently in bioclinical applications. Here, peripheral blood mononuclear cells were exposed to USSNs (silicon) and their gene expression was assessed

overall_design: Peripheral blood mononuclear cells (PBMCs) were freshly isolated from single human leukocyte cones and treated in triplicate with saline or  USSNs (DV0.5 = 3.6 +/- 0.5, treated at 150 uM Si) for 4 h and then RNA collected. RNA was also collected prior to separation and treatment of the cells (i.e. at 0 h; n=3 replicates). The whole experiment was performed in triplicate on PBMCs isolated from three different human donors.

first: Ravin

last: Jugdaohsingh

first: Rachel

middle: E

last: Hewitt

first: Mark

last: Boekschoten

first: Jonathan

last: Powell


title: Studying the mating mechanisms in Phytophthora infestans

status: Public on Jan 25 2018

city: Uppsala

first: Johan

last: Fogelqvist

address: PO- Box 7080

department: Plant Biology

country: Sweden

institute: Swdish Universitu of Agriculture

summary: Phytophthora infestans is a filamentous plant pathogen. It belongs to the class Oomycota within the Stramenopiles. Despite the importance of sexual reproduction in P. infestans, many aspects of the mating process remain unknown. In this study we are investigating its mating mechanisms using different molecular techniques. Isolates with A1 and A2 mating types from Sweden, the Netherlands and the UK, were used for this purpose because mating frequencies are known to differ among European countries. RNA was prepared from the “mating-zone” between the 4 Swedish, 1 Dutch and 1 British pairs. RNA-seq analysis was performed on an Illumina HiSeq 2500 platform and data normalized to parental isolates growing individually.

overall_design: In total 14 samples were analyzed. The mating samples (m3-m10) contained 3 biological replicates, while the control samples (s1-s8) contained 2 biological replicates

first: Georgios

last: Tzelepis

first: Ramesh

last: Vetukuri

first: Anna

last: Åsman

first: Christina

last: Dixelius


title: Transcriptional responsen of phosphorus (re-)absorbing organs to diets varying in phosphorus content in pigs (low-intake; medium intake; high-intake)

status: Public on Dec 31 2017

city: Dummerstorf

first: Klaus

last: Wimmers

address: Wilhelm-Stahl-Allee 2

department: Genome Biology

institute: FBN Dummerstorf

summary: in vivo microarray study of transcriptional changes in porcine jejunum, colon and kidney due to dietary intake of phosphorus

overall_design: per dietary group 6-7 pigs were collected for expression profiling at one time point

first: Eduard

last: Muráni

first: Siriluck

last: Ponsuksili

first: Michael

last: Oster

first: Franziska

last: Just


title: Long noncoding RNA (lncRNA) expression data from human myelodysplastic syndromes (MDS) bone marrow mononuclear cells

status: Public on Feb 13 2018

city: Taipei City

first: Chi-Yuan

last: Yao

address: No.7, Chung Shan S. Rd.

country: Taiwan

institute: National Taiwan University Hospital

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

summary:
lncRNAs not only participate in normal hematopoiesis but also contribute to the pathogenesis of acute leukemia. However, their clinical and prognostic relevance in MDS remains unclear to date.
In this study, we profiled the lncRNA expressions in 176 adult patients with primary MDS with Affymetrix GeneChip Human Transcriptome Array 2.0, and identified the lncRNAs whose expression levels were significantly associated with overall survival (OS). We then constructed a risk scoring system with the weighted sum of these lncRNAs. Patients with higher lncRNA scores had a significantly shorter OS and a higher five-year leukemic transformation rate compared with those with lower scores.

overall_design: Cryopreserved bone marrow cells were obtained from a training cohort of 176 primary MDS patients, and another independent validation cohort of 30 primary MDS patients at diagnosis. Each sample was analyzed with Affymetrix GeneChip Human Transcriptome Array 2.0.

first: Wen-Chien

last: Chou

first: Hwei-Fang

last: Tien


title: ChIP-Seq_PETAL

status: Public on Dec 27 2017

city: Shanghai

first: Yang

last: Li

address: Dongchuan Rd. 800

institute: Shanghai Jiao Tong University

summary: To test Pbodies (anibodies screened from PETAL) for more applications, we performed ChIP-seq with selected Pbodies. ChIP-seq assays in HepG2 for Pbodies against SMRC1, SATB1 and NFIC were carried out.

overall_design: ChIP-seq assays in HepG2 for Pbodies against three transcript factors (SMRC1, SATB1 and NFIC) were carried out. The results were compared with published data using commercial ChIP-seq antibodies.

first: Jian

last: Han

first: Xiao-dong

last: Zhao


title: Mir 22-3p enhances recombinant protein production from HEK 293 cell by affecting the expression of HIPK1 and FRAT2

status: Public on Dec 17 2017

first: WeiPing

last: Chen

address: Bldg 8, Room 1A11, NIDDK/NIH

department: GCL

institute: NIDDK/NIH

summary: Improving protein production in human embryonic kidney cells is important structural studies and antibody production. The use of small non-protein coding RNA, such as microRNA, has been an effective method for increasing protein expression. Our high-throughput human microRNA screen in HEK 293 cells previously identified miRNA 22-3p as a promising candidate for increasing the expression of luciferase, couple of membrane proteins and a secreted fusion protein. To explore the mechanisms of this increase in protein expression and to understand the intracellular events, we conducted a gene expression analysis of luciferase- expressing HEK 293 cells transfected with a mir-22-3p mimic and compared with cells transfected with a negative control. Following microarray analysis, down-regulated genes were identified and were cross-referenced with the predicted targets of mir-22-3p and with results from our previous high-throughput siRNA screen. By performing common seed analysis on the possible targets, the list was narrowed to two genes, HIPK1 and FRAT2. These two genes were validated as being involved in improving luciferase production using siRNA and qRT PCR.

overall_design: Identification of genes expressed in WT vs.human embryonic kidney cells that were treated with Mir 22-3p  by triplicated sample per group

first: Sarah

last: Inwood

first: Eugene

last: Buehler

last: Betenbaugh

first: Madhu

last: La

first: Joseph

last: Shiloach


title: Expression of pluripotency genes in chondrocyte-like cells differentiated from human induced pluripotent stem cells

status: Public on Oct 27 2017

city: Poznan

first: Marcin

last: Rucinski

address: Swiecicki 6

department: Histology and Embriology

country: Poland

institute: Poznan University of Medical Science

summary:
Human induced pluripotent stem cells (hiPSCs) constitute an important breakthrough in regenerative medicine, particularly in orthopedics, where more effective treatments are urgently needed. Despite the promise of hiPSCs only limited data on in vitro chondrogenic differentiation of hiPSCs are available.
Therefore, we compared the gene expression profile of pluripotent genes in hiPSC-derived chondrocytes (ChiPS) to that of an hiPSC cell line created by our group (GPCCi001-A).

overall_design: The feeder-dependent hiPSC cell line (GPCCi001-A) generated by our group were differentiated into chondrocyte-like cells (ChiPS) via monolayer culture. The experiment was performed in triplicate. We performed global gene expression analysis using the Affymetrix platform—to better understand the processes directing cell fate during chondrogenic differentiation in vitro (hiPSC served as a control). This study had three primary aims: 1) to evaluate the similarities between hiPSC-derived chondrocytes (ChiPS) and parental” hiPSCs at the gene level, 2) to assess how the differentiation process changes the expression of essential genes involved in pluripotency; and 3) to determine whether the hiPSC cells maintain their pluripotency state in long term cultures.

first: Ewelina

last: Stelcer

first: Katarzyna

last: Kulcenty

first: Karol

last: Jopek

first: Tomasz

last: Trzeciak

first: Magdalena

last: Richter

first: Wiktoria

last: Suchorska


title: The spatial position of budding yeast chromosomes affects gene expression

status: Public on Dec 20 2017

city: Barcelona

first: Marco

last: Di Stefano

address: Carrer Baldiri Reixac, 4

country: Spain

institute: CNAG-CRG

summary: The three-dimensional (3D) organization of chromosomes can influence transcription. However, the frequency and magnitude of these effects is still controversial. To determine how changes in chromosome positioning affect transcription we characterized nuclear organization and global gene expression after large-scale chromosomal rearrangements in budding yeast. We used computational modelling and single cell imaging to determine chromosome position and integrated these data with genome-wide transcriptional profiles from RNA sequencing. Chromosome displacement relative to the nuclear periphery has mild but widespread and significant effects on transcription. Our study suggests that basal transcriptional activity is sensitive to radial changes on chromosomal position, and provides support for the functional relevance of budding yeast chromosome-level 3D organization in gene expression.

