title: Liver transcriptome analysis reveals extensive transcriptional plasticity during acclimation to low salinity in Cynoglossus semilaevis

city: QINGDAO

first: YUFENG

last: SI

state: SHANDONG

address: 5 YUSHAN ROAD

department: COLLEGE OF FISHERIES

institute: OCEAN UNIVERSITY OF CHINA

summary:
Background: Salinity is an important abiotic stress that influences the physiological and metabolic activity, reproduction, growth and development of marine fish. It has been suggested that half-smooth tongue sole (Cynoglossus semilaevis), a euryhaline fish species, use a large amount of energy to maintain osmotic pressure balance when exposed to fluctuations in salinity.  To delineate the molecular response of C. semilaevis to different levels of salinity, we performed RNA-seq analysis of the liver to identify the genes and molecular and biological processes involved in responding to salinity change.
Results: The present study yielded 330.4 million clean reads, of which 83.9% were successfully mapped to the reference genome of C. semilaevis. One hundred twenty-eight differentially expressed genes (DEGs), including 43 up-regulated genes and 85 down-regulated genes, were identified. These DEGs were highly represented in metabolic pathways, steroid biosynthesis, terpenoid backbone biosynthesis, butanoate metabolism, glycerolipid metabolism and the 2-oxocarboxylic acid metabolism pathway. In addition, genes involved in metabolism, osmoregulation and ion transport, signal transduction, immune response and stress response, cytoskeleton remodeling, and apoptosis were affected during acclimation to low salinity. Genes acat2, fdps, hmgcr, hmgcs1, mvk, pmvk, ebp, lss, dhcr7, and dhcr24 were up-regulated and abat, ddc, acy1 were down-regulated in metabolic pathways. Genes aqp10 and slc6a6 were down-regulated in osmoregulation and ion transport. Genes abat, fdps, hmgcs1, mvk, pmvk and dhcr7 were first reported to be associated with salinity adaptation in teleosts.
Conclusions: Our results revealed that metabolic pathways, especially lipid metabolism were important for salinity adaptation. The candidate genes identified from this study provide a basis for further studies to investigate the molecular mechanism of salinity adaptation and transcriptional plasticity in marine fish.

overall_design: Liver mRNA profiles of 10 month old Cynoglossus semilaevis in low salinity and high salinity were generated by RNA-seq, in triplicate, using Illumina HiSeq2500.

first: Yufeng

last: Si

first: Haishen

last: Wen

first: Yun

last: Li

first: Feng

last: He

first: Jifang

first: Siping

first: Huiwen


title: Infection of RoNi cells with Sendai Cantell virus at MOI of 1.0

status: Public on Apr 26 2018

city: Frederick

first: Catherine

middle: E

last: Arnold

state: MD

address: 1425 Porter St

department: Diagnostic Systems Division

country: USA

institute: US Army Medical Research Institute of Infectious Diseases

type: Expression profiling by high throughput sequencing

summary: Study was performed in order to determine the type and scope of interferon response of Rousettus aegyptiacus-derived fibroblasts to Sendai virus infection.  This study helps to understand the function of the expanded immune repertoire of Rosettus aegyptiacus.

overall_design: 3 timepoints, three replicates.  Mock and SeV infected samples.  18 total samples.

first: Jonathan

middle: C

last: Guito


title: Enhanced wound healing of tissue-engineered human corneas through altered phosphorylation of the CREB and AKT signal transduction pathways

status: Public on Apr 21 2018

city: Québec

first: Sylvain

last: Guérin

state: QC

address: 1050 Chemin Ste-Foy

country: Canada

institute: Université Laval

summary: The cornea is a transparent organ, highly specialized and unique that is continually subjected to abrasive forces and occasional mechanical or chemical trauma because of its anatomical localization. Upon injury, the extracellular matrix (ECM) rapidly changes to promote wound healing through integrin-dependent activation of specific signal transduction mediators whose contribution is to favor faster closure of the wound by altering the adhesive and migratory properties of the cells surrounding the damaged area. In this study, we exploited the human tissue-engineered cornea (hTECs) as a model to study the signal transduction pathways that participate to corneal wound healing. By exploiting both gene profiling and activated kinases arrays, we could demonstrate the occurrence of important alterations in the level of expression and activation of a few mediators from the PI3K/Akt and CREB pathways in response to the ECM remodeling taking place during wound healing of damaged hTECs. Pharmacological inhibition of CREB with C646 considerably accelerated wound closure compared to controls. This process was considerably accelerated further when both C646 and SC79, an Akt agonist, were added together to wounded hTECs. Therefore, our study demonstrate that proper corneal wound healing requires the activation of Akt together with the inhibition of CREB and that wound healing in vitro can be altered by the use of pharmacological inhibitors (such as C646) or agonists (such as SC79) of these mediators.

overall_design: Comparison of biopsies taken from the central (wound) and external (control) sections of human tissue-engineered corneas made with 3 population of human epithelial cells (epi44, epi52 and epi71b).

first: Camille

last: Couture

first: Pascale

last: Desjardins

first: Karine

last: Zaniolo

first: Richard

last: Bazin

first: Lucie

last: Germain

middle: L


title: The bacteriophage T4 MotB protein, a DNA-binding protein, improves phage fitness

city: Bethesda

first: Jennifer

middle: Patterson

last: West

state: Md

address: 8 Center Drive

department: Laboratory of Cell and Molecular Biology

institute: NIDDK

summary:
Purpose: To investigated the role of MotB in T4 infections

Method:  NapIV NS were grown to a cell density of ~4 x 10^8 cells/mL (OD600 ~0.4) then infected with either wild-type T4D+ or T4motBam at a MOI of 10.  RNA was isolated at 5  post-infection using method II of (Hinton 1989).  rRNA subtraction was performed with the bacterial RiboMinus Kit (Ambion) according to manufacturer instructions.  cDNA was prepared using the NEBNext strand specific kit (New England BioLabs) according to manufacturer instruction for libraries with 300-450 bp insert size with the following modifications.  Illumina adaptors sequences based on TruSeq HT Sample Prep Kits were purchase from Integrated DNA Technologies and used in the ligation step.  TruSeq-1 and TruSeq-2 primer were used for PCR enrichment of adaptor ligated DNA.  Library size was verified with a Bioanalyzer using an Agilent High Sensitivity DNA kit.  The concentration of each library was determined using the KAPA Library Quantification Kit for Illumina platforms.  Sequencing was performed by the NIDDK Genomics Core facility using a MiSeq system with the MiSeq 2 x 250 bp Sequencing Kit (Illumina).

Result:  RNA-seq data revealed that the expression of only six late genes, which decreased from 2 to 4.8-fold, were significantly affected in the T4motBam infection relative to T4 wt at 5 min after infection.  The expression of early and middle genes did not change.
Conclusion:   MotB is a bactericidal DNA-binding protein that improves the fitness of T4 infections.

overall_design: To determine the effect of MotB on T4 gene expression, RNAseq was performed for NapIV nonsuppressing cells infected with either T4wt or T4motBam at 5 minutes post-infection.

last: Patterson-West

first: Melissa

last: Arroyo-Mendoza

first: Meng-Lun

last: Hsieh

first: Danielle

last: Harrison

first: MacKenzie

last: Walker

first: Leslie

last: Knipling

first: Deborah

middle: M

last: Hinton


title: Gene expression profile of SmarT-cells compared to control 1G CAR T cells

status: Public on Apr 20 2018

city: Houston

first: Juan

middle: F

last: Vera

state: Texas

address: 1102 Bates Ave

department: Center for Cell and Gene therapy

institute: Baylor College of Medicine

summary: The objective of this experiment was to compare the transcriptional profile of T cells modified to express CAR, TBBR and 4/7 ICR (i.e. SmarT-cells) against control 1G CAR T cells expressing CD3z endodomain. RNA samples were isolated from trangenic T cells generated from three independent donors.

overall_design: T cells were sorted 5 days post transduction using a SH800S cell sorter (SONY Biotechnology) to normalize for the mean fluorescence intensity (MFI) between transgenic T cells. RNA was isolated at 24 hours after stimulating the transgenic T cells with OKT3, TGFb and IL4 using the RNeasy mini plus kit (QIAGEN) and hybridized to the nCounter PanCancer immune profiling panel (human codeset).

first: Sujita

last: Sukumaran

first: Kanchana

last: Raja


title: Gene expression profile of SmarT-cells compared to control T cells modified to express ΔCAR, ΔTGFbRII and ΔIL4R

summary: The objective of this experiment was to compare the transcriptional profile of T cells modified to express CAR, TBBR and 4/7 ICR (i.e. SmarT-cells) against control T cells expressing the delta constructs (i.e. ΔCAR, ΔTGFbRII and ΔIL4R). RNA samples were isolated from trangenic T cells generated from three independent donors.

overall_design: T cells were sorted 5 days post transduction using a SH800S cell sorter (SONY Biotechnology) to normalize for the mean fluorescence intensity (MFI) between transgenic T cells. RNA was isolated at 24 hours after stimulating the transgenic T cells with OKT3, TGFb and IL4, using the RNeasy mini plus kit (QIAGEN) and hybridized to the nCounter PanCancer immune profiling panel (human codeset).


title: Gene expression profile of CAR T cells compared to control ΔCAR T cells

summary: The objective of this experiment was to compare the transcriptional profile of CAR (CD3z endodomain) vs control ΔCAR (truncated version that lacks an endodomain) modified T cells. RNA samples were isolated from trangenic T cells generated from three independent donors.

overall_design: T cells were sorted 5 days post transduction using a SH800S cell sorter (SONY Biotechnology) to normalize for the mean fluorescence intensity (MFI) between transgenic T cells. RNA was isolated at 24 hours after stimulating the transgenic T cells with PSCA antigen using the RNeasy mini plus kit (QIAGEN) and hybridized to the nCounter PanCancer immune profiling panel (human codeset).


title: Gene expression profile of 4/7 ICR modified T cells compared to control ΔIL4R T cells

summary: The objective of this experiment was to compare the transcriptional profile of 4/7 ICR (IL4R ectodomain fused to IL7R endodomain) vs control ΔIL4R (truncated version that lacks an endodomain) modified T cells. RNA samples were isolated from trangenic T cells generated from three independent donors.

overall_design: T cells were sorted 5 days post transduction using a SH800S cell sorter (SONY Biotechnology) to normalize for the mean fluorescence intensity (MFI) between transgenic T cells. RNA was isolated at 24 hours after stimulating the transgenic T cells with OKT3 and IL4, using the RNeasy mini plus kit (QIAGEN) and hybridized to the nCounter PanCancer immune profiling panel (human codeset).


title: The PKC-β selective inhibitor, Enzastaurin, impairs memory in middle-aged rats

city: Phoenix

first: Matthew

last: Huentelman

state: AZ

address: 445 N 5th St

department: Neurogenomics

institute: TGen

summary: Enzastaurin is a Protein Kinase C-β selective inhibitor that was developed to treat cancers. Protein Kinase C-β is an important enzyme for a variety of neuronal functions; in particular, previous rodent studies have reported deficits in spatial and fear-conditioned learning and memory with lower levels of Protein Kinase C-β. Due to Enzastaurin’s mechanism of action, the present study investigated the consequences of Enzastaurin exposure on learning and memory in 12-month-old Fischer-344 male rats. Rats were treated daily with subcutaneous injections of either vehicle or Enzastaurin, and behaviorally tested using the spatial reference memory Morris Water Maze. Rats treated with Enzastaurin exhibited decreased overnight retention and poorer performance on the latter testing day, indicating a mild, but significant, memory impairment. There were no differences during the probe trial indicating that all animals were able to spatially localize the platform to the proper quadrant by the end of testing. RNA isolated from the hippocampus was analyzed using Next Generation Sequencing (Illumina). No statistically significant transcriptional differences were noted. Our findings suggest that acute Enzastaurin treatment can impair hippocampal-based learning and memory performance, with no effects on transcription in the hippocampus. We propose that care should be taken in future clinical trials that utilize Protein Kinase C-ß inhibitors, to monitor for possible cognitive effects, future research should examine if these effects are fully reversible.

