title: Gene expression profile of Ba/F3 variant (#BEB1) cells that have binding ability to Ecrg4

status: Public on Mar 23 2018

city: Kobe

first: Kei

last: Enomoto

state: Hyogo

address: Chuo-ku, Minatojima-Minamimachi

country: Japan

institute: ASUBIO PHARMA CO., LTD.

summary: Esophageal cancer-related gene 4 (Ecrg4) encodes a hormone-like peptide, and is thought to be involved in a variety of physiological phenomena including tumor suppressor function.  Recent progress of Ecrg4 reveals that Ecrg4 peptides are pro-inflammatory and induce the expression of several cytokines and chemokines.  However, detailed molecular mechanisms of Ecrg4 signaling, especially the receptors for Ecrg4 peptides, remain poorly understood. Here, using retrovirus-mediated expression cloning, we identified lectin-like oxidized low-density lipoprotein receptor-1 (LOX-1) as a membrane protein bound for amino acid residues 71-132 of Ecrg4, Ecrg4(71-132).  Moreover, not only LOX-1 but also several scavenger receptors such as Scarf1, Cd36 and Stabilin-1 efficiently internalized Ecrg4(71-132) into cells.  The broad scavenger receptor competitive inhibitor polyinosinic acid reduced both the internalization of Ecrg4(71-132) and activation of NF-kB in microglia.  In addition, this activation is dependent on Myd88, an adaptor protein to recruit signaling proteins to TLR and IL-1R receptors with induction of several immune response.  These data suggest that multiple scavenger receptors recognize Ecrg4(71-132) and transduce its signals along with TLR/IL-1R receptors in microglia.

overall_design: A variant strain of Ba/F3 (#BEB1) cells that have an ability to bind Ecrg4 was obtained after five round sorting using retrovirus expression library prepared from mRNA of CG4 cells.

first: Tetsuo

last: Moriguchi


title: Gene expression in beta-cells in mice submitted to a high-fat diet

city: Pierre Bénite

first: emmanuelle

last: meugnier

address: Cens Eli Bat 2 D- Hopital Lyon Sud

country: France

summary: Gene expression in beta pancreatic cells of mice submitted to a high-fat diet.

overall_design: C57BL/6 mice were submitted to a high-fat diet or a control diet. At sacrifice, beta pancreatic cells were collected and snap frozen. RNA was extracted and global transcriptomic analysis was performed.

first: Sophie

last: Rome

first: Sandra

last: Pesenti

first: Emmanuelle

last: Meugnier


title: Analysis of altered miRNA expression profiles in the streptozotocin-induced diabetic rats compared to normal SD rats

city: Wuhan

first: Guojun

last: Guo

state: Hubei

address: 1277# Jiefang Avenue

department: Hand Surgery

country: China

institute: Union Hospital of Tongji medical college, Huazhong University of Science & Technology

summary: Diabetes mellitus (DM) is one of the most common chronic diseases around the world, and diabetic peripheral neuropathy (DPN) is one of the most common complications of DM. We used microarrays to identify the differentially expressed miRNAs in dorsal root ganglia (DRG) tissues from streptozotocin (STZ)-induced diabetic rats, taking normal SD rats as controls, and tried to find out the related genes which may be involved in the development of DPN.

overall_design: We collected bilateral L3-6 DRG tissues from three STZ-induced diabetic rats and three normal SD rats. By using Affymetrix GeneChip miRNA 4.0 Array, we tried to find out the differentially expressed miRNAs in STZ-induced diabetic rats.

first: Zhenbing

last: Chen


title: Whole genome profiling of liver biopsies discloses potential biomarkers for diagnosis of idiopathic non-cirrhotic portal hypertension

status: Public on Mar 31 2018

city: Barcelona

first: Juanjo

last: Lozano

address: C/ Rosselló 153

department: Plataforma de Bioinformatica

country: Spain

institute: CIBEREHD

summary: Background. Idiopathic non-cirrhotic portal hypertension (INCPH) is a frequently misdiagnosed cause of portal hypertension. It also lacks a specific test for its diagnosis. This study evaluates whether using new immunohistochemistry makers derived from whole genome analysis improves the diagnosis of INCPH.  Methods. We analyzed formalin-fixed, paraffin embedded (FFPE) liver tissue from 18 INCPH and 22 patients with cirrhosis (LC) as well as from 14 histologically normal livers (HNL) as controls. Microarray experiments were performed using Illumina Whole-Genome DASL HT BeadChip arrays. Selected genes showing differential expression at Illumina were confirmed using quantitative real-time PCR (qRT-PCR) gene expression performed with Fluidigm Biomark HD system in a subgroup of samples. Immunohistochemistry was used to confirm the qRT-PCR results.   Results. At Illumina, a total of 292 genes were differentially expressed (FC>+2/-2 and p-value <0.05) in INCPH compared to the control group (LC and HNL) (202 up-regulated and 90 down-regulated).

overall_design: Transcriptomic profile of liver tissue from 18 INCPH and 22 patients with cirrhosis (LC) as well as from 14 histologically normal livers (HNL) as controls.

first: S

last: Seijo

first: J

middle: J

first: D

last: Colomer

first: E

last: Reverter

middle: C

last: Garcia-Pagan


title: Expression data from pmel1 CD8+ T cells stimulated with agonist anti-CD27, blockade of PD-1/L1 or both together

status: Public on Mar 27 2018

city: Southampton

first: Sarah

middle: Louise

last: Buchan

state: Hants

address: Tremona Road

department: Cancer Sciences Unit

country: United Kingdom

institute: University of Southampton

summary:
CD8+ T cells are regulated by inhibitory and activatory receptors.  We have investigated the influence of enforced CD27 stimulation compared with blockade of PD-1 and the combination of both agents together.
Anti-CD27 and PD-1 blockade combined to enhance CD8+ T-cell accumulation, effector protein expression and tumor therapy.  This array was used to further characterize the transcriptional changes in CD8+ T cells that drive this differentiation.

overall_design: Two million Thy1.1+CD8+ T cells from pmel1 mice were adoptively transferred to naive congenic recipient mice.  Recipients (in groups of 3) were then treated with 100ug hgp100 peptide i.v. delivered with a total of 400ug antibodies comprising 200ug agonist anti-CD27 (AT124), with 100ug anti-PD-1 (RMP1-14) and 100ug anti-PD-L1 (10F.9G2) (termed 'combination'); alternatively mice were treated with peptide+ AT124 (anti-CD27), or peptide + anti-PD-1/anti-PD-L1 (anti-PD-1/L1) mixed with 200ug appropriate isotype control antibodies.  On day 4 relative to peptide injection CD8+ cells from spleens were isolated from individual mice using negative selection MACs kits, and then Thy1.1+CD8+ cells enriched to >99% purity by FACs.  RNA was extracted from a minimum of 0.4x10^6 cells using RNeasy kits and gDNA eliminator columns (Qiagen).  Samples were stored at -80C and subsequently processed for array by AROS (Applied Biotechnology (Denmark).

middle: L


title: Analysis of altered lncRNA and mRNA expression profiles in the streptozotocin-induced diabetic rats compared to normal SD rats

summary: Diabetes mellitus (DM) is one of the most common chronic diseases around the world, and diabetic peripheral neuropathy (DPN) is one of the most common complications of DM. We used microarrays to identify the differentially expressed lncRNAs and mRNAs in dorsal root ganglia (DRG) tissues from streptozotocin (STZ)-induced diabetic rats, taking normal SD rats as controls, and tried to find out the related genes which may be involved in the development of DPN.

overall_design: We collected bilateral L3-6 DRG tissues from three STZ-induced diabetic rats and three normal SD rats. By using Affymetrix GeneChip Rat Transcriptome Array 1.0, we tried to find out the differentially expressed lncRNAs and mRNAs in STZ-induced diabetic rats.


title: Gene expression from human keratinocytes isolated from limited systemic sclerosis (lcSSc) and diffuse systemic sclerosis (dcSSc) skin biopsy

status: Public on Mar 21 2018

city: Ann Arbor

first: Celine

last: Berthier

state: MI

address: 1150 W. Medical Center Dr, MSRB2

country: USA

institute: University of Michigan

summary: Systemic sclerosis (SSc) is a rare but devastating disease of fibrosis impacting the dermis and multiple organ systems.  The prevalence ranges from 4 to 489 cases per million individuals with ten year mortality rates reported around 18 percent.  Survival is related to the extent of skin involvement, yet the precise mechanisms driving skin fibrosis in SSc remain unknown. In this study, we analyzed the shared and unique transcriptomic profiles of SSc and normal keratinocytes.

overall_design: RNA from keratinocytes isolated and grown to passage 2 from human skin biopsies was extracted and processed for hybridization on Affymetrix microarrays.

middle: S

last: McCoy

first: T

last: Reed

first: C

first: P

last: Tsou

last: Khanna

middle: E

last: Gudjonsson

middle: M

last: Kahlenberg


title: β2→1-fructans modulate the immune system in vivo in a microbiota-dependent and -independent fashion

status: Public on Mar 22 2018

city: Wageningen

first: Guido

last: Hooiveld

address: HELIX, Stippeneng 4

department: Div. Human Nutrition & Health

country: Netherlands

institute: Wageningen University

summary: It has been shown in vitro that only specific dietary-fibers contribute to immunity but studies in vivo are not conclusive. Here we investigated degree of polymerization (DP) dependent effects of β2→1-fructans on immunity via microbiota-dependent and -independent effects. To this end, conventional or germ-free mice received short- or long-chain β2→1-fructan for 5 days. Immune cell populations in the spleen, mesenteric lymph nodes (MLN), and Peyer's patches (PPs) were analyzed with flow cytometry, genome-wide gene expression in the ileum was measured with microarray, and gut microbiota composition was analyzed with 16S rRNA sequencing of fecal samples. We found that β2→1-fructans modulated immunity by both microbiota and microbiota-independent effects. Moreover, effects were dependent on the chain-length of the β2→1-fructans type polymer. Both short- and long-chain β2→1-fructans enhanced T-helper 1 cells in Peyer's patches, whereas only short-chain β2→1-fructans increased regulatory T cells and CD11b-CD103- DCs in the MLN. A common feature after short- and long-chain β2→1-fructan treatment was enhanced Fut2 expression and other IL-22-dependent genes in the ileum of conventional mice. These effects were not associated with shifts in gut microbiota composition, or altered production of short-chain fatty acids. Both short- and long-chain β2→1-fructans also induced immune effects in germ-free animals, demonstrating direct effect independent from the gut microbiota. Also, these effects were dependent on the chain-length of the β2→1-fructans. Short-chain β2→1-fructan induced lower CD80 expression by CD11b-CD103- DCs in PPs, whereas long-chain β2→1-fructan specifically modulated B cell responses in germ-free mice. In conclusion, support of immunity is determined by the chemical structure of β2→1-fructans and is partially microbiota-independent.

overall_design: Conventional or germ-free mice received short-chain (oligofructose; FOS) or long-chain (inulin; IN) β2→1-fructan for 5 days. Genome-wide gene expression in the ileum was measured with microarray.