overall_design: We analysed 42 samples in total: wildtype (409) strain (4 replicas), mutant strain 524 (4 replicas), mutant strain 527 (4 replicas), mutant strain 1138 (4 replicas), mutant strain 1228 (4 replicas), mutant strain 1379 (4 replicas), mutant strain 1387 (4 replicas), mutant strain 1380 (4 replicas),  mutant strain 1388 (4 replicas),  mutant strain 1788 (3 replicas),  mutant strain 1793 (3 replicas)

first: Francesca

last: Di Giovanni

first: Davide

last: Baù

first: Lucas

last: Carey

first: Marc

middle: A

last: Marti-Renom

first: Manuel

last: Mendoza


title: Transcriptional and epigenetic regulation of adaptive NK cell responses [ChIP-Seq]

city: Ithaca

first: Colleen

last: Lau

address: 930 Campus Road

department: Microbiology & Immunology

institute: Cornell University

summary: Natural killer (NK) cells are innate lymphocytes that possess features of adaptive immunity such as clonal expansion and generation of long-lived memory. Interleukin (IL)-12 signaling through its downstream transcription factor STAT4 is required for the generation of memory NK cells following expansion, while type I interferon through STAT1 is important for NK cell expansion. Here, we identify gene loci that are highly enriched for STAT4 binding using ChIP-seq for STAT4 and the permissive histone mark H3K4me3 in activated NK cells. In addition, we identify gene loci that are high enriched for STAT1 binding in response to type I interferon signaling.

overall_design: ChIP-seq was performed on ex-vivo NK cells cultured in (stimulated with) IL-12/IL-18 or IFNa.

last: Sun


title: TRF2-ChipSeq in post mitotic cells

status: Public on Oct 17 2017

city: Nice

first: Olivier

last: Croce

address: Faculty of Medicine - Pasteur tower - 28, av. Valombrose

department: Bioinformatics

country: France

institute: IRCAN

summary: We report the TRF2 binding sites in post mitotic mammalian cells under TRF2 (protein level) modulation. By obtaining sequences from chromatin immunoprecipitated DNA, we generated genome-wide chromatin-state maps of differentiated muscle cells (myotubes). Importantly we find that TRF2 levels are correlated with age (R= 0.60) making our results of importance in regards of the changes that occur in the chromatin landscape upon aging. We found multiple TRF2 binding sites that are conserved across cell types (Young et al., 2008, Simonet et al., 2011) highlighting the central role of TRF2 as a key chromatin modifier and gene regulator.

overall_design: Identification of TRF2 binding sites in myotubes under TRF2 modulation (up and down)

first: Robin

last: Jérôme

first: Pen

last: Han


title: Transcriptomic Profiling of Circulating Tumor Cells in Multiple Myeloma: A New Model to Understand Disease Dissemination I

status: Public on Feb 26 2019

first: Juan-Jose

last: Garces

address: 321 E 61st St

institute: Memorial Sloan Kettering Cancer Center

summary:
The number of peripheral blood (PB) circulating tumor cells (CTCs) predicts risk of transformation in smoldering multiple myeloma (MM) and survival in active MM. Growing evidence suggests that as the tumor progresses and the microenvironment becomes hypoxic, clonal plasma cells (PCs) constantly invade new regions of the bone marrow (BM) through induced systemic recirculation. Of note, the frequency of CTCs is typically low and thus, it could be hypothesized that the dissemination of MM is made by few tumor cells with unique features that induce them to egress the BM and spread the disease through PB. This hypothesis has not been demonstrated because the molecular profile of CTCs in MM has not been investigated.
We used gene expression profiling (GEP) arrays to identify gene regulatory networks related to disease dissemination by comparing the molecular profile of CTCs with patient-matched BM clonal PCs.

overall_design: We used FACS and patient-specific aberrant phenotypes to isolate CTCs and BM clonal PCs of paired PB and BM samples from 24 newly-diagnosed MM, 9 relapses and 1 monoclonal gammopathy of undetermined significance.

first: Michal

last: Šimíček

last: Vicari

first: Lucie

last: Brozova

first: Leire

last: Burgos

first: Renata

last: Bezdekova

first: Diego

last: Alignani

first: Maria-Jose

last: Calasanz

first: Kateřina

last: Growková

first: Ludek

last: Pour

first: Rafel

last: Rios

first: Joaquin

last: Martinez-Lopez

first: Pamela

last: Millacoy

first: Luis

last: Palomera

last: del Orbe

first: Sonia

last: Garate

first: Laura

last: Blanco

first: Maria

last: Collantes

first: Patricia

last: Maiso

first: Zuzana

last: Chyra

first: Alexander

last: Vdovin

first: Tomas

last: Jelinek

first: Cirino

last: Botta

first: Halima

last: El Omri

first: Jonathan

last: Keats

first: Xabier

last: Agirre

first: Felipe

last: Prosper

first: Roman

last: Hajek

first: Jesús

last: San Miguel

first: Bruno

last: Paiva


title: Metabolic and Expression Regulation in Caldicellulosiruptor bescii

status: Public on Nov 28 2017

city: Oak Ridge

first: Kyle

last: Sander

state: TN

address: 1 Bethel Valley Road, MS 6038

department: Biosciences

institute: University of Tennessee/Oak Ridge National Laboratory

overall_design: A total of 27 samples were analyzed.  All samples were sequenced on one sequencing lane.  Two single-gene knockout strains (ΔfapR and Δcra) and their common parent strain (JWCB005) were each grown in three conditions of elevated osmolarity which produced a moderate growth defect in all strains and relative growth phenotypes between the strains.  Sacrifical batch samples were taken at mid log phase of growth for RNA sequencing.

first: Daehwan

last: Chung

first: Janet

last: Westpheling

first: Dawn

last: Klingeman

first: Miguel

last: Rodriguez

first: Brian

last: Davison

first: Steven

last: Brown


title: Epigenetic-scale comparison of human iPSCs generated by retrovirus, Sendai virus or episomal vectors

status: Public on Nov 06 2017

city: Setagaya-ku

first: Akihiro

last: Umezawa

state: Tokyo

department: Center for Regenerative Medicine

institute: National Center for Child Health and Development

type: Methylation profiling by genome tiling array

summary: We examined genome-wide DNA methylation with 20  human iPSC lines derived from five different cell types,and 7 human ESC lines using Illumina’s Infinium HumanMethylation450K and compared among iPSCs by retrovirus, Sendai virus or episomal vectors.

overall_design: Bisulphite converted DNA from the 30 samples were hybridised to the Illumina Infinium Human Methylation450K Beadchip

first: Koichiro

last: Nishino

first: Ken

last: Takasawa

first: Masashi

last: Toyoda

first: Mayu

last: Yamazaki-Inoue

first: Tohru

last: Sugawara

first: Hidenori

last: Akutsu

last: Nishimura

first: Manami

last: Ohtaka

first: Mahito

last: Nakanishi


title: Deep sequencing analysis of differences in miRNA expression between IBDV-infected and Mock-infected DF-1 cells

status: Public on Oct 13 2017

first: Shijun J.

last: Zheng

state: beijing

address: 2 Yuan-Ming-Yuan West Road

department: College of Veterinary Medicine

institute: China Agricultural University

summary: To evaluate the change of miRNA expression profile in DF-1 cells in respond to Infectious bursal disease virus (IBDV) infection, Deep sequencing was performed by LC Sciences (Hangzhou, China) on DF-1 cells infected with mock or IBDV  Lx strain at an MOI of 1 for 24 h.

overall_design: DF-1 cells (immortal chicken embryo fibroblast) were cultured in 100mm cell culture dish in Dulbecco modified Eagle medium (DMEM) (Invitrogen, USA) supplemented with 10% fetal bovine serum (FBS) in a 5% CO2 incubator. when cells would be 70-90% confluent, they were infected with Mock or IBDV Lx strain at an MOI of 1, and cultured in DMEM supplemented with 2% FBS . Twenty-four hours after infection, total RNA was extracted using the TRIzol reagent (LC Science, China) following the manufacturer’s protocol. The deep sequencing were performed by LC Science (hangzhou, China).

first: Shijun

first: Bin

last: Wang


title: Effects of novel antiandrogens (enzalutamide and ARN-509) on global gene expression in castration-resistant prostate cancer (CRPC) xenograft model

status: Public on Oct 09 2017

city: Turku

first: Matti

last: Poutanen

address: Kiinamyllynkatu 10

department: Institute of Biomedicine

country: Finland

institute: University of Turku

summary: Global transcriptome analysis revealed altered expression of 291 genes, including mRNAs for several AR-interacting proteins and multiple enzymes involved in steroid metabolism. The data indicate that antiandrogens modify the androgen signaling in VCaP xenografts at multiple levels by reducing concentrations of active androgens, increasing AR expression and inducing alterations in the expression of AR interacting proteins, steroid metabolizing enzymes and AR downstream target genes.

overall_design: RNA-seq analyses of vehicle (control group, n=15), enzalutamide (n=14) and ARN-509 treated (n=15) castration-resistant VCaP tumors after 4-week treatment.

first: Matias

last: Knuuttila

first: Arfa

last: Mehmood

first: Riikka

last: Huhtaniemi

first: Merja

middle: R

last: Häkkinen

last: Oksala

first: Teemu

last: Laajala

first: Henrik

last: Ryberg

first: David

last: Handelsman

first: Tero

last: Aittokallio

first: Seppo

last: Auriola

first: Claes

last: Ohlsson

first: Asta

last: Laiho

first: Laura

middle: L

last: Elo

first: Petra

last: Sipilä

first: Sari

middle: I

last: Mäkelä


title: RNA-Seq Analysis of Tetranychus cinnabarinus in Response to scopoletin

city: Chongqing

first: Xuejiao

last: Liu

state: Chongqing

address: Tiansheng

institute: Southwest university

summary: RNA-seq was employed to analyze the transcriptome changes in T. cinnabarinus treated with scopoletin or solvent. A total of 104, 783, 164 clean sequence reads were generated from the sequencing with more than 90% of the reads were successfully mapped to the reference sequence. The RNA-seq identified 70 and 102 differentially expressed genes between scopoletin and solvent treated mites at 24 h and 48 h post treatment, respectively. GO enrichment analysis showed that differentially expressed genes from 24 h post treatment were categorized into 31 GO functional groups and differentially expressed genes from 48 h post treatment were categorized into 29 GO functional groups. The cellular process under the category of biological process was dominant throughout the GO classification at both time points. Overall our results revealed the global transcriptional changes in T. cinnabarinus upon scopoletin treatment and will enable the further identification of the targets of scopoletin on mite.