overall_design: Middle-aged (12 months) virgin male Fischer-344 rats born and raised at the National Institute on Aging colony at Harlan Laboratories (Indianapolis, IN) were used. The rats were pair housed at Arizona State University, had exposure to food and water ad-lib, and were maintained on a 12-h light/dark cycle at 23°C. Rats were randomly divided into two treatment groups, receiving either vehicle (n=10) or ENZ (n=8). Rats received either daily subcutaneous injections of ENZ (25mg/kg; 0.4mL) (Selleck Chemicals, Houston, TX) suspended in polyethylene glycol (PEG, Sigma-Aldrich, St. Louis, MO) or vehicle (100% PEG) for three days concurrent to behavioral testing. Injections started the first day of behavioral testing. Maze testing commenced 30-45 minutes after injection. Animals were sacrificed immediately after the probe trial on day 3 of testing. Rats received six trials/day for three days, with a 15 min delay given between trials three and four (Markham et al. 2002). A video camera recorded each rat and a tracking system (Ethovision XT 5.1, Noldus) analyzed each rat’s path. Immediately after the probe trial on day 3 of testing, animals were anesthetized with isofluorane gas and decapitated using a guillotine, and brains were rapidly dissected and frozen. Dissected tissues were stored in pre-weighed microcentrifuge tubes at -70°C until analysis. Dissection of the CA1/CA2 region of the hippocampus (plates 39-42) was according to plate designations in Paxinos and Watson (1998). The brain was cut in the coronal plane to obtain access to the ventral CA1/CA2 region of the hippocampus. The dentate gyrus and the alveus were excluded.

first: M

middle: N

last: Willeman

first: S

last: Mennenga

first: A

last: Siniard

first: J

middle: J

last: Corneveaux

last: De Both

first: L

middle: T

last: Hewitt

first: C

middle: W

last: Tsang

last: Caselli

first: B

middle: B

last: Braden

first: H

middle: A

last: Bimonte-Nelson


title: Gene expression profile of TBBR modified T cells compared to control ΔTGFbRII T cells

summary: The objective of this experiment was to compare the transcriptional profile of TBBR (TGFbRII ectodomain fused to 41BB endodomain) vs control ΔTGFbRII (truncated version that lacks an endodomain) modified T cells. RNA samples were isolated from trangenic T cells generated from three independent donors.

overall_design: T cells were sorted 5 days post transduction using a SH800S cell sorter (SONY Biotechnology) to normalize for the mean fluorescence intensity (MFI) between transgenic T cells. RNA was isolated at 24 hours after stimulating the transgenic T cells with OKT3 and TGFb using the RNeasy mini plus kit (QIAGEN) and hybridized to the nCounter PanCancer immune profiling panel (human codeset).


title: Disruption of gul-1 decreased the culture viscosity and improved protein secretion in the filamentous fungus Neurospora crassa

status: Public on Apr 19 2018

city: Tianjin

first: liangcai

last: lin

address: 32 West 7th Avenue, Tianjin Airport Economic Area

country: China

institute: Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences

summary: In this study, we screened morphological mutants in the filamentous fungus N. crassa. Of the 90 morphological mutants screened, 14 mutants exhibited considerably higher viscosity compared with that of the wild type strain, and only 2 mutants showed low-viscosity morphologies in submerged culture. We observed that disruption of gul-1 (NCU01197), which encodes an mRNA binding protein involved in cell wall remodeling, caused pellet formation as the fermentation progressed, and resulted in the most significant decrease in viscosity of culture broth. Moreover, over-expression of gul-1 caused dramatically increased viscosity, suggesting that the gul-1 had an important function in mycelial morphology during submerged cultivation. Additionally, the deletion of gul-1 caused increased protein secretion, probably due to a defect in cell wall integrity, suggesting this as an alternative strategy of strain improvement for enzyme production. To confirm practical application, deleting gul-1 in the hyper-cellulase producing strain (∆ncw-1∆Ncap3m) significantly reduced the viscosity of culture broth.

overall_design: Conidia of △gul-1 and wild-type (WT) strains were separately inoculated into Avicel medium (1×Vogel's salt, 2% w/v crystalline cellulose, 0.75% w/v yeast extract and 0.2% v/v Tween 80) and batch cultured for 3 days. Total RNA from frozen samples was extracted and treated.

first: Liangcai

last: Lin

first: Jingen

last: Li

first: Chaoguang

last: Tian


title: Deletion of Nkx2-5 in trabecular myocardium reveals the developmental origins of pathological heterogeneity associated with ventricular non-compaction cardiomyopathy

status: Public on Apr 18 2018

city: Marseille

first: Thom

middle: Thi

last: Tran

address: 163, avenue de Luminy

department: Marseille

country: France

institute: INSERM

summary: Left ventricular non-compaction (LVNC) is a rare cardiomyopathy associated with a hypertrabeculated phenotype and a large spectrum of symptoms. The developmental origins and mechanistic basis of varying severity of this pathology are unknown. To investigate these issues, we inactivated the cardiac transcription factor Nkx2-5 in trabecular myocardium at different stages of trabecular morphogenesis.  Conditional deletion of Nkx2-5 at embryonic stages, during trabecular formation, provokes a severe hypertrabeculated phenotype associated with subendocardial fibrosis and   Purkinje fiber hypoplasia. A milder phenotype was observed after Nkx2-5 deletion at fetal stages, during trabecular compaction. A longitudinal study of cardiac function in adult Nkx2-5 conditional mutant mice demonstrates that excessive trabeculation is associated with complex ventricular conduction defects, progressively leading to strain defects, and, in 50% of mutant mice, to heart failure. Progressive impaired cardiac function correlates with conduction and strain defects independently of the degree of hypertrabeculation. Transcriptomic analysis of molecular pathways reflects myocardial remodeling with a larger number of differentially expressed genes in the severe versus mild phenotype and identifies Six1 as a marker upregulated in hypertrabeculated hearts.  Our results provide insights into the etiology of LVNC and link its pathogenicity with compromised trabecular development including compaction defects and ventricular conduction system hypoplasia.

overall_design: Fifty mice were assigned to three groups: Nkx2-5Δtrab mice received tamoxifen injections at embryonic stages (E10.5 and E11.5), Nkx2-5Δcomp mice received tamoxifen injections at fetal stages (E13.5 and E14.5), and control mice without tamoxifen injection. For transcriptomic analyse, n=4 per group at 6 month-old mutant mice.

first: Caroline

last: Choquet

first: Thi-Hong-Minh

last: Nguyen

first: Pierre

last: Sicard

first: Emeline

last: Buttigieg

first: Thi-Thom

first: Frank

last: Kober

first: Isabelle

last: Varlet

first: Mauro

last: Costa

first: Richard

middle: P

last: Harvey

first: Catherine

first: Pascal

last: Rihet

first: Sylvain

last: Richard

first: Monique

last: Bernard

first: Robert

middle: G

last: Kelly

first: Nathalie

last: Lalevée

first: Lucile

last: Miquerol


title: Transcriptomic profiling of the Cryptococcus neoformans transition to titan-like cells

city: CERDANYOLA DEL VALLES

first: JOAQUIN

last: ARINO

state: Barcelona

address: ED. IBB

department: Biochemistry & Mol. Biol.

country: Spain

institute: UNIVERSITAT AUTONOMA BARCELONA

summary: We compared the expression profile of titan-like cells with cells of regular size in C. neoformans. This was investigated at different time points of the transition: 7 and 24 h

overall_design: A total number of 10 RNA samples from Cryptococcus neoformans are analyzed. Six of them correspond to control growth conditions (three biological replicates taken after 7 hours and three after 24 h of growth). Four of them correspond to titan-like cells promoting growth conditons (two taken after 7 h and two taken after 24 h of growth).

first: Joaquin

last: Ariño

first: Zaragoza

last: Oscar


title: Expression profile of human lymphatic endothelial cells cultured on stiff (25 kPa) or soft (0.2 kPa) matrix conditions in the presence or absence of GATA2

status: Public on Apr 17 2018

city: Uppsala

first: Maike

last: Frye

address: Dag Hammarskjöldsv. 20

department: IGP

country: Sweden

institute: University Uppsala

summary:
Global transcriptome analysis showed that human lymphatic endothelial cells (LECs) grown on a soft matrix exhibit increased GATA2 expression, concomitant with a GATA2-dependent upregulation of genes involved in cell migration and lymphangiogenesis, including the key lymphangiogenic growth factor receptor VEGFR3.
Affymetrix GeneChip analysis revealed regulation of 2771 transcripts above or below a 1.4-fold change (log2 fold change >0.5 or <-0.5) threshold on soft versus stiff matrices. Moreover, 406 (27%) of the 1485 transcripts that were increased and 207 (16 %) of the 1286 transcripts that were decreased on soft matrix were regulated in a GATA2 dependent manner.

overall_design: In total 18 samples were analyzed. To identify differentially expressed genes between the ctrl stiff and ctrl soft groups, a stepwise analysis with 6 biological replicates was performed. First, exon set ID’s with an average expression lower than 5 were considered as not significantly expressed and excluded from the analysis. A threshold of 40% increase (>0.5 log2 fold change) or decrease (<-0.5 log2 fold change) of gene expression on the soft matrix (vs. stiff matrix) was considered for further analysis. For all genes with 3 or more exon probe set ID’s regulated above the defined thresholds, the average log2 fold change of the regulated exon probe ID’s was calculated and used to generate the final list of genes regulated by matrix stiffness. To determine which of the genes are regulated in a GATA2 dependent manner, a stepwise analysis with 2 biological replicates ctrl siRNA soft vs GATA2 siRNA soft groups was performed. The previously identified exon probe ID’s for genes differentially regulated between the ctrl stiff and ctrl soft groups were extracted and their average log2 fold change was calculated for the new data set. A threshold of 40% increase (>0.5 log2 fold change) or decrease (<-0.5 log2 fold change) of gene expression in the absence of the GATA2 was used to generate the final list of genes.

first: Taija

last: Mäkinen

first: Liqun

last: He

first: Hanna

last: Göransson Kultima


title: SAS cells: control siRNA (siC) vs DDX3 siRNA (siD) transfected

city: Taipei

first: Hung-Hsi

last: Chen

address: N223, IBMS, No. 128, Sec. 2, Academia Rd.

country: Taiwan

institute: Academia Sinica

summary: Transcriptional profiling of SAS cells comparing siC-transfected SAS cells with siD-transfected SAS cells. The latter decreased proliferation and migration of SAS cells. Goal was to determine the DDX3-regulated transcripts.

overall_design: Two-condition experiment, siC-transfected SAS vs. siD-transfected cells. Biological replicates: 2 siC replicates, 2 siD replicates.

