title: Decoding microglia responses to psychosocial stress reveals blood-brain barrier breakdown that may drive stress susceptibility

status: Public on Jul 31 2018

city: BETHESDA

first: abdel

middle: G

last: Elkahloun

address: 50, SOUTH DRIVE

country: USA

institute: NHGRI-NIH

summary: An animal’s ability to cope with or succumb to deleterious effects of chronic psychological stress may be rooted in the brain’s immune responses manifested in microglial activity.  Mice subjected to chronic social defeat (CSD) were categorized as susceptible (CSD-S) or resilient (CSD-R) based on behavioral phenotyping, and their microglial RNAs were isolated and analyzed by global gene expression microarrays.  Microglia transcriptome from CSD-S mice was enriched for pathways that describe phases of CNS healing to sterile injury including, inflammation, oxidative stress, debris clearance, and wound resolution.  Histochemical experiments confirmed the array predictions: CSD-S microglia showed elevated phagocytosis and oxidative stress, and the brains of CSD-S but not CSD-R or HC mice showed vascular leakage of intravenously injected fluorescent tracers.  The results suggest that the inflammatory profile of CSD-S microglia may be precipitated by leakage of blood-born substances into brain parenchyma.  We hypothesize that these CNS-centric responses contribute to the stress-susceptible behavioral phenotype.

overall_design: Microglia from mice that went through chronic social defeat were divided to either suceptible or resilient to stress and were compared to microglia from home caged animals.

first: Michale

last: Lehmann

first: Abdel

first: Miles

last: Herkenham


title: The C. difficile clnRAB operon initiates adaptations to the host environment in response to LL-37

status: Public on Jul 30 2018

city: Atlanta

first: Gregory

middle: K

last: Tharp

state: GA

address: 954 Gatewood Dr

department: Developmental and Cognitive Neuroscience

institute: Yerkes National Primate Research Center

type: Expression profiling by high throughput sequencing

summary: Clostridium difficile is a major nosocomial pathogen that causes severe diarrheal disease. Though C. difficile is known to inhabit the human gastrointestinal tract, the mechanisms that allow this pathogen to adapt to the intestine and survive host defenses are not known. In this work, we investigated the response of C. difficile to the host defense peptide, LL-37, to determine the mechanisms underlying host adaptation and survival. Expression analyses revealed a previously unknown locus, which we named clnRAB, that is highly induced by LL-37 and acts as a global regulator of gene expression in C. difficile. Mutant analyses indicate that ClnRAB is a novel regulatory system that senses LL-37 as a host signal to regulate adaptation to the intestinal environment.

overall_design: Strain 630∆erm without LL-37 served as the control strain. Expression in 630∆erm with LL-37 and expression in the clnR mutant without LL-37 were compared to this control strain. Expression in the clnR mutant with LL-37 was compared to 630∆erm with LL-37. Two independent replicates are included.

first: Emily

middle: C

last: Woods

first: Adrianne

middle: N

last: Edwards

first: Shonna

middle: M

last: McBride

first: James

last: Billingsley

first: Nirav

last: Patel


title: CLIP-seq diagram of ZAP-binding RNA mapped to JEV genome

city: Taipei

first: Hsin-Ping

last: Chiu

address: No.1 Jen Ai road section 1

department: Microbiology

country: Taiwan

institute: National Taiwan University

summary: To elucidate the possible regions of JEV genome targeted by ZAP, we performed CLIP to pull down the RNA interacting with ZAP in JEV-infected ZAP-S overexpressing cells. The enriched RNA population was subjected to NGS by use of the Ion Torrent platform.

overall_design: Regions of JEV genome bound with ZAP-S in JEV-infected A549 cells with ZAP-S overexpression

first: Yi-Ling

last: Lin


title: Genomewide miRNA profiling of colorectal cancer cell lines and colorectal cancer-derived induced pluripotent cancer cell lines

city: Sg. Long

first: Kong Bung

last: Choo

state: Selangor

address: Jalan Sungai Long

department: Preclinical Sciences

country: Malaysia

institute: Universiti Tunku Abdul Rahman

summary:
To establish a genomewide miRNA profile of colorectal cancer-derived induced pluripotent cancer cell lines (CRC-iPC). CRC-iPC clones and two parental cell lines were subjected to miRNA microarray analysis using SurePrint Human MiRNA Microarray Release 21.0 (Agilent). In order to identify the differentially-expressed miRNAs after OSKM-reprogramming, the miRNA expression of CRC-iPCs was relatively compared to that of parental colorectal cancer cell lines. Using a stringent selection criteria of log2(fold change) (FC) ≥ 2.0 or < -2.0 and p-value < 0.05, a total of 102 statistically significant differentially-expressed miRNAs were identified. Amongst the 102 miRNAs, 50 miRNAs were down-regulated and 52 miRNAs were up-regulated. Four miRNAs (miR-362-5p, miR-532-3p, miR-125b-5p, and miR199a-3p) were randomly selected for validation by quantitative real-time PCR, the results were consistent with that of the microarray results.
To establish a genomewide miRNA profile of colorectal cancer-derived induced pluripotent cancer cell lines (CRC-iPC). CRC-iPC clones and two parental cell lines were subjected to miRNA microarray analysis using SurePrint Human MiRNA Microarray Release 21.0 (Agilent). In order to identify the differentially-expressed miRNAs after OSKM-reprogramming, the miRNA expression of CRC-iPCs was relatively compared to that of parental colorectal cancer cell lines. Using a stringent selection criteria of log2(fold change) (FC) ≥ 2.0 or < -2.0 and p-value < 0.05, a total of 102 statistically significant differentially-expressed miRNAs were identified. Amongst the 102 miRNAs, 50 miRNAs were down-regulated and 52 miRNAs were up-regulated. Four miRNAs (miR-362-5p, miR-532-3p, miR-125b-5p, and miR199a-3p) were randomly selected for validation by quantitative real-time PCR, the results were consistent with that of the microarray results.

overall_design: Two CRC cell lines were reprogrammed into near pluripotent state by retroviral transduction of OSKM. Two representative iPC clones derived from each CRC cell line were selected for genomewide miRNA profiling. Four CRC-iPC clones and two parental CRC cell lines were subjected to miRNA microarray analysis using SurePrint Human MiRNA Microarray Release 21.0 (Agilent). The miRNA expression of CRC-iPC clones was relatively compared to the miRNA expression of parental CRC cell lines. The microarray data was analysed by GeneSpring GX software version 13.0.

first: Kong

middle: B

first: Chiu-Jung

last: Huang

first: Michele

middle: S

last: Yuin Hiew

first: Han

middle: P

last: Cheng


title: Setaria viridis small RNAs from panicle tissues

status: Public on Jul 28 2018

city: St. Louis

first: Blake

middle: C.

last: Meyers

state: MO

address: 975 N Warson Road

institute: Donald Danforth Plant Science Center

type: Non-coding RNA profiling by high throughput sequencing

summary: A total of 18 libraries from Setaria viridis were constructed using the Illumina TruSeq sample preparation method. We used two biological replicate libraries from the leaf, whole panicles (inside leaf sheath), whole panicles (coming out of leaf sheath), whole panicles (completely out of leaf sheath), whole panicles (completely out of leaf sheath, after pollination), spikelet (inside leaf sheath), spikelet (coming out of leaf sheath), and spikelet (completely out of leaf sheath).

overall_design: We analyzed 21- and 24-nt phasiRNAs in Setaria (Setaria viridis) to use as a cross-species test for a machine learning classifier. We used two biological replicate libraries constructed from the leaf, whole panicle (inside leaf sheath), whole panicle (coming out of leaf sheath), whole panicle (completely out of leaf sheath) , whole panicle (completely out of leaf sheath,after pollination), spikelet (inside leaf sheath), spikelet (coming out of leaf sheath), and spikelet (completely out of leaf sheath).

first: Sandra

last: Mathioni


title: Genetic response of E.coli to mild elevated pressure

city: Newcastle upon Tyne

first: Meng

last: Zhang

address: Ellison Place

department: Applied Sciences

country: United Kingdom

institute: Northumbria University

summary: The genetic response of E.coli K-12 MG 1655 to 1MPa pressure was examined using transcriptomic analysis by RNA-Seq. The results show many differentially expressed genes are invovled in oxidative stress, Fe-S cluster assesmbly and iron acquisition.

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

overall_design: Overall there were 8 samples sequenced. Four 1MPa treated samples (HPs) contained 2 biological replicates with 2 techinical replicates. Four control samples (LPs) also contained 2 biological replicates with 2 techinical replicates. After PCA analysis, LP4 was removed from further analysis

first: Martyn

middle: F

last: Dade-Robertson

first: Wendy

last: Smith

first: Aurelie

last: Guyet

first: Anil

last: Wipat

first: John

last: Casement

first: Helen

last: Mitrani


title: Zebrafish control and csf1r mutant microglia and brain transcriptomes

status: Public on Jul 20 2018

city: Rotterdam

first: Tjakko

middle: Jakob

last: Van Ham

address: Wytemaweg 80

department: Clinical Genetics

country: Netherlands

institute: Erasmus MC

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

overall_design: Refer to individual Series


title: Transcriptome analysis of the treeshrew infected with ZIKV GZ01

city: Suzhou

first: feng

last: ma

state: Jiangsu

address: 218 Xinghu Street, B5-527

department: Suzhou Institute of Systems Medicine

country: China

institute: CAMS

summary: We analyzed the gene expression profile of the PBMC from -2dpi, 2dpi, and 6dpi ZIKV-infected treeshrew

overall_design: Two treeshreews (duplicated) infected with10^5 PFU of ZIKV(GZ01 strain) by the subcutaneous (s.c.) route. Peripheral blood mononuclear cells (PBMCs) from 0, 2 and 6 dpi (two for each group) were isolated using Ficoll-Hypaque and total RNA were extracted by RNeasy mini kit (Qiagen, German) for global transcriptome analysis.

first: Na-Na

first: Li

first: Yong-Qiang

last: Deng

first: Yue

last: Feng

first: Feng

last: Ma

first: Qi

last: Wang

first: Qing

last: Ye

first: Guoqing

first: Jiejie

last: Dai

first: Yuanyuan

last: Han

first: Xiaomei

last: Sun

first: Xiaopeng

last: Qi

first: Xueshan

last: Xia

first: Cheng-Feng

last: Qin


title: Zebrafish control and csf1r mutant brain transcriptomes

summary:
Purpose: Identify zebrafish control and csf1r-mutant brain transcriptomes
Methods: RNA sequencing was performed on whole brain of control (3x), csf1ra-/- microglia (3x) and csf1ra-/-;b+/- microglia (3x) and csf1ra-/-;b-/- zebrafish. 10-20 million reads per sample were obtained. Reads were mapped to zebrafish genome GRC10.
Results: We identified that microglia gene expression was reduced in csf1ra-/-;b+/- and csf1ra-/-;b-/;- mutant transcriptomes.

overall_design: Zebrafish brain transcriptomes of control (triplicate), csf1ra-/- (triplicate), csf1ra-/-;b+/- and csf1ra-/-;b-/- brain.

first: Nynke

last: Oosterhof

first: Laura

middle: E

last: Kuil

first: Herma

last: van der Linde

first: Saskia

last: Burm

first: Woutje

last: Berdowski

first: Wilfred

last: van IJcken

first: John

last: van Swieten

first: Elly

last: Hol

first: Mark

middle: H

last: Verheijen

middle: J

last: van Ham


title: miRNA expression in hypopharyngeal carcinoma  with different survival status

status: Public on Jul 24 2018

city: Jinan

first: X.

