title: BHLHE40 modulates gene transcription in breast cancer cells exposed to hypoxia and low glucose

status: Public on Oct 30 2018

city: Memphis

first: Meiyun

last: Fan

address: 19 S. Manassas Street

country: USA

institute: University of Tennessee

summary: Knockdown of BHLHE40 expression significantly reduced primary tumor growth and spontaneous lung metastasis in an orthotopic xenograft model of human breast cancer. Gene expression analysis implicated a role of BHLHE40 in hypoxia-induced exosomic secretion of Heparin Binding Epidermal Growth Factor HBEGF, which promotes cell survival and invasion. BHLHE40 induces HBEGF transcription by blocking DNA binding of HDAC1 and HDAC2.

overall_design: A lung metastatic subline of MDA-MB-231, designated as LM, was stably transfected with MISSION shRNA (TRCN0000232187) to knockdown BHLHE40 or control vector. The cells were cultured in medium containing low glucose (1 mg/ml) under hypoxia (1% O2) for 6 or 48 hr.  Total RNA was purified by using the RNeasy kits (Qiagen). A total of 12 samples were subjected to microarray analysis, with two biological repeats for each experiment condition.

first: Aarti

last: Sethuraman

first: Martin

last: Brown

first: Tiffany

middle: N

last: Seagroves

first: Zhao-Hui

last: Wu

first: Lawrence

middle: M

last: Pfeffer


title: RNAseq of regenerating yap mutant zebrafish hearts

city: Wauwatosa

first: Michael

middle: Andrew

last: Flinn

state: WI

address: 8701 W Watertown Plank Rd

department: Physiology

institute: Medical College of Wisconsin

type: Expression profiling by high throughput sequencing

summary: A Yap knockout zebrafish line was used to observe how loss of Yap affects cardiac regeneration.

overall_design: Cryoinjury or sham surgeries were performed on 6-12 month old zebrafish ventricles. At 7 days post injury, whole hearts were collected and RNAseq was performed.

middle: A

first: Caitlin

middle: C

last: O’Meara

first: Brian

last: Link


title: Characterization of quiescent adult liver stem cells and downstream lineages [Agilent Array]

status: Public on Oct 29 2018

city: Shanghai

first: Kunshan

last: Zhang

address: 389 Xincun Road

department: Stem cell Translational Research center

country: China

institute: Tongji Hospital, Tongji University

summary: Understanding the liver stem cells (LSCs) holds great promise for new insights into liver diseases and liver regeneration. By employing single-cell RNA-seq technology with weighted gene co-expression network analyses (WGCNA), we examined transcriptome features of distinct Krt19 lineage-tracing cell types isolated from Krt19CreERT; Rosa26R-GFP reporter mice, and identified gene expression signatures of quiescent and active adult LSCs, as well as their downstream lineage-restricted progenitors and terminally differentiation hepatocytes and cholangiocytes. Importantly, we discovered a novel cell surface LSC marker, CD63, as well as CD56, which distinguished active and quiescent LSCs. Furthermore, we confirmed that CD63+CD56- quiescent LSCs resided in Canals of Hering and peribiliary glands and that these cells could be activated by a combined action of VEGF and bFGF, and subsequently underwent terminal differentiation. These findings define an authentic adult liver stem cells compartment and highlight its contribution to liver homeostasis during pathophysiologic processes.

overall_design: Examination of 6 cell-lines from adult mouse liver.

first: Yiping

last: Hu

first: Siguang

last: Li

first: Fei

last: Chen

first: Minjun

last: Wang


title: Early regulatory B cell induction and Th/Tr17 responses relates to success of long-term grass-pollen AIT

city: Munich

first: Ulrich

last: Zissler

address: Biedersteiner Str. 29

department: Center of Allergy & Environment (ZAUM)

country: Germany

institute: Technical University of Munich & Helmholtz Center Munich

summary:
The up-dosing phase is marked by increased IL-10+B-cells with allergen-specific PD-L1 up-regulation, while effector Th1/Th17 cells and CCR6+IL-17+FoxP3+T-cells decrease. The conversion phase exhibits Th17 recovery in the absence of Th2cells. The tolerance-mounting phase after three years of treatment is characterized by induction of Tregs while Th2 and phleum-specific IL-17A responses decrease. Notably, high ratios of circulating Breg/Th17 following initial AIT correlate significantly with clinical improvement after three years.
Our data imply differential shifts in the hierarchy of tolerance in three distinct phases of AIT characterized by conversion of regulatory against pro-inflammatory mechanisms, of which the Breg/Th17 ratio after initial treatment emerges as potential early prediction of AIT efficacy.

overall_design: Nasal brushings were performed in healthy controls in and out of grass pollen season, untreated patients suffering from allergic rhinitis (only in grass pollen season), and allergic rhinitis patients who received allergen-specific immunotherapy (AIT). From treated patients, samples were take before treatment (baseline - T0), 6 hours after last topdose (T4), and after 3 years of completed AIT (T9).

first: U

first: C

last: Jakwerth

first: F

last: Guerth

first: L

last: Pechtold

first: J

last: Aguilar-Pimentel

first: K

last: Dietz

last: Suttner

first: G

last: Piontek

first: B

last: Haller

first: Z

last: Hajdu

first: M

last: Schiemann

middle: B

last: Schmidt-Weber

first: A

last: Chaker


title: Genomics and response to long-term oxygen therapy in chronic obstructive pulmonary disease

city: Boston

first: Minseok

last: Seo

state: MA

address: 181 longwood ave.

department: Channing Division of Network Medicine

institute: Brigham & Women's Hospital and Harvard Medical School

summary: Longitudinal transcriptome analysis for invsetigation of the effect of long-term oxygen therapy in COPD

overall_design: A total of 51 microarray samples were available, which consisted of 37 COPD patients treated with oxygen or control, either at screening or 12 month follow-up, or at both time points.

first: Craig

middle: P

last: Hersh


title: Array CGH data of A. oryzae strains bearing translocated chromosomal duplication and triplication

status: Public on Oct 23 2018

city: Noda City

first: Tadashi

last: Takahashi

address: 399 Noda

country: Japan

institute: Noda Institute for Scientific Research

summary: In this study, we achieved translocated chromosomal duplication and triplication of a 1.4-Mb targeted chromosomal region by directly introducing I-SceI meganuclease into A. oryzae protoplast cells. Strains with duplication and triplication of chromosome 2 showed substantial increases in the activity of protease and amylase. Gene dosage effects were enhanced by combining the structural gene and its regulatory gene, indicating that segmental duplications of chromosomes play important phenotypic roles in koji mold strains.

overall_design: A. oryzae strain bearing a 1.4Mb translocated chromosomal duplication, A. oryzae strain bearing a 1.4Mb translocated chromosomal triplication, and A. oryzae RIB40 (wild type strain), were cultivated in Polypeptone-dextrin medium. After 3 days cultivation, genomic DNAs from the samples were extracted, and array CGH analysis was carried out to confirm the chromosomal duplications in the strains.

first: Masahiro

last: Ogawa

first: Atsushi

last: Sato

first: Yasuji

last: Koyama


title: Microarray analysis of NAD-treated and water-treated Pineapple sweet orange

city: Durham

first: Jian-Liang

last: Li

state: NC

address: 111 TW Alexander Dr

institute: NIEHS

summary: The goal of the microarray experiment was to identify genes that were differentially expressed in NAD-treated and water-treated sweet orange leaf tissues.  Results indicated that, compared with the water treatment, the NAD tretament triggered profound transcriptome changes in the citrus leaves, with about 1,200 genes being up-regulated or down-regulated by twofold or more.

overall_design: Three biological replicates with leaf discs from 8-12 plants were collected at 4 hours after NAD and water treatments.  After extraction, RNA concentration was determined on a NanoDrop Spectrophotometer (Thermofisher Scientific, Waltham, MA) and sample quality was assessed using the 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).  Equal amount of RNA from the 3 biological replicates were used for microarray analysis.

first: Fernando

last: Alferez

first: Kayla

last: Gerberich

first: Jian

middle: L

first: Yanping

last: Zhang

first: James

middle: H

last: Graham

first: Zhonglin

last: Mou


title: Characterizing Acinetobacter baumannii desiccation tolerance.

status: Public on Oct 27 2018

city: Austin

first: Xun

last: Wang

state: Texas

address: 2506 Speedway, NMS 3.236

department: Department of Molecular Biosciences

institute: University of Texas at Austin

summary: Desiccation tolerance has been implicated as an important characteristic that potentiates the spread of the bacterial pathogen Acinetobacter baumannii through hospitals on dry surfaces. Despite the potential importance of this stress response, scarce information is available describing the underlying mechanisms of A. baumannii desiccation tolerance. Here we characterize the factors influencing desiccation survival of A. baumannii. At the macroscale level, we find that desiccation tolerance is influenced by cell density, growth phase, and desiccation medium. Our transcriptome analysis indicates that desiccation represents a unique state for A. baumannii compared to commonly studied growth conditions and strongly influences pathways responsible for proteostasis. Remarkably, we find that an increase in total cellular protein aggregates, which is often considered deleterious, correlates positively with the ability of A. baumannii to survive desiccation. We show that artificially inducing protein aggregate formation increases desiccation survival, and more importantly, that proteins incorporated into cellular aggregates can retain activity. Our results suggest that protein aggregates may promote desiccation tolerance in A. baumannii through preserving and protecting proteins from damage during desiccation until rehydration occurs.

overall_design: mRNA profiles of desiccated A. baumannii ATCC17978 were analysed in biological duplicate. A. baumannii grown in liquid LB medium to log phase or stationary phase, and bacteria grown on LB agar plates were also analyzed and serve as controls.

first: Bryan

last: Davies


title: Comparison of the transcriptomes of hTERT-immortalized and wild type marmoset fibroblasts by next-generation RNA sequencing.

city: Goettingen

first: Gabriela

last: Salinas

state: Lower-Saxony

address: Kreuzbergring 57

department: Department of Pathology

institute: Universitaetsmedizin Goettingen

summary: Neuborn marmoset fibroblasts were immortalized by piggyBac transposition of hTERT expression cassette. The gene expression of the resulting one polyclonal and two monoclonal immortalized cell lines were then compared with the wild type cells used for their derivation.

overall_design: The mRNA profiles of one wild type, one polyclonal, and two monoclonal immortalized cell lines were generated by deep sequencing in triplicate, using Illumina.

first: Rüdiger

last: Behr

first: Tobias

last: Kahland


title: Coding and Non-coding gene expression signatures of granulosa cells from Polycystic Ovary Syndrome Patients

first: Jun

last: Zhao

address: 845 Lingshan Road

department: Renji Hospital, School of medicine

institute: Shanghai Jiao Tong university

summary: Polycystic ovary syndrome (PCOS), one of the most common endocrinal diseases among reproductive-aged women,is characterized by hyperandrogenemia, chronic oligo/anovulation and polycystic ovarian morphology. In this research, we presented microarrays to identify the differential expressed protein-coding genes and lncRNAs expression profile in the luteinized granulosa cells obtained from PCOS and healthy control patients.

overall_design: The human luteinized granulosa cells (hLGCs) were retrieved from the follicular fluid of normal and PCOS woman undergoing IVF or ICSI. RNA was extracted and hybridized to microarray screening of non-coding RNAs and mRNAs.