first: Floris

last: Fransen

first: Neha

last: Sahasrabudhe

first: Marlies

last: Elderman

first: Margaret

last: Bosveld

first: Sahar

last: El Aidy

first: Floor

last: Hugenholtz

first: Theo

last: Borghuis

first: Ben

last: Kousemaker

first: Simon

last: Winkel

first: Christa

last: van der Gaast-de Jongh

first: Marien

middle: I

last: de Jonge

first: Mark

middle: V

last: Boekschoten

first: Hauke

last: Smidt

first: Henk

middle: A

last: Schols

first: Paul

last: de Vos


title: Comparative microRNAome analysis of the petals in doubled haploid and autotetraploid Chinese cabbages

city: Tianjin

first: Yiheng

last: Wang

address: 17km Jinjing Road

institute: Tianjin Academy of Agricultural Sciences

type: Non-coding RNA profiling by high throughput sequencing

summary: We performed microRNA profiling of doubled haploids and autotetraploids that generated from a Chinese cabbage doubled haploid line ‘FT’ using the Illumina high-throughput sequencing platform and analyzed differentially expressed miRNAs.

overall_design: microRNA levels were examinated in doubled haploid and autotetraploid petals of Chinese cabbage.

first: Hui

last: Feng


title: Hydrogen peroxide positively regulates brassinosteroid signaling through oxidation of the BRASSINAZOLE-RESISTANT1 transcription factor

city: Jinan

first: Yanchen

last: Tian

state: Shandong

address: No. 27, South Shanda Road

department: School of Life Sciences

institute: Shandong university

type: Expression profiling by high throughput sequencing

summary: Hydrogen peroxide (H2O2) is an important signaling molecule in plant developmental processes and stress responses. However, whether H2O2-mediated signaling can crosstalk with plant hormone signaling is largely unclear. Here, we show that H2O2 induces oxidation of the BRASSINAZOLE-RESISTANT1 (BZR1) transcription factor, which functions as a master regulator of Brassinosteroid (BR) signaling. Oxidative modification enhances BZR1 transcriptional activity by promoting its interaction with regulators of auxin- and light-signaling, including AUXIN RESPONSE FACTOR6 (ARF6) and PHYTOCHROME INTERACTING FACTOR4 (PIF4). Genome-wide analysis shows that H2O2-dependent regulation of BZR1 activity plays a major role in modifying gene expression related to several BR-mediated biological processes. Furthermore, we show that the thioredoxin TRXh5 can interact with, and catalyze reduction of, BZR1. We conclude that reversible oxidation of BZR1 connects H2O2- and thioredoxin-mediated redox signaling to BR signaling to regulate plant development

overall_design: Wild type Col-0 and bzr1-1D were grown in ½ MS medium containing 2 µM PPZ, and/or 1 µM DPI, 0.3 mM H2O2 for six days in the dark. Total RNA was extracted with Trizaol RNA extraction kit (Transgene), and the mRNA sequencing libraries construction and sequencing on the BGISEQ-500 platform were performed at Beijing Geonomics institute (BGI). The sequence reads were mapped to the Arabidopsis genome using HISAT and Bowtie2 software, and differential gene expression was analyzed using Noiseq software. Differentially expressed genes were defined by a 1.5-fold expression difference with a possibility >0.8.

first: Min

last: Fan

first: Mingyi

last: Bai


title: Newly identified interferon tau-responded cytidine/uridine monophosphate kinase 2 and Hes family BHLH transcription factor 4 genes in bovine peripheral blood cells at peri-implantation period

status: Public on Mar 30 2018

city: Morioka

first: Keiichiro

last: Kizaki

state: Iwate

department: Vet. Med.

institute: Iwate University

summary: In cattle, interferon-stimulating genes (ISGs) such as ISG15, MX1, MX2, and OAS1 are known as classical ISGs that are intensely involved in the implantation process. Various molecules play a crucial role in the mechanism underlying ISG effects. Although microarray analysis highlighted the expression of various molecules during the implantation period, these are incompletely characterized. In the present study, some specifically expressed genes were selected and their characteristics were examined. The microarray data of peripheral blood leucocytes from artificially inseminated and embryo-transferred cows were used to identify new ISG candidates. Seven common genes, including ISG15 and OAS1, were confirmed, but only four of these were amplified by reverse transcription quantitative polymerase chain reaction. These showed significantly higher expression in pregnant cows than in non-pregnant cows. Moreover, three expressed sequence tags (ESTs) showed significantly higher expression in granulocytes after IFNT stimulation. NCBI BLAST analysis revealed the similar sequences of two ESTs on chromosome 16 that were deemed as Hes family BHLH transcription factor 4 (HES4). Another EST was identified on chromosome 11 as cytidine/uridine monophosphate kinase 2 (CMPK2). The promoter sequences of HES4 and CMPK2 were cloned and analyzed from DNA of whole blood cells in cyclic Holstein cows. In silico analysis facilitated the identification of the transcription factor-binding sequences, including interferon-stimulated response element- and interferon regulatory factor-binding sites, on the promoter region of HES4 and CMPK2. These genes may be one of the new ISGs related to embryo implantation and may participate in the coordination of feto-maternal interface in cows.

overall_design: Bovine peripheral blood granulocytes were obtained from cows on Day 21 pregnant (n=4) by embryo transfer and before embryo transfer (n=4, non-pregnant at Day 7 estrous cycle).


title: Glycyrrhizin, silymarin, and ursodeoxycholic acid regulate a common hepatoprotective pathway in HepG2 cells

city: Taichung

first: Chien-Yun

last: Hsiang

address: 91 Hsueh-Shih Road

country: Taiwan

institute: China Medical University

summary:
Background: Glycyrrhizin, silymarin, and ursodeoxycholic acid are widely used hepatoprotectants for the treatment of liver disorders, such as hepatitis C virus infection, primary biliary cirrhosis, and hepatocellular carcinoma.
Hypothesis/Purpose: However, few studies have evaluated the effects of these compounds on gene expression.
Methods: Here, we used an oligonucleotide microarray approach to study the gene expression profile in human hepatoma cells treated with 25 μM of hepatoprotective agents.
Results: Among a total of 30,968 genes, 252 genes were commonly regulated by all compounds. These compounds affected the expressions of genes involved in different biological pathways, such as neurotransmission and glucose and lipid metabolism. Genes involved in hepatocarcinogenesis, apoptosis, and anti-oxidative pathways were differentially regulated by all compounds. Moreover, interaction networks showed that nuclear factor-κB (NF-κB) might play a central role in the regulation of the gene expression network. Further analysis revealed that these hepatoprotectants inhibited NF-κB activation in a dose-dependent manner.
Conclusion: Our data suggested that glycyrrhizin, silymarin, and ursodeoxycholic acid protected livers from damage by regulating the genes involved in apoptosis and oxidative stress. Moreover, the regulation of genes by hepatoprotectants might be through the suppression of NF-κB activities.

overall_design: We used an oligonucleotide microarray approach to study the gene expression profile in human hepatoma cells treated with 25 μM of hepatoprotective agents.


title: Genome-wide expression reveals multiple systemic effects of anticoagulant poisons in bobcats (Lynx rufus)

status: Public on Mar 25 2018

city: Los Angeles

first: Alice

last: Mouton

state: CA

address: 610 Charles E. Young Dr. East

department: Ecology and Evolutionary Biology

institute: UCLA

summary: We evaluated AR-related effects on genome wide expression patterns in a population of bobcats in southern California. We identify differential expression of genes involved in xenobiotic metabolism, endoplasmic reticulum stress response, epithelial integrity, and both adaptive and innate immune function. Further, we find that differential expression of immune related genes may be attributable to AR-related effects on leukocyte differentiation. Collectively, our results provide an unprecedented understanding of the sublethal effects of AR exposure on a wild carnivore.

overall_design: Blood samples from 26 bobcats tested positive for Anticoagulant Rodenticides (Ars) and 26 samples of bobcats not tested positive for ARs.

first: Devaughn

last: Fraser

first: Robert

middle: K

last: Wayne


title: Comparison of Human Bone Marrow Stromal Cells Cultured in Human Platelet Growth Factors and Fetal Bovine Serum

city: BETHESDA

first: PING

last: JIN

state: MD

address: 9000 ROCKVILLE PIKE

department: DTM

institute: CC/DTM/NIH

summary:
Background: Bone marrow stromal cells (BMSCs) have classically been cultured in media supplemented with 20% fetal bovine serum (FBS).  As an alternative to FBS, pooled solvent detergent apheresis platelets, HPGF-C18, was evaluated for BMSC culture.
Methods: A comparison of passage 2 BMSC growth revealed that 10% HPGF-C18 produced similar cell numbers as 20% FBS. Marrow aspirates from 5 healthy subjects were cultured for 4 passages in 10% HPGF-C18 or 20% FBS and were analyzed for proliferation, colony formation efficiency (CFE), surface marker expression, suppression of mixed lymphocyte reactions (MLRs), global gene and microRNA expression analysis. BMSC supernatant cytokine and growth factor concentrations were also compared.
Results: Primary cultures of marrow aspirates in 10% HPGF-C18 and 20% FBS yielded similar numbers and CFE.  After 4 passages, 10% HPGF-C18 and 20% FBS yielded similar numbers of BMSCs, surface marker expression patterns and immunosuppression effects. Gene and microRNA expression analysis revealed that BMSCs cultured under the two conditions had distinct expression profiles. Gene Set Enrichment Analysis (GSEA) revealed HPGF-C18-cultured BMSCs were enriched in metabolic processing and biosynthetic pathways; cell proliferation and cell cycle pathways; and immune response pathways.  FBS-cultured BMSCs were enriched in MAPK signaling, TGF-beta signaling, cell adhesion and extracellular matrix pathways. Differently expressed microRNAs were related to the osteogenesis of BMSCs. Supernatant analysis found that HPGF-C18 BMSCs displayed higher levels of PEDF and TGFB1 and lower levels of IL6, VEGF, SDF1 and PLGF.
Conclusions:  Traditional measures; expansion, surface marker expression and inhibition of MLRs suggest that BMSC cultured in HPGF-C18 and FBS were similar, but analysis at the molecular level revealed many differences. BMSCs cultured in HPGF-C18 should be assessed in specific functional assays that reflect application-specific potency before substituting FBS with HPGF-C18.

first: Jiaqiang

last: Ren

first: Steven

last: Chen

first: Katherine

last: Tran

first: Ping

last: Jin

first: Marianna

last: Sabatino

first: Pamela

middle: G

last: Robey

first: David

last: Stroncek


title: Comparative transcriptome analysis of the petals in doubled haploid and autotetraploid Chinese cabbages

first: Yiheng

last: Wang

summary: We performed transcript profiling of doubled haploids and autotetraploids that generated from a Chinese cabbage doubled haploid line ‘FT’ using the Illumina high-throughput sequencing platform and analyzed differential gene expression at the transcriptional level.

overall_design: mRNA levels were examinated in doubled haploid and autotetraploid petals of Chinese cabbage, in three biological replicates.

first: Hui

last: Feng


title: Impact of Vitamine D depletion and repletion on rat skeletal muscle

status: Public on Mar 24 2018

first: emmanuelle

last: meugnier

summary: 15 months Old Wistar Rat were submitted to 3 differents diets: control, without vitamin D and  without vitamin D followed by a supplementation in vitamin D. At sacrifice, skeletal muscle were recovered, quickly frozen in liquid nitrogen. RNA profiling by microarrays was performed.

overall_design: The aim of this study was to examine the effects of vitamin D deficiency on muscle mitochondrial oxidative function in old sarcopenic rats. We hypothesized that suboptimal mitochondrial function contributes to the myopathy in vitamin D-deficient older individuals. 15-month-old Wistar rats were fed a vitamin D-deficient diet (VDD group) or a control diet (1000UI/Kg vit D) for 9 months (n=7-9/group) or a vitamin D-deficient diet followed by supplementation. Our results indicated a link between vitamin D status, muscle mitochondrial oxidative capacities, whole-body energy expenditure and change in body composition in old rats.