last: Xu

state: Shandong

address: Wenhuaxi Road 107

department: Department of Otolaryngology

institute: Qilu hospital of Shandong university

summary: The study aim to briefly profile miRNA expression differences in hypopharyngeal carcinoma patients, who underwent surgery and chemoradiotherapy, with different survival status. We applied Agilent microRNA microarray to FFPE samples from 8 patients with hypopharyngeal carcinoma.

overall_design: FFPE tissues from 8 patients with hypopharyngeal carcinoma, who underwent surgery and chemoradiotherapy, were collected. The cohort were divided into 2 group as the survival status at the time of the research. Each group (survival group, labeled as L and death group, labeled as D) contained 4 patients.

first: Xinbo

first: Guojun

last: Li


title: Zebrafish control and csf1r mutant microglia transcriptomes

first: Tjakko

last: Van Ham

summary:
Purpose: Identify zebrafish control and csf1r-mutant microglia transcriptomes
Methods: RNA sequencing was performed on FACS-sorted control microglia (3x), csf1ra-/- microglia (3x) and csf1ra-/-;b+/- microglia (3x). 10-20 million reads per sample were obtained. Reads were mapped to zebrafish genome GRC10.
Results: We identified that csf1ra-/- or csf1ra-/-;b+/- microglia transcriptomes retain most of the microglia gene expression signature but mostly show changes in chemoklines expression.

overall_design: Zebrafish microglia transcriptomes of homeostatic microglia (triplicate), other brain cells (triplicate), activated microglia 24h (duplo), activated microglia 48h (duplo). In data analysis all activated microglia samples were pooled.


title: Loss of MPZL3 Function Causes Seborrheic Dermatitis-like Phenotype in Mice

status: Public on Jul 27 2018

city: Miami

first: Tongyu

last: Wikramanayake

state: FL

address: 1600 NW 10th Avenue, RMSB 2023A

department: Dermatology and Cutaneous Surgery

summary: Seborrheic Dermatitis (SD) is a common inflammatory skin disorder.  In this study, we demonstrated SD-like clinical features with associated histology in the Mpzl3 knockout(-/-) mice.  Mpzl3-/- skin showed increased macrophage and CD4+ lymphocyte infiltration, however adaptive immunity was not required for the onset of skin inflammation.  Furthermore, we detected epidermal barrier defects as suggested by increased dye permeability in Mpzl3-/- embryos and altered gene expression by microarray analysis in pup skin.  Taken together, these findings suggest MPZL3 plays an essential role in epidermal differentiation and barrier function, and underscore the interplay between epidermal barrier and immunity in SD.  The SD-like clinical and histologic features in the Mpzl3-/- mice also resemble those in patients carrying a frame-shift mutation in ZNF750, a key regulator of epidermal differentiation and a transcriptional activator of the MPZL3 gene.  Therefore, we conclude that the ZNF750/MPZL3 pathway plays a critical role in the pathogenesis of SD, and a better understanding of skin inflammation and barrier restoration in the Mpzl3-/- mice will provide insight into the pathogenesis and treatment/prevention of recurrent SD.

overall_design: Comparison of gene expression of Mpzl3 -/- and +/+ mouse skin: Total RNA was extracted from the dorsal skin of mouse pups with TriZol Reagent (Life Technologies, Grand Island, NY) and purified with the RNeasy mini kit (Qiagen, Germantown, MD).  RNA was sent to the John P. Hussman Institute for Human Genomics Gene Expression Core Facility at the University of Miami Miller School of Medicine for microarray analysis using the Agilent Whole Mouse Genome (4x44K) array from Agilent (Santa Clara, CA).

first: Luis

last: Borda

first: Ying

last: Wang

first: Stephanie

last: Duffort

first: Andres

last: Reyes-Capo

first: Alexander

last: Barsam

first: Maite

last: Urbieta

first: Victor

middle: L

last: Perez

first: Robert

last: Kirsner


title: Acute lung injury models identify putative growth factors that promote tissue repair and biomarkers for acute lung injury

status: Public on Jul 26 2018

city: Tokyo

first: Shion

last: Miyoshi

address: 5-21-16, Omori-Nishi, Ota-Ku

country: Japan

institute: Toho University

summary:
We tried to identify growth factor(s) to promote regeneration of type 2 alveolar epitherial cells. To identify such candidates, we compared gene expression profiles of RNAs from lungs of mice of the following four different groups of bone marrow (BM) chimeric mice after diphteria toxin (DT) injection. LL, BM cells of LysM-DTR mice into LysM-DTR mice; WL, BM cells of wild-type mice into LysM-DTR mice; LW, BM cells of LysM-DTR mice into wild-type mice; WW, BM cells of wild-type mice into wild-type mice.
Transcriptome analysis revealed that a set of growth factor-related genes was upregulated in the lungs of WL mice compared to LL mice.

overall_design: The experiments were performed using two mice per each group.

first: Takeyuki

last: Kurosawa

first: Hiroyasu

last: Nakano


title: Comparison of expression profile between fibroblasts taken from young (23 years old) and aged (70 years old) donors

city: Yokohama

first: Kazuyuki

last: Yo

state: Kanagawa

address: 560 Kashio-cho, Totsuka-ku

department: Skin Research Department

institute: POLA Chemical Industries, Inc.

summary: Several features differentiate aged cells from young cells, many of which are due to changes in gene expression during the aging process. The mechanisms of altered gene expression in aging cells remain incompletely understood, and we hypothesized that long non-coding (lnc) RNAs mediate at least some of these changes. To determine candidate lncRNAs which are associated with aging process, we screened for alterations in lncRNA expression with aging in skin fibroblasts. Twenty-eight lncRNAs were found to be expressed more than 2-fold in aged fibroblasts, and thirty-five lncRNAs expressed less than 0.5-fold.

overall_design: Normal human dermal fibroblasts taken from young (23 years old) and aged (70 years old) donors' abdomen were cultured with 10% feratl bovine serum-containing Dulbecco’s modified Eagle’s medium. Cell lysate from three independent dishes were put into one tube. Total RNA was isolated using RNeasy Mini Kit (QIAGEN), and labeled with Low Input Quick Amp Labeling Kit (Agilent). Following hybridization with Gene Expression Hybridization Kit (Agilent), microarray was scanned by DNA Microarray Scanner (Agilent).


title: The major origin of seedless grapes is associated with a missense mutation in the MADS-box gene VviAGL11

city: Logrono

first: Pablo

last: Carbonell-Bejerano

state: La Rioja

address: Madre de Dios, 51

department: Instituto de las Ciencias de la Vid y del Vino

country: Spain

institute: CSIC

summary: Seedlessness is greatly prized by consumers of fresh grapes. While stenospermocarpy determined by the Seed Development Inhibitor (SDI) locus is the usual source of seedlessness in commercial grapevine cultivars, the sdi mutation underlying this locus remained unknown and we undertook an integrative approach to identify it. Quantitative genetics and fine mapping studies in two Crimson Seedless (CS)-derived F1 populations confirmed the major effect of the SDI locus and delimited the sdi mutation to a region of 323 kb on chromosome 18. Transcriptomics comparing gene expression between seeds and seed traces in RG (Red Globe) × CS progeny identified processes triggered during sdi-determined seed abortion, including the activation of salicylic acid (SA)-dependent defenses. RNA-seq and NimbleGen microarray datasets were investigated for candidate genes and, while no evidence for causal cis-acting regulatory mutations was detected, deleterious nucleotide sequence changes in the seedless haplotype were predicted in two genes within the sdi fine mapping interval, VviPPAT2 and VviAGL11. Targeted re-sequencing of the two genes in a collection of 126 cultivars showed that only the point variation causing the Arg197Leu substitution in the seed morphogenesis regulator gene VviAGL11 was fully linked with seedlessness. Remarkably, this missense mutation was not detected in seeded clonal variants of Sultanina cultivar, the original donor of the sdi mutation, providing genetic evidence that this is the major cause of seedlessness in cultivated grapevines. The identification of the dominant effects of this amino acid substitution in seed abortion can be exploited to boost seedless grape breeding.

overall_design: A total of 9 samples were hybridized. RNA from developing fruits at fruit set stage from four seeded (660-43, 660-50, 669-45, 671-19) and five seedless (660-40, 660-41, 660-57, 669-19, 671-34) Red Globe×Crimson Seedless F1 Vitis vinifera table grape hybrids was compared. Every sample was collected simultaneously on the same day and at least four replicates were analyzed for the two genotypically and phenotypically constrasting offspring classes.

first: José

last: Martínez-Zapater


title: Systematic microRNAome profiling reveals the roles of microRNAs in milk protein metabolism and quality: insights on low-quality forage utilization

status: Public on Jul 21 2018

city: Hangzhou

first: Huizeng

last: Sun

state: Zhejiang

address: 866 Yuhangtang Road

department: College of Animal Sciences

institute: Zhejiang University

summary: In this study, we investigated the molecular regulatory mechanisms of milk protein production in dairy cows by studying the miRNAomes of five key metabolic tissues involved in protein synthesis and metabolism from dairy cows fed high- and low-quality diets. In total, 340, 338, 337, 330, and 328 miRNAs were expressed in the rumen, duodenum, jejunum, liver, and mammary gland tissues, respectively. Some miRNAs were highly correlated with feed and nitrogen efficiency, with target genes involved in transportation and phosphorylation of amino acid (AA). Additionally, low-quality forage diets (corn stover and rice straw) influenced the expression of feed and nitrogen efficiency-associated miRNAs such as miR-99b in rumen, miR-2336 in duodenum, miR-652 in jejunum, miR-1 in liver, and miR-181a in mammary gland. Ruminal miR-21-3p and liver miR-2285f were predicted to regulate AA transportation by targeting ATP1A2 and SLC7A8, respectively. Furthermore, bovine-specific miRNAs regulated the proliferation and morphology of rumen epithelium, as well as the metabolism of liver lipids and branched-chain AAs, revealing bovine-specific mechanisms. Our results suggest that miRNAs expressed in these five tissues play roles in regulating transportation of AA for downstream milk production, which is an important mechanism that may be associated with low milk protein under lowquality forage feed.

overall_design: 3 different diet groups (alfalfa hay, corn stover, and rice straw based diets), 6 dairy cows per group, the rumen, duodenum, jejunum, liver, and mammary gland samples were collected frow each cow

first: Leluo

last: Guan


title: Cell-type specific transcriptional profiling of glucocorticoid receptor-dependent changes in the nucleus accumbens

city: Krakow

first: Marcin

last: Piechota

address: Smetna 12

department: Molecular Neuropharmacology

country: Poland

institute: Institute of Pharmacology PAS

summary: We have aimed to analyze dexamethasone-induced transcriptional profiling in astrocytes and neurons of the mouse nucleus accumbens (NAc).

overall_design: C57BL mice were injected with saline or dexamethasone (glucocorticoid receptor agonist, 4mg/kg), and gene expression was analyzed 4 hours later in the NAc tissue as well as magnetically sorted astrocytes and neurons. Samples from individual mice were hybridized to separate microarrays.