first: Woan-Yuh

last: Tarn


title: Chronic subacute (incl. one subchronic study) exposure of Wistar rats to (non-)carcinogenic compound

city: Basel

first: Jonathan

last: Moggs

address: Fabrikstrasse 2

country: Switzerland

institute: Novartis

summary: The carcinogenic potential of chemicals is currently evaluated with rodent life-time bioassays, which are time consuming, and expensive with respect to cost, number of animals and amount of compound required. For insight into early mechanisms of non-genotoxoc carcinogenesis and for identification of potential early biomarkers of non-genotoxic carcinogenesis, groups of rats were treated with a range of known non-genotoxic carcinogens for a period of 14, 28, or 90 days, and liver tissue was harvested for expression profiling. Control groups were treated with appropriate vehicles.

overall_design: Male Wistar rats were treated by oral gavage with different nongenotoxic hepatocarcinogens or non-hepatocarcinogens (Pioglitazone, Rosiglitazone) and corresponding vehicle controls. Depending on the administered compound, rats were treated daily for 14 or 28 days and sacrificed one day each after the last treatment for clinical chemistry analysis, histopathological evaluation and molecular profiling of the liver using Affymetrix RaGene_2.0_ST arrays.

first: Michael

last: Römer

first: Heidrun

last: Ellinger-Ziegelbauer


title: Srf destabilizes cell identity (Microarray_Agilent Technologies)

city: Kyoto

first: Takashi

last: Ikeda

address: 53 Shogoin Kawahara-cho Sakyo-ku

country: Japan

institute: Kyoto Univ.

summary: Multicellular organisms consist of multiple cell types, whose identities are maintained appropriately at locations where they are reside. The identity of each cell type is primarily maintained by cell-type-specific gene expression programs, but mechanisms that suppress these programs are poorly defined. Here we show that serum response factor (Srf), a transcription factor that is activated by various extracellular stimuli, can repress cell-type-specific genes and promote cellular reprogramming to pluripotency. Manipulations that decrease β-actin monomer resulted in nuclear accumulation of Mkl1 and the activation of Srf, which downregulated cell-type-specific genes and altered epigenetics in enhancers and chromatin organization. Mice overexpressing Srf exhibited various pathologies including an ulcerative colitis-like symptom and a metaplasia-like phenotype in the pancreas. Our results demonstrate an unexpected function of Srf via a mechanism by which extracellular stimuli actively destabilize cell identity and suggest Srf involvement in a wide range of diseases.

overall_design: Total RNAs of NPCs (over)expressing EGFP, Mkl1, Srf, shEGFP and shActb were used to analyze effects of overexpressions of Srf and Mkl1 and knockdown of Actb on changes of gene expressions.

first: Takafusa

last: Hikichi

first: Akira

last: Watanabe

first: Keisuke

last: Okita

first: Shinji

last: Masui


title: The memory of environmental chemical exposure in C. elegans is dependent on the Jumonji demethylases jmjd-2 and jmjd-3/utx-1

status: Public on Apr 16 2018

city: Los Angeles

first: Yen-Wei

address: 650 Charles E. Young Dr. South  16-035 Center for Health Sciences

department: IDP Molecular Toxicology

institute: University of California, Los Angeles

type: Genome binding/occupancy profiling by high throughput sequencing

summary: How artificial environmental cues are biologically integrated and transgenerationally inherited is still poorly understood. Here, we investigate the mechanisms of inheritance of reproductive outcomes elicited by the model environmental chemical Bisphenol A (BPA) in C. elegans. We show that BPA exposure causes the derepression of an epigenetically silenced transgene in the germline for 5 generations, regardless of ancestral response. ChIP-seq, histone modifications quantitation, and immunofluorescence assays revealed that this effect is associated with a reduction of the repressive marks H3K9me3 and H3K27me3 in whole worms and in germline nuclei in the F3 as well as with reproductive dysfunctions including germline apoptosis and embryonic lethality. Furthermore, targeting of the Jumonji demethylases JMJD-2 and JMJD-3/UTX-1 restores H3K9me3 and H3K27me3 levels, respectively, and fully alleviates the BPA-induced transgenerational effects. Together, our results demonstrate the central role of repressive histone modifications in the inheritance of reproductive defects elicited by a common environmental chemical exposure.

overall_design: First generation C. elegans were exposed to either water, DMSO or BPA for two days, followed by collection of worm body in third generation and conduct ChIP-seq experiments.

first: Patrick

last: Allard


title: Shared and unique features distinguishing follicular T helper (TFH) and regulatory (TFR) cells from peripheral lypmh node and Peyer's Patches

city: Hanover

first: Günter

last: Bernhardt

address: Carl Neuberg Strasse 1

department: Institue of Immunology

country: Germany

institute: Hannover Medical School

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

overall_design: Refer to individual Series


title: Gender Specific Differences in Expression of Neisseria gonorrhoeae Antibiotic Resistance Genes During Human Mucosal Infection

city: Boston

first: Caroline

middle: Attardo

last: Genco

state: MA

address: 136 Harrison Ave

institute: Tufts University

summary: Samples were collected from infected male patients and RNA seq was used to determine the transcriptome of Neisseria gonorrhoeae both during infection and during growth in chemically defined media (CDM). Samples were also collected from infected female patients to determine the transcriptome differences between male and female infections.

overall_design: Examination of 6 male in vivo samples compared to the 6 isolated strains grown in vitro and 7 female in vivo samples

first: Kathleen

last: Nudel

first: Ryan

last: McClure

last: Attardo Genco


title: Species-specific transcriptomic network inference of interspecies interactions

status: Public on Apr 14 2018

city: Richland

state: Washington

address: 11829272 Battelle for the US DOE, 790 6th Street

department: Microbiology

institute: Pacific Northwest National Laboratory

summary: A cyanobacterium, Thermosynechococcus elongatus BP1, was cultured with a heterotroph, Meiothermus ruber strain A, under a variety of conditions. A gene co-expression approach was used to infer a network of T. elongatus and M. ruber genes, with a focus on those genes from different species that were co-expressed, highlighting potential points of coordination and interaction.

sample_organism:
Meiothermus ruber
Thermosynechococcus vestitus BP-1

overall_design: Both species were co-cultured together under 20 different culturing conditions, RNA-seq data was collected for each condition and combined with previously existing RNA-seq data. CLR was then used to infer a network of co-expressed genes.

first: Alex

last: Beliaev


title: Shared and unique features distinguishing follicular T helper (TFH) and regulatory (TFR) cells from peripheral lypmh node and Peyer's Patches [Agilent-048306]

summary: Transcriptome analyses were done comparing gene regulation of TFH and TFR cells isolated from Peyer’s Patches (PP) and immunized peripheral lymph nodes (pLN) revealing many regulatory patterns common to all follicular cells. However, in contrast to TFH cells, the kinetic but also the extent of regulation regarding many genes was attenuated in pLN TFR cells when compared to those of PP. Additionally, PP but not pLN TFR cells were largely unresponsive to IL2 and expressed Il4 as well as Il21. Together with fundamental differences in gene expression that were found between cells of both compartments this emphasizes specific adaptations of follicular T cell functions to their micro-milieu.

overall_design: Cells from either pLN or PP were combined from 8-15 mice, the indicated CD4 T cell subtypes sorted by flow cytometry, the purity of the sorts controlled by re-analysis and RNA extracted. The obtained RNA provided the basis for one chip hybridization and subsequent data generation. For PP two independent experiments were done, for immunized pLN (12 days post immunization) three independent were done and for immunized pLN (25 days post immunization) two independent experiment were performEd.

first: Hristo

last: Georgiev


title: Shared and unique features distinguishing follicular T helper (TFH) and regulatory (TFR) cells from peripheral lypmh node and Peyer's Patches [Agilent-084107]

overall_design: Cells from either pLN or PP were combined from 8-15 mice, the indicated CD4 T cell subtypes sorted by flow cytometry, the purity of the sorts controlled by re-analysis and RNA extracted. The obtained RNA provided the basis for one chip hybridization and subsequent data generation. For PP two independent experiments were done, for immunized pLN (12 days post immunization) three independent were done and for immunized pLN (25 days post immunization) two independent experiment were perforemd.

first: Bernhardt

last: Günter

first: Georgiev

last: Hristo


title: Nanostring Immunology V2 panel comparing expression in kidney tissue from lupus nephritis patients at diagnosis (A) and at flare (B)

city: Mexico City

first: Juan

middle: Manuel

last: Mejia-Vilet

state: Mexico City

address: 15 Vasco de Quiroga, Seccion XVI

department: Nephrology

country: Mexico

institute: Instituto Nacional de Nutrición Salvador Zubirán

summary:
The purpose of the experiment was to compare the transcriptional profile of lupus nephritis kidney tissue at a first flare and expression at a repeated lupus nephritis episode.
All samples were laser microdissected into glomerular and tubular compartments and samples were ran in different cartridges.

overall_design: Fourteen lupus nephritis patients and ten normal controls (7 for glomeruli) FFPE samples were laser microdissected and then ran into 5 cartridges for glomeruli and 5 cartridges for tubulointerstitium

first: B

middle: H

last: Rovin

first: S

middle: V

last: Parikh

first: J

last: Shapiro


first: Zeyneb

last: Kurt

state: CA

address: 2000 Terasaki Life Sciences Bldg 610 Charles E. Young Drive East

department: Integrative Biology and Physiology

institute: University of California Los Angeles

overall_design: First generation C. elegans were exposed to either water, DMSO or BPA for for 48 hours, third generation (F3) worms were used for RNA-seq experiments.Total RNA was extracted from needle-dissected gonads of F3 adult worms in 4 replicates of H2O, DMSO, and BPA-exposed P0 nematodes.


title: Srf destabilizes cell identity (Microarray_affymetrix)

first: Takashi

last: Ikeda

overall_design: Total RNAs of hepatoblasts expressing EGFP and overexpressing Srf were used to analyze effects of overexpressions of Srf on changes of gene expressions.

first: Takafusa

last: Hikichi

first: Takuya

last: Yamamoto

first: Keisuke

last: Okita


title: Transcriptional profiling of microRNAs after short-term exposure of CD1-mice to carcinogenic and non-carcinogenic chemicals

status: Public on Apr 13 2018

first: Jonathan

last: Moggs

summary: Assessing the carcinogenic potential of drug candidates is a costly procedure which requires the life-long treatment of rodents at different dose levels. A promising approach, which may to a certain degree reduce the need for animal studies in the future is toxicogenomics. The idea is to employ microarray platforms for the genome-wide expression profiling of compounds, which may facilitate the discovery of biomarker genes and provide insights in molecular mechanisms.  We profiled global microRNA expression in the liver of male and female CD-1 mice treated with genotoxic, nongenotoxic, and non-hepatocarcinogenic compounds up to two weeks.

overall_design: Diverse compounds were administrated to male and female mice CD-1 mice by oral gavage up to 14 days. In order to chose appropriate dose levels for the carcinogenic substances, the dose reported to be carcinogenic in the 2-year mouse bioassay as stated in the CPDB database (http://potency.berkeley.edu/) was used. To ensure clearly visible changes in gene expression in response to treatment with non-hepatocarcinogens, a high dose was used for these compounds. Mice received a daily administration of the compounds for 3 or 14 days. One day after the last treatment, the animals were anesthetized using isoflurane, exsanguinated from the heart and then subjected to necropsy. The median lobe and left lateral liver lobe were cut in cubes with 4-5 mm side length, placed in Wheaton Cryovials, snap frozen in liquid nitrogen and kept at -80°C until extraction.

first: Michael

last: Römer

first: Nadine

last: Kossler


title: MicroRNA expression in R6/2 and wild-type mouse brain

status: Public on Apr 11 2018

city: Kodaira

first: Hirohiko

last: Hohjoh

state: Tokyo

address: 4-1-1 Ogawahigashi

institute: National Institute of Neuroscience, NCNP

summary: We investigated miRNA expression profiles in R6/2 and wild-type mice. The results suggested that there was a difference in the expression of miRNAs between the mice.