first: Jerome

last: Salles

first: Sandra

last: Pesenti

first: Emmanuelle

last: Meugnier


title: MicroRNA expression data from brainstem gliomas

status: Public on Mar 20 2018

city: beijing

first: xin

last: chen

address: 6 tiantanxili

institute: Beijing Tiantan Hospital

summary:
Gliomas arising in the brainstem are rare tumours worldwide that are difficult to surgically resect, and the involved miRNAs and signaling pathways associated with brainstem gliomas (BSGs) are largely unclear. Tumours in the control nervous system owned a WHO classification, which are of great significance to guide the treatment and to evaluate prognosis.
To determine grade-associated miRNAs in BSGs, this study performed microarray of 10 low-grade and 15 high grade BSGs.

overall_design: Brainstem gliomas tissues were selected  for RNA extraction and hybridization on Affymetrix microarrays. We sought to obtain  grade-associated miRNAs in BSGs. To that end, we selected brainstem gliomas tissues according to WHO classification: grade I,grade II,grade III and grade IV

first: Xin


title: Tumor-independent host gene expression changes induced by VEGFR2 antibody

status: Public on Mar 29 2018

city: Buffalo

first: John

last: Ebos

state: NY

address: Elm & Carlton Streets

department: Department of Cancer Genetics and Genomics

institute: Roswell Park Cancer Institute

summary: Transcriptome analysis was used to identify tumor-independent changes after treatment with mouse VEGFR2 neutralizing antibody.

overall_design: 8 week old Balb/c mice were treated for 7 days with anti-VEGFR2 clone DC101 (800ug/mouse every 3 days). Lung tissue was collected and total RNA was isolated for whole genome expression analysis.

first: Michalis

last: Mastri


title: In vivo transcriptome analysis of avian pathogenic Escherichia coli under the control of RstA/RstB two-component regulatory system

city: Yangzhou

first: Qingqing

last: Gao

state: Jiangsu

address: Yangzhou wenhui Road 12

department: Colledge of Veterianry medicine

institute: Yangzhou university

summary: APEC cause avian colibacillosis in poultry, characterized by the systematic infection, such as septicemia, airsacculitis, and pericarditis. APEC mainly use two-component regulatory systems (TCSs) to deal with the stressing environments in host during their infection. Whereas most TCSs in E.coli are well characterized, the characterization of RstA/RstB in APEC has not been thoroughly investigated. To understand the whole picture of RstA/RstB regulation, especially its role in virulence regulation, transcriptional analysis of the effect of rstAB deletion was performed in vivo. We compared the transcriptome of rstAB mutant and its wild-type strain during their growth in bloodstream of challenged chickens. In total, the transcripts of 85 genes were down-regulated by rstAB deletion while 113 were up-regulated at least twofold (cutoff limitation for fold change >2 or <0.5 and Cuffdiff P-value <0.05 was used to select differential expression genes). Our data showed that the RstA/RstB was a by-function regulator system, acting as both an activator and a repressor. The RstAB mainly regulated systems involved in nitrogen metabolism, bacterial virulence, iron acquisition and acid resistance.

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

overall_design: We contructed the rstAB mutant and compared the transcriptome of rstAB mutant and its wild-type strain during their growth in bloodstream of challenged chickens

first: Song


title: Tumor-independent host gene expression changes induced by tyrosine kinase inhibitors

summary: Transcriptome analysis was used to identify tumor-independent changes after treatment with different tyrosine kinase inhibitors (TKIs).

overall_design: 8 week old Balb/c mice were treated for 7 days with sunitinib (60 or 120 mg/kg/day), crizotinib (50mg/kg/day), axitinib (100mg/kg/day), or combination of sunitinib (60mg/kg/day) and crizotinib. Lung tissue was collected and total RNA was isolated for whole genome expression analysis.


title: Tumor-independent host gene expression changes induced by PD-1 pathway inhibitors

summary: Transcriptome analysis was used to identify tumor-independent changes after treatment with mouse neutralizing PD-1 or PD-L1 antibodies.

overall_design: 8 week olg Balb/c mice were treated for 7 days with anti-PD-1 clone RMI1-14 (250ug/mouse every 3 days) or anti-PD-L1 clone 10F.9G2 (250ug/mouse every 3 days). Lung tissue was collected and total RNA was isolated for whole genome expression analysis.


title: SWI/SNF and RSC cooperate to reposition and evict promoter nucleosomes at highly expressed genes in yeast

city: Bethesda

first: Yashpal

last: Rawal

state: Maryland

address: 6 Center Dr., Bldg 6, Room 233

department: 1Laboratory of Gene Regulation and Development

institute: NICHD-NIH

type: Genome binding/occupancy profiling by high throughput sequencing

summary: The nucleosome remodeling complex RSC functions throughout the yeast genome to set the positions of -1 and +1 nucleosomes and thereby determines the widths of nucleosome-depleted regions (NDRs). The related complex SWI/SNF participates in nucleosome remodeling/eviction and promoter activation at certain yeast genes, including those activated by transcription factor Gcn4, but does not appear to function broadly in establishing NDRs. By analyzing the large cohort of Gcn4-induced genes in mutants lacking the catalytic subunits of SWI/SNF or RSC, we uncovered cooperation between these remodelers in evicting nucleosomes from different locations in the promoter and in repositioning the +1 nucleosome downstream to produce wider NDRs, highly depleted of nucleosomes, during transcriptional activation. SWI/SNF also functions on par with RSC at the most highly transcribed constitutively expressed genes, suggesting general cooperation by these remodelers for maximal transcription. SWI/SNF and RSC occupancies are greatest at the most highly expressed genes, consistent with their cooperative functions in nucleosome remodeling and transcriptional activation. Thus, SWI/SNF acts comparably to RSC in forming wide, nucleosome-free NDRs to achieve high-level transcription, but only at the most highly expressed genes exhibiting the greatest SWI/SNF occupancies.

overall_design: Sonicated or Micrococcal Nuclease digested DNA fragments were immunopurified  and subjected to paired-end sequencing. This study includes paired-end sequencing studies of (1) ChIP samples for the histone H3, (2) ChIP samples for the histone H2B, (3) ChIP samples for the Rpb3 subunit of Pol II.

first: Razvan

last: Chereji

first: Hongfang

last: Qiu

first: Sudha

last: Ananthakrishnan

first: Chhabi

last: Govind

last: Clark

first: Alan

last: Hinnebusch


title: Gene expression profile in zebrafish D. rerio exposed to metal oxidate nanoparticles

city: Beijing

first: Jing

last: Hou

address: No. 19, XinJieKouWai St., HaiDian District

institute: Beijing Normal University

summary: Metal oxide nanoparticles can exert adverse effects on humans and aquatic organisms. However, the toxic effects and mechanisms of MO-NPs are not clearly understood.We investigated the toxic effects and mechanisms of copper oxide, zinc oxide, and nickel oxide nanoparticles in Danio rerio using microarray analysis.

overall_design: After two weeks of acclimation, D. rerio were exposed to eight concentrations of each NP solution (ZnO: 1.0, 2.0, 4.0, 8.0, 16.0, 32.0, 64.0, and 128.0 mg/L; CuO: 0.0625, 0.125, 0.25, 0.5, 1.0, 2.0, 4.0, and 8.0 mg/L; NiO: 2.0, 4.0, 8.0, 16.0, 32.0, 64.0, 128.0, and 256.0 mg/L) with a day/night cycle of 16/8 h. Three biological replicates were used in each treatment and each replicate consisted of 10 individuals. D. rerio were exposed for 96 h without feeding. Survival rates were recorded each day and the median lethal concentration (LC50) was calculated using the probit method. The subsequent exposures for the microarray were performed using one-tenth of the LC50 for each NP solution (0.2 mg/L CuO, 4.8 mg/L ZnO, and 17.5 mg/L NiO). Ten D. rerio were sacrificed for each treatment, and the gills were pooled as a sample. Three biological replicates were used for each treatment.

first: Shiguo

last: Li


title: microRNA expression data of a paired fibrosarcoma with ESCC samples

city: Shantou

first: Qian

last: Yang

state: Guangdong

address: Xinling 22 Road

institute: Medical College of Shantou University

summary: We detected the expression of miRNA in a fibrosarcoma with ESCC sample and the corresponding normal esophagus tissue. Then, we identified the differentially expressed miRNAs in this rare disease.

overall_design: miRNA molecular in total RNA was labeled by miRNA Complete Labeling and Hyb Kit (Cat#5190-0456, Agilent technologies, Santa Clara, CA, US) followed the manufacturer’s instructions, labeling section. Each slide was hybridized with 100ng Cy3-labeled RNA using miRNA Complete Labeling and Hyb Kit(Cat#5190-0456, Agilent technologies, Santa Clara, CA, US)in hybridization Oven(Cat#G2545A, Agilent technologies, Santa Clara, CA, US)at 55℃，20rpm for 20 hours according to the manufacturer’s instructions, hybridization section. After hybridization, slides were washed in staining dishes (Cat#121, Thermo Shandon, Waltham, MA, US) with Gene Expression Wash Buffer Kit(Cat#5188-5327, Agilent technologies, Santa Clara, CA, US).Slides were scanned by Agilent Microarray Scanner(Cat#G2565BA，Agilent  technologies, Santa Clara, CA, US)and Feature Extraction software 10.7 (Agilent technologies, Santa Clara, CA, US)with default settings. Raw data were normalized by Quantile algorithm, Gene Spring Software 11.0(Agilent technologies, Santa Clara, CA, US).

first: Jian-Zhong

last: He

first: En-Min

first: Li-Yan

last: Xu


title: In vitro transcriptomic profiling of P. falciparum under 4 hr artemisinin challenge (900nM), from 10 HPI

city: Singapore

first: Frances Maureen

middle: Casica

last: Rocamora

state: Singapore

address: 60 Nanyang Drive Nanyang Technological University

department: School of Biological Sciences

country: Singapore

institute: Nanyang Technological University

summary: This dataset pertains to a microarray-based transcriptomic profiling of artemisinin-resistant (6A-R, 11C-R) and artemisinin-sensitive (6A, 11C) P. falciparum under an an in vitro 4 hr artemisinin challenge (900nM), from 10 - 14 HPI

overall_design: Synchronized parasites were treated with 900nM artemisinin for 4 hrs starting from 10 HPI. Control parasites were treated in parallel with an equivalent volume of DMSO. Parasitized red blood cells (RBCs) were then harvested at 1hr after treatment with artemisinin/DMSO (TP1), 2 hours after treatment artemisinin/DMSO(TP2), and 4 hrs after treatment artemisinin/DMSO (TP3). Extraction of total RNA and amplification of total cDNA was carried out as  described in Bozdech, Z., S. Mok & A. P. Gupta, (2013) DNA microarray-based genome-wide analyses of Plasmodium parasites. Methods in molecular biology 923: 189-211.

first: Frances

first: Liong

last: Yee

first: Zbynek

last: Bozdech


title: Caveolin-1 promotes the human trophoblasts cells invasion through FAK signaling pathway in the early placental development

city: Shanghai

first: Zhihui

last: Dai

address: Xiangyin Road 800

institute: placenta

summary: mRNA expression profiles in the placenta tissues from different developmental stages in mice were analyzed by Arraystar Mouse LncRNA Microarray V3.0.

overall_design: The placenta tissues of mice were divided into three groups, including group A ( E7.5 d ),group B ( E14.5 d ) and group C ( E19.5 d ).Three  independent tissues samples were repeated at each time point.