first: Urszula

last: Skupio

first: Michal

last: Korostynski

first: Slawomir

last: Golda


title: Microarray analysis of long noncoding RNA and mRNA expression profiles in Randall’s Plaques of CaOx stones patients

city: Chang Sha

first: Chen

last: Hequn

address: xiangya road

institute: Xiangya Hospital, Central South University

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

summary: Microarray analysis was used to assess the expression levels of lncRNAs and mRNAs in three pairs of Randall’s plaques tissues of CaOx renal stones patients and normal renal papillary tissues.Randall’s Plaques tissues of CaOx renal stones patients were obtained from patients with idiopathic CaOx renal stone who underwent percutaneous nephrolithotomy. Normal renal papillary tissues were obtained from patients with renal tumor who underwent nephrectomy, the tissues were obtained from papillary without tumor invasion. Randall’s Plaques tissues of CaOx renal stones patients were obtained from patients with idiopathic CaOx renal stone who underwent percutaneous nephrolithotomy. Normal renal papillary tissues were obtained from patients with renal tumor who underwent nephrectomy, the tissues were obtained from papillary without tumor invasion.

overall_design: In the study presented here, microarray analysis was used to assess the expression levels of lncRNAs and mRNAs in three pairs of RP tissues and normal renal papillary tissues. LncRNA and mRNAs profiling screened out 1329 lncRNAs and 448 mRNAs that significant different expression in RP comparing with normal papillary tissues

first: Yu

last: Cui

first: X

last: Zu

first: H

last: Chen


city: Tel Aviv

first: Ran

last: Elkon

address: Ramat Aviv

department: Human Genetics

country: Israel

institute: Tel Aviv University

summary: We profiled gene expression levels in RPE cells derived from human ESCs using Affymetrix arrays

overall_design: Gene expression analysis in RPE cells derived from hESCs using two time points (5d and 14 d), each probed in independent triplicates.

first: Yamit

last: Cohen-Tayar

first: Rani

first: Ruth

last: Ashery-Padan


title: Expression data from in vitro healthy cells and malignant pleural mesothelioma cell lines infected by oncolytic attenuated measles virus or treated by exogenous type I interferon

city: Paris

first: Franck

last: Letourneur

address: 22 rue mechain

country: France

institute: INSERM

summary: We used microarrays to analyse antiviral response by mesothelioma cells sensitive or resistant to the oncolytic activity of measles virus

overall_design: 4 healthy cells and 12 malignant pleural mesothelioma cell lines were infected with measles virus (MV, MOI 1) or not infected (NI = basal expression) or were treated with type I interferon (IFN : IFN-alpha2 + IFN-Beta, 1000UI/mL) during 48 hours. Cells were lysed and RNA was extracted of each sample. This experiment was performed 3 times. RNA was quantified after purification and same quantity of RNA of the 3 experiments was pooled in the same tube for each sample. Then, RNA was analyzed with microarrays.

first: Tiphaine

last: Delaunay

first: JeanFrançois

last: Fonteneau


title: Transcriptomic analysis of tomato sperm cell lineage development

city: Beijing

first: Tai

last: Wang

address: Nanxincun 20, Xiangshan

institute: Institute of Botany, CAS

summary: Sperm cell (SC) lineage development from the haploid microspore to SCs represents a unique biological process. We isolated tomato (Solanum lycopersicum) microspores, generative cells and sperm cells, and performed the genome-wide transcriptomic analysis of lncRNAs and mRNAs. SC lineage development involves global repression of genes for pluripotency, somatic development and metabolism following microspore asymmetric division and coordinated upregulation of GC/SC preferential genes. This process is accompanied by progressive loss of the active marks H3K4me3 and H3K9ac, and accumulation of the repressive marks H3K9 methylation. The SC lineage has a higher ratio of lncRNAs to mRNAs and preferentially expresses a larger percentage of lncRNAs than does the non-SC lineage. A co-expression network showed that the largest set of lncRNAs in these nodes, with more than 100 links, are GC-preferential, and a small portion of lncRNAs co-express with their neighboring genes. Single molecular FISH showed that several candidate genes may be markers distinguishing the three cell types of the SC lineage. Our findings reveal the molecular programming and potential roles of lncRNAs for SC lineage development.

overall_design: Seven cell types were examined, including microspores, generative cells, sperm cells, callus, fully expanded leaves, pistil  and mature pollen grain (MPG). Each cell type has three biological replicates.

first: Yunlong

last: Lu


title: Analysis of gene expression in populations of adult undifferentiated spermatogonia [microarray]

city: CLAYTON

first: Robin

middle: Mark

last: Hobbs

state: VIC

address: 27-31 Wright Street

department: Centre for Reproductive Health

country: Australia

institute: Hudson Institute of Medical Research

summary: The undifferentiated spermatogonial population of mouse testis is known to be functionally heterogeneous and contain both stem cells and committed progenitor cells. However, gene expression patterns marking these distinct cell fractions are poorly defined. We found that a subset of undifferentiated spermatogonia were marked by expression of an Oct4-GFP transgene but properties of these cells were unclear. Undifferentiated cells were therefore isolated from adult testes and seperated according to expression of Oct4-GFP for gene expression analysis by microarray. Our goal was to correlate Oct4-GFP expression with that of known markers of stem and committed progenitor cells to determine which undifferentiated cell populations were marked by Oct4-GFP.

overall_design: 3 independent sets of Oct4-GFP-positive and Oct4-GFP-negative undifferentiated spermatogonia were isolated by flow sorting from adult mouse testes. To obtain sufficient cells for analysis, testis cells from 2-3 mice were pooled for each sample.

first: Hue

last: La

first: Juho-Antti

last: Mäkelä

first: Ai-Leen

last: Chan

first: Fernando

last: Rossello

first: Christian

last: Nefzger

first: Julien

last: Legrand

first: Mia

last: De Seram

first: Jose

last: Polo


title: Upregulation of lncRNA ADAMTS9-AS2 promotes salivary adenoid cystic carcinoma (SACC) metastasis via miR-143-3p-mediated regulation of PI3K/Akt and MEK/Erk signaling

status: Public on Jul 25 2018

city: Guangzhou

first: jinsong

last: Li

address: Yanjiang west road

institute: sun yat-sen university

summary: Neurotropic infiltrative growth and distant metastasis are the main causes of death in salivary adenoid cystic carcinoma (SACC) patients. Long noncoding RNAs (lncRNAs) are involved in many human neoplasms, however their potential roles in SACC are unclear. In our study, we found that ADAMTS9-AS2 was significantly upregulated in SACC patients with metastasis and SACC -LM cells. Moreover, ADAMTS9-AS2 expression was closely associated with the prognosis and distant metastasis in SACC patients. Next, we found that c-myc could specifically bind to the promoter of ADAMTS9-AS2 and activated its transcription. Knockdown of ADAMTS9-AS2 significantly inhibited migration and invasion of SACC cells in vitro and distant lung metastasis in vivo. Furthermore, ADAMTS9-AS2 which mainly expressed in the cytoplasm shared miRNA response elements with ITGA6. Overexpression of ADAMTS9-AS2 competitively bound to miR-143-3p that inhibited ITGA6 from miRNA-mediated degradation, thus activated the activity of PI3K/Akt and MEK/Erk signaling and facilitated SACC metastasis. In summary, ADAMTS9-AS2 promotes migration and invasion in SACC by competing with miR-143-3p. This sheds a new insight into the regulation mechanism of ADAMTS9-AS2 and provides a possible application for the SACC treatment.

overall_design: lncRNA microarray analysis of highly-metastatic cell line SACC-LM and parental cell line SACC-83

first: Shule

last: Xie

first: Xin

last: Yu

first: Yingru

first: Hanyu

last: Ma

first: Song

last: Fan

first: Weixiong

last: Chen

first: Guokai

last: Pan

first: Weiwei

first: Hanqing

last: Zhang

first: Jinsong

first: Zhaoyu

last: Lin


title: Comparative analysis of the root and leaf transcriptomes in Chelidonium majus L.

city: Isfahan

first: Aboozar

last: Soorni

address: Isfahan

department: Biotechnology

country: Iran

institute: Isfahan University of Technology

summary: To understand the biosynthesis of C. majus BIAs, we performed de novo transcriptome sequencing of leaf and root tissues of C. majus using Illumina high-throughput sequencing technology.

overall_design: Different tissues, including roots and leaves from Chelidonium majus were used for transcriptome sequencing using the Illumina HiSeq 2000 platform to generate paired-end (2×150 base) reads.

first: Mohammad

middle: R

last: Naghavi


title: Leptin stimulates cellular glycolysis through a STAT3 dependent mechanism in tilapia

city: Durham

first: Jonathan

middle: D.

last: Douros

state: NC

address: 300 N. Duke St.

department: Duke Molecular Physiology Inst.

institute: Duke University

summary:
Purpose: The goal of this study was to assess the differential gene expression between control and leptin treated pituitary rostral pars distalis' of the tilapia (Oreochromis mossambicus).
Methods: Pituitary mRNA profiles from control (PBS) and leptin (100nM) treated tilapia (Oreochromis mossambicus) pituitary rostral pars disatalis were generated by deep sequencing using Illumina MiSeq. The sequence reads that passed quality filters were analyzed at the transcript abundance level using ANOVA (ANOVA) and BowTie2 followed by Cufflinks.
Results: Differential gene expression identified 1995 genes that were differentially expressed in the pituitary rostral pars distalis treated with leptin compared to PBS treated controls. These genes were indicated to be functionally involved in numerous biological processes including glycolyiss.
Conclusions: Our study represents the first detailed pituitary rostral pars distalis transcriptomes in the tilapia and identifies leptin as a major stimulator of glycolysis at the cellular level in teleost fishes.

middle: D


title: Distinguishing reproductive phasiRNAs in grasses from other identically-sized small RNAs using machine learning methods

status: Public on Jul 23 2018

city: St. Louis

first: Blake

last: Meyers

address: 975 N Warson Road

institute: Donald Danforth Plant Science Center

summary: Small RNA libraries made from the rdr2/mop1 maize mutant, using RNA extracted from young ears (3 to 5 cm in length). Four libraries were constructed representing biological replicates.  The mop1 mutant is depleted for heterochromatic siRNAs and enriched for 22-nt siRNAs of unknown function (as shown by Nobuta et al., 2008). These libraries were made in ~2010 but used for this study to assess the properties of the 22-nt, mop1-independent siRNAs.

middle: C

first: Vicki

last: Chandler

first: Stacey

last: Simon


title: Chip-chip from mechanical stretched interfollicular epidermal stem cells (IFESCs) with YAP

city: shanghai

first: Jing

last: Wang

address: 639 Zhizaoju Road

department: Depart of Plastic & Reconstructive Surgery

institute: Shanghai 9th People's Hospital, School of Medicine, Shanghai JiaoTong University

type: Genome binding/occupancy profiling by genome tiling array

summary: The renewing human epidermis constantly senses and adapts to a wide range of mechanical cues that are ubiquitous throughout life. The mechanisms of how mechanical forces are responded by interfollicular epidermal stem cells (IFESCs) and are transmitted directly into nucleus to modify gene expression was discovered to be mediated by transcriptional coactivators YAP. Interestingly, YAP, a critical modulator in controlling organ size by regulating both cell proliferation and apoptosis, was also found to induce self-renewal or amplification of epidermal progenitor/stem cells, and balance epidermal growth and differentiation. Because growth regulation imposed by different stimuli is achieved through distinct YAP target genes even in a single cell type. This study used chromatin immunoprecipitation (ChIP) coupled with human promoter tiling microarray analysis (ChIP-on-chip) to profile YAP at promoters genome-wide. The goal of the study was to identify the target genes occupied by YAP in IFESCs under the mechanical stretch condition.

overall_design: ChIP-on-chip performed with antibodies to YAP on mechanical stretched or unstretched human interfollicular epidermal stem cells  and with technical replicates in vitro.