overall_design: Small RNA samples prepared from the striatum of R6/2 and wild-type mice were examined by 3D-Gene Mouse miRNA chips.

first: Masashi

last: Fukuoka


title: Circulating microRNA of advanced colorectal cancer patients

status: Public on Apr 12 2018

city: Sydney

first: Fatemeh

last: Vafaee

state: UNSW

address: Gate 11 Botany Street, UNSW Sydney, School of BABS

department: School of Biotechnology and Biomolecular Sciences

country: Australia

institute: University of New South Wales

summary: Recent advances in high-throughput technologies have provided an unprecedented opportunity to identify molecular markers of disease processes. This plethora of complex -omics data has simultaneously complicated the problem of extracting meaningful molecular signatures and opened up new opportunities for more sophisticated integrative and holistic approaches. In this era, effective integration of data-driven and knowledge-based approaches for biomarker identification has been recognised as key to improving the identification of high-performance biomarkers, and necessary for translational applications. Here, we have evaluated the role of circulating microRNA as a means of predicting the prognosis of patients with colorectal cancer, which is the second leading cause of cancer-related death worldwide. We have developed an innovative multi-objective optimisation method which effectively integrates a data-driven approach with the knowledge obtained from the microRNA-mediated regulatory network to identify robust plasma microRNA signatures which are reliable in terms of predictive power as well as functional relevance. We have found 9 signatures of colorectal cancer prognosis comprising a total of 19 circulating microRNAs. The identified signatures predict the patients’ survival outcome and target pathways underlying colorectal cancer progression. The altered expression of the microRNAs within these signatures was confirmed in two independent public datasets of plasma and tumour samples of patients in early stage versus advanced colorectal cancer.

overall_design: Total RNA was isolated from patient plasma samples. Global profiling of miRNA was carried out using the OpenArray platform. The entire RT reaction was used for pre-amplification and the resultant cDNA combined with OpenArray real-time PCR master mix and loaded onto OpenArray miRNA panel plates and run according to the default protocol for reaction conditions.

first: Connie

last: Diakos

first: Michaela

last: Kirschner

first: Glen

last: Reid

last: Michael

first: Lisa

last: Horvath

first: Zhangkai

last: Cheng

first: Zdenka

last: Kuncic

first: Stephen

last: Clarke


title: Profiling of Pol II occupancy in quiescent neural stem cells in Drosophila melanogaster

status: Public on Apr 06 2018

city: Cambridge

first: Andrea

last: Brand

address: Tennis Court Road

department: University of Cambridge

country: United Kingdom

institute: Gurdon Institute

type: Genome binding/occupancy profiling by genome tiling array

summary: Pol II profiling of Drosophila quiescent neural stem cells using Targeted DamID (Southall et al. 2013).

overall_design: The neural stem cell-specific wor-GAL4 driver was used to express Dam-Pol II or Dam-only reference constructs, as described by Southall et al. 2013. Two biological replicates were performed.


title: Streptococcus suis 05ZY: wt vs SSU05_0930 knockout strain

city: Wuhan

first: Zhongmin

last: Xu

state: Hubei Province

address: No.1,Shizishan Street

institute: Huazhong Agricultural University

summary: Two large-scale outbreaks of streptococcal toxic shock-like syndrome (STSLS) have revealed Streptococcus suis 2 (SS2) to be a severe, evolving pathogen in humans. We investigated the mechanism by which SS2 causes STSLS. The transcriptional regulator TstS up-regulated during experimental infection. Compared with the wild type 05ZY strain, the tstS deletion mutant (∆tstS) elicited reduced cytokine secretion in macrophages. In mice, tstS deletion decreased virulence, bacterial load, and cytokine production. Moreover, TstS expression in P1/7 strain led to induction of STSLS in the infected mice. This is noteworthy because although virulent, P1/7 does not normally induce STSLS. Through microarray-based comparative transcriptomics analysis, we found that TstS regulates multiple metabolism related genes and several virulence-related genes associated with immune evasion.

overall_design: Streptococcus suis 05ZY (wt) and its SSU05_0930 knockout strain were harvested at the logarithmic phase of growth. Four independent experiments were performed at each time

first: Bo

last: Chen

first: Qiang

last: Zhang

first: Liang

last: Liu

first: Shuxian

last: Yan

first: Junping

last: Yu

first: Xiaomei

last: Sun

first: Meilin

last: Jin


title: Mutational and Transcriptional Landscape of Spontaneous Gene Duplications and Deletions in Caenorhabditis elegans

status: Public on Apr 07 2018

city: College Station

first: Vaishali

last: Katju

address: Veterinary Integrative Bioscience, MS 4458

department: Veterinary Integrative Bioscience

institute: Texas A&M University

type: Genome variation profiling by genome tiling array

summary: Gene duplication and deletion are pivotal processes shaping the structural and functional repertoire of genomes, with implications for disease, adaptation and evolution. We employed an experimental evolution framework partnered with high-throughput genomics to assess the molecular and transcriptional characteristics of novel gene copy-number variants (CNVs) in Caenorhabditis elegans populations subjected to varying intensity of selection. Here, we report a direct spontaneous genome-wide rate of gene duplication of 2.9 × 10-5 /gene/generation in C. elegans, the highest for any species to date. The increase in average transcript abundance of new duplicates arising under minimal selection is significantly greater than two-fold compared to single-copies of the same gene, suggesting that genes in segmental duplications are frequently overactive at inception. The average increase in transcriptional activity of gene duplicates is greater in MA lines that passed through single individual bottlenecks than in MA lines with larger population bottlenecks.  Furthermore, there is an inverse relationship between the ancestral transcription levels of newly originating gene duplicates and population size, with duplicate copies of highly expressed genes less likely to accumulate in larger populations. The results demonstrate that there is a fitness cost of superfluous gene expression and purifying selection against new gene duplicates. However, on average, duplications also provide a significant increase in gene expression that can facilitate adaptation to novel environmental challenges.

overall_design: Experimental evolution study of 35 mutation accumulation lines descendant from a common ancestor: Twenty lines of size N = 1, ten lines of population size N = 10, and five lines of population size N = 100 are compared to their ancestor after up to 409 generations of mutation accumulation.

first: Anke

last: Konrad

first: Stephane

last: Flibotte

first: Jon

last: Taylor

first: Robert

last: Waterston

first: Donald

last: Moerman

first: Ulfar

last: Bergthorsson


title: Identification of differentially expressed miRNAs between SW480 and SW620 spheroid cultures [miRNA]

city: Belvaux

first: Elisabeth

last: Letellier

address: 6, Avenue du Swing

department: Life Sciences Research Unit

country: Luxembourg

institute: University of Luxembourg

summary:
The colorectal cancer (CRC) cell line pair SW480/SW620 is an accepted model to study CRC progression and metastasis formation. Studying miRNA expression differences might allow to uncover molecular mechanisms that underlie metastasis initiation
Both cell lines are derived from the same patient, but at different stages of the disease. They might show differences in tumor-initiating cell (TIC) potential.

overall_design: Spheroid cultures of both cell lines were used to specifically look for differences in the TIC compartment of both cell lines. Three technical replicates were used for both conditions.


title: Genome-wide analysis of Differential Responses of Pseudomonas aeruginosa PAO1 and  PA14 cells to Interfacial Stress

city: Pittsburgh

first: Tagbo

last: Niepa

state: PA

address: 3700 OHara Street, 926 Benedum Hall

department: Chemical and Petroleum Engineering

institute: University of Pittsburgh

summary: Analysis of gene expression level of P. aeruginosa confined to Hexadecane-water interfaces. The hypothesis tested in the present study was to determine if interfacial confinements at hexadecane-water affect microbial metabolism through regulation of stress response.

sample_organism:
Pseudomonas aeruginosa PAO1
Pseudomonas aeruginosa PA14

overall_design: Total RNA obtained from isolated PAO1 and PA14 cells subjected to 1 hour of confinement at Hexadecane-water interfaces. The Total expression level was compared to the untreated control (exposed for 1 hour  to 154 mM NaCl solution only).


title: Dysregulated genes in connexin 30 deficient mice microglia [EAE]

status: Public on Apr 04 2018

city: Fukuoka

first: Ryo

last: Yamasaki

state: Fukuoka

address: 3-1-1 Maidashi, Higashi-Ku

department: Neurology

institute: Kyushu University

summary:
Objective: Connexins are known to compose gap junctions by a pair of hemichannels connected in a head to head configuration. Each hemichannel is composed by hexameric cluster of connexins. There are 20 members of connexins known as connexin family in mice, and are expressed on each cell surface in different fashion. Connexin 30 (Cx30) is mainly expressed on the surface of oligodendroglia and astrocyte in central nervous system (CNS), but little is known about the functional relevance in neuroinflammatory diseases. To elucidate the role of Cx30 in the pathogenesis of neuroinflammatory disease, we induced experimental autoimmune encephalomyelitis (EAE) on Cx30 knock-out (Cx30-KO) mice and analyzed the clinical and neuropathological findings with wild-type control.
Methods: C57BL/6J and Cx30-KO mice > 12 weeks of age were used in this study (N > 3 in each group). EAE was induced by immunization of mice with MOG35-55 peptide emulsified in CFA at a dose of 200 μg per mouse, followed by the administration of pertussis toxin (500 ng per mouse) on days 0 and 2. Mice were sacrificed and brain, spinal cord, spleen, and optic nerve were harvested for immunohistochemical analyses at the acute and chronic phases of EAE. Mice with EAE were scored as follows: 0, no disease; 1, limp tail; 2, abnormal gait and hind limb weakness (shaking); 2.5, paralysis of one hind limb; 3, paralysis of two hind limb; 3.5, ascending paralysis (able to move around); 4, tetraplegia; and 5, moribund (death). At the onset and chronic stage of EAE, mononuclear cells were isolated and analyzed by flow cytometry to check the distinct characteristics of cellular populations in inflamed CNS lesions.
Results: Initial screening of immunohistological difference revealed basic activation of microglial cells in naïve Cx30-KO mice without any behavioral phenotype. Clinical signs of EAE were ameliorated in the Cx30-KO mice than in the control group mainly during the chronic phase of disease course. Immunohistochemical analyses of the fourth lumbar segment, brain and optic nerve revealed increased number of microglia in the Cx30-KO mice. Flow cytometric analysis also confirmed the findings. In contrast, there were no significant change in astroglial or oligodendroglial phenotype.
Conclusion: Microglial activation appears to be the key factor in the Cx30-KO mice EAE with alleviation of chronic disease scores. Unexpectedly, microglia were already activated in naïve CNS, indicating protective phenotypic change of microglia in Cx30-KO mice.

overall_design: We have collected microglia from wild type and Cx30 deficient mice with EAE. Each group cotained 3 mice. Collected microglia were pooled together for the analysis.

first: Mei

last: Fang

first: Hiroo

last: Yamaguchi

first: Jun-ichi

last: Kira


title: Expression data from knockdown of UGT8 in MDA-MB231 cells

city: Hangzhou

first: Chenfang

last: Dong

address: 866 Yuhangtang Rd

institute: Zhejiang University

summary: UGT8 is the first key enzyme that catalyzes the transfer of galactose to ceramide for the synthesis of galactosylceramide.  We used microarray analysis to identify the genes that are regulated by UGT8 in MDA-MB231 cells.