overall_design: In this study, RNA-seq was employed to analyze the transcriptome changes in T. cinnabarinus treated with scopoletin or solvent treatment 24h and 48h.

first: Hong

last: Zhou

first: Wei

last: Ding

first: Yongiang

last: Zhang

first: Ting

last: Lai


title: Whole human genome expression analysis on left ventricular free wall heart tissue samples

status: Public on Sep 30 2017

city: Marseille

first: Christophe

last: Chevillard

state: BDR

address: 27 bd Jean Moulin faculté de médecine

institute: INSERM

summary:
Human left ventricular free wall heart tissue was obtained from end-stage heart failure patients at the moment of heart transplantation
Left ventricular free wall samples were also obtained from healthy hearts of organ donors, which were not used for transplantation due to size mismatch with available recipients.

overall_design:
RNA Extraction was done on frozen tissues without stimulation. Whole genome expression analysis was conducted on 10 CCC and 7 control samples;
*CTL (control samples): left ventricular free wall samples were also obtained from healthy  hearts of organ donors, which were not used for transplantation due to size mismatch with available recipients.
*CCC (patients samples): patients have severe Chagas  Chronic  Cardiomyopathy (severe dilated cardiomyopathy). Human left ventricular free wall heart tissue was obtained from end-stage heart failure patients at the moment of heart transplantation.

first: C

first: E

last: Cunha-Neto


title: Tet-mediated DNA hydroxymethylation regulates retinal neurogenesis in zebrafish via cell-extrinsic signaling pathways

status: Public on Aug 25 2017

city: Pittsburgh

first: Jeffrey

last: Gross

state: Pennsylvania

address: 3501 Fifth Avenue

department: Ophthalmology

institute: University of Pittsburgh

summary: Using zebrafish tet2-/-;tet3-/- mutants, we identify functions for Tet enzymes and 5-hydroxymethylcytosine (5hmC) in regulating gene expression and cell type-specific differentiation during retinal development.

overall_design: RNAseq from tet2-/-;tet3-/- mutant and sibling embryonic eye tissues dissected at 72hpf and 36hpf.

first: Pawat

last: Seritrakul

first: Jeff


title: Identification of promoters and enhancers induced by carbon nanotube exposure

status: Public on Jun 21 2017

city: Hørsholm

first: Yun

last: Chen

address: Bøge Alle 10

department: Health & Nutrition

country: Denmark

institute: Chr Hansen A/S

summary: Cap Analysis of Gene Expression (CAGE) applied on carbon nanotubes exposed lung tissue to identify alternative promoter and enhancer usage after 24 hr of exposure in order to investigate the nature of the response observed in these mice.

overall_design: C57BL/6 mice was exposed to vehicle or multi walled carbon nanotubes (MWCNT) by intratracheal installation. 5 mice was exposed to 162 ug of MWCNTs ( XNRI-7;  lot05072001K28, Hadoga Chemical industry (formerly known as Mitsui) disolved in 0.9% NaCl  and 10% v/v cellfree cellular broncho alveolar lavage (BAL) fluid collected from C57BL/6 mice. 6 mice was exposed to the previously decribed saline/BAL solution but without carbon nanotubes.

first: Albin

last: Sandelin

first: Jette

last: Bornholdt


title: A transcriptional regulatory network connects mitochondrial biogenesis and metabolic shift with stem cell commitment to hepatic differentiation

status: Public on Aug 23 2017

city: Boston

first: Anaïs

last: Wanet

state: MA

address: 3 Blackfan circle

department: Hematology Oncology

institute: BIDMC

summary: Mitochondrial biogenesis and metabolism recently emerged as critical modulators of stemness properties and differentiation programmes. The increase in mitochondrial biogenesis and metabolic shift toward increased oxidative phosphorylations (OXPHOS) appear as hallmarks of stem cell differentiation processes. While several mechanisms support the involvement of mitochondrial biogenesis and function in the regulation of stem cell differentiation, the mechanisms triggering mitochondrial biogenesis in the context of cell differentiation remain elusive. In this study, we performed transcriptomic and bioinformatic analyses in order to get deeper insights into the cross-regulation of mitochondrial biogenesis and hepatogenic differentiation of human bone marrow mesenchymal stem cells (BM-MSCs). We identified a transcriptional regulatory network involved in the co-regulation of stem cell differentiation and mitochondrial biogenesis.

overall_design: Transcriptomics analyses performed at early time points of the hepatogenic differentiation of BM-MSC

first: Patricia

last: Renard


title: Dynamic gene expression response to altered gravity in human T cells (parabolic flight)

status: Public on Aug 11 2017

city: Zurich

first: Cora

middle: S.

last: Thiel

address: Winterthurerstrasse 190

department: Institute of Anatomy

institute: University of Zurich

summary: We investigated differentially regulated genes in human Jurkat T lymphocytic cells in 20s and 5min microgravity and in hypergravity and compared expression profiles to identify potential gravity-regulated genes and adaptation processes.

overall_design: Human Jurkat T cells were exposed to altered gravity during a parabolic flight

middle: S

first: Swantje

last: Hauschild

first: Andreas

last: Huge

first: Svantje

last: Tauber

first: Beatrice

last: Lauber

first: Jennifer

last: Polzer

first: Katrin

last: Paulsen

first: Hartwin

last: Lier

first: Frank

last: Engelmann

first: Burkhard

last: Schmitz

last: Schütte

first: Liliana

last: Layer

first: Oliver

last: Ullrich


title: Mapping the mouse Allelome reveals tissue-specific regulation of allelic expression

status: Public on Aug 22 2017

city: Vienna, Austria

first: Daniel

last: Andergassen

address: Lazarettgasse 14, AKH BT 25.3

country: Austria

institute: CeMM Research Center for  Molecular Medicine of the  Austrian Academy of Sciences

summary: Allele-specific expression is important in development and disease, but a complete picture is lacking. Therefore, we mapped allelic-specific expression in 23 tissues during mouse development, including 19 female tissues allowing X chromosome inactivation (XCI) escapers to also be detected. By using rRNA depleted RNA-seq we were able to map allelic expression of lncRNAs that may be lowly expressed or non-polyadenylated. Analysis of this data together with ChIP-seq and genetic models reveals previously unappreciated aspects of the regulation of allelic expression. We demonstrate that allelic expression arising from genetic differences between the alleles, or from the epigenetic processes XCI and genomic imprinting, is surprisingly highly tissue-specific. We find that tissue-specific strain-biased gene expression may be regulated by tissue-specific enhancers or by post-transcriptional differences in stability between the alleles. We detect a higher rate of XCI escapers than most previous mouse studies, (∼10% genes escaping per tissue similar to reports in human), while leg muscle shows an unexpectedly high rate of ∼50% escapers. By surveying a range of tissues during development, and by performing extensive validation including an embryo transfer experiment to exclude false positives from placental maternal contamination, we are able to provide a high confidence list of mouse imprinted genes including 18 novel genes. This increases the proportion of imprinted genes that are clustered (>90%), and shows that cluster size varies dynamically during development, and can be substantially larger than previously thought, with the Igf2r cluster extending over 10Mb in placenta, making it the largest autosomal cis-regulated region in mammals.

overall_design: Defining allele-specific genome features from the mouse in 23 tissues and developmental stages

first: Florian

middle: M

last: Pauler

first: Quanah

last: Hudson


title: Alterations in the Transcriptional Profile of the Liver Tissue and the Therapeutic Effects of Propolis Extracts in Alcohol-induced Steatosis in Rats

status: Public on Jun 20 2017

city: Yangzhou

first: Manhong

last: Ye

state: Jiangsu

address: East Wenhui road 12#

department: College of Bioscience and Biotechnology

institute: Yangzhou University

summary: Gene expression Array analysis has been an effective technique for exploring treatment-associated transcriptional changes in tissues. The main goal of this study is to explore the expression changes of transcripts in the liver tissue of rats which were treated with the ethanolic extraction of propolis (EEP) as well as alcohol. We aim to find a subset of genes which responded to the treatment of EEP and may be useful candidate genes in explaining the protective effects of EEP on fatty liver.