first: Qingfeng

first: Xiaoling

first: Jiao

first: Yifan


title: Definitive classification of ovarian mature cystic teratomas origin using B allele frequency plots with SNP array analysis

status: Public on Jul 22 2018

city: Chiba

first: Hirokazu

last: Usui

state: Chiba

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

department: Department of Reproductive Medicine

institute: Graduate School of Medicine, Chiba University

summary: Ovarian mature cystic teratomas (MCTs) originate from postmeiotic germ cells, and some are thought to result from the fusion of two ova. The aim of this study was to determine whether this mechanism is in fact involved in MCT development. MCTs can be classified by the zygosity of the centromere and distal chromosome regions. We evaluated the zygosity of all chromosomes from 38 MCT specimens using B allele frequency (BAF) plots of single nucleotide polymorphism-array data. Theoretically, MCTs originated from the fusion of two ova should have a mixed pattern of centromeric zygosity, i.e., a combination of heterozygous and homozygous regions. However, no MCTs in this series met this criterion as evidenced by BAF plots, suggesting that the fusion of two ova is not mechanistically involved in the development of ovarian teratomas. Thus, MCTs were classified into three types originating from meiosis I and meiosis II errors, and endoduplication of a mature ovum. The numbers of recombination events occurring with type I and II MCTs were somewhat higher than in regular oogenesis. In addition, BAF plots could facilitate the construction of recombination maps at the whole-genome level for type I and II MCTs. In conclusion, our findings provide evidence against the hypothesis that MCTs originate from the fusion of two ova and indicate that BAF plots could serve as useful analytical tools for analyzing MCT cytogenetics and human oocyte meiosis.

overall_design: Thirty-eight ovarian MCTs specimens from 35 MCTs were obtained from 27 patients, who were subjected to cystectomy or oophorectomy. Three sets of specimens were collected from same tumors (specimen 09 and 10 from tumor 27, specimen 23 and 24 from tumor 28, specimen 32 and 33 from tumor 12). The other specimens were sampled from independent tumors. The genomic DNAs were extracted and were analyzed by Illumina HumanCore-24v1 array.

first: H

first: K

last: Nakabayashi

last: Maehara

last: Hata

first: M

last: Shozu


title: Treponema denticola transcriptional profiles in serum-restricted conditions

city: Chiyoda-ku

first: Kazuyuki

last: Ishihara

state: Tokyo

address: Misakicho 2-1-14

department: Microbiolgy

institute: Tokyo Dental College

summary: Treponema denticola is a major pathogen in periodontal disease, frequently isolated from lesions of chronic periodontitis. The ability to adopt its environment is believed to be important for T. denticola in colonizing and proliferating in the gingival crevice. T. denticola use serum as a major nutrient source in the gingival crevices, suggesting that this microorganism utilize serum components to proliferate in gingival crevice. The purpose of this study was to identify T. denticola serum utilization genes. Precultured T. denticola were suspended in tryptone-yeast extract-gelatin-volatile fatty acids medium containing 0, 1 and 10% serum, and incubated anaerobically for 17 h. Total RNA was isolated and T. denticola gene expression was compared by microarray and reverse transcription-polymerase chain reaction. In serum-depleted conditions, the expression of a potential hydroxylamine reductase, several ABC transporters, and phosphoenolpyruvate synthase were increased, while methyl-accepting chemotaxis proteins and a transcriptional regulator were decreased. The results suggest that T. denticola may uptake serum components via ABC transporters. Decreased dmcA expression with decreased serum concentration suggests its involvement in chemotaxis toward serum-rich environments.

overall_design:
Comparison of 3 culture conditions.
Treponema denticola was cultured in medium containing 10%, 1% or 0% for 17 h. Profile of gene expression of T. denticola grown in medium containing 1% or 0% serum was compared to that grown in medium containing 10% serum.

first: Mariko

last: Tanno-Nakanishi

first: Yuichiro

last: Kikuchi

first: Satoru

last: Yamada

first: Eitoyo

last: Kokubu


title: Expression of protocadherin gamma in skeletal muscle tissue is associated with age and muscle weakness

city: Wageningen

first: Roland

last: Hangelbroek

address: Stippeneng 4

department: Division of Human Nutrition

institute: Wageningen University

summary: The skeletal muscle system plays an important role in the independence of older adults. In this study we examine differences in the skeletal muscle transcriptome between healthy young and older subjects and (pre‐)frail older adults. Additionally, we examine the effect of resistance‐type exercise training on the muscle transcriptome in healthy older subjects and (pre‐)frail older adults. Baseline transcriptome profiles were measured in muscle biopsies collected from 53 young, 73 healthy older subjects, and 61 frail older subjects. Follow‐up samples from these frail older subjects (31 samples) and healthy older subjects (41 samples) were collected after 6 months of progressive resistance‐type exercise training. Frail older subjects trained twice per week and the healthy older subjects trained three times per week. At baseline genes related to mitochondrial function and energy metabolism were differentially expressed between older and young subjects, as well as between healthy and frail older subjects. Three hundred seven genes were differentially expressed after training in both groups. Training affected expression levels of genes related to extracellular matrix, glucose metabolism, and vascularization. Expression of genes that were modulated by exercise training was indicative of muscle strength at baseline. Genes that strongly correlated with strength belonged to the protocadherin gamma gene cluster (r = −0.73). Our data suggest significant remaining plasticity of ageing skeletal muscle to adapt to resistance‐type exercise training. Some age‐related changes in skeletal muscle gene expression appear to be partially reversed by prolonged resistance‐type exercise training. The protocadherin gamma gene cluster may be related to muscle denervation and re‐innervation in ageing muscle.

overall_design: Gene expression was profiled in human skeletal muscle (vastus lateralis) in young and older subjects. Older subjects (frail and healthy) participated in progressive resistance-type exercise training.

middle: W

first: Parastoo

last: Fazelzadeh

first: Michael

last: Tieland

first: Mark

middle: V

last: Boekschoten

first: Guido

last: Hooiveld

first: John

last: van Duynhoven

first: James

middle: A

last: Timmons

first: Lex

last: Verdijk

first: Lisette

last: de Groot

first: Luc

last: van Loon

last: Müller


title: Affymetrix OncoScan CN analysis on breast cancer in women affected with Neurofibromatosis type 1

city: TAmpa

first: Yonghong

last: Zhang

address: 12902 USF Magnolia Drive

department: Biomedical Informatics

institute: Moffitt Cancer Center

summary: NF1 germline mutation predisposes to breast cancer. NF1 mutations have also been proposed as oncogenic drivers in sporadic breast cancers. To understand the genomic and histological characteristics of these breast cancers, we examined the tumors with NF1 germline mutations.

overall_design: 11 FFPE samples - no replicates

first: Wang

last: Xia


title: Carbohydrate Syntrophy enhances the establishment of Bifidobacterium breve UCC2003 in the neonatal gut

status: Public on Jul 19 2018

city: Cork

first: Mary

last: O'Connell Motherway

address: Western Road

department: Department of Microbiology and Alimentary Pharmabiotic Centre

country: Ireland

institute: University College Cork

summary: To extend our understanding of bifidobacterial mutualism and carbohydrate syntrophy in the gut we adopted advanced functional genomics to create single- and double-deletion isogenic strains of the NagA encoding genes of B. breve UCC2003. The resulting strains were examined, as compared to the parent strain, for their ability to metabolise particular host derived carbohydrates. In addition, the B. breve strains were examined for their crossfeeding capability and ability to establish, in the presence of B. bifidum ATCC29521, in the gut of dam fed neonatal mice.

overall_design: DNA-microarrays containing oligonucleotide primers representing each of the 1864 annotated genes on the genome of B. breve UCC2003 were designed by and obtained from Agilent Technologies (Palo Alto, Ca., USA). Methods for cell disruption, RNA isolation, RNA quality control, complementary DNA synthesis and labeling were performed as described previously (Pokusaeva et al., 2009). Labeled cDNA was hybridized using the Agilent Gene Expression hybridization kit (part number 5188-5242) as described in the Agilent Two-Color Microarray-Based Gene Expression Analysis v4.0 manual (G4140-90050). Following hybridization, microarrays were washed in accordance with Agilent’s standard procedures and scanned using an Agilent DNA microarray scanner (model G2565A). Generated scans were converted to data files with Agilent's Feature Extraction software (Version 9.5). DNA-microarray data were processed as previously described (Garcia De La Nava et al., 2003). Differential expression tests were performed with the Cyber-T implementation of a variant of the t-test (Long et al., 2001). A gene was considered differentially expressed when p < 0.001 and an expression ratio of >3 or <0.33 relative to the control.


title: mRNA sequencing of live and encysting cells of Colpoda aspera.

status: Public on Jul 16 2018

city: wuhan

first: Wei

last: Miao

state: hubei

address: donghu south road #7

institute: Institute of hydrobiology, CAS

summary: The goals of this study is to investigate the encystment mechanism.

overall_design: Compare the expression of genes between two samples.


title: mRNA sequencing of live and encysting cells of Colpoda aspera


title: Expression data from aged SIV-infected macaques

city: Pittsburgh

first: Stephanie

last: Bissel

state: PA

address: 3550 Terrace Street, S758 Scaife Hall

institute: University of Pittsburgh

summary:
It has been hypothesized that lentiviral infection might exacerbate age-related neurodegenerative processes.
This study used microarrays to detail gene expression in the midfrontal cortex from aged macaques chronically infected with SIVmac251 with and without antiretroviral therapy along with non-infected counterparts.

overall_design: RNA from midfrontal cortex samples was taken from aged female Rhesus macaques (Macaca mulatta) of Chinese origin (range = 14.7-24.8 years). Half of the macaques (n=12) were infected with SIVmac251, while the other half (n=11) were mock-infected controls. After 10 months of infection, half of both the infected and mock-infected macaques received daily subcutaneous doses of reverse transcriptase inhibitors TDF and FTC for an additional 6 months. The other macaques received saline in the 6 month period. At the end of the treatment period, brain sections from each animal were queried for evidence of SIV infection. Based on the histological findings, macaques were organized into the following groups for gene expression profiling by array: aged SIV-infected (n=4); aged SIV-infected with antiretroviral therapy (n=3); aged SIV-infected with meningitis (n=1); aged SIV-infected with rhesus CMV  meningoencephalitis (n=1); aged with SIV encephalitis (n=2); aged control (n=6); aged control with antiretroviral therapy (n=5). For comparison, RNA from midfrontal cortex of non-infected (n=6) and SIV encephalitic (n=2) macaques were  also examined.

first: Clayton

last: Wiley


title: Chlorovirus ATCV-1 is part of the human oropharyngeal virome and is associated with changes in cognitive functions in humans and mice

city: Baltimore

first: Robert

last: Yolken

state: MD

address: 600 N Wolfe st

department: Pediatrics

institute: Johns Hopkins

summary: Human mucosal surfaces contain a wide range of microorganisms. The biological effects of these organisms are largely unknown. Large-scale metagenomic sequencing is emerging as a method to identify novel microbes. Unexpectedly, we identified DNA sequences homologous to virus ATCV-1, an algal virus not previously known to infect humans, in oropharyngeal samples obtained from healthy adults. The presence of ATCV-1 was associated with a modest but measurable decrease in cognitive functioning. A relationship between ATCV-1 and cognitive functioning was confirmed in a mouse model, which also indicated that exposure to ATCV-1 resulted in changes in gene expression within the brain. Our study indicates that viruses in the environment not thought to infect humans can have biological effects.

overall_design: Mice that had been successfully infected with ATCV-1, n=16, were compared with matched but un-infected mice, n=7.