first: Y

middle: Z

last: Du

first: J

middle: Y

last: Xu

first: X

middle: J

last: Liu

last: Geng


title: SNV microarray data from "Genome-edited cardiac models reveal combinatorial genetic interactions in human cardiomyopathy" by Deacon et al

city: La Jolla

first: Neil

last: Chi

state: CA

address: 9500 Gilman Drive

department: Medicine

institute: University of California, San Diego

summary:
SNV microarray data from eleven family members in a family with high rates of cardiomyopathy
Source name refers to patient position in pedigree from  "Genome-edited cardiac models reveal combinatorial genetic interactions in human cardiomyopathy" by Deacon et al

overall_design: SNV microarray data from saliva samples from family members in this cohort


title: Transcriptional profiles of human CD14+ monocytes conditioned with melanoma exosomes [gene expression]

status: Public on Oct 26 2018

city: Milan

first: Matteo

last: Dugo

address: via Olgettina 60

department: Department of Medical Oncology

country: Italy

institute: IRCCS Ospedale San Raffaele

summary: We analyzed gene and microRNA expression profiles of purified CD14 monocytes isolated from blood of 5 healthy donors after 24 h of in vitro co-culture with exosomes exosomes isolated from the INT12 melanoma cell line generated in our laboratory from a human melanoma specimen. Differentially expressed genes and miRNAs were identified between treated and untreated monocytes.

overall_design: Gene and microRNA expression profiles of CD14+ monocytes co-cultered with melanoma exosomes (five biological replicates) were compared to those of untreated CD14+ monocytes (five biological replicates).

first: Licia

last: Rivoltini

first: Monica

last: Rodolfo

first: Loris

last: De Cecco


title: Gene expression in diet-induced obesity resistent  (DIO non-responder) and diet-induced obesity susceptible (DIO responder) C57BL/6J mouse strain

city: Nuthetal

first: Heike

last: Vogel

state: BRB

address: Arthur-Scheunert-Allee 114-116

department: Department of Experimental Diabetology

institute: German Institute of Human Nutrition Potsdam-Rehbruecke

summary:
Inbred C57BL/6J mice differ in their susceptibility to diet-induced obesity. Comparison of the liver transcriptomes leads to genes that are involved in the development as well as the maintenance of fatty liver during the onset of obesity upon high fat diet feeding.
Genes being upregulated in DIO responder can be seen as drivers of fatty liver development, while genes upregulated in DIO non-responder are most likely involved in the protection against fatty liver diseases.

overall_design: Male C57BL/6J mice were kept on a high-fat diet (60%kcal from fat) directly after weaning. At the age of 6  weeks livers were collected for transcriptome analysis.

first: Robert

last: Schwenk

first: Anne

last: Kammel

first: Annette

last: Schürmann


title: Acute Mechanical Unloading Prior to Reperfusion is Cardioprotective and Limits the Development of Heart Failure After Myocardial Infarction

status: Public on Oct 25 2018

first: Gavin

middle: R.

last: Schnitzler

address: 800 Washington St. Box 80

department: Molecular Cardiology Research Institute

institute: Tufts Medical Center

summary:
Ischemic heart failure after acute myocardial infarction (AMI) is a major cause of morbidity and mortality worldwide. We recently reported that activation of a trans-valvular axial-flow pump in the LV and delaying myocardial reperfusion, known as Primary Unloading, limits infarct size by reducing LV wall stress and increasing expression of the cardioprotective cytokine, stromal derived factor 1 alpha (SDF1a). The mechanisms underlying the cardioprotective benefit and sustained effect of Primary Unloading remain poorly understood. We now tested the importance of delayed reperfusion, the functional significance of SDF1a, and the late-term impact on myocardial function and scar size associated with Primary Unloading.
Adult male swine were subjected to Primary Reperfusion or Primary Unloading after 90 minutes of left anterior descending artery occlusion. Compared to Primary Reperfusion, 30 minutes of Primary Unloading was necessary and sufficient prior to reperfusion to limit infarct size. Primary Unloading was associated with a global shift in gene expression within the infarct zone favoring cardioprotection. Compared to Primary Reperfusion, Primary Unloading for 30 minutes preserved SDF1a protein levels without changing SDF1a mRNA levels within the infarct zone and further promoted a shift towards anti-apoptotic signaling within the infarct zone. Primary Unloading reduced activity levels of proteases known to degrade SDF1a and blocking the SDF1a receptor, CXCR4, attenuated the cardioprotective effect of Primary Unloading. Primary Unloading further reduced LV scar size, improved cardiac function, limited expression of markers associated with heart failure and maladaptive remodeling within the non-infarct zone 28 days after acute myocardial infarction.
In conclusion, we introduce that Primary Unloading for 30 minutes before, not after reperfusion limits infarct size, increases SDF1a levels within the infarct zone, and results in a durable reduction in LV scar size, improved cardiac function, and limits markers of heart failure and maladaptive remodeling 28 days after AMI.

overall_design: To explore the optimal duration of mechanical unloading prior to reperfusion, adult, male Yorkshire swine were divided into 4 groups (n=4/group; Figure 1A). All groups underwent 90 minutes of LAD occlusion. In Group 1, LAD occlusion followed by 120 minutes of reperfusion served as the control group (Primary Reperfusion). In Groups 2 and 3, LAD occlusion was followed by insertion and activation of a TV-Pump (Impella CP; Abiomed Inc; Danvers, MA) via a 14Fr sheath in the left femoral artery and maintained at maximal support (44,000 rotations per minute). This was followed by an additional 15 (Group 2) or 30 (Group 3; Primary Unloading) minutes of occlusion respectively, then 120 minutes of reperfusion. In Group 4, LAD occlusion was followed by reperfusion, and after 30 minutes of reperfusion, a TVP was inserted and activated for the remaining 90 minutes of reperfusion (Post Reperfusion Unloading). At the end of each study, animals were euthanized for determination of myocardial infarct size. Three sham-operated animals were intubated, anesthetized, and mechanically ventilated without myocardial infarction or mechanical unloading. LV tissue samples obtained from sham controls were used for tissue analysis. RNA was collected from the center of the infarct zone of group 1 (Primary Reperfusion), group 3 (Primary Unloading) animals, or from the same region of the left ventricle in sham operated animals. RNA was processed and hybridized to Affymetrix Porcine Gene 1.0 ST expression microarrays (3 to 4 arrays per condition), using the standard Affymetrix workflow. Gene level expression values were determined using the Robust Multiarray Average (RMA) method (1) as part of the affy package (version 1.36.1) (2) in the Bioconductor R suite (version 2.12) (3), together with Entrez Gene-specific probeset maping (17.0.0) from the Molecular and Behavioral Neuroscience Institute (Brainarray) at the University of Michigan (4)). Array quality was measured by computing Relative Log Expression (RLE) and Normalized Unscaled Standard Error (NUSE) using the affyPLM package (version 1.34.0) (5). The three best samples from each group, by RLE value, were selected for further analysis. Data was quantile normalized using normalize.quantiles in the R preprocessCore package (version 1.32.0), and differential expression was determined using Limma (6) (version 3.26.9) for three contrasts: Primary Reperfusion vs Sham, Primary Unloading vs. Sham, and Primary Unloading vs. Primary Reperfusion. Genes showing at least a 2.0 fold change in expression and a raw p.value of less than 0.01.

first: Michele

last: Esposito

first: Yali

last: Zhang

first: Xiaoying

last: Qia

first: Lara

last: Reyelt

first: Vikram

last: Paruchuri

first: Kevin

last: Morine

first: Shiva

last: Annamalai

first: Courtney

last: Bogins

first: Peter

last: Natov

last: Pedicini

first: Catalina

last: Breton

first: Andrew

last: Mullin

first: Emily

last: Mackey

first: Ayan

last: Patel

first: Ethan

last: Rowin

first: Iris

last: Jaffe

first: Richard

last: Karas

first: Navin

middle: K

last: Kapur


title: siRNA knockdown of neonatal rat cardiac myocytes and fibroblasts

first: Michael

last: Flinn

summary: Primary neonatal rat cardiac myocytes or fibroblasts were isolated and subjected to siRNA mediated Yap knockdown

overall_design: Primary cardiac myocytes and fibroblasts were isolated from two-day old rats via neonatal heart dissociation kit (Miltenyi Biotec) according to the manufacturer’s protocol followed by percoll gradient separation. Cells were transfected with siRNAs designed against Yap, or universal negative control siRNAs. Transfected cells were collected 48 hours post transfection for RNAseq.

first: Caitlin

last: O'meara

first: Brian

last: Link


title: MicroRNAomes of cattle intestinal tissues revealed possible miRNA regulated mechanisms involved in Escherichia coli O157 fecal shedding

city: Hangzhou

first: Huizeng

last: Sun

state: Zhejiang

address: 866 Yuhangtang Road

department: College of Animal Sciences

institute: Zhejiang University

type: Non-coding RNA profiling by high throughput sequencing

summary: The current study aimed to investigate whether bovine non-coding RNA play a role in regulating E. coli O157 shedding through studying miRNAomes of the whole gastrointestinal tract including duodenum, proximal jejunum, distal jejunum, cecum, spiral colon, descending colon and rectum. The number of miRNAs detected in each intestinal region ranged from 390 ± 13 to 413 ± 49. Compared between SS and NS, the number of differentially expressed (DE) miRNAs ranged from one to eight, and through the whole gut, seven miRNAs were up-regulated and seven were down-regulated in SS. The distal jejunum and rectum were the regions where the most DE miRNAs were identified (8 and 7, respectively). Functional analysis indicated that the bta-miR-378b, bta-miR-2284j and bta-miR-2284d which were down-regulated in both distal jejunum and rectum of SS, the bta-miR-2887 which was down-regulated in rectum of SS, as well as the bta-miR-211 and bta-miR-29d-3p which were up-regulated in rectum of SS were potentially regulatory to host immune functions, including hematological system development and immune cell trafficking. Our findings suggest that the alternation of miRNA expression in the gut of SS may lead to differential regulation in immune functions involved in E. coli O157 super-shedding in cattle.

overall_design: We performed a differential analysis of microRNA expression of intestinal tissues collected from E. coli O157 super-shedders and non-shedders, targets prediction for interested microRNAs, and functional analysis for interested microRNAs, to study molecular mechanisms of super-shedding phenomenon.

first: Leluo

last: Guan

first: Ou

last: Wang


title: Global transcriptional analysis of wild-type and cuf1Δ Cryptococcus neoformans cells in responses to copper availability

first: John

last: Perfect

state: North Carolina

address: 303 Research Drive, Rm.337

department: Division of Infectious Diseases

institute: Duke University School of Medicine

summary: The essential yet toxic nature of Cu ions in living cells requires exquisite control of Cu homeostasis. The fungal pathogen C. neoformans regulates Cu homeostasis for survival during a complex host colonization process. During pulmonary infection host innate immune cells use Cu in an attempt to toxify C. neoformans, which responds by activating expression of Cu detoxifying proteins. However, during brain colonization expression of the fungal Cu import machinery is activated and required for virulence. To achieve the genetic plasticity required for adaptation to a continuum of distinct Cu environments within the host, C. neoformans utilizes the Cu-responsive transcription factor, Cuf1. Cuf1 is unique as it senses and responds to both high and low Cu environments, activating different sets of genes dependent on environmental Cu status. Cells lacking Cuf1 are compromised for colonization of the lungs and brain, highlighting Cuf1 as an important virulence factor. In this study, we provide a genome-wide assessment of the Cuf1-dependent transcription changes driven by Cu status identified novel genes required for adaptation to high and low Cu environments. These genes and their regulation provide new insights with respect to adaptive responses to changes in host Cu availability and could reveal new targets for therapeutic intervention in cryptococcosis.