overall_design: Chronic alcoholic fatty liver was induced by administration of 52% alcohol to Wistar rats at the dose of 1% body weight for 7 weeks. Then animals were simultaneously treated with 50% ethanol solutions of EEP or normal saline at the dose of 0.1% body weight for 4 further weeks. Serological analyses and liver histopathology studies were performed to investigate the development of steatosis. Microarray analysis was conducted to investigate the alterations of hepatic gene expression profiling. Our results showed that long-term excessive alcohol feeding to rats caused fatty liver, which was characterized by significantly increased plasma levels of alanine aminotransferase and total cholesterol, as well as excessive accumulation of lipids in hepatocytes. After 4-week treatment of EEP, the levels of various blood indices, liver function enzymes and the histopathology of liver were restored to normal. Results from both microarray analysis and quantitative real-time PCR revealed that the hepatic expressions of genes involved in lipogenesis (such as FASN, SCD1, FABP5 and PKLR) were significantly down-regulated by EEP treatment, while the transcriptional expressions of genes involved in the oxidation of fatty acids (such as Acot1 and Acot4) were markedly increased. Our results indicated that concomitant administration of EEP with alcohol helped to restore serological parameters to the normal level and suppress lipid accumulation in the liver tissue. The ability of EEP to alleviate the adverse effects of alcohol on liver may provide a promising natural therapeutic strategy against alcoholic fatty liver.

first: Mengting

last: Xu

first: Chao

last: Ji

first: Jian

first: Fubiao

first: Wanhong

last: Wei

first: Shengmei

last: Yang

first: Bin

last: Zhou


title: Transcriptome analysis of hypothalamuses from pubertal and prepubertal goats

status: Public on Jun 12 2017

city: Hefei

first: Fugui

last: Fang

address: No. 130 of Changjiang West Road

department: College of Animal Sciences and Technology

institute: Anhui Agricultural University

summary: We applied RNA sequencing analysis to 6 hypothalamuses from pubertal and prepubertal goats. The significant differential expression transcripts were screened out. In order to validate the RNA-seq data, the expression patterns in the samples of lncRNAs and mRNA genes were confirmed by qRT-PCR. This research provides an expression profile of lncRNAs to further research on puberty.

overall_design: LncRNA profiles of pubertal and prepubertal goats were generated by deep sequencing, in triplicate for each group, using Illumina.

first: Xiaoxiao

last: Gao


title: Transcriptional network controlled by Candida glabrata Ada2, a transcription coactivator

status: Public on May 24 2017

city: Taipei city

first: Shang Jie

last: Yu

state: Taiwan (R.O.C)

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

department: Plant Pathology and Microbiology

institute: National Taiwan University

summary: In order to identify genes governed by Ada2, a transcription coactivator in C. glabrata, we compared the genome-wide expression profile in wild-type strain CBS138 and ada2 mutant via RNA sequencing. According to our analyses, 43 genes were down- and 443 genes were up-regulated in ada2 mutant when compared with the wild-type. The 43 down-regulated genes involved in ergosterol biosynthesis pathway (ERG6, ERG13), adhesin or adhesin-like genes (ICS2, AWP2, EPA7), heat shock genes (HSP30, SSB2) and other cellular functions. Among the 443 up-regulated genes, nine adhesin-like EPA family genes (EPA1, EPA6, EPA8, EPA10, EPA11, EPA12, EPA15, EPA20, EPA23) and three yapsin family genes (YPS4, YPS8, YPS10) were included.

overall_design: Total mRNAs extracted from C. glabrata wild-type CBS138 and ada2 mutant were analyzed using RNA sequencing

first: Shang-Jie

first: Ying-Lien

last: Chen


title: Rat esophagus: Control vs. NMBA vs. Tocopherols

status: Public on May 29 2017

city: Beijing

first: Hui

address: 7 Panjiayuan Nanli, Room314

department: Department of Toxicology

institute: China National Center for Food Safety Risk Assessment (CFSA)

summary: Transcriptional profiling of rat esophageal epithelium comparing control animals, NMBA treated animals, with tocopherols intervention animals. Goal was to determine the effects of tocopherols on gene expression underlying the chemoprevention of NMBA-induced esophageal carcinogenesis.

overall_design: Five experimental groups: Control, NMBA, NMBA supplemented with Alpha-, Delta, and Gamma-enriched Tocopherol. Biological replicates: 5 replicates each group.

first: Xudong

last: Jia


title: Global transcriptome profiling of AtJUB1-OX and WT fruits at mature green (MG) and breaker+7 developmental stages.

status: Public on Mar 31 2017

city: Postdam

first: Salma

last: Balazadeh

address: Am Muehlenberg 1

department: Stitt

institute: MPIMP

summary:
To understand the AtJUB1 mediated regulation of tomato fruit development.
To test how the NAC transcription factor JUNGBRUNNEN1 from Arabidopsis thaliana (AtJUB1, identical to ANAC042; At2g43000) affects the development of tomato fruits, AtJUB1-GFP was expressed in transgenic tomato plants under the control of the CaMV 35S promoter. AtJUB1-GFP fusion protein was previously shown to encode a functionally active transcription factor in Arabidopsis (Wu et al., 2012). We then performed gene expression profiling of fruits from AtJUB1-GFP lines (AtJUB1-OX plants) and non-modified wild-type (WT) plants. Fruits at two developmental stages, namely mature green (MG) and Breaker+7 days (B+7), were analysed. To this end, the pericarp was separated from the rest of the fruits and quickly frozen in liquid nitrogen for subsequent RNA extraction. Gene expression analysis was performed using GeneChip Tomato Genome Arrays (Affymetrix). Probe preparation and microarray hybridizations were performed by ATLAS Biolabs (Berlin, Germany).


title: Oncogenic BRAF disrupts thyroid morphogenesis and function via Twist expression

status: Public on Mar 28 2017

city: New York

first: Yariv

last: Houvras

state: NY

address: 1300 York Ave

department: Surgery

institute: Weill Cornell Medical College

summary: Thyroid cancer is common, yet the sequence of alterations that promote tumor formation are incompletely understood. Here we describe a novel model of thyroid carcinoma in zebrafish that reveals temporal changes due to BRAFV600E. Through the use of real-time in vivo imaging we observe disruption in thyroid follicle structure that occurs early in thyroid development. Combinatorial treatment using BRAF and MEK inhibitors reversed the developmental effects induced by BRAFV600E. Adult zebrafish expressing BRAFV600E in thyrocytes developed invasive carcinoma. We identified a gene expression signature from zebrafish thyroid cancer that is predictive of disease free survival in patients with papillary thyroid cancer. Gene expression studies nominated TWIST2 as a key effector downstream of BRAF. Using CRISPR/Cas9 to genetically inactivate a TWIST2 orthologue, we suppressed the effects of BRAFV600E and restored thyroid morphology and hormone synthesis. These data suggest that expression of TWIST2 plays a role in an early step of BRAFV600E-mediated transformation.

overall_design: 3 embryo tg-TOM (tg:TdTomato), 3 embryo tg-BRAFV600E-TOM,  3 adult tg-TOM and 5 adult tg-BRAFV600E-TOM  biological replicates were sequenced. Strains with tg:TdTomato express the TdTomato fluorophore under control of the zebrafish thyroglobulin promoter (tg).

first: Viviana

last: Anelli


title: Dynamic Reorganization of Chromatin Accessibility Signatures during Dedifferentiation of Secretory Precursors into Lgr5+ Intestinal Stem Cells

status: Public on Jun 01 2017

first: Ramesh

last: Shivdasani

address: 450 Brookline Ave. Dana 720D

department: Medical Oncology

institute: Dana Farber Cancer Institute

summary:
To define differences in chormatin accessibility and histome modifications in intestinal stem and epithelial cells, we performed ATAC-seq and ChIP-seq.
We used RNA-sequencing to profile gene expression changes during intestinal stem cell differentiation into different cell types. We find that gene expression is correlated with the chromatin accessibility and reveals differences between intestinal stem cells types.

overall_design: ATAC-seq, H3K4me1, H3K4me2 and H3K27ac ChIP-Seq analysis of isolated mouse intestinal stem cells and progenitor cells. RNA seq analysis of mouse intestinal stem, progenitor and differntiated cells.

first: Unmesh

last: Jadhav

first: Madhurima

last: Saxena

first: Nicholas

middle: K

last: O’Neill

first: Assieh

last: Saadatpour

first: Guo-Cheng

last: Yuan

first: Zachary

last: Herbert

first: Kazutaka

last: Murata


title: Activated entomopathogenic nematode infective juveniles release lethal venom proteins

status: Public on Mar 27 2017

city: Minneapolis

first: Marissa

last: Macchietto

address: 117 Pleasant Street SE

department: Minnesota Supercomputing Institute

institute: University of Minnesota, Minneapolis

summary: Entomopathogenic nematodes (EPNs) are unique parasitic nematodes due to their symbiosis with entomopathogenic bacteria and their ability to kill insect hosts quickly after infection. Although it has been widely believed that EPNs rely on their bacterial partners for killing insect hosts, compelling evidence from previous studies challenges this model. We developed an improved method of activating millions of Steinernema carpocapsae infective juveniles (IJs) in vitro to harvest excreted/secreted (ES) proteins for bioactivity tests and proteomics analysis. We found that a low dose of the ES proteins from early activated nematodes is lethal to Drosophila melanogaster adults within 2-6 hours. We analyzed the protein composition of this venom using mass spectrometry and identified 472 proteins. Many of these venom proteins share high homology with those of vertebrate-parasitic nematodes. Among many different families of proteins found in the venom, proteases and protease inhibitors are especially abundant. Some toxin-related proteins such as Shk domain-containing proteins were also detected. We further analyzed the transcriptomes of individual non-activated IJs and nematodes that were activated in vitro and in vivo, which revealed a dramatic shift in gene expression during IJ activation. By comparing the whole transcriptomes and the genes encoding venom proteins between the in vitro and in vivo activated nematodes, we confirmed that the in vitro activation is a good approximation of the in vivo process. In summary, our findings strongly support a new model that S. carpocapsae and likely other Steinernema EPNs have a more active role in contributing to the pathogenicity of the nematode-bacterium complex than simply relying on their symbiotic bacteria. Furthermore, we propose that EPNs are a good model system for investigating vertebrate- and human-parasitic nematodes, especially regarding the function of ES products.