first: C

last: Talbot

first: Emese

last: Prandovszky

last: Van Etten


title: Gene expression profiles in E. coli under different frequency signals

city: Hefei

first: Zhi

last: Liang

address: No.96, JinZhai Road

department: School of Life Sciences

institute: University of Science & Technology of C

summary: To identify the physiological effects of the multiple frequency signaling through the SIMO module of EnvZHK, we used transcriptome sequencing to study the influences of different frequency inputs to gene expressions in E.coli. From the results we found that different frequency signals through the SIMO module resulted in distinct gene expressions. Moreover, the PCA result showed a significant difference between frequency response gene expression profiles under the wildtype and the mutant EnvZHK SIMO module that the gene expression profile of the wildtype samples under middle frequencies were closer to that under high frequencies, while the gene expression profile of the mutant samples under middle frequencies were closer to that under low frequencies. Interestingly, these relationships of the expression patterns were in agreement with that of these effective frequency spectrums of the SIMO module, indicating that particular frequency signals determine the distinct gene expression profiles.

overall_design: The gene expression profiles in E. coli were analyzed by approach of transcriptome sequencing under different input LED frequencies, including 1/3600 Hz, 1/2400 Hz, 1/1800 Hz, 1/1200 Hz, 1/900 Hz and 1/600 Hz, for E. coli transcriptome sequencing.

first: Siwei

last: Luo

first: Jiarui

last: Wu


title: The effect of probiotic Lactobacilli strains, inulin-type fructans and oligofructose on gene expression profiles in intestinal Caco-2 cells

first: Nicole

last: de Wit

address: Bornse Weilanden 9

department: Food & Biobased Research

institute: Wageningen UR

summary: Background: Beneficial microbes can be actors in maintaining or stimulating barrier function, and may counteract pathogen-infection. Lactobacilli are particularly recognized for enhancing intestinal barrier function and to confer protective effects against multiresistant pathogens. Various L. acidophilus strains support intestinal immune barrier function and have been shown to improve resistance to pathogens. Although less extensively studied than beneficial bacteria, other food-based ingredients that can contribute to strengthening barrier function are dietary fibers. For instance, inulin and fructooligosaccharides (FOS) have recently been shown to enhance barrier function  and protect against barrier dysfunction. Effects of these ingredients on intestinal barrier function were evaluated by quantifying regulation of gene expression by microarray. Methods: Caco-2 cells were incubated with probiotic strains or inulin-type fibers for 6 hours, total RNA was extracted and Affymterix Human Gene 1.1 ST arrays were used to analyze the gene expression profiles. Results: Only L. acidophilus modulated a group of 26 genes related to tight-junctions. Inulin-type fructans, L. brevis W63 and L. casei W56 regulated other genes, unrelated to tight junctions. L. acidophilus also had unique effects on a group of 6 genes regulating epithelial phenotype towards follicle-associated epithelium. L. acidophilus W37 was therefore selected for a challenge with STM and prevented STM-induced barrier disruption and decreased secretion of IL-8. L. acidophilus W37 increases TEER and can protect against STM induced disruption of gut epithelial cells integrity in vitro. Conclusion: Our results suggest that selection of specific bacterial strains for enforcing barrier function may be a promising strategy to reduce or prevent STM infections.

overall_design:
Microarray analysis was performed on 21-days differentiated Caco-2 cells incubated with probiotic strains L. acidophilus W37, L. brevis W63 and L. casei W56 or inulin-like fructans and oligofructose for 6 hours. This experiment was performed two or three times, so independent biological replicates per treatment were included in the microarray analysis.
Gene expression profiling by microarray

first: Alexia

last: Lepine

first: Mark

last: Boekschoten

first: Jurriaan

last: Mes


title: lncRNA profiling in moDCs of systemic lupus erythematosus

city: Shanghai

first: Yilun

last: Wang

address: No.12 Wulumuqi Zhong Road

institute: Fudan University

summary: Recent studies have shown that alterations in the function of dendritic cells (DCs) are involved in the pathogenesis of systemic lupus erythematosus (SLE). However, the role of DCs participating in SLE remains unclear. We profiled the lncRNAs of LPS-stimulated moDCs in SLE patients compared with healthy controls.

overall_design: Two-condition experiment, DC (as controls) vs. SLG (as patients with SLE group) cells. Biological replicates: 5 control replicates, 5 patient replicates.

first: Jinhua

last: Xu


title: Suckling lamb perirenal fat transcriptome

status: Public on Jul 18 2018

city: León

first: Beatriz

last: Gutierrez Gil

state: León

address: Faculty of Veterinary, Campus de Vegazana

department: Dpto Animal Production

institute: University of León

summary: The aim of this study was to perform a comparative analysis of the perirenal fat transcriptomes of suckling lambs from two breeds with different growth and carcass characteristics. The perirenal fat tissue from 14 suckling lambs (Assaf= 8, Churra= 6) was used for the RNA-Seq analysis. The functional enrichment analysis of the 670 highly expressed genes (>150 fragments per kilobase of exon per million fragments mapped) in the perirenal fat transcriptome of both breeds revealed that the majority of these genes were involved in energy processes. The differential expression analysis performed identified 373 differentially expressed genes (DEGs) between the two compared breeds. In Assaf lambs, DEGs were enriched in Gene Ontology (GO) biological processes related to fatty-acid oxidation, while in Churra lambs, the majority of the significantly enriched GO terms were related to cholesterol synthesis, which suggests that upregulated DEGs in Assaf lambs are implicated in fat burning, while the Churra upregulated DEGs are linked to fat accumulation.

overall_design: The transcriptome analysis was performed with RNA extracted from perirenal adipose tissue from 14 suckling lambs from two different breeds (specifically, six Churra and eight Assaf lambs). All the lambs included in this study were males born between April and May 2016. After birth, lambs were maintained between 4-8 hours with their dams to suck the first colostrum. Then, in order to avoid the maternal effects, they were held in lamb pens and fed Ovilac 60 (Calfvet, Lleida, Cataluña, Spain) milk replacer powder using a milk replacer machine. Lambs were slaughtered when they reached an average live weight of (mean ± SD) 10.32 ± 0.73 kg, which is the common market weight range. Lambs ages at slaughter were from 19 to 35 days old, and carcass weight for Churra and Assaf lambs were 5.16 ± 0.44 and 5.34 ± 0.33 kg, respectively. The management, transport and sacrifice of the animals was in accordance with the Spanish and EU legislations (Spanish Laws 32/2007, 6/2013 and RD 37/2014; Council Regulation (EC) 199/2009). At slaughter, perirenal adipose tissue was collected from each lamb.

last: Gutiérrez-Gil

first: Juan

last: Arranz

first: Aroa

last: Suárez-Vega


title: Expression profiles of mRNA and lncRNA in HCT-8 cells infected with Cryptosporidium parvum IId subtype

city: shannxi

first: TingLi

last: Liu

address: xinong load

department: Northwest A&F University

institute: College of Veterinary Medicine

summary:
Cryptosporidium parvum is one of the most important opportunistic enteric parasites, causing severe diarrhea in immunocomprised human and animals. However, few effective control agents were available for this parasite. Long non-coding RNA (lncRNA) was discovered to play key roles in many diseases through regulating the gene expression.
Here, using microarray assay, we investigated the expression profiles of mRNA and lncRNA in HCT-8 cells after the infection of C. parvum IId subtype, the prevalent subtype of China. A total of 821 lncRNAs and 1,349 mRNAs were dysregulated expressed in HCT-8 cells at 24 h post infection (pi) of C. parvum IId subtype. Of them, all five types of lncRNAs were identified, including 302 of sense, 280 of antisense, 312 of intergenic, 44 of divergent, and 33 of intronic lncRNAs. Ten lncRNAs and ten mRNAs randomly selected were successfully confirmed the microarray results. The co-expression and target prediction analysis indicated 27 of mRNAs cis-regulated by 29 lncRNAs and 109 of coding genes trans-regulated by 114 lncRNAs. These predicted targets were enriched in pathways involved in the interaction between host and C. parvum, eg. hedgehog signaling pathway, Wnt signaling pathway and tight junction, suggesting that these aberrantly lncRNAs would play important regulating roles during infection of C. parvum IId subtype.

overall_design: we collected the HCT-8 cells infected with cryptosporidium parvum at 24 hours and analyzed the profiles of mRNAs and lncRNAs.

first: Tingli

first: Guanghui

last: Zhao


title: Tracking gene expression and oxidative damage of O2-stressed Clostridioides difficile by a multi-omics approach

status: Public on Jul 15 2018

city: Braunschweig

first: Michael

last: Beckstette

state: Lower Saxony

address: Inhoffenstrase 7

department: Molecular Infection Biology

country: Germany

institute: Helmholtz Centre for Infection Research

summary: Clostridioides difficile is the major pathogen causing diarrhea following antibiotic treatment. It is considered to be a strictly anaerobic bacterium, however, previous studies have shown a certain and strain-dependent oxygen tolerance. In this study, the model strain C. difficile 630Δerm was shifted to micro-aerobiosis and was found to stay growing to the same extent as anaerobically growing cells for the duration tested. However, an extensive change in gene expression was determined by RNA-Seq with 49 effected genes after 15 min and more than 400 after one hour. Effected genes exhibit a wide range of functionality, including the metabolism of amino acids, enzymes for cell wall synthesis, the uptake and metabolism of sugars, synthesis of B vitamins as well as purine synthesis and DNA repair. Our study suggests that tolerance of C. difficile towards O2 is based on a complex and far-reaching adjustment of global gene expression.

overall_design: Comparative examination of gene expression in Clostridioides difficile grown anaerobically and in the presence of 5% oygen.

first: Meina

last: Neumann-Schaal

first: Aaron

last: Nuss

first: Petra

last: Dersch

first: Susanne

last: Sievers


title: An Uncharacterized Member of the Gls24 Protein Superfamily is a Putative Sensor of Essential Amino Acid Availability in Streptococcus pneumoniae

status: Public on Jul 17 2018

city: Majadahonda

first: Antonio

middle: J.

last: Martin-Galiano

state: Madrid

address: Ctra. Majadahonda-Pozuelo, km 2.2

department: Bacterial genetics

institute: Instituto de Salud Carlos III

summary: Proteins belonging to the Gls24 superfamily are involved in survival of pathogenic Gram-positive cocci under oligotrophic conditions and other types of stress, by a still unknown molecular mechanism. In Firmicutes, this superfamily includes three different valine-rich orthologal families (Gls24A, B, C) with different potential interactive partners. Whereas the Streptococcus pneumoniae Δgls24A deletion mutant experienced a general long growth delay, the Δgls24B mutant grew as the parental strain in the semisynthetic AGCH medium but failed to grow in the complex Todd-Hewitt medium. Bovine seroalbumin (BSA) was the component responsible for this phenotype. The effect of BSA on growth was concentration-dependent and was maintained when the protein was proteolyzed but not when heat-denatured, suggesting that BSA dependence was related to oligopeptide supplementation. Global transcriptional analyses of the knockout mutant revealed catabolic derepression and induction of chaperone and oligopeptide transport genes. This mutant also showed increased sensibility to cadmium and high temperature. The Δgls24B mutant behaved as a poor colonizer in the nasopharynx of mice and showed 20-fold competence impairment. Experimental data suggest that Gls24B plays a central role as a sensor of amino acid availability and its connection to sugar catabolism. This metabolic rewiring can be compensated in vitro, at the expenses of external oligopeptide supplementation, but reduce important bacteria skills prior to efficiently address systemic virulence traits. This is an example of how metabolic factors conserved in enterococci, streptococci, and staphylococci can be essential for survival in poor oligopeptide environments prior to infection progression.