overall_design: C. neoformans wild-type and cuf1Δ cells were grown in SC media to mid-log phase, and then treated with 1 mM CuSO4 (high Cu) or 1 mM bathocuproine disulfonate (BCS) (Cu deficiency) for 3 hours. Cells were then harvested for studying the effects of the Cu status in the transcriptome by RNA-Seq. The cuf1Δ strain was used for evaluating the effect of this Cu metalloregulatory transcription factor in the regulation transcriptional changes induced by the different Cu status. These experiments were performed in triplicate.

first: Sarela

last: Garcia-Santamarina

last: Festa

first: Aaron

middle: D

last: Smith

first: Chen-Hsin

last: Yu

first: Corinna

last: Probst

first: Chen

last: Ding

first: Christina

last: Homer

first: Jun

last: Yin

first: James

last: Noonan

first: Hiten

last: Madhani

middle: R

first: Dennis

last: Thiele


title: MSC stimulate ovarian tumor growth during intercellular communication but reduce tumorigenicity after fusion with ovarian cancer cells

city: Hannover

first: Ralf

last: Hass

state: Germany

address: Carl-Neuberg-Str. 1

department: Gynecology

institute: Hannover Medical School

summary: Functional changes were investigated in vitro and in vivo following spontaneous fusion and hybrid cell formation in co-cultures of primary human mesenchymal stroma/stem-like cells (MSC) with human SK-OV-3 ovarian cancer cells. Lentiviral fluorescence-labeled MSC with eGFP and ovarian cancer cells labeled with mcherry resulted in dual-fluorescing hybrid cells. Double FACS sorting and single cell cloning revealed two different aneuploid hybrid populations (SK-hyb1 and SK-hyb2)

overall_design: A total of 4 different total RNA samples was subjected to microarray analysis according to a single-color design.

first: Catharina

last: Melzer


title: Differential gene expression analysis in clinical isolate of Leishmania donovani .

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: Differential gene expression analysis was carried out in clinical isolates of Leishmania donovani (L. donovani) parasite derived from VL patient before miltefosine treatment, post treatment and patient that relpased after miltefosine treatment

overall_design: Organism : Leishmania , Agilent custom Leishmania Gene Expression  8x15k Array (AMADID: 027511) designed by Genotypic Technology Private Limited.

first: Deepak

last: Deep

first: R

last: Singh

first: s

last: Sundar

first: M

last: Ouellette

first: P

last: Salotra


title: Genome-wide analysis of differential gene expression of contact-inhibited versus proliferating endothelial cells

status: Public on Oct 24 2018

city: Leuven

first: Bert

last: Cruys

address: Herestraat 49

country: Belgium

institute: Vesalius Research Center

summary:
Brief summary: Analysis of gene expression in endothelial cells upon contact-inhibition. With this experiments we aimed to identify genes that are associated with the induction of cellular quiescence.
Abstract from the associated publication: In contrast to the growing insight in the metabolic reprogramming underlying the angiogenic switch, little is known about the metabolic changes accompanying the quiescence of endothelial cells (ECs). Nonetheless, when dysfunctional, quiescent ECs (QECs) contribute to multiple diseases. Here, we report that QECs are not hypometabolic, but upregulate fatty acid β-oxidation (FAO), not for energy or biomass production, but for redox homeostasis. Hence, inhibition of CPT1a, a rate-controlling step of fatty acid breakdown, promotes a pro-thrombotic and pro-inflammatory signature of QECs by increasing oxidative stress. EC-specific genetic loss similarly elevates oxidative stress in vivo. Compared to proliferating ECs (PECs), QECs switch on a broad “vasculoprotective” metabolic program, involving (i) NAPDH production by the oxidative pentose phosphate pathway (oxPPP) and nicotinamide nucleotide transhydrogenase (NNT), and (ii) prostacyclin synthesis. Molecularly, pro-quiescent Notch signaling elevates FAO by upregulating CPT1a gene transcription. Thus, QECs switch on vasculoprotective metabolic reactions to ensure vascular health.

overall_design: Total RNA was extracted from human umbilical vein endothelial cells (ECs) either after induction of contact inhibition or from proliferating control ECs. ECs were isolated from four different donors. For each condition (contact-inhibited versus proliferating) three replicates were used per donor, adding up to 24 samples in total.

first: Peter

last: Carmeliet


title: Blood immune transcriptome analysis of artificially fed dairy calves and naturally suckled beef calves from birth to 7 days of age

city: Grange

first: Carla

last: Surlis

state: meath

address: Dunsany

department: Animal Bioscience

country: Ireland

institute: Teagasc

summary: The aim of the overall study was to investigate the development of immune competence in artificially reared dairy calves and in two breeds of naturally suckled beef calves over the first 168h of life. Dairy calves were fed 5% total body weight of colostrum, with beef calves monitored to ensure natural ingestion of colostrum. Blood samples were taken from all calves at 24h 48h 72h and 168h, and analysed for alterations to immunes genes.

overall_design: The animal model was designed to fully elucidate the development of immune-competence in i) Holstein dairy calves (artificially fed 5% colostrum body weight (BW) at birth) and ii), naturally suckled beef calves,  the progenies of Limousin × Friesian and Charolais × Limousin cows.

first: Bernadette

last: Earley

first: Mark

last: McGee

first: Kate

last: Keogh

first: Paul

last: Cormican

first: Gordon

last: Blackshields

first: Katie

last: Tiernan

first: Amanda

last: Dunn

first: Steven

last: Morrison

first: Anastasio

last: Arguello

first: Sinead

last: Waters


title: RNA-Seq and ChIP Seq analysis of the Cu metalloregulatory transcription factor Cuf1 in Cryptococcus neoformans in response to Cu availability

first: John

last: Perfect

type: Genome binding/occupancy profiling by high throughput sequencing

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

overall_design: Refer to individual Series


title: STAT3 promotes metastasis in melanoma through repression of the MITF pathway

city: Vienna

first: Alexander

last: Swoboda

state: Vienna

address: Waehringer Strasse 13a

country: Austria

institute: Ludwig Boltzmann Institute for Cancer Research

summary: Gene expression analysis of STAT3 deleted low passage,  lymph node derived melanoma cells, from a NRAS mouse melanoma model compared to a STAT3 wild-type control after IL-6 stimulation, OSM stimulation or unstimulated.

overall_design: 24 samples total. Four cell lines were used, two STAT3 deleted, two STAT3 wild type. All four cell lines were stimulated with IL-6, OSM or unstimulated. All conditions were analyzed in technical duplicates

first: Mario

last: Mikula

first: Richard

last: Moriggl


title: Metabolic labeling of RNAs uncovers hidden features and dynamics of the Arabidopsis thaliana transcriptome [ERIC]

status: Public on Oct 31 2018

city: Oldenburg

first: Sascha

last: Laubinger

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

institute: University of Oldenburg

summary: We provide evidence that 5-EU metabolic labeling of Arabidopsis RNAs can be used for pulse-chase experiments, which allowed us to determine Arabidopsis RNA half-lives genome-wide without chemical inhibition of transcription. Similar to BRIC-Seq, we performed 5-EU IP chase (ERIC)-Seq in seedlings of A. thaliana. Hierarchical clustering of gene expression values allowed us to define at least five clusters of mRNAs that exhibited distinct degradation kinetics. To determine the RNA half-lives of each group, we applied an exponential decay model and a locally weighted scatterplot smoothing (LOWESS) and calculated the time where the concentration was halved.  It became obvious that the half-lives determined by ERIC-Seq are much shorter than the ones determined after treatment with cordycepin or actinomycin D, respectively. We found that genes belonging to cluster A exhibiting the shortest half-lives are enriched in genes transcribed into non-coding RNAs, stress-related genes, genes involved in hormonal pathways and the metabolism of polyamines, which are also involved in stress responses. On the contrary, genes from cluster E, which have the longest half-lives, are specifically enriched in genes responsible for mitochondrial and plastic functions as well as primary metabolism (such as the TCA cycle)

overall_design: RNA was metabolically labeled with 5-ethynyl uridine for 24h, then the seedlings were transferred to media containing a high concentration of uridine to chase the 5-ethynyl uridine out. Samples were taken subsequently at 0h, 1h, 2h, 6h, 12h and 24h after end of labeling period.  A known concentration of a EU containing  RNA was used as spike-in for normalization. The poly(A) fraction of total RNA was used for NGS library preparation. Samples were taken in triplicates; an sample of timepoint zero hours was taken as reference.

first: Philipp

last: Reichert

first: Emese

middle: X

last: Szabò


title: Transcriptomic analysis revealed the mechanisms involved in the differential accumulation of taxoids, flavonoids and hormones among three Taxaceae trees

city: hangzhou

first: chengchao

last: zhang

address: Xuelin Street No.16

institute: Hangzhou Normal University

summary: The natural product taxol is an efficient and worldwide accepted anticancer drug. Taxol and other taxoids accumulate in only a few specific genera of the Taxaceae family, such as Taxus and Pseudotaxus. The comprehensive variations among three Taxaceae trees, including one taxol-producing (TP) and two non-taxol producing (NTP) trees, were compared. In total, 3,655 metabolites and 88,609 functional genes were identified through metabolomic and transcriptomic analyses, respectively.  KEGG enrichment analysis showed that many differentially expressed genes were enriched in several hormone-, flavonoid-, and terpenoid-related metabolic pathways. The hormones, abscisate and abscisic acid, highly accumulated in the NTP trees, whereas gibberellic acids substantially accumulated in the TP trees.

sample_organism:
Amentotaxus argotaenia
Torreya grandis
Pseudotaxus chienii

first: chenjia

last: shen


title: ChIP Seq analysis of the Cu metalloregulatory transcription factor Cuf1 in Cryptococcus neoformans in response to Cu availability

summary: The essential yet toxic nature of Cu ions in living cells requires exquisite control of Cu homeostasis. The fungal pathogen C. neoformans regulates Cu homeostasis for survival during a complex host colonization process. During pulmonary infection host innate immune cells use Cu in an attempt to toxify C. neoformans, which responds by activating expression of Cu detoxifying proteins. However, during brain colonization expression of the fungal Cu import machinery is activated and required for virulence. To achieve the genetic plasticity required for adaptation to a continuum of distinct Cu environments within the host, C. neoformans utilizes the Cu-responsive transcription factor, Cuf1. Cuf1 is unique as it senses and responds to both high and low Cu environments, activating different sets of genes dependent on environmental Cu status. Cells lacking Cuf1 are compromised for colonization of the lungs and brain, highlighting Cuf1 as an important virulence factor. A genome-wide assessment of the Cuf1 binding sites in the genome of C. neoformans driven by Cu status identified novel genes required for adaptation to high and low Cu environments. These genes and their regulation provide new insights with respect to adaptive responses to changes in host Cu availability and could reveal new targets for therapeutic intervention in cryptococcosis.

overall_design: ChIP-Seq was conducted in triplicate using a C. neoformans cuf1∆ strain complemented with a functional Cuf1-2xFLAG fusion protein. Cells were grown in SC until mid-log phase and treated with 1 mM CuSO4 (high Cu) or 1 mM bathocuproine disulfonate (BCS) (Cu deficiency) for three hours before cell harvesting. ChIP-Seq experiments were conducted in triplicate.