overall_design: UGT8 expression was stably knocked-down in MDA-MB231 cells. RNA from this clone and parental (control) cells were purified for microarray analysis.

first: Qianhua

last: Cao


title: Identifiation of lncRNA expression profiles and ceRNA analysis in the spinal cord of morphine tolerance rats

status: Public on Apr 05 2018

city: Changsha

first: Jiali

last: Shao

state: Hunan

address: 281 Tongzipo Road, Changsha, Hunan, China

department: Department of Anesthesiology

institute: The affiliated Cancer Hospital of Xiangya School of Medicine, Central South University

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

summary: The mechanism of morphine tolerance remains unclear, and lncRNA have been promising molecule in many pathophysiological processes. However, the role of lncRNA on morphine tolerance hasn’t been explored yet. So we explore this issue, and our results indicated that  the expression profiles of lncRNAs have changed in  morphine tolerance rats as compared with normal rats, and among those, some differentially expressed lncRNAs might be new therapeutic targets for morphine tolerance.

overall_design: Microarray expression profiling of mRNAs and lncRNAs were conducted using RNA extracted from the spinal cord of five morphine tolerance rats and five normal  rats.

first: Wangyuan

last: Zou

first: Jian

last: Wang

first: Jiangju

last: Huang

first: Chang

last: Liu

first: Yundan

last: Pan

first: Qulian

last: Guo


title: Gene expression data from yeast exposure to equitoxic doses of six different pesticides

status: Public on Apr 02 2018

city: Lisboa

first: Cristina

middle: Anjinho

last: Viegas

address: Av Rovisco Pais

department: Bioengineering

country: Portugal

institute: Instituto Superior Técnico

summary:
This study focus a comparative toxicogenomic analysis of the effects of four herbicides (alachlor, ALA, S-metolachlor, S-MET, diuron, DIU, and MCPA-methyl ester, MCPA-ME), one insecticide (carbofuran, CAB), and one fungicide (pyrimethanil, PYR), in the model yeast Saccharomyces cerevisiae, to predict potential cytotoxic effects of these xenobiotics while providing mechanistic clues possibly relevant for experimentally less accessible non-target eukaryotes. The six model pesticides selected have been used worldwide in agricultural activities, at the present time or in the past, and have different modes of action on their target-organisms. Moreover, some of them are currently in Annex 1 of EC Directive 1107/2009 (repealing 91/414), that is they are in use in the EU, but having some ecotoxicological concerns (e.g. S-MET, PYR, MCPA-ME), others have their use restricted and/or are priority substances under the Water Framework Directive (e.g. ALA, DIU), and one was banned (e.g. CAB).
We used genome microarrays to obtain gene expression profiles in S. cerevisiae strain BY4741 upon 2 hours exposure to pesticide concentrations exerting a moderate inhibition of yeast growth rate. To obtain comparable gene expression profiles representing yeast response to the six different pesticides, all exposure treatments were performed with equitoxic pesticide concentrations that generated equivalent responses at the phenotypic level (namely, 20% growth-inhibitory concentrations, hereafter designated as the pesticide IC20).

platform_organism:
Schizosaccharomyces pombe
Saccharomyces cerevisiae

overall_design: Exponential standardized cell suspensions of S. cerevisiae BY4741 in minimal growth medium were incubated in the presence of equitoxic concentrations of the pesticides (i.e. the respective IC20), or in medium non-supplemented with the pesticide (control cells, CT02) during 2 h, and used for total RNA isolation and hybridization on Affymetrix GeneChip Yeast Genome 2.0 Arrays. Exposure experiments with the IC20 concentration of each pesticide versus CT02 cells were carried out together. For each exposure condition, independent biological triplicates were processed and analyzed.

first: Jörg

middle: D

last: Becker

first: Fátima

last: Gil


title: Macrophage microRNA-150 promotes pathological angiogenesis as seen in age-related macular degeneration: part I

city: Saint Louis

first: Jonathan

last: Lin

state: MO

address: 660 S. Euclid Ave, Campus Box 8096

institute: Washington University School of Medicine

summary: Macrophage aging is pathogenic in numerous age-associated diseases, including age-related macular degeneration. The purpose of this experiment was to profile microRNA expression in young and aged macrophages at baseline and in response to oxLDL and acLDL.

overall_design: We prepared 24 samples (N=4/group with 3 treatments and 2 ages). We identified 3 outliers after principal component analysis and hierarchical clustering, which we omitted from further analysis.

first: Abdoulaye

last: Sene


title: Building a schizophrenia genetic network: Transcription Factor 4 regulates genes involved in neuronal development and schizophrenia risk

city: Richmond

first: Joseph

middle: L

last: McClay

state: VA

address: 410 N 12th Street

department: Pharmacotherapy

institute: Virginia Commonwealth University

summary: The transcription factor 4 (TCF4) locus is a robust association finding with schizophrenia (SZ), but little is known about the genes regulated by the encoded transcription factor. Therefore, we conducted chromatin immunoprecipitation sequencing (ChIP-seq) of TCF4 in neural-derived (SH-SY5Y) cells to identify genome-wide TCF4 binding sites, followed by data integration with SZ association findings. We identified 11,322 TCF4 binding sites overlapping in two ChIP-seq experiments. These sites are significantly enriched for the TCF4 Ebox binding motif (>85% having ≥1 Ebox) and implicate a gene set enriched for genes down-regulated in TCF4 siRNA knockdown experiments, indicating the validity of our findings. The TCF4 gene set was also enriched among 1) Gene Ontology categories such as axon/neuronal development, 2) genes preferentially expressed in brain, in particular pyramidal neurons of the somatosensory cortex, and 3) genes down-regulated in post-mortem brain tissue from SZ patients (OR=2.8, permutation p<4x10-5). Considering genomic alignments, TCF4 binding sites significantly overlapped those for neural DNA binding proteins such as FOXP2 and the SZ-associated EP300. TCF4 binding sites were modestly enriched among SZ risk loci from the Psychiatric Genomic Consortium (OR=1.56, p=0.03). In total, 130 TCF4 binding sites occurred in 39 of the 108 regions published in 2014. Thirteen genes within the 108 loci had both a TCF4 binding site ±10kb and were differentially expressed in siRNA knockdown experiments of TCF4, suggesting direct TCF4 regulation. These findings confirm TCF4 as an important regulator of neural genes and point towards functional interactions with potential relevance for SZ.

overall_design: ChIP-seq for TCF4 (long isoform) using two different antibodies in SH-SY5Y cells, using IgG ChIP as control


title: microRNA expression profile of MRC5-CAFs transfected with control siRNA (si-Ctrl) or Dicer1 specific siRNA (si-Dicer1) for 72 hr

status: Public on Apr 10 2018

first: Zongyuan

last: Yang

state: Hubei

address: Jiefang avenue 1095, Hankou,

department: Gyneconogical cancer

institute: cancer biology center

summary:
Ovarian cancer (OC) remains the leading cause of death in patients with gynecological malignancy. An improved understanding of the genomics has led to the separation of OC into histologically and molecularly defined subgroups. Based on molecular profiling in OC patients, subtype with a reactivated tumor stroma presented the worst prognosis, emphasizing the importance of tumor microenvironment especially stromal fibroblasts in fueling OC progression. Dicer1 is well recognized as the microRNA (miR) synthesis machinery, playing a crucial role in cellular maturation and development, and was generally considered to be a tumor suppressor gene that inhibited tumor initiation and metastasis. Dicer1 expression pattern and exact biological function was seldom studied in the stromal compartment. There was a recent study demonstrating that Dicer1 was involved in mouse embryonic fibroblast (MEF) development and maturation. Therefore, we are inspired to explore the expression and function of Dicer1 in stromal fibroblasts of OC patients. In this study, mRNA and microRNA gene expression profiling were conducted for MRC5-CAFs after silencing of Dicer1. By comparing the expression data of MRC5-CAFs transfected with control siRNA (si-Ctrl) or with Dicer1 specific siRNA (si-Dicer1) for 72 hr, we identified a set of differential expressed mRNA and microRNA in MRC5-CAFs after Dicer1 knockdown. This study was the first to investigate Dicer1 influence of stromal fibroblast gene expression and the underlying regulation mechanism, which held great importance in complementing our understanding of Dicer1 in OC initiation and development, and raises potent therapeutical targets in controlling OC metastasis
We used microarrays to profile the microRNA expression of MRC5-CAFs before and after Dicer1 knockdown, in order to identify microRNA alteration exerted by Dicer1 in the context of stromal fibroblasts.

overall_design: Transcriptome profiling analyses were performed on 6 samples of MRC5-CAFs, including 3 samples of CAFs transfected with control siRNA (si-Ctrl) and 3 samples of CAFs transfected with Dicer1 specific siRNA (si-Dicer1) for 72 hr

first: Qinglei

last: Gao


title: The large non-coding RNA ANRIL, which is associated with atherosclerosis, periodontitis and several forms of cancer, regulates ADIPOR1, VAMP3 and C11ORF10 (lncRNA ANRIL exon 13)

status: Public on Apr 09 2018

city: Kiel

first: Robert

last: Haesler

address: Schittenhelmstr. 12

department: IKMB / 1st Dept. of Medicine

institute: University Clinic of Schleswig Holstein

summary:
To identify genes that are regulated from the lncRNA ANRIL (EXON 13), we designed inducible short hairpin RNA constructs and stable integrated them into HEK cells
Changes of gene expression after induction were determined at 48h and 96h by genome-wide mRNA expression analysis.

overall_design: Tetracycline stimulated shRNA silencing of ANRIL in T-Rex 293 HECK and T-Rex HeLa cells at defined time points.

first: R

last: Häsler


title: Divergence in DNA specificity among paralogous transcription factors contributes to their differential in vivo binding [RG_Runx1Runx2_v1]

status: Public on Apr 03 2018

city: Durham

first: Raluca

last: Gordan

state: NC

address: 101 Science Dr, CIEMAS 2179

department: Center for Genomic and Computational Biology

institute: Duke University

type: Genome binding/occupancy profiling by array

summary: Members of transcription factor (TF) families, i.e. paralogous TFs, are oftentimes reported to have identical DNA-binding motifs, despite the fact that they perform distinct regulatory functions in the cell. Differential genomic targeting by paralogous TFs is generally assumed to be due to interactions with protein cofactors or the chromatin environment. Contrary to previous assumptions, we find that paralogous TFs have different intrinsic preferences for DNA, not captured by current motif models, and these differences partly explain differential genomic binding and functional specificity. Our finding was possible due to a unique combination of carefully designed high-throughput assays and rigorous computation modeling, integrated into a unified framework called iMADS. We used iMADS to quantity, model, and analyze specificity differences between 11 paralogous TFs from 4 distinct human TF families. Our finding of differential specificity between closely related TFs has important implications for the interpretation of the regulatory effects of non-coding genetic variants.

overall_design: Four genomic-context protein binding microarray (gcPBM) experiments were performed for recombinant, full-length, human transcription factors Runx1 and Runx2. Briefly, the PBMs involved binding of GST-tagged transcription factors Runx1 and Runx2 to double-stranded 180K Agilent microarrays in order to determine their binding specificity for putative DNA binding sites in native genomic context. Each genomic DNA sequence represented on the array is present in 6 replicate spots. We report the gcPBM signal intensity for each spot.