overall_design: We analyzed the transcriptomes (RNA-seq) of individual non-activated IJs and IJs that were activated in vivo (dissected from the insect Galleria mellonella) and in vitro (IJs were collected from a sponge soaked in G. mellonella hemolymph).

first: Dihong

last: Lu

first: Dennis

last: Chang

first: Mirayana

last: Barros

first: James

last: Baldwin

first: Ali

last: Mortazavi

first: Adler

last: Dillman


title: Midgut transcriptome of Culex quinquefasciatus larvae treated with LC90 doses of Bin toxin from Lysinibacillus sphaericus

status: Public on Mar 22 2017

city: Baltimore

first: George

last: Dimopoulos

state: Maryland

address: 615 N Wolfe St.

department: Molecular Microbiology and Immunology

institute: Johns Hopkins School of Public Health

summary: Lysinibacillus sphaericus produces the mosquito larvicidal binary toxin consisting of BinA and BinB, which are both required for toxicity against Culex and Anopheles larvae. The molecular mechanisms behind Bin toxin-induced damage remain unexplored. We used whole-genome microarray-based transcriptome analysis to better understand how Culex larvae respond to Bin toxin treatment at the molecular level. Our analyses of Culex quinquefasciatus larvae transcriptome changes at 6, 12, and 18 h after Bin toxin treatment revealed a wide range of transcript signatures, including genes linked to the cytoskeleton, metabolism, immunity, and cellular stress, with a greater number of down-regulated genes than up-regulated genes. Bin toxin appears to mainly repress the expression of genes involved in metabolism, the mitochondrial electron transport chain, and the protein transporter of the outer/inner mitochondrial membrane. The induced genes encode proteins linked to mitochondrial-mediated apoptosis and cellular detoxification including autophagic processes and lysosomal compartments.

overall_design: Midgut of untreated control vs. Bin toxin treated Culex quinquefasciatus larvae 4 biological replicates each

first: Chontida

last: Tangsongcharoen

first: Natapong

last: Jupatanakul

first: Boonhiang

last: Promdonkoy

first: Panadda

last: Boonserm


title: Genome-wide methylation analysis of PCNSL using Infinium HumanMethylation 450 BeadChip

status: Public on Apr 01 2017

city: Yokohama

first: Taishi

last: Nakamura

address: 3-9, Fukuura, Kanazawa-ku

department: Department of Neurosurgery

institute: Yokohama city university

summary: Genome wide DNA methylation profiling of primary CNS lymphomas. The Illumina Infinium 450k Human DNA methylation Beadchip was used to obtain DNA methylation profiles across approximately 485,500 CpGs. Samples included 95 primary CNS lymphomas and 2 metastatic DLBCLs in CNS.

overall_design: Bisulphite converted DNA from the 95 samples were hybridised to the Illumina Infinium 450k Human Methylation Beadchip


title: Transcriptome analysis of embryonic neural crest cells

status: Public on Mar 08 2017

city: Moscow

first: Maria

middle: Vladimirovna

last: Suntsova

address: Miklukho-Maklaya, 16/10

department: Department of Genetics and Postgenomic Technologies

country: Russia

institute: M.M. Shemyakin and Yu.A. Ovchinnikov  Institute of  bioorganic chemistry of the Russian Academy of Sciences

summary: The aim of this research was to explore activation/deactivation of signaling pathways in neuroblastoma samples

overall_design: Neural crest cells were used as a control for transcriptome analysis of neuroblastoma samples. Adrenal glands were taken from aborted fetuses after 25 weeks of gestation. Samples were formalin-fixed and paraffin-embedded.  Tissues were examined by histologist to confirm presence of neuroblasts.

first: Elena

last: Ilnitskaya

first: Dmitry

last: Konovalov

first: Ivan

last: Petrov

first: Maksim

last: Sorokin


title: Effects of selection on residual feed intake and diet on gene expression in pig skeletal muscle

status: Public on Mar 14 2017

city: Saint-Gilles

first: Annie

last: Vincent

address: domaine de la prise

institute: INRA

summary: Transcriptional profiling in skeletal muscle of 48 pigs (132 days of age) originated from two lines divergently selected for residual feed intake (RFI) : low-RFI pigs (RFIneg), high-RFI pigs (RFIpl). Both lines were offered isocaloric and isoproteic diets with contrasted energy source and nutrients:  low fat, low fiber (LF) diet or a high fat, high fiber (HF)diet during 10 weeks. Effects of RFI selection, diet and interaction between diet and line were investigated.

overall_design: Four experimental groups: low-RFI pigs fed high fat, high fiber diet (HF_RFIneg), high-RFI pigs fed high fat, high fiber diet(HF_RFIpl),  low-RFI pigs fed low fat, low fiber diet (LF_RFIneg) and high-RFI pigs fed low fat, low fiber diet(LF_RFIpl). 12 pigs per condition. One replicate per array.

first: Isabelle

last: Louveau

first: Florence

last: Gondret


title: Effects of selection on residual feed intake and diet on gene expression

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

overall_design: Refer to individual Series


title: Effects of selection on residual feed intake and diet on gene expression in pig liver

summary: Transcriptional profiling in liver of 48 pigs (132 days of age) originated from two lines divergently selected for residual feed intake (RFI) : low-RFI pigs (RFIneg), high-RFI pigs (RFIpl). Both lines were offered isocaloric and isoproteic diets with contrasted energy source and nutrients:  low fat, low fiber (LF) diet or a high fat, high fiber (HF)diet during 10 weeks. Effects of RFI selection, diet and interaction between diet and line were investigated.


title: Transcriptome analysis of healthy adrenal glands

overall_design: Adrenal gland tissues cells were used as a control for transcriptome analysis of neuroblastoma samples. Adrenal glands collected from autopsies of healthy adult donors killed by accidents. Samples were formalin-fixed and paraffin-embedded.

first: Daria

last: Allina

first: Anton

last: Buzdin


title: Ameloblastoma RNA profiling uncovers a distinct non-coding RNA signature

status: Public on Mar 01 2017

city: Huddinge

first: Haleh

last: Davanian

state: Stockholm

address: Alfred Nobels Allé 8

department: Department of dental medicine

institute: Karolinska Institutet

summary: Ameloblastoma of the jaws remains the top difficult to treat odontogenic tumour and has a high recurrence rate. New evidence suggests that non-coding RNAs (ncRNAs) play a critical role in tumour genesis and prognosis of cancer. However, ameloblastoma ncRNA expression data is lacking. Here we present the first report of ameloblastoma ncRNA signatures. A total of 95 ameloblastoma cases and a global array transcriptome technology covering > 285.000 full-length transcripts were used in this two-step analysis. The analysis first identified in a test cohort 31 upregulated ameloblastoma-associated ncRNAs accompanied by signalling pathways of cancer, spliceosome, mRNA surveillance and Wnt. Further validation in an independent cohort points out the long non-coding (lncRNAs) and small nucleolar RNA (snoRNAs): LINC340, LINC342, SNORD116-25, SNORA11, SNORA21, SNORA47 and SNORA65 as a distinct ncRNA signature of ameloblastoma. Importantly, the presence of these ncRNAs was independent of BRAF-V600E and SMO-L412F mutations, histology type or tumour location, but was positively correlated with the tumour size. Taken together, this study shows a systematic investigation of ncRNA expression of ameloblastoma, and illuminates new diagnostic and therapeutic targets for this invasive odontogenic tumour.

overall_design: GeneChip Human Transcriptome Array 2.0 was used to study the expression of transcriptomics in ameloblastoma 6 tumour and 4 non-tumout control tissues respectivly.

first: Anangi

last: Balasiddaiah

first: Robert

last: Heymann

first: Magnus

last: Sundström

first: Poppy

last: Redenström

first: Mikael

last: Silfverberg

first: Matti

last: Sällberg

first: Sven

last: Lindskog

first: Carina

last: Weiner

first: Margaret

last: Chen


title: Distinct Brca1 mutations differentially reduce hematopoietic stem cell function

status: Public on Feb 01 2017

city: Dallas

first: Theo

last: Ross

state: TX

address: 5323 Harry Hines Blvd.

department: Internal Medicine-Hem/Onc

institute: UT Southwestern Medical Center

summary: Mgbemena et al report that hematopoietic stem cells have an absolute requirement for Brca1 to survive. They also show that humanization of the mouse Brca1 e with a knocked-in BRCA1 cDNA, but not a mutant BRCA1/5382insC cDNA, fully substitutes for the mouse Brca1 during both embryonic development and hematopoiesis.

overall_design: Enlarged spleens from 2-3 mo. old Brca1∆/∆ mice and Brca1+/+ mice were taken for RNA extraction and processed for paired-end RNA seq.