first: Sarela

last: Garcia-Santamarina

last: Festa

first: Aaron

last: Smith

first: Chen-Hsin

last: Yu

first: Corinna

last: Probst

first: Chen

last: Ding

first: Christina

last: Homer

first: Jun

last: Yin

first: James

last: Noonan

first: Hiten

last: Madhani

first: Dennis

last: Thiele


title: Expression data from catalase stably transfected A375 human melanoma cells

city: San Martín

first: Hebe

last: Durán

state: Buenos Aires

address: Av. Gral. Paz 1499

department: Departamento de Micro y Nanotecnología

country: Argentina

institute: Comisión Nacional de Energía Atómica

summary:
Reactive oxygen species (ROS) are implicated in tumor transformation by modulating proteins involved in differentiation, proliferation and invasion. In order to identify genes that may support melanoma progression or regression after an antioxidant system (AOS) response, we developed and characterized a human melanoma cell model with different levels of ROS by stably overexpressing the antioxidant enzyme catalase in A375 amelanotic melanoma cells, and whole genome gene expression patterns were analyzed by microarrays.
We used gene expression microarrays to study the AOS global response to catalase overexpression and to identify up-regulated and down-regulated genes during progression or regression of melanoma.

overall_design: Gene expression microarrays were performed in A375 amelanotic melanoma cells stably transfected with human catalase cDNA. A375-A7 and A375-G10 cell clones were obtained by clonal dilution. A375-PCDNA3 (transfected with empty vector) and A375 cells were used as controls.

first: Candelaria

last: Bracalente

first: Irene

last: Ibañez

first: Ariel

last: Chernomoretz


title: The effects of basal LH inhibition with Cetrorelix on cumulus cell gene expression during the luteal phase under ovarian coasting stimulation in cattle.

city: Québec City

first: Marc-André

last: Sirard

state: Quebec

address: Offfice 2732, 2440 Hochelaga Blvd.

department: Sciences Animales

country: Canada

institute: Université Laval

summary: impact of suppressing LH using the GnRH antagonist Cetrorelix during an ovarian coasting stimulation protocol on the transcriptome of bovine cumulus cells (CC). Oocytes were collected twice from six dairy cows. For the first collection, the cows received FSH twice daily for three days, followed by FSH withdrawal for 68 hours as control protocol. For the second collection, the same stimulation protocol was used, but the cows also received, starting on day 2 of FSH stimulation, a GnRH antagonist once a day until recovery of the cumulus-oocyte complexes (COC). Half of the COC were subjected to in vitro maturation, fertilization and culture to assess blastocyst rates. The other half of the CC underwent microarray analysis (n=3 cows, 2 treatments, 6 oocyte collections) and qRT-PCR (n=6 cows: 3 microarray cows + 3 other cows, 2 treatments, 12 oocyte collections). The differential expression of specific genes was confirmed by RT-qPCR: ATP6AP2, SC4MOL, OSTC and PTGDS. The global transcriptomic analysis of cumulus cells demonstrated that the inhibition of LH secretion may decrease survival, and growth of the follicle. Moreover, the results suggested that LH may be important to cumulus for the maintenance of cellular mechanisms such as global RNA expression, protein and nucleic acid metabolism and energy production. These results support the hypothesis that LH support is important during the final part of follicle maturation through its influence on the cumulus cells.

overall_design: This is a 2 conditions experiment with cumulus cells collected after FSH withdrawal for 68 hours.  Three biological replicates for each treatment and each were hybridized on a dye swap design.

first: Audrey

last: Bunel

first: Anne-Laure

last: Nivet

first: Patrick

last: Blondin

first: Christian

last: Vigneault

first: François

last: Richard


title: Genetic Study of anti-EGFR Antibody Therapy Response in Colorectal Carcinoma

city: Cantanhede

first: Helena

last: Vazao

address: Biocant Park Nucleo4, 4A

department: HeartGenetics

country: Portugal

institute: HeartGenetics

summary:
Metastatic colorectal carcinoma is one of the most common cancers in the world, second most commonly diagnosed cancer in Europe. Approximately 25% of patients initially diagnosed with colorectal carcinoma have metastases at the time of the first diagnosis and almost 50% of the diagnosed patients develop metastases, which explains the high mortality rate of these tumors. The carcinogenic process can be inhibited by the inactivation of EGFR receptors, making them important therapeutic targets. However, around 90-80% of patients do not respond to the EGFR targeted therapy. Resistance is mainly due to KRAS gene mutations.
In this study, we built a 171 mutations panel (OncoAlvo®) that screens all mutations recommended by the ESMO, ASCO & NICE Medical Guidelines with 99% accuracy. The samples were simultaneously genotyped by other techniques to validate our panel and accuracy.

overall_design: 457 human colorectal samples were genotyped for 171 somatic mutations (by the analysis of 61 positions) in 6 genes. 10 negative sample controls were used. 10 positive sample controls were used. All samples were genotyped by other technologies. The baseline threshold for the measure of the variants were set up with 96 normal samples.

last: Vazão

first: Daniel

last: Luís

first: José

last: Caldas

first: Gonçalo

last: Antunes

first: Ana

last: Freitas

first: Susana

last: Santos


title: Analysis of Pseudomonas putida growth on non-trivial carbon sources using transcriptomics and genome-scale modeling

city: Kgs. Lyngby

first: Isotta

last: D'Arrigo

address: Kemitorvet

country: Denmark

institute: Technical University of Denmark

summary: Pseudomonas putida is characterized by a versatile metabolism and stress tolerance traits that allow the bacterium to cope with different environmental conditions. In this work, the mechanisms that allow P. putida KT2440 to grow in the presence of four sole carbon sources (glucose, citrate, ferulic acid, serine) were investigated by RNA sequencing (RNA-seq) and genome-scale metabolic modeling. Transcriptomic data identified uptake systems for the four carbon sources, and candidates were subjected to preliminary experimental characterization by mutant strain growth to test their involvement in substrate assimilation. The OpdH and BenF-like porins were involved in citrate and ferulic acid uptake, respectively. The citrate transporter (encoded by PP_0147) and the TctABC system were important for supporting cell growth in citrate; PcaT and VanK were associated with ferulic acid uptake; and the ABC transporter AapJPQM was involved in serine transport. A genome-scale metabolic model of P. putida KT2440 was used to integrate and analyze the transcriptomic data, identifying and confirming the active catabolic pathways for each carbon source. This study reveals novel information about transporters that are essential for understanding bacterial adaptation to different environments.

overall_design: The strain P. putida KT2440 were grown in M9 minimal medium in presence of one sole carbon sources (glucose, citrate, ferulic acid, and serine). Cells were harvested in mid-exponential phase and total RNA extracted. 3 replicas for each carbon sources, for a total of 12 samples for RNA-seq.

first: João

middle: G

last: Cardoso

first: Maja

last: Rennig

first: Nikolaus

last: Sonnenschein

first: Markus

last: Herrgård

first: Katherine

middle: S

last: Long


title: Gene expression signatures for eSAS (human tongue squamous-cell carcinoma cell line) compared with parental SAS

status: Public on Oct 22 2018

city: Suita

first: Daisuke

last: Okuzaki

state: Osaka

address: Yamadaoka 3-1

department: Immunology Frontier Research Center

institute: Osaka univ.

summary: To examine if gene expression level is altered in eSAS (human tongue squamous-cell carcinoma cell line) compared with that of parental SAS, we performed genome-wide DNA microarray analysis. For this purpose, we prepared total mRNAs from SAS and eSAS cells in their Log growth phase and compared their genome-wide expression levels.

overall_design: Two arrays (Agilent Whole Human Genome Microarray 4x44K G4112F: 014850) were performed as one color experiments.

first: Emi

last: Fujibayashi


title: Transcriptome comparison of the Streptococcus pneumoniae D39 ∆rgg144to D39 wild type grown in Mannose

status: Public on Oct 19 2018

city: STOCKHOLM

first: Sulman

last: Shafeeq

address: nobel vag 16

department: MTC

country: Sweden

institute: Karolinska Institutet

summary: Microbes communicate with each other by using quorum sensing (QS) systems and modulate their collective ‘behavior’ for in-host colonization and virulence, biofilm formation, and environmental adaptation. The recent increase in genome data availability reveals the presence of several putative QS sensing circuits in microbial pathogens, but many of these have not been functionally characterized yet, despite their possible utility as drug targets. To increase the repertoire of functionally characterized QS systems in bacteria, we studied Rgg144/Shp144 and Rgg939/Shp939, two putative QS systems in the important human pathogen Streptococcus pneumoniae. We find that both of these QS circuits are induced by short hydrophobic peptides (Shp) upon sensing sugars found in the respiratory tract, such as galactose and mannose. Microarray analyses using cultures grown on mannose and galactose revealed that the expression of a large number of genes is controlled by these QS systems, especially those encoding for essential physiological functions and virulence-related genes such as the capsular locus. Moreover, the array data revealed evidence for cross-talk between these systems. Finally, these Rgg systems play a key role in colonization and virulence, as deletion mutants of these QS systems are attenuated in the mouse models of colonization and pneumonia.

overall_design:
Transcriptome comparison of the Streptococcus pneumoniae D39 ∆rgg144 to D39 wild type grown in 55mM Mannose  until early exponential phase (corresponded to OD600 of 0.3)
One condition design comparision of two strains including a dye swap

first: Irfan

last: Manzoor

first: Hasan

last: Yesilkaya

first: Oscar

last: Kuipers


title: Transcriptome comparison of the Streptococcus pneumoniae D39 ∆rgg144to D39 wild type grown in galactose

overall_design:
Transcriptome comparison of the Streptococcus pneumoniae D39 ∆rgg144 to D39 wild type grown in 55 mM galactose until early exponential phase (corresponded to OD600 of 0.3)
One condition design comparision of two strains including a dye swap


title: Transcriptome comparison of the Streptococcus pneumoniae D39 ∆rgg939 to D39 wild type grown in galactose

overall_design:
Transcriptome comparison of the Streptococcus pneumoniae D39 ∆rgg939 to D39 wild type grown in 55mM galactose until early exponential phase (corresponded to OD600 of 0.3)
One condition design comparision of two strains including a dye swap


title: Gene expression changes in white blood cells of hypertensive patients with left ventricular remodeling

city: Toulouse

first: Philippe

middle: V

last: Rouet

address: 1 Ave Jean Poulhes

department: Cardiology

country: France

institute: INSERM U1048

summary: Using transcriptomic we looked for changes in large-scale gene expression profiling of leukocytes of hypertensive patients with left ventricular remodeling compared to hypertensive patients without left ventricular remodeling and to control and whether these changes reflect metabolic pathway regulation already shown by positron emission tomography. Genes encoding for glycolytic enzymes were found over-expressed in the group of hypertensive patients with left ventricular remodeling. Expression of master genes involved in fatty acids β-oxidation was unchanged.

overall_design: Transcriptomic analysis included 14 patients with hypertension and left ventricular hypertrophy, 14 patients with hypertension and normal left ventricular size and 8 control individuals.

first: Fatima

last: Smih

first: Michel

last: Galinier


title: Expression profiling of Hyperoxia-Tolerant Drosophila melanogaster

city: La Jolla

first: Dan

last: Zhou

address: CMG 103, 9500 Gilman Drive, MC0735

department: Pediatrics

institute: University of California, San Diego, School of Medicine

summary: One of the critical substances that mammals highly regulate via the respiratory, cardiovascular and neurologic systems is O2. Both low and high O2 levels can induce major morbidities as well as mortality. Indeed, O2 has been often considered as both an elixir and a poison in humans. In current study, we have used an experimental selection approach to generate Drosophila strains that are tolerant to severe hyperoxic environment.  Gene expression profiling is then applied to investigate the mechanisms underlying hyperoxia tolerance in the newly generated strains.