first: Fei

last: Sheng


title: Steady-state in vitro transcriptomic profiling of P. falciparum from 10-20 HPI

summary: This dataset pertains to a steady-state in vitro transcriptomic profiling of artemisinin-resistant (6A-R, 11C-R) and artemisinin-sensitive (6A, 11C) P. falciparum parasites from 10-20 HPI

overall_design: Parasitized red blood cells (RBCs) from highly synchronized parasite lines (6A-R, 11C-R, 6A and 11C) were harvested at 2-hr intervals from 10 - 20 HPI (10 HPI, 12 HPI, 14 HPI, 16 HPI, 18 HPI and 20 HPI). Extraction of total RNA and amplification of total cDNA was carried out as  described in Bozdech, Z., S. Mok & A. P. Gupta, (2013) DNA microarray-based genome-wide analyses of Plasmodium parasites. Methods in molecular biology 923: 189-211.


title: Steady-state in vitro transcriptomic profiling of P. falciparum across parasite's intraerythrocytic life cycle

summary: This dataset pertains to a steady-state in vitro transcriptomic profiling of artemisinin-resistant (6A-R, 11C-R) and artemisinin-sensitive (6A, 11C) P. falciparum parasites across its intraerythrocytic life cycle

overall_design: Parasitized red blood cells (RBCs) from highly synchronized artemisinin-resistant (6A-R, 11C-R) and artemisinin-sensitive (6A, 11C) P. falciparum parasite lines were harvested at 8-hr intervals (6 timepoints) across their intraerythrocytic developmental cycle (IDC). Prior to harvesting, all parasite lines were tighty synchronized 5 times over 2 generations using treatment with 5% sorbitol. Extraction of total RNA and amplification of total cDNA was carried out as  described in Bozdech, Z., S. Mok & A. P. Gupta, (2013) DNA microarray-based genome-wide analyses of Plasmodium parasites. Methods in molecular biology 923: 189-211.


title: In Vitro Culture of the Insect Endosymbiont Spiroplasma poulsonii Highlights Bacterial Genes Involved in Host-Symbiont Interaction

city: Lausanne

first: Sandra

last: Calderon

address: Génopode Building

department: Center for Integrative Genomics

country: Switzerland

institute: University of Lausanne

summary: Endosymbiotic bacteria associated with eukaryotic hosts are omnipresent in nature, particularly in insects. Studying the bacterial side of host-symbiont interactions is, however, often limited by the unculturability and genetic intractability of the symbionts. Spiroplasma poulsonii is a maternally transmitted bacterial endosymbiont that is naturally associated with several Drosophila species. S. poulsonii strongly affects its host’s physiology, for example by causing male killing or by protecting it against various parasites. Despite intense work on this model since the 1950s, attempts to cultivate endosymbiotic Spiroplasma in vitro have failed so far. Here, we developed a method to sustain the in vitro culture of S. poulsonii by optimizing a commercially accessible medium. We also provide a complete genome assembly, including the first sequence of a natural plasmid of an endosymbiotic Spiroplasma species. Last, by comparing the transcriptome of the in vitro culture to the transcriptome of bacteria extracted from the host, we identified genes putatively involved in host-symbiont interactions. This work provides new opportunities to study the physiology of endosymbiotic Spiroplasma and paves the way to dissect insect-endosymbiont interactions with two genetically tractable partners.

overall_design: Three independent replicates were prepared for each condition: S. poulsonii collected from Drosophila hemolymph and S. poulsonii cultured in vitro for 2 months.

first: Florent

last: Masson

last: Calderon Copete

first: Fanny

last: Schüpfer

first: Gonzalo

last: Garcia-Arraez

first: Bruno

last: Lemaitre


title: A systems biology approach for understanding the transcriptome wide modulation of cardiac gene expression under oxidative environment during early stage of cardiovascular remodeling in developing embryo

city: Coimbatore

first: Manivannan

last: Jeganathan

state: Tamilnadu

address: Maruthamalai Road

department: Environmental Sciences

country: India

institute: Bharathiar University

summary: Various internal and external factors (including environmental pollutants) elevates oxidative stress in the developing embryo. Earlier studies unveil that chick embryo developed under oxidative environment due to exposure of reactive oxygen species (ROS) leads to cardiomyocyte hypertrophy associated with modulation of signaling pathways.

overall_design: In this study, we created the oxidative environment with 2,2-azobis(2-amidinopropane) dihydrochloride (AAPH), a free radicals generator to study the effects of oxidative stress on the cardiovascular system during chick embryo development. Here we exposed the chick embryo to AAPH through injecting 100 µL of AAPH (2.6 µmol) into the air chamber of fertilized eggs containing HH 35 chick embryos. The injections were repeated on alternative days for up to 10th day. At HH37 (day 11) the hearts were harvested from all surviving embryos for total RNA isolation. Saline and AAPH exposed embryonic heart RNA was isolated for RNA-Seq using next generation sequencing (NGS) approach.

first: Manikandan

last: Venkatesan

first: Prashanth

last: Manjunath

first: Saravanakumar

first: Shairam

last: Manickaraj

first: Subburaj

last: Jeyachandran


title: Kaposi’s Sarcoma-associated Herpesvirus Reactivation by Bacteria Promotes the Hypoxia Response and Epigenetic Regulation

city: Chapel Hill

first: Jennifer

last: Webster-Cyriaque

state: NC

address: 385 S. Columbia St.

department: Dental Research

institute: University of North Carolina at Chapel Hill

summary: Herpesviruses are frequently co-present with bacterial infection at multiple sites within the body, including the mouth, gut, and genitourinary tract. The detection of replicating virus in these compartments prompted investigation into the relationship between bacterial infection and Kaposi’s Sarcoma-associated Herpesvirus (KSHV) reactivation.  Using a cell line latently infected with KSHV, we examined the ability of crude spent media containing metabolic products from periodontal and gut pathogens to reactivate KSHV. Upon incubation with crude spent media, KSHV was reactivated and we detected the up-regulation of viral early and late genes, linear viral genomes, and virions.  Furthermore, KSHV reactivation was associated with global increases in histone H3 and histone H4 acetylation, consistent with viral expression. To explore the transcriptional consequences of spent media, we compared the gene expression changes following reactivation by P. gingivalis spent medium to those of two well-established pharmacological activators of KSHV reactivation, tetradecanolyl phorbol acetate and sodium butyrate. Microarray analyses revealed a unique gene expression signature with P. gingivalis-associated reactivation. Concurrent with KSHV reactivation, P. gingivalis spent medium increased the hypoxia response.  Hypoxia was associated with effects on epigenetic regulators, including down-regulation of UHRF1, a modulator of DNA methylation. Our findings demonstrate that products secreted by oral bacteria not only stimulate a hypoxia response, but also result in global changes in epigenetic modifications and modifiers. These findings suggest that epigenetic changes induced by P. gingivalis underlie the KSHV reactivation pathway.

platform_organism:
Homo sapiens
Human alphaherpesvirus 1
Human alphaherpesvirus 2
Human alphaherpesvirus 3
Human betaherpesvirus 6
Human betaherpesvirus 7
Cucumber mosaic virus
Human gammaherpesvirus 8
Simian-Human immunodeficiency virus
human papillomavirus 72

overall_design:
Three-condition experiment using BCBL-1 cells, untreated vs. P. gingivalis (PG) spent media-treated, untreated vs. NaB-treated, untreated vs. TPA-treated. Biological replicates: 7 control, 2 PG, 3 NaB, 2 TPA. independently grown and harvested. One replicate per array.

Please note that [1] there are 2 raw data files per sample (for 4 samples); the original gpr files from GenePix and modified txt files (missing header rows but otherwise identical data) used for analysis. [2] The gpr files for three samples (out of total 7samples) are unavailable, thus only the txt files are provided. [3] The *RG_geneavg_*.txt files contain complete normalized data including gene annotations and fold-change data [4] The 'M' column (in the *RG_geneavg_*.txt file) contains the 'normalized log2 ratio (Cy5/Cy3) representing test/reference' data included in each sample data table.

first: Latres

last: Dominick

first: Janet

last: Doolittle-Hall


title: Histone deacetylation promotes transcriptional silencing at facultative heterochromatin

status: Public on Mar 19 2018

city: Oxford

first: Beth

last: Watts

address: South Parks Road

department: Biochemistry

institute: University of Oxford

summary: It is important to accurately regulate the expression of genes involved in development and environmental response. In the fission yeast Schizosaccharomyces pombe, meiotic genes are tightly repressed during vegetative growth. Despite being embedded in heterochromatin these genes are transcribed and believed to be repressed primarily at the level of RNA. However, the mechanism of facultative heterochromatin formation and the interplay with transcription regulation is not understood. We show genome-wide that HDAC-dependent histone deacetylation is a major determinant in transcriptional silencing of facultative heterochromatin domains. Indeed, mutation of class I/II HDACs leads to increased transcription of meiotic genes and accumulation of their mRNAs. Mechanistic dissection of the pho1 gene where, in response to phosphate, transient facultative heterochromatin is established by overlapping lncRNA transcription shows that the Clr3 HDAC contributes to silencing independently of SHREC, but in an lncRNA-dependent manner. We propose that HDACs promote facultative heterochromatin by establishing alternative transcriptional silencing.

overall_design: In this study, we studied the effect of trichostatin A (TSA) by RNA-seq. We also analyzed the levels of histone H3 and histone H3 lysine 14 acetylation (H3K14ac) by ChIP-seq. Samples were sequenced in duplicates and ChIP-Seq experiments include an input sample.

middle: R

first: Sina

last: Wittmann

first: Maxime

last: Wery

first: Camille

last: Gautier

first: Krzysztof

last: Kus

first: Dong-Hyuk

last: Heo

first: Cornelia

last: Kilchert

first: Antonin

last: Morillon

first: Lidia

last: Vasiljeva


title: Expression data from dorsolateral prostates of ACI rats fed corn oil diets

status: Public on Mar 17 2018

city: Cartagena

first: Niradiz

last: Reyes

address: Campus de Zaragocilla. Facultad de Medicina

country: Colombia

institute: Universidad de Cartagena

summary:
Fatty acids from corn oil for 18 months influence ACI rat prostate gene expression
We used microarrays to detail the global alterations of gene expression in the prostate of ACI rats fed high and low corn oil for 18 months

overall_design: ACI rats were placed on either a high corn oil diet or a control diet for 18 months. Prostates were resected for RNA extraction and hybridization on Affymetrix microarrays. Three replicate rats were used in each group and RNAs were used individually for chip hybridization.

first: Jan

last: Geliebter


title: Expression from Slamonella Typhimurium infected murine peritoneal macrophages

status: Public on Mar 15 2018

city: Baltimore

first: Darren

last: Perkins

address: 685 W Baltimore st suite 380

department: Microbiology and Immunology

institute: University of Maryland Baltimore

summary:
Infection of macrophages by Salmonella induces a transcriptional inflammatory response. The pattern of Salmonella induced genes is significantly altered by the expression of type I interferons.
We used microArray analysis to identify changes in global gene expressioncaused by type I interferons following Salmonella infection

overall_design: Wild type and IFN-beta null thioglycollate elicited macrophages were mock infected or infected with Salmonella typhimurium for 6 hrs and RNA was extracted

first: Stefanie

middle: N

last: Vogel


title: Esophageal epithelium of WT mice; Esophageal epithelium of Pax9 KO mice

status: Public on Mar 16 2018

city: Camden

first: Xiaoxin

middle: Luke

last: Chen

state: NJ

address: 403 Haddon Ave

institute: Coriell Institute for Medical Research

summary: To study if the Pax9 gene plays an important role in the mouse model.