title: Sox9 transcriptionally regulates Wnt signaling in intestinal epithelium stem cells under hypomethylated crypts in diabetic state

status: Public on Jan 30 2017

city: Guang-Zhou

first: Can-Ze

last: Huang

address: 107 Yan-Jiang Xi-Road

institute: Sun Yat-Sen Memorial Hospital

summary: Mammalian intestinal epithelium stem cells (IESCs) and their daughter cells require the participation of DNA methylation and the transcription factor Sox9 for proliferation and differentiation. Combining methylated DNA immunoprecipitation with microarray hybridization, we demonstrate that hypomethylation in promoter participates in the aberrant formation of crypts in diabetic db/db mice through ectopic Wnt signaling. More importantly, increased expression of Sox9 is accompanied by the loss of methylation in its promoter in IESCs. Using ChIP-seq analysis for Sox9 in IESCs, we demonstrate that Sox9 primarily targets the enhancers of Wnt signaling pathway-related genes. Sox9 is not only predominately acting as a transcriptional activator at proximal enhancer but also as a potential transcriptional inhibitor at distant enhancer. Lack of Sox9 transcriptional activation in specific repressors of Wnt signaling pathway results in loss of intrinsic inhibitory action and ultimately produces over-activation of this pathway in diabetes mellitus.

overall_design: A total of six samples are included in the experiment for promoter DNA methylation analysis, in which three are experimental group definded as db/db mice and three are control group definded as db/+ mice. The mice were maintained under a 12 h light/12 h dark cycle in a specific pathogen-free animal facility. The experiments were conducted using 16-week-old male homozygous mice, which were maintained for 8 weeks with hyperglycemia (random blood glucose level ? 16.7 mmol/l) prior to euthanasia. Identical genetic background BKS heterozygote db/+ mice (random blood glucose level < 11.1 mmol/l) were used as the control. All experiments with mice were approved by the Animal Care Committee of Sun Yat-Sen University (Permit Number: 201412000091).

first: Ji-Hao

last: Xu

first: Wa

last: Zhong

first: Zhong-Sheng

last: Xia

first: Si-Yi

last: Wang

first: Di

last: Cheng

first: Jie-Yao

last: Li

first: Ting-Feng

last: Wu

first: Qi-Kui

first: Tao

last: Yu


title: Targeted FAIRE-sequencing of breast cancer risk regions in two breast cancer cell lines

status: Public on Jan 26 2017

city: Cambridge

first: Chandra

last: Chilamakuri

address: Robinson Way

institute: Cancer Research UK Cambridge Institute

summary:
Purpose: The goal of this study was to identify allele-specific open chromatin regions in breast cancer cell lines, focusing on the fraction of the genome that has been previously associated to breast-cancer risk.
Methods: DNA obtained from Angilent SureSelect solution-based sequence capture was subjected to Illumina HiSeq 2500 paired-end sequencing (Illumina). We performed targeted sequencing of 3 replicated FAIRE samples per cell-line and the correspondent genomic DNA controls in two breast cancer cell lines (T47D and MDAMB134). Allele-specific analysis was performed with BaalChIP R package (version 0.1.9) with the default parameters and options.
Results: Using targeted sequencing, we investigated 69 genomic loci that have been previously associated to breast cancer risk. We identified a total of 21 allele-specific SNPs in MDAMB134 and allele-specific 9 SNPs in T-47D cell lines (see processed files).

overall_design: Targeted FAIRE sequencing of breast cancer risk regions. FAIRE-seq and the correspondent genomic DNA control samples were obtained in two breast cancer cell lines (T47D and MDAMB134). Three replicates per experiment.

first: Ines

last: de Santiago

first: Martin

last: O'Reilly

first: Kerstin

last: Meyer


title: Canine keratinocyte cell line: Unstimulated control (UC) vs. Samples stimulated by recombinant periostin (PO).

status: Public on Jan 20 2017

city: Sagamihara

first: TAKAYUKI

last: MINESHIGE

state: Kanagawa

address: Chuo-ku, Kyowa 4-22-6

institute: Azabu University

summary: Canine keratinocyte cell line (CPEK, CELLnTEC Advanced Cell Systems, Bern, Switzerland) : Unstimulated control (UC) vs. Samples stimulated by 4µg/mL recombinant human periostin (PO) (R&D Systems, Minneapolis, MN) for 6 or 24 hrs.

overall_design: Two-condition experiment, Canine keratinocyte cell line. UC vs. PO for 6 or 24 hrs.

first: Takayuki

last: Mineshige

first: Kinji

last: Shirota


title: Zinc finger protein overexpression improves glucose homeostasis in mice

status: Public on Jan 11 2017

city: Cleveland

first: Alyssa

last: Charrier

state: OH

address: 2109 Adelbert RT400D

institute: Case Western Reserve University

summary: Using RNA-Seq, we compared the transcriptomes of muscle from wild type C57BL/6J or Zp407 transgenic mice.

overall_design: Biceps femoris were stored in RNAlater from 5-week-old overnight-fasted male mice. 5 mice were used per group for wild type and Zp407 transgenic mice.

first: David

last: Buchner


title: Genome-wide transcriptional start site mapping and sRNA identification in the pathogen Leptospira interrogans

status: Public on Jan 23 2017

city: Paris

first: Anna

last: ZHUKOVA

address: 28 rue du Dr. Roux

institute: Institut Pasteur

summary: Leptospira are emerging zoonotic pathogens transmitted from animals to humans typically through contaminated environmental sources of water and soil. Transcriptional regulation of pathogenic Leptospira spp. underlying the adaptive response to different hosts and environmental conditions remains elusive. In this study, we provide the first global Transcriptional Start Site (TSS) map of a Leptospira species. RNA was obtained from the pathogen Leptospira interrogans grown at 30° (optimal in vitro temperature) and 37°C (host temperature) and selectively enriched for 5' ends of native transcripts. Primary TSS (pTSS) was identified for 2,865 genes, accounting for 67% of the total genome. The majority of the TSSs were located between 0 to 10 nucleotides from the translational start site. Comparative dRNA-seq analysis revealed conservation of most pTSS at 30° and 37°C. Promoter prediction algorithms allow the identification of the binding sites of the alternative sigma factor sigma 54. However, other motifs were not identified indicating that Leptospira consensus promoter sequences are inherently different from the E. coli model. RNA sequencing also identified 277 and 226 putative small regulatory RNAs (sRNAs) at 30°C and 37°C, respectively, including 8 validated sRNAs by Northern blots. These results provide the first global view of transcriptional start sites and the repertoire of sRNAs in L. interrogans, and will establish a foundation for future experimental work on gene regulation under various environmental conditions including those in the host.

overall_design: To detect the transcripts expressed by L. interrogans and identify TSS, we collected cultures grown to the exponential phase at 30 and 37°C. Total RNA was extracted and subjected to rRNA depletion. Directional cDNA libraries were prepared from enriched fragmented mRNA. To allow selective enrichment of native 5′ ends of transcripts for the determination of transcription start sites (TSS), RNA samples were also treated with terminator 5‘-phosphatedependent exonuclease (TEX) followed by tobacco acid pyrophosphatase (TAP) treatment prior to cDNA library construction. The cDNA libraries of the different samples (30-TEX(-)TAP(-) / 30-TEX(-)TAP(+) / 30-TEX(+)TAP(+) / 30-RNAseq / 37-TEX(-)TAP(-) / 37-TEX(-)TAP(+) / 37-TEX(+)TAP(+) / 37-RNAseq) were sequenced on an Illumina HiSeq2500 instrument (Illumina).

last: Zhukova

first: Luis

last: Fernandes

first: Perrine

last: Hugon

first: Christopher

last: Pappas

first: Odile

last: Sismeiro

first: Jean-Yves

last: Coppée

first: Christophe

last: Becavin

last: Malabat

first: Azad

last: Eshghi

first: Jun-Jie

last: Zhang

first: Frank

last: Yang

first: Mathieu

last: Picardeau


title: Transcriptomic profiling of egg quality in seabass (Dicentrarchus labrax)

status: Public on Dec 31 2016

city: Rennes

first: Aurelie

last: LE CAM

address: Campus de Beaulieu

department: PHASE

summary: The aim of the project was to identify differently expressed genes in eggs of European seabass (Dicentrarchus labrax) characterized by different quality. In this way it was expected to identify genes possibly being a molecular indicator of egg quality in this species, which was never studied to date. For the study microarray analysis of over 26 thousand genes in 16 egg batches was performed. Additionally, for each egg batch biological quality was determined, what allowed to compare the gene expression profile with overall egg quality (divided into two groups representing ‘high’ and ‘low’ egg quality). The analysis allowed to identify 39 differently expressed genes between the two groups representing ‘high’ and ‘low’ egg quality. From those genes, expression level of 7 were verified by real-time qPCR which confirmed significant difference in expression in 5 of them.

overall_design: Sixteen egg batches of European seabass was collected and divided into two portion. One portion was deep frozen and later used for the molecular analysis (microarray and real-time qPCR). Second portion was fertilized and incubated in order to verify the biological quality of the eggs. In this way two separate experimental groups, representing ‘low’ and ‘high’ egg quality, were created.