overall_design: 27 isogenic D. melanogaster Lines were pooled and following long-term selection over generations with increased oxygen level in the culture environment. The differences in gene expression were compared between adapted flies and generation matched naive controls by microarray.

first: Huiwen

last: Zhao

first: Gabriel

last: Haddad


title: Analysis of transcriptional profiles in Saccharomyces cerevisiae exposed to bisphenol A

city: Istanbul

first: Ceyhun

last: Bereketoglu

address: Goztepe

country: Turkey

institute: Marmara University

summary: We analyzed genome-wide transcriptional profiles of Saccharomyces cerevisiae BY4742 strain in response to BPA, focusing on two exposure scenarios: (i) low-observed-effect concentration (<10% inhibition) to examine chronic effect of BPA on yeast population, and (ii) high-inhibitory concentration (>70% inhibition) to study acute effect. Initially, yeast cells were exposed to various concentrations of BPA. 50 mg/L and 300 mg/L BPA were determined as low-observed-effect concentration and the high-inhibitory concentration, respectively. Transcriptional profiles indicated that 81 genes were repressed and 104 genes were induced in response to 50 mg/L BPA. On the other hand, in 300 mg/L BPA exposure, 378 genes were down-regulated, while 606 genes were significantly up-regulated. Our data showed that there were similar processes affected by both concentrations such as mitochondria, nucleobase-containing small molecule metabolic process, transcription from RNA polymerase II promoter, and mitotic cell cycle and associated processes. However, different modes of actions of the BPA were found between two concentrations.  300 mg/L BPA exposure showed severe effects on the processes by repressing or inducing several genes or total mechanisms with high level of expression changes, while 50 mg/L BPA exposure changed the expression of some important genes with low level of expression changes in the processes. These results suggest that yeast cells respond via different ways to the different concentrations of BPA at transcriptomic level.

platform_organism:
Schizosaccharomyces pombe
Saccharomyces cerevisiae

overall_design: Yeast cells were exposed to bisphenol A (BPA) at mid-exponential phase for 180 minutes. Then, cells were harvested and RNAs were extracted. Microarray analyses were conducted in triplicates for two different concentrations of BPA and control (in total, 9 arrays). Finally, data were analyzed and differentially expressed genes and the effected  biological processes in yeast were determined.

first: Kazim

last: Arga

first: Serpil

last: Eraslan

first: Bulent

last: Mertoglu


title: Comparison of efficacy of SHENQI compound and rosiglitazone in the treatment of diabetic vasculopathy analyzing multi-factor mediated disease-causing modules

city: harbin

first: Xiaoting

last: Li

address: haerbindajie

institute: Biotechnology

summary: Atherosclerosis-predominant vasculopathy is a common complication of diabetes with high morbidity and high mortality, which is ruining the patient's daily life. As is known to all, traditional Chinese medicine (TCM) SHENQI compound and western medicine rosiglitazone play an important role in the treatment of diabetes. In particular, SHENQI compound has a significant inhibitory effect on vascular lesions. Here, to explore and compare the therapeutic mechanism of SHENQI compound and rosiglitazone on diabetic vasculopathy, we first built 7 groups of mouse models. The behavioral, physiological and pathological morphological characteristics of these mice showed that SHENQI compound has a more comprehensive curative effect than rosiglitazone and has a stronger inhibitory effect on vascular lesions. While rosiglitazone has a more effective but no significant effect on hypoglycemic. Further, based on the gene expression of mice in each group, we performed differential expression analysis. The functional enrichment analysis of these differentially expressed genes (DEGs) revealed the potential pathogenesis and treatment mechanisms of diabetic angiopathy. In addition, we found that SHENQI compound mainly exerts comprehensive effects by regulating MCM8, IRF7, CDK7, NEDD4L by pivot regulator analysis, while rosiglitazone can rapidly lower blood glucose levels by targeting PSMD3, UBA52. Except that, we also identified some pivot TFs and ncRNAs for these potential disease-causing DEG modules, which may the mediators bridging drugs and modules. Finally, similar to pivot regulator analysis, we also identified the regulation of some drugs (e.g. bumetanide, disopyramide and glyburide etc.) which have been shown to have a certain effect on diabetes or diabetic angiopathy, proofing the scientific and objectivity of this study. Overall, this study not only provides an in-depth comparison of the efficacy of SHENQI compound and rosiglitazone in the treatment of diabetic vasculopathy, but also provides clinicians and drug designers with valuable theoretical guidance.

overall_design: Examination of 7 different gene expression profile in Healthy, Diabetic, Macroangiopathy,SHENQI, Yangyinyiqi, Huoxue, Rosiglitazone mouse

first: Hong

last: Gao

first: Yuhong

last: Duan

first: Xiaoxu

last: Fu

first: Hongyan

last: Xie

first: Ya

last: Liu

first: Haipo

last: Yuan

first: Mingyang

first: Chunguang


title: Real-time quantitative PCR miRNA expression data of normal foetal adrenal neuroblasts and cortex cells, neuroblastoma tumors and embryonic stem cells

status: Public on Oct 20 2018

city: Gent

first: Katleen

last: De Preter

address: Corneel Heymanslaan 10

department: Center for Medical Genetics

institute: Ghent University

summary: MiRNA expression of 8 embryonal stem cell lines, 7 normal foetal adrenal neuroblast samples, 7 normal foetal adrenal cortex samples and 95 neuroblastoma samples was profiled using RT-qPCR and normalized. These data are used to evaluate different miRNA expression signatures (for example an embryonic stem cell miRNA signature).

first: Frank

last: Speleman

first: Jo

last: Vandesompele

first: Pieter

last: Mestdagh

first: Karen

last: Sermon

first: Rosa

last: Noguera

first: Angelika

last: Eggert

first: Alexander

last: Schramm

first: Johannes

last: Schulte


title: Gene expression in rabbit left atrial free wall and left atrial appendage

city: Amsterdam

first: Vincent

middle: M.

last: Christoffels

state: N/A (NA)

address: Meibergdreef 15  K2-159

department: Medical Biology

country: Netherlands

institute: Amsterdam UMC

summary: RNA sequencing of dissected left atrial free wall and left atrial appendage of adult New Zealand White rabbit

overall_design: Comparison of gene expression in left atrial free wall and

first: Koen

middle: T

last: Scholman

first: Aldo

last: Jongejan

first: Bas

last: Boukens


title: Transcriptome comparison of the Streptococcus pneumoniae D39 ∆rgg939 to D39 wild type grown in Mannose

first: Sulman

last: Shafeeq

overall_design:
Transcriptome comparison of the Streptococcus pneumoniae D39 ∆rgg939 to D39 wild type grown in 55mM Mannose  until early exponential phase (corresponded to OD600 of 0.3)
One condition design comparision of two strains including a dye swap

first: Irfan

last: Manzoor

first: Hasan

last: Yesilkaya

first: Oscar

last: Kuipers


title: C. elegans stress-induced gene expression in low SAM or after histone-methytransferase RNAi

city: Worcester

first: Amy

last: Walker

address: 373 Plantation Street

department: Program in Molecular Medicine

country: USA

institute: UMASS Medical School

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

overall_design: Refer to individual Series


title: Community composition of nitrous oxide reducing bacteria investigated using a functional gene microarray

city: Princeton

first: Bess

middle: B

last: Ward

state: NJ

address: Washington Road

department: Geosciences

institute: Princeton University

summary: The diversity and environmental distribution of the nosZ gene, which encodes the enzyme responsible for the consumption of nitrous oxide, was investigated in marine and terrestrial environments using a functional gene microarray.  The microbial communities represented by the nosZ gene probes showed strong biogeographical separation, with communities from surface ocean waters and agricultural soils significantly different from each other and from those in oceanic oxygen minimum zones.  Atypical nosZ genes, usually associated with incomplete denitrification pathways, were detected in all the environments, including surface ocean waters.  The abundance of nosZ genes, as estimated by quantitative PCR, was highest in the agricultural soils and lowest in surface ocean waters.

sample_organism:
synthetic construct
soil metagenome
seawater metagenome

platform_organism:
soil metagenome
seawater metagenome

overall_design: Two color array (Cy3 and Cy5): the universal standard 20-mer oligo is printed to the slide with a 70-mer oligo (an archetype).  Environmental DNA sequences (fluoresced with Cy3) within 15% identity of the 70-mer conjugated to a 20-mer oligo (fluoresced with Cy5) complementary to the universal standard will bind to the oligo probes on the array.  Signal is the ratio of Cy3 to Cy5. Two replicate probes were printed for each archetype. Two replicate arrays were run on duplicate targets.

first: Amal

last: Jayakumar

first: Devika

last: Balachandran

first: Andrew

last: Rees

first: Patarick

last: Kearns

first: Jenifer

last: Bowen


title: Integrative analysis of transcriptomics and clinical data uncovers the tumorsuppressive activity of MITF in prostate cancer

status: Public on Oct 16 2018

city: Derio

first: Ana

middle: Maria

last: Aransay

state: BIZKAIA

address: Parque tecnologico de Bizkaia, Building 801-A

department: Genome Analysis Platform

country: Spain

institute: CIC bioGUNE

summary:
The dysregulation of gene expression is an enabling hallmark of cancer. Computational analysis of transcriptomics data from human cancer specimens, complemented with exhaustive clinical annotation, provides an opportunity to
identify core regulators of the tumorigenic process. Here we exploit well-annotated clinical datasets of prostate cancer for the discovery of transcriptional regulators relevant to prostate cancer. Following this rationale, we identify Microphthalmia-associated transcription factor (MITF) as a prostate tumor suppressor among a subset of transcription factors. Importantly, we further interrogate transcriptomics and clinical data to refine MITF perturbation-based empirical assays and unveil Crystallin Alpha B (CRYAB) as an unprecedented direct target of the transcription factor that is, at least in part, responsible for its tumor-suppressive activity in prostate cancer. This evidence was supported by the enhanced prognostic potential of a signature based on the concomitant alteration of MITF and CRYAB in prostate
cancer patients. In sum, our study provides proof-of-concept evidence of the potential of the bioinformatics screen of publicly available cancer patient databases as discovery platforms, and demonstrates that the MITF-CRYAB axis controls prostate cancer biology.

overall_design: doxycycline-treated and untreated PC3 cells

first: Lorea

last: Valcarcel-Jimenez

first: Alice

last: Macchia

first: Natalia

last: Martín-Martín

last: Cortazar

first: Ariane

last: Schaub

first: Mikel

last: Pujana

first: Ivana

last: Hermanova

first: Ianire

last: Astobiza

first: Jan

last: Trka

first: James

last: Sutherland

first: Rosa

last: Barrio

middle: M

first: Arkaitz

last: Carracedo

first: Verónica

last: Torrano


title: Comparison of  heat responsive gene expression after histone methyltransferase RNAi in C. elegans

first: Amy

last: Walker

state: MA

summary:
We resport the changes in gene expression occuring after heat exposure in C. elegans with low s-adenosylmethionine, or RNAi of two H3K4 methyltransferases
Using a C. elegans model of low SAM, we previously found that transcriptional responses response to a bacterial pathogen failed and these bacterial-response genes did not show normal H3K4me3 close to the transcriptional start sites, (Ding et al. 2015 Cell Metabolism).  We also found the HMT set-16/MLL was required for full induction, whereas set-2/SET1 appeared dispensable (Ding et al. 2015 Cell Metabolism).  We hypothesized that animals with low SAM might fail to transcriptionally respond to stress and that the HMTs may also have distinct roles in modulating stress responses.  In our present study, we set out to compare induction of transcriptional responses and survival upon stress exposure between C. elegans with reduced SAM (sams-1(RNAi)) and animals with limited H3K4me3 function, set-2/SET1, and set-16/MLL RNAi.  Because distinct stresses may rely on different transcriptional activation mechanisms, we also compared whole-genome expression patterns in three stresses: pathogenic bacteria (PA14), xenotoxic (R24) and heat in response to each RNAi.