overall_design: WT mice and K5Cre;Pax9 loxP/loxP mice.

first: Zhaohui

last: Xiong


title: Mechanical stretch induced transcriptomic profiles in cardiac myocytes

city: Kuopio

first: Jaana

last: Rysae

address: Yliopistonranta 1C

department: School of Pharmacy

country: Finland

institute: University of Eastern Finland

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

platform_organism:
Homo sapiens
Mus musculus
Rattus norvegicus
Human alphaherpesvirus 1
Human betaherpesvirus 5
Murid betaherpesvirus 1
human gammaherpesvirus 4
JC polyomavirus
Human immunodeficiency virus 1
Murid gammaherpesvirus 4
Human gammaherpesvirus 8
Betapolyomavirus hominis
Betapolyomavirus macacae

overall_design: Refer to individual Series


title: Mechanical stretch induced transcriptomic profiles in cardiac myocytes [24-48 hours]

summary: The effect of cyclic mecanical stretch on cardiac microRNA expression was studied in neonatal rat ventricular myocytes (NRVMs).

overall_design: The effect of cyclic mecanical stretch on cardiac microRNA expression was studied in neonatal rat ventricular myocytes (NRVMs) 24 and 48 hours after start of the stretching. There are 3 biological replicates at each timepoint.

last: Rysä

first: Heikki

last: Ruskoaho


title: Mechanical stretch induced transcriptomic profiles in cardiac myocytes [1-12 hours]

overall_design: The effect of cyclic mecanical stretch on cardiac microRNA expression was studied in neonatal rat ventricular myocytes (NRVMs) 1, 4, and 12 hours after start of the stretching. There are 3 biological replicates at each timepoint, except 2 replicates at one hour time point.


title: Vitamin B2 and drought stress responses in Agaricus bisporus

status: Public on Mar 14 2018

city: Bayreuth

first: Alfons

last: Weig

address: Universitaetsstrasse 30

department: Genomics and Bioinformatics

country: Germany

institute: University of Bayreuth

summary: Drought is a stressor for many soil-inhabiting organisms. Although plants have been extensively investigated for drought-adaptive mechanisms, little information is available for fungi. Antioxidants are especially relevant, since desiccation is accompanied by an excessive intracellular production of reactive oxygen species. Riboflavin (vitamin B2) is one antioxidant regulating drought tolerance in plants. A similar function may exist in fungi. Here, we examined the respiratory and transcriptional responses of Agaricus bisporus to drought and the impact of riboflavin. Mesocosm experiments with four groups were established: hyphae were treated with or without 50 µM riboflavin under drought or no drought conditions. Drought increased riboflavin content in hyphae about 5 times with, but also without, addition of riboflavin. Without addition of riboflavin, fungal respiration decreased by more than 50% at water potentials of about -20 MPa. With addition of riboflavin, respiration remained about 2-3 times higher. The transcriptional responses to only drought or only riboflavin strongly overlapped and were mainly based on factors regulating transcription and translation. This was even stronger in combined treatments. Riboflavin induced protective mechanisms in drought-stressed hyphae. Most pronounced was the methylglyoxal (cytotoxic by-product of glycolysis) detoxifying of lactoylglutathione lyase. Thus, our data suggest a stress-priming function and a role of riboflavin in drought responses of A. bisporus.

overall_design: Mycelia were grown in gas-tight mesocosm chambers. Drought stress responses were analysed three and seven days after drought application in control and Riboflavin-supplemented mycelia; biological replicates were included in dye-swap experiments;

first: Alexander

last: Guhr


title: Expression data from Hdac1 and 2 knock out microglia in 5X familial Alzheimer's disease (FAD) background

city: Freiburg

first: Ori

last: Staszewski

address: Breisacher Str. 64

department: Institute of Neuropathology

institute: University Medical Center Freiburg

summary:
Epigenetic alterations has been implicated in the pathology of several neurodegenerative diseases. To investigate the role of microglial Hdac1 and 2 in the pathogenesis of Alzheimer's disease (AD), we created microglia specific compound Hdac1 and Hdac2 knock out mice in 5X FAD background. Genetic ablation of Hdac1 and 2 from microglia reduced amyloid plaque burden and improved spatial learning and memory function.
To study how Hdac1 and 2 knock out in microglia alters gene expression profile in 5X FAD mice we carry out microarray analysis using 24-28 weeks animals

overall_design: We used FACS sorted microglia cells from wild type (WT), FAD Hdac1/2fl/fl (FAD) and FAD Hdac1/2fl/flCx3cr1CreERT2 (FAD DKO) mice at 24-28 weeks of age

first: Moumita

last: Datta

first: Marco

last: Prinz


title: Identification of gene expression patterns in spleen of TREX1-mutated mice

city: Seoul

first: Chong-Su

last: Kim

address: Gwanak-ro 1, Gwanak-gu

department: Food and nutrition

country: South Korea

institute: Seoul national university

summary:
Investigating gene expression patterns in mice with conditional expression of the most common RVCL mutation, V235fs, and another mice expressing a conditional C-terminal mutation, D272fs, associated with a case of human SLE.
Mutations at the N-terminus affecting TREX1 DNase activity are associated with autoimmune and inflammatory conditions such as Aicardi-Goutières syndrome (AGS). Mutations in the C-terminus of TREX1 cause loss of localization to the ER and dysregulation of oligosacchryltransferase (OST) activity, and are associated with retinal vasculopathy with cerebral leukodystrophy (RVCL) and in some cases with systemic lupus erythematosus (SLE).

overall_design: 12 samples were tested from 3 groups of mice - 4 samples from each group. One sample per array

first: Dong-Mi

last: Shin

first: Herbert

last: III Morse

first: Tomomi

last: Sakai


title: Characterization of human dental pulp cells grown in chemically defined serum-free medium

city: Hiroshima

first: katsumi

last: Fujimoto

address: 1-2-3 Kasumi, Minami-ku

institute: Hiroshima University

summary:
Dental pulp cells obtained from several donors proliferated actively in a serum-free medium STK2. The growth rate of dental pulp cells from most donors was higher in the serum-free medium than that in a medium containing 10% serum.
DNA microarray analyses showed that gene expression profile of dental pulp cells grown in the serum-free medium was similar to that of cells grown in a medium containing 10% serum. However, several genes related to cell proliferation were up-regulated in dental pulp cells grown in the serum-free medium.

overall_design: Three dental pulp cell lines were cultured in DMEM/10% FBS or serum-free medium for 7 days. Total RNA was extracted from these cells, and DNA microarray analysis was performed to compare the genes expressed in dental pulp cells grown in DMEM/10% FBS (three samples) to those in cells grown in serum-free medium (three samples).

first: Sakiko

last: Fujii

first: Katsumi

first: Yukio

last: Kato


title: miRNA content of extracellular vesicles released from astrocytes upon stimulation of IL-1beta and control

first: Norman

last: Haughey

address: 600N Wolfe Street, Pathology 608

department: Department of Neurology

institute: Joohns Hopkins School of Medcine

summary: Brain injury induces a peripheral acute cytokine response (ACR) that directs the transmigration of leukocytes into brain. This brain-to-peripheral immune communication affects patient recovery, thus understanding how it is regulated is important. Contrary to expectations, it is not regulated by sympathetic innervation. Using a mouse model of an inflammatory brain injury, we set out to find a soluble mediator for this phenomenon. We found that extracellular vesicles (EVs) shed from astrocytes in response to intracerebral injection of interleukin-1b (IL-1b) rapidly entered into peripheral circulation and promoted the transmigration of leukocytes through modulation of the peripheral ACR. Bioinformatic interrogation of the protein and miRNA cargo of EVs identified Peroxisome proliferator-activated receptor-α (PPAR-a)  as a primary molecular target of astrocyte-shed EVs. We confirmed in mice that astrocytic EVs promoted the transmigration of leukocytes into the brain by inhibiting PPARa resulting in the increase of NF-κB activity thus, triggering the production of cytokines in liver. These findings expand our basic understanding of the mechanisms regulating communication between the brain and peripheral immune system, and identify astrocytic EVs as a molecular regulator of the immunological response to inflammatory brain damage.

overall_design: This study characterised the miRNA content of extracellular vesicles released from cultured astrocytes when stimulated with IL-1beta. The control exosomes were generated by collecting all particles released over a 24h period.

first: Alex

last: Dickens

first: Luis

middle: B

last: Tovar-y–Romo

first: Seung

middle: W

last: Yoo

first: Amanda

last: Trout

first: Mihyun

last: Bae

first: Marlene

last: Kanmogne

first: Bezawit

last: Megra

first: Dionna

last: Williams

first: Kennith

last: Witwer

first: Mar

last: Gacias

first: Nino

last: Tabatadze

first: Robert

last: Cole

first: Patrizia

last: Casaccia

first: Joan

last: Berman

first: Daniel

last: Anthony


title: Identification differentially expressed genes in the mouse testis caused by Prss54 deficiency

city: shanghai

first: Xuan

last: Shang

state: shanghai

address: No.197, Ruijin 2nd Road, Huangpu District, Shanghai

department: Research Center for Experimental Medicine

institute: Shanghai Ruijin Hospital Affiliated to Shanghai Jiao Tong University School of Medicine

summary: To further investigate molecular mechanism of Prss54 in mouse, we have employed whole genome microarray expression profiling as a discovery platform to identify genes with the potential role to be downstream targets of Prss54.

overall_design: In the study presented here, testis from three wildtype and three Prss54 knockout adult mice were used to acquire expression profiles of a total of 41,267 unique genes, leading to the fully understand the function of Prss54.

first: Chunling

last: Shen

first: Zhugang

last: Wang


title: Expression data from HEK 293T cells overexpressing either myc-FUS or myc-R495X (miRNA)

first: Jiou

address: 615 N. Wolfe St.

institute: Johns Hopkins University

summary:
Individuals with the ALS-linked (amyotrophic lateral sclerosis) truncation mutation (R495X) in FUS (fused in sarcoma) are known to have a more aggressive form of the disease than those with point mutations.  The underlying cause for this difference is unclear.  We report that FUS is a component of miRISC (miRNA-induced silencing complex) and that overexpression of its truncation mutant R495X negatively impacts miRNA mediated RNA silencing.
In this study, we compared the impact overexpression of wild-type myc-tagged FUS versus truncation mutant R495X has on global gene expression.

overall_design: Pairwise comparisons were made based on three biological replicates from two groups: 293Ts expressing myc-tagged R495x versus those expressing wild-type myc-tagged FUS.

first: P

last: Mullane


title: Gene expression profile in kidney with experimental membranous

status: Public on Mar 13 2018

city: Taipei

first: Yen-Sung

last: Huang

address: Academia Sinica, No.128, Sec2,

department: Institute of Biomedical Sciences

institute: Academia Sinica

summary: In this study, we  try to identify dysregualted-genes in kindey with experimental membranous nephroapthy (MN).

overall_design: Using a previously described method that induces MN, we immunized mice with cationic bovine serum albumin (cBSA) to induce kidney damage. Total RNA in kidneys were extrracted from MN mice and control mice.

first: Yen

first: Hsin

middle: Y

last: Hsieh

first: Chia

middle: C

last: Wu


title: Expression profiling of lncRNAs/mRNA for H.pylori infected normal gastric epithelial cell line

city: Beijing

first: Taotao

last: Han

state: Beijing

address: NO.5 Dong Dan San Tiao, Dongcheng District

department: Department of Biochemistry and Molecular Biology

institute: Peking Union Medical College & Chinese Academy of Medical Sciences

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

summary: In this study, cultured H.pylori was used to infect the normal gastric epithelial cell line GES-1, to construct the H.pylori infection model. lncRNA microarray was applied for detecting the lncRNA in H.pylori infection model.