first: Daniel

last: Zarski

first: Thaovi

last: Nguyen

last: Le Cam

first: Iratxe

last: Rojo

first: Jerome

last: Montfort

first: Gilbert

last: Dutto

first: Marie

middle: O

last: Vidal

first: Christian

last: Fauvel

first: Julien

last: Bobe


title: An Integrative Informatics Approach to Identify Drug Targets and Therapies for Chronic Allograft Injury after Kidney Transplantation

city: Stanford

first: Li

last: Li

state: CA

address: 300 pastuer dr.,

department: Pediatric

institute: Stanford University

summary: We performed a meta-analysis of biopsy and peripheral blood samples from publicly available microarray datasets in GEO using a two-step meta-analysis method. Our in-house 22 microarray dataset is one of the datasets. We identified 85 immune-related genes that were associated with CAI. We then sought to discover novel therapeutic relationships between drug compounds and CAI through cMAP, a large-scale integration of public gene expression data for drugs and disease. We proposed that drugs that have a potentially therapeutic effect will be able to reverse the differential expression of the 85 CAI-specific gene set during drug exposure in a modeled cell line. We selected two drugs for in vivo and in vitro validations, kaempferol and esculetin, two plant-derived compounds that were ranked at the top of the 1,309 compounds.

overall_design: Biopsies obtained at 12 months post-transplantation from renal allograft recipients (n=22) were analyzed for gene expression by Affymetrix exon arrays.

first: Ilana

last: Greene

first: Benjamin

last: Readhead

first: Brian

last: Kidd

first: Rong

last: Chen

first: Joel

last: Dudley

first: Barbara

last: Murphy


title: Differentially expressed genes between the miR-506-overexpressing AsPC-1 pancreatic cancer cell line (n=3) and its negative control (n=3)

status: Public on Dec 22 2016

city: Chongqing

first: Jian

address: No.30 Gaotanyan Street, Shapingba District

institute: Southwest Hospital, Third Military Medical University

summary: To identify additional miR-506 target genes and the mechanisms behind its tumor-suppressive effect, we performed global microarray analysis of mRNA expression in a miR-506-overexpressing AsPC-1 pancreatic cancer cell line and a negative control

overall_design: mRNAs in miR-506-overexpressing AsPC-1 cell line (n=3) and its negative control (n=3) by microarray using Agilent human Gene Expression 4*44K v2

first: Huaizhi

last: Wang


title: Conserved recurrent gene mutations correlate with pathway deregulation and clinical outcomes of lung adenocarcinoma in never-smokers

status: Public on Dec 02 2016

city: Rochester

first: Zhifu

last: Sun

state: MN

address: 200 1st ST SW

department: HSR-BSI

institute: Mayo Clinic

summary: Background. Novel and targetable mutations are needed for improved understanding and treatment of lung cancer in never-smokers. Methods. Twenty-seven lung adenocarcinomas from never-smokers were sequenced by both exome and mRNA-seq with respective normal tissues. Somatic mutations were detected and compared with pathway deregulation, tumor phenotypes and clinical outcomes. Results. Although somatic mutations in DNA or mRNA ranged from hundreds to thousands in each tumor, the overlap mutations between the two were only a few to a couple of hundreds. The number of somatic mutations from either DNA or mRNA was not significantly associated with clinical variables; however, the number of overlap mutations was associated with cancer subtype. These overlap mutants were preferentially expressed in mRNA with consistently higher allele frequency in mRNA than in DNA. Ten genes (EGFR, TP53, KRAS, RPS6KB2, ATXN2, DHX9, PTPN13, SP1, SPTAN1 and MYOF) had recurrent mutations and these mutations were highly correlated with pathway deregulation and patient survival. Conclusions. The recurrent mutations present in both DNA and RNA are likely the driver for tumor biology, pathway deregulation and clinical outcomes. The information may be used for patient stratification and therapeutic target development.

overall_design: 27 pairs of tumor and normal tissues from lung adenocarcinoma patients were sequenced by both exome-seq and RNA-seq. This series contains the RNA-seq data only.

first: Yang

last: Ping

first: Sun

last: Zhifu


title: Global gene expression of hiPS cell derived cardiomyocytes from healthy volunteers

status: Public on Dec 14 2016

city: Fujisawa

first: Tadahiro

last: Shinozawa

address: Muraokahigashi 2chome

institute: Takeda pharmaceuticals

summary: To investigate the relationship between inter-individual difference of drug susceptibility and global gene expression, gene expression profiles of human iPS cell-derived cardiomyocytes (hiPSC-CMs) generated from healthy volunteers were compared with each other.

overall_design:
Three undifferentiated hiPSC lines of three individuals and hiPSC-CMs generated from 10 healthy volunteers were sampled at three different time points. Adult ventricular tissue was sampled from three different human cadavers.
iPSC_donorA, iPSC_donorE and iPSC_donorH are represented as undifferentiated iPS cells derived from donor A, E and H.

first: Masanobu

last: Shoji


title: Transcriptomic features of Pecten maximus oocyte quality and maturation

status: Public on Feb 06 2017

city: Legnaro

first: Massimo

last: Milan

state: PD

address: Viale dell'Università 16

department: Dept. of Department of Public Health, Comparative Pathology,and Veterinary Hygiene

country: Italy

institute: University of Padova

summary: The king scallop Pecten maximus is a high valuable species of great interest in Europe for both fishery and aquaculture. However, hatchery production is a relatively new industry and it is still underdeveloped. Major hurdles are spawning control and gamete quality. In the present study, a total of 14 scallops were sampled in the bay of Brest (Brittany, France) to compare transcriptomic profiles of mature oocytes collected by spawning induction or by stripping. To reach such a goal, a microarray analysis was performed by using a custom 8x60K oligonucleotide microarray

overall_design: Adult scallops (mean weight±SD: 174±32g, mean length: 111±7mm) were caught from the bay of Brest at the beginning of their natural spawning period and transferred to the experimental hatchery of Ifremer (Argenton, France) where they were conditioned for 1 month under suitable conditions for germ cells maturation. Briefly, scallops were placed in experimental raceways supplied with 1 µm-filtered running seawater at 17 ± 1.0°C and fed with a mixed diet of two microalgae (Chaetoceros gracilis and Tisochrysis lutea) at a daily ratio equal to 10 exp 9 cells of each algae species/scallop. Released oocytes were obtained by thermal stimulation to induce spawning of females, consisting on exposure to alternate cycles of 18°C (20 minutes) and 23°C (1 hour) [Gruffydd and Beaumont, 1970]. Once spawning was completed, the collected oocytes were filtered in a 20 µm sieve, to avoid self-fertilization. Oocytes from eight females were rinsed with iso-osmotic ammonium formate (3 % w/v) to remove salt. A total of 20,000 oocytes were homogenized in 1,5 ml of Extract-all (Eurobio) and stored at -80 °C for further transcriptomic analyses. Fertilization was then performed as described in Corporeau et al., 2014. Trochophores movement was estimate at 24h post fertilization using a CASA device, according to Suquet et al. [2012]. Then, the D-larval yield was assessed at 48h post fertilization (number of normal D-larvae/total number of oocytes) as described in de Sousa et al., 2015. In addition, gametes (20,000 oocytes per female) from six sexually mature females were dissected and oocytes were collected by “gamete stripping” as reported in Song et al., 2009. About 20,000 oocytes from each female were harvested and stored as described above. The remaining stripped oocytes from each female were fertilized (as described above) and D-larval rate was registered. RNA was isolated by following the Extract-all manufacturer instructions and combining the RNeasy Mini Kit (Qiagen) for the nucleic acid purification. A DNAse treatment was also carried out (Qiagen). Samples concentration was measured in a NanoDrop® ND-1000 spectrophotometer and the RNA quality was assessed through the Bioanalyzer 2010 instrument (Agilent). Gene expression profiling was performed using an Pecten maximus oligo-DNA microarray of 59,824 probes based on single-colour detection (Cyanine-3 only). Microarrays were scanned with Agilent scanner G2565BA at a resolution of 2 microns; all slides were scanned twice at two different sensitivity settings (XDRHi 100% and XDRLo 10%); the scanner software created a unique ID for each pair of XDR scans and saved it to both scan image files. FeatureExtraction v10.7.3.1 used XDR ID to link the pairs of scans together automatically when extracting data. The signal left after all the FE processing steps have been completed is ProcessedSignal that contains the Multiplicatively Detrended, Background-Subtracted Signal.

first: Pauletto

last: Marianna

first: Milan

last: Massimo

first: Bargelloni

last: Luca


title: Dietary Gluten-Induced Gut Dysbiosis is Accompanied by Selective Upregulation of microRNAs with Intestinal Tight Junction and Bacteria-Binding Motifs in Rhesus Macaque Model of Celiac Disease

status: Public on Nov 10 2016

city: San Antonio

first: Mahesh

last: Mohan

state: Texas

address: 8715 West Military Road

department: Host Pathogen Interaction Program

institute: Southwest National Primate Research Center

summary: The study describes miRNA expression in intact jejunum following feeding of gluten containing monkey chow to gluten sensitive (GS) rhesus macaques. Gluten feeding induced several inflammation associated miRNAs validated and predicted to directly target intestinal tight junction proteins. Upregulation of these microRNAs was accompanied significantly reduced mRNA expression of claudin-1, claudin-3 and occludin and severe gut dysbiosis. These findings suggest that miRNA mediated downregulation of intestinal epithelial tight junction proteins could increase intestinal permeability and facilitate translocation of dysbiotic bacteria into the systemic circulation.