title: Divergence in DNA specificity among paralogous transcription factors contributes to their differential in vivo binding [RG_E2F1-3-4_cust2_v1]

overall_design: Five genomic-context protein binding microarray (gcPBM) experiments were performed for recombinant, full-length, human transcription factors E2f1, E2f3, and E2f4. Briefly, the PBMs involved binding of GST-tagged transcription factors E2f1, E2f3, and E2f4 to double-stranded 180K Agilent microarrays in order to determine their binding specificity for putative DNA binding sites in native genomic context. Each genomic DNA sequence represented on the array is present in 6 replicate spots. We report the gcPBM signal intensity for each spot.


title: miRNA data from extracellular vesicles secreted by Nippostrongylus brasiliensis

status: Public on Apr 01 2018

city: Cairns

first: Ramon

middle: Marc

last: Eichenberger

state: QLD

address: 14 McGregor Road

department: Australian Institute of Tropical Health and Medicine

institute: James Cook University

type: Non-coding RNA profiling by high throughput sequencing

summary: miRNA-Seq analysis of the miRNA present in the extracellular vesicles secreted by the nematode Nippostrongylus brasiliensis

overall_design: Analyis of 3 biological replicates of miRNA extracted from the extracellular vesicles secreted by the nematode Nippostrongylus brasiliensis

middle: M

first: Matt

last: Field

first: Javier

last: Sotillo

first: Alex

last: Loukas


title: Expression data from Lx-2 cells in which miR214 is repressed by LNA-antimiR-214

city: Kanazawa

first: Masao

last: Honda

address: Takara-Machi 13-1

department: Gastroenterology

institute: Kanazawa University

summary:
The expression of miR-214 is up-regulated in the liver of chronic viral hepatitis. Functional relevance of miR-214 was analyzed in human stellate cell line, Lx-2.
Pro fibrotic genes were repressed, while translation related genes were up-regulated by LNA-antimiR-214

overall_design: Gene expression profiling of Lx-2 cells transfected with LNA-antimiR-214 or LAN-antimiR-control (each n = 3) was obtained.

first: Hikari

last: Okada

first: Jean

middle: S

last: Campbell

first: Junichi

last: Saito

first: Kai

last: Takegoshi

first: Yoshio

last: Sakai

first: Taro

last: Yamashita

first: Takayoshi

last: Shirasaki

first: Takayuki

last: Shiomoto

first: Riuta

last: Takabatake

first: Mikiko

last: Nakamura

first: Takuji

last: Tanaka

first: Shuichi

last: Kaneko


title: Heart tissue expression data from dTGR rats treated with or without BAY 41-8543 and Sprague Dawley control rats

status: Public on Mar 31 2018

city: Berlin

first: Ralf

last: Lesche

address: Muellerstr 178

institute: Bayer Pharma AG

summary:
We aimed to characterize the complex cardiovascular effects of NOsGC stimulation using NO-independent stimulator BAY 41-8543 in a double transgenic rat (dTGR) model of HFpEF.
We used  microarrays to detail the effect of NOsGC-stimulation on cardiac gene expression in heart failure with preserved ejection fraction.

overall_design: Rats were sacrificed at age of 7 weeks, after 4 weeks of the respective treatment and tissue biopsies of the left ventricle were obtained.

first: Nadine

last: Haase


title: Dysregulated genes in connexin 30 deficient mice microglia [naive]

first: Ryo

last: Yamasaki

overall_design: We have collected microglia from wild type and Cx30 deficient mice with naïve. Each group cotained 3 mice. Collected microglia were pooled together for the analysis.

first: Mei

last: Fang

first: Hiroo

last: Yamaguchi

first: Jun-ichi

last: Kira


title: Activation of the stringent response by loading of tRNA-RelA complexes at the ribosomal A-site

city: Copenhagen

first: Kenn

last: Gerdes

address: Ole Maaloesvej 5

country: Denmark

institute: University of Copenhagen

summary: RelA/SpoT Homologs (RSHs) are ubiquitous bacterial enzymes that synthesize and hydrolyze (p)ppGpp in response to environmental challenges. Bacteria cannot survive in hosts and produce infection without activating the (p)ppGpp-mediated stringent response, but it is not yet understood how the enzymatic activities of RSHs are controlled. Using UV crosslinking and deep sequencing, we show that Escherichia coli RelA [(p)ppGpp synthetase I] interacts with uncharged tRNA during steady-state cell growth without being activated. Amino acid starvation leads to loading of cognate tRNA·RelA complexes at vacant ribosomal A-sites. In turn, RelA is activated and synthesizes (p)ppGpp. Mutation of a single, conserved residue in RelA simultaneously prevents tRNA binding, ribosome binding, and activation of RelA, showing that all three processes are interdependent. Our results support a model in which (p)ppGpp synthesis occurs by ribosome-bound RelA interacting with the Sarcin-Ricin Loop of 23S rRNA.

overall_design: The relA locus of Escherichia coli was fused to a dual affinity His-TEV-FLAG tag. Untagged Control strain (named Control) and strains expressing relA-HTF (rela), relAΔRRM-HTF (RRM deletion, named RRM), relAΔZFDΔRRM-HTF (ZFDRRM deletion, named ZFDRRM) and relAH432E-HTF (H432E substitution, named H432E) were grown exponentially in MOPS minimal medium. Cell samples were UV-C irradiated (100sec of 1800mJ) before and after 30 min of isoleucine starvation (indicated by +val) and harvested. Cells were washed with ice-cold PBS before snap freezing in liquid nitrogen. RNA-RelA complexes were purified on M2-anti-FLAG resin and Ni-NTA resin. Sequencing libraries were prepared from purified complexes essentially per Winther et al. 2018. Amplified libraries were sequenced on an Illumina MiSeq instrument.

first: Kristoffer

last: Winther

first: Mohammad

last: Roghanian


title: Comparison of transcriptomic landscapes of different lamb muscles using RNA-Seq

status: Public on Mar 30 2018

city: Madison

first: Francisco

last: Peñagaricano

state: Wisconsin

address: 1675 Observatory Drive

department: Animal and Dairy Sciences

institute: University of Wisconsin-Madison

summary: Transcriptome deep sequencing is a powerful tool for exploring the genetic architecture of complex traits. Gene expression patterns may explain a high degree of the observed phenotypic differences in histochemical and metabolic parameters related to meat quality among different muscles. Utilizing RNA Sequencing, this study characterized the whole transcriptome of nine lamb muscles: Semimembranosus (SM), Semitendinosus (ST), Gluteobiceps (GB), Gluteus medius (GM), Rectus femoris (RF), Supraspinatus (SS), Longissimus lumborum (LL), Adductor (AD) and Psoas major (PS).

overall_design: Muscle samples were collected from four unrelated Poll Dorset cross-bred lambs. After weaning, lambs received soy crop and grain sorgum supplementation until slaughter, with final live weights ranging from 67 to 72 kg at 14 months old. Tissue samples were collected immediately after slaughter from the mid superficial belly of the following nine muscles: Semimembranosus (SM), Semitendinosus (ST), Gluteobiceps (GB), Gluteus medius (GM), Rectus femoris (RF), Supraspinatus (SS), Longissimus lumborum (LL), Adductor (AD) and Psoas major (PM). Muscle tissue samples (4 lambs x 9 muscles = 36 samples) were then subjected to RNA extraction, library generation, and sequencing.

first: Eileen

last: Armstrong

first: Andres

last: Iriarte


title: Expression data of innate or antigen-induced memory cells

city: Lyon

first: Simon

last: de Bernard

address: 30 rue Pré Gaudry

institute: AltraBio

summary:
The pool of memory-phenotype CD8 T cells is composed of antigen-induced (AI) and cytokine-induced innate (IN) cells.  Pathogen-induced AI memory cells can be distinguished from naturally-generated IN memory cells by surface expression of NKG2D. AI also differ from IN memory CD8 T cells by their capacity to migrate to the lung parenchyma upon inflammation or infection, a process dependent on their expression of ITGA1/CD49a and ITGA4/CD49d integrins.
We used microarrays to identify  gene expression signatures  that distinguish antigen-induced (AI) from cytokine-induced innate (IN) memory cells.

overall_design:
AI and IN memory CD8 T cells (CD8+CD44+) were sorted from naive or vaccinia primed C57Bl/6 mice based on the expression of  NKG2D.
Tcr Transgenic F5 CD8 T cells were transferred in naive mice before intra-nasal infection with vaccinia virus. Memory CD8 T cells F5, AI and IN were isolated from the same pool of infected mice, in the memory phase, i.e. at least 80 days post infection.
CD8 T cell samples were purified from a pool of 3 to 8 spleens. 4 to 5 biological replicates were performed for each experimental condition.

first: Jacqueline

last: Marvel

first: Morgan

last: Grau

first: Julien

last: Mafille


title: Rice (Nipponbare) transcriptome upon inoculation with Malian Xanthomonas oryzae pv. oryzae strain MAI1

city: Montpellier

first: Alvaro

middle: Luis

last: Pérez-Quintero

state: Montpellier

address: 911 Avenue Agropolis

department: RBP

institute: IRD

summary: African Xanthomonas oryzae pv. oryzae strains seem most closely related to and share several genetic features with pathovar oryzicola despite causing symptoms of bacterial leaf blight. The ability of most Xanthomonas plant pathogenic bacteria to infect their host relies on the action of a specific family of type III effectors called the TAL effectors. These microbial transcription factors are injected into the plant and manipulate the host transcriptome upon binding to the promoters of plant genes. The genes whose induction is of benefit to the pathogen are called susceptibility genes. RNA profiling experiments in rice using the Malian Xoo strain MAI1 and in silico prediction of TAL effector binding sites were carried out to identify candidate targets of TalB, revealing OsTFX1, a bZIP transcription factor previously identified as a bacterial blight S gene, and OsERF#123, which encodes a subgroup IXc AP2/ERF transcription factor.

overall_design: RNAseq libraries (paired-end strand specific TruSeq Illumina) were constructed from RNA extracted from leaf tissues of Nipponbare plants collected 24 hours post inoculation with the Xoo strain MAI1 and a water control. Libraries were sequenced in a HiSeq2000 machine (Illumina) at the INRA Unité de Recherche en Génomique Végétale (Evry, France). Library quality was verified using FastQC v0.10.1 (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/). Reads were mapped against the rice genome (Nipponbare v. MSU7) using the Tuxedo suite v2.1.1 with the following parameters: Tophat (--max-multihits 20--b2-very-fast); Cufflinks (--frag-bias-correct --library-type fr-secondstrand --multi-read-correct); Cuffdiff (--upper-quartile-norm --multi-read-correc --FDR 0.05).

last: Perez-Quintero

first: Boris

last: Szurek


title: Divergence in DNA specificity among paralogous transcription factors contributes to their differential in vivo binding [RG_MycMaxMad_v1]

first: Raluca

last: Gordan

overall_design: Genomic-context protein binding microarray (gcPBM) experiments were performed for recombinant, full-length, human transcription factors c-Myc, Max, and Mad1. Briefly, the PBMs involved binding of his-tagged transcription factor dimers to double-stranded 180K Agilent microarrays in order to determine their binding specificity for putative DNA binding sites in native genomic context. Each genomic DNA sequence represented on the array is present in 6 replicate spots. We report the gcPBM signal intensity for each spot.


title: Expression data of small and large luteal cells from bovine mature CL

city: Dummerstorf

first: Vijay simha

last: Baddela

address: Wilhelm-Stahl-Allee 2

department: Reproductive biology

institute: Leibniz institute for farm animal biology

summary: Comparative genome wide gene expression profiles of small and large luteal cells from characterized mature CL are not currently available in any species. During present study, transcriptome differences of small and large luteal cells werte comprehensively analyzed to understand the specific functional roles of small and large luteal cells in mature bovine CL.