overall_design: A three chip study using total RNA extracted from  GES-1 cells infected with H.pylori . Each chip measures the expression level of 45,697 genes  collected from the authoritative data source including NCBI

first: Juan

last: Shi


title: Detection of aberrant DNA methylation in acute myeloid leukemia samples compared to normal human monocytes

city: Regensburg

first: Michael

last: Rehli

address: F.-J.-Strauss-Allee 11

department: Internal Med III

institute: University Hospital Regensburg

type: Methylation profiling by genome tiling array

summary: To globally define CG-rich regions that show altered DNA methylation im leukemia, we analyzed the methylation status of 23,000 CpG islands of the human genome in twenty seven acute leukemia samples as well as normal blood monocytes using our previously described methyl-CpG immunoprecipitation (MCIp) technique (Gebhard et al. 2006; Schilling and Rehli 2007). This method enriches for highly CpG methylated DNA that can be directly applied to fluorescent labeling and oligonucleotide microarray hybridization without an additional amplification step.

overall_design:
CpG-methylated genomic DNA was enriched using methyl-CpG immunoprecipitation (MCIp). On each microarray, the enriched material from leukemia samples was compared to the enriched material from normal blood monocytes to identify aberrantly methylated regions.
MCIp-on-Chip; comparative genomic hybridization

first: Claudia

last: Gebhard


title: Expression data from mouse hepatocellular carcinomas developed in Axin1 hepatocyte deleted mice

city: Paris

first: Franck

last: Letourneur

address: 22 rue mechain

institute: INSERM

summary:
Mouse liver tumors (T) and non tumoral adjacent livers (NT) sorted from mice knock out for Axin1 gene specifically in the hepatocytes . 3 mice of the brother hood non deleted for Axin1 were used as controls (WT)
We used microarrays to determine the differential expression between tumoral and non tumoral tissue.

overall_design: Tumors were isolated from non-tumoral adjacent livers. Normal liver from mice of the same age and gender were used as a control.

first: Helene

last: Gilgenkrantz

first: Florent

last: Dumont


title: miRNA in CD4+ T cells: control vs. patients with myasthenia gravis

city: Chang Sha

first: jingjiao

last: chen

state: Hu Nan

address: Renmin

institute: xiangya hospital

summary: To investigate the abnormal expression amount of microRNAs in T cells of patients with myasthenia gravis

overall_design: Two-condition experiment,control vs.patients with MG. Biological replicates: 6 control replicates, 6 MG replicates.

first: Jingjiao

last: Chen

first: Jing

last: Li


title: Transcriptomic and Network Analyses Reveals Mechanistic-Based Biomarkers of Endocrine Disruption in the Marine Mussel, Mytilus edulis

city: Boston

first: Bonnie

last: Blalock

state: MA

address: 100 Morrissey Blvd

department: School for the Environment

institute: University of Massachusetts Boston

summary: Coastal monitoring in the 21st century faces challenges as measuring exposure using traditional toxicity approaches is not practical or financially feasible for the numerous contaminants entering oceans.  Transcriptomics, high-throughput assays, and adverse outcome pathways (AOP) have been one approach to overcome these obstacles but development of these methods is challenging for non-model organisms and contaminants with unknown mechanisms.  Endocrine Disrupting Compounds (EDCs) have been found to cause reproductive impairments such as intersex in bivalves, however, the mechanism linked to this adverse outcome (AO) is unknown as the estrogen receptor (ER) has been identified to be unresponsive to EDCs.  To develop mechanism-based biomarkers that may be linked through an AOP we exposed Mytilus edulis to 17-alpha-ethinylestradiol (5 and 50ng/L) and 4-nonylphenol (1 and 100μg/L), and performed gene expression analysis on digestive gland tissue using a M. edulis microarray.  Through network and targeted analyses, we identified the non-genomic estrogen signaling pathway and steroidogenesis pathway as the likely mechanism of action and identified biomarkers and potential key events (KE) for an AOP of endocrine disruption in marine mussels.  The mechanism-based biomarkers were validated in the laboratory, tested in the field, and were responsive in areas known to be contaminated with EDCs.

overall_design: 40 samples total were analyzed.  4 replicates were examined for males and female Mytilus edulis in control, 5 and 50ng/L 17-alpha-ethinylestradiol (EE2) and 1 and 100μg/L 4-nonylphenol (4NP).   Each male and female replicate came from separate experimental tanks.

middle: J

first: Helen

last: Poynton


title: Expression data in subcutaneous xenografts of Huh7 cells overexpressing or not insulin receptor isoform A

first: Christèle

last: Desbois-Mouthon

address: 15 rue de l'école de médecine

summary: Insulin receptor isoform A (IR-A) is overexpressed in human hepatocellular carcinoma. We used microarrays to investigate gene expression patterns in subcutaneous xenografts derived from Huh7 stably overexpressing IR-A

overall_design: Huh7 cells were stably transfected with the expression plasmid pRcCMVi.hIR-A(GFP) or the empty vector and selected for G418 resistance and GFP expression by cytometry. 2 x 106 cells were then sc injected to nude mice. Tumors (Control (n=3) and  IR-A overexpressing (n=3)) were harvested and RNA was extracted and hybridized on Affymetrix microarrays.


title: Transcriptome profiling of FK866 response in CCRF-CEM parental and resistant cells

city: Povo

first: Toma

last: Tebaldi

state: Trento

address: via Sommarive n. 9

department: Centre for Integrative Biology

country: Italy

institute: University of Trento

summary:
Parental and resistant CCRF-CEM cells were treated for 48 hr with a sublethal dose of FK866 (5 nM) or DMSO (Mock, control treatment).  This comparison enables the identification of the specific transcriptional alterations induced by FK866 in parental or resistant cells.
Keywords: transcriptome profiling, FK866, drug resistance

overall_design: Gene expression signals derived from parental and resistant CCRF-CEM cells after FK866 treatment were compared by microarrays analysis. Total RNA were isolated from CCRF-CEM cells treated with FK866 5 nM  or DMSO (mock, control treatment) for 48 hr. Cells lysates were collected from control cells (mock) and from treated cells (FK866). All experiments were run with biological replicates.

first: Chiara

last: Zucal

first: Vito

last: D'Agostino

first: Natthakan

last: Thongon

first: Valentina

last: Adami

first: Alessandro

last: Provenzani


title: Analysis of influence of Excretory Secretory Products from wild and laboratory Fasciola hepatica isolates on bovine macrophages

city: Warsaw

first: Piotr

last: Bąska

state: Mazowieckie

address: Ciszewskiego 8

department: Department of Preclinical Sciences

country: Poland

institute: Warsaw University of Life Sciences WULS – SGGW

summary: F. hepatica is a parasite causing losses of great importance in animal production. It is also considered a zoonosis of growing importance. During the infection the parasite releases a number of antigens (called Excretory Secretory Products - ESP) facilitating the parasites survival. A number of ESP components have immunomodulatory properties.  To determine if ES from various F. hepatica isolates have different immunomodulatory abilities “BOMA” cells were stimulated with ES from laboratory Weybridge (FhWey-ES) and wild (FhWild-ES) Fasciola hepatica isolates.

overall_design: The experiment was performed in quadruplicate. Cells were seeded in 24 deep well plates. Four wells were stimulated and four were unstimulated and treated as a controls. RNA was isolated from cells from each well followed by labelling with Cy3 (control cells) or Cy5 (stimulated cells). The material was hybrised to four bovine mRNA microarrays (Agilent).

first: Luke

last: Norbury

first: Kamil

last: Januszkiewicz


title: Copy number profiling of 556 high-risk neuroblastoma patients using aCGH or SNP arrays

city: Gent

first: Katleen

last: De Preter

address: Corneel Heymanslaan 10

department: Center for Medical Genetics

country: Belgium

institute: Ghent University

type: Genome variation profiling by genome tiling array

summary:
Purpose: Neuroblastoma is characterized by substantial clinical heterogeneity. Despite intensive treatment, the survival rates of high-risk neuroblastoma patients are still disappointingly low. Somatic chromosomal copy number aberrations have been shown to be associated with patient outcome, particularly in low- and intermediate-risk neuroblastoma patients. To improve outcome prediction in high-risk neuroblastoma, we aimed to design a prognostic classification method based on copy number aberrations.
Methods: In an international collaboration, normalized high-resolution DNA copy number data (arrayCGH and SNP arrays) from 556 high-risk neuroblastomas obtained at diagnosis were collected from nine collaborative groups and segmented using the same method. We applied logistic and Cox proportional hazard regression to identify genomic aberrations associated with poor outcome.
Results: In this study, we identified two types of copy number aberrations that are associated with extremely poor outcome. (i) Distal 6q losses were detected in 5.9% of patients and were associated with a ten-year survival probability of only 3.4%. (ii) Amplifications of regions not encompassing the MYCN locus were detected in 18% of patients and were associated with a ten-year survival probability of only 5.8%.
Conclusion: Using a unique large copy number dataset of high-risk neuroblastoma cases, we identified a small subset of high-risk neuroblastoma patients with extremely low survival probability that might be eligible for inclusion in clinical trials of new therapeutics. The amplicons may also nominate alternative treatments that target the amplified genes.

overall_design: In an international collaborative effort joining nine neuroblastoma research groups, we collected DNA copy number data from 556 high risk neuroblastoma patients, enrolled in the SIOPEN, GPOH, COG and Japanese treatment protocols. High-risk was defined as either stage 4 and older than 1 year, or MYCN amplification (any age or stage). SIOPEN and GPOH data were combined to form the training cohort while COG and Japanese data were used as separate validation cohorts. These data include 92 samples previously reported on GEO, among which 68 samples from series GSE12494 and 24 samples from series GSE25771.

first: Pauline

last: Depuydt

last: Boeva

first: Toby

middle: D

last: Hocking

first: Robrecht

last: Cannoodt

first: Inge

last: Ambros

first: Peter

middle: F

first: Shahab

last: Asgharzadeh

first: Edward

last: Attiyeh

first: Valérie

last: Combaret

first: Raffaella

last: Defferrari

first: Matthias

last: Fischer

first: Barbara

last: Hero

first: Michael

last: Hogarty

first: Meredith

middle: S

last: Irwin

first: Jan

last: Koster

first: Susan

last: Kreissman

first: Ruth

last: Ladenstein

first: Eve

last: Lapouble

first: Geneviève

last: Laureys

first: Wendy

last: London

first: Katia

last: Mazzocco

first: Akira

last: Nakagawara

first: Rosa

last: Noguera

first: Miki

last: Ohira

first: Julie

last: Park

first: Ulrike

last: Pötschger

first: Jessica

last: Theissen

first: Gian

middle: P

last: Tonini

first: Dominique

last: Valteau-Couanet

first: Luigi

last: Varesio

first: Rogier

last: Versteeg

first: Frank

last: Speleman

first: John

last: Maris

first: Gudrun

last: Schleiermacher


title: Mnemiopsis leidyi high resolution developmental transcriptomic time-course 0-20 hours

city: Saint Augustine

first: Alexandra

last: Hernandez

state: FL

address: 9505 OCEAN SHORE BLVD

department: Biology

institute: Whitney Laboratory for Marine Bioscience, University of Florida

summary: These data complement GEO accession GSE60478, a time-course of Mnemiopsis leidyi developmental gene expression for hours 0-13 and hour 20. The data here provide additional replicates for 0-13 and 20 hours as well as new timepoints 14–19. As in the original study (Levin et al. 2016 PMID: 26886793) data are from single embryos using the Cel-Seq (Single-Cell RNA-Seq by Multiplexed Linear Amplification PMID:22939981). Embryo processing, sequencing and sequence processing were performed in the same manner as the original analyses (GEO accession GSE60478) so these data should be completely compatible with that study.