overall_design: C. elegans were grown on RNAi plates, then exposed to 37°C for 90 minutes


title: Comparison of R24 responsive gene expression after histone methyltransferase RNAi in C. elegans

summary:
We resport the changes in gene expression occuring after R24 exposure in C. elegans with low s-adenosylmethionine, or RNAi of two H3K4 methyltransferases
Using a C. elegans model of low SAM, we previously found that transcriptional responses response to a bacterial pathogen failed and these bacterial-response genes did not show normal H3K4me3 close to the transcriptional start sites, (Ding et al. 2015 Cell Metabolism).  We also found the HMT set-16/MLL was required for full induction, whereas set-2/SET1 appeared dispensable (Ding et al. 2015 Cell Metabolism).  We hypothesized that animals with low SAM might fail to transcriptionally respond to stress and that the HMTs may also have distinct roles in modulating stress responses.  In our present study, we set out to compare induction of transcriptional responses and survival upon stress exposure between C. elegans with reduced SAM (sams-1(RNAi)) and animals with limited H3K4me3 function, set-2/SET1, and set-16/MLL RNAi.  Because distinct stresses may rely on different transcriptional activation mechanisms, we also compared whole-genome expression patterns in three stresses: pathogenic bacteria (PA14), xenotoxic (R24) and heat in response to each RNAi.

overall_design: C. elegans were grown on RNAi plates, then exposed to R24


title: A novel animal model for secondary progressive multiple sclerosis by oligodendroglia-specific conditional connexin 47 knockout

status: Public on Oct 17 2018

city: Fukuoka

first: Ryo

last: Yamasaki

state: Fukuoka

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

department: Neurology

institute: Kyushu University


title: A novel animal model for secondary progressive multiple sclerosis by oligodendroglia-specific conditional connexin 47 knockout [Agilent]

summary: Objective: To elucidate the role of Cx47 loss in chronic neuroinflammation and establish an SPMS model.   Methods: Plp-CreERT; Cx47fl/fl mice were generated and administered tamoxifen to induce oligodendroglia-specific conditional knockout of Cx47 (Cx47 icKO). Ten days after tamoxifen treatment, Cx47 icKO mice and their control littermates were immunized by myelin oligodendrocyte glycoprotein peptide 35-55 to induce experimental autoimmune encephalomyelitis (EAE).

overall_design: contorols: 1FL naive Ast as control.

first: Zhao

last: Yinan


title: A novel animal model for secondary progressive multiple sclerosis by oligodendroglia-specific conditional connexin 47 knockout [Affy]

overall_design: FL naive MG as control.

first: Yinan

last: Zhao


title: differentially expressed genes in NDV infected chicken brains

status: Public on Oct 18 2018

city: Yangling

first: wenbin

last: wang

state: Shannxi

address: 22#, Xinong Road

department: College of Veterinary Medicine

country: China

institute: Northwest A&F University

summary: Cellular proteins in central nervous system involved in avian neurotropic virus infection remains completely unknown. To investigate host gene expression profile in NDV infected SPF chicken brains, The microarray initial analysis was performed at LC-Bio (Hangzhou, China). A 44K Agilent chicken whole genome chip (43,803 probes) (Agilent Technologies, USA) was used for gene microarray analysis from F48E9-, LaSota-infected and mock-infected brains through intraocular-nasal routes.The chicken brains were collected at 5 day post infection. The significance analysis was used to evaluate the differences in gene expression. P and fold change (FC) values represent the alteration tendency of gene expression between experimental and control groups. The genes (FC>2) were input in Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis for DEGs.

overall_design: F48E9-, LaSota-infected and PBS (control)-infected brains through intraocular-nasal routes in 100000 pfu/100μl/chicken were collected at 5 day post infection.The data from F48E9- and LaSota-infected brains were compared to mock (PBS)-infection.

first: Wenbin

last: Wang

first: Xudong

last: Chang


title: Stenotrophomonas maltophilia FLR19 response to pH

city: Irvine

first: Katrine

last: Whiteson

state: CA

address: 3315 McGaugh Hall

institute: University of California, Irvine

summary: We sought to determine how a cystic fibrosis isolate of Stenotrophomonas maltophilia responds to relevant pH gradients (pH 5, 7, and 9) by growing the bacterium in phosphate buffered media and conducting RNAseq experiments. Our data suggests acidic conditions are stressful for strain FLR19, as it responded by increasing expression of stress-response and antibiotic-resistance genes.

overall_design: Bacterial transcriptional response to acidic, neutral and basic pH

first: Tara

last: Gallagher


title: Rgg-Shp regulators are important for pneumococcal colonization and invasion through their effect on mannose utilization and capsule synthesis

first: Sulman

last: Shafeeq


title: Comparsion of histone modifications of core and accessory chromosomes of Fusarium oxysporum

first: Like

last: Fokkens

department: Swammerdam Institute of Life Sciences

institute: University of Amsterdam

summary: To study whether there are differences in chromatin-mediated regulation between and within chromosomes in Fusarium oxysporum f. sp. lycopersici 4287 (FGSC9935), we determined the distribution of histone marks associated with euchromatin (H3K4me2) and facultative heterochromatin (H3K27me3) in vitro. We then determined whether these differences correlate with differences in dispensability and sequence divergence and gene expression.

overall_design: Examination of histone modifications H3K4me2 and H3K27me3 in vitro.

first: Michael

last: Freitag

first: Shermineh

last: Shahi

first: Lanelle

last: Connolly

first: Kristine

last: Smith


title: LGR5 promotes tumorigenicity and invasion of glioblastoma stem-like cells and is a potential therapeutic target for a subset of glioblastoma patients [shLGR5]

city: Uppsala

first: Lene

last: Uhrbom

address: Dag Hammarskjölds väg 20

department: Immunology, Genetics and Pathology

institute: Uppsala University

summary:
Glioblastoma progression and recurrence are suggested to be derived by glioblastoma stem-like cells (GSCs). There is limited knowledge about the expression and therapy response of LGR5 in GSCs.
We have investigated the role of LGR5 in glioblastoma by knocking down LGR5 using short hairpin RNA targeting LGR5 mRNA (shLGR5) and non-target RNA (shNT) as control.

overall_design: Gene expression was analysed in three glioblastoma patient derived GSC lines of proneural subtype (U3082MG, U3117MG and U3118MG) transduced with lentiviral vectors containing shLGR5 or shNT. All cells were cultured adherently under stem cell conditions.

first: Yuan

last: Xie

first: Anders

last: Sundström

first: Naga

middle: P

last: Maturi

first: E-Jean

last: Tan

first: Voichita

last: Marinescu

first: Malin

last: Jarvius

last: Tirfing

first: Chuan

last: Jin

first: Lei

last: Chen

first: Magnus

last: Essand

first: Fredrik

last: Swartling

first: Sven

last: Nelander

first: Yiwen

last: Jiang


title: Gene expression analysis between planktonic and biofilm states of Flavobacterium columnare

city: Auburn

first: Jason

last: Abernathy

state: AL

address: 990 Wire Road

institute: USDA-ARS

summary: Flavobacterium columnare, the causative agent of columnaris disease causes substantial mortality worldwide in numerous freshwater finfish species. Due to its global significance and impact on the aquaculture industry continual efforts to better understand basic mechanisms that contribute to disease are urgently needed. F. columnare naturally occurs in a planktonic, free living state where it can survive for long periods of time, even in the absence of nutrients.  In contrast, F. columnare also possesses the ability to form biofilms, broadly defined as surface bound microbial communities inhabiting an organic matrix composed of autogenously derived extracellular polymeric substances.  The advantages of adopting this life stage are not completely clear for F. columnare, but biofilm formation could increase virulence by offering protection from desiccation, augment resistance to antimicrobials, improve nutrient acquisition, and protection against other bacteria. To examine gene expression between F. columnare planktonic cells and biofilms, we conducted a study where both phases were grown with and without stimulation and then sampled for RNA sequencing.

overall_design: F. columnare isolate 94-081 was retrieved from frozen glycerol stocks and streaked onto the appropriate medium. After 24-48 h, bacterial colonies were dislodged from the agar using a sterile cotton swab and inoculated into FCGM. Bacterial broth cultures were incubated for 24 h at 28℃ prior to use in all growth assays. For planktonic and biofilm assays, an overnight broth culture of 94-081 was diluted (1:100) as needed into fresh FCGM broth into separate flasks with or without the addition of 20 µg/ml sterilized catfish mucus. After 48 h of growth at 28℃ the planktonic culture was removed from the flask prior to harvesting the biofilm. Experiments were performed in triplicate to represent biological replicates. A total of 12 samples were taken: three biological replicates, sampling two states, with two treatment groups (with or without mucus) for the isolate.

first: Miles

last: Lange


title: LGR5 promotes tumorigenicity and invasion of glioblastoma stem-like cells and is a potential therapeutic target for a subset of glioblastoma patients [oeLGR5]

summary: Glioblastoma progression and recurrence are suggested to be derived by glioblastoma stem-like cells (GSCs). There is limited knowledge about the expression and therapy response of LGR5 in GSCs. We have investigated the role of LGR5 in glioblastoma by over-expression LGR5 using lentiviral vectors containing LGR5 cDNA (oeLGR5) or control (oeCTL).

overall_design: Gene expression was analysed in two glioblastoma patient-derived GSC lines (U3020MG and U3060MG) transduced with lentiviral vectors containing oeLGR5 or oeCTL. All cells were cultured adherently under stem cell conditions.

first: E-J


title: Cdh1 and Pik3ca mutations cooperate to induce Immune-Related Invasive Lobular Carcinoma of the Breast

city: Chapel Hill

first: Charles

last: Perou

state: NC

address: 12-044 Lineberger Comprehensive Cancer Center CB# 7295

department: Professor of Genetics, and Pathology & Laboratory Medicine; Lineberger Comprehensive Cancer Center

institute: University of North Carolina at Chapel Hill

summary:
CDH1 and PIK3CA are the two most frequently mutated genes in Invasive Lobular Carcinoma (ILC) of the breast. Transcription profiling has identified molecular subtypes for ILC, one of which - Immune-Related (IR) - is associated with gene expression linked to lymphocyte and macrophage infiltration. Here we report that homozygous deletion of Cdh1 together with mutational activation of Pik3ca in mammary epithelium of genetically modified mice leads to rapid formation of IR-ILC-like tumors with immune cell infiltration, as well as gene expression signatures linked to TRegulatory (Treg) cell signaling and immune checkpoint inhibitor pathway activation. Interestingly, these tumors show enhanced Oct4-, Hif1á-, YAP-, Shh-, Rac- and Notch-dependent transcription/signaling, features in common with human IR-ILC and therefore potential targets for therapy.
Gene expression profiling reveals immune infiltration and similarities to a subtype of human Invasive Lobular carcinoma.

overall_design: Agilent gene expression profiling of mouse mammary tumors.