overall_design: RNA from small luteal cells  (4n) and large luteal cells (4n) were processed for microarray analysis

first: Vanselow

last: Jens

first: Vijay


title: Transcriptional responses of K. pneumoniae, S. maltophilia, P.aeruginosa, and B. thailandensis exposed to lung surfactant

city: Burlington

first: Matthew

middle: J

last: Wargo

state: VT

address: 95 Carrigan Dr

department: Department of Microbiology and Molecular Genetics

institute: University of Vermont

summary:
The interactions between Gram-negative respiratory pathogens and the host environment at the site of infection largely unknown. Pulmonary surfactant serves as an initial point of contact for inhaled bacteria entering the lung and is thought to contain molecular cues that aid colonization and pathogenesis. To gain insight into this ecological transition, we characterized the transcriptional responses of Pseudomonas aeruginosa PA14, Burkholderia thailandensis E264, Klebsiella pneumoniae MGH 78578, and Stenotrophomonas maltophilia K279A  exposed to purified pulmonary surfactant (Survanta) through microarrays. This study provides novel insight into the interactions occurring between Gram-negative opportunistic pathogens and the host at an important infection site, and demonstrates the utility of purified lung surfactant preparations for dissecting host-lung pathogen interactions in vitro. The goal of this study was to compare the transcriptional responses of Pseudomonas aeruginosa PA14, Burkholderia thailandensis E264, Klebsiella pneumoniae MGH 78578, and Stenotrophomonas maltophilia K279A  exposed to pulmonary surfactant using a custom affymetrix chip designed for their genomes.
The goal of this study was to compare the transcriptional responses of Pseudomonas aeruginosa PA14, Burkholderia thailandensis E264, Klebsiella pneumoniae MGH 78578, and Stenotrophomonas maltophilia K279A  exposed to pulmonary surfactant using a custom affymetrix chip designed for their genomes.

sample_organism:
Burkholderia thailandensis E264
Stenotrophomonas maltophilia K279a
Pseudomonas aeruginosa PA14
Klebsiella pneumoniae MGH 78578

overall_design: Microarrays were performed with total RNA collected from two independent gene induction experiments, where each strain was cultured in MOPS minimal media in  the presence and absence of Survanta (purified pulmonary surfactant).  Total RNA collected from these experiments were then mixed together 1:1  (P. aeruginosa & B. thailandensis, or K. pneumoniae & S. maltophilia) prior to hybridization to custom Affymetrix microarray chips (PaKpSmBta521148F).  The resulting eight chips were then processed  via RMA using Affymetrix's Expression Console and Transcriptome Analysis Console.

first: Graham

last: Willsey


title: Gene expression profiling in mouse strains carrying a knockout mutation in the vomeronasal receptor gene Vmn2r1

city: Frankfurt

first: Peter

last: Mombaerts

address: Max-von-Laue-Str. 4

institute: Max Planck Research Unit for Neurogenetics

summary: The NanoString multiplex gene expression platform was applied to examine changes in V2R gene expression in total RNA samples from the vomeronasal organ of mice of gene-targeted strains ΔC1 and ΔC1-GFP, which each carry a knockout mutation in the Vmn2r1 gene. There is significant decrease in the expression level of various V2R genes that are normally coexpressed with Vmn2r1.

overall_design: We designed a custom CodeSet Pao of NanoString probes, which includes probes for 69 V2R genes, covering a half of the mouse V2R gene repertoire, and for nine non-classical class I MHC H2-Mv genes. Total RNA samples from whole vomeronasal mucosae of mice from the ΔC1 and ΔC1-GFP strains were used. Six homozygous mutant mice and six wild-type littermate from each strain were analyzed in one cartridge.

first: Sachiko

last: Akiyoshi

first: Tomohiro

last: Ishii

first: Zhaodai

last: Bai


title: Quantitative reverse transcription PCR analysis of human breast tumor cells in the PAM50 genes

city: Salt Lake City

first: Nicola

last: Camp

state: UT

address: 2000 Cir of Hope Dr

department: Huntsman Cancer Institute

institute: University of Utah

summary: Human formalin-fixed paraffin-embedded breast tumor tissue (1-4 1.5mm punches) was processed to RNA using High Pure RNA Paraffin Kit (Roche Applied Science, Indianapolis, IN) for quantitative reverse transcription polymerase chain reaction (qRT-PCR).

overall_design: qRT-PCR expression profiling of PAM50 genes in breast cancer tumors

first: Michael

last: Madsen

first: Philip

last: Bernard


title: Gene expression in the Bmi1 knockout Huh7 and Hep3B cells

status: Public on Mar 29 2018

city: Wuhan

first: Yuyuan

last: Chen

address: Hangkong Road

institute: School of Pharmacy, Tongji Medical College, Huazhong University of Science and Technology

summary: Bmi1 plays a pivotal role in hepatic carcinoma (HCC), but its targets in HCC is unknown. To screen the potential targets, we transfected HCC cell line Huh7 and Hep3B with Bmi1 shRNA lenti-virus. After confirming the Bmi1 was knocked down using western blotting, we extracted total RNA and then run the microarray detection. Gene expression profiles in Bmi1 KO cells were compared with those in Bmi1 WT cells to screen potential targets of Bmi1.

overall_design: Bmi1 gene was knocked down using shRNA lenti-virus in HCC cell lines and the potential target genes were screened.

first: Chuanrui

last: Xu

first: Bin

last: Li


title: Identification of genes involved in symbiosis of green hydra and Chlorella

city: Setouchi

first: Mayuko

last: Hamada

state: Okayama

address: 130-17, Kashino, Ushimado

institute: Okayama University

summary: Green hydra (Hydra viridissima) harbors endosymbiotic Chlorella and have established a mutual relation. To identify the host hydra genes involved in the specific symbiotic relationship, transcriptomes of intact H. viridissima colonized with symbiotic Chlorella strain A99, aposymbiotic H.viridissima and H. viridissima  artificially infected with other symbiotic Chlorella were compared by microarray analysis. The results indicated that genes involved in nutrition supply to Chlorella were upregulated in the symbiotic hydra. In addition, it was induced by supply of photosynthates from the symbiont to the host, suggesting cooperative metabolic interaction between the host and the symbiotic algae.

overall_design: For the microarray analysis, we used intact H.viridissima A99 in asexual phase, that in sexual phase, aposymbiotic H.viridissima A99 which removed symbiotic algae, and H.viridissima A99 which removed the symbiotic algae and artificially infected Chlorella variabilis NC64A known as the symbiotic Chlorella of paramecium. The experiments using three biological replicates for each sample were performed using the total RNA from whole polyps after light exposure for six hour.

first: Sebastian

last: Fraune

first: Ulrich

last: Kürn

first: Thomas

middle: C

last: Bosch


title: Divergence in DNA specificity among paralogous transcription factors contributes to their differential in vivo binding [RG_Elk1Ets1Gabpa_v1]

first: Raluca

last: Gordan

overall_design: Four genomic-context protein binding microarray (gcPBM) experiments were performed for recombinant, full-length, human transcription factors Elk1, Ets1, and Gabpa. Briefly, the PBMs involved binding of GST-tagged transcription factors Elk1, Ets1, and Gabpa to double-stranded 180K Agilent microarrays in order to determine their binding specificity for putative DNA binding sites in native genomic context. Each genomic DNA sequence represented on the array is present in 6 replicate spots. We report the gcPBM signal intensity for each spot.


title: Transcriptome profiling reveals cleft palate-related genes in Chinese sturgeon (Acipenser sinensis)

status: Public on Mar 24 2018

city: Yichang

first: Jing

last: Yang

address: Jijin Road

institute: China Three Gorges Corporation

summary: The Chinese sturgeon (Acipenser sinensis) is anadromous fish distributed in Yangtze River and East China Sea. In this study, we reported cleft-palate Chinese sturgeons in artificial population for the first time. In order to explore the genetic basis of palate malformation in A. sinensis, Illumina RNA-seq technology was used to analyze the transcriptome data of normal and cleft-palate individuals in farmed Chinese sturgeons. Raw reads were obtained and assembled into 808,612 unigenes, with an average length of 509.33 bp and an N50 of 574 bp. Sequence similarity analyses against four public databases (Nr, Uniprot, KEGG and COGs) found 158,642 unigenes that can be annotated. GABAergic synapse and TGF-β signal pathway were the most two enriched pathways with high Richfactor in the analyses of different expressed genes. In these two signal pathways, six genes (GABRA4, GS, GNS, S6K, PITX2, and BMP8) were found as cleft-palate genes in Chinese sturgeon. These findings contribute to our understanding of the genetic basis of cleft palate in sturgeon, while simultaneously adding to our knowledge about craniofacial development.

overall_design: Palate RNA profiles of 3 noncleft-palate (NCP) and 3 cleft-palate (CP) were used for deep sequecing.

first: Hejun

last: Du


title: Integrating genomic alterations in diffuse large B-cell Lymphoma identifies new relevant pathways and potential therapeutic targets

status: Public on Mar 14 2018

city: Barcelona

first: Itziar

last: Salaverria

address: Rossello 153

institute: Hospital Clínic

summary:
Genome studies of diffuse large B-cell lymphoma (DLBCL) have revealed a large number of somatic mutations and structural alterations that may contribute to their heterogeneous behavior. However, their clinical relevance and potential interest in identifying appropriate candidate drugs for personalized management are not well known.
In this study, targeted next generation sequencing and genomic copy number alterations (CNA) were analyzed in 150 cases of diffuse large B-cell lymphoma (DLBCL) to define the clinical significance of recurrent genomic alterations and to identify potential targets for personalized management. An independent cohort of 111 patients was also analyzed to confirm the clinically significant findings.
We found a differential profile of mutations, altered pathogenic pathways and CNA in germinal center B (GCB) and activated B-cell (ABC)-DLBCL with some shared alterations in both subtypes. Mutations in genes of the NOTCH pathway and tumor suppressor genes (TP53/CDKN2A), but not individual genes, conferred an unfavorable prognosis that was independent of other parameters and confirmed in the validation cohort. Tumors with NOTCH pathway mutations had a significant overexpression of downstream target genes, emphasizing the relevance of this pathway in DLBCL. We identified other new relevant genes including TMEM30A, RHOA, EBF, and TOX, among others. In silico drug discovery analysis recognized 69 (46%) cases carrying at least one genomic alteration considered a potential target of drug response according to early clinical trials (n=66) or pre-clinical assays (n=3) in DLBCL or other lymphomas. These findings orient future preclinical and clinical intervention strategies in DLBCL.

overall_design: Genomic copy number alterations (CNA) were analyzed in 119 cases of diffuse large B-cell lymphoma (DLBCL) were analyzed by Cytoscan

first: K

last: Karube

first: A

last: Enjuanes

first: I

last: Dlouhy

last: Lopez-Guillermo

first: E

last: Campo


title: Comparison of expression data from DLD-1 subpopulations III

city: Hamburg

last: Streichert

address: Martinistr. 52, Campus Forschung N27, 2. OG

department: Institute For Clinical Chemistry / Central Laboratories

institute: University Medical Center Hamburg-Eppendorf

type:
SNP genotyping by SNP array
Genome variation profiling by SNP array

summary:
The function of cell-cell contact for radiochemosensitivity is unclear. Here, we investigate the role of the E-cadherin/catenin complex proteins under more physiological three-dimensional (3D) cell culture conditions in a panel of CRC cell lines.
To gain further insights, differential gene expression was investigated in DLD-1 subpopulations showing distinct morphology and invasion in 3D collagen type I.