overall_design: single embryo samples; a time-course of Mnemiopsis leidyi developmental gene expression for 0-13 and 20 hours as well as new timepoints 14-19

first: Itai

last: Yanai

first: Mark

middle: Q

last: Martindale

first: Joseph

last: Ryan


title: Gene expression in squash (Cucurbita pepo) nectaries

city: Duluth

first: Marshall

last: Hampton

state: MN

address: 1117 University Drive

institute: University of Minnesota Duluth

summary: Nectaries are the glands responsible for nectar secretion. To understand the genetic programming underlying nectar production, male and female squash(Cucurbita pepo)  floral nectaries at four different time points (pre-secretion #1, pre-secretion #2, secretory, and post-secretory) in biological triplicate were collected, with RNA being isolated and subjected to Illumina RNA-seq analysis.

overall_design: Cucurbita pepo (Crookneck Yellow Squash) plants were grown on Sun Gro LC8 soil under a 16 hr day/8 hr night cycle, photosynthetic photon flux of 250 μmol m-2 s-1 at leaf level, and a temperature of 21°C. Four types of RNA samples were separately prepared from the nectaries of both male and female squash flowers, including: ‘pre-secretory #1’ (24 hours prior to anthesis/nectar secretion), ‘pre-secretory #2’ (12 hours prior to anthesis/nectar secretion), ‘secretory’ (full anthesis, 3 hours after dawn), and ‘post-secretory’ (12 hours after the ‘secretory’ stage). All nectary tissues were manually dissected by hand with the RNA being immediately extracted by mechanical disruption with a microcentrifuge pestle and using an RNAqueous® RNA isolation kit (Ambion, Austin, TX) with Plant RNA Isolation Aid (Ambion, Austin, TX). Agarose gel electrophoresis and UV spectrophotometry were used to assess RNA quality for all samples prior to submission to the University of Minnesota Genomics Center for mRNA isolation, barcoded library creation and Illumina HiSeq 2500 sequencing. Twenty-three TruSeq RNA v2 libraries were created (triplicate samples for male and female nectaries at four timepoints each, except for only duplicate samples of female ‘pre-secretory #2’ nectaries) and sequenced via 50 bp, paired-end runs on the HiSeq 2500 using Rapid chemistry. All libraries were pooled and sequenced across two full lanes. This generated over 240 M reads for each lane and the average quality scores were above Q30.

first: Clay

last: Carter

first: Peter

middle: M

last: Klinkenberg


title: RNA regulated by Orb in Drosophila

status: Public on Mar 12 2018

city: Montpellier

first: Isabelle

last: Busseau

address: 141 rue de la Cardonille

department: Institut de Génétique Humaine

country: France

institute: CNRS

summary:
We used microarrays to identify mRNAs regulated by Orb, the Drosophila CPEB homolog, during oogenesis. We analyzed RNA recovered from immunoprecipitation experiments and transcriptomes of wild-type and orb mutant females.
Keywords: mRNA targets of a regulatory protein

overall_design:
All samples from wild-type (w1118) females
RNA from females CS: one sample
RNA from females orbdec: one sample
Seven hybridization (5 and 2 dye-swap)
DrosophilaFemale_CSCy3xorbdecCy5_rep1 (3000203462)
DrosophilaFemale_CSCy3xorbdecCy5_rep2 (3000207295)
DrosophilaFemale_CSCy3xorbdecCy5_rep3 (3000207846)
DrosophilaFemale_CSCy3xorbdecCy5_rep4 (3000207861)
DrosophilaFemale_CSCy3xorbdecCy5_rep5 (3000207876)
DrosophilaFemale_CSCy5xorbdecCy3_rep1 (3000203463)
DrosophilaFemale_CSCy5xorbdecCy3_rep2 (3000207833)
IP from ovarian extracts with 6H4 anti-Orb monoclonal antibody: 3 samples
IP from ovarian extracts with 12CA5 anti-HA-Tag monoclonal antibody: 1 sample
poly(A+) RNA from ovaries: 1 sample
One hybridization IP-6H4 x IP-12CA5
Two hybridizations IP-6H4 x poly(A+) RNAfrom ovaries, with dye swap
IP_Orb_6H4Cy3xIP_12CA5Cy3 (3000203456)
IP_Orb_6H4Cy3 x ovarian_pACy5 (3000207835)
IP_Orb_6H4Cy5 x ovarian_pACy3 (3000207834)

first: Martine

last: Simonelig

first: Dany

last: Severac

first: Cindy

last: Aknin


title: The cold shock response of Bacillus subtilis analyzed by RNA-sequencing: YplP regulates pyruvate transport at low temperatures

city: Groningen

first: Anne

middle: de

last: Jong

address: Nijenborgh 7

department: Molecular Genetics

institute: university of Groningen

summary: The cold shock response of B. subtilis was defined after 0.5 hr and 2 hr cold shock using RNA sequencing. We identified novel RNAs (including non-coding RNAs) that play a role during growth at low temperatures. Deletion of the cold induced protein YplP results in a cold sensitive phenotype, and a comparative RNA sequencing analysis suggests that YplP induces pftAB expression after prolonged incubation at low temperatures, thereby optimizing pyruvate transport under cold shock conditions.

overall_design: 2 conditions, 2 strains, 2 timepoints

first: Marielle

middle: H

last: van den Esker

first: Oscar

last: Kuipers

last: de Jong


title: MalR regulon of B. breve UCC2003; malto-oligosachrides and beyond

status: Public on Mar 09 2018

city: Cork

first: Noreen

last: Lanigan

state: Cork

address: Biosciences Institute, University college Cork, cork, ireland.

department: Microbiology

country: Ireland

institute: University college cork

summary: Bifidobacteria resident in the gastrointestinal tract are subject to many stresses such as bile stress, osmotic stress and starvation. Adaption to these stresses requires a high amount of energy and rapid changes in gene transcription. Four Bifidobacterium breve UCC2003-encoded Lac I type transcriptional regulators had been proposed to be involved in the utilisation of maltose, maltodextrins and related polymers such as starch, amylopectin, amylose, glycogen and pullulan. However, it now appears that these regulators are also involved in the utilisation of other carbon sources such as ribose and cellobiose. Interestingly, in vitro these regulators often cross regulate the same carbohydrate utilization genes, along with regulating each other.  This hierarchical regulatory system controls the transcription of genes involved in carbohydrate uptake, storage, breakdown and central metabolism. These four regulators respond to differing effectors in vitro, these effectors include sugars such as turanose or galactose, thus indicating that each regulator is responsible for a different aspect of carbon metabolism.  This complex network of gene regulation provide novel insights into the decision making process of the cell and the metabolic adaption of bifidobacteria to its environment.

overall_design: DNA-microarrays containing oligonucleotide primers representing each of the 1864 annotated genes on the genome of B. breve UCC2003 (O'Connell Motherway et al., 2011) 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.

first: Emer

last: Kelly

first: Douwe

last: van Sinderen


title: High-throughput sequencing reveals microRNAs in response to heat stress in head kidney of rainbow trout (Oncorhynchus mykiss)

city: Tianshui

first: Fang

last: Ma

state: Qinzhou District

address: South Xihe Road

department: College of Bioengineering and Technology

country: China

institute: Tianshui normal university

summary:
Purpose:Our data significantly advance understanding of heat stress regulatory mechanism of miRNA in the head kidney of rainbow trout
Methods:miRNAs of rainbow trout were involved in heat stress were identified by high-throughput sequencing of six small RNA libraries of the kidney tissues under control (18℃) and heat-treated (24℃) conditions
Results:high-throughput sequencing was performed to identify miRNAs responsive to heat stress. We obtained 41,991,119 and 43,882,123 raw reads and 39,756,736  and 42,538,331 clean reads from under control (18℃) and heat-treated (24℃) .A total of 392 conserved miRNAs and 989 novel miRNAs were identified, of which 78 miRNAs were expressed in different response to heat stress. In addition to, including 393 negative correlation miRNA-target gene pairs
Conclusions:through high-throughput sequencing of the six libraries from head kidney tissue of rainbow trout, the expression level of miRNA has significant changes after heat stress.

overall_design: The head kidney samples of 3 females at 18°C (control group, CK) and 3 females at 24°C (heat-treated group, HK)

first: Zhe

last: Liu


title: Molecular signatures of maturing dendritic cells: implications for testing the quality dendritic cell therapies

status: Public on Mar 08 2018

city: BETHESDA

first: PING

last: JIN

state: MD

address: 9000 ROCKVILLE PIKE

department: DTM

institute: CC/DTM/NIH

summary:
Abstract
Background: Dendritic cells (DCs) are often produced by granulocyte-macrophage colony-stimulating factor (GMCSF)  and interleukin-4 (IL-4) stimulation of monocytes. To improve the effectiveness of DC adoptive immune  cancer therapy, many different agents have been used to mature DCs. We analyzed the kinetics of DC maturation  by lipopolysaccharide (LPS) and interferon-g (IFN-g) induction in order to characterize the usefulness of mature DCs  (mDCs) for immune therapy and to identify biomarkers for assessing the quality of mDCs.  Methods: Peripheral blood mononuclear cells were collected from 6 healthy subjects by apheresis, monocytes  were isolated by elutriation, and immature DCs (iDCs) were produced by 3 days of culture with GM-CSF and IL-4.  The iDCs were sampled after 4, 8 and 24 hours in culture with LPS and IFN-g and were then assessed by flow  cytometry, ELISA, and global gene and microRNA (miRNA) expression analysis.  Results: After 24 hours of LPS and IFN-g stimulation, DC surface expression of CD80, CD83, CD86, and HLA Class II  antigens were up-regulated. Th1 attractant genes such as CXCL9, CXCL10, CXCL11 and CCL5 were up-regulated  during maturation but not Treg attractants such as CCL22 and CXCL12. The expression of classical mDC biomarker  genes CD83, CCR7, CCL5, CCL8, SOD2, MT2A, OASL, GBP1 and HES4 were up-regulated throughout maturation  while MTIB, MTIE, MTIG, MTIH, GADD45A and LAMP3 were only up-regulated late in maturation. The expression of  miR-155 was up-regulated 8-fold in mDCs.  Conclusion: DCs, matured with LPS and IFN-g, were characterized by increased levels of Th1 attractants as  opposed to Treg attractants and may be particularly effective for adoptive immune cancer therapy.

first: Ping

last: Jin

first: Tae

last: Han

first: Jiaqiang

last: Ren

first: Stefanie

last: Saunders

first: Ena

last: Wang

first: Francesco

last: Marincola


title: Analysis of differential gene expression during Bacillus subtilis spore outgrowth

summary: The transcriptome of 8 strains were studied during 7 stages of the Morphological phases of sporulation P0 = Resuspention of cells in sporulation medium; P1 = Onset of sporulation before asymmetric division; P2 = Visible asymmetric septum; P3 = Ongoing engulfment of the forespore compartment by the mother cell compartment of sporulating cells; P4 = Completed engulfment (engulfed phase-dark forespores are surrounded by the mother-cell cytoplasm); P5 = Maturation (ongoing dehydration of the forespore core seen as a transition of phase-dark forespores into phase-bright foresppores); P6 = Phase-bright forespores (sporulation almost completed, mother-cells contain phase-bright dehydrated forespores).