overall_design: Total RNA was extracted from S. pneumoniae R6 wild-type and spr0399 deletion mutant cultures during exponential growth (with 500 or 50 µg/mL BSA), amplified and used for microarray hibridization. Two independent replicates were performed.


title: Piglet weight gain during the first two weeks of lactation influences the immune system development

status: Public on Jul 14 2018

city: Sherbrooke

first: Martin

last: Lessard

state: Qc

address: 2000 College

department: Sherbrooke Research Centre

country: Canada

institute: Agriculture and AgriFood Canada

summary: gene expression in ileum of low birth weight piglets was compared to the one in high birth weight piglets at 16 days of age.

overall_design: RNA pooled from the two piglets born with the lowest weight were compared to RNA pooled from the piglets born with the highest weight


title: RNA-seq, YY1 ChIP-seq and MeDIP-seq of radiation-induced skin fibrosis of rats

status: Public on Jul 13 2018

city: suzhou

first: zhang

middle: shu

last: yu

address: No. 199, Ren'ai Road

department: soochow university

institute: Soochow University

type: Genome binding/occupancy profiling by high throughput sequencing

type: Methylation profiling by high throughput sequencing

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

overall_design: Refer to individual Series


title: DNA methylation analysis of radiation-induced skin fibrosis of rats

summary: This study aims to compared the genome-wide DNA methylation status in radiation-induced fibrotic skin and adjacent normal tissues of rats by methylated DNA immunoprecipitation sequencing (MeDIP-Seq). Male Sprague-Dawley (SD) rats (4 weeks old) were irradiated with a single 45-Gy dose of irradiation was administered to the treatment area at a rate of 750 cGy/min using a 6-MeV electron beam accelerator (Clinac 2100EX, Varian Medical Systems, Inc., CA). Skin tissues from nonirradated skin areas and irradietd areas were collected and subjected to DNA methylation analysis by MeDIP.

overall_design: Male Sprague-Dawley (SD) rats (4 weeks old) were irradiated with a single 45-Gy dose of irradiation was administered to the treatment area at a rate of 750 cGy/min using a 6-MeV electron beam accelerator (Clinac 2100EX, Varian Medical Systems, Inc., CA). Skin tissues from nonirradated skin areas (NC) and irradietd areas were collected and subjected to DNA methylation analysis by MeDIP.

first: Shuyu

last: Zhang


title: mRNA expression analysis of radiation-induced skin fibrosis of rats

summary: This study aims to compared mRNA expression between radiation-induced fibrotic skin and adjacent normal tissues of rats by RNA-Seq. Male Sprague-Dawley (SD) rats (4 weeks old) were irradiated with a single 45-Gy dose of irradiation was administered to the treatment area at a rate of 750 cGy/min using a 6-MeV electron beam accelerator (Clinac 2100EX, Varian Medical Systems, Inc., CA). Skin tissues from nonirradated skin areas and irradietd areas were collected and subjected to mRNA expression analysis.

overall_design: Male Sprague-Dawley (SD) rats (4 weeks old) were irradiated with a single 45-Gy dose of irradiation was administered to the treatment area at a rate of 750 cGy/min using a 6-MeV electron beam accelerator (Clinac 2100EX, Varian Medical Systems, Inc., CA). Skin tissues from nonirradated skin areas and irradietd areas were collected and subjected to RNA sequencing.


title: Comprehensive circRNAs expression profiling reveals the potential role of circRNAs in systemic lupus erythematosus [Human circRNA Array v2.0]

first: Lian-Ju

last: Li

state: Anhui

address: 81 Meishan Road

department: Department of Epidemiology and Biostatistics, School of Public Health

institute: Anhui Medical University

summary: CircRNAs are novel non-coding RNAs which  can serve as microRNA sponge and regulate gene transcription through promoting expression of their parent genes or competing with splicing of their parent genes. Moveover, there is increasing evidence showing that aberrant expressions of circRNAs are implicated in various cancers. Yet, their roles in systemic lupus erythematosus (SLE), a prototypical autoimmune disease, remain unknown. To reveal the implications of circRNAs in SLE, we used Human circRNA Array v2.0 microarrays to measure the expression profiles of circRNAs in T cells of patients with SLE and healthy controls. We found 129 differentially expressed circRNAs (fold change >2; P <0.05) in SLE patients compared with controls. Home-made computer program based on TargetScan and miRanda was applied to predict miRNA targets of circRNAs and identify 5 miRNAs with the highest mirSVR score for each circRNA.Downregulation of circRNA hsa_circ_0045272 was established using Real-time quantitative PCR. These results showed abrrant expression profiles of circRNAs in T cells of SLE patients and revealed their potential role in SLE.

overall_design: In this study, we determined expression profile of circRNAs in T cells of six SLE patients (S5, S9, S11, S15, S18, S25) and three healthy controls (C1, C2, C3) using Human circRNA Array v2.0 microarray (8×15K, Arraystar).

first: Dong-Qing

last: Ye


title: Transcriptomics effects of ingestion of food additive titanium dioxide (E171) in the colon of a chemically induced colorectal cancer model

city: Maastricht

first: Héloïse

last: Proquin

address: Universiteitssingel 50

institute: Maastricht University

summary: Titanium dioxide, a white colorant, is the mineral the most produced worldwide. It is used in food under the name of E171. Previous studies showed that in a chemically induced colorectal cancer mouse model, E171 increase significantly the number of tumours. The aim of this study was to understand the molecular mechanisms behind these effects of E171 exposure. BALB/c mice were exposed by gavage to 5 mg/kg bw/day of E171 for 2, 7, 14 and 21 days. Whole genome mRNA microarray analyses on the distal colon were performed. The results show that E171 induced a downregulation of genes involved in the innate and adaptive immune system, suggesting impairment of this system. In addition, over time, signalling genes involved in colorectal cancer and other types of cancers were modulated. In relation to cancer development, effects potentially associated with oxidative stress were observed through modulation of genes related to antioxidant production. E171 affected genes involved in biotransformation of xenobiotics which can form reactive intermediates resulting in toxicological effects. These transcriptomics data reflect the early biological responses induced by E171 which precede tumour formation in an AOM/DSS mouse model.

overall_design: Total of 31 colon of mice samples, every sample was in duplicate. Two different type of exposure: exposed to AOM and DSS (CRC), exposed to AOM/DSS and 5mg/kg bw/day of E171 (CRCE). Four time points: 2, 7, 14 and 21 days. At each time point 4 mice are euthanised (2 males, 2 females)'

first: Marlon

last: Jetten

first: Marloes

last: Jonkhout

first: Luis

last: Guillermo Garduño-Balderas

first: Jacob

last: Briedé

first: Theo

middle: M

last: de Kok

first: Henk

last: van Loveren

first: Yolanda

middle: I

last: Chirino


title: Effects of larval density on gene regulation in C. elegans during routine L1 synchronization

city: Philadelphia

first: Colin

last: Conine

state: Pennsylvania

address: 421 Curie Blvd BRB 1213

department: Genetics and Neonatology

institute: UPenn Perelman SOM and CHOP

summary: Bleaching gravid C. elegans followed by a short period of starvation of the L1 larvae is a routine method performed by worm researchers for generating synchronous populations for experiments. During the process of investigating dietary effects on gene regulation in L1 stage worms by single-worm RNA-Seq, we found that the density of resuspended L1 larvae affects expression of many mRNAs. Specifically, a number of genes related to metabolism and signalling are highly expressed in worms arrested at low density, but are repressed at higher arrest densities. We generated a GFP reporter strain based on one of the most density-dependent genes in our dataset – lips-15 – and confirmed that this reporter was expressed specifically in worms arrested at relatively low density. Finally, we show that conditioned media from high density L1 cultures was able to downregulate lips-15 even in L1 animals arrested at low density, and experiments using daf-22 mutant animals demonstrated that this effect is not mediated by the ascaroside family of signalling pheromones. Together, our data implicate a soluble signalling molecule in density sensing by L1 stage C. elegans, and provide guidance for design of experiments focused on early developmental gene regulation.

overall_design: L1 Larvae arrested in M9 media at different densities were isolated for single L1 RNA-sequencing

first: Oliver

last: Rando


title: The value of circulating microRNAs for early diagnosis of B-cell lymphoma: A case-control study on historical samples

city: Naestved

first: Steffen

last: Jørgensen

address: Parkvej 190

country: Denmark

institute: absalon university college

summary: MicroRNAs are small regulatory RNAs that are deregulated in a wide variety of human cancers, including different types of B-cell lymphoma. Nevertheless, the feasibility of circulating microRNA for early diagnosis of B-cell lymphoma has not been established. To address the possibility of detecting specific circulating microRNAs years before a B-cell lymphoma is diagnosed, we studied the plasma expression of microRNA first in pre-treatment samples from patients with diffuse large B-cell lymphoma and subsequently in repository samples from blood donors who later developed B-cell lymphomas. In addition, we studied the microRNA expression in the diagnostic lymphoma biopsy and in plasma samples taken after end of treatment. The most strongly induced (miR-326) and suppressed (miR-375) plasma microRNA at diagnosis, when compared with healthy blood donors, were also substantially up- or down-regulated in plasma repository samples taken from several months to up to two years before the blood donors were diagnosed with B-cell lymphoma. Importantly, at these time points the donors had no signs of disease and felt healthy enough to donate blood. In conclusion, this first study of plasma microRNA profiles from apparently healthy individuals, taken several years before B-cell lymphoma diagnosis, suggests that plasma microRNA profiles may be predictive of lymphoma development.

overall_design: Plasma samples from 14 healthy controls and 16 plasma samples from patients diagnosed with Diffuse large B-cell lymphoma

first: Isabella

last: Paulsen

first: Jakob

last: Hansen

first: Dorte

last: Tholstrup

first: Christoffer

last: Hother

first: Erik

last: Sørensen

first: Mikkel

middle: S

last: Petersen

first: Kaspar

last: Nielsen

first: Klaus

last: Rostgaard

first: Margit

last: Larsen

first: Peter

last: de Nully Brown

first: Elisabeth

last: Ralfkiær

first: Keld

last: Homburg

first: Henrik

last: Hjalgrim

first: Christian

last: Erikstrup

last: Ullum

first: Jesper

last: Troelsen

first: Kirsten

last: Grønbæk

first: Ole

middle: B

last: Pedersen


title: ChIP-Sequencing analysis of YY1 binding DNA in radiation-induced skin fibrosis of rats

first: zhang

last: yu

summary: This study aims to compared the genome-wide Ying Yang-1 (YY1) binding DNA sequences in radiation-induced fibrotic skin and adjacent normal tissues of rats by ChIP-Seq. Male Sprague-Dawley (SD) rats (4 weeks old) were irradiated with a single 45-Gy dose of irradiation was administered to the treatment area at a rate of 750 cGy/min using a 6-MeV electron beam accelerator (Clinac 2100EX, Varian Medical Systems, Inc., CA). Skin tissues from nonirradated skin areas and irradietd areas were collected and subjected to ChIP of YY1.

overall_design: Male Sprague-Dawley (SD) rats (4 weeks old) were irradiated with a single 45-Gy dose of irradiation was administered to the treatment area at a rate of 750 cGy/min using a 6-MeV electron beam accelerator (Clinac 2100EX, Varian Medical Systems, Inc., CA). Skin tissues from nonirradated skin areas and irradietd areas were collected and subjected to ChIP-sequencing of YY1.

first: Shuyu

last: Zhang


title: Forms of Selenium in Vitamin-mineral Mixes Differentially Affect Hepatic Gene Expression of Steers Grazing Endophyte-infected Tall Fescue.