first: Egan

last: Sean

first: Perou

last: Charles


title: Differential, cyclical transcription of genes in Sm1021 and ntrX18

city: Shanghai

first: Shenghui

last: Xing

address: nancheng road 333

institute: shanghai university

summary: By application of cell synchronization and RNA-Seq technologies, we first described the cyclical expression of the entire genome in Sm1021, and the differential gene expression in ntrX18

overall_design: The total RNA was extracted at three phases of a cell cycle from both Sm1021 and ntrX18, which was used for cDNA production, library construction and deep sequecing.

first: Li

last: Luo


title: Timing and order of the molecular events marking the onset of berry ripening in grapevine

status: Public on Oct 15 2018

city: Verona

first: Silvia

last: Dal Santo

address: Strada Le Grazie, 15

department: Department of Biotechnology

institute: University of Verona


title: Effect of small molecule IKKε/TBK1 inhibitors on cell lines from activated B-cell of diffuse large B-cell lymphoma

status: Public on Oct 13 2018

city: Leicester

first: Nicolas

last: Sylvius

address: University Road

department: CBS-Genetics

country: United Kingdom

institute: University of Leicester

summary: Outcomes in activated B-cell diffuse large B-cell lymphoma (ABC-DLBCL) remain poor and new targets for treatment are needed. NF-κB signalling pathways from the B-cell receptor and Toll-like receptors bear mutations and are constitutively active in ABC-DLBCL but inhibitors of the major components of these signalling pathways have not yet entered clinical practice. The IKK related kinases, IKKε/TBK1, have essential roles in innate immunity and regulate aspects of NF-κB signalling and other pathways. TBK1 mRNA expression is associated with clinical outcome and TBK1 and IKKε are variably expressed in human DLBCL.

overall_design: We explored the effects of small molecule IKKε/TBK1 inhibitors on DLBCL cell lines. Gene expression differences due to drug treatment were determined in both DMX3433 sensitive and resistant cell lines. GSEA showed four biologically relevant gene sets: “TNFα signalling via NF-κB” (MSigDB M5890) “Inflammatory Response” (MSigDB M10617), “Oxidative phosphorylation” (MSigDB M5936) and “IFNA response” (MSigDB M5911). There was enrichment for NF-κB pathway genes and for inflammatory response and oxidative phosphorylation genes in untreated cells but lower levels of leading edge genes in untreated cells in “IFNA response” such that type I IFN genes ISG15, IFIT2, IFIT3, MX1 and USP18 44 were induced on DMX3433 administration.

first: Simon

last: Wagner

first: Matthew

last: Carr

first: Spencer

last: Gibson


title: Gene expression profiles in villin- and PTK7-knockdown HepG2 human hepatocarcinoma cells

status: Public on Oct 12 2018

city: Kamakura

first: Satoshi

last: Kondo

state: Kanagawa

address: 10-1 tebiro 6-chome

country: Japan

institute: Toray Industries,Inc.

summary: Effects of villin or PTK7 knockdown on gene expression were evaluated by microarray analysis in HepG2 cells

overall_design: Villin or PTK7 was knocked down using siRNA in hepG2 cells. After 72 hrs, total RNA was prepared and gene expression profiles were obtained by microarray analysis


title: RNA-sequencing of mouse E14.5 embryonic neural stem cells transduced in vitro with a shRNA against Sox4 or a scrambled shRNA

city: Utrecht

first: Paul

last: Coffer

address: Uppsalalaan 6

department: Regenerative Medicine Center

institute: UMC Utrecht

summary: Through RNA-sequencing we analyzed the differentially expressed genes upon in vitro knockdown of Sox4 in mouse E14.5 embryonic neural stem cells using one shRNA against Sox4

overall_design: RNA-sequencing of mouse E14.5 embryonic neural stem cells transduced with lentivirus carrying 1 shRNA scrambled or 1 shRNA  against Sox4 in biological duplicate (different passages)

first: L

last: Braccioli

first: S

last: Vervoort

first: P


title: Dehalococcoides ethenogenes strain 195 in mixed culture continuous (PSS) PCE and TCE fed versus batch PCE fed

city: Ithaca

first: Cresten

last: Mansfeldt

state: NY

address: 220 Hollister Hall

institute: Cornell University

summary:
Bacteria of the group “Dehalococcoides” display the ability to respire recalcitrant chlorinated organic compounds in laboratory and field site applications. Though reductive dehalogenases (RDases) have been shown to directly catalyze dechlorination reactions, the respiratory pathways and function of most genome-encoded RDases in Dehalococcoides strains remain incompletely described. In order to broaden the understanding of the biological organization of “Dehalococcoides”, this study monitored the trancriptomic response of “Dehalococcoides ethenogenes” stain 195 through microarray technology.
Batch versus continuously fed cultures were examined and compared. When similarly respiring (~120 μeeq PCE/(L-hr)) batch and pseudo steady-state cultures were contrasted, the reductive dehalogenases (RDases) DET1545 and DET0180 were up-regulated in the PSS system indicating their activity at lower overall electron acceptor concentration.

overall_design: 6 arrays total, 2 biological replicates of continous PCE fed, 2 biological replicates of continous TCE fed, and 1 technical replicate of the PCE/TCE comparsion. Control is a sample of the Donna II mixed culture after 6 hours of batch PCE feeding. 1 Control versus Control array.

first: Annette

last: Rowe

first: Gretchen

last: Heavner

first: Ruth

last: Richardson


title: A slow cycling Lgr5 tumour population mediates basal cell carcinoma relapse after therapy

status: Public on Oct 11 2018

city: Bruxelles

first: Adriana

last: Sanchez-Danes

address: Route de Lennik 808

institute: Université Libre de Bruxelles

summary: We used microarray analysis to molecularly profile distinct tumour cell populations present in untreated and vismodegib-treated basal cell carcinomas.

overall_design: We FACS-sorted the basal cell carcinoma tumour cells according to their levels of Lgr5-GFP and Lrig1 expression and we performed microarray analysis on the different FACS-sorted tumour cell populations.

last: Sánchez-Danés

first: Cédric

last: Blanpain


title: Dehalococcoides mccartyi strain 195's genome-wide transcriptomic response to batch feeding of 1,2,3,4-Tetrachlorobenzene

summary: Transcriptional profiling of the Donna II mixed community containing Dehalococcoides mccartyi strain 195 comparing a batch starved control to the mixed community being fed 1,2,3,4-tetrachlorobenzene as an electron acceptor. The goal was to determine which transcripts are regulated in response to a shift in a different electron acceptor rather than the consistent tetrachloroethene (PCE) that the parent reactor was maintained on.

overall_design: Three-condition experiment, triplicate Donna II batch fed 1,2,3,4-tetrachlorobenzene sampled at 2 days vs. pooled Donna II batch fed PCE sampled at 3 days; triplicate Donna II batch fed 1,2,3,4-tetrachlorobenzene sampled at 3 days vs. pooled Donna II batch fed PCE sampled at 3 days . The additional two microarrays are the technical dye-swap of the 3 day starved control.


title: Expression data from HeLa cells transfected with 3'-mivaRNAII-138 mimic.

city: Suita

first: Keisaku

last: Wakabayashi

address: 1-6 Yamadaoka

institute: Osaka University

summary:
The adenovirus (Ad) serotype 5 genome encodes two non-coding small RNAs (virus-associated RNAs: VA-RNAI and II), which are approximately 160nt-long RNAs transcribed by RNA polymerase III. Recent studies revealed that VA-RNAs are processed into VA-RNA-derived microRNAs (miRNAs) (mivaRNAI, II); however, we and another group recently demonstrated that mivaRNAI does not promote Ad replication. On the other hand, roles of VA-RNAII and VA-RNAII-derived miRNA (mivaRNAII) in Ad replication have remained to be clarified. In this study, we showed mivaRNAII-mediated promotion of Ad replication. Transfection with chemically synthesized 3'-mivaRNAII-138, one of the most abundant mivaRNAII, significantly enhanced Ad replication, while the other species of mivaRNAII did not.
We used microarrays to detail gene expression profiles in HeLa cells transfected with 3'-miaRNAII-138 mimic and demonstarted that expression levels of various genes were down- or up-regulated following transfection with 3'-mivaRNAII-138 mimic.

overall_design: Hela cells were transfected with 3'-mivaRNAII-138 mimic at 50 nM. After 48 h incubation, the cells were collected and gene expression profiles in the cells were analyzed by microarray analysis.

first: Mitsuhiro

last: Machitani

first: Masashi

last: Tachibana

first: Fuminori

last: Sakurai

first: Hiroyuki

last: Mizuguchi


title: Genome-wide mapping and functional analysis of DNA methylation in clonal invasive crayfish

city: Heidelberg

first: Fanny

last: Gatzmann

address: Im Neuenheimer Feld 580

department: A130 Epigenetics

country: Germany

institute: DKFZ

type: Methylation profiling by high throughput sequencing

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

sample_organism:
Procambarus fallax
Procambarus virginalis

overall_design: Refer to individual Series


title: A Qualitative Transcriptional Signature for the Histological Classification of Non-Small Cell Lung Cancer

city: harbin

first: Lishuang

last: Qi

address: No. 157, Baojian Road, Nangang District

department: College of Bioinformatics Science and Technology

institute: Harbin Medical University

summary: Histological classification by routine pathology assessment with hematoxylin-eosin staining and immunostaining for poorly differentiated tumors, particularly those from small biopsies, is still challenging. In this study, using gene expression profiles of pathologically-determined lung squamous cell carcinomas and adenocarcinomas, denoted as pSCC and pADC respectively, we developed a qualitative transcriptional signature, based on the within-sample relative gene expression orderings (REOs) of gene pairs, to individually distinguish ADC from SCC. The signature was validated in the frozen tissues, FFPE materials, mixed tumors, small biopsy specimens and poorly differentiated samples.In summary, the qualitative signature, independent of the subjective diagnosis of pathologists, would be an effective auxiliary tool in distinguishing ADC from SCC.

overall_design: Total RNA was extracted using Trizol reagent (Invitrogen) according to the manufacture's protocol. The purity and concentration of RNA was determined by Nano Drop ND-1000 spectrophotometer according to OD260/280 reading. Total RNAs were hybridized using mRNA + lncRNA Human Gene Expression Microarray

first: Zheng

last: Guo


title: Analysis of LOV-FPs-mediated stress response in E. coli.

status: Public on Oct 09 2018

city: Juelich

first: Tino

last: Polen

state: NRW

address: Wilhelm-Johnen-Str 1

department: IBG-1: Biotechnology

institute: Forschungszentrum Jülich GmbH

summary: Flavin-binding fluorescent proteins (FPs) are genetically encoded in vivo reporters, which are derived from microbial and plant LOV photoreceptors. In this study, we comparatively analyzed the ROS-induced stress responses of the two variants DsFbFP M49I and Pp2FbFP, exhibiting preferential photosensitization of superoxide and singlet oxygen, respectively, in E.coli.