sample_organism:
Bacillus amyloliquefaciens
Bacillus subtilis

overall_design: 8 strains 7 time points

first: Tonia

last: Krawczyk


title: Whole human genome expression analysis on left ventricular free wall heart tissue samples (Dilated Cardiomyopathy)

city: Marseille

first: Christophe

last: Chevillard

state: BDR

address: 27 bd Jean Moulin faculté de médecine

summary: Human left ventricular free wall heart tissue was obtained from end-stage heart failure patients at the moment of heart transplantation

overall_design: RNA Extraction was done on frozen tissues without stimulation. Whole genome expression analysis was conducted on 14 dilated cardimyopathy (DCM) samples.

first: C

first: E

last: Cunha-Neto


title: Gene expression profiling of dSur knock-out flies.

city: Padova

first: Cristiano

last: De Pitta

address: Via U. Bassi, 58/B

institute: University of Padova

summary: In order to investigate the functional relevance of SUR2 (the protein encoded by ABCC9 in humans) for sleep duration, we knocked down the expression of its Drosophila homologue (dSur) in the flies’ nervous system (both central and peripheral). Unlike humans, flies are active predominantly around dawn and dusk and show two large sleep episodes during the day and during the night. Knockdown of dSur dramatically reduced night-sleep, particularly during the first half of the dark period, but had little effect on the flies’ day-sleep. This was true for both elavgal4 UAS-Sur RNAi genotypes compared with their parental control strains. These differences in sleep duration were not due to changes in the circadian clock, as the period of the free-running locomotor activity rhythm in constant darkness was indistinguishable between knockdown flies and controls. Furthermore, no systematic differences in activity levels were found between experimental genotypes and control. Thus, the major effect of knocking down  the ABCC9 homologue in flies is shortening nighttime sleep due to a delay of its onset by 3 h.

overall_design: To elucidate the functional role of dSur we performed the gene expression profiling of elavgal4 UAS-Sur RNAi genotype compared with their parental control strain (wt) in two time points: Day and Night. The time point Day corresponds to pooled samples every three hours over a 24h period, instead the time point Night corresponds to a single ZT (three hours in the dark phase: ZT15). We used the Drosophila 1.0 custom platform (Agilent Technologies). Total RNA was obtained from the head of 30 flies for each genotype. Four biological replicates were analyzed for dSur-/- and control (wt) samples respectively for the two time points. In total we carried out 16 microarray experiments.

first: Paola

last: Cusumano

first: Rodolfo

last: Costa

first: Karla

last: Allebrandt


title: Renal tubular Sirt1 attenuates diabetic albuminuria by epigenetically suppressing Claudin-1 overexpression in podocytes.

city: Tokushima

first: Kazuhiro

last: Hasegawa

address: 3-18-15 Kuramoto-cho

department: Department of Nephrology

country: Japan

institute: Tokushima University Graduate School of Biomedical Sciences

summary:
We aim to investigate the role of renal Sirt1 on albuminuria. To further development of our gene expression approach to biodosimetry, we have employed whole genome microarray expression profiling as a discovery platform to identify genes with the potential to distinguish between wild type(C57BL/6J) mice treated with streptozotocin (WT+STZ) and Sirt1-overexpressing transgenic mice treated with streptozotocin (TG+STZ) mice.
To elucidate the molecular mechanisms underlying the amelioration of albuminuria by our TG (Sirt1-overexpressing transgenic) mice, we performed DNA microarray analysis using micro-dissected glomerular regions to examine the differences in gene expression between WT+STZ and TG+STZ mice.

overall_design: Mice in the WT+STZ and TG+STZ groups were killed at 32weeks of age. We dissected the glomerular regions. Micro-dissected glomeruli were immediately used for total RNA isolation and subjected to analysis on microarray chips.


title: Expression of circular RNA in tuberculosis patient and healthy control

status: Public on Mar 07 2018

city: NanJing

first: Musheng

last: Li

address: sipailou 2

institute: Southeast University

summary: A comprehensive profiling of known human circular RNA is performed on both TB patient and healthy control.

overall_design:
2 patient and 2 healthy case are included.

RNA-seq was performed on the same samples and the data are available in SRA under BioProject PRJNA397016.


title: The LsrB protein is required for Agrobacterium tumefaciens interaction with host plants

status: Public on Mar 05 2018

city: 上海

first: tang

middle: gui

last: rong

address: fenglin road 300

department: Shanghai Institutes for Biological Sciences

institute: University of Chinese Academy of Sciences

summary: We found 465 genes were significantly differentially expressed (upregulation of 162 genes and downregulation of 303 genes) in the mutant compared to the wild-type strain by RNA-sequencing.

overall_design: Examination of genes differentially expresssion in wild-type and mutant stains.

first: Guirong

last: Tang

first: Qiong

first: Shenghui

last: Xing

first: Ningning

first: Liangliang

last: Yu

first: Junhui

last: Yan

first: Xuan

first: Li

last: Luo


title: miRNA Expression in 4 mouse Hepatocellular Carcinoma cells with different lymphatic metastasis potentials

status: Public on Mar 10 2018

city: Panjin

first: HUANG

last: HUANG

state: Liaoning

address: NO.2 Dagong Road, New District of Liaodong Bay

department: School of Life and Medical Sciences

institute: Dalian University of Technology

summary: The purpose of this study is to screen for microRNAs related to  lymphatic metastasis in mouse Hepatocellular Carcinoma cells, named H22, Hepa1-6, Hca-P, and Hca-F. The lymphatic metastasis abilities of the cell lines are different.

overall_design: Total RNA was isolated using TRIzol Reagent (Invitrogen life technologies) from Hepa1-6 and Hca-F cells. RNA samples were analyzed by Exiqon A/S using miRCURYTM Array Power Labeling kit and the miRCURYTM Array. Hybridization signals were scanned and analyzed by Genepix 4000B microarray scanner.

first: Huang

last: Huang

first: Yanjie

last: Guo


title: Expression alterations of miRNAs in SW620, HCT116, HUVEC cells exposed to 200 μg/mL PEP06 for 24 h relative to control cells without drugs.

city: Harbin

first: SIMING

last: YU

address: No.194 XueFu Road

institute: Department of Pharmacology,Harbin Medical University,

summary: Using the highly sensitive miRNA array, we screened the abundance of 2043 microRNAs in 2 colorectal cancer cell lines SW620 and HCT116, as well as HUVEC post treatment of PEP06. Among the 2043 microRNAs, 23 were found to be aberrantly expressed with statistical significances between the control and the PEP06 treated group. In the validating study with real-time PCR and Northern blot, miR-146b-5p was revealed significantly regulated by treatment of PEP06 in vivo and in vitro. We next explored the functions of miR-146b-5p in the EMT process in colorectal cancer. Our findings gave new insights in disclosing the mechanism by which PEP06 induces colorectal cancer inhibition.

platform_organism:
Homo sapiens
Mus musculus
Rattus norvegicus

overall_design: In this study, two samples from each group were used to acquire the miRNA expression profiling and the function of the abundant miRNAs in the CRC were analyzed by bioinformatic methods, finally, miR-146b-5p was experimentally validated to be an important target in the process of PEP06 in the treatment of CRC.

first: Siming

first: Wei

last: Tian

first: Dan

last: Nie


title: Comprehensive lncRNAs expression profiling reveals the potential role of lncRNAs in systemic lupus erythematosus [Human LncRNA Array v3.0]

city: Hefei

first: Lian-Ju

state: Anhui

address: 81 Meishan Road

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

institute: Anhui Medical University

summary: long non-coding RNAs (lncRNAs) are novel non-coding RNAs which play an important part in regulating gene transcription and translation, modulating protein function, and acting as competing endogeneous RNA. Moveover, there is increasing evidence showing that aberrant expressions of lncRNAs are implicated in various cancers. Yet, their roles in systemic lupus erythematosus (SLE), a prototypical autoimmune disease, remain unknown. To reveal the implications of LncRNAs in SLE, we used Human LncRNA Array v3.0 microarrays to measure the expression profiles of lncRNAs in T cells of patients with SLE and healthy controls. we found 869 upregulated lncRNAs and 1066 downregulated lncRNAs in SLE patients compared with controls. Coding-non-coding gene coexpression (CNC) network was constructed based on the correlation analysis between the differentially expressed lncRNA and mRNA. Downregulation of two lncRNAs, uc001ykl.1 and ENST00000448942 was established using Real-time quantitative PCR. These results showed abrrant expression profiles of lncRNAs in T cells of SLE patients and revealed their potential role in SLE.

overall_design: In this study, we determined expression profile of lncRNAs in T cells of six SLE patients (S5, S9, S11, S15, S18, S25) and three healthy controls (C1, C2, C3) using Human LncRNA Array v3.0 microarray.

first: Dong-Qing

last: Ye


title: DNA methylation profiling in GC2 cells exposed to bisphenol A

status: Public on Mar 03 2018

city: ChongqingPR China

last: Yin

address: 69 Hongguang Road Huaxi Street, Banan District

department: College of Pharmacy and Biological Engineering

institute: Chongqing University of Technology

summary:
Aberrant DNA mehylation expression has been related to diethylstilbestrol exposure, but little is known about effect of diethylstilbestrol exposure on DNA mehylation in male reproductive system.
To identify DNA mehylation varied in GC2 cells treated with DMSO and diethylstilbestrol, we performed Gene promoter methylation  using an Affymetrix Mouse Promoter 1.0R Array to analysis different DNA methylation pattern.

overall_design: Mouse spermatocyte-derived GC-2 cells were treated with 2×10-5M diethylstilbestrol for 72h, and DMSO was added to control cells. DNA mehylation expression was profiled using Affymetrix GeneChip Mouse Promoter 1.0R Array.

first: Jin-yi

last: Liu


title: Indole-3-carboxaldehyde (ICA) mitigates morbidity and mortality in a mouse model of Graft-versus-Host-Disease

city: ATLANTA

first: Daniel

last: Kalman

state: Georgia

address: 615 Michael Street Rm 155-1

department: Pathology and Laboratory Medicine

country: USA

institute: Emory University

summary: ICA-treatment following allogeneic bone marrow transplant in mice limited GvHD pathology and GVHD mortality, augmented the integrity of the intestinal mucosal barrier, and limited production of inflammatory cytokines, but did not compromise donor T cell-mediated Graft vs. Leukemia (GvL) responses. Following protracted exposure, ICA treatment also induced donor-strain-specific tolerance of engrafted T cells. We used microarray to assess gene expression changes induced by ICA in the small intestine in animals with GvHD.

overall_design: Mice undergoing allogeneic bone marrow transplant (BMT) were treated daily with ICA starting one day prior to transplant and continuing until samples were harvested for RNA isolation on day 21 post-transplant.  The transplant model used was C57Bl/6 donors and B10.BR recipients. On day -1, recipient mice received 11Gy lethal total body irradiation. On day 0, recipient mice were transplanted with 5 x 106 allogeneic T cell depleted BM (TCD-BM) cells, with or without 2 x 106 purified allogeneic T cells.  Both TCD-BM only transplanted control animals, and TCD-BM + T cell transplanted animals, which develop GvHD, received a daily oral gavage of either 150 mg/kg ICA or Vehicle (DMSO (20%), PEG400 (40%), Citric Acid (2%)). Samples (ileum) were collected on day 21post-transplant.

first: A

middle: I

last: Swimm

first: C

middle: R

last: Giver

first: Z

last: Defillip

first: S

last: Rangaraju

last: Sharma

first: R

last: Sonowal

first: D

last: Powell

first: M

last: Qayed

first: E

middle: K

last: Waller