overall_design: Four age and weight matched gluten sensitive (GS) Indian rhesus macaques were fed gluten containing monkey chow. Five rhesus macaques served as normal healthy controls. Jejunal segments were collected at necropsy from both groups. All animals were necropsied at 60 days post SIV infection. ~100 ng of total RNA was first reverse transcribed and preamplified according to the manufacturer’s recommendation. microRNA expression profiling was performed using TaqMan ®OpenArray® Human microRNA panels. Data analysis was performed using ExpressionSuite® software. Data was normalized to two endogenous controls (RNU44 and RNU48). Delta CT values were calculated by subtracting individual miRNA CT values from an average of both endogenous controls.  Comparisons were made between gluten sensitive and normal healthy control macaques.      Four age and weight matched gluten sensitive Indian rhesus macaques were fed gluten containing monkey chow. Five rhesus macaques served as normal healthy controls. Jejunal segments were collected at necropsy from both groups. All animals were necropsied at 60 days post SIV infection. ~100 ng of total RNA was first reverse transcribed and preamplified according to the manufacturer’s recommendation. microRNA expression profiling was performed using TaqMan ®OpenArray® Human microRNA panels. Data analysis was performed using ExpressionSuite® software. Data was normalized to two endogenous controls (RNU44 and RNU48). Delta CT values were calculated by subtracting individual miRNA CT values from an average of both endogenous controls.  Comparisons were made between gluten sensitive and normal healthy control macaques.      Four age and weight matched gluten sensitive Indian rhesus macaques were fed gluten containing monkey chow. Five rhesus macaques served as normal healthy controls. Jejunal segments were collected at necropsy from both groups. All animals were necropsied at 60 days post SIV infection. ~100 ng of total RNA was first reverse transcribed and preamplified according to the manufacturer’s recommendation. microRNA expression profiling was performed using TaqMan ®OpenArray® Human microRNA panels. Data analysis was performed using ExpressionSuite® software. Data was normalized to two endogenous controls (RNU44 and RNU48). Delta CT values were calculated by subtracting individual miRNA CT values from an average of both endogenous controls.  Comparisons were made between gluten sensitive and normal healthy control macaques.

first: M


title: Genome-wide RNA-sequencing of mouse islets 48 hour after transduction with adenoviruses expressing either GFP (control), or constitutively active forms of the transcription factors, Nfatc1 or Nfatc2.

status: Public on Nov 17 2016

city: Madison

first: Ning

last: Leng

state: WI

address: 330 N Orchard St

institute: Morgridge Institute for Research

summary: Genetic variation at ~160 gene loci is associated with type 2 diabetes (T2D). Using an F2 mouse intercross segregating for T2D, we searched for a driver of GWAS gene expression and found that ~40% of the GWAS genes are regulated in trans by a locus on chromosome 2 in islets. We identified Nfatc2 as a candidate driver of GWAS gene expression. Overexpression of Nfatc2 induced β-cell proliferation in mouse and human islets. We show that many T2D GWAS genes are responsive to NFAT and thus may act coordinately as intermediate traits to promote diabetes.

overall_design: On each of 5 separate days ~1,200 islets were isolated and pooled from 6 B6 mice, and then separated into 3 portions for adenoviral transduction to overexpress GFP (control), or constitutively active (ca) forms of mouse Nfatc1 or Nfatc2. 48 hr later, whole islet RNA was isolated using RNeasy purification columns (Qiagen), quantified (Nanodrop) and integrity verified (Agilent) prior to sequencing. The 15 separate RNA samples (N = 5 each for GFP, ca-Nfatc1 and ca-Nfatc2) were bar-coded and randomized for multiplexing across three lanes of an Illumina HiSeq 2000, which yielded ~24M total RNA-sequencing reads/sample.

first: Mark

middle: P

last: Keller


title: Bisulfite sequencing of Parhyale hawaiensis

status: Public on Oct 28 2016

city: London

first: Peter

last: Sarkies

address: Du Cane Road

department: MRC Clinical Sciences Centre

institute: Imperial College London

type: Methylation profiling by high throughput sequencing

summary: Whole genome Bisulfite sequencing

overall_design: Genomic DNA from a single male was subjected to bisulfite conversion and sequencing.

first: Aziz

last: Aboobaker


title: Apelin, a novel predictive biomarker for bevacizumab response in colorectal cancer

status: Public on Oct 29 2016

city: Leiden

first: Martijn

last: Cordes

state: Zuid-Holland

address: Albinusdreef 2

department: Immunology

country: Netherlands

institute: Leiden University Medical Centre

summary:
Gene expression profiles of various isolated normal and tumour cell types
The goal was to identify genes differentially expressed in different cell types between normal and tumour tissues. To this end, different cell types (endothelial cells, macrophages and epithelial cells) were isolated from non-paired primary normal colon tissues and colorectal carcinomas and subsequently RNA was isolated. Endothelial cells and epithelial cells were isolated using facs-sorting, whereas macrophages were isolated by means of plastic adherence. For comparison RNA was also isolated from non-paired whole normal colon tissue and whole tumour colorectal carcinomas (so called “bulk”). RNA was processed and hybridized onto Agilent microarrays. Primary goal was to establish an endothelial cell genetic profile. For this we compared the gene expression of tumour endothelial cells (TECs) with normal endothelial cells (NECs).

overall_design: The analysis consisted of 3 batches that were hybridized at 3 different time points. Besides colon tissues, but outside the scope of these analyses, also RNA of whole kidney or liver (metastasis) tissues and cell fractions were hybridized on these arrays. Some replicate samples within and between batches served as technical replicates and as reference within one batch. References for batch 2 were colon tumour bulk 94 and for batch 3 colon tumour bulk 121. Technical replicates were: colon adenocarcinoma 104 (n=2), colon tumour EC 109 (n=2), colon tumour EC 118 (n=2), colon tumour epithelial cells 124 (n=2), kidney normal EC 4 (n=2), kidney tumour EC 4 (n=2), kidney normal EC 5 (n=2), kidney normal EC 6 (n=2), colon normal EC 68 (n=2), kidney normal EC 7 (n=2), colon tumour EC 71 (n=2), liver metastasis 72 (n=2), colon tumour EC 80 (n=2), colon normal EC 81 (n=2), colon normal EC 82 (n=2), colon normal EC 89 (n=2), kidney tumour EC 8II (n=2), kidney normal EC 9 (n=2), colon tumour EC 94 (n=2), colon tumour bulk 99 (n=2), colon tumour EC 99 (n=2), colon tumour bulk 94 (n=3, reference batch 2), colon tumour bulk 121 (n=13, reference batch 3).

first: Linda

last: Zuurbier

first: Arman

last: Rahman

first: Jennifer

last: Scheick

first: Tse

last: Wong

first: Francois

last: Rustenburg

first: Jesuchristopher

last: Joseph

last: Dynoodt

first: Rory

last: Casey

first: Paul

last: Drillenburg

first: Michael

last: Gerhards

first: Ana

last: Barat

first: Rut

last: Klinger

first: Bozena

last: Fender

first: Darran

last: O'Connor

first: Johannes

last: Betge

first: Matthias

last: Ebert

first: Timo

last: Gaiser

first: Jochen

middle: H

last: Prehn

first: Henk

last: Verheul

first: Arjan

last: Griffioen

first: Nicole

last: van Grieken

first: Bauke

last: Ylstra

first: Annette

middle: T

last: Byrne

first: Laurens

last: van der Flier

first: William

last: Gallagher

first: Ruben

last: Postel


title: Global DNA methylation patterns in Barrett’s esophagus, dysplastic Barrett’s, dysplastic Barrett’s, and esophageal adenocarcinoma are associated with BMI, gender, and tobacco use

status: Public on Oct 25 2016

city: Seattle

last: Grady

state: WASHINGTON

address: 1100 Fairview N.Ave

department: Department of Clinical Research

institute: Fred Hutchinson Cancer Research Center

summary: Background: The risk of developing Barrett’s esophagus (BE) and/or esophageal adenocarcinoma (EAC) is associated with specific demographic and behavioral factors, including gender, obesity/elevated body-mass index (BMI), and tobacco use.  Alterations in DNA methylation, an epigenetic modification that can affect gene expression and that can be influenced by environmental factors, is frequently present in both BE and EAC and is believed to play a role in the formation of BE and its progression to EAC. It is currently unknown whether obesity or tobacco smoking influence the risk of developing BE/EAC via the induction of alterations in DNA methylation.  To investigate this possibility, we assessed the genome-wide methylation status of 81 esophageal tissues, including BE, dysplastic BE, and EAC epithelia using HumanMethylation450 BeadChips (Illumina). Results: We found numerous differentially methylated loci in the esophagus tissues when comparing males to females, obese to lean individuals, and smokers to nonsmokers. Differences in DNA methylation between these groups were seen in a variety of functional genomic regions, and both within and outside of CpG islands.  Several cancer-related pathways were found to have differentially methylated genes between these comparison groups. Conclusions: Our findings suggest obesity and tobacco smoking may influence DNA methylation in the esophagus and raise the possibility that these risk factors affect the development of BE, dysplastic BE, and EAC through influencing the epigenetic status of specific loci that have a biologically plausible role in cancer formation.

overall_design: A total of 127 esophageal samples with different histology and 81 samples were analyzed for the publication, including N=21 BE, 18 BE+LGD, 18 BE+HGD, and 24 EAC. There were no replicates or control samples

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