city: Lexington

first: James

last: Matthews

state: KY - Kentucky

address: 325 Cooper Drive

department: Animal and Food Sciences

country: USA

institute: University of Kentucky

summary: The goal of this study was to test the hypothesis that sodium selenite (ISe), SEL-PLEX (OSe), vs. a 1:1 blend (MIX) of ISe and OSe in a basal vitamin-mineral (VM) mix would differetianlly alter hepatic transcriptome profiles in growing beef steers commonly grazing an endophyte-infected tall fescue (E+) pasture. Predominately-Angus steers (BW = 183 ± 34 kg) were randomly selected from herds of fall-calving cows grazing E+ pasture and consuming VM mixes that contained 35 ppm Se as ISe, OSe, and MIX forms. Steers were weaned, depleted of Se for 98 d, and subjected to summer-long common grazing of an E+ pasture (0.51 ppm total ergovaline per ergovalinine; 10.1 ha). Steers were assigned (n = 8 per treatment) to the same Se-form treatments upon which they were raised. Selenium treatments were administered by daily top-dressing 85 g of VM mix onto 0.23 kg soyhulls, using in-pasture Calan gates. We collected liver samples and examined for changes in global expression pattern by microarray analysis.

overall_design: 21 total samples were analyzed (n = 6 for ISe, n=7 for MIX, and n=8 for OSe ).

first: Yang

last: Jia


title: Mixed baits reduce the oxidative stress of common carp (Cyprinus carpio): Based on microRNA sequencing

city: Chengdu

first: Jie

last: Luo

state: Sichuan

address: Huimin road

department: College of Animal Science and Technology

institute: Sichuan Agricultural University

summary:
Purpose:In order to elucidate the molecular mechanism of the effects of different diets on the antioxidant capacity of fish, three groups of adult common carp (Cyprinus carpio) (initial weight 517.8 ±50 g) were fed with earthworm, earthworm + duckweed and duckweed, respectively, which were performed by  miRNA sequencing.
Methods:MiRNA profiles of  common carp fed with earthworm, earthworm + duckweed and duckweed were generated by deep sequencing, in duplicate, using Illumina Hiseq 2500 platform.  qRT–PCR validation was performed using  SYBR Green assays
Results: We built microRNA libraries by using total RNA and contained filtered 20,868,000, 18,984,242, 22,300,487, 19,538,683, 17,110,676 and 14,747,090 high-quality reads that were obtained from sample A1, A2, M1, M2, P1 and P2 respectively.In total, we discovered 236 known carp miRNAs (225, 225, 222, 227, 228 and 219 in A1, A2, M1, M2, P1and P2, respectively).For the known miRNA, 9 differentially expressed miRNAs (DEM) were found between A and M and 8 known miRNAs differentially expressed between P and M, and 11 of these were validated with qRT–PCR. The expression level of 11 known microRNAs via miRNA-seq had highly similar with the relative expression level of 11 known microRNAs via qRT-PCR.
Conclusions:  In present study, we demonstrated the transcriptional profiles, identification of 5 differentially expressed miRNAs be reported related to oxidative stress, including miR-137-3p, miR-143-3p, miR-146a-5p, miR-21-5p and miR-125b-5p. For omnivorous fish, feed a single bait may might cause oxidative stress inordinately.

first: Song

last: Yang


title: Transcriptome analysis of Streptomyces natalensis HW-2 to valine using RNA-sequencing

city: Luoyang

first: Ying

state: Henan

address: Kaiyuan Road

institute: Henan University of Science and Technology

summary: To characterize the differentially expressed genes between adding Valine and without Valine on Streptomyces natalensis HW-2

overall_design: The Valine was added to the fermentation medium of S. natalensis HW-2 after fermentation for 36 h at 28oC with the shaking of 180r/min.using RNA-sequencing，we determine the difference of gene expression in different time of Valine on Streptomyces natalensis


title: Marginal selenium deficiency down-regulates inflammation-related genes in splenic leukocytes of the mouse

city: Wageningen

first: Evert

middle: M.

last: van Schothorst

address: De Elst 1

institute: Wageningen University

summary: Moderate selenium deficiency may lead to an impaired capacity to cope with health challenges. Functional effects of suboptimal selenium intake are not fully known, and biomarkers for an insufficient selenium supply are inadequate. We therefore fed mice diets of moderately deficient or adequate selenium intake for 6 weeks. Changes in global gene expression were monitored by microarray analysis in splenic leukocytes. Genes for four selenoproteins, Sepw1, Gpx1, Selh and Sep15, were the most significantly down-regulated in moderate selenium deficiency, and this was confirmed by quantitative polymerase chain reaction (qPCR). Classification of significantly affected genes revealed that processes related to inflammation, heme biosynthesis, DNA replication and transcription, cell cycle and transport were affected by selenium restriction. Down-regulation by moderate selenium deficiency of specific genes involved in inflammation and heme biosynthesis was confirmed by qPCR. Myeloperoxidase and lysozyme activities were decreased in selenium-restricted leukocytes, providing evidence for functional consequences. Genes for 31 nuclear factor (NF)-κB targets were down-regulated in moderate selenium deficiency, indicating an impaired NF-κB signaling. Together, the observed changes point to a disturbance in inflammatory response. The selenoproteins found here to be sensitive to selenium intake in murine leukocytes might also be useful as biomarkers for a moderate selenium deficiency in humans.

overall_design: Male C57BL/6J mice (3–4 wk of age) from Charles River (Sulzfeld, Germany) were randomly assigned to the selenium-deficient or selenium-adequate group (12 mice per group) with free access to food and water. The selenium-adequate diet (Se-adeq) was produced by mixing selenomethionine (Acros, Geel, Belgium) into the selenium-deficient diet (Se-def; No. C1045 with 50% carbohydrates, 17% protein, 5% fat, 4% fibre, and mixture of micronutrients; Altromin, Lage, Germany) containing 0.086mg Se/kg (Riese et al., Endocrinology 2006) to yield a selenium content of 0.15 mg/kg corresponding to the dietary reference intake for mice. Diets were fed as powder for 6wk until mice were killed in the non-fasted state. Animals were anesthetized with isofluran and blood with heparinized capillaries by puncture of the retroorbital plexus. Anesthetized animals were killed by cervical dislocation. Spleens were removed aseptically, placed on a sterile microscope slide and crushed with the end of a 6-ml syringe plunger. Released cells were diluted in 5ml of cell culture medium (RPMI with 5% fetal calf serum; Gibco, Karlsruhe, Germany). Clumps were dispersed by drawing and expelling the suspension repeatedly through a 6-ml syringe with a 20-gauge needle. A 100-μmmesh was used to remove clumps and particles and to receive a single cell suspension. The mesh was rinsed with 5 ml RPMI. After centrifugation (5 min, 200g) and washing with 10 ml RPMI, erythrocytes were lysed for 5 min in 5 ml of ammonium chloride lysis buffer (0.15 mol/L NH4Cl, 10 mmol/L KHCO3, 0.1 mmol/L Na2EDTA, pH 7.4). Thereafter, 15 ml of balanced salt solution containing 0.2% bovine serum albumin was added, and the suspension was centrifuged for 5 min at 200g. The pellet was suspended in 1 ml phosphate-buffered saline (PBS) and transferred into a 2-ml tube. Thirty microliters of the suspension was smeared on microscope slides and dried on air for counting. The cells of the remaining suspension were pelleted (5 min, 200g) and washed with 1 ml PBS. The pellet was frozen at−80°C until RNA isolation. As determined with May–Grünwald–Giemsa staining, the leukocyte population was independent of the selenium status and on average was composed of 79% lymphocytes, 18% granulocytes and 2% monocytes.

first: Anna

last: Kipp

first: Antje

last: Banning

first: Regina

last: Brigelius-Flohe

first: Jaap

last: Keijer


title: Four selenoproteins, protein biosynthesis, and Wnt signalling are particularly sensitive to limited selenium intake in mouse colon

summary: Selenium is an essential micronutrient. Its recommended daily allowance is not attained by a significant proportion of the population in many countries and its intake has been suggested to affect colorectal carcinogenesis. Therefore, microarrays were used to determine how both selenoprotein and global gene expression patterns in the mouse colon were affected by marginal selenium deficiency comparable to variations in human dietary intakes. Two groups of 12 mice each were fed a selenium-deficient (0.086mg Se/kg) or a selenium-adequate (0.15mg Se/kg) diet. After 6wk, plasma selenium level, liver, and colon glutathione peroxidase (GPx) activity in the deficient group was 12, 34, and 50%, respectively, of that of the adequate group. Differential gene expression was analysed with mouse 44K whole genome microarrays. Pathway analysis by GenMAPP identified the protein biosynthesis pathway as most significantly affected, followed by inflammation, Delta-Notch and Wnt pathways. Selected gene expression changes were confirmed by quantitative real-time PCR. GPx1 and the selenoproteins W, H, and M, responded significantly to selenium intake making them candidates as biomarkers for selenium status. Thus, feeding a marginal selenium-deficient diet resulted in distinct changes in global gene expression in the mouse colon. Modulation of cancer-related pathways may contribute to the higher susceptibility to colon carcinogenesis in low selenium status.

overall_design: Male C57BL/6J mice (3–4 wk of age) from Charles River (Sulzfeld, Germany) were randomly assigned to the selenium-deficient or selenium-adequate group (12 mice per group) with free access to food and water. The selenium-adequate diet (Se-adeq) was produced by mixing selenomethionine (Acros, Geel, Belgium) into the selenium-deficient diet (Se-def; No. C1045 with 50% carbohydrates, 17% protein, 5% fat, 4% fibre, and mixture of micronutrients; Altromin, Lage, Germany) containing 0.086mg Se/kg (Riese et al., Endocrinology 2006) to yield a selenium content of 0.15 mg/kg corresponding to the dietary reference intake for mice. Diets were fed as powder for 6wk until mice were killed in the non-fasted state. Animals were anesthetized with isofluran and blood was withdrawn from the retro-orbital plexus. Anesthetized animals were killed by cervical dislocation. Plasma and tissues freeze clamped in liquid nitrogen were stored at -80C.


title: Genetic analysis of residual feed intake and its molecular pathways in coloured broiler chicken [duodenum]

status: Public on Jul 12 2018

city: BAREILLY

first: ANAND

last: PRAKASH

state: UTTAR PRADESH

address: IZATNAGAR

department: CARI

country: India

institute: ICAR

summary: Transcriptome analysis was performed in duodenum of high and low RFI chicks for finding out differentially expressing genes and molecular pathways for RFI in colored broiler chicken. The sample of 4 birds each from high and low RFI group from the whole lot of 225 broilers was taken for transcriptome analysis. The expression of genes influencing low and high feed efficiency and the pathways of these genes was studied out to examine the molecular mechanism influencing feed efficiency.

overall_design: In this experiment 4-5 birds at the age of 5-weeks were humanely slaughtered each organ wise in each group (high and low RFI). Each pool was divided in duplicate resulting two biological replicate in each group. Finally, two complementary RNA from each group were used for hybridization reaction. The RNAs from low FE group were used as a control for RNA from high FE group.