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

platform_organism: Bacillus subtilis subsp. subtilis str. 168

overall_design: To analyze differences in global oxidative stress response in E. coli that were induced by Pp2FbFP and DsFbFP M49I, a DNA microarray-based analysis was conducted. E. coli cells expressing the respective photosensitizers were cultivated in LB media. LOV-FP expression was induced by addition of 0.4 mM IPTG during the  logarithmic growth phase (~OD580 = 0.7). Three hours after induction, cultures were divided into two test cultures with a volume of 25 ml in 500 ml Erlenmeyer flaks and an OD580 of 0.5. For light treatment one of these cultures was placed between two blue-light emitting LED-panels, whereas the second culture was kept in the dark. Detailed transcriptome analyses of light-induced stress-response based on independent biological triplicates were finally carried out under best illumination conditions (i.e. Pp2FbFP: 5 min, DsFbFP M49I: 15 min).

first: Stephan

last: Endres

first: Thomas

last: Drepper


title: The protective effect of betacellulin against acute pancreatitis is ERBB4-dependent

status: Public on Oct 10 2018

city: Munich

first: Alexander

last: Graf

address: Feodor-Lynen-Str. 25

department: Gene Center Munich

institute: Ludwig-Maximilians-Universität München

summary: We investigated the pancreatic transcriptome of Btc mice and control littermates by microarrays to identify regulated genes that could mechanistically explain the protection of BTC against AP.

overall_design: Gene expression in murine pancreas was measured  3 hours after an intraperitoneal application of a single dosis of cerulein (cerulein group; 50 µg/kg body weight) or saline (sham group: 0 hours).  Four animals per group were investigated at each point of time (cerulein group and sham group).

first: Kathrin

last: Hedegger

first: Franziska

last: Stumpf

first: Helmut

last: Blum

first: Roland

last: Schmid

first: Marina

last: Lesina

first: Hana

last: Algül

first: Marlon

last: Schneider

first: Maik

last: Dahlhoff


title: Investigation of spatial vulnerabilities of Bacterium Escherichia coli genome to spontaneous mutations by molecularly barcoded deep Sequencing

status: Public on Oct 08 2018

city: Dalian

first: Jinsong

last: Yan

address: 9 west section, Lvshun south road, Dalian, Liaoning Province, China

department: Institute of Cancer Stem Cell

institute: Dalian Medical University

summary: Investigation of spontaneous mutations by Next-Generation Sequencing technology has attracted extensive attention lately due to the fundamental roles of spontaneous mutations in evolution and pathological processes. However, these studies only focused on the mutations accumulated through many generations during long term --could be years of-- culturing, but not the freshly-generated spontaneous mutations that occurs at very low frequencies. In this study, we established a molecularly-barcoded deep sequencing strategy to detect low abundant spontaneous mutations in genomes of bacteria cell cultures. Genome-wide spontaneous mutations in 15 E. coli cell culture samples were defined with a high confidence (P < 0.01). We also developed a hotspot region-calling approach based on Run-Length Encoding algorithm to find the genomic regions that are vulnerable to the spontaneous mutations. The hotspots for the mutations appeared to be highly conserved across the bacteria samples. Further biological annotation of these regions indicated that most of the spontaneous mutations were located at the repeat domains or nonfunctional domains of the genomes, suggesting the existence of mechanisms that could somehow prevent the occurrence of mutations in crucial genic areas. This study provides a more faithful picture of mutation occurrence and spectra without the distortion of long term culturing.

overall_design: We conducted RNA-seq analysis for E.coli lines of E3C to study the relationship between mutation and gene expression.

first: Zhiguang

last: Li

first: Xuehong

last: Zhang


title: Expression data from rat bone marrow mesenchymal stem cells

city: Beijing

first: XIN

last: FU

address: 33 Ba-Da-Chu Road

department: Research Center

institute: Plastic Surgery Hospital (Institute), Peking Union Medical College & Chinese Academy of Medical Sciences

summary:
Mesenchymal stem cells (MSCs) are involved in tissue homeostasis and repair, and can be impaired in subjects with high fat diet (HFD)-induced metabolic disorders.
We used microarrays to detail the global programme of gene expression bone marrow MSCs (BMSCs) underlying HFD-induced progression of metabolic disorders in rat and identified distinct classes of differentiatilly expressed genes during this process.

overall_design: Six-week old Sprague-Dawley (SD) rats were randomized to normal diet (ND) and high-fat diet (HFD) groups, fed a normal diet (ND, 100% basal diet) and a customized high-fat diet (60% basal diet, 10% sucrose, 20% lard and 10% egg yolk powder), respectively. The total mRNA of BMSCs (P1) from both groups (n= 3 per group) at the specified feeding time points (1, 2 and 4 months) was purified and hybridized on Affymetrix microarrays. BMSCs were isolated and characterized for the expression of cell surface markers before RNA extraction, to improve the accuracy of expression profiles.

first: Jianhai

last: Bi

first: Qiuchen


title: Dysfunction of circadian clock component PERIOD2 in oncogenic cells confers chemoresistance by up-regulation of Aldh3a1 gene

city: Fukuoka

first: Satoru

last: Koyanagi

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

department: Pharmaceutics

institute: Kyushu University

summary: Disruption of circadian rhythms is implicated in increasing the risk of cancer development. The Period2 (Per2) gene is one of the major components of mammalian circadian clock, which plays a key role in controlling the circadian rhythms in physiology and behavior. PER2 also has tumor suppression function, but its role in the regulation of susceptibility to chemotherapeutic drugs remains unclear. In this study, we identified up-regulation of Aldehyde dehydrogenase 3a1 (Aldh3a1) gene in oncogenic transformed mouse embryo fibroblasts prepared from Per2-mutant (Per2m/m) mice, which were associated with the resistance against chemotherapeutic drugs. Co-expression of H-rasV12 and SV40 large T antigen induced malignant transformation of both wild-type and Per2m/m cells, but the cytotoxic effects of methotrexate, gemcitabine, etoposide, vincristine, and oxaliplatin were significantly alleviated in oncogenic transformed Per2m/m cells. Although introduction of oncogenes increased the expression of Aldh3a1 in both wild-type and Per2m/m cells, the levels of ALDH3A1 protein in oncogenic transformed Per2m/m cells were 10-fold higher than those in wild-type cells. Elevated ALDH3A1 levels in oncogenic transformed Per2m/m cells were sufficient to prevent chemotherapeutic drug-induced production of reactive oxygen species. Consequently, suppression of Aldh3a1 expression by siRNA relived chemoresistance of Per2m/m cells. These results suggest an uncovered role for PER2 in the development of multiple drug resistance and offers new therapeutic strategies for treatment of cancers.

overall_design: Total 6 samples were derived from [1] mock or [2] H-Ras and SV40T expressing vector-transfected wild-type mouse embryonic fibroblasts (MEFs), [3] mock or [4] H-Ras and SV40T expressing vector-transfected Clock mutant MEFs, and [5] mock or [6] H-Ras and SV40T expressing vector-transfected Per2m/m MEFs

first: Chiharu

last: Katamune

first: Ken-ichi

last: Hashikawa

first: Naoki

last: Kusunose

first: Takahiro

last: Akamine

first: Naoya

last: Matsunaga

first: Shigehiro

last: Ohdo


title: Gene expression analysis in rat liver after exposure to pregnenolone-16α-carbonitrile

city: Osaka

first: Ayako

last: Ohara

address: 1-98, Kasugade-naka 3-chome, Konohana-ku

institute: Sumitomo Chemical Co., Ltd.

summary:
RCCHanTM:WIST male rats were administered for 7 days by oral gavage with vehicle (corn oil) or 100 mg/kg/day of pregnenolone-16α-carbonitrile(PCN).
We used microarrays to evaluate gene expression profiling in rat liver at the early phase of treatment with PCN.

overall_design: After treatment periods, livers of 6 rats (3 rats in each group) were excised for RNA extraction and hybridization on Agilent microarrays.

first: Takako

last: Fukuda

first: Fumihiro

last: Yamada


title: Histone deacetylase 3 deletion in the embryonic heart at day E9.5

city: Philadelphia

first: Michael

middle: Patrick

last: Morley

state: PA

address: 3400 Civic Center Blvd, Bldg 421

department: Penn Cardiovascular Institute

institute: Perelman School of Medicine at the University of Pennsylvania

summary:
Analysis of whole hearts from e9.5 embryos from Nkx2.5Cre; Hdac3f/f embryos and littermate controls.  Results provide insight into gene programs regulated by Hdac3 in cardiac development.
Progenitor cells require coordinated expression of lineage-specific genes to regulate differentiation into daughter cell types. Epigenetic regulators are ideally positioned to synchronize transcription of disparate genomic loci. Using cardiac development to model progenitor cell behavior, we demonstrate that Histone deacetylase 3 (Hdac3) functions in a deacetylase-independent manner to repress cardiac differentiation. Loss of Hdac3 promotes differentiation into cardiomyocytes by de-repressing a myocyte gene program.

overall_design: 4 biological replicates of mutant vs 4 biological replicates of wild-type E9.5 microdissected hearts (3 pooled hearts per biological replicate)

first: Jonathan

middle: A

last: Epstein

first: Mudit

last: Gupta


title: Reduced representation bisulfite sequencing (RRBS) of cultured cells derived from Parkinson's disease patient [RRBS-seq]

city: Regensburg

first: Markus

last: Schulze

address: Franz-Josef-Strauss Allee 11

department: Neuropathology

institute: University Hospital Regensburg

summary: High throughput sequencing of MSPI digested, size selected and  bisulfite converted genomic DNA from control- and sporadic Parkinson´s disease patient derived fibroblasts (n=15), induced pluripotent stem cells (n=26) and differentiated midbrain neurons (n=10). We were able to sequence more than 400,000 CpGs at ≥5x coverage in all samples. Nonetheless, statistical analysis with RnBeads did not identify major differences on single CpG or promoter methylation level between control- and Parkinson´s disease patient derived cells in any cell type.

overall_design:
Two-condition experiment in three cell types: Control- and Parkinson´s disease patient derived fibroblasts, induced pluripotent stem cells and differentiated midbrain neurons were compared. Fibroblast cell cultures were established from skin biopsies from six control patients and nine sporadic Parkinson´s disease patients and reprogrammed with the OSKM cocktail. Reduced representation bisulfite sequencing libraries were prepared with the NEXTflex™ Bisulfite Library Prep Kit (BIOO Scientific) and sequencing was performed on an Illumina HiSeq1000 instrument (1x50 bp). Differential expression analysis was performed comparing control- and Parkinson´s disease patient derived cells within each cell type (fibroblasts, induced pluripotent stem cells or neurons).
Please note that Raw data is only available via dbGAP due to privacy concerns

middle: J

last: Riemenschneider

first: Winkler

last: Jürgen

first: Winner

last: Beate


title: RNA-seq of cultured cells derived from Parkinson's disease patients [PolyA RNA-seq]

summary: High throughput sequencing of poly-A RNA from control- and sporadic Parkinson´s disease patient derived fibroblasts (n=15), induced pluripotent stem cells (n=31) and differentiated midbrain neurons (n=15). Fibroblasts and iPSCs do not show major differences on single gene level. In contrast, midbrain neurons derived from  Parkinson´s disease patients show changes known to be associated with neurodegenerative diseases.

overall_design:
Two-condition experiment in three cell types: Control- and Parkinson´s disease patient derived fibroblasts, induced pluripotent stem cells and differentiated midbrain neurons were compared. Fibroblast cell cultures were established from skin biopsies from six control patients and nine sporadic Parkinson´s disease patients and reprogrammed with the OSKM cocktail. Poly-A RNA libraries were prepared with the Illumina TruSeq® RNA Sample Preparation Kit v2 and sequencing was performed on an Illumina HiSeq1000 instrument (1x50 bp). Differential expression analysis was performed comparing control- and Parkinson´s disease patient derived cells within each cell type (fibroblasts, induced pluripotent stem cells or neurons)
Please note that Raw data is only available via dbGAP due to privacy concerns