overall_design: RNA extracted from DLD-1 subpopulations grown in 3D collagen type I (n=3 per subpopulation) was used for Affymetrix microarrays.

first: Nils

last: Cordes


title: CIRCULATING MICRORNAs PREDICT SURVIVAL OF PATIENTS WITH TUMORS OF GLIAL ORIGIN

city: Columbus

first: Alessandra

last: Drusco

address: 460 W. 12th Ave.  Biological Research Tower 1094

department: Department of Cancer Biology and Genetics

institute: The Ohio State University

summary: We analyzed serum extracellular vescicles (SEV) of 28 patients with glioma tumors and 8 normal samples by Nanostring, and validated a microRNA profile that can differentiate between and among some classes of CNS tumors.

overall_design: A total of 28 glial tumor SEV samples were collected from UCFS, and 8 SEV normal control samples from The Ohio State University, Columbus, OH.

first: C

last: Croce


title: Comprehensive expression profiling reveals the potential role of lncRNAs and circRNAs in systemic lupus erythematosus

status: Public on Mar 08 2018

city: Hefei

first: Lian-Ju

last: Li

state: Anhui

address: 81 Meishan Road

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

institute: Anhui Medical University

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

overall_design: Refer to individual Series


title: Gene expression in human bone marrow Mesenchymal Stem cell line (hMSC-TERTs) during proliferation, quiescence (G0-arrest) and re-activation.

status: Public on Mar 02 2018

city: Bangalore

first: Genotypic

last: technology

state: Karnataka

address: 259, Apoorva 4th cross,80 feet Road,RMV 2ND STAGE

country: India

institute: Genotypic Technology

summary: A microarray study using human Mesenchymal Stem cell line (hMSC-TERTs), was designed in order to detect the differences in global gene expression during proliferation, quiescence (G0) and reactivation post quiescence for 1 hr (R1), 3 hrs (R3) and 24 hrs (R24). Proliferating and re-activated cells were harvested at 70-75% confluency. To induce quiescence, MSCs were cultured in suspension in methyl cellulose in presence of full serum complement. The raw data from gene arrays were normalized and the five samples were compared to each other in order to detect differences in gene expression between the samples.

overall_design: Asynchronously proliferating hMSCs-TERTs was cultured in two different culture conditions, in adherent condition (proliferating) and in non-adherent suspension condition (quiescent). Gene expression profiling of proliferating, quiescent and re-activated hMSCs was performed using agilent arrays. All the samples were taken in triplicates. Thus the numeber of samples for microarray analysis was 15.

first: M

last: Rumman

last: Majumder

first: L

last: Harkness

first: B

last: Venugopal

middle: R

last: Vinay

last: Pillai

last: Kassem

first: J

last: Dhawan


title: Efficacy of the highly selective focal adhesion kinase inhibitor BI 853520 in adenocarcinoma xenograft models is linked to a mesenchymal tumor phenotype [miRNA]

status: Public on Feb 27 2018

city: Vienna

first: Daniel

last: Gerlach

address: Dr.-Boehringer-Gasse 5-11

department: Global Computational Biology and Digital Sciences

country: Austria

institute: Boehringer Ingelheim RCV GmbH & Co KG

summary:
microRNA expression profiling of untreated CDX samples and correlation with sensitivity data derived from treatments with BI 853520.

Focal adhesion kinase (FAK), a non-receptor tyrosine kinase, has attracted interest as a target for pharmacological intervention in malignant diseases. Here, we describe BI 853520, a novel ATP-competitive inhibitor distinguished by high potency and selectivity. In vitro, the compound inhibits FAK autophosphorylation in PC-3 prostate carcinoma cells with an IC50 of 1 nmol/L and blocks anchorage-independent proliferation of PC-3 cells with an EC50 of 3 nmol/L, whereas cells grown in conventional surface culture are 1000-fold less sensitive. In mice, the compound shows long half-life, high volume of distribution and high oral bioavailability; oral dosing of immunodeficient mice bearing subcutaneous PC-3 prostate adenocarcinoma xenografts resulted in rapid, long-lasting repression of FAK autophosphorylation in tumor tissue. Daily oral administration of BI 853520 to nude mice at doses of 50 mg/kg was well tolerated for prolonged periods of time. In a diverse panel of 16 subcutaneous adenocarcinoma xenograft models in nude mice, drug treatment resulted in a broad spectrum of outcomes, ranging from group median tumor growth inhibition values >100% and tumor regression in subsets of animals to complete lack of sensitivity. Biomarker analysis indicated that high sensitivity is linked to a mesenchymal tumor phenotype, initially defined by loss of E-cadherin expression and subsequently substantiated by gene set enrichment analysis. Further, we obtained microRNA expression profiles for 13 models and observed that hsa-miR-200c-3p expression is strongly correlated with efficacy (R2 = 0.889). BI 853520 is undergoing evaluation in early clinical trials.

overall_design: In total 37 cell line derived xenografts were analyzed from 15 individual cell lines with either 2 or 3 biological replicates.

first: Norbert

last: Schweifer

first: Christian

last: Haslinger


title: YAP and RUNX co-regulated genes in MCF10A

status: Public on Feb 26 2018

city: Singapore

first: Tuan Zea

last: Tan

address: 14 Medical Drive, #11-01, Singapore

department: Cancer Science Institute Singapore

country: Singapore

institute: National University of Singapore

summary: An antagonistic interplay between YAP and RUNX where RUNX proteins abrogate YAP-mediated transcription of EMT and Stemness associated genes in mammary epithelial cells in an interaction dependent manner.

overall_design: YAP and RUNX1 or RUNX3 were stably expressed together or alone in MCF10A cell line. Genes that are co-regulated by both were studied in the context of breast cancer.

first: Madhura

last: Kulkarni

first: Henry

last: Yang

first: Yoshiaki

last: Ito


title: Gene expression data of microRNA from liver of pig breed German Landrace

status: Public on Feb 14 2018

first: Siriluck

last: Ponsuksili

address: Wilhelm-stahl-allee 2

institute: FBN

summary: Gene expression data of micro RNA of pig, in the first part of this study, they were analysed for correlation of transcripts levels with body weight and meat quality grade traits

overall_design: miRNAs of liver at adult stage were hybridized to Affymetrix miRNA-3 Array.

first: Klaus

last: Wimmers


title: The E. coli global regulator DksA attenuates transcription during T4 infection

status: Public on Mar 15 2018

city: Bethesda

first: Jennifer

middle: Patterson

last: West

state: Md

address: 8 Center Drive

department: Laboratory of Cell and Molecular Biology

country: USA

institute: NIDDK

summary:
Purpose: We investigated how deletion of DksA or ppGpp, two E. coli global transcription regulators, affects T4 infection.

Method: B606, B606 DdksA, and B606 ppGpp0 were grown at 37C to early/mid log phase (OD600 ~ 0.4) then infected with moi of 10 of either wt T4 or T4motAam and total RNA was isolated. 2.5 µg total RNA from each sample was treated with a Ribo-Zero rRNA Removal Kit (Gram-Negative Bacteria; Illumina San Diego, CA) to deplete rRNA. The enriched mRNA was fragmented, reverse-transcribed, ligated with dual indexes, and amplified using a TruSeq Stranded mRNA Library Prep Kit (Illumina, San Diego, CA).
    The resulting RNA-Seq libraries were pooled at equal concentrations and sequenced using on an Illumina MiSeq to generate 2 x 100 bp paired-end reads.   Read data in fastq format was demultiplexed and aligned to E. coli B str. DE3 (NC_012971.2) reference genome using STAR v2.5.2, retaining unmapped reads (Dobin, Davis et al. 2013).  Unmapped reads were then mapped in a second step to T4 reference (NC_000866.4).  In both cases, default alignment behavior was altered with the following arguments: --outFilterScoreMinOverLread 0 --outFilterMatchNmin 30 --outFilterMatchNminOverLread 0 --clip3pAdapterSeq AGATCGGAAGAGCGTCGTGTA --alignIntronMax 1.
RNA gene counts in both reference genomes were then quantified using the same NCBI gene definitions utilized in mapping index construction using the subread featureCounts v1.4.6-p3 package (Liao, Smyth et al. 2014).  Differential expression between samples fchanges in gene expression was predetermined to entail a fold change of more than or equal to 2 and P value less than or equal to 0.05. at 5 minutes post-infection.

Result: Both ppGpp0 and delta(dksA) increase wt T4 plaque size.  However, ppGpp0 does not significantly alter burst size/latent period and only modestly affects T4 transcript abundance, while delta(dskA) increases burst size (2-fold), does not affect latent period, and increases the abundance of several Pe RNAs at 5 min post-transcription. delta(dskA) also increases T4motAam plaque size with a much shorter latent period compared to T4motAam/wt infection, and the levels of specific middle RNAs increase due to more transcription from Pe's that extend into these middle genes.

Conclusion:  We conclude that DksA attenuates T4 early gene expression. Consequently, delta(dksA) results in a more productive wt infection and ameliorates the poor expression of middle genes in a T4motAam infection.

overall_design: Three strains of E. coli were used to determine the role of dksA and ppGpp in bacteriophage T4 infections: wt, delta(dksA), and ppGpp0. To determine the effect of MotA on global transcription, 2 strains of bacteriophage T4 were used: wt and motAam

last: Patterson-West

first: Tamara

last: James

first: Llorenç

last: Fernández-Coll

first: James

last: Iben

first: Kyung

last: Moon

first: Leslie

last: Knipling

first: Michael

last: Cashel

first: Deborah

last: Hinton


title: The gene expression profiles of hypoxia-resistant (HR) human multiple myeloma cell lines

status: Public on Feb 06 2018

city: Shinjyuku

first: Tomohiro

last: Umezu

state: Tokyo

address: 6-1-1 Shinjyuku

department: Department of Molecular Pathology

institute: Tokyo Medical University

summary: In multiple myeloma (MM), abnormal plasma cells interact with bone marrow (BM) stromal cells and vascular cells among others. A part of the BM milieu is considered highly hypoxic, and myeloma cells in situ may be influenced by circumstances other than normoxia in vitro. Hence, we attempted to confirm the role of hypoxic MM-derived exosomes in the BM milieu. We established a novel hypoxia-resistant cell line, RPMI8226-HR derived from RPMI8226 cells, KMS-11-HR derived from KMS-11, U266-HR derived from U266, and IM-9-HR derived from IM-9 cultured for >4 months under hypoxia (1% O2), as a model of MM cells localizing in an extensively hypoxic milieu. We used RPMI8226 cells and RPMI8226-HR cells, as donor cells, and HUVECs as recipient cells. Exosomes derived from RPMI8226 cells (normoxia or hypoxia) and exosomes derived from RPMI8226-HR cells (hypoxia-resistant, HR sub-line) were used for validation of angiogeneic activity, such as tube formation assay. Exosomes derived from the RPMI8226-HR cells significantly increased tube formation of HUVECs than those from RPMI8226 cells.

overall_design: Parental cells (RPMI8226, KMS-11, U266, IM-9) were cultured for 24 hours under normoxic conditions (20% O2). Hypoxia-resistant (HR) cells (RPMI8226-HR, KMS-11-HR, U266-HR, IM-9-HR) were cultured for 24 hours under hypoxic conditions (1% O2). Total RNA from each sample (Normal-BMSCs, MM-BMSCs and MGUS-BMSCs) was processed for hybridization onto GeneChip® human Gene 2.0 ST Array (Affymetrix) according to the manufacturer's protocol and scanned.