first: A

last: Prakash

first: V

middle: K

last: Saxena

first: Ravi

last: Kumar

first: Simmi

last: Tomar


title: Genetic analysis of residual feed intake and its molecular pathways in coloured broiler chicken


title: FPX is a Novel Chemical Inducer That Promotes Callus Formation and Shoot Regeneration in Plants

city: Ikoma

first: Misato

last: Ohtani

address: 8916-5 Takayama-cho

department: Graduate School of Biological Sciences

institute: NAIST


title: Genetic analysis of residual feed intake and its molecular pathways in coloured broiler chicken [liver]

summary: Transcriptome analysis was performed in liver of high and low RFI chicks for finding out differentially expressing genes and molecular pathways for RFI in colored broiler chicken. The sample of 4 birds each from high and low RFI group from the whole lot of 225 broilers was taken for transcriptome analysis. The expression of genes influencing low and high feed efficiency and the pathways of these genes was studied out to examine the molecular mechanism influencing feed efficiency.


title: FPX is a Novel Chemical Inducer That Promotes Callus Formation and Shoot Regeneration in Plants [auxin & cytokinin]

summary: Auxin and cytokinin can regulate callus formation from developed plant organs and shoot regeneration from callus. The regulation of dedifferentiation and regeneration of plant cells by auxin and cytokinin stimulation was considered to be caused by the regulation of reprograming of callus cells, but the hypothesis had been argued still in now. Although elucidation of the regulatory mechanisms of callus formation and shoot regeneration has helped advance plant biotechnology research, many plant species are intractable to transformation because of difficulties with callus regulation. In this study, we identified the compound Fipexide (FPX) as a useful regulatory compound through chemical biology-based screening. Compared with the activity of auxin and cytokinin, FPX showed higher efficiency as a chemical inducer in callus formation, shoot regeneration, and Agrobacterium infection. In regards to morphology, the cellular organization of FPX-induced callus differed from that produced under auxin/cytokinin conditions. According to a microarray analysis, the expressions of approximately 971 genes were two-fold up-regulated by FPX treatment for 2 days. Among these genes, 598 genes were also induced by auxin/cytokinin, while 373 genes, including metabolic regulation-related genes, were specifically expressed only under FPX treatment. FPX can promote callus formations in rice, poplar, and several vegetables. FPX should be a useful tool to reveal unknown mechanisms of plant development and to increase the number of transgenic plant species.

overall_design: Total RNAs of the 4-d-old wild-type seedlings treated with 2.26 μM 2,4-D and 0.46 μM kinetin  for 0, 2, and 8 days. The total RNAs were used for microarray analysis to reveal genes affected by the FPX treatment to compare with auxin and cytokinin treatment.

first: Takeshi

last: Nakano


title: FPX is a Novel Chemical Inducer That Promotes Callus Formation and Shoot Regeneration in Plants [FPX]

overall_design:
Total RNAs of the 4-d-old wild-type seedlings treated with 45 μM FPX for 0, 2, and 8 days. The total RNAs were used for microarray analysis to reveal genes affected by the FPX treatment to compare with auxin and cytokinin treatment.

The 0 day samples have been re-analyzed from GSE116937-- the raw data are identical but the normalized values differ.


title: EP2 receptor modulates macrophage activity for cardiac repair

status: Public on Jul 11 2018

city: Taipei

first: Yuan-Yuan

last: Cheng

address: Academia road

country: Taiwan

institute: Academia Sinica

summary: To examine the functional changes of macrophages isolated from wild-type or EP2-KO mice

overall_design: LPS-induced immune responses were performed in wild-type and EP2-KO mice, and the macrophages were isolated separately for microarray analaysis

first: Jasmine

last: Wu

first: Patrick

last: Hsieh


title: Tead1 is required to maintain adult cardiomyocyte function

city: Pittsburgh

first: Vijay

middle: K.

last: Yechoor

address: 200 Lothrop Street, BST 1058W

institute: University of Pittsburgh

summary: Since Tead1 binds to MCAT promoter elements to regulate many muscle-specific genes, we performed a global transcriptome analysis in Tead1-deleted adult mouse hearts to assess Tead1 regulated pathways critical to CM function.

overall_design: Heart samples from inducible Tead1 icKO (Tead1F/F; Myh6-CreER with Tamoxifen) and control (Tead1 flox mice with Tamoxifen) mice were sent for microarray analysis.

first: Ruya

last: Liu

first: Mousumi

last: Moulik


title: Real time quantitative PCR analysis of serum samples obtained from transgenic and wildtype mice

status: Public on Jul 10 2018

city: Athens

first: Mandi

last: Murph

state: GA

address: 250 West Green Street, Room 312

department: Pharmaceutical & Biomedical Sciences

institute: University of Georgia

summary:
Wildtype mice and Autotaxin-overexpressing transgenic mice, both with and without spontaneous tumor formation, were maintained in a colony. Serum samples from mice in the aforementioned three groups were collected and a random subset of mice were selected for microarray analysis.
RNA was extracted from serum and subsequently cDNA was generated and run on two 384-well plates probing for 373 viable targets, including microRNAs, control probes and interplate calibrators. Raw Ct values obtained from qPCR analysis were analyzed using GenEx and graphed using GraphPad Prism.

platform_organism:
Mus musculus
Rattus norvegicus

overall_design: microRNA expression analysis was performed with RNA extracted from serum samples of wildtype and Autotaxin transgenic mice with and without spontaneous tumor formation.

first: Sudeepti

last: Kuppa


title: microRNAs expression of human submandibular gland cell lines

city: Tokushima

first: noriko

last: mizusawa

address: 3-18-15 Kuramoto-cho

department: Department of Medical Pharmacology

institute: The University of Tokushima Graduate School, Institute of Health Biosciences

summary: The immortalized normal human salivary gland ductal cells (NS-SV-DC) and acinar cells (NS-SV-AC) have characteristic morphologic differences and useful for organizing knowledge of bio-functional mechanisms of human salivary gland.

overall_design: Comprehensive characterization of molecular levels to clarify the differences between NS-SV-AC and NS-SV-DC cells.

first: Noriko

last: Mizusawa

first: Wan

last: Shahidan

first: Katsuhiko

last: Yoshimoto


title: miRNAs regulated by TTF-1 in small cell lung cancer cell lines

city: Los Angeles

first: Masafumi

last: Horie

address: 2011 Zonal Ave

institute: University of Southern California

summary: To determine miRNAs regulated by TTF-1 in SCLC cell lines, miRNA array analyses were carried out in NCI-H209 cells following TTF-1 knockdown

overall_design: RNA was collected from NCI-H209 cell lines transfected with control and TTF-1 siRNAs.

first: Naoya

last: Miyashita

first: Johanna

last: Mattsson

last: Micke

first: Takahide

last: Nagase

first: Akira

last: Saito


title: Development of in vitro enteroids derived from bovine small intestinal crypts

city: Edinburgh

first: Neil

last: Mabbott

state: Midlothian

address: Easter Bush

country: United Kingdom

institute: The Roslin Institute & Royal (Dick) School of Veterinary Sciences, University of Edinburgh

summary: In vitro 2D cultures of intestinal epithelial cells or epithelial cell lines have been widely used to study cell function and host-pathogen interactions in the bovine intestine.  However, these cultures lack the cellular diversity encountered in the intestinal epithelium, and the physiological relevance of monocultures of transformed cell lines is uncertain.  Little is also known of the factors that influence cell differentiation and homeostasis in the bovine intestinal epithelium, and few cell-specific markers that can distinguish the different intestinal epithelial cell lineages have been reported.  Here we describe a simple and reliable procedure to establish in vitro 3D enteroid, or “mini gut”, cultures from bovine small intestinal (ileal) crypts.  These enteroids contained a continuous central lumen lined with a single layer of polarized enterocytes, bound by tight junctions with abundant microvilli on their apical surfaces.  Histological and transcriptional analyses suggested that the enteroids comprised a mixed population of intestinal epithelial cell lineages including intestinal stem cells, enterocytes, Paneth cells, goblet cells and enteroendocrine cells.  We show that bovine enteroids can be successfully maintained long-term through multiple serial passages without observable changes to their growth characteristics, morphology or transcriptome.  Furthermore, the bovine enteroids can be cryopreserved and viable cultures recovered from frozen stocks.   Our data suggest that these 3D bovine enteroid cultures represent a novel, physiologically-relevant and tractable in vitro system in which epithelial cell differentiation and function, and host-pathogen interactions in the bovine small intestine can be studied.

overall_design: The aim of this study was to assess global gene expression of bovine intestinal crypts, and bovine intestinal organoids across different passage numbers (P0-P5), by RNA-seq.

first: Carly

last: Hamilton

first: Rachel

last: Young

first: Siddharth

last: Jayaraman

first: Anuj

last: Sehgal

first: Edith

last: Paxton

first: Sarah

last: Thomson

first: Frank

last: Katzer

first: Jayne

last: Hope

first: Elisabeth

last: Innes

first: Liam

last: Morrison


title: Expression data from MCAO or Sham operated rat brain [mRNA]

city: Bunkyo-ku

first: Ayako

last: Takuma

department: Graduate School of Agricultural and Life Sciences

institute: The University of Tokyo

summary:
To analyze the gene expression alteration after stroke, we used Middle Cerebral Artery Occlusion model of rats. By comparing with Sham operated rats, we extracted the mRNAs whose expressions are alterated by stroke.
Using microarray analysis, we aimed to grasp the overall expression alteration of mRNA in brain after stroke.

overall_design: 12 Sprague-Dawley rats were subjected to Middle Cerebral Artery Occlusion (MCAO, n=7) or Sham operation (n=5), and the mRNA expression in the brain was compared between the two group.

first: Yoshikazu

first: Arata

last: Abe

first: Tomiko

last: Asakura

first: Keiko


title: Expression profiling in exosomal miRNAs of patients with late-onset acute graft-versus-host disease in Allogeneic Hematopoietic Stem Cell Transplantation

status: Public on Jul 08 2018

city: Shinjyuku

first: Tomohiro

last: Umezu

address: 6-1-1 Shinjyuku

department: Department of Molecular Pathology

institute: Tokyo Medical University

summary: Recent studies have demonstrated exosomal microRNAs are potential in facilitating molecular diagnosis. Currently, little is known about the underlying mechanism of late-onset acute GVHD (LA GVHD). Identification of altered differential expression profiling of miRNAs in exosome will be useful for understanding role of miRNA in the LA GVHD. The purpose of this study is to investigate the relevance of miRNAs in exosome derived from patients developing LA GVHD after allogeneic HSCT.

overall_design: Plasma samples were collected from patients with LA GVHD (n = 5), non-GVHD (n = 5) and controls (n = 8) for exosomal miRNA expression profiling by a TaqMan low-density array. Exosomes were extracted by using Total Exosome Isolation Reagent, and the exosomal miRNA profiling was performed with a TaqMan Low-Density Array. The relative expression level of each gene was calculated by using the comparative thresholds cycle (Ct) method. Synthetic spike control (ath-miR-159) was used as an invariant control for the exosomal miRNA.


title: Long noncoding RNAs expression profile in rat extra-synaptic and synaptic NMDAR activation neurons

status: Public on Jul 07 2018

city: Wuhan

first: Huang

last: Fang

address: Jiefang  Avenue, qiaokou district, wuhan city, hubei province

institute: Tongji medical college huazhong university of science and technology

summary: The study revealed differentially expressed lncRNAs in synaptic and extrasynaptic NMDAR activation and suggested that lncRNAs might be responsible for extrasynaptic NMDAR-induced neurodegeneration

overall_design: Synaptic NMDAR was activated with Bic/4AP treatment. After blocking activated synaptic NMDAR with  MK-801, NMDA and Glycine were applied to selectively activate extrasynaptic NMDAR.Cells were thereafter incubated for 6 h for total RNA extraction and lncRNAs were analised

first: Fang

last: Huang

first: Sun

last: Xuying